diff --git a/.gitignore b/.gitignore
index cea500f..3ddfac0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -258,4 +258,6 @@ pip-log.txt
/Umpire-SpectrumParser/nbproject/private/
/Umpire-UmpireSearch/nbproject/private/
/Umpire-Utility/nbproject/private/
-/DIA-Umpire/nbproject/private/
\ No newline at end of file
+/DIA-Umpire/nbproject/private/
+/DIA_Umpire_To_Skyline/nbproject/private/
+/MS1Quant/nbproject/private/
\ No newline at end of file
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/Alignment.java b/DIA-Umpire/src/ExternalPackages/JAligner/Alignment.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/JAligner/Alignment.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/Alignment.java
index 9f5ff7a..a875823 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/Alignment.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/Alignment.java
@@ -14,10 +14,10 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner;
+package ExternalPackages.JAligner;
-import ExtPackages.JAligner.matrix.Matrix;
-import ExtPackages.JAligner.util.Commons;
+import ExternalPackages.JAligner.matrix.Matrix;
+import ExternalPackages.JAligner.util.Commons;
import java.text.DecimalFormat;
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/Cell.java b/DIA-Umpire/src/ExternalPackages/JAligner/Cell.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/JAligner/Cell.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/Cell.java
index 6d803e4..10a8bad 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/Cell.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/Cell.java
@@ -14,7 +14,7 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner;
+package ExternalPackages.JAligner;
/**
* A cell in a similarity matrix, to hold row, column and score.
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/Directions.java b/DIA-Umpire/src/ExternalPackages/JAligner/Directions.java
similarity index 96%
rename from DIA-Umpire/src/ExtPackages/JAligner/Directions.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/Directions.java
index 26feb22..261f355 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/Directions.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/Directions.java
@@ -14,7 +14,7 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner;
+package ExternalPackages.JAligner;
/**
* Traceback directions.
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/Markups.java b/DIA-Umpire/src/ExternalPackages/JAligner/Markups.java
similarity index 97%
rename from DIA-Umpire/src/ExtPackages/JAligner/Markups.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/Markups.java
index 5ed4d9d..16379d5 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/Markups.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/Markups.java
@@ -14,7 +14,7 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner;
+package ExternalPackages.JAligner;
/**
* Markups line characters.
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/NeedlemanWunsch.java b/DIA-Umpire/src/ExternalPackages/JAligner/NeedlemanWunsch.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/JAligner/NeedlemanWunsch.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/NeedlemanWunsch.java
index 6ab8f60..62b4c40 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/NeedlemanWunsch.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/NeedlemanWunsch.java
@@ -14,9 +14,9 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner;
+package ExternalPackages.JAligner;
-import ExtPackages.JAligner.matrix.Matrix;
+import ExternalPackages.JAligner.matrix.Matrix;
/**
* An implementation of the Needleman-Wunsch algorithm for biological global
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/NeedlemanWunschGotoh.java b/DIA-Umpire/src/ExternalPackages/JAligner/NeedlemanWunschGotoh.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/JAligner/NeedlemanWunschGotoh.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/NeedlemanWunschGotoh.java
index 5fbb0eb..9518c94 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/NeedlemanWunschGotoh.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/NeedlemanWunschGotoh.java
@@ -13,9 +13,9 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner;
+package ExternalPackages.JAligner;
-import ExtPackages.JAligner.matrix.Matrix;
+import ExternalPackages.JAligner.matrix.Matrix;
import java.util.logging.Logger;
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/Sequence.java b/DIA-Umpire/src/ExternalPackages/JAligner/Sequence.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/JAligner/Sequence.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/Sequence.java
index b759a60..b73de04 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/Sequence.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/Sequence.java
@@ -14,9 +14,9 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner;
+package ExternalPackages.JAligner;
-import ExtPackages.JAligner.util.Commons;
+import ExternalPackages.JAligner.util.Commons;
import java.io.Serializable;
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/SmithWatermanGotoh.java b/DIA-Umpire/src/ExternalPackages/JAligner/SmithWatermanGotoh.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/JAligner/SmithWatermanGotoh.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/SmithWatermanGotoh.java
index f09b248..3cab266 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/SmithWatermanGotoh.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/SmithWatermanGotoh.java
@@ -14,9 +14,9 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner;
+package ExternalPackages.JAligner;
-import ExtPackages.JAligner.matrix.Matrix;
+import ExternalPackages.JAligner.matrix.Matrix;
import java.util.logging.Logger;
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/TracebackNode.java b/DIA-Umpire/src/ExternalPackages/JAligner/TracebackNode.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/JAligner/TracebackNode.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/TracebackNode.java
index 2405ee6..3b94541 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/TracebackNode.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/TracebackNode.java
@@ -14,7 +14,7 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner;
+package ExternalPackages.JAligner;
/**
* Traceback node
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/example/NeedlemanWunschExample.java b/DIA-Umpire/src/ExternalPackages/JAligner/example/NeedlemanWunschExample.java
similarity index 80%
rename from DIA-Umpire/src/ExtPackages/JAligner/example/NeedlemanWunschExample.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/example/NeedlemanWunschExample.java
index 30a09d5..aea831a 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/example/NeedlemanWunschExample.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/example/NeedlemanWunschExample.java
@@ -14,22 +14,22 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.example;
+package ExternalPackages.JAligner.example;
-import ExtPackages.JAligner.Alignment;
-import ExtPackages.JAligner.NeedlemanWunsch;
-import ExtPackages.JAligner.Sequence;
-import ExtPackages.JAligner.formats.Pair;
-import ExtPackages.JAligner.matrix.Matrix;
-import ExtPackages.JAligner.matrix.MatrixGenerator;
-import ExtPackages.JAligner.util.SequenceParser;
+import ExternalPackages.JAligner.Alignment;
+import ExternalPackages.JAligner.NeedlemanWunsch;
+import ExternalPackages.JAligner.Sequence;
+import ExternalPackages.JAligner.formats.Pair;
+import ExternalPackages.JAligner.matrix.Matrix;
+import ExternalPackages.JAligner.matrix.MatrixGenerator;
+import ExternalPackages.JAligner.util.SequenceParser;
import java.util.logging.Level;
import java.util.logging.Logger;
/**
* Example of using JAligner API to perform global pairwise sequence alignment
- * with Needleman-Wunsch algorithm {@link ExtPackages.JAligner.NeedlemanWunsch}.
+ * with Needleman-Wunsch algorithm {@link ExternalPackages.JAligner.NeedlemanWunsch}.
*
* @author Ahmed Moustafa
*/
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/example/NeedlemanWunschGotohExample.java b/DIA-Umpire/src/ExternalPackages/JAligner/example/NeedlemanWunschGotohExample.java
similarity index 86%
rename from DIA-Umpire/src/ExtPackages/JAligner/example/NeedlemanWunschGotohExample.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/example/NeedlemanWunschGotohExample.java
index 355414c..7382826 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/example/NeedlemanWunschGotohExample.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/example/NeedlemanWunschGotohExample.java
@@ -16,7 +16,7 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.example;
+package ExternalPackages.JAligner.example;
/*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
@@ -33,20 +33,20 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-import ExtPackages.JAligner.Alignment;
-import ExtPackages.JAligner.NeedlemanWunschGotoh;
-import ExtPackages.JAligner.Sequence;
-import ExtPackages.JAligner.formats.Pair;
-import ExtPackages.JAligner.matrix.Matrix;
-import ExtPackages.JAligner.matrix.MatrixGenerator;
-import ExtPackages.JAligner.util.SequenceParser;
+import ExternalPackages.JAligner.Alignment;
+import ExternalPackages.JAligner.NeedlemanWunschGotoh;
+import ExternalPackages.JAligner.Sequence;
+import ExternalPackages.JAligner.formats.Pair;
+import ExternalPackages.JAligner.matrix.Matrix;
+import ExternalPackages.JAligner.matrix.MatrixGenerator;
+import ExternalPackages.JAligner.util.SequenceParser;
import java.util.logging.Level;
import java.util.logging.Logger;
/**
* Example of using JAligner API to perform global pairwise sequence alignment
- * with {@link ExtPackages.JAligner.NeedlemanWunschGotoh}.
+ * with {@link ExternalPackages.JAligner.NeedlemanWunschGotoh}.
*
* @author Ahmed Moustafa
*/
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/example/SmithWatermanGotohExample.java b/DIA-Umpire/src/ExternalPackages/JAligner/example/SmithWatermanGotohExample.java
similarity index 89%
rename from DIA-Umpire/src/ExtPackages/JAligner/example/SmithWatermanGotohExample.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/example/SmithWatermanGotohExample.java
index 8085641..22ba924 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/example/SmithWatermanGotohExample.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/example/SmithWatermanGotohExample.java
@@ -14,14 +14,14 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.example;
+package ExternalPackages.JAligner.example;
-import ExtPackages.JAligner.Alignment;
-import ExtPackages.JAligner.Sequence;
-import ExtPackages.JAligner.SmithWatermanGotoh;
-import ExtPackages.JAligner.formats.Pair;
-import ExtPackages.JAligner.matrix.MatrixLoader;
-import ExtPackages.JAligner.util.SequenceParser;
+import ExternalPackages.JAligner.Alignment;
+import ExternalPackages.JAligner.Sequence;
+import ExternalPackages.JAligner.SmithWatermanGotoh;
+import ExternalPackages.JAligner.formats.Pair;
+import ExternalPackages.JAligner.matrix.MatrixLoader;
+import ExternalPackages.JAligner.util.SequenceParser;
import java.io.IOException;
import java.io.InputStream;
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/example/package.html b/DIA-Umpire/src/ExternalPackages/JAligner/example/package.html
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/example/package.html
rename to DIA-Umpire/src/ExternalPackages/JAligner/example/package.html
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/example/sequences/p53_human.fasta b/DIA-Umpire/src/ExternalPackages/JAligner/example/sequences/p53_human.fasta
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/example/sequences/p53_human.fasta
rename to DIA-Umpire/src/ExternalPackages/JAligner/example/sequences/p53_human.fasta
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/example/sequences/p53_mouse.fasta b/DIA-Umpire/src/ExternalPackages/JAligner/example/sequences/p53_mouse.fasta
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/example/sequences/p53_mouse.fasta
rename to DIA-Umpire/src/ExternalPackages/JAligner/example/sequences/p53_mouse.fasta
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/formats/CLUSTAL.java b/DIA-Umpire/src/ExternalPackages/JAligner/formats/CLUSTAL.java
similarity index 97%
rename from DIA-Umpire/src/ExtPackages/JAligner/formats/CLUSTAL.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/formats/CLUSTAL.java
index b0a4dd6..f07d85d 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/formats/CLUSTAL.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/formats/CLUSTAL.java
@@ -14,9 +14,9 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.formats;
+package ExternalPackages.JAligner.formats;
-import ExtPackages.JAligner.Alignment;
+import ExternalPackages.JAligner.Alignment;
/**
* CLUSTAL format.
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/formats/FASTA.java b/DIA-Umpire/src/ExternalPackages/JAligner/formats/FASTA.java
similarity index 94%
rename from DIA-Umpire/src/ExtPackages/JAligner/formats/FASTA.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/formats/FASTA.java
index c5ee7cd..dce591a 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/formats/FASTA.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/formats/FASTA.java
@@ -14,10 +14,10 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.formats;
+package ExternalPackages.JAligner.formats;
-import ExtPackages.JAligner.Alignment;
-import ExtPackages.JAligner.Sequence;
+import ExternalPackages.JAligner.Alignment;
+import ExternalPackages.JAligner.Sequence;
/**
* FASTA format.
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/formats/Format.java b/DIA-Umpire/src/ExternalPackages/JAligner/formats/Format.java
similarity index 93%
rename from DIA-Umpire/src/ExtPackages/JAligner/formats/Format.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/formats/Format.java
index ef6ced0..6154e38 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/formats/Format.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/formats/Format.java
@@ -14,9 +14,9 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.formats;
+package ExternalPackages.JAligner.formats;
-import ExtPackages.JAligner.Alignment;
+import ExternalPackages.JAligner.Alignment;
/**
* Abstract format
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/formats/FormatFactory.java b/DIA-Umpire/src/ExternalPackages/JAligner/formats/FormatFactory.java
similarity index 97%
rename from DIA-Umpire/src/ExtPackages/JAligner/formats/FormatFactory.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/formats/FormatFactory.java
index 555225e..1350e5b 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/formats/FormatFactory.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/formats/FormatFactory.java
@@ -14,7 +14,7 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.formats;
+package ExternalPackages.JAligner.formats;
import java.util.Collection;
import java.util.HashMap;
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/formats/Pair.java b/DIA-Umpire/src/ExternalPackages/JAligner/formats/Pair.java
similarity index 97%
rename from DIA-Umpire/src/ExtPackages/JAligner/formats/Pair.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/formats/Pair.java
index b951b6d..f6f94e3 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/formats/Pair.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/formats/Pair.java
@@ -14,10 +14,10 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.formats;
+package ExternalPackages.JAligner.formats;
-import ExtPackages.JAligner.Alignment;
-import ExtPackages.JAligner.util.Commons;
+import ExternalPackages.JAligner.Alignment;
+import ExternalPackages.JAligner.util.Commons;
/**
* Alignment Formats.
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/formats/package.html b/DIA-Umpire/src/ExternalPackages/JAligner/formats/package.html
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/formats/package.html
rename to DIA-Umpire/src/ExternalPackages/JAligner/formats/package.html
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/MatricesCompartor.java b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/MatricesCompartor.java
similarity index 97%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/MatricesCompartor.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/MatricesCompartor.java
index 6125e66..20084e3 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/matrix/MatricesCompartor.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/MatricesCompartor.java
@@ -14,7 +14,7 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.matrix;
+package ExternalPackages.JAligner.matrix;
import java.util.Comparator;
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/Matrix.java b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/Matrix.java
similarity index 97%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/Matrix.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/Matrix.java
index 563bbfb..bb9185b 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/matrix/Matrix.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/Matrix.java
@@ -13,7 +13,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.matrix;
+package ExternalPackages.JAligner.matrix;
import java.io.Serializable;
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/MatrixGenerator.java b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/MatrixGenerator.java
similarity index 97%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/MatrixGenerator.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/MatrixGenerator.java
index b1df668..3053589 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/matrix/MatrixGenerator.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/MatrixGenerator.java
@@ -14,7 +14,7 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.matrix;
+package ExternalPackages.JAligner.matrix;
/**
* A utility class to generate a scoring matrix from a fixed match and mismatch
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/MatrixLoader.java b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/MatrixLoader.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/MatrixLoader.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/MatrixLoader.java
index fedbed3..71009bf 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/matrix/MatrixLoader.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/MatrixLoader.java
@@ -13,10 +13,10 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.matrix;
+package ExternalPackages.JAligner.matrix;
-import ExtPackages.JAligner.ui.filechooser.NamedInputStream;
-import ExtPackages.JAligner.util.Commons;
+import ExternalPackages.JAligner.ui.filechooser.NamedInputStream;
+import ExternalPackages.JAligner.util.Commons;
import java.io.BufferedReader;
import java.io.File;
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/MatrixLoaderException.java b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/MatrixLoaderException.java
similarity index 96%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/MatrixLoaderException.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/MatrixLoaderException.java
index b67cb2b..d8378c9 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/matrix/MatrixLoaderException.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/MatrixLoaderException.java
@@ -14,7 +14,7 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.matrix;
+package ExternalPackages.JAligner.matrix;
/**
*
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUM100 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUM100
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUM100
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUM100
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUM30 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUM30
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUM30
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUM30
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUM35 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUM35
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUM35
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUM35
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUM40 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUM40
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUM40
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUM40
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUM45 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUM45
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUM45
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUM45
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUM50 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUM50
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUM50
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUM50
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUM55 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUM55
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUM55
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUM55
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUM60 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUM60
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUM60
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUM60
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUM62 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUM62
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUM62
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUM62
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUM65 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUM65
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUM65
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUM65
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUM70 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUM70
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUM70
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUM70
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUM75 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUM75
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUM75
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUM75
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUM80 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUM80
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUM80
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUM80
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUM85 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUM85
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUM85
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUM85
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUM90 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUM90
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUM90
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUM90
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUMN b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUMN
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/BLOSUMN
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/BLOSUMN
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/DAYHOFF b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/DAYHOFF
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/DAYHOFF
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/DAYHOFF
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/EDNAFULL b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/EDNAFULL
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/EDNAFULL
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/EDNAFULL
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/GONNET b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/GONNET
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/GONNET
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/GONNET
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/IDENTITY b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/IDENTITY
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/IDENTITY
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/IDENTITY
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/MATCH b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/MATCH
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/MATCH
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/MATCH
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM10 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM10
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM10
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM10
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM100 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM100
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM100
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM100
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM110 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM110
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM110
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM110
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM120 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM120
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM120
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM120
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM130 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM130
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM130
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM130
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM140 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM140
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM140
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM140
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM150 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM150
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM150
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM150
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM160 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM160
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM160
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM160
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM170 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM170
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM170
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM170
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM180 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM180
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM180
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM180
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM190 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM190
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM190
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM190
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM20 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM20
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM20
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM20
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM200 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM200
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM200
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM200
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM210 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM210
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM210
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM210
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM220 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM220
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM220
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM220
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM230 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM230
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM230
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM230
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM240 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM240
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM240
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM240
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM250 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM250
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM250
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM250
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM260 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM260
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM260
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM260
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM270 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM270
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM270
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM270
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM280 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM280
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM280
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM280
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM290 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM290
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM290
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM290
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM30 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM30
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM30
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM30
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM300 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM300
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM300
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM300
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM310 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM310
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM310
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM310
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM320 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM320
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM320
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM320
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM330 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM330
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM330
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM330
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM340 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM340
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM340
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM340
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM350 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM350
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM350
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM350
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM360 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM360
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM360
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM360
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM370 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM370
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM370
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM370
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM380 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM380
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM380
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM380
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM390 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM390
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM390
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM390
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM40 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM40
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM40
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM40
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM400 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM400
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM400
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM400
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM410 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM410
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM410
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM410
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM420 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM420
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM420
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM420
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM430 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM430
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM430
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM430
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM440 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM440
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM440
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM440
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM450 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM450
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM450
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM450
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM460 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM460
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM460
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM460
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM470 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM470
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM470
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM470
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM480 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM480
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM480
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM480
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM490 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM490
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM490
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM490
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM50 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM50
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM50
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM50
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM500 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM500
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM500
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM500
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM60 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM60
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM60
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM60
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM70 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM70
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM70
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM70
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM80 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM80
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM80
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM80
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM90 b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM90
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/matrices/PAM90
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/matrices/PAM90
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/matrix/package.html b/DIA-Umpire/src/ExternalPackages/JAligner/matrix/package.html
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/matrix/package.html
rename to DIA-Umpire/src/ExternalPackages/JAligner/matrix/package.html
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/package.html b/DIA-Umpire/src/ExternalPackages/JAligner/package.html
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/package.html
rename to DIA-Umpire/src/ExternalPackages/JAligner/package.html
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/test/NeedlemanWunschGotohTester.java b/DIA-Umpire/src/ExternalPackages/JAligner/test/NeedlemanWunschGotohTester.java
similarity index 90%
rename from DIA-Umpire/src/ExtPackages/JAligner/test/NeedlemanWunschGotohTester.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/test/NeedlemanWunschGotohTester.java
index a550a56..727cc4d 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/test/NeedlemanWunschGotohTester.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/test/NeedlemanWunschGotohTester.java
@@ -14,15 +14,15 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.test;
+package ExternalPackages.JAligner.test;
-import ExtPackages.JAligner.Alignment;
-import ExtPackages.JAligner.NeedlemanWunschGotoh;
-import ExtPackages.JAligner.Sequence;
-import ExtPackages.JAligner.formats.Format;
-import ExtPackages.JAligner.formats.Pair;
-import ExtPackages.JAligner.matrix.Matrix;
-import ExtPackages.JAligner.matrix.MatrixLoader;
+import ExternalPackages.JAligner.Alignment;
+import ExternalPackages.JAligner.NeedlemanWunschGotoh;
+import ExternalPackages.JAligner.Sequence;
+import ExternalPackages.JAligner.formats.Format;
+import ExternalPackages.JAligner.formats.Pair;
+import ExternalPackages.JAligner.matrix.Matrix;
+import ExternalPackages.JAligner.matrix.MatrixLoader;
import java.util.ArrayList;
import java.util.Iterator;
@@ -30,7 +30,7 @@
import java.util.Random;
/**
- * Testing the scores of the alignments of {@link ExtPackages.JAligner.NeedlemanWunschGotoh}.
+ * Testing the scores of the alignments of {@link ExternalPackages.JAligner.NeedlemanWunschGotoh}.
*
* @author Bram Minnaert
*/
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/test/NeedlemanWunschTester.java b/DIA-Umpire/src/ExternalPackages/JAligner/test/NeedlemanWunschTester.java
similarity index 91%
rename from DIA-Umpire/src/ExtPackages/JAligner/test/NeedlemanWunschTester.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/test/NeedlemanWunschTester.java
index b8f657e..0bdfff4 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/test/NeedlemanWunschTester.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/test/NeedlemanWunschTester.java
@@ -14,15 +14,15 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.test;
+package ExternalPackages.JAligner.test;
-import ExtPackages.JAligner.Alignment;
-import ExtPackages.JAligner.NeedlemanWunsch;
-import ExtPackages.JAligner.Sequence;
-import ExtPackages.JAligner.formats.Format;
-import ExtPackages.JAligner.formats.Pair;
-import ExtPackages.JAligner.matrix.Matrix;
-import ExtPackages.JAligner.matrix.MatrixLoader;
+import ExternalPackages.JAligner.Alignment;
+import ExternalPackages.JAligner.NeedlemanWunsch;
+import ExternalPackages.JAligner.Sequence;
+import ExternalPackages.JAligner.formats.Format;
+import ExternalPackages.JAligner.formats.Pair;
+import ExternalPackages.JAligner.matrix.Matrix;
+import ExternalPackages.JAligner.matrix.MatrixLoader;
import java.util.ArrayList;
import java.util.Iterator;
@@ -30,7 +30,7 @@
import java.util.Random;
/**
- * Testing the scores of the alignments of {@link ExtPackages.JAligner.NeedlemanWunsch}.
+ * Testing the scores of the alignments of {@link ExternalPackages.JAligner.NeedlemanWunsch}.
*
* @author Ahmed Moustafa
*/
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/test/RandomSequenceGenerator.java b/DIA-Umpire/src/ExternalPackages/JAligner/test/RandomSequenceGenerator.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/JAligner/test/RandomSequenceGenerator.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/test/RandomSequenceGenerator.java
index 2c217d6..ab7f7c9 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/test/RandomSequenceGenerator.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/test/RandomSequenceGenerator.java
@@ -14,7 +14,7 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.test;
+package ExternalPackages.JAligner.test;
import java.util.Random;
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/test/SmithWatermanGotohTester.java b/DIA-Umpire/src/ExternalPackages/JAligner/test/SmithWatermanGotohTester.java
similarity index 91%
rename from DIA-Umpire/src/ExtPackages/JAligner/test/SmithWatermanGotohTester.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/test/SmithWatermanGotohTester.java
index 9ba6602..c653758 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/test/SmithWatermanGotohTester.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/test/SmithWatermanGotohTester.java
@@ -14,15 +14,15 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.test;
+package ExternalPackages.JAligner.test;
-import ExtPackages.JAligner.Alignment;
-import ExtPackages.JAligner.Sequence;
-import ExtPackages.JAligner.SmithWatermanGotoh;
-import ExtPackages.JAligner.formats.Format;
-import ExtPackages.JAligner.formats.Pair;
-import ExtPackages.JAligner.matrix.Matrix;
-import ExtPackages.JAligner.matrix.MatrixLoader;
+import ExternalPackages.JAligner.Alignment;
+import ExternalPackages.JAligner.Sequence;
+import ExternalPackages.JAligner.SmithWatermanGotoh;
+import ExternalPackages.JAligner.formats.Format;
+import ExternalPackages.JAligner.formats.Pair;
+import ExternalPackages.JAligner.matrix.Matrix;
+import ExternalPackages.JAligner.matrix.MatrixLoader;
import java.util.ArrayList;
import java.util.Iterator;
@@ -30,7 +30,7 @@
import java.util.Random;
/**
- * Testing the scores of the alignments of {@link ExtPackages.JAligner.SmithWatermanGotoh}.
+ * Testing the scores of the alignments of {@link ExternalPackages.JAligner.SmithWatermanGotoh}.
*
* @author Bram Minnaert
*/
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/test/package.html b/DIA-Umpire/src/ExternalPackages/JAligner/test/package.html
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/test/package.html
rename to DIA-Umpire/src/ExternalPackages/JAligner/test/package.html
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/AlignCommandLine.java b/DIA-Umpire/src/ExternalPackages/JAligner/ui/AlignCommandLine.java
similarity index 86%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/AlignCommandLine.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/AlignCommandLine.java
index f606393..b82bedc 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/ui/AlignCommandLine.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/ui/AlignCommandLine.java
@@ -14,16 +14,16 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.ui;
+package ExternalPackages.JAligner.ui;
-import ExtPackages.JAligner.Alignment;
-import ExtPackages.JAligner.Sequence;
-import ExtPackages.JAligner.SmithWatermanGotoh;
-import ExtPackages.JAligner.formats.Pair;
-import ExtPackages.JAligner.matrix.Matrix;
-import ExtPackages.JAligner.matrix.MatrixLoader;
-import ExtPackages.JAligner.util.Commons;
-import ExtPackages.JAligner.util.SequenceParser;
+import ExternalPackages.JAligner.Alignment;
+import ExternalPackages.JAligner.Sequence;
+import ExternalPackages.JAligner.SmithWatermanGotoh;
+import ExternalPackages.JAligner.formats.Pair;
+import ExternalPackages.JAligner.matrix.Matrix;
+import ExternalPackages.JAligner.matrix.MatrixLoader;
+import ExternalPackages.JAligner.util.Commons;
+import ExternalPackages.JAligner.util.SequenceParser;
import java.io.File;
import java.util.logging.Level;
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/AlignWindow.form b/DIA-Umpire/src/ExternalPackages/JAligner/ui/AlignWindow.form
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/AlignWindow.form
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/AlignWindow.form
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/AlignWindow.java b/DIA-Umpire/src/ExternalPackages/JAligner/ui/AlignWindow.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/AlignWindow.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/AlignWindow.java
index 487f025..8f68c45 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/ui/AlignWindow.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/ui/AlignWindow.java
@@ -14,28 +14,28 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.ui;
-
-import ExtPackages.JAligner.Alignment;
-import ExtPackages.JAligner.Sequence;
-import ExtPackages.JAligner.SmithWatermanGotoh;
-import ExtPackages.JAligner.example.SmithWatermanGotohExample;
-import ExtPackages.JAligner.formats.CLUSTAL;
-import ExtPackages.JAligner.formats.FASTA;
-import ExtPackages.JAligner.formats.FormatFactory;
-import ExtPackages.JAligner.formats.Pair;
-import ExtPackages.JAligner.matrix.Matrix;
-import ExtPackages.JAligner.matrix.MatrixLoader;
-import ExtPackages.JAligner.ui.clipboard.ClipboardListener;
-import ExtPackages.JAligner.ui.clipboard.ClipboardPoller;
-import ExtPackages.JAligner.ui.filechooser.FileChooserFactory;
-import ExtPackages.JAligner.ui.filechooser.NamedInputStream;
-import ExtPackages.JAligner.ui.images.ToolbarIcons;
-import ExtPackages.JAligner.ui.logging.DocumentHandler;
-import ExtPackages.JAligner.ui.util.TextComponentUtil;
-import ExtPackages.JAligner.ui.util.TextComponentUtilException;
-import ExtPackages.JAligner.util.Commons;
-import ExtPackages.JAligner.util.SequenceParser;
+package ExternalPackages.JAligner.ui;
+
+import ExternalPackages.JAligner.Alignment;
+import ExternalPackages.JAligner.Sequence;
+import ExternalPackages.JAligner.SmithWatermanGotoh;
+import ExternalPackages.JAligner.example.SmithWatermanGotohExample;
+import ExternalPackages.JAligner.formats.CLUSTAL;
+import ExternalPackages.JAligner.formats.FASTA;
+import ExternalPackages.JAligner.formats.FormatFactory;
+import ExternalPackages.JAligner.formats.Pair;
+import ExternalPackages.JAligner.matrix.Matrix;
+import ExternalPackages.JAligner.matrix.MatrixLoader;
+import ExternalPackages.JAligner.ui.clipboard.ClipboardListener;
+import ExternalPackages.JAligner.ui.clipboard.ClipboardPoller;
+import ExternalPackages.JAligner.ui.filechooser.FileChooserFactory;
+import ExternalPackages.JAligner.ui.filechooser.NamedInputStream;
+import ExternalPackages.JAligner.ui.images.ToolbarIcons;
+import ExternalPackages.JAligner.ui.logging.DocumentHandler;
+import ExternalPackages.JAligner.ui.util.TextComponentUtil;
+import ExternalPackages.JAligner.ui.util.TextComponentUtilException;
+import ExternalPackages.JAligner.util.Commons;
+import ExternalPackages.JAligner.util.SequenceParser;
import java.awt.Color;
import java.awt.Component;
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/clipboard/ClipboardHandler.java b/DIA-Umpire/src/ExternalPackages/JAligner/ui/clipboard/ClipboardHandler.java
similarity index 96%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/clipboard/ClipboardHandler.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/clipboard/ClipboardHandler.java
index d8d3776..4b350d1 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/ui/clipboard/ClipboardHandler.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/ui/clipboard/ClipboardHandler.java
@@ -14,7 +14,7 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.ui.clipboard;
+package ExternalPackages.JAligner.ui.clipboard;
/**
* Abstract class to handle setting and getting "text" contents of
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/clipboard/ClipboardHandlerAWT.java b/DIA-Umpire/src/ExternalPackages/JAligner/ui/clipboard/ClipboardHandlerAWT.java
similarity index 97%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/clipboard/ClipboardHandlerAWT.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/clipboard/ClipboardHandlerAWT.java
index 62d145b..1be5e95 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/ui/clipboard/ClipboardHandlerAWT.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/ui/clipboard/ClipboardHandlerAWT.java
@@ -14,7 +14,7 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.ui.clipboard;
+package ExternalPackages.JAligner.ui.clipboard;
import java.awt.Toolkit;
import java.awt.datatransfer.Clipboard;
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/clipboard/ClipboardHandlerFactory.java b/DIA-Umpire/src/ExternalPackages/JAligner/ui/clipboard/ClipboardHandlerFactory.java
similarity index 88%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/clipboard/ClipboardHandlerFactory.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/clipboard/ClipboardHandlerFactory.java
index 886a6e4..3a0db02 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/ui/clipboard/ClipboardHandlerFactory.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/ui/clipboard/ClipboardHandlerFactory.java
@@ -14,12 +14,12 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.ui.clipboard;
+package ExternalPackages.JAligner.ui.clipboard;
-import ExtPackages.JAligner.util.Commons;
+import ExternalPackages.JAligner.util.Commons;
/**
- * A factory for {@link ExtPackages.JAligner.ui.clipboard.ClipboardHandler}.
+ * A factory for {@link ExternalPackages.JAligner.ui.clipboard.ClipboardHandler}.
*
* @author Ahmed Moustafa
*/
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/clipboard/ClipboardHandlerJNLP.java b/DIA-Umpire/src/ExternalPackages/JAligner/ui/clipboard/ClipboardHandlerJNLP.java
similarity index 97%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/clipboard/ClipboardHandlerJNLP.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/clipboard/ClipboardHandlerJNLP.java
index fdc99ae..266e25f 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/ui/clipboard/ClipboardHandlerJNLP.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/ui/clipboard/ClipboardHandlerJNLP.java
@@ -14,7 +14,7 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.ui.clipboard;
+package ExternalPackages.JAligner.ui.clipboard;
import java.awt.datatransfer.DataFlavor;
import java.awt.datatransfer.StringSelection;
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/clipboard/ClipboardListener.java b/DIA-Umpire/src/ExternalPackages/JAligner/ui/clipboard/ClipboardListener.java
similarity index 95%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/clipboard/ClipboardListener.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/clipboard/ClipboardListener.java
index 9593c23..39382d4 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/ui/clipboard/ClipboardListener.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/ui/clipboard/ClipboardListener.java
@@ -14,7 +14,7 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.ui.clipboard;
+package ExternalPackages.JAligner.ui.clipboard;
/**
* Listener interface to get notified with the clipboard contents.
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/clipboard/ClipboardPoller.java b/DIA-Umpire/src/ExternalPackages/JAligner/ui/clipboard/ClipboardPoller.java
similarity index 97%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/clipboard/ClipboardPoller.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/clipboard/ClipboardPoller.java
index 0d1f8cf..e3d6475 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/ui/clipboard/ClipboardPoller.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/ui/clipboard/ClipboardPoller.java
@@ -14,7 +14,7 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.ui.clipboard;
+package ExternalPackages.JAligner.ui.clipboard;
import java.util.logging.Level;
import java.util.logging.Logger;
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/clipboard/package.html b/DIA-Umpire/src/ExternalPackages/JAligner/ui/clipboard/package.html
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/clipboard/package.html
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/clipboard/package.html
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/filechooser/FileChooser.java b/DIA-Umpire/src/ExternalPackages/JAligner/ui/filechooser/FileChooser.java
similarity index 97%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/filechooser/FileChooser.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/filechooser/FileChooser.java
index dd2ffb1..7c47290 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/ui/filechooser/FileChooser.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/ui/filechooser/FileChooser.java
@@ -14,7 +14,7 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.ui.filechooser;
+package ExternalPackages.JAligner.ui.filechooser;
import java.io.InputStream;
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/filechooser/FileChooserException.java b/DIA-Umpire/src/ExternalPackages/JAligner/ui/filechooser/FileChooserException.java
similarity index 95%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/filechooser/FileChooserException.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/filechooser/FileChooserException.java
index f1bc246..b4d907a 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/ui/filechooser/FileChooserException.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/ui/filechooser/FileChooserException.java
@@ -14,7 +14,7 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.ui.filechooser;
+package ExternalPackages.JAligner.ui.filechooser;
/**
* File chooser exception
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/filechooser/FileChooserFactory.java b/DIA-Umpire/src/ExternalPackages/JAligner/ui/filechooser/FileChooserFactory.java
similarity index 88%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/filechooser/FileChooserFactory.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/filechooser/FileChooserFactory.java
index c6f0190..88b8631 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/ui/filechooser/FileChooserFactory.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/ui/filechooser/FileChooserFactory.java
@@ -14,12 +14,12 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.ui.filechooser;
+package ExternalPackages.JAligner.ui.filechooser;
-import ExtPackages.JAligner.util.Commons;
+import ExternalPackages.JAligner.util.Commons;
/**
- * A factory for {@link ExtPackages.JAligner.ui.filechooser.FileChooser}.
+ * A factory for {@link ExternalPackages.JAligner.ui.filechooser.FileChooser}.
*
* @author Ahmed Moustafa
*/
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/filechooser/FileChooserJNLP.java b/DIA-Umpire/src/ExternalPackages/JAligner/ui/filechooser/FileChooserJNLP.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/filechooser/FileChooserJNLP.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/filechooser/FileChooserJNLP.java
index d0190c3..6fb290e 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/ui/filechooser/FileChooserJNLP.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/ui/filechooser/FileChooserJNLP.java
@@ -14,7 +14,7 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.ui.filechooser;
+package ExternalPackages.JAligner.ui.filechooser;
import java.io.InputStream;
import java.util.logging.Logger;
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/filechooser/FileChooserTrusted.java b/DIA-Umpire/src/ExternalPackages/JAligner/ui/filechooser/FileChooserTrusted.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/filechooser/FileChooserTrusted.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/filechooser/FileChooserTrusted.java
index c139391..2330b21 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/ui/filechooser/FileChooserTrusted.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/ui/filechooser/FileChooserTrusted.java
@@ -14,7 +14,7 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.ui.filechooser;
+package ExternalPackages.JAligner.ui.filechooser;
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/filechooser/NamedInputStream.java b/DIA-Umpire/src/ExternalPackages/JAligner/ui/filechooser/NamedInputStream.java
similarity index 96%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/filechooser/NamedInputStream.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/filechooser/NamedInputStream.java
index 40f3174..8958289 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/ui/filechooser/NamedInputStream.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/ui/filechooser/NamedInputStream.java
@@ -14,7 +14,7 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.ui.filechooser;
+package ExternalPackages.JAligner.ui.filechooser;
import java.io.InputStream;
import java.io.Serializable;
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/filechooser/package.html b/DIA-Umpire/src/ExternalPackages/JAligner/ui/filechooser/package.html
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/filechooser/package.html
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/filechooser/package.html
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/images/ToolbarIcons.java b/DIA-Umpire/src/ExternalPackages/JAligner/ui/images/ToolbarIcons.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/images/ToolbarIcons.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/images/ToolbarIcons.java
index deb545e..a00bb6b 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/ui/images/ToolbarIcons.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/ui/images/ToolbarIcons.java
@@ -14,7 +14,7 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.ui.images;
+package ExternalPackages.JAligner.ui.images;
import javax.swing.ImageIcon;
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/images/gifs/about.gif b/DIA-Umpire/src/ExternalPackages/JAligner/ui/images/gifs/about.gif
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/images/gifs/about.gif
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/images/gifs/about.gif
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/images/gifs/close.gif b/DIA-Umpire/src/ExternalPackages/JAligner/ui/images/gifs/close.gif
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/images/gifs/close.gif
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/images/gifs/close.gif
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/images/gifs/copy.gif b/DIA-Umpire/src/ExternalPackages/JAligner/ui/images/gifs/copy.gif
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/images/gifs/copy.gif
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/images/gifs/copy.gif
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/images/gifs/cut.gif b/DIA-Umpire/src/ExternalPackages/JAligner/ui/images/gifs/cut.gif
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/images/gifs/cut.gif
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/images/gifs/cut.gif
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/images/gifs/delete.gif b/DIA-Umpire/src/ExternalPackages/JAligner/ui/images/gifs/delete.gif
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/images/gifs/delete.gif
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/images/gifs/delete.gif
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/images/gifs/jaligner.gif b/DIA-Umpire/src/ExternalPackages/JAligner/ui/images/gifs/jaligner.gif
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/images/gifs/jaligner.gif
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/images/gifs/jaligner.gif
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/images/gifs/open.gif b/DIA-Umpire/src/ExternalPackages/JAligner/ui/images/gifs/open.gif
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/images/gifs/open.gif
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/images/gifs/open.gif
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/images/gifs/paste.gif b/DIA-Umpire/src/ExternalPackages/JAligner/ui/images/gifs/paste.gif
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/images/gifs/paste.gif
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/images/gifs/paste.gif
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/images/gifs/print.gif b/DIA-Umpire/src/ExternalPackages/JAligner/ui/images/gifs/print.gif
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/images/gifs/print.gif
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/images/gifs/print.gif
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/images/gifs/save.gif b/DIA-Umpire/src/ExternalPackages/JAligner/ui/images/gifs/save.gif
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/images/gifs/save.gif
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/images/gifs/save.gif
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/images/package.html b/DIA-Umpire/src/ExternalPackages/JAligner/ui/images/package.html
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/images/package.html
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/images/package.html
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/logging/DocumentHandler.java b/DIA-Umpire/src/ExternalPackages/JAligner/ui/logging/DocumentHandler.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/logging/DocumentHandler.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/logging/DocumentHandler.java
index 0fc18c9..e17e888 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/ui/logging/DocumentHandler.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/ui/logging/DocumentHandler.java
@@ -14,7 +14,7 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.ui.logging;
+package ExternalPackages.JAligner.ui.logging;
import java.awt.Color;
import java.util.logging.ErrorManager;
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/logging/RecordFormatter.java b/DIA-Umpire/src/ExternalPackages/JAligner/ui/logging/RecordFormatter.java
similarity index 97%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/logging/RecordFormatter.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/logging/RecordFormatter.java
index c704606..0f00080 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/ui/logging/RecordFormatter.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/ui/logging/RecordFormatter.java
@@ -14,7 +14,7 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.ui.logging;
+package ExternalPackages.JAligner.ui.logging;
import java.util.Date;
import java.util.logging.Formatter;
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/logging/package.html b/DIA-Umpire/src/ExternalPackages/JAligner/ui/logging/package.html
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/logging/package.html
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/logging/package.html
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/package.html b/DIA-Umpire/src/ExternalPackages/JAligner/ui/package.html
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/package.html
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/package.html
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/util/PrintJobMointor.java b/DIA-Umpire/src/ExternalPackages/JAligner/ui/util/PrintJobMointor.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/util/PrintJobMointor.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/util/PrintJobMointor.java
index 4d0e7b0..6e21cea 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/ui/util/PrintJobMointor.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/ui/util/PrintJobMointor.java
@@ -14,7 +14,7 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.ui.util;
+package ExternalPackages.JAligner.ui.util;
import java.util.logging.Level;
import java.util.logging.Logger;
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/util/TextComponentUtil.java b/DIA-Umpire/src/ExternalPackages/JAligner/ui/util/TextComponentUtil.java
similarity index 96%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/util/TextComponentUtil.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/util/TextComponentUtil.java
index ab7423d..c1cb20c 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/ui/util/TextComponentUtil.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/ui/util/TextComponentUtil.java
@@ -14,12 +14,12 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.ui.util;
+package ExternalPackages.JAligner.ui.util;
-import ExtPackages.JAligner.ui.clipboard.ClipboardHandlerFactory;
-import ExtPackages.JAligner.ui.filechooser.FileChooserFactory;
-import ExtPackages.JAligner.ui.filechooser.NamedInputStream;
-import ExtPackages.JAligner.util.Commons;
+import ExternalPackages.JAligner.ui.clipboard.ClipboardHandlerFactory;
+import ExternalPackages.JAligner.ui.filechooser.FileChooserFactory;
+import ExternalPackages.JAligner.ui.filechooser.NamedInputStream;
+import ExternalPackages.JAligner.util.Commons;
import java.io.BufferedReader;
import java.io.ByteArrayInputStream;
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/util/TextComponentUtilException.java b/DIA-Umpire/src/ExternalPackages/JAligner/ui/util/TextComponentUtilException.java
similarity index 95%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/util/TextComponentUtilException.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/util/TextComponentUtilException.java
index 1179e6b..e97b46d 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/ui/util/TextComponentUtilException.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/ui/util/TextComponentUtilException.java
@@ -14,7 +14,7 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.ui.util;
+package ExternalPackages.JAligner.ui.util;
/**
*
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/ui/util/package.html b/DIA-Umpire/src/ExternalPackages/JAligner/ui/util/package.html
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/ui/util/package.html
rename to DIA-Umpire/src/ExternalPackages/JAligner/ui/util/package.html
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/util/Commons.java b/DIA-Umpire/src/ExternalPackages/JAligner/util/Commons.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/JAligner/util/Commons.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/util/Commons.java
index a16468f..28a5e73 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/util/Commons.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/util/Commons.java
@@ -13,7 +13,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.util;
+package ExternalPackages.JAligner.util;
import java.net.JarURLConnection;
import java.net.URL;
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/util/SequenceParser.java b/DIA-Umpire/src/ExternalPackages/JAligner/util/SequenceParser.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/JAligner/util/SequenceParser.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/util/SequenceParser.java
index e03cff7..a534a40 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/util/SequenceParser.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/util/SequenceParser.java
@@ -14,10 +14,10 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.util;
+package ExternalPackages.JAligner.util;
-import ExtPackages.JAligner.Sequence;
+import ExternalPackages.JAligner.Sequence;
import java.io.BufferedReader;
import java.io.File;
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/util/SequenceParserException.java b/DIA-Umpire/src/ExternalPackages/JAligner/util/SequenceParserException.java
similarity index 96%
rename from DIA-Umpire/src/ExtPackages/JAligner/util/SequenceParserException.java
rename to DIA-Umpire/src/ExternalPackages/JAligner/util/SequenceParserException.java
index 8582d33..35f6a14 100644
--- a/DIA-Umpire/src/ExtPackages/JAligner/util/SequenceParserException.java
+++ b/DIA-Umpire/src/ExternalPackages/JAligner/util/SequenceParserException.java
@@ -14,7 +14,7 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-package ExtPackages.JAligner.util;
+package ExternalPackages.JAligner.util;
/**
*
diff --git a/DIA-Umpire/src/ExtPackages/JAligner/util/package.html b/DIA-Umpire/src/ExternalPackages/JAligner/util/package.html
similarity index 100%
rename from DIA-Umpire/src/ExtPackages/JAligner/util/package.html
rename to DIA-Umpire/src/ExternalPackages/JAligner/util/package.html
diff --git a/DIA-Umpire/src/ExtPackages/SortedListLib/Alteration.java b/DIA-Umpire/src/ExternalPackages/SortedListLib/Alteration.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/SortedListLib/Alteration.java
rename to DIA-Umpire/src/ExternalPackages/SortedListLib/Alteration.java
index 6b8d6aa..c5838fe 100644
--- a/DIA-Umpire/src/ExtPackages/SortedListLib/Alteration.java
+++ b/DIA-Umpire/src/ExternalPackages/SortedListLib/Alteration.java
@@ -1,4 +1,4 @@
-package ExtPackages.SortedListLib;
+package ExternalPackages.SortedListLib;
/**
* Represents the alterations to the backingList of a {@code PatchWorkArray}.
diff --git a/DIA-Umpire/src/ExtPackages/SortedListLib/AlterationList.java b/DIA-Umpire/src/ExternalPackages/SortedListLib/AlterationList.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/SortedListLib/AlterationList.java
rename to DIA-Umpire/src/ExternalPackages/SortedListLib/AlterationList.java
index a82290d..323afe4 100644
--- a/DIA-Umpire/src/ExtPackages/SortedListLib/AlterationList.java
+++ b/DIA-Umpire/src/ExternalPackages/SortedListLib/AlterationList.java
@@ -1,4 +1,4 @@
-package ExtPackages.SortedListLib;
+package ExternalPackages.SortedListLib;
import java.util.ConcurrentModificationException;
import java.util.Iterator;
diff --git a/DIA-Umpire/src/ExtPackages/SortedListLib/ArrayLocation.java b/DIA-Umpire/src/ExternalPackages/SortedListLib/ArrayLocation.java
similarity index 97%
rename from DIA-Umpire/src/ExtPackages/SortedListLib/ArrayLocation.java
rename to DIA-Umpire/src/ExternalPackages/SortedListLib/ArrayLocation.java
index fe7474e..72fbc07 100644
--- a/DIA-Umpire/src/ExtPackages/SortedListLib/ArrayLocation.java
+++ b/DIA-Umpire/src/ExternalPackages/SortedListLib/ArrayLocation.java
@@ -1,4 +1,4 @@
-package ExtPackages.SortedListLib;
+package ExternalPackages.SortedListLib;
/**
* Simple class to define a location within the a patch work array.
diff --git a/DIA-Umpire/src/ExtPackages/SortedListLib/NaturalSortedList.java b/DIA-Umpire/src/ExternalPackages/SortedListLib/NaturalSortedList.java
similarity index 94%
rename from DIA-Umpire/src/ExtPackages/SortedListLib/NaturalSortedList.java
rename to DIA-Umpire/src/ExternalPackages/SortedListLib/NaturalSortedList.java
index 74ea572..33b3ac1 100644
--- a/DIA-Umpire/src/ExtPackages/SortedListLib/NaturalSortedList.java
+++ b/DIA-Umpire/src/ExternalPackages/SortedListLib/NaturalSortedList.java
@@ -1,4 +1,4 @@
-package ExtPackages.SortedListLib;
+package ExternalPackages.SortedListLib;
import java.util.Comparator;
diff --git a/DIA-Umpire/src/ExtPackages/SortedListLib/PatchWorkArray.java b/DIA-Umpire/src/ExternalPackages/SortedListLib/PatchWorkArray.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/SortedListLib/PatchWorkArray.java
rename to DIA-Umpire/src/ExternalPackages/SortedListLib/PatchWorkArray.java
index a902056..559a243 100644
--- a/DIA-Umpire/src/ExtPackages/SortedListLib/PatchWorkArray.java
+++ b/DIA-Umpire/src/ExternalPackages/SortedListLib/PatchWorkArray.java
@@ -1,4 +1,4 @@
-package ExtPackages.SortedListLib;
+package ExternalPackages.SortedListLib;
import java.io.Serializable;
import java.util.*;
diff --git a/DIA-Umpire/src/ExtPackages/SortedListLib/SortedList.java b/DIA-Umpire/src/ExternalPackages/SortedListLib/SortedList.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/SortedListLib/SortedList.java
rename to DIA-Umpire/src/ExternalPackages/SortedListLib/SortedList.java
index e1a1e9e..36dd021 100644
--- a/DIA-Umpire/src/ExtPackages/SortedListLib/SortedList.java
+++ b/DIA-Umpire/src/ExternalPackages/SortedListLib/SortedList.java
@@ -1,4 +1,4 @@
-package ExtPackages.SortedListLib;
+package ExternalPackages.SortedListLib;
import java.io.Serializable;
import java.lang.reflect.Array;
diff --git a/DIA-Umpire/src/ExtPackages/SortedListLib/UnsortedList.java b/DIA-Umpire/src/ExternalPackages/SortedListLib/UnsortedList.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/SortedListLib/UnsortedList.java
rename to DIA-Umpire/src/ExternalPackages/SortedListLib/UnsortedList.java
index 18c6bc0..8860ff8 100644
--- a/DIA-Umpire/src/ExtPackages/SortedListLib/UnsortedList.java
+++ b/DIA-Umpire/src/ExternalPackages/SortedListLib/UnsortedList.java
@@ -1,4 +1,4 @@
-package ExtPackages.SortedListLib;
+package ExternalPackages.SortedListLib;
import java.util.*;
diff --git a/DIA-Umpire/src/ExtPackages/jMEF/Bernoulli.java b/DIA-Umpire/src/ExternalPackages/jMEF/Bernoulli.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/jMEF/Bernoulli.java
rename to DIA-Umpire/src/ExternalPackages/jMEF/Bernoulli.java
index 601ecd7..f58c506 100644
--- a/DIA-Umpire/src/ExtPackages/jMEF/Bernoulli.java
+++ b/DIA-Umpire/src/ExternalPackages/jMEF/Bernoulli.java
@@ -1,6 +1,6 @@
-package ExtPackages.jMEF;
+package ExternalPackages.jMEF;
-import ExtPackages.jMEF.Parameter.TYPE;
+import ExternalPackages.jMEF.Parameter.TYPE;
/**
* @author Vincent Garcia
diff --git a/DIA-Umpire/src/ExtPackages/jMEF/BinomialFixedN.java b/DIA-Umpire/src/ExternalPackages/jMEF/BinomialFixedN.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/jMEF/BinomialFixedN.java
rename to DIA-Umpire/src/ExternalPackages/jMEF/BinomialFixedN.java
index 4566873..0d12c18 100644
--- a/DIA-Umpire/src/ExtPackages/jMEF/BinomialFixedN.java
+++ b/DIA-Umpire/src/ExternalPackages/jMEF/BinomialFixedN.java
@@ -1,6 +1,6 @@
-package ExtPackages.jMEF;
+package ExternalPackages.jMEF;
-import ExtPackages.jMEF.Parameter.TYPE;
+import ExternalPackages.jMEF.Parameter.TYPE;
/**
* @author Vincent Garcia
diff --git a/DIA-Umpire/src/ExtPackages/jMEF/BregmanHardClustering.java b/DIA-Umpire/src/ExternalPackages/jMEF/BregmanHardClustering.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/jMEF/BregmanHardClustering.java
rename to DIA-Umpire/src/ExternalPackages/jMEF/BregmanHardClustering.java
index a57e7de..5683f7e 100644
--- a/DIA-Umpire/src/ExtPackages/jMEF/BregmanHardClustering.java
+++ b/DIA-Umpire/src/ExternalPackages/jMEF/BregmanHardClustering.java
@@ -1,6 +1,6 @@
-package ExtPackages.jMEF;
+package ExternalPackages.jMEF;
-import ExtPackages.jMEF.Clustering.CLUSTERING_TYPE;
+import ExternalPackages.jMEF.Clustering.CLUSTERING_TYPE;
import java.util.Arrays;
import java.util.Random;
diff --git a/DIA-Umpire/src/ExtPackages/jMEF/BregmanHierarchicalClustering.java b/DIA-Umpire/src/ExternalPackages/jMEF/BregmanHierarchicalClustering.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/jMEF/BregmanHierarchicalClustering.java
rename to DIA-Umpire/src/ExternalPackages/jMEF/BregmanHierarchicalClustering.java
index 2b09650..c84f075 100644
--- a/DIA-Umpire/src/ExtPackages/jMEF/BregmanHierarchicalClustering.java
+++ b/DIA-Umpire/src/ExternalPackages/jMEF/BregmanHierarchicalClustering.java
@@ -1,6 +1,6 @@
-package ExtPackages.jMEF;
+package ExternalPackages.jMEF;
-import ExtPackages.jMEF.Clustering.CLUSTERING_TYPE;
+import ExternalPackages.jMEF.Clustering.CLUSTERING_TYPE;
/**
* @author Vincent Garcia
diff --git a/DIA-Umpire/src/ExtPackages/jMEF/BregmanSoftClustering.java b/DIA-Umpire/src/ExternalPackages/jMEF/BregmanSoftClustering.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/jMEF/BregmanSoftClustering.java
rename to DIA-Umpire/src/ExternalPackages/jMEF/BregmanSoftClustering.java
index 0cbfd87..070da31 100644
--- a/DIA-Umpire/src/ExtPackages/jMEF/BregmanSoftClustering.java
+++ b/DIA-Umpire/src/ExternalPackages/jMEF/BregmanSoftClustering.java
@@ -1,8 +1,8 @@
-package ExtPackages.jMEF;
+package ExternalPackages.jMEF;
import java.util.Vector;
-import ExtPackages.jMEF.Parameter.TYPE;
+import ExternalPackages.jMEF.Parameter.TYPE;
/**
* @author Vincent Garcia
diff --git a/DIA-Umpire/src/ExtPackages/jMEF/Clustering.java b/DIA-Umpire/src/ExternalPackages/jMEF/Clustering.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/jMEF/Clustering.java
rename to DIA-Umpire/src/ExternalPackages/jMEF/Clustering.java
index fc84f39..7062b6c 100644
--- a/DIA-Umpire/src/ExtPackages/jMEF/Clustering.java
+++ b/DIA-Umpire/src/ExternalPackages/jMEF/Clustering.java
@@ -1,4 +1,4 @@
-package ExtPackages.jMEF;
+package ExternalPackages.jMEF;
/**
* @author Vincent Garcia
diff --git a/DIA-Umpire/src/ExtPackages/jMEF/ExpectationMaximization1D.java b/DIA-Umpire/src/ExternalPackages/jMEF/ExpectationMaximization1D.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/jMEF/ExpectationMaximization1D.java
rename to DIA-Umpire/src/ExternalPackages/jMEF/ExpectationMaximization1D.java
index 7d3e63c..4c8d6e3 100644
--- a/DIA-Umpire/src/ExtPackages/jMEF/ExpectationMaximization1D.java
+++ b/DIA-Umpire/src/ExternalPackages/jMEF/ExpectationMaximization1D.java
@@ -1,4 +1,4 @@
-package ExtPackages.jMEF;
+package ExternalPackages.jMEF;
import java.util.Vector;
diff --git a/DIA-Umpire/src/ExtPackages/jMEF/ExponentialFamily.java b/DIA-Umpire/src/ExternalPackages/jMEF/ExponentialFamily.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/jMEF/ExponentialFamily.java
rename to DIA-Umpire/src/ExternalPackages/jMEF/ExponentialFamily.java
index dedc1ce..eae2bcd 100644
--- a/DIA-Umpire/src/ExtPackages/jMEF/ExponentialFamily.java
+++ b/DIA-Umpire/src/ExternalPackages/jMEF/ExponentialFamily.java
@@ -1,4 +1,4 @@
-package ExtPackages.jMEF;
+package ExternalPackages.jMEF;
import java.io.Serializable;
diff --git a/DIA-Umpire/src/ExtPackages/jMEF/HierarchicalMixtureModel.java b/DIA-Umpire/src/ExternalPackages/jMEF/HierarchicalMixtureModel.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/jMEF/HierarchicalMixtureModel.java
rename to DIA-Umpire/src/ExternalPackages/jMEF/HierarchicalMixtureModel.java
index 2cf02c6..dc7af78 100644
--- a/DIA-Umpire/src/ExtPackages/jMEF/HierarchicalMixtureModel.java
+++ b/DIA-Umpire/src/ExternalPackages/jMEF/HierarchicalMixtureModel.java
@@ -1,6 +1,6 @@
-package ExtPackages.jMEF;
+package ExternalPackages.jMEF;
-import ExtPackages.jMEF.Clustering.CLUSTERING_TYPE;
+import ExternalPackages.jMEF.Clustering.CLUSTERING_TYPE;
/**
* @author Vincent Garcia
diff --git a/DIA-Umpire/src/ExtPackages/jMEF/Laplacian.java b/DIA-Umpire/src/ExternalPackages/jMEF/Laplacian.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/jMEF/Laplacian.java
rename to DIA-Umpire/src/ExternalPackages/jMEF/Laplacian.java
index 2fb5ef6..1059896 100644
--- a/DIA-Umpire/src/ExtPackages/jMEF/Laplacian.java
+++ b/DIA-Umpire/src/ExternalPackages/jMEF/Laplacian.java
@@ -1,6 +1,6 @@
-package ExtPackages.jMEF;
+package ExternalPackages.jMEF;
-import ExtPackages.jMEF.Parameter.TYPE;
+import ExternalPackages.jMEF.Parameter.TYPE;
/**
* @author Vincent Garcia
diff --git a/DIA-Umpire/src/ExtPackages/jMEF/MixtureModel.java b/DIA-Umpire/src/ExternalPackages/jMEF/MixtureModel.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/jMEF/MixtureModel.java
rename to DIA-Umpire/src/ExternalPackages/jMEF/MixtureModel.java
index 8635731..3b1df56 100644
--- a/DIA-Umpire/src/ExtPackages/jMEF/MixtureModel.java
+++ b/DIA-Umpire/src/ExternalPackages/jMEF/MixtureModel.java
@@ -1,4 +1,4 @@
-package ExtPackages.jMEF;
+package ExternalPackages.jMEF;
import java.io.FileInputStream;
import java.io.FileOutputStream;
diff --git a/DIA-Umpire/src/ExtPackages/jMEF/MultinomialFixedN.java b/DIA-Umpire/src/ExternalPackages/jMEF/MultinomialFixedN.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/jMEF/MultinomialFixedN.java
rename to DIA-Umpire/src/ExternalPackages/jMEF/MultinomialFixedN.java
index 20eea84..137b876 100644
--- a/DIA-Umpire/src/ExtPackages/jMEF/MultinomialFixedN.java
+++ b/DIA-Umpire/src/ExternalPackages/jMEF/MultinomialFixedN.java
@@ -1,6 +1,6 @@
-package ExtPackages.jMEF;
+package ExternalPackages.jMEF;
-import ExtPackages.jMEF.Parameter.TYPE;
+import ExternalPackages.jMEF.Parameter.TYPE;
/**
* @author Vincent Garcia
diff --git a/DIA-Umpire/src/ExtPackages/jMEF/MultivariateGaussian.java b/DIA-Umpire/src/ExternalPackages/jMEF/MultivariateGaussian.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/jMEF/MultivariateGaussian.java
rename to DIA-Umpire/src/ExternalPackages/jMEF/MultivariateGaussian.java
index 9376cb2..939b2de 100644
--- a/DIA-Umpire/src/ExtPackages/jMEF/MultivariateGaussian.java
+++ b/DIA-Umpire/src/ExternalPackages/jMEF/MultivariateGaussian.java
@@ -1,6 +1,6 @@
-package ExtPackages.jMEF;
+package ExternalPackages.jMEF;
-import ExtPackages.jMEF.Parameter.TYPE;
+import ExternalPackages.jMEF.Parameter.TYPE;
import java.util.Random;
diff --git a/DIA-Umpire/src/ExtPackages/jMEF/MultivariateIsotropicGaussian.java b/DIA-Umpire/src/ExternalPackages/jMEF/MultivariateIsotropicGaussian.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/jMEF/MultivariateIsotropicGaussian.java
rename to DIA-Umpire/src/ExternalPackages/jMEF/MultivariateIsotropicGaussian.java
index 6adb3f9..d3971da 100644
--- a/DIA-Umpire/src/ExtPackages/jMEF/MultivariateIsotropicGaussian.java
+++ b/DIA-Umpire/src/ExternalPackages/jMEF/MultivariateIsotropicGaussian.java
@@ -1,6 +1,6 @@
-package ExtPackages.jMEF;
+package ExternalPackages.jMEF;
-import ExtPackages.jMEF.Parameter.TYPE;
+import ExternalPackages.jMEF.Parameter.TYPE;
import java.util.Random;
diff --git a/DIA-Umpire/src/ExtPackages/jMEF/PMatrix.java b/DIA-Umpire/src/ExternalPackages/jMEF/PMatrix.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/jMEF/PMatrix.java
rename to DIA-Umpire/src/ExternalPackages/jMEF/PMatrix.java
index cce6333..accca03 100644
--- a/DIA-Umpire/src/ExtPackages/jMEF/PMatrix.java
+++ b/DIA-Umpire/src/ExternalPackages/jMEF/PMatrix.java
@@ -1,4 +1,4 @@
-package ExtPackages.jMEF;
+package ExternalPackages.jMEF;
import java.util.Arrays;
import java.util.Locale;
diff --git a/DIA-Umpire/src/ExtPackages/jMEF/PVector.java b/DIA-Umpire/src/ExternalPackages/jMEF/PVector.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/jMEF/PVector.java
rename to DIA-Umpire/src/ExternalPackages/jMEF/PVector.java
index 21aff75..5cd421b 100644
--- a/DIA-Umpire/src/ExtPackages/jMEF/PVector.java
+++ b/DIA-Umpire/src/ExternalPackages/jMEF/PVector.java
@@ -1,4 +1,4 @@
-package ExtPackages.jMEF;
+package ExternalPackages.jMEF;
import java.util.Arrays;
import java.util.Locale;
diff --git a/DIA-Umpire/src/ExtPackages/jMEF/PVectorMatrix.java b/DIA-Umpire/src/ExternalPackages/jMEF/PVectorMatrix.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/jMEF/PVectorMatrix.java
rename to DIA-Umpire/src/ExternalPackages/jMEF/PVectorMatrix.java
index 8d6b5b6..670a1e9 100644
--- a/DIA-Umpire/src/ExtPackages/jMEF/PVectorMatrix.java
+++ b/DIA-Umpire/src/ExternalPackages/jMEF/PVectorMatrix.java
@@ -1,4 +1,4 @@
-package ExtPackages.jMEF;
+package ExternalPackages.jMEF;
/**
* @author Vincent Garcia
diff --git a/DIA-Umpire/src/ExtPackages/jMEF/Parameter.java b/DIA-Umpire/src/ExternalPackages/jMEF/Parameter.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/jMEF/Parameter.java
rename to DIA-Umpire/src/ExternalPackages/jMEF/Parameter.java
index 94df70a..7b551d0 100644
--- a/DIA-Umpire/src/ExtPackages/jMEF/Parameter.java
+++ b/DIA-Umpire/src/ExternalPackages/jMEF/Parameter.java
@@ -1,4 +1,4 @@
-package ExtPackages.jMEF;
+package ExternalPackages.jMEF;
import java.io.Serializable;
diff --git a/DIA-Umpire/src/ExtPackages/jMEF/Poisson.java b/DIA-Umpire/src/ExternalPackages/jMEF/Poisson.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/jMEF/Poisson.java
rename to DIA-Umpire/src/ExternalPackages/jMEF/Poisson.java
index 02e87f0..167eb8a 100644
--- a/DIA-Umpire/src/ExtPackages/jMEF/Poisson.java
+++ b/DIA-Umpire/src/ExternalPackages/jMEF/Poisson.java
@@ -1,6 +1,6 @@
-package ExtPackages.jMEF;
+package ExternalPackages.jMEF;
-import ExtPackages.jMEF.Parameter.TYPE;
+import ExternalPackages.jMEF.Parameter.TYPE;
/**
* @author Vincent Garcia
diff --git a/DIA-Umpire/src/ExtPackages/jMEF/Quicksort.java b/DIA-Umpire/src/ExternalPackages/jMEF/Quicksort.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/jMEF/Quicksort.java
rename to DIA-Umpire/src/ExternalPackages/jMEF/Quicksort.java
index 18fbf9e..6f00d4b 100644
--- a/DIA-Umpire/src/ExtPackages/jMEF/Quicksort.java
+++ b/DIA-Umpire/src/ExternalPackages/jMEF/Quicksort.java
@@ -1,4 +1,4 @@
-package ExtPackages.jMEF;
+package ExternalPackages.jMEF;
/**
* @author Vincent Garcia
diff --git a/DIA-Umpire/src/ExtPackages/jMEF/Rayleigh.java b/DIA-Umpire/src/ExternalPackages/jMEF/Rayleigh.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/jMEF/Rayleigh.java
rename to DIA-Umpire/src/ExternalPackages/jMEF/Rayleigh.java
index c70da29..5799087 100644
--- a/DIA-Umpire/src/ExtPackages/jMEF/Rayleigh.java
+++ b/DIA-Umpire/src/ExternalPackages/jMEF/Rayleigh.java
@@ -1,6 +1,6 @@
-package ExtPackages.jMEF;
+package ExternalPackages.jMEF;
-import ExtPackages.jMEF.Parameter.TYPE;
+import ExternalPackages.jMEF.Parameter.TYPE;
/**
* @author Vincent Garcia
diff --git a/DIA-Umpire/src/ExtPackages/jMEF/UnivariateGaussian.java b/DIA-Umpire/src/ExternalPackages/jMEF/UnivariateGaussian.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/jMEF/UnivariateGaussian.java
rename to DIA-Umpire/src/ExternalPackages/jMEF/UnivariateGaussian.java
index 8c4d9d4..a608f77 100644
--- a/DIA-Umpire/src/ExtPackages/jMEF/UnivariateGaussian.java
+++ b/DIA-Umpire/src/ExternalPackages/jMEF/UnivariateGaussian.java
@@ -1,6 +1,6 @@
-package ExtPackages.jMEF;
+package ExternalPackages.jMEF;
-import ExtPackages.jMEF.Parameter.TYPE;
+import ExternalPackages.jMEF.Parameter.TYPE;
import java.util.Random;
diff --git a/DIA-Umpire/src/ExtPackages/jMEF/UnivariateGaussianFixedVariance.java b/DIA-Umpire/src/ExternalPackages/jMEF/UnivariateGaussianFixedVariance.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/jMEF/UnivariateGaussianFixedVariance.java
rename to DIA-Umpire/src/ExternalPackages/jMEF/UnivariateGaussianFixedVariance.java
index 2bf5bfd..e55844b 100644
--- a/DIA-Umpire/src/ExtPackages/jMEF/UnivariateGaussianFixedVariance.java
+++ b/DIA-Umpire/src/ExternalPackages/jMEF/UnivariateGaussianFixedVariance.java
@@ -1,8 +1,8 @@
-package ExtPackages.jMEF;
+package ExternalPackages.jMEF;
import java.util.Random;
-import ExtPackages.jMEF.Parameter.TYPE;
+import ExternalPackages.jMEF.Parameter.TYPE;
/**
* @author Vincent Garcia
diff --git a/DIA-Umpire/src/ExtPackages/jMEF/jMEFException.java b/DIA-Umpire/src/ExternalPackages/jMEF/jMEFException.java
similarity index 96%
rename from DIA-Umpire/src/ExtPackages/jMEF/jMEFException.java
rename to DIA-Umpire/src/ExternalPackages/jMEF/jMEFException.java
index dd26c36..bbe4470 100644
--- a/DIA-Umpire/src/ExtPackages/jMEF/jMEFException.java
+++ b/DIA-Umpire/src/ExternalPackages/jMEF/jMEFException.java
@@ -1,4 +1,4 @@
-package ExtPackages.jMEF;
+package ExternalPackages.jMEF;
/**
* @author Vincent Garcia
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/CompoundListType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/CompoundListType.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/CompoundListType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/CompoundListType.java
index a79c9e2..0be3fd7 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/CompoundListType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/CompoundListType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/CompoundType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/CompoundType.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/CompoundType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/CompoundType.java
index 8b773a6..7fb9c08 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/CompoundType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/CompoundType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ConfigurationListType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ConfigurationListType.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ConfigurationListType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ConfigurationListType.java
index 8739dd6..9419d8c 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ConfigurationListType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ConfigurationListType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ConfigurationType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ConfigurationType.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ConfigurationType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ConfigurationType.java
index 62a912d..84eed08 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ConfigurationType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ConfigurationType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ContactListType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ContactListType.java
similarity index 97%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ContactListType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ContactListType.java
index 1159525..655e0d9 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ContactListType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ContactListType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ContactType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ContactType.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ContactType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ContactType.java
index 09dc66b..095e953 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ContactType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ContactType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/CvListType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/CvListType.java
similarity index 97%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/CvListType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/CvListType.java
index d706d8d..022d9e5 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/CvListType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/CvListType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/CvParamType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/CvParamType.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/CvParamType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/CvParamType.java
index 7bb1f54..87c2fd7 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/CvParamType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/CvParamType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/CvType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/CvType.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/CvType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/CvType.java
index 1021603..fb3dbc6 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/CvType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/CvType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/EvidenceType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/EvidenceType.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/EvidenceType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/EvidenceType.java
index fe383ac..001f7fe 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/EvidenceType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/EvidenceType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/InstrumentListType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/InstrumentListType.java
similarity index 97%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/InstrumentListType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/InstrumentListType.java
index 52f0978..81a3efe 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/InstrumentListType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/InstrumentListType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/InstrumentType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/InstrumentType.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/InstrumentType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/InstrumentType.java
index 31b9cef..377d8fc 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/InstrumentType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/InstrumentType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/IntermediateProductType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/IntermediateProductType.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/IntermediateProductType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/IntermediateProductType.java
index 8a66a3a..aafef59 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/IntermediateProductType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/IntermediateProductType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/InterpretationListType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/InterpretationListType.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/InterpretationListType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/InterpretationListType.java
index 8c366ac..a0eecdf 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/InterpretationListType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/InterpretationListType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/InterpretationType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/InterpretationType.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/InterpretationType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/InterpretationType.java
index 93b5f44..d9aa148 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/InterpretationType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/InterpretationType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ModificationType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ModificationType.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ModificationType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ModificationType.java
index abf6e6a..6e4e2b0 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ModificationType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ModificationType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ObjectFactory.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ObjectFactory.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ObjectFactory.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ObjectFactory.java
index 325f8c2..b245589 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ObjectFactory.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ObjectFactory.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import javax.xml.bind.JAXBElement;
import javax.xml.bind.annotation.XmlElementDecl;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/PeptideType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/PeptideType.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/PeptideType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/PeptideType.java
index c3559fb..401a7c6 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/PeptideType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/PeptideType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/PrecursorType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/PrecursorType.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/PrecursorType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/PrecursorType.java
index 102e3ff..daa3eb6 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/PrecursorType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/PrecursorType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/PredictionType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/PredictionType.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/PredictionType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/PredictionType.java
index 80bf10f..4088fd8 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/PredictionType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/PredictionType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ProductType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ProductType.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ProductType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ProductType.java
index 4fc6723..702961e 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ProductType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ProductType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ProteinListType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ProteinListType.java
similarity index 97%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ProteinListType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ProteinListType.java
index d4874d2..907a472 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ProteinListType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ProteinListType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ProteinRefType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ProteinRefType.java
similarity index 97%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ProteinRefType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ProteinRefType.java
index 7146a07..73e7212 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ProteinRefType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ProteinRefType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ProteinType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ProteinType.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ProteinType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ProteinType.java
index abf8480..714d171 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ProteinType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ProteinType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/PublicationListType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/PublicationListType.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/PublicationListType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/PublicationListType.java
index a023f46..441458a 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/PublicationListType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/PublicationListType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/PublicationType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/PublicationType.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/PublicationType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/PublicationType.java
index 690ce32..b92e1bb 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/PublicationType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/PublicationType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/RetentionTimeListType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/RetentionTimeListType.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/RetentionTimeListType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/RetentionTimeListType.java
index 52c1c34..72587f4 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/RetentionTimeListType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/RetentionTimeListType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/RetentionTimeType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/RetentionTimeType.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/RetentionTimeType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/RetentionTimeType.java
index 9b0e5f0..80a9cf2 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/RetentionTimeType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/RetentionTimeType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/SequenceType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/SequenceType.java
similarity index 97%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/SequenceType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/SequenceType.java
index 7a9c19e..0be0f24 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/SequenceType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/SequenceType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/SoftwareListType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/SoftwareListType.java
similarity index 97%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/SoftwareListType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/SoftwareListType.java
index 503f77a..e9915a3 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/SoftwareListType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/SoftwareListType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/SoftwareType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/SoftwareType.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/SoftwareType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/SoftwareType.java
index 96aaee9..9154068 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/SoftwareType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/SoftwareType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/SourceFileListType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/SourceFileListType.java
similarity index 97%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/SourceFileListType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/SourceFileListType.java
index 13e5b54..5be93a5 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/SourceFileListType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/SourceFileListType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/SourceFileType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/SourceFileType.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/SourceFileType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/SourceFileType.java
index 292d24f..5f93f00 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/SourceFileType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/SourceFileType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/TargetExcludeListType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/TargetExcludeListType.java
similarity index 97%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/TargetExcludeListType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/TargetExcludeListType.java
index 1aad352..2c89711 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/TargetExcludeListType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/TargetExcludeListType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/TargetIncludeListType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/TargetIncludeListType.java
similarity index 97%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/TargetIncludeListType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/TargetIncludeListType.java
index a5913c9..f8f9c0c 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/TargetIncludeListType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/TargetIncludeListType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/TargetListType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/TargetListType.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/TargetListType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/TargetListType.java
index 80ca799..e6d650f 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/TargetListType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/TargetListType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/TargetType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/TargetType.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/TargetType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/TargetType.java
index 8fb04a0..cc20467 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/TargetType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/TargetType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/TraMLType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/TraMLType.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/TraMLType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/TraMLType.java
index 726abed..ace6ded 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/TraMLType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/TraMLType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/TransitionListType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/TransitionListType.java
similarity index 97%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/TransitionListType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/TransitionListType.java
index 12e5979..fe06ab0 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/TransitionListType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/TransitionListType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/TransitionType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/TransitionType.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/TransitionType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/TransitionType.java
index 496fadc..5eaa6ef 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/TransitionType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/TransitionType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/UserParamType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/UserParamType.java
similarity index 99%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/UserParamType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/UserParamType.java
index 1a50d8a..a782600 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/UserParamType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/UserParamType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ValidationStatusType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ValidationStatusType.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ValidationStatusType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ValidationStatusType.java
index 31d869d..fd473c5 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ValidationStatusType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ValidationStatusType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ValidationType.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ValidationType.java
similarity index 97%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ValidationType.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ValidationType.java
index 0bedf1d..9934889 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/ValidationType.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/ValidationType.java
@@ -6,7 +6,7 @@
//
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
import java.util.ArrayList;
import java.util.List;
diff --git a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/package-info.java b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/package-info.java
similarity index 91%
rename from DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/package-info.java
rename to DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/package-info.java
index 03c04f6..e7be66a 100644
--- a/DIA-Umpire/src/ExtPackages/org/hupo/psi/ms/traml/package-info.java
+++ b/DIA-Umpire/src/ExternalPackages/org/hupo/psi/ms/traml/package-info.java
@@ -6,4 +6,4 @@
//
@javax.xml.bind.annotation.XmlSchema(namespace = "http://psi.hupo.org/ms/traml", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
-package ExtPackages.org.hupo.psi.ms.traml;
+package ExternalPackages.org.hupo.psi.ms.traml;
diff --git a/DIA-Umpire/src/ExtPackages/org/systemsbiology/apps/tramlcreator/TraMLCreator.java b/DIA-Umpire/src/ExternalPackages/org/systemsbiology/apps/tramlcreator/TraMLCreator.java
similarity index 91%
rename from DIA-Umpire/src/ExtPackages/org/systemsbiology/apps/tramlcreator/TraMLCreator.java
rename to DIA-Umpire/src/ExternalPackages/org/systemsbiology/apps/tramlcreator/TraMLCreator.java
index b2a8d5a..a525edd 100644
--- a/DIA-Umpire/src/ExtPackages/org/systemsbiology/apps/tramlcreator/TraMLCreator.java
+++ b/DIA-Umpire/src/ExternalPackages/org/systemsbiology/apps/tramlcreator/TraMLCreator.java
@@ -21,11 +21,11 @@
* mbrusniak@systemsbiology.org
*
*/
-package ExtPackages.org.systemsbiology.apps.tramlcreator;
+package ExternalPackages.org.systemsbiology.apps.tramlcreator;
-import ExtPackages.org.hupo.psi.ms.traml.TraMLType;
-import ExtPackages.org.systemsbiology.constants.JTRAML_URL;
+import ExternalPackages.org.hupo.psi.ms.traml.TraMLType;
+import ExternalPackages.org.systemsbiology.constants.JTRAML_URL;
import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBElement;
diff --git a/DIA-Umpire/src/ExtPackages/org/systemsbiology/apps/tramlparser/TraMLParser.java b/DIA-Umpire/src/ExternalPackages/org/systemsbiology/apps/tramlparser/TraMLParser.java
similarity index 96%
rename from DIA-Umpire/src/ExtPackages/org/systemsbiology/apps/tramlparser/TraMLParser.java
rename to DIA-Umpire/src/ExternalPackages/org/systemsbiology/apps/tramlparser/TraMLParser.java
index 622b193..00ab29a 100644
--- a/DIA-Umpire/src/ExtPackages/org/systemsbiology/apps/tramlparser/TraMLParser.java
+++ b/DIA-Umpire/src/ExternalPackages/org/systemsbiology/apps/tramlparser/TraMLParser.java
@@ -49,13 +49,13 @@
* dcampbell@systemsbiology.org
*
*/
-package ExtPackages.org.systemsbiology.apps.tramlparser;
+package ExternalPackages.org.systemsbiology.apps.tramlparser;
// Core
import org.apache.log4j.Logger;
-import ExtPackages.org.hupo.psi.ms.traml.TraMLType;
-import ExtPackages.org.systemsbiology.constants.JTRAML_URL;
+import ExternalPackages.org.hupo.psi.ms.traml.TraMLType;
+import ExternalPackages.org.systemsbiology.constants.JTRAML_URL;
import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBElement;
diff --git a/DIA-Umpire/src/ExtPackages/org/systemsbiology/apps/tramlparser/TraMLParserApp.java b/DIA-Umpire/src/ExternalPackages/org/systemsbiology/apps/tramlparser/TraMLParserApp.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/org/systemsbiology/apps/tramlparser/TraMLParserApp.java
rename to DIA-Umpire/src/ExternalPackages/org/systemsbiology/apps/tramlparser/TraMLParserApp.java
index 4f19279..3a2072f 100644
--- a/DIA-Umpire/src/ExtPackages/org/systemsbiology/apps/tramlparser/TraMLParserApp.java
+++ b/DIA-Umpire/src/ExternalPackages/org/systemsbiology/apps/tramlparser/TraMLParserApp.java
@@ -49,7 +49,7 @@
* dcampbell@systemsbiology.org
*
*/
-package ExtPackages.org.systemsbiology.apps.tramlparser;
+package ExternalPackages.org.systemsbiology.apps.tramlparser;
// org.apache
diff --git a/DIA-Umpire/src/ExtPackages/org/systemsbiology/apps/tramlvalidator/TraMLValidator.java b/DIA-Umpire/src/ExternalPackages/org/systemsbiology/apps/tramlvalidator/TraMLValidator.java
similarity index 93%
rename from DIA-Umpire/src/ExtPackages/org/systemsbiology/apps/tramlvalidator/TraMLValidator.java
rename to DIA-Umpire/src/ExternalPackages/org/systemsbiology/apps/tramlvalidator/TraMLValidator.java
index 0cba105..e603158 100644
--- a/DIA-Umpire/src/ExtPackages/org/systemsbiology/apps/tramlvalidator/TraMLValidator.java
+++ b/DIA-Umpire/src/ExternalPackages/org/systemsbiology/apps/tramlvalidator/TraMLValidator.java
@@ -36,7 +36,7 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package ExtPackages.org.systemsbiology.apps.tramlvalidator;
+package ExternalPackages.org.systemsbiology.apps.tramlvalidator;
import psidev.psi.tools.ontology_manager.impl.local.OntologyLoaderException;
import psidev.psi.tools.validator.Validator;
@@ -65,7 +65,7 @@ public TraMLValidator(InputStream ontoConfig) throws OntologyLoaderException {
}
- public Collection validate(ExtPackages.org.hupo.psi.ms.traml.TraMLType traml) throws ValidatorException {
+ public Collection validate(ExternalPackages.org.hupo.psi.ms.traml.TraMLType traml) throws ValidatorException {
final Collection messages = new ArrayList();
diff --git a/DIA-Umpire/src/ExtPackages/org/systemsbiology/apps/tramlvalidator/TraMLValidatorRunner.java b/DIA-Umpire/src/ExternalPackages/org/systemsbiology/apps/tramlvalidator/TraMLValidatorRunner.java
similarity index 98%
rename from DIA-Umpire/src/ExtPackages/org/systemsbiology/apps/tramlvalidator/TraMLValidatorRunner.java
rename to DIA-Umpire/src/ExternalPackages/org/systemsbiology/apps/tramlvalidator/TraMLValidatorRunner.java
index 9d9f26a..b581801 100644
--- a/DIA-Umpire/src/ExtPackages/org/systemsbiology/apps/tramlvalidator/TraMLValidatorRunner.java
+++ b/DIA-Umpire/src/ExternalPackages/org/systemsbiology/apps/tramlvalidator/TraMLValidatorRunner.java
@@ -36,7 +36,7 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package ExtPackages.org.systemsbiology.apps.tramlvalidator;
+package ExternalPackages.org.systemsbiology.apps.tramlvalidator;
import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBElement;
@@ -57,7 +57,7 @@
import java.io.IOException;
import java.util.Collection;
-import ExtPackages.org.hupo.psi.ms.traml.TraMLType;
+import ExternalPackages.org.hupo.psi.ms.traml.TraMLType;
public class TraMLValidatorRunner {
diff --git a/DIA-Umpire/src/ExtPackages/org/systemsbiology/constants/JTRAML_URL.java b/DIA-Umpire/src/ExternalPackages/org/systemsbiology/constants/JTRAML_URL.java
similarity index 96%
rename from DIA-Umpire/src/ExtPackages/org/systemsbiology/constants/JTRAML_URL.java
rename to DIA-Umpire/src/ExternalPackages/org/systemsbiology/constants/JTRAML_URL.java
index 103ffea..6a2731b 100644
--- a/DIA-Umpire/src/ExtPackages/org/systemsbiology/constants/JTRAML_URL.java
+++ b/DIA-Umpire/src/ExternalPackages/org/systemsbiology/constants/JTRAML_URL.java
@@ -1,4 +1,4 @@
-package ExtPackages.org.systemsbiology.constants;
+package ExternalPackages.org.systemsbiology.constants;
/**
* This class is a
diff --git a/DIA-Umpire/src/MSUmpire/BaseDataStructure/ScanCollection.java b/DIA-Umpire/src/MSUmpire/BaseDataStructure/ScanCollection.java
index 7631bd5..33f6728 100644
--- a/DIA-Umpire/src/MSUmpire/BaseDataStructure/ScanCollection.java
+++ b/DIA-Umpire/src/MSUmpire/BaseDataStructure/ScanCollection.java
@@ -20,7 +20,6 @@
package MSUmpire.BaseDataStructure;
import java.util.*;
-import java.util.Map.Entry;
import org.apache.avalon.framework.activity.Disposable;
/**
@@ -96,10 +95,7 @@ public void AddScan(ScanData scan) {
}
}
- public ScanData GetParentMSScan(int ScanNo) {
- //ScanData scan = null;
- //Entry floorEntry = ScanHashMap.floorEntry(ScanNo);
- //Set entryset = ScanHashMap.entrySet();
+ public ScanData GetParentMSScan(int ScanNo) {
Integer preScanNo = null;
ScanData PreScan = null;
while ((preScanNo = ScanHashMap.lowerKey(ScanNo)) != null) {
@@ -149,8 +145,8 @@ public ScanCollection GetSubCollectionByElutionTimeAndMZ(float startTime, float
if (endTime == -1) {
endTime = 9999999f;
}
+
//Find the start scan num and end scan num
-
int StartScanNo = 0;
int EndScanNo = 0;
@@ -232,6 +228,7 @@ public void dispose() {
}
}
+ //Remove peaks whose the intensity low than the threshold
public void RemoveBackground(int mslevel, float background) {
for (ScanData scan : ScanHashMap.values()) {
if(scan.MsLevel==mslevel){
diff --git a/DIA-Umpire/src/MSUmpire/BaseDataStructure/SortedListFloat.java b/DIA-Umpire/src/MSUmpire/BaseDataStructure/SortedListFloat.java
index 2ca71dc..64b495a 100644
--- a/DIA-Umpire/src/MSUmpire/BaseDataStructure/SortedListFloat.java
+++ b/DIA-Umpire/src/MSUmpire/BaseDataStructure/SortedListFloat.java
@@ -22,7 +22,7 @@
*
*/
-import ExtPackages.SortedListLib.SortedList;
+import ExternalPackages.SortedListLib.SortedList;
import java.io.Serializable;
import java.util.Comparator;
diff --git a/DIA-Umpire/src/MSUmpire/BaseDataStructure/SortedXYCollectionClass.java b/DIA-Umpire/src/MSUmpire/BaseDataStructure/SortedXYCollectionClass.java
index c5075df..f98affb 100644
--- a/DIA-Umpire/src/MSUmpire/BaseDataStructure/SortedXYCollectionClass.java
+++ b/DIA-Umpire/src/MSUmpire/BaseDataStructure/SortedXYCollectionClass.java
@@ -22,7 +22,7 @@
*
*/
-import ExtPackages.SortedListLib.SortedList;
+import ExternalPackages.SortedListLib.SortedList;
import java.io.IOException;
import java.io.Serializable;
import java.util.Arrays;
diff --git a/DIA-Umpire/src/MSUmpire/BaseDataStructure/SortedXYZCollection.java b/DIA-Umpire/src/MSUmpire/BaseDataStructure/SortedXYZCollection.java
index 69f2cb4..88ca834 100644
--- a/DIA-Umpire/src/MSUmpire/BaseDataStructure/SortedXYZCollection.java
+++ b/DIA-Umpire/src/MSUmpire/BaseDataStructure/SortedXYZCollection.java
@@ -19,7 +19,7 @@
*/
package MSUmpire.BaseDataStructure;
-import ExtPackages.SortedListLib.SortedList;
+import ExternalPackages.SortedListLib.SortedList;
import java.io.Serializable;
import java.util.Comparator;
diff --git a/DIA-Umpire/src/MSUmpire/DIA/CorrCalcCluster2CurveUnit.java b/DIA-Umpire/src/MSUmpire/DIA/CorrCalcCluster2CurveUnit.java
index 3a13691..34c10df 100644
--- a/DIA-Umpire/src/MSUmpire/DIA/CorrCalcCluster2CurveUnit.java
+++ b/DIA-Umpire/src/MSUmpire/DIA/CorrCalcCluster2CurveUnit.java
@@ -38,16 +38,14 @@ public class CorrCalcCluster2CurveUnit implements Runnable {
public PeakCluster MS1PeakCluster;
private SortedCurveCollectionApexRT PeakCurveSortedListApexRT;
- InstrumentParameter parameter;
- //HashMap FragmentPeaks = new HashMap<>();
+ InstrumentParameter parameter;
public ArrayList GroupedFragmentList = new ArrayList<>();
- //TreeMap[] IsotopePatternMap;
+
public CorrCalcCluster2CurveUnit(PeakCluster MS1PeakCluster, SortedCurveCollectionApexRT PeakCurveSortedListApexRT, InstrumentParameter parameter) {
this.MS1PeakCluster = MS1PeakCluster;
this.PeakCurveSortedListApexRT = PeakCurveSortedListApexRT;
this.parameter = parameter;
- //this.IsotopePatternMap = IsotopePatternMap;
}
@Override
@@ -55,11 +53,8 @@ public void run() {
int startRTidx = PeakCurveSortedListApexRT.BinarySearchLower(MS1PeakCluster.PeakHeightRT[0] - parameter.ApexDelta);
int endRTidx = PeakCurveSortedListApexRT.BinarySearchHigher(MS1PeakCluster.PeakHeightRT[0] + parameter.ApexDelta);
- //XYPoint[] PatternRange = MS1PeakCluster.GetPatternRange(IsotopePatternMap);
PeakCurve targetMS1Curve = MS1PeakCluster.MonoIsotopePeak;
-// if (PatternRange[0].Y > 1) {
-// targetMS1Curve = MS1PeakCluster.IsoPeaksCurves[1];
-// }
+
float ms1rtrange = targetMS1Curve.EndRT() - targetMS1Curve.StartRT();
int highCorrCnt = 0;
diff --git a/DIA-Umpire/src/MSUmpire/DIA/DIAAssignQuantUnit.java b/DIA-Umpire/src/MSUmpire/DIA/DIAAssignQuantUnit.java
index 5b02ad5..c26aba3 100644
--- a/DIA-Umpire/src/MSUmpire/DIA/DIAAssignQuantUnit.java
+++ b/DIA-Umpire/src/MSUmpire/DIA/DIAAssignQuantUnit.java
@@ -139,77 +139,5 @@ private void MatchFragmentByTargetCluster(PeakCluster peakCluster) {
pepIonID.FragmentPeaks.add(fragmentpeak);
}
}
- }
-
- private void MatchFragment() {
- for (Ion frag : pepIonID.GetFragments()) {
- PrecursorFragmentPairEdge bestfragment = null;
- float targetmz = (float) frag.getTheoreticMz(1);
- for (PeakCluster peakCluster : pepIonID.MS1PeakClusters) {
- for (PrecursorFragmentPairEdge fragmentClusterUnit : peakCluster.GroupedFragmentPeaks) {
- if (InstrumentParameter.CalcPPM(targetmz, fragmentClusterUnit.FragmentMz) <= parameter.MS2PPM) {
- if (bestfragment == null || fragmentClusterUnit.Correlation > bestfragment.Correlation) {
- bestfragment = fragmentClusterUnit;
- }
- }
- }
- }
- for (PeakCluster peakCluster : pepIonID.MS2UnfragPeakClusters) {
- for (PrecursorFragmentPairEdge fragmentClusterUnit : peakCluster.GroupedFragmentPeaks) {
- if (InstrumentParameter.CalcPPM(targetmz, fragmentClusterUnit.FragmentMz) <= parameter.MS2PPM) {
- if (bestfragment == null || fragmentClusterUnit.Correlation > bestfragment.Correlation) {
- bestfragment = fragmentClusterUnit;
- }
- }
- }
- }
- if (bestfragment != null) {
- FragmentPeak fragmentpeak = new FragmentPeak();
- fragmentpeak.ObservedMZ = bestfragment.FragmentMz;
- fragmentpeak.FragMZ = targetmz;
- fragmentpeak.corr = bestfragment.Correlation;
- fragmentpeak.intensity = bestfragment.Intensity;
- fragmentpeak.ApexDelta = bestfragment.ApexDelta;
- fragmentpeak.RTOverlapP = bestfragment.RTOverlapP;
- fragmentpeak.Charge = 1;
- fragmentpeak.ppm = InstrumentParameter.CalcSignedPPM(bestfragment.FragmentMz, targetmz);
- fragmentpeak.IonType = frag.getSubTypeAsString() + ((PeptideFragmentIon) frag).getNumber();
- pepIonID.FragmentPeaks.add(fragmentpeak);
- }
-
- targetmz = (float) frag.getTheoreticMz(2);
- bestfragment = null;
- for (PeakCluster peakCluster : pepIonID.MS1PeakClusters) {
- for (PrecursorFragmentPairEdge fragmentClusterUnit : peakCluster.GroupedFragmentPeaks) {
- if (InstrumentParameter.CalcPPM(targetmz, fragmentClusterUnit.FragmentMz) <= parameter.MS2PPM) {
- if (bestfragment == null || fragmentClusterUnit.Correlation > bestfragment.Correlation) {
- bestfragment = fragmentClusterUnit;
- }
- }
- }
- }
- for (PeakCluster peakCluster : pepIonID.MS2UnfragPeakClusters) {
- for (PrecursorFragmentPairEdge fragmentClusterUnit : peakCluster.GroupedFragmentPeaks) {
- if (InstrumentParameter.CalcPPM(targetmz, fragmentClusterUnit.FragmentMz) <= parameter.MS2PPM) {
- if (bestfragment == null || fragmentClusterUnit.Correlation > bestfragment.Correlation) {
- bestfragment = fragmentClusterUnit;
- }
- }
- }
- }
- if (bestfragment != null) {
- FragmentPeak fragmentpeak = new FragmentPeak();
- fragmentpeak.ObservedMZ = bestfragment.FragmentMz;
- fragmentpeak.FragMZ = targetmz;
- fragmentpeak.corr = bestfragment.Correlation;
- fragmentpeak.intensity = bestfragment.Intensity;
- fragmentpeak.ApexDelta = bestfragment.ApexDelta;
- fragmentpeak.RTOverlapP = bestfragment.RTOverlapP;
- fragmentpeak.Charge = 2;
- fragmentpeak.ppm = InstrumentParameter.CalcSignedPPM(bestfragment.FragmentMz, targetmz);
- fragmentpeak.IonType = frag.getSubTypeAsString() + ((PeptideFragmentIon) frag).getNumber();
- pepIonID.FragmentPeaks.add(fragmentpeak);
- }
- }
- }
+ }
}
diff --git a/DIA-Umpire/src/MSUmpire/DIA/DIAPack.java b/DIA-Umpire/src/MSUmpire/DIA/DIAPack.java
index 92f8ee8..e4c2bce 100644
--- a/DIA-Umpire/src/MSUmpire/DIA/DIAPack.java
+++ b/DIA-Umpire/src/MSUmpire/DIA/DIAPack.java
@@ -31,12 +31,9 @@
import MSUmpire.PSMDataStructure.LCMSID;
import MSUmpire.PSMDataStructure.PSM;
import MSUmpire.PSMDataStructure.PepIonID;
-import MSUmpire.PSMDataStructure.ProtID;
-import MSUmpire.PSMDataStructure.SortedPepListMass;
import MSUmpire.PeakDataStructure.PeakCluster;
import MSUmpire.PeakDataStructure.PrecursorFragmentPairEdge;
import MSUmpire.SearchResultParser.PepXMLParser;
-import MSUmpire.SearchResultParser.TPPResult;
import MSUmpire.SearchResultWriter.PepXMLWriter;
import MSUmpire.SpectrumParser.DIA_Setting;
import MSUmpire.SpectrumParser.mzXMLParser;
@@ -52,7 +49,6 @@
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
-import java.util.Objects;
import java.util.TreeMap;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.ExecutorService;
@@ -61,7 +57,6 @@
import java.util.zip.DataFormatException;
import javax.xml.parsers.ParserConfigurationException;
import org.apache.commons.io.FilenameUtils;
-import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang.exception.ExceptionUtils;
import org.apache.log4j.Logger;
import org.xml.sax.SAXException;
@@ -197,7 +192,6 @@ public mzXMLParser GetMzXML() {
public void process() throws SQLException, IOException, InterruptedException, ExecutionException, ParserConfigurationException, SAXException, FileNotFoundException, DataFormatException, Exception {
BuildDIAWindows();
MS1PeakDetection();
- //ms1lcms.ExportPeakClusterResultCSV();
DIAMS2PeakDetection();
}
@@ -211,7 +205,7 @@ public void BuildDIAWindows() throws IOException, DataFormatException, IOExcepti
LastWinMz = (XYData) WindowRange[i + 1];
}
LCMSPeakDIAMS2 diawindow = new LCMSPeakDIAMS2(Filename, this, parameter, DiaWinMz, LastWinMz, GetMzXML(), NoCPUs);
- //diawindow.SetMySQLConnection(connectionManager);
+
diawindow.datattype = dIA_Setting.dataType;
diawindow.ExportPeakCurveTable = ExportFragmentPeak;
diawindow.ExportPeakClusterTable = ExportPrecursorPeak;
@@ -317,28 +311,6 @@ public void ReadScanNoMapping() throws FileNotFoundException, IOException {
reader4.close();
}
- public void LinkIDClustersToScanKey() {
- HashMap Q1Hash = new HashMap<>();
- HashMap Q2Hash = new HashMap<>();
-
- for (Integer ScanNo : ScanClusterMap_Q1.keySet()) {
- Q1Hash.put(ScanClusterMap_Q1.get(ScanNo), ScanNo);
- }
- for (Integer ScanNo : ScanClusterMap_Q2.keySet()) {
- Q2Hash.put(ScanClusterMap_Q2.get(ScanNo), ScanNo);
- }
-
- for (PepIonID pepIonID : IDsummary.GetPepIonList().values()) {
- for (PeakCluster peakCluster : pepIonID.MS1PeakClusters) {
- if (peakCluster.IsoPeakIndex[2] != 0) {
- peakCluster.SpectrumKey = GetQ1Name() + "." + Q1Hash.get(peakCluster.Index) + "." + Q1Hash.get(peakCluster.Index) + "." + peakCluster.Charge;
- } else {
- peakCluster.SpectrumKey = GetQ2Name() + "." + Q2Hash.get(peakCluster.Index) + "." + Q2Hash.get(peakCluster.Index) + "." + peakCluster.Charge;
- }
- }
- }
- }
-
public String GetForLibQ1Name() {
//return FilenameUtils.getBaseName(ScanCollectionName) + ".Q1";
return FilenameUtils.getBaseName(Filename) + ".ForLibQ1";
@@ -369,11 +341,6 @@ public String GetQ3Name() {
return FilenameUtils.getBaseName(Filename) + "_Q3";
}
- public String GetQ4Name() {
- //return FilenameUtils.getBaseName(ScanCollectionName) + ".Q4";
- return FilenameUtils.getBaseName(Filename) + "_Q4";
- }
-
public String GetiProphExtPepxml(String tag) {
return FilenameUtils.separatorsToUnix(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename) + "_"+tag+".iproph.pep.xml");
}
@@ -488,412 +455,7 @@ public void GenerateClusterScanNomapping() throws IOException {
}
ReadScanNoMapping();
}
-
- public void FilterDeamidateGlycoPep() throws IOException {
- HashSet PeakCurveIndexMS1 = new HashSet<>();
- ArrayList SharedPeakCurveMS1 = new ArrayList<>();
- HashSet PeakCurveIndexMS2 = new HashSet<>();
- ArrayList SharedPeakCurveMS2 = new ArrayList<>();
- ArrayList IDPeakClusterMS1 = new ArrayList<>();
- ArrayList IDPeakClusterMS2 = new ArrayList<>();
- ArrayList AllPepSeq = new ArrayList<>();
- for (String PepSeq : IDsummary.PeptideList.keySet()) {
- if (!AllPepSeq.contains(PepSeq)) {
- AllPepSeq.add(PepSeq);
- }
- }
- for (String PepSeq : IDsummary.MappedPeptideList.keySet()) {
- if (!AllPepSeq.contains(PepSeq)) {
- AllPepSeq.add(PepSeq);
- }
- }
- for (PepIonID pepIonID : IDsummary.GetPepIonList().values()) {
- if (!pepIonID.MS1PeakClusters.isEmpty()) {
- pepIonID.GlycoMS1Valid = true;
- }
- if (!pepIonID.MS2UnfragPeakClusters.isEmpty()) {
- pepIonID.GlycoMS2Valid = true;
- }
- }
- for (PepIonID pepIonID : IDsummary.GetMappedPepIonList().values()) {
- if (!pepIonID.MS1PeakClusters.isEmpty()) {
- pepIonID.GlycoMS1Valid = true;
- }
- if (!pepIonID.MS2UnfragPeakClusters.isEmpty()) {
- pepIonID.GlycoMS2Valid = true;
- }
- }
-
- FileWriter writer = new FileWriter(FilenameUtils.getFullPath(Filename) + "/" + FilenameUtils.getBaseName(Filename) + "_GlycoSharePeakResult.xls");
- writer.write("MSlevel\tSharedPeakCurve\tPeptideIndex\tSequence\tPepModSeq\tMass\tCharge\tmz\tRT\tNoClusters\tClusterIndex\tIsoScore\tIDIsoScore\tValid\n");
-
- for (String PepSeq : AllPepSeq) {
- PeakCurveIndexMS1.clear();
- SharedPeakCurveMS1.clear();
- PeakCurveIndexMS2.clear();
- SharedPeakCurveMS2.clear();
- IDPeakClusterMS1.clear();
- IDPeakClusterMS2.clear();
-
- if (IDsummary.PeptideList.containsKey(PepSeq)) {
- for (PepIonID pepion : IDsummary.PeptideList.get(PepSeq).values()) {
- AddShareIndexMS1(pepion, PeakCurveIndexMS1, SharedPeakCurveMS1);
- AddShareIndexMS2(pepion, PeakCurveIndexMS2, SharedPeakCurveMS2);
- for (PeakCluster cluster : pepion.MS1PeakClusters) {
- cluster.IDIsoPatternProb = cluster.GetChiSquareProbByTheoIso(pepion.IsotopicDistrubtion(parameter.MinNoPeakCluster));
- IDPeakClusterMS1.add(cluster.Index);
- }
- for (PeakCluster cluster : pepion.MS2UnfragPeakClusters) {
- cluster.IDIsoPatternProb = cluster.GetChiSquareProbByTheoIso(pepion.IsotopicDistrubtion(parameter.MinNoPeakCluster));
- IDPeakClusterMS2.add(cluster.Index);
- }
- }
- }
- if (IDsummary.MappedPeptideList.containsKey(PepSeq)) {
- for (PepIonID pepion : IDsummary.MappedPeptideList.get(PepSeq).values()) {
- for (PeakCluster cluster : pepion.MS1PeakClusters) {
- cluster.IDIsoPatternProb = cluster.GetChiSquareProbByTheoIso(pepion.IsotopicDistrubtion(parameter.MinNoPeakCluster));
- if (IDPeakClusterMS1.contains(cluster.Index)) {
- pepion.GlycoMS1Valid = false;
- }
- }
- for (PeakCluster cluster : pepion.MS2UnfragPeakClusters) {
- cluster.IDIsoPatternProb = cluster.GetChiSquareProbByTheoIso(pepion.IsotopicDistrubtion(parameter.MinNoPeakCluster));
- if (IDPeakClusterMS2.contains(cluster.Index)) {
- pepion.GlycoMS2Valid = false;
- }
- }
- if (pepion.GlycoMS1Valid) {
- AddShareIndexMS1(pepion, PeakCurveIndexMS1, SharedPeakCurveMS1);
- }
- if (pepion.GlycoMS2Valid) {
- AddShareIndexMS2(pepion, PeakCurveIndexMS2, SharedPeakCurveMS2);
- }
- }
- }
-
- for (Integer sharedindex : SharedPeakCurveMS1) {
- //System.out.println("Share MS1 peak curve index :" +sharedindex);
- SortedPepListMass ShareIDs = new SortedPepListMass();
- if (IDsummary.PeptideList.containsKey(PepSeq)) {
- for (PepIonID pepion : IDsummary.PeptideList.get(PepSeq).values()) {
- for (PeakCluster cluster : pepion.MS1PeakClusters) {
- AddShareID(cluster, sharedindex, pepion, ShareIDs);
- }
- }
- }
- if (IDsummary.MappedPeptideList.containsKey(PepSeq)) {
- for (PepIonID pepion : IDsummary.MappedPeptideList.get(PepSeq).values()) {
- for (PeakCluster cluster : pepion.MS1PeakClusters) {
- AddShareID(cluster, sharedindex, pepion, ShareIDs);
- }
- }
- }
- boolean CorrectFound = false;
- float CorrectMass = 0f;
- for (PepIonID pepion : ShareIDs) {
- writer.write("MS1\t" + sharedindex + "\t" + pepion.Index + "\t" + pepion.Sequence + "\t" + pepion.ModSequence + "\t" + pepion.CalcNeutralPepMass() + "\t" + pepion.Charge + "\t" + pepion.ObservedMz + "\t" + pepion.PeakRT + "\t" + pepion.MS1PeakClusters.size() + "\t");
- PeakCluster targetcluster = null;
-
- for (PeakCluster cluster : pepion.MS1PeakClusters) {
- for (int i = 0; i < cluster.IsoPeakIndex.length; i++) {
- Integer index = cluster.IsoPeakIndex[i];
- if (Objects.equals(sharedindex, index)) {
- writer.write(cluster.Index + "_" + cluster.mz[i] + ";");
- if (targetcluster == null || targetcluster.IDIsoPatternProb < cluster.IDIsoPatternProb) {
- targetcluster = cluster;
- }
- }
- }
- }
- if ((CorrectFound && pepion.NeutralPrecursorMz() > CorrectMass) || targetcluster.IDIsoPatternProb < 0.8f) {
- pepion.GlycoMS1Valid = false;
- } else {
- CorrectFound = true;
- CorrectMass = pepion.NeutralPrecursorMz();
- }
- writer.write("\t" + targetcluster.IsoMapProb + "\t" + targetcluster.IDIsoPatternProb + "\t" + pepion.GlycoMS1Valid + "\n");
- }
- }
- for (Integer sharedindex : SharedPeakCurveMS2) {
- //System.out.println("Share MS2 peak curve index :" + sharedindex);
- SortedPepListMass ShareIDs = new SortedPepListMass();
- if (IDsummary.PeptideList.containsKey(PepSeq)) {
- for (PepIonID pepion : IDsummary.PeptideList.get(PepSeq).values()) {
- for (PeakCluster cluster : pepion.MS2UnfragPeakClusters) {
- AddShareID(cluster, sharedindex, pepion, ShareIDs);
- }
- }
- }
-
- if (IDsummary.MappedPeptideList.containsKey(PepSeq)) {
- for (PepIonID pepion : IDsummary.MappedPeptideList.get(PepSeq).values()) {
- for (PeakCluster cluster : pepion.MS2UnfragPeakClusters) {
- AddShareID(cluster, sharedindex, pepion, ShareIDs);
- }
- }
- }
-
- /////MS2
- boolean CorrectFound = false;
- float CorrectMass = 0f;
- for (PepIonID pepion : ShareIDs) {
- writer.write("MS2\t" + sharedindex + "\t" + pepion.Index + "\t" + pepion.Sequence + "\t" + pepion.ModSequence + "\t" + pepion.CalcNeutralPepMass() + "\t" + pepion.Charge + "\t" + pepion.ObservedMz + "\t" + pepion.PeakRT + "\t" + pepion.MS1PeakClusters.size() + "\t");
-
- PeakCluster targetcluster = null;
- for (PeakCluster cluster : pepion.MS2UnfragPeakClusters) {
- for (int i = 0; i < cluster.IsoPeakIndex.length; i++) {
- Integer index = cluster.IsoPeakIndex[i];
- if (Objects.equals(sharedindex, index)) {
- writer.write(cluster.Index + "_" + cluster.mz[i] + ";");
- if (targetcluster == null || targetcluster.IDIsoPatternProb < cluster.IDIsoPatternProb) {
- targetcluster = cluster;
- }
- }
- }
- }
- if ((CorrectFound && pepion.NeutralPrecursorMz() > CorrectMass) || targetcluster.IDIsoPatternProb < 0.8f) {
- pepion.GlycoMS2Valid = false;
- } else {
- CorrectFound = true;
- CorrectMass = pepion.NeutralPrecursorMz();
- }
- writer.write("\t" + targetcluster.IsoMapProb + "\t" + targetcluster.IDIsoPatternProb + "\t" + pepion.GlycoMS2Valid + "\n");
- }
- }
- }
- writer.close();
-
- HashMap> DeglycoSeq = new HashMap<>();
- HashMap NIndex = new HashMap<>();
- for (String PepSeq : AllPepSeq) {
- DeglycoSeq.clear();
- if (IDsummary.PeptideList.containsKey(PepSeq)) {
- for (PepIonID pepion : IDsummary.PeptideList.get(PepSeq).values()) {
- String deglyco = pepion.ModSequence.replace("[0.984(N)]", "") + "_" + pepion.Charge;
- if (!DeglycoSeq.containsKey(deglyco)) {
- DeglycoSeq.put(deglyco, new ArrayList());
- }
- DeglycoSeq.get(deglyco).add(pepion);
- }
- }
- if (IDsummary.MappedPeptideList.containsKey(PepSeq)) {
- for (PepIonID pepion : IDsummary.MappedPeptideList.get(PepSeq).values()) {
- String deglyco = pepion.ModSequence.replace("[0.984(N)]", "") + "_" + pepion.Charge;
- if (!DeglycoSeq.containsKey(deglyco)) {
- DeglycoSeq.put(deglyco, new ArrayList());
- }
- DeglycoSeq.get(deglyco).add(pepion);
- }
- }
-
- for (ArrayList list : DeglycoSeq.values()) {
- //Multiple glyco forms
- NIndex.clear();
- for (int i = 0; i < list.get(0).Sequence.length(); i++) {
- if (String.valueOf(list.get(0).Sequence.charAt(i)).equals("N")) {
- NIndex.put(i + 1, false);
- }
- }
- for (PepIonID pepIonID : list) {
- for (Integer site : NIndex.keySet()) {
- NIndex.put(site, false);
- }
- for (FragmentPeak frag : pepIonID.FragmentPeaks) {
- String type = String.valueOf(frag.IonType.charAt(0));
- Integer matchindex = Integer.parseInt(frag.IonType.substring(1));
- if ("b".equals(type)) {
- for (Integer index : NIndex.keySet()) {
- if (index <= matchindex) {
- NIndex.put(index, true);
- }
- }
- } else if ("y".equals(type)) {
- for (Integer index : NIndex.keySet()) {
- if (index <= matchindex) {
- NIndex.put(index, true);
- }
- }
- }
- }
- pepIonID.NoNsite = NIndex.size();
- pepIonID.NoNsiteFragObs = 0;
- for (Boolean obs : NIndex.values()) {
- if (obs) {
- pepIonID.NoNsiteFragObs++;
- }
- }
- }
- }
- }
- FileWriter writer2 = new FileWriter(FilenameUtils.getFullPath(Filename) + "/" + FilenameUtils.getBaseName(Filename) + "_GlycoAllResult.xls");
- writer2.write("PeptideIndex\tSequence\tPepModSeq\tMass\tCharge\tmz\tRT\tMS1IsoScore\tMS1IDIsoScore\tMS2IsoScore\tMS2IDIsoScore\tGlycoMS1Valid\tGlycoMS2Valid\tNoSite\tNoSiteObs\n");
- for (PepIonID pepion : IDsummary.GetPepIonList().values()) {
- writer2.write("ID_" + pepion.Index + "\t" + pepion.Sequence + "\t" + pepion.ModSequence + "\t" + pepion.CalcNeutralPepMass() + "\t" + pepion.Charge + "\t" + pepion.ObservedMz + "\t" + pepion.PeakRT + "\t");
- PeakCluster targetcluster = null;
- float IsoMapProb = 0f;
- float IDIsoPatternProb = 0f;
- for (PeakCluster cluster : pepion.MS1PeakClusters) {
- if (targetcluster == null || targetcluster.IDIsoPatternProb < cluster.IDIsoPatternProb) {
- targetcluster = cluster;
- }
- }
- if (targetcluster != null) {
- IsoMapProb = targetcluster.IsoMapProb;
- IDIsoPatternProb = targetcluster.IDIsoPatternProb;
- }
- writer2.write(IsoMapProb + "\t" + IDIsoPatternProb + "\t");
- IsoMapProb = 0f;
- IDIsoPatternProb = 0f;
- for (PeakCluster cluster : pepion.MS2UnfragPeakClusters) {
- if (targetcluster == null || targetcluster.IDIsoPatternProb < cluster.IDIsoPatternProb) {
- targetcluster = cluster;
- }
- }
- if (targetcluster != null) {
- IsoMapProb = targetcluster.IsoMapProb;
- IDIsoPatternProb = targetcluster.IDIsoPatternProb;
- }
- writer2.write(IsoMapProb + "\t" + IDIsoPatternProb + "\t" + pepion.GlycoMS1Valid + "\t" + pepion.GlycoMS2Valid + "\t" + pepion.NoNsite + "\t" + pepion.NoNsiteFragObs + "\n");
- }
- for (PepIonID pepion : IDsummary.GetMappedPepIonList().values()) {
- writer2.write("ID_" + pepion.Index + "\t" + pepion.Sequence + "\t" + pepion.ModSequence + "\t" + pepion.CalcNeutralPepMass() + "\t" + pepion.Charge + "\t" + pepion.ObservedMz + "\t" + pepion.PeakRT + "\t");
- PeakCluster targetcluster = null;
- float IsoMapProb = 0f;
- float IDIsoPatternProb = 0f;
- for (PeakCluster cluster : pepion.MS1PeakClusters) {
- if (targetcluster == null || targetcluster.IDIsoPatternProb < cluster.IDIsoPatternProb) {
- targetcluster = cluster;
- }
- }
- if (targetcluster != null) {
- IsoMapProb = targetcluster.IsoMapProb;
- IDIsoPatternProb = targetcluster.IDIsoPatternProb;
- }
- writer2.write(IsoMapProb + "\t" + IDIsoPatternProb + "\t");
- IsoMapProb = 0f;
- IDIsoPatternProb = 0f;
- for (PeakCluster cluster : pepion.MS2UnfragPeakClusters) {
- if (targetcluster == null || targetcluster.IDIsoPatternProb < cluster.IDIsoPatternProb) {
- targetcluster = cluster;
- }
- }
- if (targetcluster != null) {
- IsoMapProb = targetcluster.IsoMapProb;
- IDIsoPatternProb = targetcluster.IDIsoPatternProb;
- }
- writer2.write(IsoMapProb + "\t" + IDIsoPatternProb + "\t" + pepion.GlycoMS1Valid + "\t" + pepion.GlycoMS2Valid + "\t" + pepion.NoNsite + "\t" + pepion.NoNsiteFragObs + "\n");
- }
-
- writer2.close();
-
- Logger.getRootLogger().info("No. of ID peptide ions:" + IDsummary.GetPepIonList().size() + " No. of mapped ions:" + IDsummary.GetMappedPepIonList().size());
- ArrayList removlist = new ArrayList<>();
-
- for (PepIonID pepIonID : IDsummary.GetPepIonList().values()) {
- if (!pepIonID.GlycoMS1Valid && !pepIonID.GlycoMS2Valid) {
- removlist.add(pepIonID);
- }
- }
- for (PepIonID pepIonID : removlist) {
- IDsummary.GetPepIonList().remove(pepIonID.GetKey());
- IDsummary.PeptideList.get(pepIonID.Sequence).remove(pepIonID.GetKey());
- }
- removlist.clear();
- for (PepIonID pepIonID : IDsummary.GetMappedPepIonList().values()) {
- if (!pepIonID.GlycoMS1Valid && !pepIonID.GlycoMS2Valid) {
- removlist.add(pepIonID);
- }
- }
- for (PepIonID pepIonID : removlist) {
- IDsummary.GetMappedPepIonList().remove(pepIonID.GetKey());
- IDsummary.MappedPeptideList.get(pepIonID.Sequence).remove(pepIonID.GetKey());
- }
-
- Logger.getRootLogger().info("No. of ID peptide ions:" + IDsummary.GetPepIonList().size() + " No. of mapped ions:" + IDsummary.GetMappedPepIonList().size());
-
-// removlist=new ArrayList<>();
-//
-// for (PepIonID pepIonID : IDsummary.GetPepIonList().values()) {
-// if (pepIonID.NoNsiteFragObs == 0) {
-// removlist.add(pepIonID);
-// }
-// }
-// for(PepIonID pepIonID : removlist){
-// IDsummary.GetPepIonList().remove(pepIonID.GetKey());
-// IDsummary.PeptideList.get(pepIonID.Sequence).remove(pepIonID.GetKey());
-// }
-// removlist.clear();
-// for(PepIonID pepIonID : IDsummary.GetMappedPepIonList().values()){
-// if (pepIonID.NoNsiteFragObs == 0) {
-// removlist.add(pepIonID);
-// }
-// }
-// for(PepIonID pepIonID : removlist){
-// IDsummary.GetMappedPepIonList().remove(pepIonID.GetKey());
-// IDsummary.MappedPeptideList.get(pepIonID.Sequence).remove(pepIonID.GetKey());
-// }
-//
-// System.out.println("No. of ID peptide ions:"+IDsummary.GetPepIonList().size() +" No. of mapped ions:"+IDsummary.GetMappedPepIonList().size());
-//
- IDsummary.ClearProPeplist();
- IDsummary.AssignProtForPepIon();
- IDsummary.AssignProtForMappedIon();
- IDsummary.GenearteAssignIonList();
- }
-
- private void AddShareID(PeakCluster cluster, Integer sharedindex, PepIonID pepion, SortedPepListMass ShareIDs) {
- for (Integer index : cluster.IsoPeakIndex) {
- if (Objects.equals(sharedindex, index)) {
- ShareIDs.add(pepion);
- }
- }
- }
-
- private void AddShareIndexMS1(PepIonID pepion, HashSet PeakCurveIndexMS1, ArrayList SharedPeakCurveMS1) {
- for (PeakCluster cluster : pepion.MS1PeakClusters) {
- for (Integer index : cluster.IsoPeakIndex) {
- if (index > 0) {
- if (!PeakCurveIndexMS1.contains(index)) {
- PeakCurveIndexMS1.add(index);
- } else {
- SharedPeakCurveMS1.add(index);
- }
- }
- }
- }
- }
-
- private void AddShareIndexMS2(PepIonID pepion, HashSet PeakCurveIndexMS2, ArrayList SharedPeakCurveMS2) {
-
- for (PeakCluster cluster : pepion.MS2UnfragPeakClusters) {
- for (Integer index : cluster.IsoPeakIndex) {
- if (index > 0) {
- if (!PeakCurveIndexMS2.contains(index)) {
- PeakCurveIndexMS2.add(index);
- } else {
- SharedPeakCurveMS2.add(index);
- }
- }
- }
- }
- }
-
- public void MapPSM2Cluster() throws IOException, SQLException {
- GenerateClusterScanNomapping();
- for (PSM psm : IDsummary.PSMList.values()) {
- int ClusterIndex = -1;
- if (psm.GetRawNameString().equals(FilenameUtils.getBaseName(GetQ1Name()))) {
- ClusterIndex = ScanClusterMap_Q1.get(psm.ScanNo);
- PeakCluster Cluster = ms1lcms.PeakClusters.get(ClusterIndex - 1);
- Cluster.AssignedPepIon = psm.Sequence;
- } else if (psm.GetRawNameString().equals(FilenameUtils.getBaseName(GetQ2Name()))) {
- ClusterIndex = ScanClusterMap_Q2.get(psm.ScanNo);
- PeakCluster Cluster = ms1lcms.PeakClusters.get(ClusterIndex - 1);
- Cluster.AssignedPepIon = psm.Sequence;
- }
- }
- }
+
public void AssignQuant() throws IOException, SQLException {
AssignQuant(true);
@@ -902,51 +464,35 @@ public void AssignQuant() throws IOException, SQLException {
public void AssignQuant(boolean export) throws IOException, SQLException {
Logger.getRootLogger().info("Assign peak cluster to identified peptides");
GenerateClusterScanNomapping();
- //ReadScanNomapping();
+
ExecutorService executorPool = null;
for (PeakCluster cluster : ms1lcms.PeakClusters) {
cluster.Identified = false;
}
- //UpdateProcess progress = new UpdateProcess();
- //progress.SetTotal(IDsummary.GetPepIonList().size());
- //Thread thread = new Thread(progress);
- //thread.start();
- //executorPool = Executors.newFixedThreadPool(NoCPUs);
+
for (PepIonID pepIonID : IDsummary.GetPepIonList().values()) {
pepIonID.MS1PeakClusters = new ArrayList<>();
pepIonID.MS2UnfragPeakClusters = new ArrayList<>();
}
- for (LCMSPeakDIAMS2 DIAWindow : DIAWindows) {
- //if (DIAWindow.DIA_MZ_Range.getX() < 401f) {
- DIA_window_Quant dia_w = new DIA_window_Quant(GetQ1Name(), GetQ2Name(), GetQ3Name(), ScanClusterMap_Q1, ScanClusterMap_Q2, ScanClusterMap_Q3, ms1lcms, DIAWindow, IDsummary, NoCPUs);
- //executorPool.execute(dia_w);
- dia_w.run();
- //}
+ for (LCMSPeakDIAMS2 DIAWindow : DIAWindows) {
+ DIA_window_Quant dia_w = new DIA_window_Quant(GetQ1Name(), GetQ2Name(), GetQ3Name(), ScanClusterMap_Q1, ScanClusterMap_Q2, ScanClusterMap_Q3, ms1lcms, DIAWindow, IDsummary, NoCPUs);
+ dia_w.run();
}
-// executorPool.shutdown();
-// while (!executorPool.isTerminated()) {
-// }
executorPool = Executors.newFixedThreadPool(NoCPUs);
- //executorPool = Executors.newFixedThreadPool(1);
+
for (PepIonID pepIonID : IDsummary.GetPepIonList().values()) {
DIAAssignQuantUnit quantunit = new DIAAssignQuantUnit(pepIonID, ms1lcms, parameter);
executorPool.execute(quantunit);
}
executorPool.shutdown();
-// while (!executorPool.isTerminated()) {
-// }
+
try {
executorPool.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS);
} catch (InterruptedException e) {
Logger.getRootLogger().info("interrupted..");
}
- //thread = null;
- //progress.ClearMSG();
- //progress = null;
- //ms1lcms.DetermineMS1PeakClusterScore();
- //ms1lcms.ExportPeakCluster();
if (export) {
ExportID();
}
@@ -969,14 +515,7 @@ public void AssignMappedPepQuant(boolean export, FragmentLibManager libManager,
}
parameter.RT_window_Targeted=RTWindow;
GenerateClusterScanNomapping();
-// FragmentLibManager libManager = new FragmentLibManager(LibID,connectionManager);
-// libManager.ReadFromDB();
ExecutorService executorPool = null;
-
- //UpdateProcess progress = new UpdateProcess();
- //progress.SetTotal(IDsummary.GetMappedPepIonList().size());
- //Thread thread = new Thread(progress);
- //thread.start();
TScoring = new TargetMatchScoring(Filename, libManager.LibID);
@@ -1011,18 +550,15 @@ public void AssignMappedPepQuant(boolean export, FragmentLibManager libManager,
executorPool = Executors.newFixedThreadPool(NoCPUs);
for (PepIonID pepIonID : SearchList) {
- //if(pepIonID.GetKey().equals("ELVLDN[57.021(C)]CK_2")){
if (DIAWindow.DIA_MZ_Range.getX() <= pepIonID.NeutralPrecursorMz() && DIAWindow.DIA_MZ_Range.getY() >= pepIonID.NeutralPrecursorMz()) {
if (libManager.GetFragmentLib(pepIonID.GetKey()).FragmentGroups.size() >= 3) {
UmpireSpecLibMatch matchunit = new UmpireSpecLibMatch(ms1lcms, DIAWindow, pepIonID, libManager.GetFragmentLib(pepIonID.GetKey()), libManager.GetDecoyFragmentLib(pepIonID.GetKey()), parameter);
- executorPool.execute(matchunit);
- //matchunit.run();
+ executorPool.execute(matchunit);
TScoring.libTargetMatches.add(matchunit);
} else {
Logger.getRootLogger().warn("skipping " + pepIonID.GetKey() + ", it has only " + libManager.GetFragmentLib(pepIonID.GetKey()).FragmentGroups.size() + " matched fragments");
}
}
- //}
}
for (PepIonID pepIonID : IDsummary.GetPepIonList().values()) {
@@ -1038,8 +574,7 @@ public void AssignMappedPepQuant(boolean export, FragmentLibManager libManager,
}
}
executorPool.shutdown();
-// while (!executorPool.isTerminated()) {
-// }
+
try {
executorPool.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS);
} catch (InterruptedException e) {
@@ -1071,158 +606,15 @@ public void AssignMappedPepQuant(boolean export, FragmentLibManager libManager,
executorPool.execute(quantunit);
}
executorPool.shutdown();
-// while (!executorPool.isTerminated()) {
-// }
+
try {
executorPool.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS);
} catch (InterruptedException e) {
Logger.getRootLogger().info("interrupted..");
}
- //thread = null;
- //progress.ClearMSG();
- //progress = null;
+
if (export) {
ExportID();
-// if (connectionManager != null) {
-// ExportMappedIDQuant();
-// }
- }
- }
-
- public void ExtractFragmentForMS1PeakCluster() {
- for (LCMSPeakDIAMS2 DIAWindow : DIAWindows) {
- Logger.getRootLogger().info("Extracting fragments for MS1 clusters in MS2 isolation window:" + FilenameUtils.getBaseName(DIAWindow.ScanCollectionName));
-
- if (!DIAWindow.ReadPrecursorFragmentClu2Cur()) {
- Logger.getRootLogger().error("Reading results for " + DIAWindow.ScanCollectionName + " failed");
- System.exit(2);
- }
- for (PeakCluster cluster : ms1lcms.PeakClusters) {
- DIAWindow.ExtractFragmentForPeakCluser(cluster);
- }
- }
- }
-
-// public void ReadIDFromDBAndSkylineQuant(String mzxmlname, String SkylineExport, LCMSID RefProtID) throws SQLException, IOException {
-//
-// this.IDsummary = new LCMSID(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(mzxmlname),RefProtID.DecoyTag, RefProtID.FastaPath);
-// this.IDsummary.ReadFromSkylineExport(SkylineExport);
-// this.IDsummary.CreateProtByRefID(RefProtID);
-// this.IDsummary.GenearteAssignIonList();
-// connectionManager.CloseConnection();
-// }
-
- private void AssignMS2Cluster() throws SQLException {
- for (LCMSPeakDIAMS2 DIAWindow : DIAWindows) {
- DIAWindow.ReadPeakCluster();
- for (PepIonID peptide : IDsummary.GetPepIonList().values()) {
- if (DIAWindow.DIA_MZ_Range.getX() <= peptide.ObservedMz && DIAWindow.DIA_MZ_Range.getY() >= peptide.ObservedMz) {
-
- for (String indexint : peptide.MS2ClusIndex.split(";")) {
- if (!"".equals(indexint)) {
- try {
- PeakCluster cluster = DIAWindow.PeakClusters.get(Integer.parseInt(indexint) - 1);
- if (Math.abs(cluster.TargetMz() - peptide.ObservedMz) < 0.1f && cluster.Charge == peptide.Charge) {
- peptide.MS2UnfragPeakClusters.add(cluster);
- }
- } catch (Exception e) {
- //System.err.println(peptide.ObservedMz+"\t"+DIAWindow.DIA_MZ_Range.getX()+"\t"+DIAWindow.DIA_MZ_Range.getY());
- }
- }
- }
- }
- if (peptide.PeakRT == -1f) {
- PeakCluster target = null;
- for (PeakCluster cluster : peptide.MS2UnfragPeakClusters) {
- if (target == null || cluster.PeakHeight[0] > target.PeakHeight[0]) {
- target = cluster;
- }
- }
- if (target != null) {
- peptide.PeakRT = target.PeakHeightRT[0];
- peptide.ObservedMz = target.mz[0];
- }
- }
- }
- if (IDsummary.GetMappedPepIonList() != null) {
- for (PepIonID peptide : IDsummary.GetMappedPepIonList().values()) {
- if (DIAWindow.DIA_MZ_Range.getX() <= peptide.ObservedMz && DIAWindow.DIA_MZ_Range.getY() >= peptide.ObservedMz) {
- for (String indexint : peptide.MS2ClusIndex.split(";")) {
- if (!"".equals(indexint)) {
- try {
- PeakCluster cluster = DIAWindow.PeakClusters.get(Integer.parseInt(indexint) - 1);
- if (Math.abs(cluster.TargetMz() - peptide.ObservedMz) < 0.1f && cluster.Charge == peptide.Charge) {
- peptide.MS2UnfragPeakClusters.add(cluster);
- }
- } catch (Exception e) {
- //System.err.println(peptide.ObservedMz + "\t" + DIAWindow.DIA_MZ_Range.getX() + "\t" + DIAWindow.DIA_MZ_Range.getY());
- }
- }
- }
- }
- if (peptide.PeakRT == -1f) {
- PeakCluster target = null;
- for (PeakCluster cluster : peptide.MS2UnfragPeakClusters) {
- if (target == null || cluster.PeakHeight[0] > target.PeakHeight[0]) {
- target = cluster;
- }
- }
- if (target != null) {
- peptide.PeakRT = target.PeakHeightRT[0];
- peptide.ObservedMz = target.mz[0];
- }
- }
- }
- }
- }
- for (PepIonID peptide : IDsummary.GetMappedPepIonList().values()) {
- if (StringUtils.countMatches(peptide.MS2ClusIndex, ";") != peptide.MS2UnfragPeakClusters.size()) {
- System.err.println("MS2 peak cluster not found " + peptide.GetKey() + ";" + peptide.MS2ClusIndex);
- }
- }
- for (PepIonID peptide : IDsummary.GetPepIonList().values()) {
- if (StringUtils.countMatches(peptide.MS2ClusIndex, ";") != peptide.MS2UnfragPeakClusters.size()) {
- System.err.println("MS2 peak cluster not found " + peptide.GetKey() + ";" + peptide.MS2ClusIndex);
- }
- }
- }
-
- private void CheckPSM() {
- for (PepIonID pepIonID : IDsummary.GetPepIonList().values()) {
- if (pepIonID.GetPSMList().isEmpty()) {
- for (PSM psm : templcmsid.PSMList.values()) {
- if ((psm.Sequence == null ? pepIonID.Sequence == null : psm.Sequence.equals(pepIonID.Sequence)) && psm.Charge == pepIonID.Charge) {
- if (Math.abs(pepIonID.NeutralPrecursorMz() - psm.NeutralPrecursorMz()) < 0.1f) {
- psm.ModSeq = pepIonID.ModSequence;
- pepIonID.AddPSM(psm);
- }
- }
- }
- if (pepIonID.GetPSMList().isEmpty()) {
- Logger.getRootLogger().error("PSM list is empty:" + pepIonID.GetKey());
- }
- }
- if (Math.abs(pepIonID.ObservedMass() - pepIonID.CalcNeutralPepMass()) > 0.1f) {
- Logger.getRootLogger().error(pepIonID.ObservedMass());
- float mass = pepIonID.CalcNeutralPepMass();
- Logger.getRootLogger().error(mass);
- pepIonID.GetPepFactory().estimateTheoreticMass();
- mass = pepIonID.CalcNeutralPepMass();
- Logger.getRootLogger().error(mass);
- }
- }
- }
-
- private void CheckOverlap() {
- for (PepIonID pepIonID : IDsummary.GetPepIonList().values()) {
- if (IDsummary.GetMappedPepIonList().containsKey(pepIonID.GetKey())) {
- Logger.getRootLogger().error("overlap");
- }
- }
- for (PepIonID pepIonID : IDsummary.GetMappedPepIonList().values()) {
- if (IDsummary.GetPepIonList().containsKey(pepIonID.GetKey())) {
- Logger.getRootLogger().error("overlap");
- }
}
}
@@ -1242,18 +634,6 @@ public boolean ReadSerializedLCMSID(String tag) throws Exception {
this.IDsummary.mzXMLFileName=Filename;
return true;
}
-
- public void ParseCombinePepXML(DBSearchParam searchPara, LCMSID ReferenceID) throws ParserConfigurationException, SAXException, IOException, XmlPullParserException, ClassNotFoundException, InterruptedException {
- IDsummary = new LCMSID(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename),searchPara.DecoyPrefix,searchPara.FastaPath);
- TPPResult tppresult = new TPPResult(searchPara.PepFDR, searchPara.ProtFDR, searchPara.DecoyPrefix);
- tppresult.ReadSearchResultByRefIDProt(IDsummary, GetCombinePepXML(), ReferenceID);
- Logger.getRootLogger().info("No. of peptide ions:" + IDsummary.ProteinList.size() + "; Assigned Peptide No.:" + IDsummary.AssignedPepIonList.size() + "; All peptide No.:" + IDsummary.GetPepIonList().size());
- if (ms1lcms != null) {
- this.ms1lcms.IDsummary = IDsummary;
- }
- }
- LCMSID templcmsid;
-
public void SetPepXMLPath(){
iProphPepXMLs = new ArrayList();
@@ -1352,72 +732,6 @@ public void LableMatchedFragmentFromMS1Cluster(String mgfname, HashMap ScanClusterMap) {
- for (PepIonID peptide : IDsummary.GetPepIonList().values()) {
- PSM psm = null;
- for (PSM psm2 : peptide.GetPSMList()) {
- if (psm == null || psm2.Probability > psm.Probability) {
- psm = psm2;
- }
- }
- if (psm != null && psm.GetRawNameString().equals(mgfname)) {
- int ClusterIndex = Integer.parseInt(ScanClusterMap.get(psm.ScanNo));
- for (LCMSPeakDIAMS2 DIAWindow : DIAWindows) {
- if (DIAWindow.DIA_MZ_Range.getX() <= psm.ObserPrecursorMz() && DIAWindow.DIA_MZ_Range.getY() >= psm.ObserPrecursorMz()) {
- if (DIAWindow.UnFragIonClu2Cur.containsKey(ClusterIndex)) {
- for (PrecursorFragmentPairEdge fragmentClusterUnit : DIAWindow.UnFragIonClu2Cur.get(ClusterIndex)) {
- for (FragmentPeak frag : peptide.FragmentPeaks) {
- if (InstrumentParameter.CalcPPM(fragmentClusterUnit.FragmentMz, frag.FragMZ) < parameter.MS2PPM) {
- if (!DIAWindow.MatchedFragmentMap.containsKey(fragmentClusterUnit.PeakCurveIndexB)) {
- ArrayList ClusterList = new ArrayList<>();
- DIAWindow.MatchedFragmentMap.put(fragmentClusterUnit.PeakCurveIndexB, ClusterList);
- }
- DIAWindow.MatchedFragmentMap.get(fragmentClusterUnit.PeakCurveIndexB).add(fragmentClusterUnit);
- break;
- }
- }
- }
- }
- }
- }
- }
- }
- }
-
- public void ReportSharedFrag() throws InterruptedException, IOException, ParserConfigurationException, SAXException, FileNotFoundException, ExecutionException, XmlPullParserException, DataFormatException, ClassNotFoundException {
- Logger.getRootLogger().info("Removing matched fragments for 2nd stage searching.......");
- for (LCMSPeakDIAMS2 DIAwindow : DIAWindows) {
- DIAwindow.ReadIfProcessed();
- }
- LableMatchedFragmentFromMS1Cluster(GetQ1Name(), ScanClusterMap_Q1);
- LableMatchedFragmentFromMS1Cluster(GetQ2Name(), ScanClusterMap_Q2);
- //LableMatchedFragmentFromUnfragMS1Cluster(GetQ3Name(), ScanClusterMap_Q3);
- //ms1lcms.ReadPeakCluster();
- FileWriter writer = new FileWriter(FilenameUtils.getFullPath(Filename) + "/" + FilenameUtils.getBaseName(Filename) + "_SharedFragment.xls");
- writer.write("ID\tWindow\tFragIndex\tPrecursorIndex\tmz\tCorr\tApexDelta\tintensity\tPrecursorMz\tPrecursorCharge\n");
- for (LCMSPeakDIAMS2 DIAWindow : DIAWindows) {
- for (ArrayList fragmments : DIAWindow.MatchedFragmentMap.values()) {
- for (PrecursorFragmentPairEdge frag : fragmments) {
- //PeakCluster cluster=ms1lcms.PeakClusters.get(frag.PeakCurveIndexA-1);
- writer.write(DIAWindow.WindowID + "_" + frag.PeakCurveIndexB + "\t" + DIAWindow.WindowID + "\t" + frag.PeakCurveIndexB + "\t" + frag.PeakCurveIndexA + "\t" + frag.FragmentMz + "\t" + frag.Correlation + "\t" + frag.ApexDelta + "\t" + frag.Intensity + "\n");
- //writer.write(DIAWindow.WindowID+"_"+ frag.PeakCurveIndexB+"\t"+DIAWindow.WindowID+"\t"+frag.PeakCurveIndexB+"\t"+frag.PeakCurveIndexA+"\t"+frag.FragmentMz+"\t"+frag.Correlation+"\t"+frag.ApexDelta+"\t"+frag.Intensity+"\t"+cluster.TargetMz()+"\t"+cluster.Charge+"\n");
- }
- }
- }
- writer.close();
- }
-
- public void RemoveMatchedFragment() throws InterruptedException, IOException, ParserConfigurationException, SAXException, FileNotFoundException, ExecutionException, XmlPullParserException, DataFormatException, ClassNotFoundException {
- Logger.getRootLogger().info("Removing matched fragments for 2nd stage searching.......");
- for (LCMSPeakDIAMS2 DIAwindow : DIAWindows) {
- DIAwindow.ReadIfProcessed();
- }
- LableMatchedFragmentFromMS1Cluster(GetQ1Name(), ScanClusterMap_Q1);
- LableMatchedFragmentFromMS1Cluster(GetQ2Name(), ScanClusterMap_Q2);
- LableMatchedFragmentFromUnfragMS1Cluster(GetQ3Name(), ScanClusterMap_Q3);
- GenerateMGF_2ndStage();
- }
-
private String GetSkylineFolder(){
return FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename) + "_Skyline/";
}
@@ -1484,8 +798,6 @@ public void GenerateRawMGF() throws IOException, Exception {
Logger.getRootLogger().info("(Memory usage:" + Math.round((Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory()) / 1048576) + "MB)");
}
executorPool.shutdown();
-// while (!executorPool.isTerminated()) {
-// }
try {
executorPool.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS);
@@ -1578,13 +890,6 @@ public void GenerateRawMGF() throws IOException, Exception {
mgfWriter3.close();
}
- public void GenerateMGF_2ndStage() throws IOException, InterruptedException {
- for (LCMSPeakDIAMS2 DIAwindow : DIAWindows) {
- DIAwindow.GenerateMGF(ms1lcms);
- }
- RenameMGF("_RC");
- }
-
private void FindPSMRT(){
try {
if(!new File(FilenameUtils.getFullPath(Filename) + GetQ1Name() + ".mzXML").exists()){
@@ -1617,31 +922,7 @@ private void FindPSMRT(){
Logger.getRootLogger().warn("Exception trying to fill PSM RTs");
}
}
- public void ParseSearchEngineResultiProphet(DBSearchParam param) throws ParserConfigurationException, SAXException, IOException, XmlPullParserException, ClassNotFoundException, InterruptedException, Exception {
- ParseSearchEngineResultiProphet(param,null);
- }
-
- public void SetIPROPHETPepXML(){
- iProphPepXMLs = new ArrayList();
- iProphPepXMLs.add(FilenameUtils.getFullPath(Filename) + GetQ1Name() + ".iproph.pep.xml");
- iProphPepXMLs.add(FilenameUtils.getFullPath(Filename) + GetQ2Name() + ".iproph.pep.xml");
- iProphPepXMLs.add(FilenameUtils.getFullPath(Filename) + GetQ3Name() + ".iproph.pep.xml");
- }
- public void ParseSearchEngineResultiProphet(DBSearchParam param, final LCMSID RefPepID) throws ParserConfigurationException, SAXException, IOException, XmlPullParserException, ClassNotFoundException, InterruptedException, Exception {
- SetIPROPHETPepXML();
- TPPResult tppresult = new TPPResult(param.PepFDR, param.ProtFDR, param.DecoyPrefix);
- IDsummary = new LCMSID(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename),param.DecoyPrefix,param.FastaPath);
- if (RefPepID != null) {
- tppresult.ReadSearchResultByRefPepID(IDsummary, iProphPepXMLs, GetCombineiProphProtXML(), RefPepID);
- } else {
- tppresult.ReadSearchResult(IDsummary, iProphPepXMLs, GetCombineiProphProtXML());
- }
- CheckPSMRT();
- if (ms1lcms != null) {
- this.ms1lcms.IDsummary = IDsummary;
- }
- }
-
+
public void CheckPSMRT() {
boolean PSMRT0=false;
for(PSM psm : IDsummary.PSMList.values()){
@@ -1654,46 +935,8 @@ public void CheckPSMRT() {
FindPSMRT();
}
}
- public void ParseiProphetPepXML(DBSearchParam param) throws ParserConfigurationException, SAXException, IOException, XmlPullParserException, ClassNotFoundException, InterruptedException, Exception {
- iProphPepXMLs = new ArrayList();
- iProphPepXMLs.add(FilenameUtils.getFullPath(Filename) + GetQ1Name() + ".iproph.pep.xml");
- iProphPepXMLs.add(FilenameUtils.getFullPath(Filename) + GetQ2Name() + ".iproph.pep.xml");
- iProphPepXMLs.add(FilenameUtils.getFullPath(Filename) + GetQ3Name() + ".iproph.pep.xml");
- TPPResult tppresult = new TPPResult(param.PepFDR, param.ProtFDR, param.DecoyPrefix);
- IDsummary = new LCMSID(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename),param.DecoyPrefix,param.FastaPath);
- for (String pepxml : iProphPepXMLs) {
- LCMSID pepxmlid = new LCMSID(pepxml, IDsummary.DecoyTag, IDsummary.FastaPath);
- PepXMLParser pepxmlparser = new PepXMLParser(pepxmlid, pepxml, 0f);
- for (PepIonID pepion : pepxmlid.GetPepIonList().values()) {
- IDsummary.AddPeptideID(pepion);
- }
- }
- CheckPSMRT();
- if (ms1lcms != null) {
- this.ms1lcms.IDsummary = IDsummary;
- }
- }
-
- public void ParseTPP(DBSearchParam searchPara) throws ParserConfigurationException, SAXException, IOException, XmlPullParserException, ClassNotFoundException, InterruptedException {
-
- iProphPepXMLs = new ArrayList();
- String PepXMLPath1 = FilenameUtils.separatorsToUnix(FilenameUtils.getFullPath(Filename) + "interact-" + GetQ1Name() + ".pep.xml");
- String PepXMLPath2 = FilenameUtils.separatorsToUnix(FilenameUtils.getFullPath(Filename) + "interact-" + GetQ2Name() + ".pep.xml");
- String PepXMLPath3 = FilenameUtils.separatorsToUnix(FilenameUtils.getFullPath(Filename) + "interact-" + GetQ3Name() + ".pep.xml");
- iProphPepXMLs.add(PepXMLPath1);
- iProphPepXMLs.add(PepXMLPath2);
- iProphPepXMLs.add(PepXMLPath3);
- TPPResult tppresult = new TPPResult(searchPara.PepFDR, searchPara.ProtFDR, searchPara.DecoyPrefix);
-
- String CombinedProt = FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename) + "_combine.prot.xml";
- IDsummary = new LCMSID(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename),searchPara.DecoyPrefix,searchPara.FastaPath);
- tppresult.ReadSearchResult(IDsummary, iProphPepXMLs, CombinedProt);
- if (ms1lcms != null) {
- this.ms1lcms.IDsummary = IDsummary;
- }
- }
-
-
+
+
public void ClearStructure() {
ms1lcms = null;
DIAWindows = null;
@@ -1702,18 +945,16 @@ public void ClearStructure() {
}
public void BuildStructure() throws SQLException, FileNotFoundException, IOException, InterruptedException, ExecutionException, ParserConfigurationException, SAXException, DataFormatException {
- //System.out.println("building peak clusters.....");
+
LoadDIASetting();
ms1lcms = new LCMSPeakMS1(Filename, NoCPUs);
ms1lcms.datattype = dIA_Setting.dataType;
ms1lcms.SetParameter(parameter);
- //ms1lcms.SetMySQLConnection(connectionManager);
-
+
if (IDsummary != null) {
ms1lcms.IDsummary = IDsummary;
}
- //System.out.print("Querying SWATH:");
if (dIA_Setting.DIAWindows == null || dIA_Setting.DIAWindows.isEmpty()) {
GetMzXML();
}
@@ -1732,14 +973,13 @@ private void MS1PeakDetection() throws SQLException, InterruptedException, Execu
ms1lcms = new LCMSPeakMS1(Filename, NoCPUs);
ms1lcms.datattype = dIA_Setting.dataType;
ms1lcms.SetParameter(parameter);
- //ms1lcms.SetMySQLConnection(connectionManager);
+
ms1lcms.SetMS1Windows(dIA_Setting.MS1Windows);
ms1lcms.CreatePeakFolder();
ms1lcms.ExportPeakCurveTable = false;
- //ms1lcms.SwathWindows = DIAWindows;
+
ms1lcms.SetmzXML(GetMzXML());
- Logger.getRootLogger().info("Processing MS1 peak detection");
- //ms1lcms.AssignIDResult(DDAIDsummary);
+ Logger.getRootLogger().info("Processing MS1 peak detection");
ms1lcms.ExportPeakClusterTable = ExportPrecursorPeak;
ms1lcms.PeakClusterDetection();
@@ -1813,7 +1053,6 @@ public void DIAMS2PeakDetection() throws SQLException, IOException, InterruptedE
Logger.getRootLogger().info("==================================================================================");
}
RenameMGF("");
- //}
}
private void RenameMGF(String tag) {
@@ -1848,8 +1087,7 @@ public void GenerateMassCalibrationRTMap() {
}
public void ReplaceProtByRefIDByTheoPep(LCMSID protID) {
- IDsummary.GenerateProteinByRefIDByPepSeq(protID, UseMappedIon);
- //IDsummary.GenearteAssignIonList();
+ IDsummary.GenerateProteinByRefIDByPepSeq(protID, UseMappedIon);
}
public void SaveParams() {
@@ -1873,92 +1111,4 @@ public boolean LoadDIASetting() {
public InstrumentParameter GetParameter() {
return parameter;
}
-
- public void ParseiProphet(DBSearchParam param) throws ParserConfigurationException, SAXException, IOException, XmlPullParserException, ClassNotFoundException, InterruptedException {
- IDsummary = new LCMSID(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename),param.DecoyPrefix,param.FastaPath);
- TPPResult tppresult = new TPPResult(param.PepFDR, param.ProtFDR, param.DecoyPrefix);
- tppresult.ReadSearchResult(IDsummary, GetIPROPHETPepXML(), GetIPROPHETProtXML());
- }
-
- public void ExportSkylineFilesProt() throws IOException, XmlPullParserException {
-
- FileWriter writerT =new FileWriter(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename) + "_ProtTransitions.tsv");
- FileWriter writerP =new FileWriter(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename) + "_PeakBoundary.txt");
- writerP.write("PeptideModifiedSequence\tPrecursorCharge\tMinStartTime\tMaxEndTime\tFileName\n");
- //writerT.write("PeptideModifiedSequence\tPrecursorCharge\tPrecursorMZ\tTransitionMZ\tLibraryIntensity\tTr_recalibrated\n");
- //writerT.write("PeptideModifiedSequence\tPrecursorMZ\tTransitionMZ\tLibraryIntensity\tTr_recalibrated\n");
- writerT.write("Protein\tPeptideModifiedSequence\tPrecursorMZ\tTransitionMZ\tTr_recalibrated\n");
- for (ProtID prot : IDsummary.ProteinList.values()) {
- for (PepIonID pep : prot.PeptideID.values()) {
- ExportSkylineForPepProt(prot, pep, writerP, writerT);
- }
- }
- writerP.close();
- writerT.close();
- }
-
- public void ExportSkylineFiles() throws IOException, XmlPullParserException {
-
- FileWriter writerT =new FileWriter(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename) + "_TransitionsRT.tsv");
- FileWriter writerP =new FileWriter(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename) + "_PeakBoundary.txt");
- writerP.write("PeptideModifiedSequence\tPrecursorCharge\tMinStartTime\tMaxEndTime\tFileName\n");
- writerT.write("PeptideModifiedSequence\tPrecursorMZ\tTransitionMZ\tTr_recalibrated\n");
- for (PepIonID pep : IDsummary.GetPepIonList().values()) {
- ExportSkylineForPep(pep, writerP, writerT);
- }
- for (PepIonID pep : IDsummary.GetMappedPepIonList().values()) {
- ExportSkylineForPep(pep, writerP, writerT);
- }
- writerP.close();
- writerT.close();
- }
-
- private void ExportSkylineForPepProt(ProtID protein, PepIonID pep, FileWriter writerP, FileWriter writerT) throws IOException, XmlPullParserException {
- PeakCluster targetcluster = null;
- for (PeakCluster cluster : pep.MS2UnfragPeakClusters) {
- if (targetcluster == null || targetcluster.PeakHeight[0] < cluster.PeakHeight[0]) {
- targetcluster = cluster;
- }
- }
- for (PeakCluster cluster : pep.MS1PeakClusters) {
- if (targetcluster == null || targetcluster.PeakHeight[0] < cluster.PeakHeight[0]) {
- targetcluster = cluster;
- }
- }
- writerP.write(pep.GetSkylineModSeq() + "\t" + pep.Charge + "\t" + targetcluster.startRT + "\t" + targetcluster.endRT + "\t" + FilenameUtils.getName(Filename) + "\n");
- for (int i = 0; i < targetcluster.PeakHeight.length; i++) {
- //writerT.write(pep.GetSkylineModSeq() + "\t" + pep.Charge + "\t" + pep.NeutralPrecursorMz() + "\t" + targetcluster.mz[i] + "\t" + targetcluster.PeakHeight[i] + "\t" + targetcluster.PeakHeightRT[i] + "\n");
- //writerT.write(pep.GetSkylineModSeq() + "\t" + pep.NeutralPrecursorMz() + "\t" + targetcluster.mz[i] + "\n");
- writerT.write(protein.getAccNo()+"\t"+ pep.GetSkylineModSeq() + "\t" + pep.NeutralPrecursorMz() + "\t" + targetcluster.mz[i] + "\t" + targetcluster.PeakHeightRT[0] + "\n");
- }
- for (FragmentPeak frag : pep.FragmentPeaks) {
- writerT.write(protein.getAccNo()+"\t"+pep.GetSkylineModSeq() + "\t" + pep.NeutralPrecursorMz() + "\t" + frag.FragMZ + "\t" + targetcluster.PeakHeightRT[0] + "\n");
- }
- }
- private void ExportSkylineForPep(PepIonID pep, FileWriter writerP, FileWriter writerT) throws IOException, XmlPullParserException {
- PeakCluster targetcluster = null;
- for (PeakCluster cluster : pep.MS2UnfragPeakClusters) {
- if (targetcluster == null || targetcluster.PeakHeight[0] < cluster.PeakHeight[0]) {
- targetcluster = cluster;
- }
- }
- for (PeakCluster cluster : pep.MS1PeakClusters) {
- if (targetcluster == null || targetcluster.PeakHeight[0] < cluster.PeakHeight[0]) {
- targetcluster = cluster;
- }
- }
- if(targetcluster==null){
- Logger.getRootLogger().warn("Peptide "+ pep.ModSequence+" doesn't have peak cluster assigned.");
- return;
- }
- writerP.write(pep.GetSkylineModSeq() + "\t" + pep.Charge + "\t" + targetcluster.startRT + "\t" + targetcluster.endRT + "\t" + FilenameUtils.getName(Filename) + "\n");
- for (int i = 0; i < targetcluster.PeakHeight.length; i++) {
- //writerT.write(pep.GetSkylineModSeq() + "\t" + pep.Charge + "\t" + pep.NeutralPrecursorMz() + "\t" + targetcluster.mz[i] + "\t" + targetcluster.PeakHeight[i] + "\t" + targetcluster.PeakHeightRT[i] + "\n");
- //writerT.write(pep.GetSkylineModSeq() + "\t" + pep.NeutralPrecursorMz() + "\t" + targetcluster.mz[i] + "\n");
- writerT.write(pep.GetSkylineModSeq() + "\t" + pep.NeutralPrecursorMz() + "\t" + targetcluster.mz[i] + "\t" + targetcluster.PeakHeightRT[0] + "\n");
- }
- for (FragmentPeak frag : pep.FragmentPeaks) {
- writerT.write(pep.GetSkylineModSeq() + "\t" + pep.NeutralPrecursorMz() + "\t" + frag.FragMZ + "\t" + targetcluster.PeakHeightRT[0] + "\n");
- }
- }
}
diff --git a/DIA-Umpire/src/MSUmpire/DIA/DIA_window_Quant.java b/DIA-Umpire/src/MSUmpire/DIA/DIA_window_Quant.java
index e50856f..c100801 100644
--- a/DIA-Umpire/src/MSUmpire/DIA/DIA_window_Quant.java
+++ b/DIA-Umpire/src/MSUmpire/DIA/DIA_window_Quant.java
@@ -76,8 +76,7 @@ public void run() {
}
}
executorPool.shutdown();
-// while (!executorPool.isTerminated()) {
-// }
+
try {
executorPool.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS);
} catch (InterruptedException e) {
diff --git a/DIA-Umpire/src/MSUmpire/DIA/MixtureModelKDESemiParametric.java b/DIA-Umpire/src/MSUmpire/DIA/MixtureModelKDESemiParametric.java
index 0980e4b..6be4b3e 100644
--- a/DIA-Umpire/src/MSUmpire/DIA/MixtureModelKDESemiParametric.java
+++ b/DIA-Umpire/src/MSUmpire/DIA/MixtureModelKDESemiParametric.java
@@ -20,9 +20,9 @@
package MSUmpire.DIA;
import MSUmpire.MathPackage.KMeans;
-import ExtPackages.jMEF.ExpectationMaximization1D;
-import ExtPackages.jMEF.MixtureModel;
-import ExtPackages.jMEF.PVector;
+import ExternalPackages.jMEF.ExpectationMaximization1D;
+import ExternalPackages.jMEF.MixtureModel;
+import ExternalPackages.jMEF.PVector;
import java.awt.Color;
import java.io.File;
import java.io.FileWriter;
@@ -143,15 +143,7 @@ public void GeneratePlot(String pngfile) throws IOException {
chart.setBackgroundPaint(Color.white);
XYLineAndShapeRenderer render = new XYLineAndShapeRenderer();
-// render.setSeriesPaint(0, Color.DARK_GRAY);
-// render.setSeriesPaint(1, Color.DARK_GRAY);
-// render.setSeriesPaint(2, Color.GREEN);
-// render.setSeriesShape(0, new Ellipse2D.Double(0, 0, 2, 2));
-// render.setSeriesShape(1, new Ellipse2D.Double(0, 0, 2, 2));
-// render.setSeriesShape(2, new Ellipse2D.Double(0, 0, 2.5f, 2.5f));
-// render.setSeriesStroke(1, new BasicStroke(1.0f));
-// render.setSeriesStroke(0, new BasicStroke(1.0f));
-// render.setSeriesStroke(2, new BasicStroke(2.0f));
+
plot.setDataset(1, dataset);
plot.setRenderer(1, render);
plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);
@@ -178,11 +170,6 @@ public void Modeling() {
weight_incorrect = targetlowidcdf/ decoylowidcdf;
weight_correct = 1-weight_incorrect;
-// weight_incorrect = mmc.weight[0];
-// weight_correct = mmc.weight[1];
-// weight_incorrect = 0.8f;
-// weight_correct = 0.2f;
-
//initialization
GenerateIniCorrectDensity();
GenerateDecoyDensity();
@@ -240,7 +227,6 @@ private void Update() {
for (int i = 0; i < TargetEmpiricalDist.getN(); i++) {
f1[i] = CorrectKDELookUp(TargetEmpiricalDist.getObs(i));
f0[i] = DecoyKDELookUp(TargetEmpiricalDist.getObs(i));
- //p[i] = f1[i] / TargetKDELookUp(TargetEmpiricalDist.getObs(i));
p[i] = f1[i] / (f1[i]+f0[i]);
pisum += p[i];
}
@@ -359,18 +345,6 @@ private double DecoyKDELookUp(double x) {
return decoy_kde_y[NoBinPoints - 1];
}
- private double TargetKDELookUp(double x) {
- if (x <= model_kde_x[0]) {
- return model_kde_y[0];
- }
- for (int i = 0; i < NoBinPoints - 1; i++) {
- if (x >= model_kde_x[i] && x < model_kde_x[i + 1]) {
- return model_kde_y[i];
- }
- }
- return model_kde_y[NoBinPoints - 1];
- }
-
private double ProbBasedKDE(EmpiricalDist dist, double x) {
// Computes and returns the kernel density estimate at $y$, where the
// kernel is the density kern.density(x), and the bandwidth is $h$.
@@ -413,14 +387,5 @@ private double TargetKDE(double x) {
private double DecoyKDE(double x) {
return KDE(DecoyEmpiricalDist, x);
- }
-
- private double[] ArrayKDE(EmpiricalDist dist, double[] X) {
- int m = X.length;
- double[] u = new double[m];
- for (int j = 0; j < m; j++) {
- u[j] = KDE(dist, X[j]);
- }
- return u;
- }
+ }
}
diff --git a/DIA-Umpire/src/MSUmpire/DIA/TargetHitPepXMLWriter.java b/DIA-Umpire/src/MSUmpire/DIA/TargetHitPepXMLWriter.java
index e06e36d..a4f18fb 100644
--- a/DIA-Umpire/src/MSUmpire/DIA/TargetHitPepXMLWriter.java
+++ b/DIA-Umpire/src/MSUmpire/DIA/TargetHitPepXMLWriter.java
@@ -20,7 +20,7 @@
package MSUmpire.DIA;
import MSUmpire.BaseDataStructure.UmpireInfo;
-import MSUmpire.FastaParser.FastaParser_V2;
+import MSUmpire.FastaParser.FastaParser;
import MSUmpire.PSMDataStructure.PepIonID;
import MSUmpire.Utility.DateTimeTag;
import java.io.FileWriter;
@@ -78,9 +78,9 @@ public void write() throws IOException, XmlPullParserException {
}
}
- FastaParser_V2 fastaparser = new FastaParser_V2(Fasta);
+ FastaParser fastaparser = new FastaParser(Fasta);
fastaparser.RemoveDecoy(Decoytag);
- //FastaParser_V2 fastaparser = FastaParser_V2.FasterSerialzationRead(Fasta);
+ //FastaParser_V2 fastaparser = FastaParser.FasterSerialzationRead(Fasta);
fastaparser.digestion(maxmiss, minlength, maxlength,Decoytag);
Header();
@@ -274,15 +274,6 @@ private void SearchSummary() {
+ "\n"
+ "\n"
+ "\n"
-// + "\n"
-// + "\n"
-// + "\n"
-// + "\n"
-// + "\n"
-// + "\n"
-// + "\n"
-// + "\n"
-// + "\n"
+ " \n");
}
diff --git a/DIA-Umpire/src/MSUmpire/DIA/TargetMatchScoring.java b/DIA-Umpire/src/MSUmpire/DIA/TargetMatchScoring.java
index e73d441..0416541 100644
--- a/DIA-Umpire/src/MSUmpire/DIA/TargetMatchScoring.java
+++ b/DIA-Umpire/src/MSUmpire/DIA/TargetMatchScoring.java
@@ -24,9 +24,9 @@
import MSUmpire.MathPackage.KernelDensityEstimator;
import MSUmpire.MathPackage.Regression;
import MSUmpire.PSMDataStructure.PepIonID;
-import ExtPackages.jMEF.ExpectationMaximization1D;
-import ExtPackages.jMEF.MixtureModel;
-import ExtPackages.jMEF.PVector;
+import ExternalPackages.jMEF.ExpectationMaximization1D;
+import ExternalPackages.jMEF.MixtureModel;
+import ExternalPackages.jMEF.PVector;
import java.awt.Color;
import java.io.File;
import java.io.FileInputStream;
@@ -88,21 +88,13 @@ public class TargetMatchScoring implements Serializable {
public transient int NoBinPoints = 1000;
MatchSubscore matchSubscore = new MatchSubscore(0);
Float[][] MixtureModelProb;
- ArrayList decoyModelingList = new ArrayList<>();
- public transient TrainingModel model = TrainingModel.LDA;
- transient Instances TrainingData = null;
- transient LibSVM svm = null;
+ ArrayList decoyModelingList = new ArrayList<>();
private transient boolean UseOldVersion=false;
public void SetUseOldVersion(){
UseOldVersion=true;
matchSubscore=new MatchSubscore(1);
}
- public enum TrainingModel {
- SVR,
- SVM,
- LDA,
- }
public TargetMatchScoring(String Filename, String LibID) {
libTargetMatches = new ArrayList<>();
@@ -137,21 +129,11 @@ public void Process() throws IOException {
AssignMixtureModelProb();
}
else {
- if (model == TrainingModel.SVM) {
- SVMTraining();
- AssignProbSVM();
- } else {
- if (model == TrainingModel.LDA) {
- EM_LDATraining();
- } else if (model == TrainingModel.SVR) {
- SVRTraining();
- }
-
- //MixtureModeling();
- MixtureModelingSemiSupervised();
- //GeneratePrecursorCentrolRanking();
- AssignMixtureModelProb();
- }
+ EM_LDATraining();
+ //MixtureModeling();
+ MixtureModelingSemiSupervised();
+ //GeneratePrecursorCentrolRanking();
+ AssignMixtureModelProb();
}
ExportAlignmentResult();
RemoveLowScoreEntry();
@@ -272,29 +254,9 @@ public void AssignUmpireScore(PeakGroupScore peakgroup) {
float[] Subs = matchSubscore.GetSubScoreArray(peakgroup);
peakgroup.UmpireScore = 0f;
int idx = 0;
- if (model == TrainingModel.LDA) {
- for (int i = 0; i < Subs.length; i++) {
- if (matchSubscore.Subscores[i].enable) {
- peakgroup.UmpireScore += (float) (matchSubscore.SubSCoeff[idx++] * Subs[i]);
- }
- }
- } else if (model == TrainingModel.SVR) {
- Instance ins = matchSubscore.GetFeatureInstance(peakgroup);
- ins.setDataset(TrainingData);
- try {
- peakgroup.UmpireScore = (float) svm.classifyInstance(ins);
- } catch (Exception ex) {
- Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
- }
- } else if (model == TrainingModel.SVM) {
- Instance ins = matchSubscore.GetFeatureInstance(peakgroup);
- ins.setDataset(TrainingData);
- try {
- double[] temp = svm.distributionForInstance(ins);
- peakgroup.MixtureModelLocalProb = (float) temp[0];
- peakgroup.UmpireScore = (float) temp[0];
- } catch (Exception ex) {
- Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
+ for (int i = 0; i < Subs.length; i++) {
+ if (matchSubscore.Subscores[i].enable) {
+ peakgroup.UmpireScore += (float) (matchSubscore.SubSCoeff[idx++] * Subs[i]);
}
}
}
@@ -319,9 +281,6 @@ private void EM_LDATraining() throws IOException {
ArrayList decoyList = new ArrayList<>();
for (UmpireSpecLibMatch match : libTargetMatches) {
-// for (PeakGroupScore peakGroupScore : match.DecoyHits) {
-// decoyList.add(peakGroupScore);
-// }
if (match.BestDecoyHit != null) {
decoyList.add(match.BestDecoyHit);
}
@@ -333,16 +292,8 @@ private void EM_LDATraining() throws IOException {
if (match.BestHit != null) {
IDList.add(match.BestHit);
}
-// for (PeakGroupScore peakGroupScore : match.DecoyHits) {
-// //decoyList.add(peakGroupScore);
-// }
}
-// FileWriter writer=new FileWriter(FilenameUtils.getFullPath(Filename) + "/" + FilenameUtils.getBaseName(Filename) + "_LDATraining.xls");
-// writer.write("File:"+Filename+"\n");
-// writer.write("No. of identified groups:"+idcount+"\n");
-// writer.write("No. of target groups:"+targetcount+"\n");
-// writer.write("No. of decoy groups:"+decoyList.size()+"\n");
Collections.shuffle(decoyList);
ArrayList decoyTList = new ArrayList<>();
for (int i = 0; i < decoyList.size() / 2; i++) {
@@ -352,9 +303,6 @@ private void EM_LDATraining() throws IOException {
decoyTList.add(decoyList.get(i));
}
decoyList = decoyTList;
-// for (PeakGroupScore score : decoyModelingList) {
-// decoyList.remove(score);
-// }
int targetNo = (int) (IDList.size() * samplingratio);
int TrainNo = Math.min(targetNo, decoyList.size());
@@ -366,16 +314,7 @@ private void EM_LDATraining() throws IOException {
Logger.getRootLogger().warn("No. of training data is less than 5, the training process will exit.");
return;
}
- //writer.write("Training set size:"+TrainNo+"\n\n");
- //writer.write("Iteration\t");
-// for (int i = 0; i < NoFeatures; i++) {
-// writer.write(LDACompName[i] + "\t");
-// }
-// writer.write(iteration + "\t");
-// for (int i = 0; i < NoFeatures; i++) {
-// writer.write(SubSCoeff[i] + "\t");
-// }
-// writer.write(LDASimialrity + "\n");
+
while (LDASimialrity < StopThreshold && iteration < MaxIterations) {
Collections.shuffle(decoyList);
Collections.shuffle(IDList);
@@ -439,269 +378,9 @@ private void EM_LDATraining() throws IOException {
Logger.getRootLogger().debug("LDA weight similarity to previous iteration:" + df.format(LDASimialrity));
CalcUmpireScore();
-// writer.write(iteration + "\t");++) {
-// writer.write(SubSCoeff[i] + "\t");
-// }
-// writer.write(LDASimialrity + "\n");
-// for (int i = 0; i < NoFeatures; i
- }
- //writer.close();
- }
-
- private void SVRTraining() throws IOException {
- try {
- float samplingratio = 0.5f;
- model = TrainingModel.LDA;
- matchSubscore.InitializeLDACoeff();
- CalcUmpireScore();
- model = TrainingModel.SVR;
- ArrayList IDList = new ArrayList<>();
- ArrayList decoyList = new ArrayList<>();
-
- for (UmpireSpecLibMatch match : libTargetMatches) {
- if (match.BestDecoyHit != null) {
- decoyList.add(match.BestDecoyHit);
- }
- if (match.BestMS2DecoyHit != null) {
- decoyList.add(match.BestMS2DecoyHit);
- }
- }
- for (UmpireSpecLibMatch match : libIDMatches) {
- if (match.BestHit != null) {
- IDList.add(match.BestHit);
- }
- }
-
- svm = new LibSVM();
- //svm.setShrinking(false);
- svm.setSVMType(new SelectedTag(LibSVM.SVMTYPE_NU_SVR, LibSVM.TAGS_SVMTYPE));
- svm.setKernelType(new SelectedTag(LibSVM.KERNELTYPE_RBF, LibSVM.TAGS_KERNELTYPE));
-
- FastVector Features = matchSubscore.GetFeatureFastVectorSVR();
-
- Collections.shuffle(decoyList);
- ArrayList decoyTList = new ArrayList<>();
- for (int i = 0; i < decoyList.size() / 2; i++) {
- decoyModelingList.add(decoyList.get(i));
- }
- for (int i = decoyList.size() / 2; i < decoyList.size(); i++) {
- decoyTList.add(decoyList.get(i));
- }
- decoyList = decoyTList;
-
- int targetNo = (int) (IDList.size() * samplingratio);
- int TrainNo = Math.min(targetNo, decoyList.size());
-
- if (TrainNo < 5) {
- Terminate = true;
- return;
- }
-
- Collections.shuffle(decoyList);
- Collections.shuffle(IDList);
- TrainingData = new Instances("Training", Features, TrainNo * 2);
- TrainingData.setClassIndex(TrainingData.numAttributes() - 1);
-
- for (int i = 0; i < TrainNo; i++) {
- PeakGroupScore peakgroup = IDList.get(i);
- Instance feature = matchSubscore.GetFeatureInstance(peakgroup);
- feature.setValue((Attribute) matchSubscore.GetFeatureFastVectorSVR().elementAt(TrainingData.numAttributes() - 1), 100);
- TrainingData.add(feature);
- }
-
- for (int i = 0; i < TrainNo; i++) {
- PeakGroupScore peakgroup = decoyList.get(i);
- Instance feature = matchSubscore.GetFeatureInstance(peakgroup);
- feature.setValue((Attribute) matchSubscore.GetFeatureFastVectorSVR().elementAt(TrainingData.numAttributes() - 1), 0);
- TrainingData.add(feature);
- }
- svm.buildClassifier(TrainingData);
-
- Evaluation eTest = new Evaluation(TrainingData);
- eTest.evaluateModel(svm, TrainingData);
-
- DecimalFormat df = new DecimalFormat("#.####");
- Logger.getRootLogger().debug("----------------------------------------------------------------------------------------");
- Logger.getRootLogger().debug("SVR model:");
- Logger.getRootLogger().debug(eTest.toSummaryString());
-
- CalcUmpireScore();
- } catch (Exception ex) {
- Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
- }
- }
-
- private void SVMTraining() throws IOException {
- try {
- ArrayList IDList = new ArrayList<>();
- ArrayList decoyList = new ArrayList<>();
-
- for (UmpireSpecLibMatch match : libTargetMatches) {
- for (PeakGroupScore hit : match.DecoyHits) {
- decoyList.add(hit);
- }
- }
- for (UmpireSpecLibMatch match : libIDMatches) {
- for (PeakGroupScore hit : match.TargetHits) {
- IDList.add(hit);
- }
- }
-
- svm = new LibSVM();
- svm.setShrinking(false);
- svm.setSVMType(new SelectedTag(LibSVM.SVMTYPE_NU_SVC, LibSVM.TAGS_SVMTYPE));
- svm.setKernelType(new SelectedTag(LibSVM.KERNELTYPE_RBF, LibSVM.TAGS_KERNELTYPE));
- svm.setProbabilityEstimates(true);
-
- FastVector Features = matchSubscore.GetFeatureFastVectorSVM();
-
- int TrainNo = Math.min(IDList.size(), decoyList.size());
-
- Collections.shuffle(decoyList);
- Collections.shuffle(IDList);
-
- TrainingData = new Instances("Training", Features, TrainNo);
- TrainingData.setClassIndex(TrainingData.numAttributes() - 1);
-
- for (int i = 0; i < TrainNo; i++) {
- PeakGroupScore peakgroup = IDList.get(i);
- Instance feature = matchSubscore.GetFeatureInstance(peakgroup);
- feature.setValue((Attribute) matchSubscore.GetFeatureFastVectorSVM().elementAt(TrainingData.numAttributes() - 1), "ID");
- TrainingData.add(feature);
- }
-
- for (int i = 0; i < TrainNo; i++) {
- PeakGroupScore peakgroup = decoyList.get(i);
- Instance feature = matchSubscore.GetFeatureInstance(peakgroup);
- feature.setValue((Attribute) matchSubscore.GetFeatureFastVectorSVM().elementAt(TrainingData.numAttributes() - 1), "Decoy");
- TrainingData.add(feature);
- }
-
- int seed = 319;
- int folds = 5;
- Random rand = new Random(seed); // create seeded number generator
- Instances randData = new Instances(TrainingData); // create copy of original data
- randData.randomize(rand); // randomize data with number generator
- if (randData.classAttribute().isNominal()) {
- randData.stratify(folds);
- }
- //////////////////////////
- // perform cross-validation
-
- Evaluation eval = new Evaluation(randData);
- for (int n = 0; n < folds; n++) {
- Instances train = randData.trainCV(folds, n);
- Instances test = randData.testCV(folds, n);
- Classifier clsCopy = Classifier.makeCopy(svm);
- clsCopy.buildClassifier(train);
- eval.evaluateModel(clsCopy, test);
- }
-
- // output evaluation
- System.out.println();
- System.out.println("=== Setup ===");
- System.out.println("Classifier: " + svm.getClass().getName() + " " + Utils.joinOptions(svm.getOptions()));
- System.out.println("Dataset: " + TrainingData.relationName());
- System.out.println("Folds: " + folds);
- System.out.println("Seed: " + seed);
- System.out.println();
- System.out.println(eval.toSummaryString("=== " + folds + "-fold Cross-validation ===", false));
- ////////////////////////////
- CalcUmpireScore();
- } catch (Exception ex) {
- Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
- }
- }
-
- public void MixtureModelingByNormalKDE() {
-
- if (libTargetMatches.isEmpty()) {
- return;
- }
- int targetNo = 0;
- int decoyNo = 0;
- for (UmpireSpecLibMatch match : libTargetMatches) {
- targetNo += match.TargetHits.size();
- decoyNo += match.DecoyHits.size();
- }
-
- String pngfile = FilenameUtils.getFullPath(Filename) + "/" + FilenameUtils.getBaseName(Filename) + "_LibMatchModel.png";
-
- double Decoymean = 0d;
- double Decoysigma = 0d;
-
- for (UmpireSpecLibMatch match : libTargetMatches) {
- for (PeakGroupScore peakscore : match.DecoyHits) {
- Decoymean += peakscore.UmpireScore;
- }
- }
-
- Decoymean /= decoyNo;
-
- for (UmpireSpecLibMatch match : libTargetMatches) {
- for (PeakGroupScore peakscore : match.DecoyHits) {
- Decoysigma += (peakscore.UmpireScore - Decoymean) * (peakscore.UmpireScore - Decoymean);
- }
- }
- Decoysigma /= decoyNo;
- Decoysigma = Math.sqrt(Decoysigma);
-
- int idx = 0;
- int didx = 0;
- double[] TargetObs = new double[targetNo];
- double[] DecoyObs = new double[decoyNo];
- for (UmpireSpecLibMatch match : libTargetMatches) {
- for (PeakGroupScore peakscore : match.TargetHits) {
- TargetObs[idx++] = peakscore.UmpireScore;
- }
- for (PeakGroupScore peakscore : match.DecoyHits) {
- DecoyObs[didx++] = peakscore.UmpireScore;
- }
- }
- //Arrays.sort(IDObs);
-
- KernelDensityEstimator kde = new KernelDensityEstimator();
- List density = null;
-
- NormalDistribution nor = new NormalDistribution(Decoymean, Decoysigma);
-
- double DecoyDensityRatio = 0f;
- for (idx = 0; idx < density.get(0).length - 1; idx++) {
- if (density.get(0)[idx] < Decoymean && density.get(0)[idx + 1] > Decoymean) {
- DecoyDensityRatio = density.get(1)[idx] * targetNo / nor.probability(Decoymean);
- break;
- }
- }
-
- XYSeries model1 = new XYSeries("Decoy model");
- XYSeries model2 = new XYSeries("Kernel density");
- XYSeriesCollection dataset = new XYSeriesCollection();
-
- HistogramDataset histogramDataset = new HistogramDataset();
- histogramDataset.setType(HistogramType.RELATIVE_FREQUENCY);
- histogramDataset.addSeries("Target matches", TargetObs, 100);
- histogramDataset.addSeries("Decoy matches", DecoyObs, 100);
-
- for (idx = 0; idx < density.get(0).length - 1; idx++) {
- model2.add(density.get(0)[idx], density.get(1)[idx] * targetNo);
- model1.add(density.get(0)[idx], nor.probability(density.get(0)[idx]) * DecoyDensityRatio);
- }
-
- dataset.addSeries(model1);
- dataset.addSeries(model2);
- JFreeChart chart = ChartFactory.createXYLineChart(FilenameUtils.getBaseName(pngfile), "Score", "Frequency", dataset, PlotOrientation.VERTICAL, true, true, false);
- XYPlot plot = chart.getXYPlot();
- plot.setBackgroundPaint(Color.white);
- plot.setDomainGridlinePaint(Color.white);
- plot.setRangeGridlinePaint(Color.white);
- plot.setForegroundAlpha(0.8f);
- chart.setBackgroundPaint(Color.white);
- try {
- ChartUtilities.saveChartAsPNG(new File(pngfile), chart, 1000, 600);
- } catch (IOException e) {
}
}
-
+
public void MixtureModelingSemiSupervised() throws IOException {
if (libTargetMatches.isEmpty() || Terminate) {
@@ -761,161 +440,6 @@ public void MixtureModelingSemiSupervised() throws IOException {
MixtureModelProb = mixkde.MixtureModelProb;
}
- public void MixtureModelingByGammaKDE() {
-
- if (libTargetMatches.isEmpty()) {
- return;
- }
- int IDNo = 0;
- int decoyNo = 0;
- int modelNo = 0;
- double IDmean = 0d;
- double Decoymean = 0d;
-
- for (UmpireSpecLibMatch match : libIDMatches) {
- if (match.BestHit != null) {
- IDNo++;
- IDmean += match.BestHit.UmpireScore;
- }
- }
-
- decoyNo = decoyModelingList.size();
- double[] DecoyObs = new double[decoyNo];
-
- int didx = 0;
- for (PeakGroupScore peakGroupScore : decoyModelingList) {
- Decoymean += peakGroupScore.UmpireScore;
- DecoyObs[didx++] = peakGroupScore.UmpireScore;
- }
-
- float max = Float.NEGATIVE_INFINITY;
- float min = Float.POSITIVE_INFINITY;
- for (UmpireSpecLibMatch match : libTargetMatches) {
- for (PeakGroupScore peakscore : match.TargetHits) {
- if (peakscore.UmpireScore > max) {
- max = peakscore.UmpireScore;
- }
- if (peakscore.UmpireScore < min) {
- min = peakscore.UmpireScore;
- }
- }
- for (PeakGroupScore peakscore : match.DecoyHits) {
- if (peakscore.UmpireScore > max) {
- max = peakscore.UmpireScore;
- }
- if (peakscore.UmpireScore < min) {
- min = peakscore.UmpireScore;
- }
- }
-
- if (match.BestMS1Hit != null) {
- modelNo++;
- }
- if (match.BestMS2Hit != null) {
- modelNo++;
- }
- }
-
- Decoymean /= decoyNo;
- IDmean /= IDNo;
-
- double[] IDObs = new double[IDNo];
- double[] ModelObs = new double[modelNo];
-
- int midx = 0;
- int idx = 0;
- for (UmpireSpecLibMatch match : libIDMatches) {
- if (match.BestHit != null) {
- IDObs[idx++] = match.BestHit.UmpireScore;
- }
- }
- for (UmpireSpecLibMatch match : libTargetMatches) {
- if (match.BestMS1Hit != null) {
- ModelObs[midx++] = match.BestMS1Hit.UmpireScore;
- }
- if (match.BestMS2Hit != null) {
- ModelObs[midx++] = match.BestMS2Hit.UmpireScore;
- }
- }
-
- String pngfile = FilenameUtils.getFullPath(Filename) + "/" + FilenameUtils.getBaseName(Filename) + "_LibMatchModel.png";
- XYSeries model1 = new XYSeries("Incorrect matches");
- XYSeries model2 = new XYSeries("Correct matches");
- XYSeries model3 = new XYSeries("All target hits");
-
- KernelDensityEstimator Modelkde = new KernelDensityEstimator();
- Modelkde.SetData(ModelObs);
-
- //CurveFitter fitter=new CurveFitter(IDObs, IDObs)
- WeibullDist DecoyDensity = WeibullDist.getInstanceFromMLE(DecoyObs, DecoyObs.length);
-
- double[] model_kde_x = new double[NoBinPoints];
-
- float intv = (max - min) / NoBinPoints;
- for (int i = 0; i < NoBinPoints; i++) {
- model_kde_x[i] = max - i * intv;
- }
-
- double[] model_kde_y = Modelkde.Density(model_kde_x);
- double[] decoy_kde_y = new double[model_kde_x.length];
- for (int i = 0; i < model_kde_x.length; i++) {
- decoy_kde_y[i] = DecoyDensity.density(model_kde_x[i]);
- }
- float maxdecoy = 0f;
- int maxindex = 1;
- for (int i = 0; i < NoBinPoints; i++) {
- if (decoy_kde_y[i] > maxdecoy) {
- maxindex = i;
- maxdecoy = (float) decoy_kde_y[i];
- }
- }
- float weight = (float) (model_kde_y[maxindex] / maxdecoy);
- float positiveaccu = 0f;
- float negativeaccu = 0f;
- MixtureModelProb = new Float[NoBinPoints + 1][3];
-
- for (int i = 0; i < NoBinPoints; i++) {
- float positiveNumber = (float) (model_kde_y[i] - decoy_kde_y[i] * weight);
- float negativeNumber = (float) (decoy_kde_y[i] * weight);
- model2.add(model_kde_x[i], positiveNumber);
- model1.add(model_kde_x[i], negativeNumber);
- model3.add(model_kde_x[i], model_kde_y[i]);
- positiveaccu += positiveNumber;
- negativeaccu += negativeNumber;
- MixtureModelProb[i][0] = (float) model_kde_x[i];
- MixtureModelProb[i][2] = positiveNumber / (negativeNumber + positiveNumber);
- MixtureModelProb[i][1] = positiveaccu / (negativeaccu + positiveaccu);
- }
- XYSeriesCollection dataset = new XYSeriesCollection();
- dataset.addSeries(model1);
- dataset.addSeries(model2);
- dataset.addSeries(model3);
-
- HistogramDataset histogramDataset = new HistogramDataset();
- histogramDataset.setType(HistogramType.SCALE_AREA_TO_1);
- histogramDataset.addSeries("ID hits", IDObs, 100);
- histogramDataset.addSeries("Decoy hits", DecoyObs, 100);
- //histogramDataset.addSeries("Model hits", ModelObs, 100);
-
- JFreeChart chart = ChartFactory.createHistogram(FilenameUtils.getBaseName(pngfile), "Score", "Hits", histogramDataset, PlotOrientation.VERTICAL, true, false, false);
- XYPlot plot = chart.getXYPlot();
-
- plot.setBackgroundPaint(Color.white);
- plot.setDomainGridlinePaint(Color.white);
- plot.setRangeGridlinePaint(Color.white);
- plot.setForegroundAlpha(0.8f);
- chart.setBackgroundPaint(Color.white);
-
- XYLineAndShapeRenderer render = new XYLineAndShapeRenderer();
- plot.setDataset(1, dataset);
- plot.setRenderer(1, render);
- plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);
- try {
- ChartUtilities.saveChartAsPNG(new File(pngfile), chart, 1000, 600);
- } catch (IOException e) {
- }
- }
-
public void MixtureModeling() throws IOException {
if (libTargetMatches.isEmpty()) {
return;
@@ -1151,229 +675,6 @@ public void MixtureModeling() throws IOException {
}
}
- public void MixtureModelingMixDecoy() throws IOException {
- if (libTargetMatches.isEmpty()) {
- return;
- }
- int IDNo = 0;
- int decoyNo = 0;
- int modelNo = 0;
- double IDmean = 0d;
- double Decoymean = 0d;
-
- for (UmpireSpecLibMatch match : libIDMatches) {
- if (match.BestHit != null) {
- IDNo++;
- IDmean += match.BestHit.UmpireScore;
- }
- }
-
- decoyNo = decoyModelingList.size();
- for (PeakGroupScore peakGroupScore : decoyModelingList) {
- Decoymean += peakGroupScore.UmpireScore;
- }
-
- for (UmpireSpecLibMatch match : libTargetMatches) {
- modelNo += match.TargetHits.size();
- }
- modelNo += decoyModelingList.size();
-
- Decoymean /= decoyNo;
- IDmean /= IDNo;
-
- PVector[] points = new PVector[modelNo];
- PVector[] centroids = new PVector[2];
-
- int idx = 0;
- for (UmpireSpecLibMatch match : libTargetMatches) {
- for (PeakGroupScore peak : match.TargetHits) {
- points[idx] = new PVector(1);
- points[idx].array[0] = peak.UmpireScore;
- idx++;
- }
- }
- for (PeakGroupScore peak : decoyModelingList) {
- points[idx] = new PVector(1);
- points[idx].array[0] = peak.UmpireScore;
- idx++;
- }
-
- MixtureModel mmc;
- centroids[0] = new PVector(1);
- centroids[0].array[0] = Decoymean;
- centroids[1] = new PVector(1);
- centroids[1].array[0] = IDmean;
- Vector[] clusters = KMeans.run(points, 2, centroids);
- MixtureModel mm = ExpectationMaximization1D.initialize(clusters);
- mmc = ExpectationMaximization1D.run(points, mm);
- DecimalFormat df = new DecimalFormat("#.####");
- Logger.getRootLogger().debug("----------------------------------------------------------------------------------------");
- Logger.getRootLogger().debug("No. of modeling points=" + modelNo);
- Logger.getRootLogger().debug("ID hits mean=" + df.format(IDmean));
- Logger.getRootLogger().debug("Decoy hits mean=" + df.format(Decoymean));
- //System.out.print("T-test: p-value=" + df.format(model.ttest.pValue).toString() + "\n");
- Logger.getRootLogger().debug("Incorrect hits model mean=" + df.format(((PVector) mmc.param[0]).array[0]) + " variance=" + df.format(((PVector) mmc.param[0]).array[1]) + " weight=" + df.format(mmc.weight[0]));
- Logger.getRootLogger().debug("Correct hits model mean=" + df.format(((PVector) mmc.param[1]).array[0]) + " variance=" + df.format(((PVector) mmc.param[1]).array[1]) + " weight=" + df.format(mmc.weight[1]));
-
- if (((PVector) mmc.param[0]).array[0] > ((PVector) mmc.param[1]).array[0]) {
- return;
- }
-
- float max = (float) (((PVector) mmc.param[1]).array[0] + 4 * Math.sqrt(((PVector) mmc.param[1]).array[1]));
- float min = (float) (((PVector) mmc.param[0]).array[0] - 4 * Math.sqrt(((PVector) mmc.param[0]).array[1]));
-
- ///////////////////////////////////////////////////////////////////////////////////////////////
- IDNo = 0;
- decoyNo = 0;
- modelNo = 0;
-
- for (PeakGroupScore peakGroupScore : decoyModelingList) {
- if (peakGroupScore.UmpireScore > min && peakGroupScore.UmpireScore < max) {
- decoyNo++;
- }
- }
-
- for (UmpireSpecLibMatch match : libIDMatches) {
- if (match.BestHit != null && match.BestHit.UmpireScore > min && match.BestHit.UmpireScore < max) {
- IDNo++;
- }
- }
-
- for (UmpireSpecLibMatch match : libTargetMatches) {
- for (PeakGroupScore peak : match.TargetHits) {
- if (peak.UmpireScore > min && peak.UmpireScore < max) {
- modelNo++;
- }
- }
- }
-
- double[] IDObs = new double[IDNo];
- double[] DecoyObs = new double[decoyNo];
- double[] ModelObs = new double[modelNo];
- idx = 0;
- int didx = 0;
- int midx = 0;
- for (UmpireSpecLibMatch match : libIDMatches) {
- if (match.BestHit != null && match.BestHit.UmpireScore > min && match.BestHit.UmpireScore < max) {
- IDObs[idx++] = match.BestHit.UmpireScore;
- }
- }
- for (PeakGroupScore peakGroupScore : decoyModelingList) {
- if (peakGroupScore.UmpireScore > min && peakGroupScore.UmpireScore < max) {
- DecoyObs[didx++] = peakGroupScore.UmpireScore;
- }
- }
-
- for (UmpireSpecLibMatch match : libTargetMatches) {
- for (PeakGroupScore peak : match.TargetHits) {
- if (peak.UmpireScore > min && peak.UmpireScore < max) {
- ModelObs[midx++] = peak.UmpireScore;
- }
- }
- }
-
- int NoPoints = 1000;
- double[] model_kde_x = new double[NoPoints];
- float intv = (max - min) / NoPoints;
- for (int i = 0; i < NoPoints; i++) {
- model_kde_x[i] = max - i * intv;
- }
-
- KernelDensityEstimator kde_decoy = new KernelDensityEstimator();
- kde_decoy.SetData(DecoyObs);
- double[] model_kde_decoy_y = kde_decoy.Density(model_kde_x);
-
- String pngfile = FilenameUtils.getFullPath(Filename) + "/" + FilenameUtils.getBaseName(Filename) + "_" + LibID + "_LibMatchModel.png";
- String modelfile = FilenameUtils.getFullPath(Filename) + "/" + FilenameUtils.getBaseName(Filename) + "_" + LibID + "_ModelPoints.txt";
- FileWriter writer = new FileWriter(modelfile);
- XYSeries model1 = new XYSeries("Incorrect matches");
- XYSeries model2 = new XYSeries("Correct matches");
- XYSeries model3 = new XYSeries("All target hits");
- double x = 0f;
- double y_c = 0f;
- double y_i = 0f;
- PVector point = new PVector(2);
- for (int i = 0; i < NoPoints; i++) {
- point.array[0] = model_kde_x[i];
- x = point.array[0];
- point.array[1] = (mmc.EF.density(point, mmc.param[0]) - model_kde_decoy_y[i]) * mmc.weight[0];
- model1.add(point.array[0], point.array[1]);
- y_i = point.array[1];
- point.array[1] = (mmc.EF.density(point, mmc.param[1]) - model_kde_decoy_y[i]) * mmc.weight[1];
- model2.add(point.array[0], point.array[1]);
- y_c = point.array[1];
- writer.write(x + "\t" + y_i + "\t" + y_c + "\n");
- }
- writer.close();
-
- KernelDensityEstimator kde = new KernelDensityEstimator();
- kde.SetData(ModelObs);
- double[] model_kde_y = kde.Density(model_kde_x);
-
- for (int i = 0; i < NoPoints; i++) {
- if (model_kde_x[i] > min && model_kde_x[i] < max) {
- model3.add(model_kde_x[i], model_kde_y[i]);
- }
- }
- MixtureModelProb = new Float[NoPoints + 1][3];
- float positiveaccu = 0f;
- float negativeaccu = 0f;
-
- MixtureModelProb[0][0] = (float) model2.getMaxX() + Float.MIN_VALUE;
- MixtureModelProb[0][1] = 1f;
- MixtureModelProb[0][2] = 1f;
-
- for (int i = 1; i < NoPoints + 1; i++) {
- float positiveNumber = model2.getY(NoPoints - i).floatValue();
- float negativeNumber = model1.getY(NoPoints - i).floatValue();
- MixtureModelProb[i][0] = model2.getX(NoPoints - i).floatValue();
- positiveaccu += positiveNumber;
- negativeaccu += negativeNumber;
- MixtureModelProb[i][2] = 0.999999f * positiveNumber / (negativeNumber + positiveNumber);
- MixtureModelProb[i][1] = 0.999999f * positiveaccu / (negativeaccu + positiveaccu);
- }
-
- XYSeriesCollection dataset = new XYSeriesCollection();
- dataset.addSeries(model1);
- dataset.addSeries(model2);
- dataset.addSeries(model3);
-
- HistogramDataset histogramDataset = new HistogramDataset();
- histogramDataset.setType(HistogramType.SCALE_AREA_TO_1);
- histogramDataset.addSeries("ID hits", IDObs, 100);
- histogramDataset.addSeries("Decoy hits", DecoyObs, 100);
- //histogramDataset.addSeries("Model hits", ModelObs, 100);
-
- JFreeChart chart = ChartFactory.createHistogram(FilenameUtils.getBaseName(pngfile), "Score", "Hits", histogramDataset, PlotOrientation.VERTICAL, true, false, false);
- XYPlot plot = chart.getXYPlot();
-
- NumberAxis domain = (NumberAxis) plot.getDomainAxis();
- domain.setRange(min, max);
- plot.setBackgroundPaint(Color.white);
- plot.setDomainGridlinePaint(Color.white);
- plot.setRangeGridlinePaint(Color.white);
- plot.setForegroundAlpha(0.8f);
- chart.setBackgroundPaint(Color.white);
-
- XYLineAndShapeRenderer render = new XYLineAndShapeRenderer();
-// render.setSeriesPaint(0, Color.DARK_GRAY);
-// render.setSeriesPaint(1, Color.DARK_GRAY);
-// render.setSeriesPaint(2, Color.GREEN);
-// render.setSeriesShape(0, new Ellipse2D.Double(0, 0, 2, 2));
-// render.setSeriesShape(1, new Ellipse2D.Double(0, 0, 2, 2));
-// render.setSeriesShape(2, new Ellipse2D.Double(0, 0, 2.5f, 2.5f));
-// render.setSeriesStroke(1, new BasicStroke(1.0f));
-// render.setSeriesStroke(0, new BasicStroke(1.0f));
-// render.setSeriesStroke(2, new BasicStroke(2.0f));
- plot.setDataset(1, dataset);
- plot.setRenderer(1, render);
- plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);
- try {
- ChartUtilities.saveChartAsPNG(new File(pngfile), chart, 1000, 600);
- } catch (IOException e) {
- }
- }
-
public void AssignMixtureModelProb() {
if (Terminate) {
return;
@@ -1408,29 +709,6 @@ private void AssignProb(UmpireSpecLibMatch match) {
match.AssignProbToPepIon();
}
- public void AssignProbSVM() {
- if (Terminate) {
- return;
- }
-
- for (UmpireSpecLibMatch match : libTargetMatches) {
- PepIonID pepIonID = match.pepIonID;
- pepIonID.MS1AlignmentLocalProbability = 0f;
- pepIonID.MS1AlignmentProbability = 0f;
- pepIonID.MS2AlignmentLocalProbability = 0f;
- pepIonID.MS2AlignmentProbability = 0f;
-
- for (PeakGroupScore peakscore : match.TargetHits) {
- if (peakscore.MSlevel == 1 && peakscore.UmpireScore > pepIonID.MS1AlignmentLocalProbability) {
- pepIonID.MS1AlignmentLocalProbability = peakscore.MixtureModelLocalProb;
- }
- if (peakscore.MSlevel == 2 && peakscore.UmpireScore > pepIonID.MS2AlignmentLocalProbability) {
- pepIonID.MS2AlignmentLocalProbability = peakscore.MixtureModelLocalProb;
- }
- }
- }
- }
-
public static TargetMatchScoring LibraryMatchRead(String Filename, String LibID) throws FileNotFoundException {
if (!new File(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename) + "_" + LibID + "_LibMatch.serFS").exists()) {
diff --git a/DIA-Umpire/src/MSUmpire/DIA/UmpireSpecLibMatch.java b/DIA-Umpire/src/MSUmpire/DIA/UmpireSpecLibMatch.java
index 6878d23..a8366b5 100644
--- a/DIA-Umpire/src/MSUmpire/DIA/UmpireSpecLibMatch.java
+++ b/DIA-Umpire/src/MSUmpire/DIA/UmpireSpecLibMatch.java
@@ -157,12 +157,6 @@ private void CalMatchScoreNew(PeakCluster cluster, PepFragmentLib fragmentLib, P
matchFragments.add(new MatchFragment(frag, bestfragment));
}
- //float maxint = 0f;
-// for (MatchFragment matchFragment : matchFragments) {
-// if (matchFragment.peakfrag != null && matchFragment.peakfrag.Intensity > maxint) {
-// maxint = matchFragment.peakfrag.Intensity;
-// }
-// }
for (MatchFragment matchFragment : matchFragments) {
if (matchFragment.peakfrag != null) {
pointset.AddPoint(matchFragment.libfrag.GetAvgInt(), matchFragment.peakfrag.Intensity);
@@ -210,12 +204,6 @@ public void run() {
if (fragmentLib != null) {
if (IdentifiedPeptideIon) {
IDPeak();
-// if (decoyfragmentLib != null) {
-// Decoy();
-// }
-// else{
-// Logger.getRootLogger().error("decoy spectrum is null : "+pepIonID.GetKey());
-// }
} else {
Target();
if (decoyfragmentLib != null) {
diff --git a/DIA-Umpire/src/MSUmpire/FastaParser/FastaParser.java b/DIA-Umpire/src/MSUmpire/FastaParser/FastaParser.java
index 4684281..bf1210f 100644
--- a/DIA-Umpire/src/MSUmpire/FastaParser/FastaParser.java
+++ b/DIA-Umpire/src/MSUmpire/FastaParser/FastaParser.java
@@ -22,14 +22,19 @@
import MSUmpire.PSMDataStructure.EnzymeManager;
import java.io.BufferedReader;
import java.io.File;
+import java.io.FileInputStream;
import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.IOException;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.HashMap;
+import org.apache.commons.io.FilenameUtils;
import org.apache.commons.lang.exception.ExceptionUtils;
import org.apache.log4j.Logger;
+import org.nustaq.serialization.FSTObjectInput;
+import org.nustaq.serialization.FSTObjectOutput;
import org.xmlpull.v1.XmlPullParserException;
/**
@@ -39,37 +44,103 @@
public class FastaParser implements Serializable{
private static final long serialVersionUID = 19398249L;
- public HashMap ProteinList;
- public transient HashMap> PeptideList;
+ public HashMap ProteinList;
+ public HashMap PeptideList;
+
+ public void RemoveDecoy(String DecoyTag) {
+ HashMap newlist=new HashMap<>();
+ for(ProteinEntry protein : ProteinList.values()){
+ if(!protein.ACC.startsWith(DecoyTag)){
+ newlist.put(protein.ACC, protein);
+ }
+ }
+ ProteinList=newlist;
+ }
+
+ public class ProteinEntry implements Serializable{
+ private static final long serialVersionUID = -2002064228475586294L;
+ public String ACC;
+ public String Des;
+ public String Seq;
+ public ArrayList Peptides=new ArrayList<>();
+ }
+
+ public class PeptideEntry implements Serializable {
+ private static final long serialVersionUID = -6343751134961266096L;
+ public ArrayList Proteins=new ArrayList<>();
+ public String Sequence;
+ public String Decoy;
+ }
public FastaParser(String filename){
ProteinList=new HashMap<>();
try {
Parse(filename);
} catch (IOException ex) {
- Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
+ Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
}
}
+
+ public static FastaParser FasterSerialzationRead(String Filename) throws FileNotFoundException {
+
+ if (!new File(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename)+ ".FastaSer").exists()) {
+ return null;
+ }
+ FastaParser fastareader=null;
+ try {
+ org.apache.log4j.Logger.getRootLogger().info("Loading fasta serialization to file:" + FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename)+ ".FastaSer..");
+ FileInputStream fileIn = new FileInputStream(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename)+ ".FastaSer");
+ FSTObjectInput in = new FSTObjectInput(fileIn);
+ fastareader = (FastaParser) in.readObject();
+ in.close();
+ fileIn.close();
+ } catch (Exception ex) {
+ org.apache.log4j.Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
+ return null;
+ }
+
+ return fastareader;
+ }
+
+ public boolean FasterSerialzationWrite(String Filename) throws FileNotFoundException {
+ try {
+ org.apache.log4j.Logger.getRootLogger().info("Writing fasta serialization to file:" + FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename)+ ".FastaSer...");
+ FileOutputStream fout = new FileOutputStream(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename)+ ".FastaSer", false);
+ FSTObjectOutput out = new FSTObjectOutput(fout);
+ out.writeObject(this);
+ out.close();
+ fout.close();
+ } catch (Exception ex) {
+ org.apache.log4j.Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
+ return false;
+ }
+ return true;
+ }
+
private void Parse(String filename) throws FileNotFoundException, IOException {
if(!new File(filename).exists()){
- Logger.getRootLogger().warn("Fasta file cannot be found: "+filename);
+ org.apache.log4j.Logger.getRootLogger().warn("Fasta file cannot be found: "+filename);
}
- BufferedReader reader = new BufferedReader(new FileReader(filename));
+ BufferedReader reader = new BufferedReader(new FileReader(filename));
String line = "";
String ACC = "";
- String des="";
+ String des = "";
StringBuilder Seq = new StringBuilder();
while ((line = reader.readLine()) != null) {
if (line.startsWith(">")) {
if (!"".equals(ACC) && !"".equals(Seq.toString())) {
- ProteinList.put(ACC, new String[]{Seq.toString().replace("*", ""),des});
- Seq=new StringBuilder();
+ ProteinEntry protein = new ProteinEntry();
+ protein.ACC = ACC;
+ protein.Des = des;
+ protein.Seq = Seq.toString().replace("*", "");
+ ProteinList.put(ACC, protein);
+ Seq = new StringBuilder();
}
ACC = line.trim().split(" ")[0].substring(1);
- des=line.replace(">"+ACC+" ", "");
+ des = line.replace(">" + ACC + " ", "");
} else {
if (!"".equals(line.trim())) {
Seq.append(line);
@@ -77,22 +148,37 @@ private void Parse(String filename) throws FileNotFoundException, IOException {
}
}
if (!"".equals(ACC) && !"".equals(Seq.toString())) {
- ProteinList.put(ACC, new String[]{Seq.toString().replace("*", ""),des});
+ ProteinEntry protein = new ProteinEntry();
+ protein.ACC = ACC;
+ protein.Des = des;
+ protein.Seq = Seq.toString().replace("*", "");
+ ProteinList.put(ACC, protein);
}
reader.close();
}
- public void digestion(int missedcleave, int minlength, int maxlength) throws XmlPullParserException, IOException {
+ public void digestion(int missedcleave, int minlength, int maxlength, String Decoytag) throws XmlPullParserException, IOException {
PeptideList=new HashMap<>();
- for (String acc : ProteinList.keySet()) {
- String Sequence = ProteinList.get(acc)[0];
+ for (ProteinEntry protein : ProteinList.values()) {
+ if(protein.ACC.startsWith(Decoytag)){
+ continue;
+ }
+ String Sequence = protein.Seq;
ArrayList TheoPeptides = EnzymeManager.GetInstance().GetTrypsinNoP().digest(Sequence, missedcleave, minlength, maxlength);
AddFirstMetDroppedPep(Sequence, missedcleave, minlength, maxlength, TheoPeptides);
for (String pep : TheoPeptides) {
if (!PeptideList.containsKey(pep)) {
- PeptideList.put(pep, new ArrayList());
+ PeptideEntry pepentry=new PeptideEntry();
+ pepentry.Sequence=pep;
+ String rev=new StringBuilder(pepentry.Sequence.subSequence(0, pepentry.Sequence.length()-1)).reverse().toString();
+ if (Sequence.indexOf(pepentry.Sequence) > 0) {
+ rev += String.valueOf(Sequence.charAt(Sequence.indexOf(pepentry.Sequence) - 1));
+ }
+ pepentry.Decoy=rev;
+ PeptideList.put(pep, pepentry);
}
- PeptideList.get(pep).add(acc);
+ PeptideList.get(pep).Proteins.add(protein.ACC);
+ protein.Peptides.add(pep);
}
}
}
diff --git a/DIA-Umpire/src/MSUmpire/FastaParser/FastaParser_V2.java b/DIA-Umpire/src/MSUmpire/FastaParser/FastaParser_V2.java
deleted file mode 100644
index 23254fd..0000000
--- a/DIA-Umpire/src/MSUmpire/FastaParser/FastaParser_V2.java
+++ /dev/null
@@ -1,205 +0,0 @@
-/*
- * Author: Chih-Chiang Tsou
- * Nesvizhskii Lab, Department of computational medicine and bioinformatics,
- * University of Michigan, Ann Arbor
- *
- * Copyright 2014 University of Michigan, Ann Arbor, MI
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package MSUmpire.FastaParser;
-
-import MSUmpire.PSMDataStructure.EnzymeManager;
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.HashMap;
-import org.apache.commons.io.FilenameUtils;
-import org.apache.commons.lang.exception.ExceptionUtils;
-import org.apache.log4j.Logger;
-import org.nustaq.serialization.FSTObjectInput;
-import org.nustaq.serialization.FSTObjectOutput;
-import org.xmlpull.v1.XmlPullParserException;
-
-/**
- *
- * @author Chih-Chiang Tsou
- */
-public class FastaParser_V2 implements Serializable{
- private static final long serialVersionUID = 19398249L;
-
- public HashMap ProteinList;
- public HashMap PeptideList;
-
- public void RemoveDecoy(String DecoyTag) {
- HashMap newlist=new HashMap<>();
- for(ProteinEntry protein : ProteinList.values()){
- if(!protein.ACC.startsWith(DecoyTag)){
- newlist.put(protein.ACC, protein);
- }
- }
- ProteinList=newlist;
- }
-
-
- public class ProteinEntry implements Serializable{
- private static final long serialVersionUID = -2002064228475586294L;
- public String ACC;
- public String Des;
- public String Seq;
- public ArrayList Peptides=new ArrayList<>();
- }
-
- public class PeptideEntry implements Serializable {
- private static final long serialVersionUID = -6343751134961266096L;
- public ArrayList Proteins=new ArrayList<>();
- public String Sequence;
- public String Decoy;
- }
-
- public FastaParser_V2(String filename){
- ProteinList=new HashMap<>();
- try {
- Parse(filename);
- } catch (IOException ex) {
- Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
- }
- }
-
-
- public static FastaParser_V2 FasterSerialzationRead(String Filename) throws FileNotFoundException {
-
- if (!new File(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename)+ ".FastaSer").exists()) {
- return null;
- }
- FastaParser_V2 fastareader=null;
- try {
- org.apache.log4j.Logger.getRootLogger().info("Loading fasta serialization to file:" + FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename)+ ".FastaSer..");
- FileInputStream fileIn = new FileInputStream(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename)+ ".FastaSer");
- FSTObjectInput in = new FSTObjectInput(fileIn);
- fastareader = (FastaParser_V2) in.readObject();
- in.close();
- fileIn.close();
- } catch (Exception ex) {
- org.apache.log4j.Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
- return null;
- }
-
- return fastareader;
- }
-
- public boolean FasterSerialzationWrite(String Filename) throws FileNotFoundException {
- try {
- org.apache.log4j.Logger.getRootLogger().info("Writing fasta serialization to file:" + FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename)+ ".FastaSer...");
- FileOutputStream fout = new FileOutputStream(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename)+ ".FastaSer", false);
- FSTObjectOutput out = new FSTObjectOutput(fout);
- out.writeObject(this);
- out.close();
- fout.close();
- } catch (Exception ex) {
- org.apache.log4j.Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
- return false;
- }
- return true;
- }
-
- private void Parse(String filename) throws FileNotFoundException, IOException {
-
- if(!new File(filename).exists()){
- org.apache.log4j.Logger.getRootLogger().warn("Fasta file cannot be found: "+filename);
- }
- BufferedReader reader = new BufferedReader(new FileReader(filename));
- String line = "";
- String ACC = "";
- String des = "";
- StringBuilder Seq = new StringBuilder();
- while ((line = reader.readLine()) != null) {
- if (line.startsWith(">")) {
- if (!"".equals(ACC) && !"".equals(Seq.toString())) {
- ProteinEntry protein = new ProteinEntry();
- protein.ACC = ACC;
- protein.Des = des;
- protein.Seq = Seq.toString().replace("*", "");
- ProteinList.put(ACC, protein);
- Seq = new StringBuilder();
- }
- ACC = line.trim().split(" ")[0].substring(1);
- des = line.replace(">" + ACC + " ", "");
- } else {
- if (!"".equals(line.trim())) {
- Seq.append(line);
- }
- }
- }
- if (!"".equals(ACC) && !"".equals(Seq.toString())) {
- ProteinEntry protein = new ProteinEntry();
- protein.ACC = ACC;
- protein.Des = des;
- protein.Seq = Seq.toString().replace("*", "");
- ProteinList.put(ACC, protein);
- }
- reader.close();
- }
-
- public void digestion(int missedcleave, int minlength, int maxlength, String Decoytag) throws XmlPullParserException, IOException {
- PeptideList=new HashMap<>();
- for (ProteinEntry protein : ProteinList.values()) {
- if(protein.ACC.startsWith(Decoytag)){
- continue;
- }
- String Sequence = protein.Seq;
- ArrayList TheoPeptides = EnzymeManager.GetInstance().GetTrypsinNoP().digest(Sequence, missedcleave, minlength, maxlength);
- AddFirstMetDroppedPep(Sequence, missedcleave, minlength, maxlength, TheoPeptides);
- for (String pep : TheoPeptides) {
- if (!PeptideList.containsKey(pep)) {
- PeptideEntry pepentry=new PeptideEntry();
- pepentry.Sequence=pep;
- String rev=new StringBuilder(pepentry.Sequence.subSequence(0, pepentry.Sequence.length()-1)).reverse().toString();
- if (Sequence.indexOf(pepentry.Sequence) > 0) {
- rev += String.valueOf(Sequence.charAt(Sequence.indexOf(pepentry.Sequence) - 1));
- }
- pepentry.Decoy=rev;
- PeptideList.put(pep, pepentry);
- }
- PeptideList.get(pep).Proteins.add(protein.ACC);
- protein.Peptides.add(pep);
- }
- }
- }
-
- public void AddFirstMetDroppedPep(String Sequence, int missedcleave, int minlength, int maxlength, ArrayList TheoPeptides) {
- if (String.valueOf(Sequence.charAt(0)).equals("M")) {
- int mc = 0;
- for (int i = 1; i < Sequence.length(); i++) {
- if (String.valueOf(Sequence.charAt(i)).equals("K") || String.valueOf(Sequence.charAt(i)).equals("R")) {
- mc++;
- if (mc > missedcleave) {
- return;
- }
- String pep = Sequence.substring(1, i + 1);
- if (pep.length() >= minlength && pep.length() <= maxlength && !TheoPeptides.contains(pep)) {
- TheoPeptides.add(pep);
- }
- }
- }
- }
- }
-
-
-}
diff --git a/DIA-Umpire/src/MSUmpire/FragmentLib/FragmentLibManager.java b/DIA-Umpire/src/MSUmpire/FragmentLib/FragmentLibManager.java
index 4c5366b..efb121a 100644
--- a/DIA-Umpire/src/MSUmpire/FragmentLib/FragmentLibManager.java
+++ b/DIA-Umpire/src/MSUmpire/FragmentLib/FragmentLibManager.java
@@ -35,9 +35,9 @@
import com.compomics.util.experiment.biology.Peptide;
import com.compomics.util.experiment.biology.ions.PeptideFragmentIon;
import com.compomics.util.experiment.identification.matches.ModificationMatch;
-import ExtPackages.JAligner.matrix.Matrix;
-import ExtPackages.JAligner.matrix.MatrixLoader;
-import ExtPackages.JAligner.matrix.MatrixLoaderException;
+import ExternalPackages.JAligner.matrix.Matrix;
+import ExternalPackages.JAligner.matrix.MatrixLoader;
+import ExternalPackages.JAligner.matrix.MatrixLoaderException;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
@@ -45,8 +45,6 @@
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
-import java.io.ObjectInputStream;
-import java.io.ObjectOutputStream;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.HashMap;
@@ -54,14 +52,14 @@
import java.util.regex.Pattern;
import org.apache.commons.lang.exception.ExceptionUtils;
import org.apache.log4j.Logger;
-import ExtPackages.org.hupo.psi.ms.traml.CvParamType;
-import ExtPackages.org.hupo.psi.ms.traml.ModificationType;
-import ExtPackages.org.hupo.psi.ms.traml.PeptideType;
-import ExtPackages.org.hupo.psi.ms.traml.RetentionTimeType;
-import ExtPackages.org.hupo.psi.ms.traml.TransitionType;
+import ExternalPackages.org.hupo.psi.ms.traml.CvParamType;
+import ExternalPackages.org.hupo.psi.ms.traml.ModificationType;
+import ExternalPackages.org.hupo.psi.ms.traml.PeptideType;
+import ExternalPackages.org.hupo.psi.ms.traml.RetentionTimeType;
+import ExternalPackages.org.hupo.psi.ms.traml.TransitionType;
import org.nustaq.serialization.FSTObjectInput;
import org.nustaq.serialization.FSTObjectOutput;
-import ExtPackages.org.systemsbiology.apps.tramlparser.TraMLParser;
+import ExternalPackages.org.systemsbiology.apps.tramlparser.TraMLParser;
import org.xmlpull.v1.XmlPullParserException;
/**
@@ -96,7 +94,6 @@ public FragmentLibManager(String LibID) {
public void WriteFragmentLibSerialization(String path) {
- //JavaSerializationFragmentLibWrite(path, LibID);
FSFragmentLibWrite(path, LibID);
}
@@ -116,7 +113,6 @@ private void FSFragmentLibWrite(String path, String LibID1) {
public static FragmentLibManager ReadFragmentLibSerialization(String path, String LibID) {
FragmentLibManager lib = FSFragmentLibRead(path, LibID);
if (lib == null) {
- //lib = JavaSerializationFragmentLibRead(path, LibID);
lib=FSFragmentLibRead_Old(path, LibID);
if (lib != null) {
lib.WriteFragmentLibSerialization(path);
diff --git a/DIA-Umpire/src/MSUmpire/LCMSBaseStructure/LCMSPeakBase.java b/DIA-Umpire/src/MSUmpire/LCMSBaseStructure/LCMSPeakBase.java
index ba97836..871cc8f 100644
--- a/DIA-Umpire/src/MSUmpire/LCMSBaseStructure/LCMSPeakBase.java
+++ b/DIA-Umpire/src/MSUmpire/LCMSBaseStructure/LCMSPeakBase.java
@@ -25,7 +25,6 @@
import MSUmpire.PSMDataStructure.PepIonID;
import MSUmpire.PeakDataStructure.PeakCluster;
import MSUmpire.PeakDataStructure.PeakCurve;
-import MSUmpire.PeakDataStructure.SortedClusterCollectionClassApexRT;
import MSUmpire.PeakDataStructure.SortedCurveCollectionApexRT;
import MSUmpire.SpectrumParser.mzXMLParser;
import java.io.File;
@@ -35,7 +34,6 @@
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
-import java.sql.SQLException;
import java.util.*;
import java.util.logging.Level;
import net.sf.javaml.core.kdtree.KDTree;
@@ -55,8 +53,7 @@
*/
public class LCMSPeakBase {
- public ArrayList PeakClusters = new ArrayList<>(1000);
- private SortedClusterCollectionClassApexRT PeakClusterListRT=null;
+ public ArrayList PeakClusters = new ArrayList<>(1000);
private KDTree PeakClusterMassSearchTree=null;
private KDTree PeakCurveSearchTree=null;
public String ScanCollectionName;
@@ -85,7 +82,6 @@ public void ClearAllPeaks(){
}
public void BaseClearAllPeaks() {
PeakClusters = null;
- PeakClusterListRT = null;
PeakCurveListRT = null;
UnSortedPeakCurves=null;
PeakCurveSearchTree=null;
@@ -145,37 +141,6 @@ public ArrayList FindAllPeakClustersForMappedPep(PepIonID pep) {
}
return allclusterList;
}
-
- public ArrayList FindPeakCurveByMZRT(float mz, float RT, float ppm) {
- ArrayList ReturnList = new ArrayList<>();
- float lowrt = RT - parameter.MaxCurveRTRange;
- float highrt = RT + parameter.MaxCurveRTRange;
- float lowmz = InstrumentParameter.GetMzByPPM(mz, 1, ppm);
- float highmz = InstrumentParameter.GetMzByPPM(mz, 1, -ppm);
-
- Object[] found=null;
- try {
- found = GetPeakCurveSearchTree().range(new double[]{lowrt,lowmz}, new double[]{highrt,highmz});
- } catch (KeySizeException ex) {
-
- }
- if(found==null || found.length==0){
- return ReturnList;
- }
- for(Object obj : found){
- PeakCurve peakcurve = (PeakCurve)obj;
- if (InstrumentParameter.CalcPPM(peakcurve.TargetMz, mz) < ppm) {
- if (peakcurve.StartRT() <= RT && peakcurve.EndRT() >= RT) {
- ReturnList.add(peakcurve);
- }
- } else {
- if (peakcurve.TargetMz > mz) {
- return ReturnList;
- }
- }
- }
- return ReturnList;
- }
public ArrayList FindPeakClustersByMassIDTime(float mass, int charge, float RT, float RTtol) {
ArrayList ReturnList = new ArrayList<>();
@@ -324,7 +289,6 @@ public void ExportPeakClusterResultCSV() throws IOException {
writer.close();
//System.out.print("Finished multithreading\n");
}
-
public void ExportPeakCluster() throws IOException {
WritePeakClusterSerialization();
@@ -499,12 +463,4 @@ public SortedCurveCollectionApexRT GetPeakCurveListRT() {
}
return PeakCurveListRT;
}
- public SortedClusterCollectionClassApexRT GetPeakClusterListRT() {
- if (PeakClusterListRT == null) {
- PeakClusterListRT=new SortedClusterCollectionClassApexRT();
- PeakClusterListRT.addAll(PeakClusters);
- }
- return PeakClusterListRT;
- }
-
}
diff --git a/DIA-Umpire/src/MSUmpire/LCMSBaseStructure/LCMSPeakDIAMS2.java b/DIA-Umpire/src/MSUmpire/LCMSBaseStructure/LCMSPeakDIAMS2.java
index 855068c..c0dcf01 100644
--- a/DIA-Umpire/src/MSUmpire/LCMSBaseStructure/LCMSPeakDIAMS2.java
+++ b/DIA-Umpire/src/MSUmpire/LCMSBaseStructure/LCMSPeakDIAMS2.java
@@ -130,7 +130,6 @@ public void PeakDetectionPFGrouping(LCMSPeakMS1 ms1lcms) throws InterruptedExcep
}
ExportPeakCluster();
- //GenerateRTSoretedClusterList(false);
if(parameter.MassDefectFilter){
RemoveFragmentPeakByMassDefect();
}
@@ -155,10 +154,6 @@ public String GetQ3Name() {
return FilenameUtils.getBaseName(ParentmzXMLName) + "_Q3";
}
- public String GetQ4Name() {
- return FilenameUtils.getBaseName(ParentmzXMLName) + "_Q3";
- }
-
private void PrepareMGF_MS1Cluster(LCMSPeakMS1 ms1lcms) throws IOException {
ArrayList ScanList = new ArrayList<>();
@@ -180,8 +175,7 @@ private void PrepareMGF_MS1Cluster(LCMSPeakMS1 ms1lcms) throws IOException {
executorPool.execute(proc);
}
executorPool.shutdown();
-// while (!executorPool.isTerminated()) {
-// }
+
try {
executorPool.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS);
} catch (InterruptedException e) {
@@ -457,19 +451,6 @@ private void WriteCluster2CurveCorrSerialization() {
FSCluster2CurveWrite();
}
- private void JavaSerializationCluster2CurveWrite() {
- try {
- Logger.getRootLogger().debug("Writing PrecursorFragmentCorr serialization to file:" + FilenameUtils.getBaseName(ScanCollectionName) + "_Clus2Cur.ser...");
- FileOutputStream fout = new FileOutputStream(FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName) + "_Peak/" + FilenameUtils.getBaseName(ScanCollectionName) + "_Clus2Cur.ser", false);
- ObjectOutputStream oos = new ObjectOutputStream(fout);
- oos.writeObject(FragmentsClu2Cur);
- oos.close();
- fout.close();
- } catch (Exception ex) {
- Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
- }
- }
-
private void FSCluster2CurveWrite() {
try {
Logger.getRootLogger().debug("Writing PrecursorFragmentCorr serialization to file:" + FilenameUtils.getBaseName(ScanCollectionName) + "_Clus2Cur.serFS...");
@@ -483,8 +464,7 @@ private void FSCluster2CurveWrite() {
}
}
- private boolean ReadCluster2CurveCorrSerialization() {
- //return JavaSerializationCluster2CurveRead();
+ private boolean ReadCluster2CurveCorrSerialization() {
if (!FSCluster2CurveRead()) {
if (JavaSerializationCluster2CurveRead()) {
FSCluster2CurveWrite();
@@ -557,8 +537,7 @@ private boolean JavaSerializationCluster2CurveRead() {
return true;
}
- private void WriteUnfragmentedCluster2CurveCorrSerialization() {
- //JavaSerializationCluster2CurveUnfragWrite();
+ private void WriteUnfragmentedCluster2CurveCorrSerialization() {
FSCluster2CurveUnfragWrite();
}
@@ -575,19 +554,6 @@ private void FSCluster2CurveUnfragWrite() {
}
}
- private void JavaSerializationCluster2CurveUnfragWrite() {
- try {
- Logger.getRootLogger().debug("Writing UnfragPrecursorFragCorr serialization to file:" + FilenameUtils.getBaseName(ScanCollectionName) + "_UnfClus2Cur.ser...");
- FileOutputStream fout = new FileOutputStream(FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName) + "_Peak/" + FilenameUtils.getBaseName(ScanCollectionName) + "_UnfClus2Cur.ser", false);
- ObjectOutputStream oos = new ObjectOutputStream(fout);
- oos.writeObject(UnFragIonClu2Cur);
- oos.close();
- fout.close();
- } catch (Exception ex) {
- Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
- }
- }
-
private boolean ReadUnfragmentedCluster2CurveCorrSerialization() {
if (!FSCluster2CurveUnfragRead()) {
if (JavaSerializationCluster2CurveUnfragRead()) {
diff --git a/DIA-Umpire/src/MSUmpire/LCMSBaseStructure/LCMSPeakMS1.java b/DIA-Umpire/src/MSUmpire/LCMSBaseStructure/LCMSPeakMS1.java
index 03f834f..d0856ee 100644
--- a/DIA-Umpire/src/MSUmpire/LCMSBaseStructure/LCMSPeakMS1.java
+++ b/DIA-Umpire/src/MSUmpire/LCMSBaseStructure/LCMSPeakMS1.java
@@ -138,44 +138,6 @@ public void SetDefaultPath(DBSearchParam para) {
para.PepXMLPath = GetDefaultPepXML();
para.ProtXMLPath = GetDefaultProtXML();
}
-
- public void ParseTPP(DBSearchParam para, boolean UserDefinedPath) throws ParserConfigurationException, IOException, InterruptedException, ClassNotFoundException, XmlPullParserException, SAXException {
- this.IDsummary = new LCMSID(ScanCollectionName,para.DecoyPrefix,para.FastaPath);
- if (!UserDefinedPath) {
- SetDefaultPath(para);
- }
- TPPResult tppresult = new TPPResult(para.PepFDR, para.ProtFDR, para.DecoyPrefix);
- ParseLuciphor(IDsummary);
- tppresult.ReadSearchResult(IDsummary, para.PepXMLPath, para.ProtXMLPath);
- }
-
- public void ParseTPP(DBSearchParam para) throws ParserConfigurationException, IOException, InterruptedException, ClassNotFoundException, XmlPullParserException, SAXException {
- ParseTPP(para, false);
- }
-
- public void ParseTPPByRefID(DBSearchParam para, LCMSID ReferenceID) throws ParserConfigurationException, IOException, InterruptedException, XmlPullParserException, SAXException, ClassNotFoundException {
- SetDefaultPath(para);
- //para.PepXMLPath = FilenameUtils.separatorsToUnix(FilenameUtils.getFullPath(ScanCollectionName) + FilenameUtils.getBaseName(ScanCollectionName) + ".Comet.pep.xml");
- this.IDsummary = new LCMSID(ScanCollectionName,para.DecoyPrefix,para.FastaPath);
- TPPResult tppresult = new TPPResult(para.PepFDR, para.ProtFDR,para.DecoyPrefix);
- ParseLuciphor(IDsummary);
- tppresult.ReadSearchResultByRefID(IDsummary, para.PepXMLPath, para.ProtXMLPath, ReferenceID);
- }
-
- public void ParseLuciphor(LCMSID IDsummary) throws FileNotFoundException, IOException {
- if (!new File(ScanCollectionName.replace(".mzXML", ".luciphor.tsv")).exists()) {
- return;
- }
- IDsummary.LuciphorResult = new HashMap<>();
- BufferedReader reader = new BufferedReader(new FileReader(ScanCollectionName.replace(".mzXML", ".luciphor.tsv")));
- String line = "";
- reader.readLine();
- while ((line = reader.readLine()) != null) {
- IDsummary.LuciphorResult.put(line.split("\t")[0], line);
- }
- reader.close();
- }
-
public void AssignMS1Cluster() {
for (PepIonID pepIonID : IDsummary.GetPepIonList().values()) {
@@ -195,11 +157,7 @@ public void AssignMS1Cluster() {
}
}
}
-
- public void AssignIDResult(LCMSID summary) {
- this.IDsummary = summary;
- }
-
+
public void SetmzXML(mzXMLParser mzxml) {
this.mzxml = mzxml;
}
@@ -252,7 +210,6 @@ public void PeakClusterDetection() throws FileNotFoundException, IOException, In
MapScanNoForPeakClusters();
if (ExportPeakClusterTable) {
- //ExportPeakCurveResult();
ExportPeakClusterResultCSV();
}
@@ -388,30 +345,7 @@ public void ExportID(String tag) throws IOException {
}
IDsummary.WriteLCMSIDSerialization(ParentmzXMLName,tag);
}
-
- public void GenerateMassCalibrationMWMap() throws IOException {
- //FileWriter writer = new FileWriter(FilenameUtils.getFullPath(ScanCollectionName) + "/" + FilenameUtils.getBaseName(ScanCollectionName) + "_masscali.txt");
- String pngfile = FilenameUtils.getFullPath(ScanCollectionName) + "/" + FilenameUtils.getBaseName(ScanCollectionName) + "_masscaliMW.png";
- XYSeries series = new XYSeries("PSM");
- XYSeriesCollection xySeriesCollection = new XYSeriesCollection();
- for (PSM psm : this.IDsummary.PSMList.values()) {
- float ppm = InstrumentParameter.CalcSignedPPM(psm.ObserPrecursorMass, psm.NeutralPepMass);
- series.add(new XYDataItem(psm.NeutralPepMass, ppm));
- }
- xySeriesCollection.addSeries(series);
- JFreeChart chart = ChartFactory.createScatterPlot("Mass calibration", "Mass", "Mass error (ppm)", xySeriesCollection,
- PlotOrientation.VERTICAL, true, true, false);
- XYPlot xyPlot = (XYPlot) chart.getPlot();
- xyPlot.setDomainCrosshairVisible(true);
- xyPlot.setRangeCrosshairVisible(true);
- XYItemRenderer renderer = xyPlot.getRenderer();
- renderer.setSeriesPaint(0, Color.blue);
- renderer.setSeriesShape(0, new Ellipse2D.Double(0, 0, 3, 3));
- renderer.setSeriesStroke(0, new BasicStroke(1.0f));
- xyPlot.setBackgroundPaint(Color.white);
- ChartUtilities.saveChartAsPNG(new File(pngfile), chart, 1000, 600);
- }
-
+
public void GenerateMassCalibrationRTMap() throws IOException {
String pngfile = FilenameUtils.getFullPath(ScanCollectionName) + "/" + FilenameUtils.getBaseName(ScanCollectionName) + "_masscaliRT.png";
XYSeries series = new XYSeries("PSM");
@@ -463,11 +397,7 @@ public void GenerateMassCalibrationRTMap() throws IOException {
xyPlot.setBackgroundPaint(Color.white);
ChartUtilities.saveChartAsPNG(new File(pngfile), chart, 1000, 600);
}
-
- public void ReplaceProtByRefID(LCMSID protID) {
- IDsummary.GenerateProteinByRefIDByPepSeq(protID, UseMappedIon);
- }
-
+
public String GetIPROPHETPepXML(){
return FilenameUtils.getFullPath(ParentmzXMLName) + "interact-"+FilenameUtils.getBaseName(ParentmzXMLName) + ".iproph.pep.xml";
}
@@ -475,33 +405,13 @@ public String GetIPROPHETPepXML(){
public String GetIPROPHETProtXML(){
return FilenameUtils.getFullPath(ParentmzXMLName) + "interact-"+FilenameUtils.getBaseName(ParentmzXMLName) + ".iproph.prot.xml";
}
-
- public void ParseiProphet(DBSearchParam param) throws ParserConfigurationException, IOException, SAXException, XmlPullParserException, ClassNotFoundException, InterruptedException {
- ParseiProphet(param,null);
- }
-
- public void ParseiProphet(DBSearchParam param,LCMSID RefPepID) throws ParserConfigurationException, IOException, SAXException, XmlPullParserException, ClassNotFoundException, InterruptedException {
- IDsummary = new LCMSID(FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName),param.DecoyPrefix,param.FastaPath);
- TPPResult tppresult = new TPPResult(param.PepFDR,param.ProtFDR, param.DecoyPrefix);
- if (RefPepID == null) {
- tppresult.ReadSearchResult(IDsummary, GetIPROPHETPepXML(), GetIPROPHETProtXML());
- } else {
- tppresult.ReadSearchResultByRefPepID(IDsummary, GetIPROPHETPepXML(), GetIPROPHETProtXML(), RefPepID);
- }
- CheckPSMRT();
- }
public void ParsePepXML(DBSearchParam param, float prob) throws ParserConfigurationException, IOException, SAXException, XmlPullParserException, ClassNotFoundException, InterruptedException {
IDsummary = new LCMSID(FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName),param.DecoyPrefix,param.FastaPath);
PepXMLParser pepxmlparser = new PepXMLParser(IDsummary, param.InteractPepXMLPath, prob);
CheckPSMRT();
}
- public void ParseiProphetPepXML(DBSearchParam param, float prob) throws ParserConfigurationException, IOException, SAXException, XmlPullParserException, ClassNotFoundException, InterruptedException {
- IDsummary = new LCMSID(FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName),param.DecoyPrefix,param.FastaPath);
- PepXMLParser pepxmlparser = new PepXMLParser(IDsummary, GetIPROPHETPepXML(), prob);
- CheckPSMRT();
- }
-
+
private void CheckPSMRT() {
for(PSM psm : IDsummary.PSMList.values()){
if(psm.RetentionTime==-1f){
diff --git a/DIA-Umpire/src/MSUmpire/MSMSDBSearch/DBSearchParam.java b/DIA-Umpire/src/MSUmpire/MSMSDBSearch/DBSearchParam.java
index 3a83948..f00314a 100644
--- a/DIA-Umpire/src/MSUmpire/MSMSDBSearch/DBSearchParam.java
+++ b/DIA-Umpire/src/MSUmpire/MSMSDBSearch/DBSearchParam.java
@@ -43,18 +43,7 @@ public abstract class DBSearchParam implements Cloneable{
public int MissCleavage = 1;
public boolean SemiCleavage = false;
public boolean NonSpecificCleavage=false;
- public boolean IsotopeError = false;
-
- //
- // [-m FragmentMethodID] (0: As written in the spectrum or CID if no info (Default), 1: CID, 2: ETD, 3: HCD)
- //[-inst MS2DetectorID] (0: Low-res LCQ/LTQ (Default), 1: Orbitrap/FTICR, 2: TOF, 3: Q-Exactive)
- //[-e EnzymeID] (0: unspecific cleavage, 1: Trypsin (Default), 2: Chymotrypsin, 3: Lys-C, 4: Lys-N, 5: glutamyl endopeptidase, 6: Arg-C, 7: Asp-N, 8: alphaLP, 9: no cleavage)
- public int MSGFInstrumentID=2;
- public int MSGFFragmentMethodID=0;
- public int MSGFEnzymeID=1;
-
-//
-
+ public boolean IsotopeError = false;
public String parameterPath;
public String templateParamFile;
public SearchInstrumentType defaultType;
@@ -62,11 +51,7 @@ public abstract class DBSearchParam implements Cloneable{
public float PepFDR = 0.01f;
public float ProtFDR = 0.01f;
public boolean Overwrite = false;
- public String xinteractpath = "C:/inetpub/tpp-bin/xinteract";
- public String msconvertpath = "C:/inetpub/tpp-bin/msconvert";
public String DecoyPrefix="rev_";
- public String xinteractpara = "-OpdEAP -PPM -drev -p0.1";
-
public enum SearchInstrumentType {
Orbitrap,
@@ -87,8 +72,7 @@ public Object clone() throws CloneNotSupportedException {
public abstract void SetResultFilePath(String mzXMLfile);
public abstract void SetCombineFileName(String filename, String tag);
- public abstract void GenerateParamFile();
-
+
protected void SetParameter(SearchInstrumentType type) {
switch (type) {
case Orbit_Velos: {
diff --git a/DIA-Umpire/src/MSUmpire/MSMSDBSearch/TandemParam.java b/DIA-Umpire/src/MSUmpire/MSMSDBSearch/TandemParam.java
index 90ce15e..542571d 100644
--- a/DIA-Umpire/src/MSUmpire/MSMSDBSearch/TandemParam.java
+++ b/DIA-Umpire/src/MSUmpire/MSMSDBSearch/TandemParam.java
@@ -19,58 +19,18 @@
*/
package MSUmpire.MSMSDBSearch;
-import java.io.*;
-import java.util.ArrayList;
-import org.apache.avalon.framework.ExceptionUtil;
import org.apache.commons.io.FilenameUtils;
-import org.apache.log4j.Logger;
/**
*
* @author Chih-Chiang Tsou
*/
public class TandemParam extends DBSearchParam {
-
- public String PotentialModification = "15.994915@M,57.021464@C";
- public String PotentialModMotif = "";
- public String FixModification = "";
- public ArrayList LabelingModification = new ArrayList<>();
- public String tandempath = "C:/inetpub/tpp-bin/tandem.exe";
- public String tandem2XML = "C:/inetpub/tpp-bin/Tandem2XML";
- public String Scoring = "Native";
- public boolean SpectrumConditioning = true;
-
+
public TandemParam(SearchInstrumentType type) {
defaultType = type;
SetParameter(type);
}
-
- private String AddPotentialModification(String output, String Modinfo) {
- if (!"".equals(Modinfo)) {
- output = output.replace("", "" + Modinfo + "");
- }
- return output;
- }
-
- private String AddFixModification(String output, String Modinfo) {
- if (!"".equals(Modinfo)) {
- output = output.replace("", "" + Modinfo + "");
- }
- return output;
- }
-
- private String AddPotentialModMotif(String output, String ModMotif) {
- if (!"".equals(ModMotif)) {
- output = output.replace("", "" + ModMotif + "");
- }
- return output;
- }
-
- private String AddlableingModification(String output, int Index, String Modinfo) {
- output = output.replace(" Add labeling modification by replacing this line", "" + Modinfo + "\n Add labeling modification by replacing this line");
- return output;
- }
-
public void SetCombineFileName(String filename, String tag) {
CombinedPepXML = FilenameUtils.separatorsToUnix(FilenameUtils.getFullPath(filename) + "interact-" + FilenameUtils.getBaseName(filename) + tag + ".tandem.combine.pep.xml");
CombinedProt = FilenameUtils.getFullPath(filename) + FilenameUtils.getBaseName(filename) + tag + ".tandem.Qcombine.prot.xml";
@@ -85,103 +45,4 @@ public void SetResultFilePath(String mzXMLfile) {
parameterPath = FilenameUtils.separatorsToUnix(FilenameUtils.getFullPath(mzXMLfile) + FilenameUtils.getBaseName(mzXMLfile) + ".tandem.param");
RawSearchResult = FilenameUtils.separatorsToUnix(FilenameUtils.getFullPath(mzXMLfile) + FilenameUtils.getBaseName(mzXMLfile) + ".tandem");
}
-
- @Override
- public void GenerateParamFile() {
- FileWriter writer = null;
- try {
- InputStream is = DBSearchParam.class.getClassLoader().getResourceAsStream("resource/tandem.xml");
- if (templateParamFile != null && new File(templateParamFile).exists()) {
- Logger.getRootLogger().info("Using X! Tandem parameter template: " + templateParamFile);
- is = new FileInputStream(templateParamFile);
- }
- BufferedReader reader = new BufferedReader(new InputStreamReader(is));
- String line = "";
- StringBuffer sb = new StringBuffer();
- while ((line = reader.readLine()) != null) {
- sb.append(line + "\n");
- }
- String output = sb.toString();
- if (Scoring.equals("Kscore")) {
- output = output.replace("isb_default_input_native.xml", "" + FilenameUtils.getFullPath(parameterPath) + "/isb_default_input_kscore.xml");
- } else if (Scoring.equals("Native")) {
- output = output.replace("isb_default_input_native.xml", "" + FilenameUtils.getFullPath(parameterPath) + "/isb_default_input_native.xml");
- }
- output = output.replace("15", "" + FragPPM + "");
- output = output.replace("20", "" + PrecursorPPM + "");
- output = output.replace("20", "" + PrecursorPPM + "");
- output = output.replace("", "" + SpectrumPath + "");
- if (NonSpecificCleavage) {
- output = output.replace("[RK]|{P}", "[X]|[X]");
- }
- if (!SpectrumConditioning) {
- output = output.replace("yes", "no");
- }
- output = output.replace("", "" + RawSearchResult + "");
- //output=output.replace("", "" + OutputSeqPath + "");
- output = output.replace("3", "" + MinNoPeaksScoring + "");
- output = output.replace("0", "" + MissCleavage + "");
- output = output.replace("taxnomy.xml", "" + FilenameUtils.getFullPath(parameterPath) + "taxonomy.xml" + "");
- output = output.replace("3", "" + MinNoPeaks + "");
- output = output.replace("100", "" + TotalPeaks + "");
- for (int i = 0; i < LabelingModification.size(); i++) {
- output = AddlableingModification(output, i + 1, LabelingModification.get(i));
- }
- output = AddPotentialModification(output, PotentialModification);
- output = AddFixModification(output, FixModification);
- output = AddPotentialModMotif(output, PotentialModMotif);
- if (SemiCleavage) {
- output = output.replace("no", "yes");
- }
- if (IsotopeError) {
- output = output.replace("no", "yes");
- }
- output = output.replace("6", "" + NoCPUs + "");
- writer = new FileWriter(parameterPath);
- writer.write(output);
- writer.close();
- is = DBSearchParam.class.getClassLoader().getResourceAsStream("resource/taxonomy.xml");
- reader = new BufferedReader(new InputStreamReader(is));
- line = "";
- sb = new StringBuffer();
- while ((line = reader.readLine()) != null) {
- sb.append(line);
- }
- output = sb.toString();
- output = output.replace("", "");
- output = output.replace("", "");
- writer = new FileWriter(FilenameUtils.getFullPath(parameterPath) + "taxonomy.xml");
- writer.write(output);
- writer.close();
- is = DBSearchParam.class.getClassLoader().getResourceAsStream("resource/isb_default_input_kscore.xml");
- reader = new BufferedReader(new InputStreamReader(is));
- line = "";
- sb = new StringBuffer();
- while ((line = reader.readLine()) != null) {
- sb.append(line);
- }
- output = sb.toString();
- if (!(new File(FilenameUtils.getFullPath(parameterPath) + "isb_default_input_kscore.xml")).exists()) {
- writer = new FileWriter(FilenameUtils.getFullPath(parameterPath) + "isb_default_input_kscore.xml");
- writer.write(output);
- writer.close();
- }
- is = DBSearchParam.class.getClassLoader().getResourceAsStream("resource/isb_default_input_native.xml");
- reader = new BufferedReader(new InputStreamReader(is));
- line = "";
- sb = new StringBuffer();
- while ((line = reader.readLine()) != null) {
- sb.append(line);
- }
- output = sb.toString();
- if (!(new File(FilenameUtils.getFullPath(parameterPath) + "isb_default_input_native.xml")).exists()) {
- writer = new FileWriter(FilenameUtils.getFullPath(parameterPath) + "isb_default_input_native.xml");
- writer.write(output);
- writer.close();
- }
- writer.close();
- } catch (Exception ex) {
- Logger.getRootLogger().error(ExceptionUtil.printStackTrace(ex));
- }
- }
}
diff --git a/DIA-Umpire/src/MSUmpire/MathPackage/KMeans.java b/DIA-Umpire/src/MSUmpire/MathPackage/KMeans.java
index aac682b..146d15f 100644
--- a/DIA-Umpire/src/MSUmpire/MathPackage/KMeans.java
+++ b/DIA-Umpire/src/MSUmpire/MathPackage/KMeans.java
@@ -19,7 +19,7 @@
*/
package MSUmpire.MathPackage;
-import ExtPackages.jMEF.PVector;
+import ExternalPackages.jMEF.PVector;
import java.util.Arrays;
import java.util.Random;
diff --git a/DIA-Umpire/src/MSUmpire/MathPackage/KernelDensityEstimator.java b/DIA-Umpire/src/MSUmpire/MathPackage/KernelDensityEstimator.java
index 2941c2b..59f5098 100644
--- a/DIA-Umpire/src/MSUmpire/MathPackage/KernelDensityEstimator.java
+++ b/DIA-Umpire/src/MSUmpire/MathPackage/KernelDensityEstimator.java
@@ -37,19 +37,6 @@ public class KernelDensityEstimator {
private EmpiricalDist empiricalDist;
private KernelDensityGen kernelDensityGen;
private int ObsDataSize=0;
-
- private double [] GussianRandomPointGenerator(int NoPoints) {
- RandomStream stream = new MRG31k3p();
- NormalGen normalKernelDensityGen = new NormalGen(stream);
- kernelDensityGen = new KernelDensityGen(stream, empiricalDist, normalKernelDensityGen);
- double[] randomSamples = new double[NoPoints];
-
- for (int i = 0; i < NoPoints; i++) {
- double nextDouble = kernelDensityGen.nextDouble();
- randomSamples[i] = nextDouble;
- }
- return randomSamples;
- }
public void SetData(double [] data){
Arrays.sort(data);
diff --git a/DIA-Umpire/src/MSUmpire/MathPackage/PearsonCorr.java b/DIA-Umpire/src/MSUmpire/MathPackage/PearsonCorr.java
index 401456e..5aea804 100644
--- a/DIA-Umpire/src/MSUmpire/MathPackage/PearsonCorr.java
+++ b/DIA-Umpire/src/MSUmpire/MathPackage/PearsonCorr.java
@@ -106,8 +106,6 @@ public double CalcCorrV2(XYPointCollection CollectionA, XYPointCollection Collec
return 0f;
}
-// double[] arrayA = new double[num];
-// double[] arrayB = new double[num];
double[] arrayA = new double[num];
double[] arrayB = new double[num];
@@ -185,8 +183,6 @@ public float CalcCorr(XYPointCollection CollectionA, XYPointCollection Collectio
return 0f;
}
-// double[] arrayA = new double[num];
-// double[] arrayB = new double[num];
float[] arrayA = new float[num];
float[] arrayB = new float[num];
@@ -253,9 +249,6 @@ public float CalcCorr(XYPointCollection CollectionA, XYPointCollection Collectio
R2 = regression.GetR2();
}
}
- //PearsonsCorrelation correlation=new PearsonsCorrelation();
- //double R2_2=correlation.correlation(arrayA, arrayB);
-
pointset.dispose();
regression.dispose();
regression = null;
diff --git a/DIA-Umpire/src/MSUmpire/PSMDataStructure/LCMSID.java b/DIA-Umpire/src/MSUmpire/PSMDataStructure/LCMSID.java
index 363c71a..756a5c9 100644
--- a/DIA-Umpire/src/MSUmpire/PSMDataStructure/LCMSID.java
+++ b/DIA-Umpire/src/MSUmpire/PSMDataStructure/LCMSID.java
@@ -25,7 +25,7 @@
import MSUmpire.BaseDataStructure.XYData;
import MSUmpire.FastaParser.FastaParser;
import MSUmpire.PeakDataStructure.PeakCluster;
-import ExtPackages.SortedListLib.SortedList;
+import ExternalPackages.SortedListLib.SortedList;
import com.compomics.util.experiment.biology.AminoAcid;
import com.compomics.util.experiment.biology.Ion;
import com.compomics.util.experiment.biology.PTM;
@@ -73,16 +73,10 @@ public class LCMSID implements Serializable {
private HashMap PepIonList;
private HashMap PepIonIndexList;
public HashMap> PeptideList;
-//
+
private HashMap MappedPepIonList;
private HashMap MappedPepIonIndexList;
public HashMap> MappedPeptideList;
-//
-// private HashMap ExtLibPepIonList;
-// private HashMap ExtLibPepIonIndexList;
-// public HashMap> ExtLibPeptideSeqList;
-
-
public HashMap AssignedPepIonList;
public HashMap ProtXMLPepIonList;
@@ -111,11 +105,9 @@ public class LCMSID implements Serializable {
public String DecoyTag = "rev_";
public String FastaPath;
private float NorFactor = 1f;
- //SequenceFactory sequenceFactory = null;
- FastaParser fastaParser;
- //transient FastaParser_V2 fastaParser;//removed 02032015
+ private transient FastaParser fastaParser;
public HashMap LuciphorResult;
- public String Filename; //added 0828, needs to set as transient for older serialization
+ public String Filename;
private FastaParser GetFastaParser() {
if (fastaParser == null) {
@@ -645,14 +637,7 @@ public void ReadFromDBPSM(Connection connection) throws SQLException {
psm.NeutralPepMass = rsQuery.getFloat("NeutralPepMass");
} catch (Exception e) {
}
- try {
- psm.LuciphorScore = rsQuery.getFloat("LuciphorScore");
- psm.LuciphorLFLR = rsQuery.getFloat("LuciphorLFLR");
- psm.LuciphorFLR = rsQuery.getFloat("LuciphorFLR");
-
- } catch (Exception ex) {
- Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
- }
+
psm.Charge = rsQuery.getInt("Charge");
psm.RetentionTime = rsQuery.getFloat("RT");
psm.ObserPrecursorMass = rsQuery.getFloat("ObservedMass");
@@ -892,10 +877,10 @@ private void ExportPepPSMCSV(String folder) throws IOException {
}
Logger.getRootLogger().info("Writing PSM result to file:" + folder + FilenameUtils.getBaseName(mzXMLFileName) + "_PSMs.csv...");
FileWriter writer = new FileWriter(folder + FilenameUtils.getBaseName(mzXMLFileName) + "_PSMs.csv");
- writer.write("SpecID,Sequence,ModSeq,TPPModSeq,LuciphorScore,LuciphorLFLR,LuciphorFLR,Modification,Charge,mz,NeutralPepMass,ObservedMass,RT,AdjustedRT,Rank,ScanNo,PreAA,NextAA,MissedCleavage,ExpectValue,MassError,Prob,Rawname,ParentPepIndex,MS1Quant\n");
+ writer.write("SpecID,Sequence,ModSeq,TPPModSeq,Modification,Charge,mz,NeutralPepMass,ObservedMass,RT,AdjustedRT,Rank,ScanNo,PreAA,NextAA,MissedCleavage,ExpectValue,MassError,Prob,Rawname,ParentPepIndex,MS1Quant\n");
for (PepIonID pepion : PepIonList.values()) {
for (PSM psm : pepion.GetPSMList()) {
- writer.write(psm.SpecNumber + "," + psm.Sequence + "," + psm.ModSeq + "," + psm.TPPModSeq + "," + psm.LuciphorScore + "," + psm.LuciphorLFLR + "," + psm.LuciphorFLR + "," + psm.GetModificationString() + "," + psm.Charge + "," + psm.ObserPrecursorMz() + "," + psm.NeutralPepMass + "," + psm.ObserPrecursorMass + "," + psm.RetentionTime + "," + psm.NeighborMaxRetentionTime + "," + psm.Rank + "," + psm.ScanNo + "," + psm.PreAA + "," + psm.NextAA + "," + psm.MissedCleavage + "," + psm.expect + "," + psm.MassError + "," + psm.Probability + "," + psm.RawDataName + "," + pepion.Index + "," + pepion.GetMS1() + "\n");
+ writer.write(psm.SpecNumber + "," + psm.Sequence + "," + psm.ModSeq + "," + psm.TPPModSeq + "," + psm.GetModificationString() + "," + psm.Charge + "," + psm.ObserPrecursorMz() + "," + psm.NeutralPepMass + "," + psm.ObserPrecursorMass + "," + psm.RetentionTime + "," + psm.NeighborMaxRetentionTime + "," + psm.Rank + "," + psm.ScanNo + "," + psm.PreAA + "," + psm.NextAA + "," + psm.MissedCleavage + "," + psm.expect + "," + psm.MassError + "," + psm.Probability + "," + psm.RawDataName + "," + pepion.Index + "," + pepion.GetMS1() + "\n");
}
}
writer.close();
@@ -919,9 +904,9 @@ private void ExportPepIonCSV(String folder) throws IOException {
Logger.getRootLogger().info("Writing PepIon result to file:" + folder + FilenameUtils.getBaseName(mzXMLFileName) + "_PepIonIDs.csv...");
FileWriter writer = new FileWriter(folder + FilenameUtils.getBaseName(mzXMLFileName) + "_PepIonIDs.csv");
- writer.write("PepIndex,Sequence,ModSeq,TPPModSeq,LuciphorScore,LuciphorLFLR,LuciphorFLR, IsNonDegenerate,Charge,mz,IDRT,PeakRT,NoPSMs,MS1ClusIndex,MS2ClusIndex,PeakScore,PeakHeight1,PeakHeight2,PeakHeight3,PeakArea1,PeakArea2,PeakArea3\n");
+ writer.write("PepIndex,Sequence,ModSeq,TPPModSeq,IsNonDegenerate,Charge,mz,IDRT,PeakRT,NoPSMs,MS1ClusIndex,MS2ClusIndex,PeakScore,PeakHeight1,PeakHeight2,PeakHeight3,PeakArea1,PeakArea2,PeakArea3\n");
for (PepIonID pepion : PepIonList.values()) {
- writer.write(pepion.Index + "," + pepion.Sequence + "," + pepion.ModSequence + "," + pepion.TPPModSeq + "," + pepion.GetMaxLuciphorScore() + "," + pepion.GetMinLuciphorLFLR() + "," + pepion.GetMinLuciphorFLR() + "," + (pepion.Is_NonDegenerate ? 1 : 0) + "," + pepion.Charge + "," + pepion.NeutralPrecursorMz() + "," + pepion.GetIDRT() + "," + pepion.PeakRT + "," + pepion.GetSpectralCount() + "," + pepion.GetMS1ClusIndex() + "," + pepion.GetMS2ClusIndex() + "," + pepion.PeakClusterScore + "," + pepion.PeakHeight[0] + "," + pepion.PeakHeight[1] + "," + pepion.PeakHeight[2] + "," + pepion.PeakArea[0] + "," + pepion.PeakArea[1] + "," + pepion.PeakArea[2] + "\n");
+ writer.write(pepion.Index + "," + pepion.Sequence + "," + pepion.ModSequence + "," + pepion.TPPModSeq + "," + (pepion.Is_NonDegenerate ? 1 : 0) + "," + pepion.Charge + "," + pepion.NeutralPrecursorMz() + "," + pepion.GetIDRT() + "," + pepion.PeakRT + "," + pepion.GetSpectralCount() + "," + pepion.GetMS1ClusIndex() + "," + pepion.GetMS2ClusIndex() + "," + pepion.PeakClusterScore + "," + pepion.PeakHeight[0] + "," + pepion.PeakHeight[1] + "," + pepion.PeakHeight[2] + "," + pepion.PeakArea[0] + "," + pepion.PeakArea[1] + "," + pepion.PeakArea[2] + "\n");
}
writer.close();
}
@@ -994,7 +979,7 @@ public void LoadSequence() throws IOException, XmlPullParserException {
//String Sequence = GetSequenceFactory().getProtein(protID.UniProtID).getSequence();
//String Sequence = GetFastaParser().ProteinList.get(protID.getAccNo()).Seq;
try {
- String Sequence = GetFastaParser().ProteinList.get(protID.getAccNo())[0];
+ String Sequence = GetFastaParser().ProteinList.get(protID.getAccNo()).Seq;
if (Sequence != null) {
protID.SetSequence(Sequence);
} else {
@@ -1026,27 +1011,6 @@ public ArrayList FindPsmsBymzRT(float mz, float RT, int charge, float PPM,
return psms;
}
- private void FindSpecExpectThresholdByFDR() {
-
- SortedPSMListEvalue sortedlist = new SortedPSMListEvalue();
- sortedlist.addAll(PSMList.values());
-
- int positive = 0;
- int negative = 0;
- for (int i = 0; i < sortedlist.size(); i++) {
- PSM psm = sortedlist.get(i);
- if (psm.IsDecoy(DecoyTag)) {
- negative++;
- } else {
- positive++;
- }
- if ((float) negative / (float) (positive + negative) >= FDR) {
- ExpectThreshold = psm.expect;
- return;
- }
- }
- }
-
public void ROCProtByMaxIniProb(String decoytag) throws IOException {
if (ProteinList.isEmpty()) {
return;
@@ -1154,107 +1118,6 @@ private void FindMaxIniProbThresholdByFDR() {
Logger.getRootLogger().info("Protein maxiniprob threshold=" + ProteinProbThreshold + " Estimated raw protein FDR:" + (float) negative / (float) (positive) + "(Target/Decoy)=(" + positive + "/" + negative + ")");
}
- private void FindLocalPWThresholdByFDR() {
- //FileWriter writer = null;
- //try {
- if (ProteinList.isEmpty()) {
- return;
- }
- SortedProteinListProb sortedlist = new SortedProteinListProb();
- sortedlist.addAll(ProteinList.values());
-
- //writer = new FileWriter(FilenameUtils.getFullPath(mzXMLFileName)+"/" + FilenameUtils.getBaseName(mzXMLFileName)+"_Pro.txt");
- int positive = 0;
- int negative = 0;
- ProtID protein = sortedlist.get(0);
- if (protein.IsDecoy(DecoyTag)) {
- negative++;
- } else {
- positive++;
- }
- for (int i = 1; i < sortedlist.size(); i++) {
- protein = sortedlist.get(i);
- if (protein.IsDecoy(DecoyTag)) {
- negative++;
- //System.out.println(protein.getAccNo()+"-"+protein.ProteinGroup+"-Decoy");
- } else {
- positive++;
- //System.out.println(protein.getAccNo()+"-"+ protein.ProteinGroup);
- }
- if (protein.Probability < sortedlist.get(i - 1).Probability && (float) negative / (float) (positive) >= ProteinFDR) {
- ProteinProbThreshold = protein.Probability;
- Logger.getRootLogger().info("Protein probability threshold=" + ProteinProbThreshold + " Estimated raw protein FDR:" + (float) negative / (float) (positive) + "(Target/Decoy)=(" + positive + "/" + negative + ")");
- return;
- }
- }
- }
-
- private void FindProteinMaxLocalPWThresholdByFDR() {
- if (ProteinList.isEmpty()) {
- return;
- }
- SortedProteinListMaxLocalPW sortedlist = new SortedProteinListMaxLocalPW();
- sortedlist.addAll(ProteinList.values());
-
- //writer = new FileWriter(FilenameUtils.getFullPath(mzXMLFileName)+"/" + FilenameUtils.getBaseName(mzXMLFileName)+"_Pro.txt");
- int positive = 0;
- int negative = 0;
- ProtID protein = sortedlist.get(0);
- if (protein.IsDecoy(DecoyTag)) {
- negative++;
- } else {
- positive++;
- }
- for (int i = 1; i < sortedlist.size(); i++) {
- protein = sortedlist.get(i);
- if (protein.IsDecoy(DecoyTag)) {
- negative++;
- } else {
- positive++;
- //System.out.println(protein.getAccNo()+"-"+ protein.ProteinGroup);
- }
- if (protein.MaxLocalPW < sortedlist.get(i - 1).MaxLocalPW && (float) negative / (float) (positive) >= ProteinFDR) {
- ProteinProbThreshold = protein.MaxLocalPW;
- Logger.getRootLogger().info("Protein probability threshold=" + ProteinProbThreshold + " Estimated raw protein FDR:" + (float) negative / (float) (positive) + "(Target/Decoy)=(" + positive + "/" + negative + ")");
- return;
- }
- }
- }
-
- private void FindSpecProbThresholdByFDR() {
- if (PSMList.isEmpty()) {
- return;
- }
- SortedPSMListProb sortedlist = new SortedPSMListProb();
- sortedlist.addAll(PSMList.values());
-
- //writer = new FileWriter(FilenameUtils.getFullPath(mzXMLFileName)+"/" + FilenameUtils.getBaseName(mzXMLFileName)+"_Pep.txt");
- int positive = 0;
- int negative = 0;
- PSM psm = sortedlist.get(0);
- if (psm.IsDecoy(DecoyTag)) {
- negative++;
- } else {
- positive++;
- }
- for (int i = 1; i < sortedlist.size(); i++) {
- psm = sortedlist.get(i);
- if (psm.Probability < 0.1f) {
- break;
- }
- if (psm.IsDecoy(DecoyTag)) {
- negative++;
- } else {
- positive++;
- }
- if (psm.Probability < sortedlist.get(i - 1).Probability && ((float) negative / (float) (positive) >= FDR)) {
- SpecProbThreshold = psm.Probability;
- Logger.getRootLogger().info("Spectrum probability threshold=" + SpecProbThreshold + " Estimated Spectrum FDR:" + (float) negative / (float) (positive) + "(Target/Decoy)=(" + positive + "/" + negative + ")");
- return;
- }
- }
- }
-
public void ClearPeakData() {
for (PepIonID pepIonID : PepIonList.values()) {
for (PeakCluster peak : pepIonID.MS1PeakClusters) {
@@ -1326,15 +1189,7 @@ public void ReMapProPep() {
GenearteAssignIonList();
}
- public void RemoveRedundantFrag() {
- for (PepIonID pep : GetPepIonList().values()) {
- pep.RemoveRedundantFrag();
- }
- for (PepIonID pep : GetMappedPepIonList().values()) {
- pep.RemoveRedundantFrag();
- }
- }
-
+
public void SetFilterByGroupWeight() {
for (PepIonID pep : GetPepIonList().values()) {
pep.FilteringWeight = pep.GroupWeight;
diff --git a/DIA-Umpire/src/MSUmpire/PSMDataStructure/PSM.java b/DIA-Umpire/src/MSUmpire/PSMDataStructure/PSM.java
index e9dc104..d5a1117 100644
--- a/DIA-Umpire/src/MSUmpire/PSMDataStructure/PSM.java
+++ b/DIA-Umpire/src/MSUmpire/PSMDataStructure/PSM.java
@@ -60,9 +60,6 @@ public class PSM implements Serializable{
public float xscore;
public float expect;
public PepIonID pepIonID;
- public float LuciphorLFLR;
- public float LuciphorFLR;
- public float LuciphorScore;
public String GetRawNameString() {
return SpecNumber.substring(0, SpecNumber.indexOf("."));
diff --git a/DIA-Umpire/src/MSUmpire/PSMDataStructure/PepIonID.java b/DIA-Umpire/src/MSUmpire/PSMDataStructure/PepIonID.java
index 3c8b7c4..bfef9bf 100644
--- a/DIA-Umpire/src/MSUmpire/PSMDataStructure/PepIonID.java
+++ b/DIA-Umpire/src/MSUmpire/PSMDataStructure/PepIonID.java
@@ -23,7 +23,6 @@
import MSUmpire.PeakDataStructure.PeakCluster;
import com.compomics.util.experiment.biology.Ion;
import com.compomics.util.experiment.biology.IonFactory;
-import com.compomics.util.experiment.biology.PTM;
import com.compomics.util.experiment.biology.Peptide;
import com.compomics.util.experiment.biology.ions.ElementaryIon;
import com.compomics.util.experiment.biology.ions.PeptideFragmentIon;
@@ -31,13 +30,11 @@
import com.compomics.util.general.IsotopicDistribution;
import com.compomics.util.protein.AASequenceImpl;
import com.compomics.util.protein.MolecularFormula;
-import java.io.IOException;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import org.apache.log4j.Logger;
-import org.xmlpull.v1.XmlPullParserException;
/**
*
@@ -76,10 +73,9 @@ public class PepIonID implements Serializable {
private float RT = -1f;
public float PeakRT = -1f;
public ArrayList PredictRT = new ArrayList<>();
- //public int PeakClusterIndex = -1;
+
private float RTSD = -1f;
private ArrayList Fragments;
- private SortedFragmentSet FragmentMZSet;
public ArrayList Modifications = new ArrayList<>();
public ArrayList FragmentPeaks = new ArrayList<>();
private Peptide peptide = null;
@@ -129,42 +125,6 @@ public float GetMS1PPM(){
return ppm;
}
- public String GetSkylineModSeq() throws XmlPullParserException, IOException {
- if (skylinemod == null || "".equals(skylinemod)) {
- skylinemod = Sequence;
-
- double FirstAAmoddiff=0d;
- for (ModificationMatch mod : Modifications) {
- int site = mod.getModificationSite() - 1;
- PTM ptm = PTMManager.GetInstance().GetPTMByName(mod.getTheoreticPtm());
- double massdiff = ptm.getMass();
- if (mod.getTheoreticPtm().contains("n-term") || site == 0) {
- FirstAAmoddiff += massdiff;
- } else {
- String modstring = "";
- if (massdiff > 0) {
- modstring = "[+" + massdiff + "]";
- } else {
- modstring = "[" + massdiff + "]";
- }
- skylinemod = ModStringConvert.AddModIntoSeqAfterSite(skylinemod, modstring, site);
- }
- }
-
- if (FirstAAmoddiff != 0d) {
- String modstring = "";
- if (FirstAAmoddiff > 0) {
- modstring = "[+" + FirstAAmoddiff + "]";
- } else {
- modstring = "[" + FirstAAmoddiff + "]";
- }
- skylinemod = ModStringConvert.AddModIntoSeqAfterSite(skylinemod, modstring, 0);
- }
-
- }
- return skylinemod;
- }
-
transient int fragcount=-1;
public int GetFragCount(){
if (fragcount == 0) {
@@ -217,44 +177,13 @@ public int getNMissedCleavages() {
public void ClearPepFragFactory(){
peptide=null;
- FragmentMZSet=null;
Fragments=null;
}
-
- public float GetMaxLuciphorScore() {
- float score = 0f;
- for (PSM psm : PSMList) {
- if (psm.LuciphorScore > score) {
- score = psm.LuciphorScore;
- }
- }
- return score;
- }
-
- public float GetMinLuciphorLFLR() {
- float flr = 1f;
- for (PSM psm : PSMList) {
- if (psm.LuciphorLFLR < flr) {
- flr = psm.LuciphorLFLR;
- }
- }
- return flr;
- }
-
+
public float TargetedProbability(){
return Math.max(MS1AlignmentLocalProbability, MS2AlignmentLocalProbability);
}
- public float GetMinLuciphorFLR() {
- float flr = 1f;
- for (PSM psm : PSMList) {
- if (psm.LuciphorFLR < flr) {
- flr = psm.LuciphorFLR;
- }
- }
- return flr;
- }
-
public void ReFreshPepFactory() {
peptide = new Peptide(Sequence, Modifications);
mz = -1f;
@@ -289,9 +218,6 @@ public PepIonID ClonePepIonID() {
newpeptide.PeakArea = new float[PeakArea.length];
newpeptide.PeakHeight = new float[PeakHeight.length];
}
-// if (PSMList != null) {
-// newpeptide.PSMList = (ArrayList) PSMList.clone();
-// }
return newpeptide;
}
@@ -314,32 +240,9 @@ public float GetPepAbundanceByTopCorrFragAcrossSample(ArrayList PepFrag)
}
}
}
-// if(count<2){
-// totalabundance=0;
-// }
return totalabundance;
}
- public float GetPepAbundanceByTopCorrFragments(int topN) {
- ArrayList includelist = new ArrayList<>();
- for (int i = 0; i < topN; i++) {
- FragmentPeak bestfrag=null;
- for (FragmentPeak fragment : FragmentPeaks) {
- if (!includelist.contains(fragment) && (bestfrag == null || fragment.intensity > bestfrag.intensity)) {
- bestfrag = fragment;
- }
- }
- if (bestfrag != null) {
- includelist.add(bestfrag);
- }
- }
- float totalabundance = 0f;
- for (FragmentPeak frag : includelist ) {
- totalabundance+=frag.intensity;
- }
- return totalabundance;
- }
-
public float GetPepAbundanceByTopFragments(int topN) {
ArrayList includelist = new ArrayList<>();
for (int i = 0; i < topN; i++) {
@@ -360,14 +263,6 @@ public float GetPepAbundanceByTopFragments(int topN) {
return totalabundance;
}
- public float GetPepAbundanceByAllFragments() {
- float totalabundance = 0f;
- for (FragmentPeak fragment : FragmentPeaks) {
- totalabundance += fragment.intensity;
- }
- return totalabundance;
- }
-
public PSM GetBestExpectValuePSM() {
PSM top = GetPSMList().get(0);
for (int psmidx = 1; psmidx < GetPSMList().size(); psmidx++) {
@@ -415,31 +310,6 @@ public float LookUpFragmentMZ(PeptideFragmentIon.IonType fragmentIonType, int nu
}
return 0f;
}
-
- public SortedFragmentSet GetFragmentMZ() {
-
- if (FragmentMZSet == null) {
- FragmentMZSet = new SortedFragmentSet();
- double protonMass = ElementaryIon.proton.getTheoreticMass();
- for (Ion frag : GetFragments()) {
- float targetmz = (float) frag.getTheoreticMz(1);
- PeptideFragment fragment = new PeptideFragment();
- fragment.IonType = frag.getSubTypeAsString() + ((PeptideFragmentIon) frag).getNumber();
- fragment.Charge = 1;
- fragment.FragMZ = targetmz;
- //fragment.Number = ((PeptideFragmentIon) frag).getNumber();
- FragmentMZSet.add(fragment);
- float targetmz2 = (float) frag.getTheoreticMz(2);
- PeptideFragment fragment2 = new PeptideFragment();
- fragment2.IonType = frag.getSubTypeAsString() + ((PeptideFragmentIon) frag).getNumber();
- fragment2.Charge = 2;
- fragment2.FragMZ = targetmz2;
- //fragment2.Number = ((PeptideFragmentIon) frag).getNumber();
- FragmentMZSet.add(fragment2);
- }
- }
- return FragmentMZSet;
- }
private void SetFragments() {
peptide = GetPepFactory();
@@ -558,13 +428,7 @@ public void AddModifications(PSM psm) {
}
}
-
- //private transient int spc=-1;
-
public int GetSpectralCount(){
-// if(spc==-1){
-// spc=PSMList.size();
-// }
return PSMList.size();
}
@@ -609,8 +473,7 @@ public String GetModificationString() {
}
public MolecularFormula GetMolecularFormula() {
- MolecularFormula formula = new MolecularFormula(GetAASequenceImpl());
- //formula.addMolecularFormula(GetModMolecularFormula());
+ MolecularFormula formula = new MolecularFormula(GetAASequenceImpl());
return formula;
}
AASequenceImpl AAimple = null;
diff --git a/DIA-Umpire/src/MSUmpire/PSMDataStructure/ProtID.java b/DIA-Umpire/src/MSUmpire/PSMDataStructure/ProtID.java
index bcc54c0..ad53752 100644
--- a/DIA-Umpire/src/MSUmpire/PSMDataStructure/ProtID.java
+++ b/DIA-Umpire/src/MSUmpire/PSMDataStructure/ProtID.java
@@ -33,10 +33,11 @@
*
* @author Chih-Chiang Tsou
*/
-public class ProtID implements Serializable{
+public class ProtID implements Serializable {
+
private static final long serialVersionUID = 863236278237L;
- public transient boolean IDByDBSearch=false;
+ public transient boolean IDByDBSearch = false;
public ArrayList IndisProteins;
public transient ArrayList IndisProtDes;
private String AccNo;
@@ -48,7 +49,7 @@ public class ProtID implements Serializable{
public float Mass;
public float Probability;
public float GroupProb;
- public float MaxLocalPW;
+ public float MaxLocalPW;
public float MaxIniProb = 0f;
public String Sequence;
public HashMap PeptideID;
@@ -71,14 +72,14 @@ public void SetDescription(String Des) {
GeneName = Description.substring(Description.indexOf("GeneName=") + 9, Description.indexOf("OtherGeneNames") - 2).trim();
}
}
-
+
public ProtID CloneProtein() {
ProtID newprotein = new ProtID();
try {
if (Sequence != null) {
newprotein.SetSequence(Sequence);
} else {
- Logger.getRootLogger().error("Sequence of protein:"+getAccNo()+" is null");
+ Logger.getRootLogger().error("Sequence of protein:" + getAccNo() + " is null");
}
} catch (Exception ex) {
Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
@@ -100,10 +101,11 @@ public float GetAbundanceByFragment_IBAQ(int topNfragment) {
}
public float GetAbundanceByTopPepFrag(int toppep, int topfrag) {
- return GetAbundanceByTopPepFrag(toppep,topfrag,-1f);
+ return GetAbundanceByTopPepFrag(toppep, topfrag, -1f);
}
+
public float GetAbundanceByTopPepFrag(int toppep, int topfrag, float pepweight) {
- if(PeptideID.isEmpty()){
+ if (PeptideID.isEmpty()) {
return 0;
}
PriorityQueue TopQueue = new PriorityQueue<>(PeptideID.size(), Collections.reverseOrder());
@@ -121,50 +123,15 @@ public float GetAbundanceByTopPepFrag(int toppep, int topfrag, float pepweight)
return totalabundance / num;
}
- public float GetAbundanceByAllFragment_IBAQ() {
- return GetAbundanceByAllFragment_IBAQ(-1);
- }
-
- public float GetAbundanceByAllFragment_IBAQ(float pepweight) {
- float totalabundance = 0f;
- for (PepIonID peptide : PeptideID.values()) {
- if (peptide.FilteringWeight>pepweight) {
- totalabundance += peptide.GetPepAbundanceByAllFragments();
- }
- }
- return totalabundance / TheoPeptides.size();
- }
-
- public int GetSILAC_H_Count(String Mod) {
- int spc = 0;
- for (PepIonID pep : PeptideID.values()) {
- if (pep.ModSequence.contains(Mod)) {
- spc += pep.GetSpectralCount();
- }
- }
- return spc;
- }
-
- public int GetSILAC_L_Count(String AA, String Mod) {
- int spc = 0;
- for (PepIonID pep : PeptideID.values()) {
- if (pep.ModSequence.contains(AA) && !pep.ModSequence.contains(Mod)) {
- spc += pep.GetSpectralCount();
- }
- }
- return spc;
- }
-
-
public int GetSpectralCount() {
int spc = 0;
for (PepIonID pep : PeptideID.values()) {
- spc += pep.GetSpectralCount();
+ spc += pep.GetSpectralCount();
}
return spc;
}
-
- public int GetFragCount() {
+
+ public int GetFragCount() {
int frag = 0;
for (PepIonID pep : PeptideID.values()) {
frag += pep.GetFragCount();
@@ -172,34 +139,14 @@ public int GetFragCount() {
return frag;
}
- public float GetAbundanceByMS1_IBAQ_SILAC_H(String Mod) {
- float totalabundance = 0f;
- for (PepIonID peptide : PeptideID.values()) {
- if (peptide.PeakHeight != null && peptide.ModSequence.contains(Mod)) {
- totalabundance += peptide.PeakHeight[0];
- }
- }
- return totalabundance / TheoPeptides.size();
- }
-
- public float GetAbundanceByMS1_IBAQ_SILAC_L(String AA, String Mod) {
- float totalabundance = 0f;
- for (PepIonID peptide : PeptideID.values()) {
- if (peptide.PeakHeight != null && peptide.ModSequence.contains(AA) && !peptide.ModSequence.contains(Mod)) {
- totalabundance += peptide.PeakHeight[0];
- }
- }
- return totalabundance / TheoPeptides.size();
- }
-
public float GetAbundanceByMS1_IBAQ() {
return GetAbundanceByMS1_IBAQ(-1f);
}
-
+
public float GetAbundanceByMS1_IBAQ(float pepweight) {
float totalabundance = 0f;
for (PepIonID peptide : PeptideID.values()) {
- if (peptide.PeakHeight != null && peptide.FilteringWeight>pepweight) {
+ if (peptide.PeakHeight != null && peptide.FilteringWeight > pepweight) {
totalabundance += peptide.PeakHeight[0];
}
}
@@ -207,15 +154,16 @@ public float GetAbundanceByMS1_IBAQ(float pepweight) {
}
public float GetAbundanceByMS1_TopN(int topN) {
- return GetAbundanceByMS1_TopN(topN,-1f);
+ return GetAbundanceByMS1_TopN(topN, -1f);
}
+
public float GetAbundanceByMS1_TopN(int topN, float pepweight) {
- if(PeptideID.isEmpty()){
+ if (PeptideID.isEmpty()) {
return 0;
}
- PriorityQueue TopQueue = new PriorityQueue<>(PeptideID.size(), Collections.reverseOrder());
+ PriorityQueue TopQueue = new PriorityQueue<>(PeptideID.size(), Collections.reverseOrder());
for (PepIonID peptide : PeptideID.values()) {
- if (peptide.PeakHeight != null && peptide.FilteringWeight>pepweight) {
+ if (peptide.PeakHeight != null && peptide.FilteringWeight > pepweight) {
TopQueue.add(peptide.PeakHeight[0]);
}
}
@@ -229,7 +177,7 @@ public float GetAbundanceByMS1_TopN(int topN, float pepweight) {
return totalabundance / num;
}
- public float GetAbundanceByTopAcrossSample(ArrayList ProPep) {
+ public float GetAbundanceByTopAcrossSample(ArrayList ProPep) {
float totalabundance = 0f;
if (ProPep != null) {
for (PepIonID pepIonID : PeptideID.values()) {
@@ -240,41 +188,25 @@ public float GetAbundanceByTopAcrossSample(ArrayList ProPep) {
}
return totalabundance;
}
-
- public float GetAbundanceByTopAcrossSampleTopN(ArrayList ProPep, int TopN) {
- float totalabundance = 0f;
- if (ProPep != null) {
- for (PepIonID pepIonID : PeptideID.values()) {
- if (ProPep.contains(pepIonID.GetKey())) {
- totalabundance += pepIonID.PeakHeight[0];
- }
- }
- }
- return totalabundance;
- }
-
-
+
public float GetAbundanceByTopCorrFragAcrossSample(ArrayList ProPep, HashMap> PepFrag) {
float totalabundance = 0f;
- int count=0;
+ int count = 0;
if (ProPep != null) {
for (PepIonID pepIonID : PeptideID.values()) {
if (ProPep.contains(pepIonID.GetKey())) {
- totalabundance += pepIonID.GetPepAbundanceByTopCorrFragAcrossSample(PepFrag.get(pepIonID.GetKey()));
+ totalabundance += pepIonID.GetPepAbundanceByTopCorrFragAcrossSample(PepFrag.get(pepIonID.GetKey()));
count++;
}
}
}
-// if(count<2){
-// totalabundance=0;
-// }
return totalabundance;
}
-
+
public ProtID() {
PeptideID = new HashMap<>();
IndisProteins = new ArrayList<>();
- IndisProtDes=new ArrayList<>();
+ IndisProtDes = new ArrayList<>();
ProtPeptideID = new HashMap<>();
ProtPepSeq = new ArrayList<>();
}
@@ -291,17 +223,17 @@ public void SetSequence(String Seq) throws IOException, XmlPullParserException {
}
public void InsilicosDigestion(int missedcleave, int minlength, int maxlength) throws XmlPullParserException, IOException {
- TheoPeptides = EnzymeManager.GetInstance().GetTrypsin().digest(Sequence, missedcleave, minlength, maxlength);
+ TheoPeptides = EnzymeManager.GetInstance().GetTrypsin().digest(Sequence, missedcleave, minlength, maxlength);
if (String.valueOf(Sequence.charAt(0)).equals("M")) {
- int mc=0;
+ int mc = 0;
for (int i = 1; i < Sequence.length(); i++) {
if (String.valueOf(Sequence.charAt(i)).equals("K") || String.valueOf(Sequence.charAt(i)).equals("R")) {
mc++;
- if(mc>missedcleave){
+ if (mc > missedcleave) {
return;
}
- String pep=Sequence.substring(1,i+1);
- if (pep.length()>=minlength && pep.length()<=maxlength && !TheoPeptides.contains(pep)) {
+ String pep = Sequence.substring(1, i + 1);
+ if (pep.length() >= minlength && pep.length() <= maxlength && !TheoPeptides.contains(pep)) {
TheoPeptides.add(pep);
}
}
@@ -327,7 +259,6 @@ public boolean IsDecoy(String decoytag) {
* @return the AccNo
*/
public String getAccNo() {
- //return AccNo.replace("|", "_");
return AccNo;
}
@@ -337,8 +268,7 @@ public String getAccNo() {
public void setAccNo(String AccNo) {
this.AccNo = AccNo;
}
-
-
+
public void UpdateMaxIniProb() {
MaxIniProb = 0f;
for (PepIonID pepion : PeptideID.values()) {
@@ -347,24 +277,24 @@ public void UpdateMaxIniProb() {
}
}
}
-
+
public void RemoveLowWeightPepID(float threshold) {
- ArrayList removelist=new ArrayList<>();
- MaxIniProb=0f;
- for(PepIonID pepion: PeptideID.values()){
- if(pepion.FilteringWeight removelist = new ArrayList<>();
+ MaxIniProb = 0f;
+ for (PepIonID pepion : PeptideID.values()) {
+ if (pepion.FilteringWeight < threshold) {
removelist.add(pepion);
}
}
- for(PepIonID pepIonID : removelist){
+ for (PepIonID pepIonID : removelist) {
PeptideID.remove(pepIonID.GetKey());
}
- for(PepIonID pepion: ProtPeptideID.values()){
- if(pepion.FilteringWeight
- * Nesvizhskii Lab, Department of Computational Medicine and Bioinformatics,
- * University of Michigan, Ann Arbor
- *
- * Copyright 2014 University of Michigan, Ann Arbor, MI
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package MSUmpire.PSMDataStructure;
-
-import ExtPackages.SortedListLib.SortedList;
-import java.io.Serializable;
-import java.util.Comparator;
-
-/**
- *
- * @author Chih-Chiang Tsou
- */
-public class SortedFragmentSet extends SortedList implements Serializable {
- private static final long serialVersionUID = 836465863L;
-
- public SortedFragmentSet() {
- super(new Comparator() {
- @Override
- public int compare(PeptideFragment x, PeptideFragment y) {
- if (x.FragMZ == y.FragMZ) {
- return 1;
- }
- return -Float.compare(y.FragMZ, x.FragMZ);
- }
- });
- }
-
- public PeptideFragment GetCloset(float value) {
- return get(BinarySearchClosest(value));
- }
-
- public int BinarySearchClosest(float value) {
-
- if (isEmpty()) {
- return 0;
- }
- int lower = 0;
- int upper = size() - 1;
-
- if (value - get(upper).FragMZ >= 0) {
- return upper;
- }
- if (value - get(0).FragMZ <= 0) {
- return 0;
- }
-
- while (lower <= upper) {
- int middle = (lower + upper) / 2;
- float comparisonResult = value - get(middle).FragMZ;
- if (comparisonResult == 0) {
- return middle;
- } else if (comparisonResult < 0) {
- upper = middle - 1;
- } else {
- lower = middle + 1;
- }
- }
-
- if (Math.abs(value - get(lower).FragMZ) > Math.abs(value - get(upper).FragMZ)) {
- return upper;
- } else {
- return lower;
- }
- }
-
-}
diff --git a/DIA-Umpire/src/MSUmpire/PSMDataStructure/SortedPSMListEvalue.java b/DIA-Umpire/src/MSUmpire/PSMDataStructure/SortedPSMListEvalue.java
deleted file mode 100644
index dfd1375..0000000
--- a/DIA-Umpire/src/MSUmpire/PSMDataStructure/SortedPSMListEvalue.java
+++ /dev/null
@@ -1,43 +0,0 @@
-/*
- * Author: Chih-Chiang Tsou
- * Nesvizhskii Lab, Department of Computational Medicine and Bioinformatics,
- * University of Michigan, Ann Arbor
- *
- * Copyright 2014 University of Michigan, Ann Arbor, MI
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package MSUmpire.PSMDataStructure;
-
-import ExtPackages.SortedListLib.SortedList;
-import java.util.Comparator;
-
-/**
- *
- * @author Chih-Chiang Tsou
- */
-public class SortedPSMListEvalue extends SortedList {
-
- public SortedPSMListEvalue() {
- super(new Comparator() {
- @Override
- public int compare(PSM x, PSM y) {
- if (x.expect == y.expect) {
- return Integer.compare(x.ScanNo, y.ScanNo);
- }
- return -Float.compare(y.expect, x.expect);
- }
- });
- }
-
-}
diff --git a/DIA-Umpire/src/MSUmpire/PSMDataStructure/SortedPSMListProb.java b/DIA-Umpire/src/MSUmpire/PSMDataStructure/SortedPSMListProb.java
deleted file mode 100644
index ac1ea52..0000000
--- a/DIA-Umpire/src/MSUmpire/PSMDataStructure/SortedPSMListProb.java
+++ /dev/null
@@ -1,43 +0,0 @@
-/*
- * Author: Chih-Chiang Tsou
- * Nesvizhskii Lab, Department of Computational Medicine and Bioinformatics,
- * University of Michigan, Ann Arbor
- *
- * Copyright 2014 University of Michigan, Ann Arbor, MI
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package MSUmpire.PSMDataStructure;
-
-import ExtPackages.SortedListLib.SortedList;
-import java.util.Comparator;
-
-/**
- *
- * @author Chih-Chiang Tsou
- */
-public class SortedPSMListProb extends SortedList {
-
- public SortedPSMListProb() {
- super(new Comparator() {
- @Override
- public int compare(PSM x, PSM y) {
- if (x.Probability == y.Probability) {
- return Integer.compare(x.ScanNo, y.ScanNo);
- }
- return Float.compare(y.Probability, x.Probability);
- }
- });
- }
-
-}
diff --git a/DIA-Umpire/src/MSUmpire/PSMDataStructure/SortedPepListMass.java b/DIA-Umpire/src/MSUmpire/PSMDataStructure/SortedPepListMass.java
deleted file mode 100644
index 93b32ad..0000000
--- a/DIA-Umpire/src/MSUmpire/PSMDataStructure/SortedPepListMass.java
+++ /dev/null
@@ -1,40 +0,0 @@
-/*
- * Author: Chih-Chiang Tsou
- * Nesvizhskii Lab, Department of Computational Medicine and Bioinformatics,
- * University of Michigan, Ann Arbor
- *
- * Copyright 2014 University of Michigan, Ann Arbor, MI
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package MSUmpire.PSMDataStructure;
-
-import ExtPackages.SortedListLib.SortedList;
-import java.util.Comparator;
-
-/**
- *
- * @author Chih-Chiang Tsou
- */
-public class SortedPepListMass extends SortedList {
-
- public SortedPepListMass() {
- super(new Comparator() {
- @Override
- public int compare(PepIonID x, PepIonID y) {
- return -Float.compare(y.CalcNeutralPepMass(), x.CalcNeutralPepMass());
- }
- });
- }
-
-}
diff --git a/DIA-Umpire/src/MSUmpire/PSMDataStructure/SortedPepListProb.java b/DIA-Umpire/src/MSUmpire/PSMDataStructure/SortedPepListProb.java
index e92d8fa..2aa6d6f 100644
--- a/DIA-Umpire/src/MSUmpire/PSMDataStructure/SortedPepListProb.java
+++ b/DIA-Umpire/src/MSUmpire/PSMDataStructure/SortedPepListProb.java
@@ -19,7 +19,7 @@
*/
package MSUmpire.PSMDataStructure;
-import ExtPackages.SortedListLib.SortedList;
+import ExternalPackages.SortedListLib.SortedList;
import java.util.Comparator;
/**
diff --git a/DIA-Umpire/src/MSUmpire/PSMDataStructure/SortedProteinListMaxIniProb.java b/DIA-Umpire/src/MSUmpire/PSMDataStructure/SortedProteinListMaxIniProb.java
index 2f9a916..3d6743b 100644
--- a/DIA-Umpire/src/MSUmpire/PSMDataStructure/SortedProteinListMaxIniProb.java
+++ b/DIA-Umpire/src/MSUmpire/PSMDataStructure/SortedProteinListMaxIniProb.java
@@ -19,7 +19,7 @@
*/
package MSUmpire.PSMDataStructure;
-import ExtPackages.SortedListLib.SortedList;
+import ExternalPackages.SortedListLib.SortedList;
import java.util.Comparator;
/**
diff --git a/DIA-Umpire/src/MSUmpire/PSMDataStructure/SortedProteinListMaxLocalPW.java b/DIA-Umpire/src/MSUmpire/PSMDataStructure/SortedProteinListMaxLocalPW.java
deleted file mode 100644
index 506ae2f..0000000
--- a/DIA-Umpire/src/MSUmpire/PSMDataStructure/SortedProteinListMaxLocalPW.java
+++ /dev/null
@@ -1,43 +0,0 @@
-/*
- * Author: Chih-Chiang Tsou
- * Nesvizhskii Lab, Department of Computational Medicine and Bioinformatics,
- * University of Michigan, Ann Arbor
- *
- * Copyright 2014 University of Michigan, Ann Arbor, MI
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package MSUmpire.PSMDataStructure;
-
-import ExtPackages.SortedListLib.SortedList;
-import java.util.Comparator;
-
-/**
- *
- * @author Chih-Chiang Tsou
- */
-public class SortedProteinListMaxLocalPW extends SortedList {
-
- public SortedProteinListMaxLocalPW() {
- super(new Comparator() {
- @Override
- public int compare(ProtID x, ProtID y) {
- if (x.MaxLocalPW == y.MaxLocalPW) {
- return Float.compare(x.Mass, y.Mass);
- }
- return Float.compare(y.MaxLocalPW, x.MaxLocalPW);
- }
- });
- }
-
-}
diff --git a/DIA-Umpire/src/MSUmpire/PSMDataStructure/SortedProteinListProb.java b/DIA-Umpire/src/MSUmpire/PSMDataStructure/SortedProteinListProb.java
deleted file mode 100644
index ee86a52..0000000
--- a/DIA-Umpire/src/MSUmpire/PSMDataStructure/SortedProteinListProb.java
+++ /dev/null
@@ -1,43 +0,0 @@
-/*
- * Author: Chih-Chiang Tsou
- * Nesvizhskii Lab, Department of Computational Medicine and Bioinformatics,
- * University of Michigan, Ann Arbor
- *
- * Copyright 2014 University of Michigan, Ann Arbor, MI
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package MSUmpire.PSMDataStructure;
-
-import ExtPackages.SortedListLib.SortedList;
-import java.util.Comparator;
-
-/**
- *
- * @author Chih-Chiang Tsou
- */
-public class SortedProteinListProb extends SortedList {
-
- public SortedProteinListProb() {
- super(new Comparator() {
- @Override
- public int compare(ProtID x, ProtID y) {
- if (x.Probability == y.Probability) {
- return Float.compare(x.Mass, y.Mass);
- }
- return Float.compare(y.Probability, x.Probability);
- }
- });
- }
-
-}
diff --git a/DIA-Umpire/src/MSUmpire/PeakDataStructure/PeakCluster.java b/DIA-Umpire/src/MSUmpire/PeakDataStructure/PeakCluster.java
index 8400989..a6c717e 100644
--- a/DIA-Umpire/src/MSUmpire/PeakDataStructure/PeakCluster.java
+++ b/DIA-Umpire/src/MSUmpire/PeakDataStructure/PeakCluster.java
@@ -72,7 +72,6 @@ public class PeakCluster implements Serializable {
public float RightInt;
public boolean Identified;
public String AssignedPepIon = "";
- //public PeakOverlapRegion[] overlapRegions;
public ArrayList GroupedFragmentPeaks = new ArrayList<>();
public float MS1Score;
public float MS1ScoreLocalProb;
@@ -96,7 +95,6 @@ public PeakCluster(int IsotopicNum, int Charge) {
for (int i = 0; i < IsotopicNum; i++) {
SNR[i] = -1f;
}
- //overlapRegions = new PeakOverlapRegion[IsotopicNum - 1];
this.Charge = Charge;
}
@@ -416,7 +414,6 @@ private float GetChiSquareProbByIsoMap(TreeMap[] IsotopePatternMa
return prob;
}
- //
public boolean IsotopeComplete(int minIsonum) {
for (int i = 0; i < minIsonum; i++) {
if ((IsoPeaksCurves==null || IsoPeaksCurves[i] == null) && mz[i] == 0.0f) {
@@ -425,7 +422,6 @@ public boolean IsotopeComplete(int minIsonum) {
}
return true;
}
- //
public void CreateLock() {
lock=new ReentrantReadWriteLock();
diff --git a/DIA-Umpire/src/MSUmpire/PeakDataStructure/PeakCurve.java b/DIA-Umpire/src/MSUmpire/PeakDataStructure/PeakCurve.java
index 00edd7e..6f1d2a4 100644
--- a/DIA-Umpire/src/MSUmpire/PeakDataStructure/PeakCurve.java
+++ b/DIA-Umpire/src/MSUmpire/PeakDataStructure/PeakCurve.java
@@ -23,17 +23,10 @@
import MSUmpire.BaseDataStructure.XYData;
import MSUmpire.BaseDataStructure.XYPointCollection;
import MSUmpire.BaseDataStructure.XYZData;
-import java.io.FileWriter;
-import java.io.IOException;
import java.io.Serializable;
-import java.sql.Connection;
-import java.sql.ResultSet;
-import java.sql.SQLException;
-import java.sql.Statement;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.PriorityQueue;
-import org.apache.commons.io.FilenameUtils;
import org.jfree.data.xy.XYSeries;
/**
@@ -560,26 +553,6 @@ public void ReleaseRawPeak() {
this.waveletMassDetector = null;
}
- public XYSeries GetChartXYDatasetRAW() {
- XYSeries series1 = new XYSeries("Curve:" + Index + "_RAW");
- for (XYZData xYZPoint : PeakList) {
- series1.add(xYZPoint.getX(), xYZPoint.getZ());
- }
- return series1;
- }
-
- public XYSeries GetChartXYDatasetSmooth(String titleString) {
- XYSeries series1 = new XYSeries("Curve(" + TargetMz + "):" + Index);
- if (titleString != null) {
- series1.setKey(titleString);
- }
- for (int i = 0; i < SmoothData.PointCount(); i++) {
- XYData xYPoint = SmoothData.Data.get(i);
- series1.add(xYPoint.getX(), xYPoint.getY());
- }
- return series1;
- }
-
public void AddPeak(XYZData xYZPoint) {
PeakList.add(xYZPoint);
diff --git a/DIA-Umpire/src/MSUmpire/PeakDataStructure/SortedClusterCollectionClassApexRT.java b/DIA-Umpire/src/MSUmpire/PeakDataStructure/SortedClusterCollectionClassApexRT.java
deleted file mode 100644
index 527fa44..0000000
--- a/DIA-Umpire/src/MSUmpire/PeakDataStructure/SortedClusterCollectionClassApexRT.java
+++ /dev/null
@@ -1,146 +0,0 @@
-/*
- * Author: Chih-Chiang Tsou
- * Nesvizhskii Lab, Department of Computational Medicine and Bioinformatics,
- * University of Michigan, Ann Arbor
- *
- * Copyright 2014 University of Michigan, Ann Arbor, MI
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package MSUmpire.PeakDataStructure;
-
-import ExtPackages.SortedListLib.SortedList;
-import java.util.Comparator;
-
-/**
- *
- * @author Chih-Chiang Tsou
- */
-public class SortedClusterCollectionClassApexRT extends SortedList {
- private static final long serialVersionUID = 1413738555834427635L;
-
- public SortedClusterCollectionClassApexRT() {
- super(new Comparator() {
- @Override
- public int compare(PeakCluster x, PeakCluster y) {
- if (x.PeakHeightRT[0] == y.PeakHeightRT[0]) {
- if (x.TargetMz() == y.TargetMz()) {
- return Integer.compare(x.Charge, y.Charge);
- }
- return Float.compare(x.TargetMz(), y.TargetMz());
- }
- return Float.compare(x.PeakHeightRT[0], y.PeakHeightRT[0]);
- }
- });
- }
-
- public int BinarySearchLower(float value) {
- if (isEmpty()) {
- return 0;
- }
- int lower = 0;
- int upper = size() - 1;
-
- if (value - get(upper).PeakHeightRT[0] >= 0) {
- return upper;
- }
- if (value - get(0).PeakHeightRT[0] <= 0) {
- return 0;
- }
-
- while (lower <= upper) {
- int middle = (lower + upper) / 2;
- float comparisonResult = value - get(middle).PeakHeightRT[0];
- if (comparisonResult == 0) {
- return middle;
- } else if (comparisonResult < 0) {
- upper = middle - 1;
- } else {
- lower = middle + 1;
- }
- }
- if (upper < 0) {
- return 0;
- }
- while (upper > 0 && get(upper).PeakHeightRT[0] >= value) {
- upper--;
- }
- return upper;
- }
-
- public int BinarySearchHigher(float value) {
- if (isEmpty()) {
- return 0;
- }
- int lower = 0;
- int upper = size() - 1;
-
- if (value - get(upper).PeakHeightRT[0] >= 0) {
- return upper;
- }
- if (value - get(0).PeakHeightRT[0] <= 0) {
- return 0;
- }
-
- while (lower <= upper) {
- int middle = (lower + upper) / 2;
- float comparisonResult = value - get(middle).PeakHeightRT[0];
- if (comparisonResult == 0) {
- return middle;
- } else if (comparisonResult < 0) {
- upper = middle - 1;
- } else {
- lower = middle + 1;
- }
- }
- if (lower > size() - 1) {
- return size() - 1;
- }
- while (upper < size() && get(upper).PeakHeightRT[0] <= value) {
- upper++;
- }
- return upper;
- }
-
- public int BinarySearchClosest(float value) {
- if (isEmpty()) {
- return 0;
- }
- int lower = 0;
- int upper = size() - 1;
-
- if (value - get(upper).PeakHeightRT[0] >= 0) {
- return upper;
- }
- if (value - get(0).PeakHeightRT[0] <= 0) {
- return 0;
- }
-
- while (lower <= upper) {
- int middle = (lower + upper) / 2;
- float comparisonResult = value - get(middle).PeakHeightRT[0];
- if (comparisonResult == 0) {
- return middle;
- } else if (comparisonResult < 0) {
- upper = middle - 1;
- } else {
- lower = middle + 1;
- }
- }
- if (Math.abs(value - get(lower).PeakHeightRT[0]) > Math.abs(value - get(upper).PeakHeightRT[0])) {
- return upper;
- } else {
- return lower;
- }
- }
-}
diff --git a/DIA-Umpire/src/MSUmpire/PeakDataStructure/SortedClusterCollectionClassMZ.java b/DIA-Umpire/src/MSUmpire/PeakDataStructure/SortedClusterCollectionClassMZ.java
deleted file mode 100644
index 566a6c6..0000000
--- a/DIA-Umpire/src/MSUmpire/PeakDataStructure/SortedClusterCollectionClassMZ.java
+++ /dev/null
@@ -1,147 +0,0 @@
-/*
- * Author: Chih-Chiang Tsou
- * Nesvizhskii Lab, Department of Computational Medicine and Bioinformatics,
- * University of Michigan, Ann Arbor
- *
- * Copyright 2014 University of Michigan, Ann Arbor, MI
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package MSUmpire.PeakDataStructure;
-
-import ExtPackages.SortedListLib.SortedList;
-import java.util.Comparator;
-
-/**
- *
- * @author Chih-Chiang Tsou
- */
-public class SortedClusterCollectionClassMZ extends SortedList {
- private static final long serialVersionUID = 7300471440319024208L;
-
- public SortedClusterCollectionClassMZ() {
- super(new Comparator() {
- @Override
- public int compare(PeakCluster x, PeakCluster y) {
- if (x.TargetMz() == y.TargetMz()) {
- if (x.startRT == y.startRT) {
- return Integer.compare(x.Charge, y.Charge);
- }
- return Float.compare(x.startRT, y.startRT);
- }
- return Float.compare(x.TargetMz(), y.TargetMz());
- }
- });
- }
-
- public int BinarySearchLower(float value) {
- if (isEmpty()) {
- return 0;
- }
- int lower = 0;
- int upper = size() - 1;
-
- if (value - get(upper).TargetMz() >= 0) {
- return upper;
- }
- if (value - get(0).TargetMz() <= 0) {
- return 0;
- }
-
- while (lower <= upper) {
- int middle = (lower + upper) / 2;
- float comparisonResult = value - get(middle).TargetMz();
- if (comparisonResult == 0) {
- return middle;
- } else if (comparisonResult < 0) {
- upper = middle - 1;
- } else {
- lower = middle + 1;
- }
- }
- if (upper < 0) {
- return 0;
- }
- while (upper > 0 && get(upper).TargetMz() >= value) {
- upper--;
- }
- return upper;
- }
-
- public int BinarySearchHigher(float value) {
- if (isEmpty()) {
- return 0;
- }
- int lower = 0;
- int upper = size() - 1;
-
- if (value - get(upper).TargetMz() >= 0) {
- return upper;
- }
- if (value - get(0).TargetMz() <= 0) {
- return 0;
- }
-
- while (lower <= upper) {
- int middle = (lower + upper) / 2;
- float comparisonResult = value - get(middle).TargetMz();
- if (comparisonResult == 0) {
- return middle;
- } else if (comparisonResult < 0) {
- upper = middle - 1;
- } else {
- lower = middle + 1;
- }
- }
- if (lower > size() - 1) {
- return size() - 1;
- }
- while (upper < size() && get(upper).TargetMz() <= value) {
- upper++;
- }
- return upper;
- }
-
- public int BinarySearchClosest(float value) {
- if (isEmpty()) {
- return 0;
- }
- int lower = 0;
- int upper = size() - 1;
-
- if (value - get(upper).TargetMz() >= 0) {
- return upper;
- }
- if (value - get(0).TargetMz() <= 0) {
- return 0;
- }
-
- while (lower <= upper) {
- int middle = (lower + upper) / 2;
- float comparisonResult = value - get(middle).TargetMz();
- if (comparisonResult == 0) {
- return middle;
- } else if (comparisonResult < 0) {
- upper = middle - 1;
- } else {
- lower = middle + 1;
- }
- }
- if (Math.abs(value - get(lower).TargetMz()) > Math.abs(value - get(upper).TargetMz())) {
- return upper;
- } else {
- return lower;
- }
- }
-
-}
diff --git a/DIA-Umpire/src/MSUmpire/PeakDataStructure/SortedClusterCollectionClassStartRT.java b/DIA-Umpire/src/MSUmpire/PeakDataStructure/SortedClusterCollectionClassStartRT.java
deleted file mode 100644
index 950262b..0000000
--- a/DIA-Umpire/src/MSUmpire/PeakDataStructure/SortedClusterCollectionClassStartRT.java
+++ /dev/null
@@ -1,145 +0,0 @@
-/*
- * Author: Chih-Chiang Tsou
- * Nesvizhskii Lab, Department of Computational Medicine and Bioinformatics,
- * University of Michigan, Ann Arbor
- *
- * Copyright 2014 University of Michigan, Ann Arbor, MI
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package MSUmpire.PeakDataStructure;
-
-import ExtPackages.SortedListLib.SortedList;
-import java.util.Comparator;
-
-/**
- *
- * @author Chih-Chiang Tsou
- */
-public class SortedClusterCollectionClassStartRT extends SortedList {
-
- public SortedClusterCollectionClassStartRT() {
- super(new Comparator() {
- @Override
- public int compare(PeakCluster x, PeakCluster y) {
- if (x.startRT == y.startRT) {
- if (x.TargetMz() == y.TargetMz()) {
- return Integer.compare(x.Charge, y.Charge);
- }
- return Float.compare(x.TargetMz(), y.TargetMz());
- }
- return Float.compare(x.startRT, y.startRT);
- }
- });
- }
-
- public int BinarySearchLower(float value) {
- if (isEmpty()) {
- return 0;
- }
- int lower = 0;
- int upper = size() - 1;
-
- if (value - get(upper).startRT >= 0) {
- return upper;
- }
- if (value - get(0).startRT <= 0) {
- return 0;
- }
-
- while (lower <= upper) {
- int middle = (lower + upper) / 2;
- float comparisonResult = value - get(middle).startRT;
- if (comparisonResult == 0) {
- return middle;
- } else if (comparisonResult < 0) {
- upper = middle - 1;
- } else {
- lower = middle + 1;
- }
- }
- if (upper < 0) {
- return 0;
- }
- while (upper > 0 && get(upper).startRT >= value) {
- upper--;
- }
- return upper;
- }
-
- public int BinarySearchHigher(float value) {
- if (isEmpty()) {
- return 0;
- }
- int lower = 0;
- int upper = size() - 1;
-
- if (value - get(upper).startRT >= 0) {
- return upper;
- }
- if (value - get(0).startRT <= 0) {
- return 0;
- }
-
- while (lower <= upper) {
- int middle = (lower + upper) / 2;
- float comparisonResult = value - get(middle).startRT;
- if (comparisonResult == 0) {
- return middle;
- } else if (comparisonResult < 0) {
- upper = middle - 1;
- } else {
- lower = middle + 1;
- }
- }
- if (lower > size() - 1) {
- return size() - 1;
- }
- while (upper < size() && get(upper).startRT <= value) {
- upper++;
- }
- return upper;
- }
-
- public int BinarySearchClosest(float value) {
- if (isEmpty()) {
- return 0;
- }
- int lower = 0;
- int upper = size() - 1;
-
- if (value - get(upper).startRT >= 0) {
- return upper;
- }
- if (value - get(0).startRT <= 0) {
- return 0;
- }
-
- while (lower <= upper) {
- int middle = (lower + upper) / 2;
- float comparisonResult = value - get(middle).startRT;
- if (comparisonResult == 0) {
- return middle;
- } else if (comparisonResult < 0) {
- upper = middle - 1;
- } else {
- lower = middle + 1;
- }
- }
- if (Math.abs(value - get(lower).startRT) > Math.abs(value - get(upper).startRT)) {
- return upper;
- } else {
- return lower;
- }
- }
-}
diff --git a/DIA-Umpire/src/MSUmpire/PeakDataStructure/SortedCorrFrag.java b/DIA-Umpire/src/MSUmpire/PeakDataStructure/SortedCorrFrag.java
index 9a835f9..05d48e2 100644
--- a/DIA-Umpire/src/MSUmpire/PeakDataStructure/SortedCorrFrag.java
+++ b/DIA-Umpire/src/MSUmpire/PeakDataStructure/SortedCorrFrag.java
@@ -19,7 +19,7 @@
*/
package MSUmpire.PeakDataStructure;
-import ExtPackages.SortedListLib.SortedList;
+import ExternalPackages.SortedListLib.SortedList;
import java.util.Comparator;
/**
diff --git a/DIA-Umpire/src/MSUmpire/PeakDataStructure/SortedCurveCollectionApexRT.java b/DIA-Umpire/src/MSUmpire/PeakDataStructure/SortedCurveCollectionApexRT.java
index 259f6df..2e6fbe4 100644
--- a/DIA-Umpire/src/MSUmpire/PeakDataStructure/SortedCurveCollectionApexRT.java
+++ b/DIA-Umpire/src/MSUmpire/PeakDataStructure/SortedCurveCollectionApexRT.java
@@ -19,7 +19,7 @@
*/
package MSUmpire.PeakDataStructure;
-import ExtPackages.SortedListLib.SortedList;
+import ExternalPackages.SortedListLib.SortedList;
import java.io.Serializable;
import java.util.Comparator;
diff --git a/DIA-Umpire/src/MSUmpire/PeakDataStructure/SortedCurveCollectionMZ.java b/DIA-Umpire/src/MSUmpire/PeakDataStructure/SortedCurveCollectionMZ.java
index 111a232..d06707a 100644
--- a/DIA-Umpire/src/MSUmpire/PeakDataStructure/SortedCurveCollectionMZ.java
+++ b/DIA-Umpire/src/MSUmpire/PeakDataStructure/SortedCurveCollectionMZ.java
@@ -19,7 +19,7 @@
*/
package MSUmpire.PeakDataStructure;
-import ExtPackages.SortedListLib.SortedList;
+import ExternalPackages.SortedListLib.SortedList;
import java.io.Serializable;
import java.util.Comparator;
diff --git a/DIA-Umpire/src/MSUmpire/PeakDataStructure/SortedRidgeCollectionClass.java b/DIA-Umpire/src/MSUmpire/PeakDataStructure/SortedRidgeCollectionClass.java
index e15d7e4..cfb39a3 100644
--- a/DIA-Umpire/src/MSUmpire/PeakDataStructure/SortedRidgeCollectionClass.java
+++ b/DIA-Umpire/src/MSUmpire/PeakDataStructure/SortedRidgeCollectionClass.java
@@ -19,7 +19,7 @@
*/
package MSUmpire.PeakDataStructure;
-import ExtPackages.SortedListLib.SortedList;
+import ExternalPackages.SortedListLib.SortedList;
import java.io.Serializable;
import java.util.Comparator;
diff --git a/DIA-Umpire/src/MSUmpire/PeptidePeakClusterDetection/CurveCorrUnit.java b/DIA-Umpire/src/MSUmpire/PeptidePeakClusterDetection/CurveCorrUnit.java
deleted file mode 100644
index 5530355..0000000
--- a/DIA-Umpire/src/MSUmpire/PeptidePeakClusterDetection/CurveCorrUnit.java
+++ /dev/null
@@ -1,71 +0,0 @@
-/*
- * Author: Chih-Chiang Tsou
- * Nesvizhskii Lab, Department of Computational Medicine and Bioinformatics,
- * University of Michigan, Ann Arbor
- *
- * Copyright 2014 University of Michigan, Ann Arbor, MI
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package MSUmpire.PeptidePeakClusterDetection;
-
-import MSUmpire.BaseDataStructure.InstrumentParameter;
-import MSUmpire.MathPackage.PearsonCorr;
-import MSUmpire.PeakDataStructure.PeakCurve;
-
-/**
- *
- * @author Chih-Chiang Tsou
- */
-public class CurveCorrUnit implements Runnable {
-
- public PeakCurve peakA;
- public PeakCurve peakB;
- public int i;
- public int j;
- public float corr = 0f;
- public InstrumentParameter parameter;
-
- public CurveCorrUnit(PeakCurve peakA, PeakCurve peakB, int i, int j, InstrumentParameter parameter) {
- this.peakA = peakA;
- this.peakB = peakB;
- this.i = i;
- this.j = j;
- this.parameter = parameter;
- }
-
- private float CalPeakCorr(PeakCurve peakA, PeakCurve peakB) {
- //System.out.print("Doing "+i+"_"+j+"\n");
- PearsonCorr corr = new PearsonCorr();
- float corre = corr.CalcCorr(peakA.GetPeakCollection(), peakB.GetPeakCollection(), parameter.NoPeakPerMin);
- corr = null;
- return corre;
- }
-
- @Override
- public void run() {
- boolean overlap = false;
- if (peakA.StartRT() >= peakB.StartRT() && peakA.StartRT() <= peakB.EndRT()) {
- overlap = true;
- } else if (peakA.EndRT() >= peakB.StartRT() && peakA.EndRT() <= peakB.EndRT()) {
- overlap = true;
- } else if (peakB.StartRT() >= peakA.StartRT() && peakB.StartRT() <= peakA.EndRT()) {
- overlap = true;
- } else if (peakB.EndRT() >= peakA.StartRT() && peakB.EndRT() <= peakA.EndRT()) {
- overlap = true;
- }
- if (overlap) {
- corr = CalPeakCorr(peakA, peakB);
- }
- }
-}
diff --git a/DIA-Umpire/src/MSUmpire/PeptidePeakClusterDetection/PDHandlerBase.java b/DIA-Umpire/src/MSUmpire/PeptidePeakClusterDetection/PDHandlerBase.java
index 5db7866..9981737 100644
--- a/DIA-Umpire/src/MSUmpire/PeptidePeakClusterDetection/PDHandlerBase.java
+++ b/DIA-Umpire/src/MSUmpire/PeptidePeakClusterDetection/PDHandlerBase.java
@@ -37,6 +37,7 @@
import net.sf.javaml.core.kdtree.KDTree;
import net.sf.javaml.core.kdtree.KeyDuplicateException;
import net.sf.javaml.core.kdtree.KeySizeException;
+import org.apache.commons.lang.exception.ExceptionUtils;
import org.apache.log4j.Logger;
/**
@@ -55,7 +56,6 @@ public class PDHandlerBase {
public TreeMap[] IsotopePatternFragMap;
protected LCMSPeakBase LCMSPeakBase;
protected InstrumentParameter parameter;
- //protected ConnectionManager connectionManager;
protected boolean ReleaseScans = true;
protected boolean TargetedOnly = false;
protected float PPM;
@@ -89,10 +89,8 @@ public void AddToInclusionList(float mz, float rt){
InclusionRT.AddPoint(rt,mz);
try {
InclusionRange.insert(new double[]{rt,mz}, point);
- } catch (KeySizeException ex) {
- java.util.logging.Logger.getLogger(PDHandlerBase.class.getName()).log(Level.SEVERE, null, ex);
- } catch (KeyDuplicateException ex) {
- java.util.logging.Logger.getLogger(PDHandlerBase.class.getName()).log(Level.SEVERE, null, ex);
+ } catch (Exception ex) {
+ Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
}
}
@@ -105,7 +103,6 @@ public void ClearRawPeaks() {
peakCurve.CalculateMzVar();
peakCurve.StartRT();
peakCurve.EndRT();
- //peakCurve.StartInt();
peakCurve.ReleaseRawPeak();
}
}
@@ -115,8 +112,6 @@ protected void FindAllPeakCurve(ScanCollection scanCollection) throws IOExceptio
IncludedHashMap = new HashSet<>();
Logger.getRootLogger().info("Processing all scans to detect possible peak curves....");
- //Get the ms1 scanNo array
- //LCMSPeakBase.PeakCurveListMZ = new SortedCurveCollectionMZ();
float preRT = 0f;
for (int idx = 0; idx < scanCollection.GetScanNoArray(MSlevel).size(); idx++) {
@@ -125,9 +120,6 @@ protected void FindAllPeakCurve(ScanCollection scanCollection) throws IOExceptio
if(TargetedOnly && !FoundInInclusionRTList(scanData.RetentionTime)){
continue;
}
-// if(scanData.RetentionTime>27){
-// System.out.println("");
-// }
if (idx == 0) {
preRT = scanData.RetentionTime - 0.01f;
}
@@ -223,9 +215,6 @@ protected void FindAllPeakCurve(ScanCollection scanCollection) throws IOExceptio
}
Peakcurve.AddPeak(new XYZData(endrt, Peakcurve.TargetMz, bk));
Peakcurve.EndScan=endScan;
-// if (Peakcurve.TargetMz > 1238.85 && Peakcurve.TargetMz < 1238.89 && Peakcurve.StartRT() < 25 && Peakcurve.EndRT() > 25) {
-// System.out.println("");
-// }
if (FoundInInclusionList(Peakcurve.TargetMz, Peakcurve.StartRT(), Peakcurve.EndRT())) {
LCMSPeakBase.UnSortedPeakCurves.add(Peakcurve);
@@ -273,7 +262,7 @@ private boolean FoundInInclusionMZList(float rt, float mz) {
try {
found = InclusionRange.range(new double[]{lowrt,lowmz}, new double[]{highrt,highmz});
} catch (KeySizeException ex) {
- java.util.logging.Logger.getLogger(PDHandlerBase.class.getName()).log(Level.SEVERE, null, ex);
+ Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
}
if(found!=null && found.length>0){
return true;
@@ -294,7 +283,7 @@ private boolean FoundInInclusionList(float mz, float startrt, float endrt){
try {
found = InclusionRange.range(new double[]{lowrt,lowmz}, new double[]{highrt,highmz});
} catch (KeySizeException ex) {
- java.util.logging.Logger.getLogger(PDHandlerBase.class.getName()).log(Level.SEVERE, null, ex);
+ Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
}
if(found!=null && found.length>0){
for(Object point: found){
@@ -383,13 +372,12 @@ protected void ReadPepIsoMS1PatternMap() throws FileNotFoundException, IOExcepti
reader.close();
}
- protected void PeakCurveCorrClustering_V2(XYData mzRange) throws IOException {
+ protected void PeakCurveCorrClustering(XYData mzRange) throws IOException {
Logger.getRootLogger().info("Grouping isotopic peak curves........");
LCMSPeakBase.PeakClusters = new ArrayList<>();
ExecutorService executorPool = null;
- executorPool = Executors.newFixedThreadPool(NoCPUs);
- //executorPool = Executors.newFixedThreadPool(1);
+ executorPool = Executors.newFixedThreadPool(NoCPUs);
ArrayList ResultList = new ArrayList<>();
for (PeakCurve Peakcurve : LCMSPeakBase.UnSortedPeakCurves) {
diff --git a/DIA-Umpire/src/MSUmpire/PeptidePeakClusterDetection/PDHandlerDIAMS2.java b/DIA-Umpire/src/MSUmpire/PeptidePeakClusterDetection/PDHandlerDIAMS2.java
index e4ee247..c8748a9 100644
--- a/DIA-Umpire/src/MSUmpire/PeptidePeakClusterDetection/PDHandlerDIAMS2.java
+++ b/DIA-Umpire/src/MSUmpire/PeptidePeakClusterDetection/PDHandlerDIAMS2.java
@@ -70,8 +70,7 @@ public void pSMARTGrouping(ScanCollection scanCollection) throws FileNotFoundExc
PrecursorFragmentPair.RTOverlapP = 1f;
PrecursorFragmentPair.ApexDelta = Math.abs(peakCluster.MonoIsotopePeak.ApexRT - scan.RetentionTime);
float rtrange = peakCluster.endRT - peakCluster.startRT;
- PrecursorFragmentPair.Correlation = (rtrange - PrecursorFragmentPair.ApexDelta) / rtrange;
- //FragmentPeaks.put(peakCurve.Index, peakCurve);
+ PrecursorFragmentPair.Correlation = (rtrange - PrecursorFragmentPair.ApexDelta) / rtrange;
ResultList.add(PrecursorFragmentPair);
}
}
@@ -83,21 +82,18 @@ public void pSMARTGrouping(ScanCollection scanCollection) throws FileNotFoundExc
}
public void DetectPeakCurves(ScanCollection scanCollection) throws FileNotFoundException, IOException {
- //ReadFragIsoPatternMap();
+
LCMSPeakBase.UnSortedPeakCurves = new ArrayList<>();
FindAllPeakCurve(scanCollection);
- //PeaksCheckingStage1AND2(1);
PeakCurveSmoothing();
- //CreateSortedPeakCurveList();
ClearRawPeaks();
ReadPepIsoMS1PatternMap();
- PeakCurveCorrClustering_V2(DIAWindowMz);
+ PeakCurveCorrClustering(DIAWindowMz);
}
public void FragmentGrouping() throws SQLException, IOException {
PrecursorFragmentPairBuildingForMS1();
PrecursorFragmentPairBuildingForUnfragmentedIon();
- //PrecursorFragmentPairBuildingForIsolatedPeakCurve();
}
@@ -118,8 +114,7 @@ private void PrecursorFragmentPairBuildingForUnfragmentedIon() throws SQLExcepti
executorPool.execute(unit);
}
executorPool.shutdown();
-// while (!executorPool.isTerminated()) {
-// }
+
try {
executorPool.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS);
} catch (InterruptedException e) {
@@ -137,8 +132,7 @@ private void PrecursorFragmentPairBuildingForUnfragmentedIon() throws SQLExcepti
((LCMSPeakDIAMS2) LCMSPeakBase).BuildFragmentUnfragranking();
((LCMSPeakDIAMS2) LCMSPeakBase).FilterByCriteriaUnfrag();
((LCMSPeakDIAMS2) LCMSPeakBase).ExportUnfragmentedClusterCurve();
- //ExportParentClusterCurveCorrToDB(ResultArrayList);
- //GenerateMGF(ResultArrayList);
+
UnfragmentedIonPairList.clear();
UnfragmentedIonPairList = null;
executorPool = null;
diff --git a/DIA-Umpire/src/MSUmpire/PeptidePeakClusterDetection/PDHandlerMS1.java b/DIA-Umpire/src/MSUmpire/PeptidePeakClusterDetection/PDHandlerMS1.java
index e38e312..768bfc1 100644
--- a/DIA-Umpire/src/MSUmpire/PeptidePeakClusterDetection/PDHandlerMS1.java
+++ b/DIA-Umpire/src/MSUmpire/PeptidePeakClusterDetection/PDHandlerMS1.java
@@ -42,7 +42,7 @@ public PDHandlerMS1(LCMSPeakBase lcmspeak, int NoCPUs, float PPM) {
public void DetectPeakClusters(ArrayList scanCollections) throws InterruptedException, ExecutionException, IOException {
DetectSingleMZTraces(scanCollections);
- PeakCurveCorrClustering_V2(new XYData(Float.NEGATIVE_INFINITY, Float.POSITIVE_INFINITY));
+ PeakCurveCorrClustering(new XYData(Float.NEGATIVE_INFINITY, Float.POSITIVE_INFINITY));
}
public void DetectSingleMZTraces(ArrayList scanCollections) throws IOException {
@@ -53,7 +53,6 @@ public void DetectSingleMZTraces(ArrayList scanCollections) thro
}
Logger.getRootLogger().info("Inclusion mz values found: "+InclusionCheckInfo());
PeakCurveSmoothing();
- //CreateSortedPeakCurveList();
ClearRawPeaks();
}
diff --git a/DIA-Umpire/src/MSUmpire/PostProcessing/PeakClusterMatch.java b/DIA-Umpire/src/MSUmpire/PostProcessing/PeakClusterMatch.java
deleted file mode 100644
index ccfa7ec..0000000
--- a/DIA-Umpire/src/MSUmpire/PostProcessing/PeakClusterMatch.java
+++ /dev/null
@@ -1,57 +0,0 @@
-/*
- * Author: Chih-Chiang Tsou
- * Nesvizhskii Lab, Department of Computational Medicine and Bioinformatics,
- * University of Michigan, Ann Arbor
- *
- * Copyright 2014 University of Michigan, Ann Arbor, MI
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package MSUmpire.PostProcessing;
-import MSUmpire.BaseDataStructure.InstrumentParameter;
-import MSUmpire.BaseDataStructure.XYPointCollection;
-import MSUmpire.PeakDataStructure.PeakCluster;
-import MSUmpire.SpectralProcessingModule.ScoreFunction;
-import org.apache.log4j.Logger;
-
-/**
- *
- * @author Chih-Chiang Tsou
- */
-public class PeakClusterMatch implements Runnable{
-
- PeakCluster peakClusterA;
- PeakCluster peakClusterB;
- InstrumentParameter parameter;
- public float similiarity=0f;
- public PeakClusterMatch(PeakCluster peakClusterA, PeakCluster peakClusterB, InstrumentParameter parameter){
- this.peakClusterA=peakClusterA;
- this.peakClusterB=peakClusterB;
- this.parameter=parameter;
- }
-
- @Override
- public void run() {
- try {
- similiarity=0f;
- XYPointCollection Scan1=peakClusterA.GetNormalizedFragmentScan();
- XYPointCollection Scan2=peakClusterB.GetNormalizedFragmentScan();
- if(Scan1.PointCount()>2 && Scan2.PointCount()>2){
- similiarity=ScoreFunction.CalcDotProductForScan(Scan1,Scan2);
- }
- } catch (InterruptedException ex) {
- Logger.getRootLogger().error("error");
- }
- }
-
-}
diff --git a/DIA-Umpire/src/MSUmpire/PostProcessing/PrecursorGroupAlignment.java b/DIA-Umpire/src/MSUmpire/PostProcessing/PrecursorGroupAlignment.java
deleted file mode 100644
index 09b7074..0000000
--- a/DIA-Umpire/src/MSUmpire/PostProcessing/PrecursorGroupAlignment.java
+++ /dev/null
@@ -1,107 +0,0 @@
-/*
- * Author: Chih-Chiang Tsou
- * Nesvizhskii Lab, Department of Computational Medicine and Bioinformatics,
- * University of Michigan, Ann Arbor
- *
- * Copyright 2014 University of Michigan, Ann Arbor, MI
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package MSUmpire.PostProcessing;
-
-import MSUmpire.BaseDataStructure.InstrumentParameter;
-import MSUmpire.DIA.DIAPack;
-import MSUmpire.PeakDataStructure.PeakCluster;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-import java.util.concurrent.TimeUnit;
-import org.apache.log4j.Logger;
-
-/**
- *
- * @author Chih-Chiang Tsou
- */
-public class PrecursorGroupAlignment {
- ArrayList DIAfiles;
- InstrumentParameter parameter;
-
- public PrecursorGroupAlignment(ArrayList DIAFiles, InstrumentParameter parameter){
- this.DIAfiles=DIAFiles;
- this.parameter=parameter;
- }
-
- public void CreateScoreMatrix(String path) throws IOException{
- System.out.println("Calculate matrix");
- for (int i = 0; i < DIAfiles.size(); i++) {
- for (PeakCluster cluster : DIAfiles.get(i).ms1lcms.PeakClusters) {
- cluster.CreateLock();
- }
- }
-
- for (int i = 0; i < DIAfiles.size(); i++) {
- for (int j = i + 1; j < DIAfiles.size(); j++) {
- FileWriter writer = new FileWriter(path + i + "_" + j + "_score.txt");
- ArrayList IncludedIndex=new ArrayList<>();
- ExecutorService executorPool = null;
- executorPool = Executors.newFixedThreadPool(20);
- ArrayList ResultList = new ArrayList<>();
-// for (PeakCluster cluster : DIAfiles.get(i).ms1lcms.MZSortedClusters) {
-// int startindex = DIAfiles.get(j).ms1lcms.MZSortedClusters.BinarySearchLower(InstrumentParameter.GetMzByPPM(cluster.TargetMz(), cluster.Charge, parameter.MS1PPM));
-// int endindex = DIAfiles.get(j).ms1lcms.MZSortedClusters.BinarySearchLower(InstrumentParameter.GetMzByPPM(cluster.TargetMz(), cluster.Charge, -parameter.MS1PPM));
-// for(int idx=startindex;idx<=endindex;idx++){
-// PeakCluster cluster2=DIAfiles.get(j).ms1lcms.MZSortedClusters.get(idx);
-// if (Math.abs(cluster2.PeakHeightRT[0] - cluster.PeakHeightRT[0]) < 10f) {
-// if (!IncludedIndex.contains(cluster.Index + "_" + cluster2.Index)) {
-// PeakClusterMatch match=new PeakClusterMatch(cluster, cluster2, parameter);
-// ResultList.add(match);
-// executorPool.execute(match);
-// IncludedIndex.add(cluster.Index + "_" + cluster2.Index);
-// }
-// }
-// }
-// }
-// for (PeakCluster cluster : DIAfiles.get(j).ms1lcms.MZSortedClusters) {
-// int startindex = DIAfiles.get(i).ms1lcms.MZSortedClusters.BinarySearchLower(InstrumentParameter.GetMzByPPM(cluster.TargetMz(), cluster.Charge, parameter.MS1PPM));
-// int endindex = DIAfiles.get(i).ms1lcms.MZSortedClusters.BinarySearchLower(InstrumentParameter.GetMzByPPM(cluster.TargetMz(), cluster.Charge, -parameter.MS1PPM));
-// for (int idx = startindex; idx <= endindex; idx++) {
-// PeakCluster cluster2 = DIAfiles.get(i).ms1lcms.MZSortedClusters.get(idx);
-// if (Math.abs(cluster2.PeakHeightRT[0] - cluster.PeakHeightRT[0]) < 10f) {
-// if (!IncludedIndex.contains(cluster2.Index + "_" + cluster.Index)) {
-// PeakClusterMatch match=new PeakClusterMatch(cluster2, cluster, parameter);
-// ResultList.add(match);
-// executorPool.execute(match);
-// IncludedIndex.add(cluster2.Index + "_" + cluster.Index);
-// }
-// }
-// }
-// }
- executorPool.shutdown();
-// while (!executorPool.isTerminated()) {
-// }
- try {
- executorPool.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS);
- } catch (InterruptedException e) {
- Logger.getRootLogger().info("interrupted..");
- }
-
- for(PeakClusterMatch match : ResultList){
- writer.write(match.peakClusterA.PeakHeightRT[0] + "\t" + match.peakClusterB.PeakHeightRT[0]+ "\t" +match.similiarity+"\n");
- }
- writer.close();
- }
- }
- }
-}
diff --git a/DIA-Umpire/src/MSUmpire/SearchResultParser/IDParser.java b/DIA-Umpire/src/MSUmpire/SearchResultParser/IDParser.java
deleted file mode 100644
index 72f45e8..0000000
--- a/DIA-Umpire/src/MSUmpire/SearchResultParser/IDParser.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * Author: Chih-Chiang Tsou
- * Nesvizhskii Lab, Department of Computational Medicine and Bioinformatics,
- * University of Michigan, Ann Arbor
- *
- * Copyright 2014 University of Michigan, Ann Arbor, MI
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package MSUmpire.SearchResultParser;
-
-/**
- *
- * @author Chih-Chiang Tsou
- */
-
-
-public interface IDParser {
-
-}
diff --git a/DIA-Umpire/src/MSUmpire/SearchResultParser/PepXMLParseHandler.java b/DIA-Umpire/src/MSUmpire/SearchResultParser/PepXMLParseHandler.java
index 322d79e..1dcffd8 100644
--- a/DIA-Umpire/src/MSUmpire/SearchResultParser/PepXMLParseHandler.java
+++ b/DIA-Umpire/src/MSUmpire/SearchResultParser/PepXMLParseHandler.java
@@ -30,7 +30,6 @@
import com.compomics.util.experiment.identification.matches.ModificationMatch;
import com.vseravno.solna.SolnaHandler;
import java.io.IOException;
-import org.apache.commons.lang3.StringUtils;
import org.apache.log4j.Logger;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
@@ -53,7 +52,6 @@ public PepXMLParseHandler(LCMSID singleLCMSID, float StartRT, float EndRT, float
float EndRT;
float threshold;
boolean CorrectMassDiff=true;
- //public String FileBaseNameFilter="";
LCMSID singleLCMSID;
@Override
@@ -125,12 +123,6 @@ private void ParseSearchSummary(Element node) throws XmlPullParserException, Xml
}
float massdiff = Float.parseFloat(node.getChildNodes().item(k).getAttributes().getNamedItem("massdiff").getNodeValue());
CheckAndAddModification(site, massdiff);
-// PTM ptm = PTMManager.GetInstance().GetPTM(site, massdiff);
-// if (ptm == null) {
-// Logger.getRootLogger().warn("Warning! term-modification:" + site + "(" + massdiff + ") cannot be found in the library.\n");
-// } else {
-// singleLCMSID.AddModification(ptm, site);
-// }
}
}
}
@@ -148,12 +140,6 @@ private void CheckAndAddModification(String site, float massdiff) throws XmlPull
}
private void ParseSpectrumNode(Element spectrum) throws XmlPullParserException, IOException {
-
-// if(!"".equals(FileBaseNameFilter)){
-// if(!spectrum.getAttributes().getNamedItem("spectrum").getNodeValue().substring(0, spectrum.getAttributes().getNamedItem("spectrum").getNodeValue().indexOf(".")).startsWith(FileBaseNameFilter)){
-// return;
-// }
-// }
PSM psm = new PSM();
psm.SpecNumber = spectrum.getAttributes().getNamedItem("spectrum").getNodeValue();
@@ -386,68 +372,5 @@ private void GetModificationInfo(PSM psmid, Node node) throws XmlPullParserExcep
}
psmid.ModSeq = modseq;
psmid.TPPModSeq = TPPmodseq;
- //UpdateFromLuciphor(psmid, modseq);
}
-
- private void UpdateFromLuciphor(PSM psmid, String modseq) throws NumberFormatException {
- if (singleLCMSID.LuciphorResult != null && singleLCMSID.LuciphorResult.containsKey(psmid.SpecNumber)) {
- String line = singleLCMSID.LuciphorResult.get(psmid.SpecNumber);
- if (Integer.parseInt(line.split("\t")[5]) < Integer.parseInt(line.split("\t")[6])) {
- for (int i = 0; i < 2; i++) {
- boolean isdecoy = line.split("\t")[12 + i].equals("1");
- if (!isdecoy) {
- String lumodseq = line.split("\t")[2 + i];
- String resultseq = modseq.replace("[79.96637(S)]", "").replace("[79.96637(Y)]", "").replace("[79.96633(T)]", "");
-
- while (lumodseq.contains("[167]")) {
- int aaindex = StringUtils.countMatches(lumodseq.substring(0, lumodseq.indexOf("[167]")).replaceAll("\\[(.*?)\\]", "$1"), "S");
- int cont = 0;
- for (int idx = 0; idx < resultseq.length(); idx++) {
- if ("S".equals(String.valueOf(resultseq.charAt(idx)))) {
- cont++;
- if (cont == aaindex) {
- resultseq = resultseq.substring(0, idx) + "[79.96637(S)]" + resultseq.substring(idx);
- }
- }
- }
- lumodseq = lumodseq.substring(0, lumodseq.indexOf("[167]")) + lumodseq.substring(lumodseq.indexOf("[167]") + 5);
- }
- while (lumodseq.contains("[181]")) {
- int aaindex = StringUtils.countMatches(lumodseq.substring(0, lumodseq.indexOf("[181]")).replaceAll("\\[(.*?)\\]", "$1"), "T");
- int cont = 0;
- for (int idx = 0; idx < resultseq.length(); idx++) {
- if ("T".equals(String.valueOf(resultseq.charAt(idx)))) {
- cont++;
- if (cont == aaindex) {
- resultseq = resultseq.substring(0, idx) + "[79.96633(T)]" + resultseq.substring(idx);
- }
- }
- }
- lumodseq = lumodseq.substring(0, lumodseq.indexOf("[181]")) + lumodseq.substring(lumodseq.indexOf("[181]") + 5);
- }
- while (lumodseq.contains("[243]")) {
- int aaindex = StringUtils.countMatches(lumodseq.substring(0, lumodseq.indexOf("[243]")).replaceAll("\\[(.*?)\\]", "$1"), "Y");
- int cont = 0;
- for (int idx = 0; idx < resultseq.length(); idx++) {
- if ("Y".equals(String.valueOf(resultseq.charAt(idx)))) {
- cont++;
- if (cont == aaindex) {
- resultseq = resultseq.substring(0, idx) + "[79.96637(Y)]" + resultseq.substring(idx);
- }
- }
- }
- lumodseq = lumodseq.substring(0, lumodseq.indexOf("[243]")) + lumodseq.substring(lumodseq.indexOf("[243]") + 5);
- }
- psmid.LuciphorLFLR = Float.parseFloat(line.split("\t")[7].replace("NA", "1"));
- psmid.LuciphorFLR = Float.parseFloat(line.split("\t")[8].replace("NA", "1"));
- psmid.LuciphorScore = Float.parseFloat(line.split("\t")[10 + i].replace("NA", "0"));
- psmid.ModSeq = resultseq;
- psmid.TPPModSeq = lumodseq;
- return;
- }
- }
- }
- }
- }
-
}
diff --git a/DIA-Umpire/src/MSUmpire/SearchResultParser/TPPResult.java b/DIA-Umpire/src/MSUmpire/SearchResultParser/TPPResult.java
index dd7f1d0..9ecdd01 100644
--- a/DIA-Umpire/src/MSUmpire/SearchResultParser/TPPResult.java
+++ b/DIA-Umpire/src/MSUmpire/SearchResultParser/TPPResult.java
@@ -70,114 +70,7 @@ public void ReadSearchResult(LCMSID lcmsid, String pepxml, String protxml) throw
lcmsid.CreateInstanceForAllPepIon();
Logger.getRootLogger().info("Protein No.:" + lcmsid.ProteinList.size() + "; Assigned Peptide No.:" + lcmsid.AssignedPepIonList.size() + "; All peptide No.:" + lcmsid.GetPepIonList().size() + "; Spectrum level threshold: " + lcmsid.SpecProbThreshold + "; Peptide level threshold: " + lcmsid.PepProbThreshold + "; Protein level threshold: " + lcmsid.ProteinProbThreshold );
}
- public void ReadSearchResultByRefPepID(LCMSID lcmsid, String pepxml, String protxml, LCMSID RefPepID) throws ParserConfigurationException, IOException, SAXException, XmlPullParserException, ClassNotFoundException, InterruptedException {
-
- LCMSID pepxmlid = new LCMSID(pepxml, lcmsid.DecoyTag, lcmsid.FastaPath);
- PepXMLParser pepxmlparser = new PepXMLParser(pepxmlid, pepxml, 0f);
- for (PepIonID pepion : pepxmlid.GetPepIonList().values()) {
- if (RefPepID.GetPepIonList().containsKey(pepion.GetKey())) {
- lcmsid.AddPeptideID(pepion);
- }
- }
- ProtXMLParser protxmlparser = new ProtXMLParser(lcmsid, protxml, 0f);
- //lcmsid.FilterByProteinDecoyFDR(DecoyTag, ProtFDR);
- lcmsid.RemoveLowLocalPWProtein(0.5f);
- //IDsummary.RemoveLowMaxIniProbProtein(0.9f);
- lcmsid.FilterByProteinDecoyFDRUsingMaxIniProb(DecoyTag, ProtFDR);
- lcmsid.LoadSequence();
- lcmsid.ReMapProPep();
- lcmsid.CreateInstanceForAllPepIon();
- Logger.getRootLogger().info("Protein No.:" + lcmsid.ProteinList.size() + "; Assigned Peptide No.:" + lcmsid.AssignedPepIonList.size() + "; All peptide No.:" + lcmsid.GetPepIonList().size() + "; Spectrum level threshold: " + lcmsid.SpecProbThreshold + "; Peptide level threshold: " + lcmsid.PepProbThreshold + "; Protein level threshold: " + lcmsid.ProteinProbThreshold );
- }
-
- public void ReadSearchResultByRefIDProt(LCMSID lcmsid, String pepxml, LCMSID RefID) throws ParserConfigurationException, IOException, SAXException, XmlPullParserException, ClassNotFoundException, InterruptedException {
- PepXMLParser pepxmlparser = new PepXMLParser(lcmsid, pepxml, 0f);
- pepxmlparser.FilteredID = FilterIDBymzXMLname;
- lcmsid.FilterByPepDecoyFDR(DecoyTag, FDR);
- lcmsid.GenerateProteinByRefIDByPepSeq(RefID,false);
- lcmsid.LoadSequence();
- lcmsid.ReMapProPep();
- lcmsid.CreateInstanceForAllPepIon();
- Logger.getRootLogger().info("Protein No.:" + lcmsid.ProteinList.size() + "; Assigned Peptide No.:" + lcmsid.AssignedPepIonList.size() + "; All peptide No.:" + lcmsid.GetPepIonList().size() + "; Spectrum level threshold: " + lcmsid.SpecProbThreshold + "; Peptide level threshold: " + lcmsid.PepProbThreshold + "; Protein level threshold: " + lcmsid.ProteinProbThreshold );
- }
- public void ReadSearchResultByRefID(LCMSID lcmsid, String pepxml, String protxml, LCMSID RefID) throws ParserConfigurationException, IOException, SAXException, XmlPullParserException, ClassNotFoundException, InterruptedException {
- PepXMLParser pepxmlparser = new PepXMLParser(lcmsid, pepxml, 0f);
- pepxmlparser.FilteredID = FilterIDBymzXMLname;
- lcmsid.FilterByPepDecoyFDR(DecoyTag, FDR);
- ProtXMLParser protxmlparser = new ProtXMLParser(lcmsid, protxml, 0f);
- lcmsid.FilterProteinByRefID(RefID);
- lcmsid.LoadSequence();
- lcmsid.ReMapProPep();
- lcmsid.CreateInstanceForAllPepIon();
- Logger.getRootLogger().info("Protein No.:" + lcmsid.ProteinList.size() + "; Assigned Peptide No.:" + lcmsid.AssignedPepIonList.size() + "; All peptide No.:" + lcmsid.GetPepIonList().size() + "; Spectrum level threshold: " + lcmsid.SpecProbThreshold + "; Peptide level threshold: " + lcmsid.PepProbThreshold + "; Protein level threshold: " + lcmsid.ProteinProbThreshold );
- }
-
- public void ReadSearchResultAndFilterByProb(LCMSID lcmsid, String pepxml, String protxml, float prob) throws ParserConfigurationException, IOException, SAXException, XmlPullParserException, ClassNotFoundException, InterruptedException {
- PepXMLParser pepxmlparser = new PepXMLParser(lcmsid, pepxml, prob);
- pepxmlparser.FilteredID = FilterIDBymzXMLname;
- ProtXMLParser protxmlparser = new ProtXMLParser(lcmsid, protxml, prob);
- lcmsid.LoadSequence();
- lcmsid.ReMapProPep();
- lcmsid.CreateInstanceForAllPepIon();
- Logger.getRootLogger().info("Protein No.:" + lcmsid.ProteinList.size() + "; Assigned Peptide No.:" + lcmsid.AssignedPepIonList.size() + "; All peptide No.:" + lcmsid.GetPepIonList().size() + "; Spectrum level threshold: " + lcmsid.SpecProbThreshold + "; Peptide level threshold: " + lcmsid.PepProbThreshold + "; Protein level threshold: " + lcmsid.ProteinProbThreshold );
- }
-
- public void ReadSearchResultByRefPepID(LCMSID lcmsid, ArrayList pepxmls, String protxml, final LCMSID RefPepID) throws ParserConfigurationException, IOException, SAXException, XmlPullParserException, ClassNotFoundException, InterruptedException {
- for (String pepxml : pepxmls) {
- LCMSID pepxmlid = new LCMSID(pepxml, lcmsid.DecoyTag, lcmsid.FastaPath);
- PepXMLParser pepxmlparser = new PepXMLParser(pepxmlid, pepxml, 0f);
- for (PepIonID pepion : pepxmlid.GetPepIonList().values()) {
- if (RefPepID.GetPepIonList().containsKey(pepion.GetKey())) {
- lcmsid.AddPeptideID(pepion);
- }
- }
- }
- ProtXMLParser protxmlparser = new ProtXMLParser(lcmsid, protxml, 0f);
- lcmsid.RemoveLowLocalPWProtein(0.5f);
- lcmsid.FilterByProteinDecoyFDRUsingMaxIniProb(DecoyTag, ProtFDR);
- lcmsid.LoadSequence();
- lcmsid.ReMapProPep();
- lcmsid.CreateInstanceForAllPepIon();
- Logger.getRootLogger().info("Protein No.:" + lcmsid.ProteinList.size() + "; Assigned Peptide No.:" + lcmsid.AssignedPepIonList.size() + "; All peptide No.:" + lcmsid.GetPepIonList().size() + "; Spectrum level threshold: " + lcmsid.SpecProbThreshold + "; Peptide level threshold: " + lcmsid.PepProbThreshold + "; Protein level threshold: " + lcmsid.ProteinProbThreshold );
- }
- public void ReadSearchResult(LCMSID lcmsid, ArrayList pepxmls, String protxml) throws ParserConfigurationException, IOException, SAXException, XmlPullParserException, ClassNotFoundException, InterruptedException {
- for (String pepxml : pepxmls) {
- LCMSID pepxmlid = new LCMSID(FilenameUtils.getFullPath(pepxml) + FilenameUtils.getBaseName(pepxml),DecoyTag,lcmsid.FastaPath);
- PepXMLParser pepxmlparser = new PepXMLParser(pepxmlid, pepxml, 0f);
- pepxmlid.FilterByPepDecoyFDR(DecoyTag, FDR);
- Logger.getRootLogger().info( "peptide No.:" + pepxmlid.GetPepIonList().size() + "; Peptide level threshold: " + pepxmlid.PepProbThreshold);
- for (PepIonID pepID : pepxmlid.GetPepIonList().values()) {
- lcmsid.AddPeptideID(pepID);
- }
- }
- ProtXMLParser protxmlparser = new ProtXMLParser(lcmsid, protxml, 0f);
- lcmsid.RemoveLowLocalPWProtein(0.5f);
- //lcmsid.RemoveLowMaxIniProbProtein(0.9f);
- lcmsid.FilterByProteinDecoyFDRUsingMaxIniProb(DecoyTag, ProtFDR);
- lcmsid.LoadSequence();
- lcmsid.ReMapProPep();
- lcmsid.CreateInstanceForAllPepIon();
- Logger.getRootLogger().info("Protein No.:" + lcmsid.ProteinList.size() + "; Assigned Peptide No.:" + lcmsid.AssignedPepIonList.size() + "; All peptide No.:" + lcmsid.GetPepIonList().size() + "; Spectrum level threshold: " + lcmsid.SpecProbThreshold + "; Peptide level threshold: " + lcmsid.PepProbThreshold + "; Protein level threshold: " + lcmsid.ProteinProbThreshold);
- }
-
- public void ReadSearchResultByRefIDUseRefProtID(LCMSID lcmsid, ArrayList pepxmls, LCMSID RefID,boolean UseMappIon) throws ParserConfigurationException, IOException, SAXException, XmlPullParserException, ClassNotFoundException, InterruptedException {
- for (String pepxml : pepxmls) {
- LCMSID pepxmlid = new LCMSID(FilenameUtils.getFullPath(lcmsid.mzXMLFileName) + FilenameUtils.getBaseName(lcmsid.mzXMLFileName),DecoyTag,lcmsid.FastaPath);
- PepXMLParser pepxmlparser = new PepXMLParser(pepxmlid, pepxml, 0f);
- pepxmlid.FilterByPepDecoyFDR(DecoyTag, FDR);
- Logger.getRootLogger().info( "peptide No.:" + pepxmlid.GetPepIonList().size() + "; Peptide level threshold: " + pepxmlid.PepProbThreshold);
- for (PepIonID pepID : pepxmlid.GetPepIonList().values()) {
- lcmsid.AddPeptideID(pepID);
- }
- }
- lcmsid.GenerateProteinByRefIDByPepSeq(RefID,UseMappIon);
- lcmsid.LoadSequence();
- lcmsid.ReMapProPep();
- lcmsid.CreateInstanceForAllPepIon();
- Logger.getRootLogger().info("Protein No.:" + lcmsid.ProteinList.size() + "; Assigned Peptide No.:" + lcmsid.AssignedPepIonList.size() + "; All peptide No.:" + lcmsid.GetPepIonList().size() + "; Spectrum level threshold: " + lcmsid.SpecProbThreshold + "; Peptide level threshold: " + lcmsid.PepProbThreshold + "; Protein level threshold: " + lcmsid.ProteinProbThreshold );
- }
-
-
+
@Override
public void run() {
try {
diff --git a/DIA-Umpire/src/MSUmpire/SearchResultWriter/PepXMLWriter.java b/DIA-Umpire/src/MSUmpire/SearchResultWriter/PepXMLWriter.java
index aace985..444348c 100644
--- a/DIA-Umpire/src/MSUmpire/SearchResultWriter/PepXMLWriter.java
+++ b/DIA-Umpire/src/MSUmpire/SearchResultWriter/PepXMLWriter.java
@@ -20,7 +20,7 @@
package MSUmpire.SearchResultWriter;
import MSUmpire.BaseDataStructure.UmpireInfo;
-import MSUmpire.FastaParser.FastaParser_V2;
+import MSUmpire.FastaParser.FastaParser;
import MSUmpire.PSMDataStructure.PepIonID;
import MSUmpire.Utility.DateTimeTag;
import java.io.FileWriter;
@@ -82,9 +82,9 @@ public void Write() throws IOException, XmlPullParserException {
}
}
- FastaParser_V2 fastaparser = FastaParser_V2.FasterSerialzationRead(Fasta);
+ FastaParser fastaparser = FastaParser.FasterSerialzationRead(Fasta);
if (fastaparser == null) {
- fastaparser = new FastaParser_V2(Fasta);
+ fastaparser = new FastaParser(Fasta);
fastaparser.digestion(maxmiss, minlength, maxlength,"DECOY");
}
Header();
diff --git a/DIA-Umpire/src/MSUmpire/SeqUtility/ShuffledSeqGen.java b/DIA-Umpire/src/MSUmpire/SeqUtility/ShuffledSeqGen.java
index 15f4691..118d46a 100644
--- a/DIA-Umpire/src/MSUmpire/SeqUtility/ShuffledSeqGen.java
+++ b/DIA-Umpire/src/MSUmpire/SeqUtility/ShuffledSeqGen.java
@@ -19,11 +19,11 @@
*/
package MSUmpire.SeqUtility;
-import ExtPackages.JAligner.Alignment;
-import ExtPackages.JAligner.NeedlemanWunschGotoh;
-import ExtPackages.JAligner.Sequence;
-import ExtPackages.JAligner.matrix.Matrix;
-import ExtPackages.JAligner.matrix.MatrixLoaderException;
+import ExternalPackages.JAligner.Alignment;
+import ExternalPackages.JAligner.NeedlemanWunschGotoh;
+import ExternalPackages.JAligner.Sequence;
+import ExternalPackages.JAligner.matrix.Matrix;
+import ExternalPackages.JAligner.matrix.MatrixLoaderException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.logging.Level;
diff --git a/DIA_Umpire_Quant/build.xml b/DIA_Umpire_Quant/build.xml
new file mode 100644
index 0000000..0487ff7
--- /dev/null
+++ b/DIA_Umpire_Quant/build.xml
@@ -0,0 +1,73 @@
+
+
+
+
+
+
+
+
+
+
+ Builds, tests, and runs the project DIA_Umpire_Quant.
+
+
+
diff --git a/DIA_Umpire_Quant/manifest.mf b/DIA_Umpire_Quant/manifest.mf
new file mode 100644
index 0000000..328e8e5
--- /dev/null
+++ b/DIA_Umpire_Quant/manifest.mf
@@ -0,0 +1,3 @@
+Manifest-Version: 1.0
+X-COMMENT: Main-Class will be added automatically by build
+
diff --git a/DIA_Umpire_Quant/nbproject/build-impl.xml b/DIA_Umpire_Quant/nbproject/build-impl.xml
new file mode 100644
index 0000000..7054a37
--- /dev/null
+++ b/DIA_Umpire_Quant/nbproject/build-impl.xml
@@ -0,0 +1,1429 @@
+
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+
+
+ Must set src.dir
+ Must set test.src.dir
+ Must set build.dir
+ Must set dist.dir
+ Must set build.classes.dir
+ Must set dist.javadoc.dir
+ Must set build.test.classes.dir
+ Must set build.test.results.dir
+ Must set build.classes.excludes
+ Must set dist.jar
+
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+ Must set javac.includes
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+ No tests executed.
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+
+
+ Must set JVM to use for profiling in profiler.info.jvm
+ Must set profiler agent JVM arguments in profiler.info.jvmargs.agent
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must select some files in the IDE or set javac.includes
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ To run this application from the command line without Ant, try:
+
+ java -jar "${dist.jar.resolved}"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must select one file in the IDE or set run.class
+
+
+
+ Must select one file in the IDE or set run.class
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must select one file in the IDE or set debug.class
+
+
+
+
+ Must select one file in the IDE or set debug.class
+
+
+
+
+ Must set fix.includes
+
+
+
+
+
+
+
+
+
+ This target only works when run from inside the NetBeans IDE.
+
+
+
+
+
+
+
+
+ Must select one file in the IDE or set profile.class
+ This target only works when run from inside the NetBeans IDE.
+
+
+
+
+
+
+
+
+ This target only works when run from inside the NetBeans IDE.
+
+
+
+
+
+
+
+
+
+
+
+
+ This target only works when run from inside the NetBeans IDE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must select one file in the IDE or set run.class
+
+
+
+
+
+ Must select some files in the IDE or set test.includes
+
+
+
+
+ Must select one file in the IDE or set run.class
+
+
+
+
+ Must select one file in the IDE or set applet.url
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must select some files in the IDE or set javac.includes
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Some tests failed; see details above.
+
+
+
+
+
+
+
+
+ Must select some files in the IDE or set test.includes
+
+
+
+ Some tests failed; see details above.
+
+
+
+ Must select some files in the IDE or set test.class
+ Must select some method in the IDE or set test.method
+
+
+
+ Some tests failed; see details above.
+
+
+
+
+ Must select one file in the IDE or set test.class
+
+
+
+ Must select one file in the IDE or set test.class
+ Must select some method in the IDE or set test.method
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must select one file in the IDE or set applet.url
+
+
+
+
+
+
+
+
+ Must select one file in the IDE or set applet.url
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/DIA_Umpire_Quant/nbproject/genfiles.properties b/DIA_Umpire_Quant/nbproject/genfiles.properties
new file mode 100644
index 0000000..c71f109
--- /dev/null
+++ b/DIA_Umpire_Quant/nbproject/genfiles.properties
@@ -0,0 +1,8 @@
+build.xml.data.CRC32=29605d81
+build.xml.script.CRC32=95b98002
+build.xml.stylesheet.CRC32=8064a381@1.75.2.48
+# This file is used by a NetBeans-based IDE to track changes in generated files such as build-impl.xml.
+# Do not edit this file. You may delete it but then the IDE will never regenerate such files for you.
+nbproject/build-impl.xml.data.CRC32=29605d81
+nbproject/build-impl.xml.script.CRC32=e2d6c772
+nbproject/build-impl.xml.stylesheet.CRC32=876e7a8f@1.75.2.48
diff --git a/DIA_Umpire_Quant/nbproject/project.properties b/DIA_Umpire_Quant/nbproject/project.properties
new file mode 100644
index 0000000..7bd2bb0
--- /dev/null
+++ b/DIA_Umpire_Quant/nbproject/project.properties
@@ -0,0 +1,350 @@
+annotation.processing.enabled=true
+annotation.processing.enabled.in.editor=false
+annotation.processing.processor.options=
+annotation.processing.processors.list=
+annotation.processing.run.all.processors=true
+annotation.processing.source.output=${build.generated.sources.dir}/ap-source-output
+build.classes.dir=${build.dir}/classes
+build.classes.excludes=**/*.java,**/*.form
+# This directory is removed when the project is cleaned:
+build.dir=build
+build.generated.dir=${build.dir}/generated
+build.generated.sources.dir=${build.dir}/generated-sources
+# Only compile against the classpath explicitly listed here:
+build.sysclasspath=ignore
+build.test.classes.dir=${build.dir}/test/classes
+build.test.results.dir=${build.dir}/test/results
+# Uncomment to specify the preferred debugger connection transport:
+#debug.transport=dt_socket
+debug.classpath=\
+ ${run.classpath}
+debug.test.classpath=\
+ ${run.test.classpath}
+# Files in build.classes.dir which should be excluded from distribution jar
+dist.archive.excludes=
+# This directory is removed when the project is cleaned:
+dist.dir=dist
+dist.jar=${dist.dir}/DIA_Umpire_Quant.jar
+dist.javadoc.dir=${dist.dir}/javadoc
+excludes=
+file.reference.activation-1.1.jar=..\\Library\\activation-1.1.jar
+file.reference.ajt-1.20.jar=..\\Library\\ajt-1.20.jar
+file.reference.axis-1.4.jar=..\\Library\\axis-1.4.jar
+file.reference.axis-jaxrpc-1.4.jar=..\\Library\\axis-jaxrpc-1.4.jar
+file.reference.axis-saaj-1.4.jar=..\\Library\\axis-saaj-1.4.jar
+file.reference.axis-wsdl4j-1.5.1.jar=..\\Library\\axis-wsdl4j-1.5.1.jar
+file.reference.batik-all-1.6.jar=..\\Library\\batik-all-1.6.jar
+file.reference.biojava3-aa-prop-3.0.7.jar=..\\Library\\biojava3-aa-prop-3.0.7.jar
+file.reference.biojava3-alignment-3.0.7.jar=..\\Library\\biojava3-alignment-3.0.7.jar
+file.reference.biojava3-core-3.0.7.jar=..\\Library\\biojava3-core-3.0.7.jar
+file.reference.biojava3-modfinder-3.0.7.jar=..\\Library\\biojava3-modfinder-3.0.7.jar
+file.reference.biojava3-structure-3.0.7.jar=..\\Library\\biojava3-structure-3.0.7.jar
+file.reference.Blas.jar=..\\Library\\Blas.jar
+file.reference.braf-1.0.1.jar=..\\Library\\braf-1.0.1.jar
+file.reference.chardet-1.0.jar=..\\Library\\chardet-1.0.jar
+file.reference.colt-1.2.0.jar=..\\Library\\colt-1.2.0.jar
+file.reference.com.springsource.antlr-2.7.7.jar=..\\Library\\com.springsource.antlr-2.7.7.jar
+file.reference.com.springsource.org.apache.commons.io-1.4.0.jar=..\\Library\\com.springsource.org.apache.commons.io-1.4.0.jar
+file.reference.com.springsource.org.apache.commons.logging-1.1.1.jar=..\\Library\\com.springsource.org.apache.commons.logging-1.1.1.jar
+file.reference.com.springsource.org.apache.log4j-1.2.15.jar=..\\Library\\com.springsource.org.apache.log4j-1.2.15.jar
+file.reference.combinatoricslib-2.0.jar=..\\Library\\combinatoricslib-2.0.jar
+file.reference.comirva-0.36.jar=..\\Library\\comirva-0.36.jar
+file.reference.commons-cli-1.2.jar=..\\Library\\commons-cli-1.2.jar
+file.reference.commons-codec-1.4.jar=..\\Library\\commons-codec-1.4.jar
+file.reference.commons-collections-3.2.1.jar=..\\Library\\commons-collections-3.2.1.jar
+file.reference.commons-compress-1.7.jar=..\\Library\\commons-compress-1.7.jar
+file.reference.commons-discovery-0.4.jar=..\\Library\\commons-discovery-0.4.jar
+file.reference.commons-io-2.3.jar=..\\Library\\commons-io-2.3.jar
+file.reference.commons-lang3-3.1.jar=..\\Library\\commons-lang3-3.1.jar
+file.reference.commons-logging-1.0.4.jar=..\\Library\\commons-logging-1.0.4.jar
+file.reference.commons-math-1.2.jar=..\\Library\\commons-math-1.2.jar
+file.reference.commons-math-2.2.jar=..\\Library\\commons-math-2.2.jar
+file.reference.commons-math3-3.2.jar=..\\Library\\commons-math3-3.2.jar
+file.reference.commons-net-2.2.jar=..\\Library\\commons-net-2.2.jar
+file.reference.concurrent-1.3.4.jar=..\\Library\\concurrent-1.3.4.jar
+file.reference.cpdetector-1.0.7.jar=..\\Library\\cpdetector-1.0.7.jar
+file.reference.csvjdbc-1.0.12.jar=..\\Library\\csvjdbc-1.0.12.jar
+file.reference.derby-10.10.1.1.jar=..\\Library\\derby-10.10.1.1.jar
+file.reference.dom4j-1.6.1.jar=..\\Library\\dom4j-1.6.1.jar
+file.reference.easymock-2.2.jar=..\\Library\\easymock-2.2.jar
+file.reference.event-1.6.5.jar=..\\Library\\event-1.6.5.jar
+file.reference.fastutil-6.5.1.jar=..\\Library\\fastutil-6.5.1.jar
+file.reference.forms-1.2.1.jar=..\\Library\\forms-1.2.1.jar
+file.reference.fst-2.05.jar=..\\Library\\fst-2.05.jar
+file.reference.fst-2.24-onejar.jar=..\\Library\\fst-2.24-onejar.jar
+file.reference.fst-2.27-onejar.jar=..\\Library\\fst-2.27-onejar.jar
+file.reference.fst-2.40-onejar.jar=..\\Library\\fst-2.40-onejar.jar
+file.reference.gentyref-1.1.0.jar=..\\Library\\gentyref-1.1.0.jar
+file.reference.guava-15.0.jar=..\\Library\\guava-15.0.jar
+file.reference.guava-17.0.jar=..\\Library\\guava-17.0.jar
+file.reference.hamcrest-core-1.1.jar=..\\Library\\hamcrest-core-1.1.jar
+file.reference.hsqldb.jar=..\\Library\\hsqldb.jar
+file.reference.ij.jar=..\\Library\\ij.jar
+file.reference.interpreter-1.6.8.jar=..\\Library\\interpreter-1.6.8.jar
+file.reference.isorelax-20050913.jar=..\\Library\\isorelax-20050913.jar
+file.reference.jackson-core-asl-1.8.8.jar=..\\Library\\jackson-core-asl-1.8.8.jar
+file.reference.jackson-mapper-asl-1.8.8.jar=..\\Library\\jackson-mapper-asl-1.8.8.jar
+file.reference.Jama-1.0.2.jar=..\\Library\\Jama-1.0.2.jar
+file.reference.jargs-1.0.jar=..\\Library\\jargs-1.0.jar
+file.reference.javaml-0.1.5.jar=..\\Library\\javaml-0.1.5.jar
+file.reference.javassist-3.18.1-GA.jar=..\\Library\\javassist-3.18.1-GA.jar
+file.reference.javastat_beta1.4.jar=..\\Library\\javastat_beta1.4.jar
+file.reference.javaws.jar=..\\Library\\javaws.jar
+file.reference.javax.mail.jar=..\\Library\\javax.mail.jar
+file.reference.jaxb-api-2.1.jar=..\\Library\\jaxb-api-2.1.jar
+file.reference.jaxb-impl-2.1.7.jar=..\\Library\\jaxb-impl-2.1.7.jar
+file.reference.jaxb-xjc-2.1.7.jar=..\\Library\\jaxb-xjc-2.1.7.jar
+file.reference.jaxrpc-api-1.1.jar=..\\Library\\jaxrpc-api-1.1.jar
+file.reference.jboss-jsfunit-microdeployer-1.3.0.Final.jar=..\\Library\\jboss-jsfunit-microdeployer-1.3.0.Final.jar
+file.reference.jcommon-1.0.17.jar=..\\Library\\jcommon-1.0.17.jar
+file.reference.jdom-2.0.2.jar=..\\Library\\jdom-2.0.2.jar
+file.reference.jdom-legacy-1.1.3.jar=..\\Library\\jdom-legacy-1.1.3.jar
+file.reference.jehep.jar=..\\Library\\jehep.jar
+file.reference.jfreechart-1.0.14-swt.jar=..\\Library\\jfreechart-1.0.14-swt.jar
+file.reference.jfreechart-1.0.14.jar=..\\Library\\jfreechart-1.0.14.jar
+file.reference.jmock-1.1.0.jar=..\\Library\\jmock-1.1.0.jar
+file.reference.jmzidentml-1.1.9.jar=..\\Library\\jmzidentml-1.1.9.jar
+file.reference.jmzml-1.6.8.jar=..\\Library\\jmzml-1.6.8.jar
+file.reference.jsc.jar=..\\Library\\jsc.jar
+file.reference.jshortcut-0.4-oberzalek.jar=..\\Library\\jshortcut-0.4-oberzalek.jar
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+file.reference.ontology-manager-2.0.5-SNAPSHOT.jar=..\\Library\\ontology-manager-2.0.5-SNAPSHOT.jar
+file.reference.optimization.jar=..\\Library\\optimization.jar
+file.reference.org-openide-util-lookup-RELEASE73.jar=..\\Library\\org-openide-util-lookup-RELEASE73.jar
+file.reference.pdf-transcoder-1.0.jar=..\\Library\\pdf-transcoder-1.0.jar
+file.reference.poi-3.9.jar=..\\Library\\poi-3.9.jar
+file.reference.relaxngDatatype-20050913.jar=..\\Library\\relaxngDatatype-20050913.jar
+file.reference.servlet-api-2.2.jar=..\\Library\\servlet-api-2.2.jar
+file.reference.slf4j-api-1.6.1.jar=..\\Library\\slf4j-api-1.6.1.jar
+file.reference.slf4j-log4j12-1.6.1.jar=..\\Library\\slf4j-log4j12-1.6.1.jar
+file.reference.solna-0.5.1.jar=..\\Library\\solna-0.5.1.jar
+file.reference.sqlite-jdbc-3.7.2.jar=..\\Library\\sqlite-jdbc-3.7.2.jar
+file.reference.ssj.jar=..\\Library\\ssj.jar
+file.reference.stax-api-1.0-2.jar=..\\Library\\stax-api-1.0-2.jar
+file.reference.swing-layout-1.0.3.jar=..\\Library\\swing-layout-1.0.3.jar
+file.reference.swingx-1.6.1.jar=..\\Library\\swingx-1.6.1.jar
+file.reference.swtgraphics2d.jar=..\\Library\\swtgraphics2d.jar
+file.reference.tcode.jar=..\\Library\\tcode.jar
+file.reference.trove4j-3.0.3.jar=..\\Library\\trove4j-3.0.3.jar
+file.reference.utilities-3.43.18.jar=..\\Library\\utilities-3.43.18.jar
+file.reference.utilities-4.0.14.jar=..\\Library\\utilities-4.0.14.jar
+file.reference.validator-2.0.5-SNAPSHOT.jar=..\\Library\\validator-2.0.5-SNAPSHOT.jar
+file.reference.weka.jar=..\\Library\\weka.jar
+file.reference.wsdl4j-1.6.1.jar=..\\Library\\wsdl4j-1.6.1.jar
+file.reference.xalan-2.7.0.jar=..\\Library\\xalan-2.7.0.jar
+file.reference.xercesImpl-2.11.0.jar=..\\Library\\xercesImpl-2.11.0.jar
+file.reference.xml-apis-2.10.0.jar=..\\Library\\xml-apis-2.10.0.jar
+file.reference.xmlenc-0.52.jar=..\\Library\\xmlenc-0.52.jar
+file.reference.xmlunit-1.4.jar=..\\Library\\xmlunit-1.4.jar
+file.reference.xmlwriter-2.2.2.jar=..\\Library\\xmlwriter-2.2.2.jar
+file.reference.xom-1.2.5.jar=..\\Library\\xom-1.2.5.jar
+file.reference.xpp3-1.1.3.4-RC3.jar=..\\Library\\xpp3-1.1.3.4-RC3.jar
+file.reference.xsdlib-20050913.jar=..\\Library\\xsdlib-20050913.jar
+file.reference.xtandem-parser-1.4.jar=..\\Library\\xtandem-parser-1.4.jar
+file.reference.xxindex-0.14.jar=..\\Library\\xxindex-0.14.jar
+file.reference.xz-1.4.jar=..\\Library\\xz-1.4.jar
+includes=**
+jar.compress=false
+javac.classpath=\
+ ${reference.DIA-Umpire.jar}:\
+ ${file.reference.Blas.jar}:\
+ ${file.reference.Jama-1.0.2.jar}:\
+ ${file.reference.activation-1.1.jar}:\
+ ${file.reference.ajt-1.20.jar}:\
+ ${file.reference.axis-1.4.jar}:\
+ ${file.reference.axis-jaxrpc-1.4.jar}:\
+ ${file.reference.axis-saaj-1.4.jar}:\
+ ${file.reference.axis-wsdl4j-1.5.1.jar}:\
+ ${file.reference.batik-all-1.6.jar}:\
+ ${file.reference.biojava3-aa-prop-3.0.7.jar}:\
+ ${file.reference.biojava3-alignment-3.0.7.jar}:\
+ ${file.reference.biojava3-core-3.0.7.jar}:\
+ ${file.reference.biojava3-modfinder-3.0.7.jar}:\
+ ${file.reference.biojava3-structure-3.0.7.jar}:\
+ ${file.reference.braf-1.0.1.jar}:\
+ ${file.reference.chardet-1.0.jar}:\
+ ${file.reference.colt-1.2.0.jar}:\
+ ${file.reference.com.springsource.antlr-2.7.7.jar}:\
+ ${file.reference.com.springsource.org.apache.commons.io-1.4.0.jar}:\
+ ${file.reference.com.springsource.org.apache.commons.logging-1.1.1.jar}:\
+ ${file.reference.com.springsource.org.apache.log4j-1.2.15.jar}:\
+ ${file.reference.combinatoricslib-2.0.jar}:\
+ ${file.reference.comirva-0.36.jar}:\
+ ${file.reference.commons-cli-1.2.jar}:\
+ ${file.reference.commons-codec-1.4.jar}:\
+ ${file.reference.commons-collections-3.2.1.jar}:\
+ ${file.reference.commons-compress-1.7.jar}:\
+ ${file.reference.commons-discovery-0.4.jar}:\
+ ${file.reference.commons-io-2.3.jar}:\
+ ${file.reference.commons-lang3-3.1.jar}:\
+ ${file.reference.commons-logging-1.0.4.jar}:\
+ ${file.reference.commons-math-1.2.jar}:\
+ ${file.reference.commons-math-2.2.jar}:\
+ ${file.reference.commons-math3-3.2.jar}:\
+ ${file.reference.commons-net-2.2.jar}:\
+ ${file.reference.concurrent-1.3.4.jar}:\
+ ${file.reference.cpdetector-1.0.7.jar}:\
+ ${file.reference.csvjdbc-1.0.12.jar}:\
+ ${file.reference.derby-10.10.1.1.jar}:\
+ ${file.reference.dom4j-1.6.1.jar}:\
+ ${file.reference.easymock-2.2.jar}:\
+ ${file.reference.event-1.6.5.jar}:\
+ ${file.reference.fastutil-6.5.1.jar}:\
+ ${file.reference.forms-1.2.1.jar}:\
+ ${file.reference.fst-2.05.jar}:\
+ ${file.reference.fst-2.24-onejar.jar}:\
+ ${file.reference.fst-2.27-onejar.jar}:\
+ ${file.reference.fst-2.40-onejar.jar}:\
+ ${file.reference.gentyref-1.1.0.jar}:\
+ ${file.reference.guava-15.0.jar}:\
+ ${file.reference.guava-17.0.jar}:\
+ ${file.reference.hamcrest-core-1.1.jar}:\
+ ${file.reference.hsqldb.jar}:\
+ ${file.reference.ij.jar}:\
+ ${file.reference.interpreter-1.6.8.jar}:\
+ ${file.reference.isorelax-20050913.jar}:\
+ ${file.reference.jackson-core-asl-1.8.8.jar}:\
+ ${file.reference.jackson-mapper-asl-1.8.8.jar}:\
+ ${file.reference.jargs-1.0.jar}:\
+ ${file.reference.javaml-0.1.5.jar}:\
+ ${file.reference.javassist-3.18.1-GA.jar}:\
+ ${file.reference.javastat_beta1.4.jar}:\
+ ${file.reference.javaws.jar}:\
+ ${file.reference.javax.mail.jar}:\
+ ${file.reference.jaxb-api-2.1.jar}:\
+ ${file.reference.jaxb-impl-2.1.7.jar}:\
+ ${file.reference.jaxb-xjc-2.1.7.jar}:\
+ ${file.reference.jaxrpc-api-1.1.jar}:\
+ ${file.reference.jboss-jsfunit-microdeployer-1.3.0.Final.jar}:\
+ ${file.reference.jcommon-1.0.17.jar}:\
+ ${file.reference.jdom-2.0.2.jar}:\
+ ${file.reference.jdom-legacy-1.1.3.jar}:\
+ ${file.reference.jehep.jar}:\
+ ${file.reference.jfreechart-1.0.14-swt.jar}:\
+ ${file.reference.jfreechart-1.0.14.jar}:\
+ ${file.reference.jmock-1.1.0.jar}:\
+ ${file.reference.jmzidentml-1.1.9.jar}:\
+ ${file.reference.jmzml-1.6.8.jar}:\
+ ${file.reference.jsc.jar}:\
+ ${file.reference.jshortcut-0.4-oberzalek.jar}:\
+ ${file.reference.jsparklines-0.8.0.jar}:\
+ ${file.reference.jtattoo-1.3.jar}:\
+ ${file.reference.junit-4.10.jar}:\
+ ${file.reference.language-1.6.7.jar}:\
+ ${file.reference.libsvm.jar}:\
+ ${file.reference.lmjunit-1.0.2.jar}:\
+ ${file.reference.log4j-api-2.0.2.jar}:\
+ ${file.reference.log4j-core-2.0.2.jar}:\
+ ${file.reference.logger-1.6.4.jar}:\
+ ${file.reference.looks-2.2.2.jar}:\
+ ${file.reference.mascotdatfile-3.3.jar}:\
+ ${file.reference.mockito-all-1.9.0.jar}:\
+ ${file.reference.ms-data-core-api-2.0.5.jar}:\
+ ${file.reference.msv-20050913.jar}:\
+ ${file.reference.mysql-connector-java-5.1.30-bin.jar}:\
+ ${file.reference.mzjava-biojava-1.0.0.jar}:\
+ ${file.reference.mzjava-core-1.0.0.jar}:\
+ ${file.reference.mzjava-proteomics-1.0.0.jar}:\
+ ${file.reference.ols-1.14.1.jar}:\
+ ${file.reference.ols-client-1.18.jar}:\
+ ${file.reference.ols-dialog-3.4.0.jar}:\
+ ${file.reference.omssa-parser-1.4.7.jar}:\
+ ${file.reference.ontology-manager-2.0.5-SNAPSHOT.jar}:\
+ ${file.reference.optimization.jar}:\
+ ${file.reference.org-openide-util-lookup-RELEASE73.jar}:\
+ ${file.reference.pdf-transcoder-1.0.jar}:\
+ ${file.reference.poi-3.9.jar}:\
+ ${file.reference.relaxngDatatype-20050913.jar}:\
+ ${file.reference.servlet-api-2.2.jar}:\
+ ${file.reference.slf4j-api-1.6.1.jar}:\
+ ${file.reference.slf4j-log4j12-1.6.1.jar}:\
+ ${file.reference.solna-0.5.1.jar}:\
+ ${file.reference.sqlite-jdbc-3.7.2.jar}:\
+ ${file.reference.ssj.jar}:\
+ ${file.reference.stax-api-1.0-2.jar}:\
+ ${file.reference.swing-layout-1.0.3.jar}:\
+ ${file.reference.swingx-1.6.1.jar}:\
+ ${file.reference.swtgraphics2d.jar}:\
+ ${file.reference.tcode.jar}:\
+ ${file.reference.trove4j-3.0.3.jar}:\
+ ${file.reference.utilities-3.43.18.jar}:\
+ ${file.reference.utilities-4.0.14.jar}:\
+ ${file.reference.validator-2.0.5-SNAPSHOT.jar}:\
+ ${file.reference.weka.jar}:\
+ ${file.reference.wsdl4j-1.6.1.jar}:\
+ ${file.reference.xalan-2.7.0.jar}:\
+ ${file.reference.xercesImpl-2.11.0.jar}:\
+ ${file.reference.xml-apis-2.10.0.jar}:\
+ ${file.reference.xmlenc-0.52.jar}:\
+ ${file.reference.xmlunit-1.4.jar}:\
+ ${file.reference.xmlwriter-2.2.2.jar}:\
+ ${file.reference.xom-1.2.5.jar}:\
+ ${file.reference.xpp3-1.1.3.4-RC3.jar}:\
+ ${file.reference.xsdlib-20050913.jar}:\
+ ${file.reference.xtandem-parser-1.4.jar}:\
+ ${file.reference.xxindex-0.14.jar}:\
+ ${file.reference.xz-1.4.jar}
+# Space-separated list of extra javac options
+javac.compilerargs=
+javac.deprecation=false
+javac.processorpath=\
+ ${javac.classpath}
+javac.source=1.7
+javac.target=1.7
+javac.test.classpath=\
+ ${javac.classpath}:\
+ ${build.classes.dir}
+javac.test.processorpath=\
+ ${javac.test.classpath}
+javadoc.additionalparam=
+javadoc.author=false
+javadoc.encoding=${source.encoding}
+javadoc.noindex=false
+javadoc.nonavbar=false
+javadoc.notree=false
+javadoc.private=false
+javadoc.splitindex=true
+javadoc.use=true
+javadoc.version=false
+javadoc.windowtitle=
+main.class=dia_umpire_quant.DIA_Umpire_Quant
+manifest.file=manifest.mf
+meta.inf.dir=${src.dir}/META-INF
+mkdist.disabled=false
+platform.active=default_platform
+project.DIA-Umpire=../DIA-Umpire
+reference.DIA-Umpire.jar=${project.DIA-Umpire}/dist/DIA-Umpire.jar
+run.classpath=\
+ ${javac.classpath}:\
+ ${build.classes.dir}
+# Space-separated list of JVM arguments used when running the project.
+# You may also define separate properties like run-sys-prop.name=value instead of -Dname=value.
+# To set system properties for unit tests define test-sys-prop.name=value:
+run.jvmargs=
+run.test.classpath=\
+ ${javac.test.classpath}:\
+ ${build.test.classes.dir}
+source.encoding=UTF-8
+src.dir=src
+test.src.dir=test
diff --git a/DIA_Umpire_Quant/nbproject/project.xml b/DIA_Umpire_Quant/nbproject/project.xml
new file mode 100644
index 0000000..adcde34
--- /dev/null
+++ b/DIA_Umpire_Quant/nbproject/project.xml
@@ -0,0 +1,25 @@
+
+
+ org.netbeans.modules.java.j2seproject
+
+
+ DIA_Umpire_Quant
+
+
+
+
+
+
+
+
+
+ DIA-Umpire
+ jar
+
+ jar
+ clean
+ jar
+
+
+
+
diff --git a/DIA-Umpire/src/DIA_Umpire_Quant/DIA_Umpire_Quant.java b/DIA_Umpire_Quant/src/dia_umpire_quant/DIA_Umpire_Quant.java
similarity index 100%
rename from DIA-Umpire/src/DIA_Umpire_Quant/DIA_Umpire_Quant.java
rename to DIA_Umpire_Quant/src/dia_umpire_quant/DIA_Umpire_Quant.java
diff --git a/DIA-Umpire/src/DIA_Umpire_Quant/diaumpire.quant_params b/DIA_Umpire_Quant/src/dia_umpire_quant/diaumpire.quant_params
similarity index 100%
rename from DIA-Umpire/src/DIA_Umpire_Quant/diaumpire.quant_params
rename to DIA_Umpire_Quant/src/dia_umpire_quant/diaumpire.quant_params
diff --git a/DIA_Umpire_SE/build.xml b/DIA_Umpire_SE/build.xml
new file mode 100644
index 0000000..e53dd23
--- /dev/null
+++ b/DIA_Umpire_SE/build.xml
@@ -0,0 +1,73 @@
+
+
+
+
+
+
+
+
+
+
+ Builds, tests, and runs the project DIA_Umpire_SE.
+
+
+
diff --git a/DIA_Umpire_SE/manifest.mf b/DIA_Umpire_SE/manifest.mf
new file mode 100644
index 0000000..328e8e5
--- /dev/null
+++ b/DIA_Umpire_SE/manifest.mf
@@ -0,0 +1,3 @@
+Manifest-Version: 1.0
+X-COMMENT: Main-Class will be added automatically by build
+
diff --git a/DIA_Umpire_SE/nbproject/build-impl.xml b/DIA_Umpire_SE/nbproject/build-impl.xml
new file mode 100644
index 0000000..d73d5cd
--- /dev/null
+++ b/DIA_Umpire_SE/nbproject/build-impl.xml
@@ -0,0 +1,1429 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must set src.dir
+ Must set test.src.dir
+ Must set build.dir
+ Must set dist.dir
+ Must set build.classes.dir
+ Must set dist.javadoc.dir
+ Must set build.test.classes.dir
+ Must set build.test.results.dir
+ Must set build.classes.excludes
+ Must set dist.jar
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must set javac.includes
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
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+
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+
+
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+
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+
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+
+
+
+
+
+
+ No tests executed.
+
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must set JVM to use for profiling in profiler.info.jvm
+ Must set profiler agent JVM arguments in profiler.info.jvmargs.agent
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must select some files in the IDE or set javac.includes
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ To run this application from the command line without Ant, try:
+
+ java -jar "${dist.jar.resolved}"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must select one file in the IDE or set run.class
+
+
+
+ Must select one file in the IDE or set run.class
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must select one file in the IDE or set debug.class
+
+
+
+
+ Must select one file in the IDE or set debug.class
+
+
+
+
+ Must set fix.includes
+
+
+
+
+
+
+
+
+
+ This target only works when run from inside the NetBeans IDE.
+
+
+
+
+
+
+
+
+ Must select one file in the IDE or set profile.class
+ This target only works when run from inside the NetBeans IDE.
+
+
+
+
+
+
+
+
+ This target only works when run from inside the NetBeans IDE.
+
+
+
+
+
+
+
+
+
+
+
+
+ This target only works when run from inside the NetBeans IDE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must select one file in the IDE or set run.class
+
+
+
+
+
+ Must select some files in the IDE or set test.includes
+
+
+
+
+ Must select one file in the IDE or set run.class
+
+
+
+
+ Must select one file in the IDE or set applet.url
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must select some files in the IDE or set javac.includes
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Some tests failed; see details above.
+
+
+
+
+
+
+
+
+ Must select some files in the IDE or set test.includes
+
+
+
+ Some tests failed; see details above.
+
+
+
+ Must select some files in the IDE or set test.class
+ Must select some method in the IDE or set test.method
+
+
+
+ Some tests failed; see details above.
+
+
+
+
+ Must select one file in the IDE or set test.class
+
+
+
+ Must select one file in the IDE or set test.class
+ Must select some method in the IDE or set test.method
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must select one file in the IDE or set applet.url
+
+
+
+
+
+
+
+
+ Must select one file in the IDE or set applet.url
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/DIA_Umpire_SE/nbproject/genfiles.properties b/DIA_Umpire_SE/nbproject/genfiles.properties
new file mode 100644
index 0000000..cd5e6ef
--- /dev/null
+++ b/DIA_Umpire_SE/nbproject/genfiles.properties
@@ -0,0 +1,8 @@
+build.xml.data.CRC32=5d5c3ac7
+build.xml.script.CRC32=f67cc717
+build.xml.stylesheet.CRC32=8064a381@1.75.2.48
+# This file is used by a NetBeans-based IDE to track changes in generated files such as build-impl.xml.
+# Do not edit this file. You may delete it but then the IDE will never regenerate such files for you.
+nbproject/build-impl.xml.data.CRC32=5d5c3ac7
+nbproject/build-impl.xml.script.CRC32=09002b48
+nbproject/build-impl.xml.stylesheet.CRC32=876e7a8f@1.75.2.48
diff --git a/DIA_Umpire_SE/nbproject/project.properties b/DIA_Umpire_SE/nbproject/project.properties
new file mode 100644
index 0000000..ee0d272
--- /dev/null
+++ b/DIA_Umpire_SE/nbproject/project.properties
@@ -0,0 +1,350 @@
+annotation.processing.enabled=true
+annotation.processing.enabled.in.editor=false
+annotation.processing.processor.options=
+annotation.processing.processors.list=
+annotation.processing.run.all.processors=true
+annotation.processing.source.output=${build.generated.sources.dir}/ap-source-output
+build.classes.dir=${build.dir}/classes
+build.classes.excludes=**/*.java,**/*.form
+# This directory is removed when the project is cleaned:
+build.dir=build
+build.generated.dir=${build.dir}/generated
+build.generated.sources.dir=${build.dir}/generated-sources
+# Only compile against the classpath explicitly listed here:
+build.sysclasspath=ignore
+build.test.classes.dir=${build.dir}/test/classes
+build.test.results.dir=${build.dir}/test/results
+# Uncomment to specify the preferred debugger connection transport:
+#debug.transport=dt_socket
+debug.classpath=\
+ ${run.classpath}
+debug.test.classpath=\
+ ${run.test.classpath}
+# Files in build.classes.dir which should be excluded from distribution jar
+dist.archive.excludes=
+# This directory is removed when the project is cleaned:
+dist.dir=dist
+dist.jar=${dist.dir}/DIA_Umpire_SE.jar
+dist.javadoc.dir=${dist.dir}/javadoc
+excludes=
+file.reference.activation-1.1.jar=..\\Library\\activation-1.1.jar
+file.reference.ajt-1.20.jar=..\\Library\\ajt-1.20.jar
+file.reference.axis-1.4.jar=..\\Library\\axis-1.4.jar
+file.reference.axis-jaxrpc-1.4.jar=..\\Library\\axis-jaxrpc-1.4.jar
+file.reference.axis-saaj-1.4.jar=..\\Library\\axis-saaj-1.4.jar
+file.reference.axis-wsdl4j-1.5.1.jar=..\\Library\\axis-wsdl4j-1.5.1.jar
+file.reference.batik-all-1.6.jar=..\\Library\\batik-all-1.6.jar
+file.reference.biojava3-aa-prop-3.0.7.jar=..\\Library\\biojava3-aa-prop-3.0.7.jar
+file.reference.biojava3-alignment-3.0.7.jar=..\\Library\\biojava3-alignment-3.0.7.jar
+file.reference.biojava3-core-3.0.7.jar=..\\Library\\biojava3-core-3.0.7.jar
+file.reference.biojava3-modfinder-3.0.7.jar=..\\Library\\biojava3-modfinder-3.0.7.jar
+file.reference.biojava3-structure-3.0.7.jar=..\\Library\\biojava3-structure-3.0.7.jar
+file.reference.Blas.jar=..\\Library\\Blas.jar
+file.reference.braf-1.0.1.jar=..\\Library\\braf-1.0.1.jar
+file.reference.chardet-1.0.jar=..\\Library\\chardet-1.0.jar
+file.reference.colt-1.2.0.jar=..\\Library\\colt-1.2.0.jar
+file.reference.com.springsource.antlr-2.7.7.jar=..\\Library\\com.springsource.antlr-2.7.7.jar
+file.reference.com.springsource.org.apache.commons.io-1.4.0.jar=..\\Library\\com.springsource.org.apache.commons.io-1.4.0.jar
+file.reference.com.springsource.org.apache.commons.logging-1.1.1.jar=..\\Library\\com.springsource.org.apache.commons.logging-1.1.1.jar
+file.reference.com.springsource.org.apache.log4j-1.2.15.jar=..\\Library\\com.springsource.org.apache.log4j-1.2.15.jar
+file.reference.combinatoricslib-2.0.jar=..\\Library\\combinatoricslib-2.0.jar
+file.reference.comirva-0.36.jar=..\\Library\\comirva-0.36.jar
+file.reference.commons-cli-1.2.jar=..\\Library\\commons-cli-1.2.jar
+file.reference.commons-codec-1.4.jar=..\\Library\\commons-codec-1.4.jar
+file.reference.commons-collections-3.2.1.jar=..\\Library\\commons-collections-3.2.1.jar
+file.reference.commons-compress-1.7.jar=..\\Library\\commons-compress-1.7.jar
+file.reference.commons-discovery-0.4.jar=..\\Library\\commons-discovery-0.4.jar
+file.reference.commons-io-2.3.jar=..\\Library\\commons-io-2.3.jar
+file.reference.commons-lang3-3.1.jar=..\\Library\\commons-lang3-3.1.jar
+file.reference.commons-logging-1.0.4.jar=..\\Library\\commons-logging-1.0.4.jar
+file.reference.commons-math-1.2.jar=..\\Library\\commons-math-1.2.jar
+file.reference.commons-math-2.2.jar=..\\Library\\commons-math-2.2.jar
+file.reference.commons-math3-3.2.jar=..\\Library\\commons-math3-3.2.jar
+file.reference.commons-net-2.2.jar=..\\Library\\commons-net-2.2.jar
+file.reference.concurrent-1.3.4.jar=..\\Library\\concurrent-1.3.4.jar
+file.reference.cpdetector-1.0.7.jar=..\\Library\\cpdetector-1.0.7.jar
+file.reference.csvjdbc-1.0.12.jar=..\\Library\\csvjdbc-1.0.12.jar
+file.reference.derby-10.10.1.1.jar=..\\Library\\derby-10.10.1.1.jar
+file.reference.dom4j-1.6.1.jar=..\\Library\\dom4j-1.6.1.jar
+file.reference.easymock-2.2.jar=..\\Library\\easymock-2.2.jar
+file.reference.event-1.6.5.jar=..\\Library\\event-1.6.5.jar
+file.reference.fastutil-6.5.1.jar=..\\Library\\fastutil-6.5.1.jar
+file.reference.forms-1.2.1.jar=..\\Library\\forms-1.2.1.jar
+file.reference.fst-2.05.jar=..\\Library\\fst-2.05.jar
+file.reference.fst-2.24-onejar.jar=..\\Library\\fst-2.24-onejar.jar
+file.reference.fst-2.27-onejar.jar=..\\Library\\fst-2.27-onejar.jar
+file.reference.fst-2.40-onejar.jar=..\\Library\\fst-2.40-onejar.jar
+file.reference.gentyref-1.1.0.jar=..\\Library\\gentyref-1.1.0.jar
+file.reference.guava-15.0.jar=..\\Library\\guava-15.0.jar
+file.reference.guava-17.0.jar=..\\Library\\guava-17.0.jar
+file.reference.hamcrest-core-1.1.jar=..\\Library\\hamcrest-core-1.1.jar
+file.reference.hsqldb.jar=..\\Library\\hsqldb.jar
+file.reference.ij.jar=..\\Library\\ij.jar
+file.reference.interpreter-1.6.8.jar=..\\Library\\interpreter-1.6.8.jar
+file.reference.isorelax-20050913.jar=..\\Library\\isorelax-20050913.jar
+file.reference.jackson-core-asl-1.8.8.jar=..\\Library\\jackson-core-asl-1.8.8.jar
+file.reference.jackson-mapper-asl-1.8.8.jar=..\\Library\\jackson-mapper-asl-1.8.8.jar
+file.reference.Jama-1.0.2.jar=..\\Library\\Jama-1.0.2.jar
+file.reference.jargs-1.0.jar=..\\Library\\jargs-1.0.jar
+file.reference.javaml-0.1.5.jar=..\\Library\\javaml-0.1.5.jar
+file.reference.javassist-3.18.1-GA.jar=..\\Library\\javassist-3.18.1-GA.jar
+file.reference.javastat_beta1.4.jar=..\\Library\\javastat_beta1.4.jar
+file.reference.javaws.jar=..\\Library\\javaws.jar
+file.reference.javax.mail.jar=..\\Library\\javax.mail.jar
+file.reference.jaxb-api-2.1.jar=..\\Library\\jaxb-api-2.1.jar
+file.reference.jaxb-impl-2.1.7.jar=..\\Library\\jaxb-impl-2.1.7.jar
+file.reference.jaxb-xjc-2.1.7.jar=..\\Library\\jaxb-xjc-2.1.7.jar
+file.reference.jaxrpc-api-1.1.jar=..\\Library\\jaxrpc-api-1.1.jar
+file.reference.jboss-jsfunit-microdeployer-1.3.0.Final.jar=..\\Library\\jboss-jsfunit-microdeployer-1.3.0.Final.jar
+file.reference.jcommon-1.0.17.jar=..\\Library\\jcommon-1.0.17.jar
+file.reference.jdom-2.0.2.jar=..\\Library\\jdom-2.0.2.jar
+file.reference.jdom-legacy-1.1.3.jar=..\\Library\\jdom-legacy-1.1.3.jar
+file.reference.jehep.jar=..\\Library\\jehep.jar
+file.reference.jfreechart-1.0.14-swt.jar=..\\Library\\jfreechart-1.0.14-swt.jar
+file.reference.jfreechart-1.0.14.jar=..\\Library\\jfreechart-1.0.14.jar
+file.reference.jmock-1.1.0.jar=..\\Library\\jmock-1.1.0.jar
+file.reference.jmzidentml-1.1.9.jar=..\\Library\\jmzidentml-1.1.9.jar
+file.reference.jmzml-1.6.8.jar=..\\Library\\jmzml-1.6.8.jar
+file.reference.jsc.jar=..\\Library\\jsc.jar
+file.reference.jshortcut-0.4-oberzalek.jar=..\\Library\\jshortcut-0.4-oberzalek.jar
+file.reference.jsparklines-0.8.0.jar=..\\Library\\jsparklines-0.8.0.jar
+file.reference.jtattoo-1.3.jar=..\\Library\\jtattoo-1.3.jar
+file.reference.junit-4.10.jar=..\\Library\\junit-4.10.jar
+file.reference.language-1.6.7.jar=..\\Library\\language-1.6.7.jar
+file.reference.libsvm.jar=..\\Library\\libsvm.jar
+file.reference.lmjunit-1.0.2.jar=..\\Library\\lmjunit-1.0.2.jar
+file.reference.log4j-api-2.0.2.jar=..\\Library\\log4j-api-2.0.2.jar
+file.reference.log4j-core-2.0.2.jar=..\\Library\\log4j-core-2.0.2.jar
+file.reference.logger-1.6.4.jar=..\\Library\\logger-1.6.4.jar
+file.reference.looks-2.2.2.jar=..\\Library\\looks-2.2.2.jar
+file.reference.mascotdatfile-3.3.jar=..\\Library\\mascotdatfile-3.3.jar
+file.reference.mockito-all-1.9.0.jar=..\\Library\\mockito-all-1.9.0.jar
+file.reference.ms-data-core-api-2.0.5.jar=..\\Library\\ms-data-core-api-2.0.5.jar
+file.reference.msv-20050913.jar=..\\Library\\msv-20050913.jar
+file.reference.mysql-connector-java-5.1.30-bin.jar=..\\Library\\mysql-connector-java-5.1.30-bin.jar
+file.reference.mzjava-biojava-1.0.0.jar=..\\Library\\mzjava-biojava-1.0.0.jar
+file.reference.mzjava-core-1.0.0.jar=..\\Library\\mzjava-core-1.0.0.jar
+file.reference.mzjava-proteomics-1.0.0.jar=..\\Library\\mzjava-proteomics-1.0.0.jar
+file.reference.ols-1.14.1.jar=..\\Library\\ols-1.14.1.jar
+file.reference.ols-client-1.18.jar=..\\Library\\ols-client-1.18.jar
+file.reference.ols-dialog-3.4.0.jar=..\\Library\\ols-dialog-3.4.0.jar
+file.reference.omssa-parser-1.4.7.jar=..\\Library\\omssa-parser-1.4.7.jar
+file.reference.ontology-manager-2.0.5-SNAPSHOT.jar=..\\Library\\ontology-manager-2.0.5-SNAPSHOT.jar
+file.reference.optimization.jar=..\\Library\\optimization.jar
+file.reference.org-openide-util-lookup-RELEASE73.jar=..\\Library\\org-openide-util-lookup-RELEASE73.jar
+file.reference.pdf-transcoder-1.0.jar=..\\Library\\pdf-transcoder-1.0.jar
+file.reference.poi-3.9.jar=..\\Library\\poi-3.9.jar
+file.reference.relaxngDatatype-20050913.jar=..\\Library\\relaxngDatatype-20050913.jar
+file.reference.servlet-api-2.2.jar=..\\Library\\servlet-api-2.2.jar
+file.reference.slf4j-api-1.6.1.jar=..\\Library\\slf4j-api-1.6.1.jar
+file.reference.slf4j-log4j12-1.6.1.jar=..\\Library\\slf4j-log4j12-1.6.1.jar
+file.reference.solna-0.5.1.jar=..\\Library\\solna-0.5.1.jar
+file.reference.sqlite-jdbc-3.7.2.jar=..\\Library\\sqlite-jdbc-3.7.2.jar
+file.reference.ssj.jar=..\\Library\\ssj.jar
+file.reference.stax-api-1.0-2.jar=..\\Library\\stax-api-1.0-2.jar
+file.reference.swing-layout-1.0.3.jar=..\\Library\\swing-layout-1.0.3.jar
+file.reference.swingx-1.6.1.jar=..\\Library\\swingx-1.6.1.jar
+file.reference.swtgraphics2d.jar=..\\Library\\swtgraphics2d.jar
+file.reference.tcode.jar=..\\Library\\tcode.jar
+file.reference.trove4j-3.0.3.jar=..\\Library\\trove4j-3.0.3.jar
+file.reference.utilities-3.43.18.jar=..\\Library\\utilities-3.43.18.jar
+file.reference.utilities-4.0.14.jar=..\\Library\\utilities-4.0.14.jar
+file.reference.validator-2.0.5-SNAPSHOT.jar=..\\Library\\validator-2.0.5-SNAPSHOT.jar
+file.reference.weka.jar=..\\Library\\weka.jar
+file.reference.wsdl4j-1.6.1.jar=..\\Library\\wsdl4j-1.6.1.jar
+file.reference.xalan-2.7.0.jar=..\\Library\\xalan-2.7.0.jar
+file.reference.xercesImpl-2.11.0.jar=..\\Library\\xercesImpl-2.11.0.jar
+file.reference.xml-apis-2.10.0.jar=..\\Library\\xml-apis-2.10.0.jar
+file.reference.xmlenc-0.52.jar=..\\Library\\xmlenc-0.52.jar
+file.reference.xmlunit-1.4.jar=..\\Library\\xmlunit-1.4.jar
+file.reference.xmlwriter-2.2.2.jar=..\\Library\\xmlwriter-2.2.2.jar
+file.reference.xom-1.2.5.jar=..\\Library\\xom-1.2.5.jar
+file.reference.xpp3-1.1.3.4-RC3.jar=..\\Library\\xpp3-1.1.3.4-RC3.jar
+file.reference.xsdlib-20050913.jar=..\\Library\\xsdlib-20050913.jar
+file.reference.xtandem-parser-1.4.jar=..\\Library\\xtandem-parser-1.4.jar
+file.reference.xxindex-0.14.jar=..\\Library\\xxindex-0.14.jar
+file.reference.xz-1.4.jar=..\\Library\\xz-1.4.jar
+includes=**
+jar.compress=false
+javac.classpath=\
+ ${reference.DIA-Umpire.jar}:\
+ ${file.reference.Blas.jar}:\
+ ${file.reference.Jama-1.0.2.jar}:\
+ ${file.reference.activation-1.1.jar}:\
+ ${file.reference.ajt-1.20.jar}:\
+ ${file.reference.axis-1.4.jar}:\
+ ${file.reference.axis-jaxrpc-1.4.jar}:\
+ ${file.reference.axis-saaj-1.4.jar}:\
+ ${file.reference.axis-wsdl4j-1.5.1.jar}:\
+ ${file.reference.batik-all-1.6.jar}:\
+ ${file.reference.biojava3-aa-prop-3.0.7.jar}:\
+ ${file.reference.biojava3-alignment-3.0.7.jar}:\
+ ${file.reference.biojava3-core-3.0.7.jar}:\
+ ${file.reference.biojava3-modfinder-3.0.7.jar}:\
+ ${file.reference.biojava3-structure-3.0.7.jar}:\
+ ${file.reference.braf-1.0.1.jar}:\
+ ${file.reference.chardet-1.0.jar}:\
+ ${file.reference.colt-1.2.0.jar}:\
+ ${file.reference.com.springsource.antlr-2.7.7.jar}:\
+ ${file.reference.com.springsource.org.apache.commons.io-1.4.0.jar}:\
+ ${file.reference.com.springsource.org.apache.commons.logging-1.1.1.jar}:\
+ ${file.reference.com.springsource.org.apache.log4j-1.2.15.jar}:\
+ ${file.reference.combinatoricslib-2.0.jar}:\
+ ${file.reference.comirva-0.36.jar}:\
+ ${file.reference.commons-cli-1.2.jar}:\
+ ${file.reference.commons-codec-1.4.jar}:\
+ ${file.reference.commons-collections-3.2.1.jar}:\
+ ${file.reference.commons-compress-1.7.jar}:\
+ ${file.reference.commons-discovery-0.4.jar}:\
+ ${file.reference.commons-io-2.3.jar}:\
+ ${file.reference.commons-lang3-3.1.jar}:\
+ ${file.reference.commons-logging-1.0.4.jar}:\
+ ${file.reference.commons-math-1.2.jar}:\
+ ${file.reference.commons-math-2.2.jar}:\
+ ${file.reference.commons-math3-3.2.jar}:\
+ ${file.reference.commons-net-2.2.jar}:\
+ ${file.reference.concurrent-1.3.4.jar}:\
+ ${file.reference.cpdetector-1.0.7.jar}:\
+ ${file.reference.csvjdbc-1.0.12.jar}:\
+ ${file.reference.derby-10.10.1.1.jar}:\
+ ${file.reference.dom4j-1.6.1.jar}:\
+ ${file.reference.easymock-2.2.jar}:\
+ ${file.reference.event-1.6.5.jar}:\
+ ${file.reference.fastutil-6.5.1.jar}:\
+ ${file.reference.forms-1.2.1.jar}:\
+ ${file.reference.fst-2.05.jar}:\
+ ${file.reference.fst-2.24-onejar.jar}:\
+ ${file.reference.fst-2.27-onejar.jar}:\
+ ${file.reference.fst-2.40-onejar.jar}:\
+ ${file.reference.gentyref-1.1.0.jar}:\
+ ${file.reference.guava-15.0.jar}:\
+ ${file.reference.guava-17.0.jar}:\
+ ${file.reference.hamcrest-core-1.1.jar}:\
+ ${file.reference.hsqldb.jar}:\
+ ${file.reference.ij.jar}:\
+ ${file.reference.interpreter-1.6.8.jar}:\
+ ${file.reference.isorelax-20050913.jar}:\
+ ${file.reference.jackson-core-asl-1.8.8.jar}:\
+ ${file.reference.jackson-mapper-asl-1.8.8.jar}:\
+ ${file.reference.jargs-1.0.jar}:\
+ ${file.reference.javaml-0.1.5.jar}:\
+ ${file.reference.javassist-3.18.1-GA.jar}:\
+ ${file.reference.javastat_beta1.4.jar}:\
+ ${file.reference.javaws.jar}:\
+ ${file.reference.javax.mail.jar}:\
+ ${file.reference.jaxb-api-2.1.jar}:\
+ ${file.reference.jaxb-impl-2.1.7.jar}:\
+ ${file.reference.jaxb-xjc-2.1.7.jar}:\
+ ${file.reference.jaxrpc-api-1.1.jar}:\
+ ${file.reference.jboss-jsfunit-microdeployer-1.3.0.Final.jar}:\
+ ${file.reference.jcommon-1.0.17.jar}:\
+ ${file.reference.jdom-2.0.2.jar}:\
+ ${file.reference.jdom-legacy-1.1.3.jar}:\
+ ${file.reference.jehep.jar}:\
+ ${file.reference.jfreechart-1.0.14-swt.jar}:\
+ ${file.reference.jfreechart-1.0.14.jar}:\
+ ${file.reference.jmock-1.1.0.jar}:\
+ ${file.reference.jmzidentml-1.1.9.jar}:\
+ ${file.reference.jmzml-1.6.8.jar}:\
+ ${file.reference.jsc.jar}:\
+ ${file.reference.jshortcut-0.4-oberzalek.jar}:\
+ ${file.reference.jsparklines-0.8.0.jar}:\
+ ${file.reference.jtattoo-1.3.jar}:\
+ ${file.reference.junit-4.10.jar}:\
+ ${file.reference.language-1.6.7.jar}:\
+ ${file.reference.libsvm.jar}:\
+ ${file.reference.lmjunit-1.0.2.jar}:\
+ ${file.reference.log4j-api-2.0.2.jar}:\
+ ${file.reference.log4j-core-2.0.2.jar}:\
+ ${file.reference.logger-1.6.4.jar}:\
+ ${file.reference.looks-2.2.2.jar}:\
+ ${file.reference.mascotdatfile-3.3.jar}:\
+ ${file.reference.mockito-all-1.9.0.jar}:\
+ ${file.reference.ms-data-core-api-2.0.5.jar}:\
+ ${file.reference.msv-20050913.jar}:\
+ ${file.reference.mysql-connector-java-5.1.30-bin.jar}:\
+ ${file.reference.mzjava-biojava-1.0.0.jar}:\
+ ${file.reference.mzjava-core-1.0.0.jar}:\
+ ${file.reference.mzjava-proteomics-1.0.0.jar}:\
+ ${file.reference.ols-1.14.1.jar}:\
+ ${file.reference.ols-client-1.18.jar}:\
+ ${file.reference.ols-dialog-3.4.0.jar}:\
+ ${file.reference.omssa-parser-1.4.7.jar}:\
+ ${file.reference.ontology-manager-2.0.5-SNAPSHOT.jar}:\
+ ${file.reference.optimization.jar}:\
+ ${file.reference.org-openide-util-lookup-RELEASE73.jar}:\
+ ${file.reference.pdf-transcoder-1.0.jar}:\
+ ${file.reference.poi-3.9.jar}:\
+ ${file.reference.relaxngDatatype-20050913.jar}:\
+ ${file.reference.servlet-api-2.2.jar}:\
+ ${file.reference.slf4j-api-1.6.1.jar}:\
+ ${file.reference.slf4j-log4j12-1.6.1.jar}:\
+ ${file.reference.solna-0.5.1.jar}:\
+ ${file.reference.sqlite-jdbc-3.7.2.jar}:\
+ ${file.reference.ssj.jar}:\
+ ${file.reference.stax-api-1.0-2.jar}:\
+ ${file.reference.swing-layout-1.0.3.jar}:\
+ ${file.reference.swingx-1.6.1.jar}:\
+ ${file.reference.swtgraphics2d.jar}:\
+ ${file.reference.tcode.jar}:\
+ ${file.reference.trove4j-3.0.3.jar}:\
+ ${file.reference.utilities-3.43.18.jar}:\
+ ${file.reference.utilities-4.0.14.jar}:\
+ ${file.reference.validator-2.0.5-SNAPSHOT.jar}:\
+ ${file.reference.weka.jar}:\
+ ${file.reference.wsdl4j-1.6.1.jar}:\
+ ${file.reference.xalan-2.7.0.jar}:\
+ ${file.reference.xercesImpl-2.11.0.jar}:\
+ ${file.reference.xml-apis-2.10.0.jar}:\
+ ${file.reference.xmlenc-0.52.jar}:\
+ ${file.reference.xmlunit-1.4.jar}:\
+ ${file.reference.xmlwriter-2.2.2.jar}:\
+ ${file.reference.xom-1.2.5.jar}:\
+ ${file.reference.xpp3-1.1.3.4-RC3.jar}:\
+ ${file.reference.xsdlib-20050913.jar}:\
+ ${file.reference.xtandem-parser-1.4.jar}:\
+ ${file.reference.xxindex-0.14.jar}:\
+ ${file.reference.xz-1.4.jar}
+# Space-separated list of extra javac options
+javac.compilerargs=
+javac.deprecation=false
+javac.processorpath=\
+ ${javac.classpath}
+javac.source=1.7
+javac.target=1.7
+javac.test.classpath=\
+ ${javac.classpath}:\
+ ${build.classes.dir}
+javac.test.processorpath=\
+ ${javac.test.classpath}
+javadoc.additionalparam=
+javadoc.author=false
+javadoc.encoding=${source.encoding}
+javadoc.noindex=false
+javadoc.nonavbar=false
+javadoc.notree=false
+javadoc.private=false
+javadoc.splitindex=true
+javadoc.use=true
+javadoc.version=false
+javadoc.windowtitle=
+main.class=dia_umpire_se.DIA_Umpire_SE
+manifest.file=manifest.mf
+meta.inf.dir=${src.dir}/META-INF
+mkdist.disabled=false
+platform.active=default_platform
+project.DIA-Umpire=../DIA-Umpire
+reference.DIA-Umpire.jar=${project.DIA-Umpire}/dist/DIA-Umpire.jar
+run.classpath=\
+ ${javac.classpath}:\
+ ${build.classes.dir}
+# Space-separated list of JVM arguments used when running the project.
+# You may also define separate properties like run-sys-prop.name=value instead of -Dname=value.
+# To set system properties for unit tests define test-sys-prop.name=value:
+run.jvmargs=
+run.test.classpath=\
+ ${javac.test.classpath}:\
+ ${build.test.classes.dir}
+source.encoding=UTF-8
+src.dir=src
+test.src.dir=test
diff --git a/DIA_Umpire_SE/nbproject/project.xml b/DIA_Umpire_SE/nbproject/project.xml
new file mode 100644
index 0000000..00ab041
--- /dev/null
+++ b/DIA_Umpire_SE/nbproject/project.xml
@@ -0,0 +1,25 @@
+
+
+ org.netbeans.modules.java.j2seproject
+
+
+ DIA_Umpire_SE
+
+
+
+
+
+
+
+
+
+ DIA-Umpire
+ jar
+
+ jar
+ clean
+ jar
+
+
+
+
diff --git a/DIA-Umpire/src/DIA_Umpire_SE/DIA_Umpire_SE.java b/DIA_Umpire_SE/src/dia_umpire_se/DIA_Umpire_SE.java
similarity index 100%
rename from DIA-Umpire/src/DIA_Umpire_SE/DIA_Umpire_SE.java
rename to DIA_Umpire_SE/src/dia_umpire_se/DIA_Umpire_SE.java
diff --git a/DIA-Umpire/src/DIA_Umpire_SE/diaumpire.se_params b/DIA_Umpire_SE/src/dia_umpire_se/diaumpire.se_params
similarity index 100%
rename from DIA-Umpire/src/DIA_Umpire_SE/diaumpire.se_params
rename to DIA_Umpire_SE/src/dia_umpire_se/diaumpire.se_params
diff --git a/DIA_Umpire_To_Skyline/build.xml b/DIA_Umpire_To_Skyline/build.xml
new file mode 100644
index 0000000..e3d0f5a
--- /dev/null
+++ b/DIA_Umpire_To_Skyline/build.xml
@@ -0,0 +1,73 @@
+
+
+
+
+
+
+
+
+
+
+ Builds, tests, and runs the project DIA_Umpire_To_Skyline.
+
+
+
diff --git a/DIA_Umpire_To_Skyline/manifest.mf b/DIA_Umpire_To_Skyline/manifest.mf
new file mode 100644
index 0000000..328e8e5
--- /dev/null
+++ b/DIA_Umpire_To_Skyline/manifest.mf
@@ -0,0 +1,3 @@
+Manifest-Version: 1.0
+X-COMMENT: Main-Class will be added automatically by build
+
diff --git a/DIA_Umpire_To_Skyline/nbproject/build-impl.xml b/DIA_Umpire_To_Skyline/nbproject/build-impl.xml
new file mode 100644
index 0000000..08f94dd
--- /dev/null
+++ b/DIA_Umpire_To_Skyline/nbproject/build-impl.xml
@@ -0,0 +1,1429 @@
+
+
+
+
+
+
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+
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+
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+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must set src.dir
+ Must set test.src.dir
+ Must set build.dir
+ Must set dist.dir
+ Must set build.classes.dir
+ Must set dist.javadoc.dir
+ Must set build.test.classes.dir
+ Must set build.test.results.dir
+ Must set build.classes.excludes
+ Must set dist.jar
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must set javac.includes
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
+ No tests executed.
+
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must set JVM to use for profiling in profiler.info.jvm
+ Must set profiler agent JVM arguments in profiler.info.jvmargs.agent
+
+
+
+
+
+
+
+
+
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must select some files in the IDE or set javac.includes
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ To run this application from the command line without Ant, try:
+
+ java -jar "${dist.jar.resolved}"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must select one file in the IDE or set run.class
+
+
+
+ Must select one file in the IDE or set run.class
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must select one file in the IDE or set debug.class
+
+
+
+
+ Must select one file in the IDE or set debug.class
+
+
+
+
+ Must set fix.includes
+
+
+
+
+
+
+
+
+
+ This target only works when run from inside the NetBeans IDE.
+
+
+
+
+
+
+
+
+ Must select one file in the IDE or set profile.class
+ This target only works when run from inside the NetBeans IDE.
+
+
+
+
+
+
+
+
+ This target only works when run from inside the NetBeans IDE.
+
+
+
+
+
+
+
+
+
+
+
+
+ This target only works when run from inside the NetBeans IDE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must select one file in the IDE or set run.class
+
+
+
+
+
+ Must select some files in the IDE or set test.includes
+
+
+
+
+ Must select one file in the IDE or set run.class
+
+
+
+
+ Must select one file in the IDE or set applet.url
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must select some files in the IDE or set javac.includes
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Some tests failed; see details above.
+
+
+
+
+
+
+
+
+ Must select some files in the IDE or set test.includes
+
+
+
+ Some tests failed; see details above.
+
+
+
+ Must select some files in the IDE or set test.class
+ Must select some method in the IDE or set test.method
+
+
+
+ Some tests failed; see details above.
+
+
+
+
+ Must select one file in the IDE or set test.class
+
+
+
+ Must select one file in the IDE or set test.class
+ Must select some method in the IDE or set test.method
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must select one file in the IDE or set applet.url
+
+
+
+
+
+
+
+
+ Must select one file in the IDE or set applet.url
+
+
+
+
+
+
+
+
+
+
+
+
+
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diff --git a/DIA_Umpire_To_Skyline/nbproject/genfiles.properties b/DIA_Umpire_To_Skyline/nbproject/genfiles.properties
new file mode 100644
index 0000000..b0f7754
--- /dev/null
+++ b/DIA_Umpire_To_Skyline/nbproject/genfiles.properties
@@ -0,0 +1,8 @@
+build.xml.data.CRC32=ca05f657
+build.xml.script.CRC32=4445318a
+build.xml.stylesheet.CRC32=8064a381@1.75.2.48
+# This file is used by a NetBeans-based IDE to track changes in generated files such as build-impl.xml.
+# Do not edit this file. You may delete it but then the IDE will never regenerate such files for you.
+nbproject/build-impl.xml.data.CRC32=ca05f657
+nbproject/build-impl.xml.script.CRC32=8c6bc1c7
+nbproject/build-impl.xml.stylesheet.CRC32=876e7a8f@1.75.2.48
diff --git a/DIA_Umpire_To_Skyline/nbproject/project.properties b/DIA_Umpire_To_Skyline/nbproject/project.properties
new file mode 100644
index 0000000..db3d4f6
--- /dev/null
+++ b/DIA_Umpire_To_Skyline/nbproject/project.properties
@@ -0,0 +1,350 @@
+annotation.processing.enabled=true
+annotation.processing.enabled.in.editor=false
+annotation.processing.processor.options=
+annotation.processing.processors.list=
+annotation.processing.run.all.processors=true
+annotation.processing.source.output=${build.generated.sources.dir}/ap-source-output
+build.classes.dir=${build.dir}/classes
+build.classes.excludes=**/*.java,**/*.form
+# This directory is removed when the project is cleaned:
+build.dir=build
+build.generated.dir=${build.dir}/generated
+build.generated.sources.dir=${build.dir}/generated-sources
+# Only compile against the classpath explicitly listed here:
+build.sysclasspath=ignore
+build.test.classes.dir=${build.dir}/test/classes
+build.test.results.dir=${build.dir}/test/results
+# Uncomment to specify the preferred debugger connection transport:
+#debug.transport=dt_socket
+debug.classpath=\
+ ${run.classpath}
+debug.test.classpath=\
+ ${run.test.classpath}
+# Files in build.classes.dir which should be excluded from distribution jar
+dist.archive.excludes=
+# This directory is removed when the project is cleaned:
+dist.dir=dist
+dist.jar=${dist.dir}/DIA_Umpire_To_Skyline.jar
+dist.javadoc.dir=${dist.dir}/javadoc
+excludes=
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+includes=**
+jar.compress=false
+javac.classpath=\
+ ${reference.DIA-Umpire.jar}:\
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+ ${file.reference.wsdl4j-1.6.1.jar}:\
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+ ${file.reference.xml-apis-2.10.0.jar}:\
+ ${file.reference.xmlenc-0.52.jar}:\
+ ${file.reference.xmlunit-1.4.jar}:\
+ ${file.reference.xmlwriter-2.2.2.jar}:\
+ ${file.reference.xom-1.2.5.jar}:\
+ ${file.reference.xpp3-1.1.3.4-RC3.jar}:\
+ ${file.reference.xsdlib-20050913.jar}:\
+ ${file.reference.xtandem-parser-1.4.jar}:\
+ ${file.reference.xxindex-0.14.jar}:\
+ ${file.reference.xz-1.4.jar}
+# Space-separated list of extra javac options
+javac.compilerargs=
+javac.deprecation=false
+javac.processorpath=\
+ ${javac.classpath}
+javac.source=1.7
+javac.target=1.7
+javac.test.classpath=\
+ ${javac.classpath}:\
+ ${build.classes.dir}
+javac.test.processorpath=\
+ ${javac.test.classpath}
+javadoc.additionalparam=
+javadoc.author=false
+javadoc.encoding=${source.encoding}
+javadoc.noindex=false
+javadoc.nonavbar=false
+javadoc.notree=false
+javadoc.private=false
+javadoc.splitindex=true
+javadoc.use=true
+javadoc.version=false
+javadoc.windowtitle=
+main.class=dia_umpire_to_skyline.DIA_Umpire_To_Skyline
+manifest.file=manifest.mf
+meta.inf.dir=${src.dir}/META-INF
+mkdist.disabled=false
+platform.active=default_platform
+project.DIA-Umpire=../DIA-Umpire
+reference.DIA-Umpire.jar=${project.DIA-Umpire}/dist/DIA-Umpire.jar
+run.classpath=\
+ ${javac.classpath}:\
+ ${build.classes.dir}
+# Space-separated list of JVM arguments used when running the project.
+# You may also define separate properties like run-sys-prop.name=value instead of -Dname=value.
+# To set system properties for unit tests define test-sys-prop.name=value:
+run.jvmargs=
+run.test.classpath=\
+ ${javac.test.classpath}:\
+ ${build.test.classes.dir}
+source.encoding=UTF-8
+src.dir=src
+test.src.dir=test
diff --git a/DIA_Umpire_To_Skyline/nbproject/project.xml b/DIA_Umpire_To_Skyline/nbproject/project.xml
new file mode 100644
index 0000000..d042493
--- /dev/null
+++ b/DIA_Umpire_To_Skyline/nbproject/project.xml
@@ -0,0 +1,25 @@
+
+
+ org.netbeans.modules.java.j2seproject
+
+
+ DIA_Umpire_To_Skyline
+
+
+
+
+
+
+
+
+
+ DIA-Umpire
+ jar
+
+ jar
+ clean
+ jar
+
+
+
+
diff --git a/DIA-Umpire/src/DIA_Umpire_To_Skyline/DIA_Umpire_To_Skyline.java b/DIA_Umpire_To_Skyline/src/dia_umpire_to_skyline/DIA_Umpire_To_Skyline.java
similarity index 100%
rename from DIA-Umpire/src/DIA_Umpire_To_Skyline/DIA_Umpire_To_Skyline.java
rename to DIA_Umpire_To_Skyline/src/dia_umpire_to_skyline/DIA_Umpire_To_Skyline.java
diff --git a/DIA-Umpire/src/DIA_Umpire_To_Skyline/FileThread.java b/DIA_Umpire_To_Skyline/src/dia_umpire_to_skyline/FileThread.java
similarity index 100%
rename from DIA-Umpire/src/DIA_Umpire_To_Skyline/FileThread.java
rename to DIA_Umpire_To_Skyline/src/dia_umpire_to_skyline/FileThread.java
diff --git a/Library/CopyLibs/org-netbeans-modules-java-j2seproject-copylibstask.jar b/Library/CopyLibs/org-netbeans-modules-java-j2seproject-copylibstask.jar
new file mode 100644
index 0000000..a26b6f4
Binary files /dev/null and b/Library/CopyLibs/org-netbeans-modules-java-j2seproject-copylibstask.jar differ
diff --git a/Library/nblibraries.properties b/Library/nblibraries.properties
new file mode 100644
index 0000000..6d0afb5
--- /dev/null
+++ b/Library/nblibraries.properties
@@ -0,0 +1,4 @@
+libs.CopyLibs.classpath=\
+ ${base}/CopyLibs/org-netbeans-modules-java-j2seproject-copylibstask.jar
+libs.CopyLibs.displayName=CopyLibs Task
+libs.CopyLibs.prop-version=2.0
diff --git a/MS1Quant/build.xml b/MS1Quant/build.xml
new file mode 100644
index 0000000..3246db9
--- /dev/null
+++ b/MS1Quant/build.xml
@@ -0,0 +1,73 @@
+
+
+
+
+
+
+
+
+
+
+ Builds, tests, and runs the project MS1Quant.
+
+
+
diff --git a/MS1Quant/manifest.mf b/MS1Quant/manifest.mf
new file mode 100644
index 0000000..328e8e5
--- /dev/null
+++ b/MS1Quant/manifest.mf
@@ -0,0 +1,3 @@
+Manifest-Version: 1.0
+X-COMMENT: Main-Class will be added automatically by build
+
diff --git a/MS1Quant/nbproject/build-impl.xml b/MS1Quant/nbproject/build-impl.xml
new file mode 100644
index 0000000..834be5b
--- /dev/null
+++ b/MS1Quant/nbproject/build-impl.xml
@@ -0,0 +1,1429 @@
+
+
+
+
+
+
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+
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+
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+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must set src.dir
+ Must set test.src.dir
+ Must set build.dir
+ Must set dist.dir
+ Must set build.classes.dir
+ Must set dist.javadoc.dir
+ Must set build.test.classes.dir
+ Must set build.test.results.dir
+ Must set build.classes.excludes
+ Must set dist.jar
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must set javac.includes
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
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+
+
+
+
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+ No tests executed.
+
+
+
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must set JVM to use for profiling in profiler.info.jvm
+ Must set profiler agent JVM arguments in profiler.info.jvmargs.agent
+
+
+
+
+
+
+
+
+
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+
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+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must select some files in the IDE or set javac.includes
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ To run this application from the command line without Ant, try:
+
+ java -jar "${dist.jar.resolved}"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must select one file in the IDE or set run.class
+
+
+
+ Must select one file in the IDE or set run.class
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must select one file in the IDE or set debug.class
+
+
+
+
+ Must select one file in the IDE or set debug.class
+
+
+
+
+ Must set fix.includes
+
+
+
+
+
+
+
+
+
+ This target only works when run from inside the NetBeans IDE.
+
+
+
+
+
+
+
+
+ Must select one file in the IDE or set profile.class
+ This target only works when run from inside the NetBeans IDE.
+
+
+
+
+
+
+
+
+ This target only works when run from inside the NetBeans IDE.
+
+
+
+
+
+
+
+
+
+
+
+
+ This target only works when run from inside the NetBeans IDE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must select one file in the IDE or set run.class
+
+
+
+
+
+ Must select some files in the IDE or set test.includes
+
+
+
+
+ Must select one file in the IDE or set run.class
+
+
+
+
+ Must select one file in the IDE or set applet.url
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must select some files in the IDE or set javac.includes
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Some tests failed; see details above.
+
+
+
+
+
+
+
+
+ Must select some files in the IDE or set test.includes
+
+
+
+ Some tests failed; see details above.
+
+
+
+ Must select some files in the IDE or set test.class
+ Must select some method in the IDE or set test.method
+
+
+
+ Some tests failed; see details above.
+
+
+
+
+ Must select one file in the IDE or set test.class
+
+
+
+ Must select one file in the IDE or set test.class
+ Must select some method in the IDE or set test.method
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Must select one file in the IDE or set applet.url
+
+
+
+
+
+
+
+
+ Must select one file in the IDE or set applet.url
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/MS1Quant/nbproject/genfiles.properties b/MS1Quant/nbproject/genfiles.properties
new file mode 100644
index 0000000..e46ec64
--- /dev/null
+++ b/MS1Quant/nbproject/genfiles.properties
@@ -0,0 +1,8 @@
+build.xml.data.CRC32=abdbd957
+build.xml.script.CRC32=4ff79844
+build.xml.stylesheet.CRC32=8064a381@1.75.2.48
+# This file is used by a NetBeans-based IDE to track changes in generated files such as build-impl.xml.
+# Do not edit this file. You may delete it but then the IDE will never regenerate such files for you.
+nbproject/build-impl.xml.data.CRC32=abdbd957
+nbproject/build-impl.xml.script.CRC32=b060f1b3
+nbproject/build-impl.xml.stylesheet.CRC32=876e7a8f@1.75.2.48
diff --git a/MS1Quant/nbproject/project.properties b/MS1Quant/nbproject/project.properties
new file mode 100644
index 0000000..a788905
--- /dev/null
+++ b/MS1Quant/nbproject/project.properties
@@ -0,0 +1,350 @@
+annotation.processing.enabled=true
+annotation.processing.enabled.in.editor=false
+annotation.processing.processor.options=
+annotation.processing.processors.list=
+annotation.processing.run.all.processors=true
+annotation.processing.source.output=${build.generated.sources.dir}/ap-source-output
+build.classes.dir=${build.dir}/classes
+build.classes.excludes=**/*.java,**/*.form
+# This directory is removed when the project is cleaned:
+build.dir=build
+build.generated.dir=${build.dir}/generated
+build.generated.sources.dir=${build.dir}/generated-sources
+# Only compile against the classpath explicitly listed here:
+build.sysclasspath=ignore
+build.test.classes.dir=${build.dir}/test/classes
+build.test.results.dir=${build.dir}/test/results
+# Uncomment to specify the preferred debugger connection transport:
+#debug.transport=dt_socket
+debug.classpath=\
+ ${run.classpath}
+debug.test.classpath=\
+ ${run.test.classpath}
+# Files in build.classes.dir which should be excluded from distribution jar
+dist.archive.excludes=
+# This directory is removed when the project is cleaned:
+dist.dir=dist
+dist.jar=${dist.dir}/MS1Quant.jar
+dist.javadoc.dir=${dist.dir}/javadoc
+excludes=
+file.reference.activation-1.1.jar=..\\Library\\activation-1.1.jar
+file.reference.ajt-1.20.jar=..\\Library\\ajt-1.20.jar
+file.reference.axis-1.4.jar=..\\Library\\axis-1.4.jar
+file.reference.axis-jaxrpc-1.4.jar=..\\Library\\axis-jaxrpc-1.4.jar
+file.reference.axis-saaj-1.4.jar=..\\Library\\axis-saaj-1.4.jar
+file.reference.axis-wsdl4j-1.5.1.jar=..\\Library\\axis-wsdl4j-1.5.1.jar
+file.reference.batik-all-1.6.jar=..\\Library\\batik-all-1.6.jar
+file.reference.biojava3-aa-prop-3.0.7.jar=..\\Library\\biojava3-aa-prop-3.0.7.jar
+file.reference.biojava3-alignment-3.0.7.jar=..\\Library\\biojava3-alignment-3.0.7.jar
+file.reference.biojava3-core-3.0.7.jar=..\\Library\\biojava3-core-3.0.7.jar
+file.reference.biojava3-modfinder-3.0.7.jar=..\\Library\\biojava3-modfinder-3.0.7.jar
+file.reference.biojava3-structure-3.0.7.jar=..\\Library\\biojava3-structure-3.0.7.jar
+file.reference.Blas.jar=..\\Library\\Blas.jar
+file.reference.braf-1.0.1.jar=..\\Library\\braf-1.0.1.jar
+file.reference.chardet-1.0.jar=..\\Library\\chardet-1.0.jar
+file.reference.colt-1.2.0.jar=..\\Library\\colt-1.2.0.jar
+file.reference.com.springsource.antlr-2.7.7.jar=..\\Library\\com.springsource.antlr-2.7.7.jar
+file.reference.com.springsource.org.apache.commons.io-1.4.0.jar=..\\Library\\com.springsource.org.apache.commons.io-1.4.0.jar
+file.reference.com.springsource.org.apache.commons.logging-1.1.1.jar=..\\Library\\com.springsource.org.apache.commons.logging-1.1.1.jar
+file.reference.com.springsource.org.apache.log4j-1.2.15.jar=..\\Library\\com.springsource.org.apache.log4j-1.2.15.jar
+file.reference.combinatoricslib-2.0.jar=..\\Library\\combinatoricslib-2.0.jar
+file.reference.comirva-0.36.jar=..\\Library\\comirva-0.36.jar
+file.reference.commons-cli-1.2.jar=..\\Library\\commons-cli-1.2.jar
+file.reference.commons-codec-1.4.jar=..\\Library\\commons-codec-1.4.jar
+file.reference.commons-collections-3.2.1.jar=..\\Library\\commons-collections-3.2.1.jar
+file.reference.commons-compress-1.7.jar=..\\Library\\commons-compress-1.7.jar
+file.reference.commons-discovery-0.4.jar=..\\Library\\commons-discovery-0.4.jar
+file.reference.commons-io-2.3.jar=..\\Library\\commons-io-2.3.jar
+file.reference.commons-lang3-3.1.jar=..\\Library\\commons-lang3-3.1.jar
+file.reference.commons-logging-1.0.4.jar=..\\Library\\commons-logging-1.0.4.jar
+file.reference.commons-math-1.2.jar=..\\Library\\commons-math-1.2.jar
+file.reference.commons-math-2.2.jar=..\\Library\\commons-math-2.2.jar
+file.reference.commons-math3-3.2.jar=..\\Library\\commons-math3-3.2.jar
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+file.reference.guava-17.0.jar=..\\Library\\guava-17.0.jar
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+file.reference.isorelax-20050913.jar=..\\Library\\isorelax-20050913.jar
+file.reference.jackson-core-asl-1.8.8.jar=..\\Library\\jackson-core-asl-1.8.8.jar
+file.reference.jackson-mapper-asl-1.8.8.jar=..\\Library\\jackson-mapper-asl-1.8.8.jar
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+file.reference.jargs-1.0.jar=..\\Library\\jargs-1.0.jar
+file.reference.javaml-0.1.5.jar=..\\Library\\javaml-0.1.5.jar
+file.reference.javassist-3.18.1-GA.jar=..\\Library\\javassist-3.18.1-GA.jar
+file.reference.javastat_beta1.4.jar=..\\Library\\javastat_beta1.4.jar
+file.reference.javaws.jar=..\\Library\\javaws.jar
+file.reference.javax.mail.jar=..\\Library\\javax.mail.jar
+file.reference.jaxb-api-2.1.jar=..\\Library\\jaxb-api-2.1.jar
+file.reference.jaxb-impl-2.1.7.jar=..\\Library\\jaxb-impl-2.1.7.jar
+file.reference.jaxb-xjc-2.1.7.jar=..\\Library\\jaxb-xjc-2.1.7.jar
+file.reference.jaxrpc-api-1.1.jar=..\\Library\\jaxrpc-api-1.1.jar
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+file.reference.jcommon-1.0.17.jar=..\\Library\\jcommon-1.0.17.jar
+file.reference.jdom-2.0.2.jar=..\\Library\\jdom-2.0.2.jar
+file.reference.jdom-legacy-1.1.3.jar=..\\Library\\jdom-legacy-1.1.3.jar
+file.reference.jehep.jar=..\\Library\\jehep.jar
+file.reference.jfreechart-1.0.14-swt.jar=..\\Library\\jfreechart-1.0.14-swt.jar
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+file.reference.jmzml-1.6.8.jar=..\\Library\\jmzml-1.6.8.jar
+file.reference.jsc.jar=..\\Library\\jsc.jar
+file.reference.jshortcut-0.4-oberzalek.jar=..\\Library\\jshortcut-0.4-oberzalek.jar
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+file.reference.libsvm.jar=..\\Library\\libsvm.jar
+file.reference.lmjunit-1.0.2.jar=..\\Library\\lmjunit-1.0.2.jar
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+file.reference.log4j-core-2.0.2.jar=..\\Library\\log4j-core-2.0.2.jar
+file.reference.logger-1.6.4.jar=..\\Library\\logger-1.6.4.jar
+file.reference.looks-2.2.2.jar=..\\Library\\looks-2.2.2.jar
+file.reference.mascotdatfile-3.3.jar=..\\Library\\mascotdatfile-3.3.jar
+file.reference.mockito-all-1.9.0.jar=..\\Library\\mockito-all-1.9.0.jar
+file.reference.ms-data-core-api-2.0.5.jar=..\\Library\\ms-data-core-api-2.0.5.jar
+file.reference.msv-20050913.jar=..\\Library\\msv-20050913.jar
+file.reference.mysql-connector-java-5.1.30-bin.jar=..\\Library\\mysql-connector-java-5.1.30-bin.jar
+file.reference.mzjava-biojava-1.0.0.jar=..\\Library\\mzjava-biojava-1.0.0.jar
+file.reference.mzjava-core-1.0.0.jar=..\\Library\\mzjava-core-1.0.0.jar
+file.reference.mzjava-proteomics-1.0.0.jar=..\\Library\\mzjava-proteomics-1.0.0.jar
+file.reference.ols-1.14.1.jar=..\\Library\\ols-1.14.1.jar
+file.reference.ols-client-1.18.jar=..\\Library\\ols-client-1.18.jar
+file.reference.ols-dialog-3.4.0.jar=..\\Library\\ols-dialog-3.4.0.jar
+file.reference.omssa-parser-1.4.7.jar=..\\Library\\omssa-parser-1.4.7.jar
+file.reference.ontology-manager-2.0.5-SNAPSHOT.jar=..\\Library\\ontology-manager-2.0.5-SNAPSHOT.jar
+file.reference.optimization.jar=..\\Library\\optimization.jar
+file.reference.org-openide-util-lookup-RELEASE73.jar=..\\Library\\org-openide-util-lookup-RELEASE73.jar
+file.reference.pdf-transcoder-1.0.jar=..\\Library\\pdf-transcoder-1.0.jar
+file.reference.poi-3.9.jar=..\\Library\\poi-3.9.jar
+file.reference.relaxngDatatype-20050913.jar=..\\Library\\relaxngDatatype-20050913.jar
+file.reference.servlet-api-2.2.jar=..\\Library\\servlet-api-2.2.jar
+file.reference.slf4j-api-1.6.1.jar=..\\Library\\slf4j-api-1.6.1.jar
+file.reference.slf4j-log4j12-1.6.1.jar=..\\Library\\slf4j-log4j12-1.6.1.jar
+file.reference.solna-0.5.1.jar=..\\Library\\solna-0.5.1.jar
+file.reference.sqlite-jdbc-3.7.2.jar=..\\Library\\sqlite-jdbc-3.7.2.jar
+file.reference.ssj.jar=..\\Library\\ssj.jar
+file.reference.stax-api-1.0-2.jar=..\\Library\\stax-api-1.0-2.jar
+file.reference.swing-layout-1.0.3.jar=..\\Library\\swing-layout-1.0.3.jar
+file.reference.swingx-1.6.1.jar=..\\Library\\swingx-1.6.1.jar
+file.reference.swtgraphics2d.jar=..\\Library\\swtgraphics2d.jar
+file.reference.tcode.jar=..\\Library\\tcode.jar
+file.reference.trove4j-3.0.3.jar=..\\Library\\trove4j-3.0.3.jar
+file.reference.utilities-3.43.18.jar=..\\Library\\utilities-3.43.18.jar
+file.reference.utilities-4.0.14.jar=..\\Library\\utilities-4.0.14.jar
+file.reference.validator-2.0.5-SNAPSHOT.jar=..\\Library\\validator-2.0.5-SNAPSHOT.jar
+file.reference.weka.jar=..\\Library\\weka.jar
+file.reference.wsdl4j-1.6.1.jar=..\\Library\\wsdl4j-1.6.1.jar
+file.reference.xalan-2.7.0.jar=..\\Library\\xalan-2.7.0.jar
+file.reference.xercesImpl-2.11.0.jar=..\\Library\\xercesImpl-2.11.0.jar
+file.reference.xml-apis-2.10.0.jar=..\\Library\\xml-apis-2.10.0.jar
+file.reference.xmlenc-0.52.jar=..\\Library\\xmlenc-0.52.jar
+file.reference.xmlunit-1.4.jar=..\\Library\\xmlunit-1.4.jar
+file.reference.xmlwriter-2.2.2.jar=..\\Library\\xmlwriter-2.2.2.jar
+file.reference.xom-1.2.5.jar=..\\Library\\xom-1.2.5.jar
+file.reference.xpp3-1.1.3.4-RC3.jar=..\\Library\\xpp3-1.1.3.4-RC3.jar
+file.reference.xsdlib-20050913.jar=..\\Library\\xsdlib-20050913.jar
+file.reference.xtandem-parser-1.4.jar=..\\Library\\xtandem-parser-1.4.jar
+file.reference.xxindex-0.14.jar=..\\Library\\xxindex-0.14.jar
+file.reference.xz-1.4.jar=..\\Library\\xz-1.4.jar
+includes=**
+jar.compress=false
+javac.classpath=\
+ ${reference.DIA-Umpire.jar}:\
+ ${file.reference.Blas.jar}:\
+ ${file.reference.Jama-1.0.2.jar}:\
+ ${file.reference.activation-1.1.jar}:\
+ ${file.reference.ajt-1.20.jar}:\
+ ${file.reference.axis-1.4.jar}:\
+ ${file.reference.axis-jaxrpc-1.4.jar}:\
+ ${file.reference.axis-saaj-1.4.jar}:\
+ ${file.reference.axis-wsdl4j-1.5.1.jar}:\
+ ${file.reference.batik-all-1.6.jar}:\
+ ${file.reference.biojava3-aa-prop-3.0.7.jar}:\
+ ${file.reference.biojava3-alignment-3.0.7.jar}:\
+ ${file.reference.biojava3-core-3.0.7.jar}:\
+ ${file.reference.biojava3-modfinder-3.0.7.jar}:\
+ ${file.reference.biojava3-structure-3.0.7.jar}:\
+ ${file.reference.braf-1.0.1.jar}:\
+ ${file.reference.chardet-1.0.jar}:\
+ ${file.reference.colt-1.2.0.jar}:\
+ ${file.reference.com.springsource.antlr-2.7.7.jar}:\
+ ${file.reference.com.springsource.org.apache.commons.io-1.4.0.jar}:\
+ ${file.reference.com.springsource.org.apache.commons.logging-1.1.1.jar}:\
+ ${file.reference.com.springsource.org.apache.log4j-1.2.15.jar}:\
+ ${file.reference.combinatoricslib-2.0.jar}:\
+ ${file.reference.comirva-0.36.jar}:\
+ ${file.reference.commons-cli-1.2.jar}:\
+ ${file.reference.commons-codec-1.4.jar}:\
+ ${file.reference.commons-collections-3.2.1.jar}:\
+ ${file.reference.commons-compress-1.7.jar}:\
+ ${file.reference.commons-discovery-0.4.jar}:\
+ ${file.reference.commons-io-2.3.jar}:\
+ ${file.reference.commons-lang3-3.1.jar}:\
+ ${file.reference.commons-logging-1.0.4.jar}:\
+ ${file.reference.commons-math-1.2.jar}:\
+ ${file.reference.commons-math-2.2.jar}:\
+ ${file.reference.commons-math3-3.2.jar}:\
+ ${file.reference.commons-net-2.2.jar}:\
+ ${file.reference.concurrent-1.3.4.jar}:\
+ ${file.reference.cpdetector-1.0.7.jar}:\
+ ${file.reference.csvjdbc-1.0.12.jar}:\
+ ${file.reference.derby-10.10.1.1.jar}:\
+ ${file.reference.dom4j-1.6.1.jar}:\
+ ${file.reference.easymock-2.2.jar}:\
+ ${file.reference.event-1.6.5.jar}:\
+ ${file.reference.fastutil-6.5.1.jar}:\
+ ${file.reference.forms-1.2.1.jar}:\
+ ${file.reference.fst-2.05.jar}:\
+ ${file.reference.fst-2.24-onejar.jar}:\
+ ${file.reference.fst-2.27-onejar.jar}:\
+ ${file.reference.fst-2.40-onejar.jar}:\
+ ${file.reference.gentyref-1.1.0.jar}:\
+ ${file.reference.guava-15.0.jar}:\
+ ${file.reference.guava-17.0.jar}:\
+ ${file.reference.hamcrest-core-1.1.jar}:\
+ ${file.reference.hsqldb.jar}:\
+ ${file.reference.ij.jar}:\
+ ${file.reference.interpreter-1.6.8.jar}:\
+ ${file.reference.isorelax-20050913.jar}:\
+ ${file.reference.jackson-core-asl-1.8.8.jar}:\
+ ${file.reference.jackson-mapper-asl-1.8.8.jar}:\
+ ${file.reference.jargs-1.0.jar}:\
+ ${file.reference.javaml-0.1.5.jar}:\
+ ${file.reference.javassist-3.18.1-GA.jar}:\
+ ${file.reference.javastat_beta1.4.jar}:\
+ ${file.reference.javaws.jar}:\
+ ${file.reference.javax.mail.jar}:\
+ ${file.reference.jaxb-api-2.1.jar}:\
+ ${file.reference.jaxb-impl-2.1.7.jar}:\
+ ${file.reference.jaxb-xjc-2.1.7.jar}:\
+ ${file.reference.jaxrpc-api-1.1.jar}:\
+ ${file.reference.jboss-jsfunit-microdeployer-1.3.0.Final.jar}:\
+ ${file.reference.jcommon-1.0.17.jar}:\
+ ${file.reference.jdom-2.0.2.jar}:\
+ ${file.reference.jdom-legacy-1.1.3.jar}:\
+ ${file.reference.jehep.jar}:\
+ ${file.reference.jfreechart-1.0.14-swt.jar}:\
+ ${file.reference.jfreechart-1.0.14.jar}:\
+ ${file.reference.jmock-1.1.0.jar}:\
+ ${file.reference.jmzidentml-1.1.9.jar}:\
+ ${file.reference.jmzml-1.6.8.jar}:\
+ ${file.reference.jsc.jar}:\
+ ${file.reference.jshortcut-0.4-oberzalek.jar}:\
+ ${file.reference.jsparklines-0.8.0.jar}:\
+ ${file.reference.jtattoo-1.3.jar}:\
+ ${file.reference.junit-4.10.jar}:\
+ ${file.reference.language-1.6.7.jar}:\
+ ${file.reference.libsvm.jar}:\
+ ${file.reference.lmjunit-1.0.2.jar}:\
+ ${file.reference.log4j-api-2.0.2.jar}:\
+ ${file.reference.log4j-core-2.0.2.jar}:\
+ ${file.reference.logger-1.6.4.jar}:\
+ ${file.reference.looks-2.2.2.jar}:\
+ ${file.reference.mascotdatfile-3.3.jar}:\
+ ${file.reference.mockito-all-1.9.0.jar}:\
+ ${file.reference.ms-data-core-api-2.0.5.jar}:\
+ ${file.reference.msv-20050913.jar}:\
+ ${file.reference.mysql-connector-java-5.1.30-bin.jar}:\
+ ${file.reference.mzjava-biojava-1.0.0.jar}:\
+ ${file.reference.mzjava-core-1.0.0.jar}:\
+ ${file.reference.mzjava-proteomics-1.0.0.jar}:\
+ ${file.reference.ols-1.14.1.jar}:\
+ ${file.reference.ols-client-1.18.jar}:\
+ ${file.reference.ols-dialog-3.4.0.jar}:\
+ ${file.reference.omssa-parser-1.4.7.jar}:\
+ ${file.reference.ontology-manager-2.0.5-SNAPSHOT.jar}:\
+ ${file.reference.optimization.jar}:\
+ ${file.reference.org-openide-util-lookup-RELEASE73.jar}:\
+ ${file.reference.pdf-transcoder-1.0.jar}:\
+ ${file.reference.poi-3.9.jar}:\
+ ${file.reference.relaxngDatatype-20050913.jar}:\
+ ${file.reference.servlet-api-2.2.jar}:\
+ ${file.reference.slf4j-api-1.6.1.jar}:\
+ ${file.reference.slf4j-log4j12-1.6.1.jar}:\
+ ${file.reference.solna-0.5.1.jar}:\
+ ${file.reference.sqlite-jdbc-3.7.2.jar}:\
+ ${file.reference.ssj.jar}:\
+ ${file.reference.stax-api-1.0-2.jar}:\
+ ${file.reference.swing-layout-1.0.3.jar}:\
+ ${file.reference.swingx-1.6.1.jar}:\
+ ${file.reference.swtgraphics2d.jar}:\
+ ${file.reference.tcode.jar}:\
+ ${file.reference.trove4j-3.0.3.jar}:\
+ ${file.reference.utilities-3.43.18.jar}:\
+ ${file.reference.utilities-4.0.14.jar}:\
+ ${file.reference.validator-2.0.5-SNAPSHOT.jar}:\
+ ${file.reference.weka.jar}:\
+ ${file.reference.wsdl4j-1.6.1.jar}:\
+ ${file.reference.xalan-2.7.0.jar}:\
+ ${file.reference.xercesImpl-2.11.0.jar}:\
+ ${file.reference.xml-apis-2.10.0.jar}:\
+ ${file.reference.xmlenc-0.52.jar}:\
+ ${file.reference.xmlunit-1.4.jar}:\
+ ${file.reference.xmlwriter-2.2.2.jar}:\
+ ${file.reference.xom-1.2.5.jar}:\
+ ${file.reference.xpp3-1.1.3.4-RC3.jar}:\
+ ${file.reference.xsdlib-20050913.jar}:\
+ ${file.reference.xtandem-parser-1.4.jar}:\
+ ${file.reference.xxindex-0.14.jar}:\
+ ${file.reference.xz-1.4.jar}
+# Space-separated list of extra javac options
+javac.compilerargs=
+javac.deprecation=false
+javac.processorpath=\
+ ${javac.classpath}
+javac.source=1.7
+javac.target=1.7
+javac.test.classpath=\
+ ${javac.classpath}:\
+ ${build.classes.dir}
+javac.test.processorpath=\
+ ${javac.test.classpath}
+javadoc.additionalparam=
+javadoc.author=false
+javadoc.encoding=${source.encoding}
+javadoc.noindex=false
+javadoc.nonavbar=false
+javadoc.notree=false
+javadoc.private=false
+javadoc.splitindex=true
+javadoc.use=true
+javadoc.version=false
+javadoc.windowtitle=
+main.class=ms1quant.MS1Quant
+manifest.file=manifest.mf
+meta.inf.dir=${src.dir}/META-INF
+mkdist.disabled=false
+platform.active=default_platform
+project.DIA-Umpire=../DIA-Umpire
+reference.DIA-Umpire.jar=${project.DIA-Umpire}/dist/DIA-Umpire.jar
+run.classpath=\
+ ${javac.classpath}:\
+ ${build.classes.dir}
+# Space-separated list of JVM arguments used when running the project.
+# You may also define separate properties like run-sys-prop.name=value instead of -Dname=value.
+# To set system properties for unit tests define test-sys-prop.name=value:
+run.jvmargs=
+run.test.classpath=\
+ ${javac.test.classpath}:\
+ ${build.test.classes.dir}
+source.encoding=UTF-8
+src.dir=src
+test.src.dir=test
diff --git a/MS1Quant/nbproject/project.xml b/MS1Quant/nbproject/project.xml
new file mode 100644
index 0000000..9425b6b
--- /dev/null
+++ b/MS1Quant/nbproject/project.xml
@@ -0,0 +1,25 @@
+
+
+ org.netbeans.modules.java.j2seproject
+
+
+ MS1Quant
+
+
+
+
+
+
+
+
+
+ DIA-Umpire
+ jar
+
+ jar
+ clean
+ jar
+
+
+
+
diff --git a/DIA-Umpire/src/MS1Quant/MS1Quant.java b/MS1Quant/src/ms1quant/MS1Quant.java
similarity index 99%
rename from DIA-Umpire/src/MS1Quant/MS1Quant.java
rename to MS1Quant/src/ms1quant/MS1Quant.java
index 9c0d5a1..b61f9d2 100644
--- a/DIA-Umpire/src/MS1Quant/MS1Quant.java
+++ b/MS1Quant/src/ms1quant/MS1Quant.java
@@ -3,7 +3,7 @@
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
-package MS1Quant;
+package ms1quant;
import MSUmpire.BaseDataStructure.InstrumentParameter;
import MSUmpire.BaseDataStructure.UmpireInfo;
diff --git a/DIA-Umpire/src/MS1Quant/MS1TargetQuantThread.java b/MS1Quant/src/ms1quant/MS1TargetQuantThread.java
similarity index 99%
rename from DIA-Umpire/src/MS1Quant/MS1TargetQuantThread.java
rename to MS1Quant/src/ms1quant/MS1TargetQuantThread.java
index 4ccffa3..a2f019f 100644
--- a/DIA-Umpire/src/MS1Quant/MS1TargetQuantThread.java
+++ b/MS1Quant/src/ms1quant/MS1TargetQuantThread.java
@@ -4,7 +4,7 @@
* and open the template in the editor.
*/
-package MS1Quant;
+package ms1quant;
import MSUmpire.BaseDataStructure.InstrumentParameter;
import MSUmpire.LCMSBaseStructure.LCMSPeakMS1;
diff --git a/DIA-Umpire/src/MS1Quant/ms1quant.params b/MS1Quant/src/ms1quant/ms1quant.params
similarity index 100%
rename from DIA-Umpire/src/MS1Quant/ms1quant.params
rename to MS1Quant/src/ms1quant/ms1quant.params