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 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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 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Must set javac.includes + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + No tests executed. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Must set JVM to use for profiling in profiler.info.jvm + Must set profiler agent JVM arguments in profiler.info.jvmargs.agent + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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_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 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+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 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${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}:\ + ${file.reference.jfreechart-1.0.14.jar}:\ 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${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 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Must set javac.includes + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + No tests executed. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Must set JVM to use for profiling in profiler.info.jvm + Must set profiler agent JVM arguments in profiler.info.jvmargs.agent + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 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+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 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Must set javac.includes + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + No tests executed. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Must set JVM to use for profiling in profiler.info.jvm + Must set profiler agent JVM arguments in profiler.info.jvmargs.agent + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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_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= +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 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${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}:\ + ${file.reference.guava-17.0.jar}:\ + 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${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_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 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Must set javac.includes + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + No tests executed. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Must set JVM to use for profiling in profiler.info.jvm + Must set profiler agent JVM arguments in profiler.info.jvmargs.agent + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 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${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