v1.4271

ignore "*" in protein sequence, it causes error in compomics sequence digestion
cctsou · Nov 12, 2015 · 2fb5f4c · 2fb5f4c
1 parent 83d7e5d
commit 2fb5f4c
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Showing 43 changed files with 53 additions and 1,436 deletions.
diff --git a/...rc/MSUmpire/SortedListLib/Alteration.java → ...ExtPackages/SortedListLib/Alteration.java b/...rc/MSUmpire/SortedListLib/Alteration.java → ...ExtPackages/SortedListLib/Alteration.java
@@ -1,4 +1,4 @@
-package MSUmpire.SortedListLib;
+package ExtPackages.SortedListLib;
 
 /**
  * Represents the alterations to the backingList of a {@code PatchWorkArray}.

diff --git a/...SUmpire/SortedListLib/AlterationList.java → ...ackages/SortedListLib/AlterationList.java b/...SUmpire/SortedListLib/AlterationList.java → ...ackages/SortedListLib/AlterationList.java
@@ -1,4 +1,4 @@
-package MSUmpire.SortedListLib;
+package ExtPackages.SortedListLib;
 
 import java.util.ConcurrentModificationException;
 import java.util.Iterator;

diff --git a/...MSUmpire/SortedListLib/ArrayLocation.java → ...Packages/SortedListLib/ArrayLocation.java b/...MSUmpire/SortedListLib/ArrayLocation.java → ...Packages/SortedListLib/ArrayLocation.java
@@ -1,4 +1,4 @@
-package MSUmpire.SortedListLib;
+package ExtPackages.SortedListLib;
 
 /**
  * Simple class to define a location within the a patch work array.

diff --git a/...pire/SortedListLib/NaturalSortedList.java → ...ages/SortedListLib/NaturalSortedList.java b/...pire/SortedListLib/NaturalSortedList.java → ...ages/SortedListLib/NaturalSortedList.java
@@ -1,4 +1,4 @@
-package MSUmpire.SortedListLib;
+package ExtPackages.SortedListLib;
 
 import java.util.Comparator;
 

diff --git a/...SUmpire/SortedListLib/PatchWorkArray.java → ...ackages/SortedListLib/PatchWorkArray.java b/...SUmpire/SortedListLib/PatchWorkArray.java → ...ackages/SortedListLib/PatchWorkArray.java
@@ -1,4 +1,4 @@
-package MSUmpire.SortedListLib;
+package ExtPackages.SortedListLib;
 
 import java.io.Serializable;
 import java.util.*;

diff --git a/...rc/MSUmpire/SortedListLib/SortedList.java → ...ExtPackages/SortedListLib/SortedList.java b/...rc/MSUmpire/SortedListLib/SortedList.java → ...ExtPackages/SortedListLib/SortedList.java
@@ -1,4 +1,4 @@
-package MSUmpire.SortedListLib;
+package ExtPackages.SortedListLib;
 
 import java.io.Serializable;
 import java.lang.reflect.Array;

diff --git a/.../MSUmpire/SortedListLib/UnsortedList.java → ...tPackages/SortedListLib/UnsortedList.java b/.../MSUmpire/SortedListLib/UnsortedList.java → ...tPackages/SortedListLib/UnsortedList.java
@@ -1,4 +1,4 @@
-package MSUmpire.SortedListLib;
+package ExtPackages.SortedListLib;
 
 import java.util.*;
 

diff --git a/DIA-Umpire/src/MSUmpire/BaseDataStructure/MapFloatComparator.java b/DIA-Umpire/src/MSUmpire/BaseDataStructure/MapFloatComparator.java
diff --git a/DIA-Umpire/src/MSUmpire/BaseDataStructure/SortedListFloat.java b/DIA-Umpire/src/MSUmpire/BaseDataStructure/SortedListFloat.java
@@ -22,7 +22,7 @@
  * 
  */
 
-import MSUmpire.SortedListLib.SortedList;
+import ExtPackages.SortedListLib.SortedList;
 import java.io.Serializable;
 import java.util.Comparator;
 

diff --git a/DIA-Umpire/src/MSUmpire/BaseDataStructure/SortedListInteger.java b/DIA-Umpire/src/MSUmpire/BaseDataStructure/SortedListInteger.java
diff --git a/DIA-Umpire/src/MSUmpire/BaseDataStructure/SortedXYCollectionClass.java b/DIA-Umpire/src/MSUmpire/BaseDataStructure/SortedXYCollectionClass.java
@@ -22,7 +22,7 @@
  * 
  */
 
-import MSUmpire.SortedListLib.SortedList;
+import ExtPackages.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
@@ -19,7 +19,7 @@
  */
 package MSUmpire.BaseDataStructure;
 
-import MSUmpire.SortedListLib.SortedList;
+import ExtPackages.SortedListLib.SortedList;
 import java.io.Serializable;
 import java.util.Comparator;
 

diff --git a/DIA-Umpire/src/MSUmpire/BaseDataStructure/UmpireInfo.java b/DIA-Umpire/src/MSUmpire/BaseDataStructure/UmpireInfo.java
@@ -26,7 +26,7 @@
 public class UmpireInfo {
 
     private static UmpireInfo umpireInfo = null;
-    public String Version = "v1.427";
+    public String Version = "v2.0";
 
     private UmpireInfo() {
 

diff --git a/DIA-Umpire/src/MSUmpire/BaseDataStructure/XYComparator.java b/DIA-Umpire/src/MSUmpire/BaseDataStructure/XYComparator.java
diff --git a/DIA-Umpire/src/MSUmpire/DIA/DIA_ParseiProphet.java b/DIA-Umpire/src/MSUmpire/DIA/DIA_ParseiProphet.java
diff --git a/DIA-Umpire/src/MSUmpire/DIA/DIA_window_Quant.java b/DIA-Umpire/src/MSUmpire/DIA/DIA_window_Quant.java
@@ -62,14 +62,6 @@ public DIA_window_Quant(String Q1Name,String Q2Name,String Q3Name,HashMap<Intege
     }
     @Override
     public void run() {
-
-        //System.out.println("Assigning clusters for peak groups in MS2 isolation window:" + FilenameUtils.getBaseName(DIAWindow.ScanCollectionName));
-        //Restore serialization files for old projects
-        //DIAWindow.ReadPeakFromDB();
-        //DIAWindow.WritePeakClusterSerialization();
-        //DIAWindow.WritePrecursorFragmentGrouping();
-        ////////////////////////////////////
-        //Needed to reactivate
 
         if(!DIAWindow.ReadPeakCluster()){
             Logger.getRootLogger().error("Reading Peak cluster result for " + DIAWindow.ScanCollectionName + " failed");