From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 17 Aug 2016 11:22:19 +0000 (+0100)
Subject: JAL-2172 reverted to not sorting column selection
X-Git-Tag: Release_2_10_0~104
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=898cc82d963669a958a7666eb4bc63d90b9b9614;p=jalview.git

JAL-2172 reverted to not sorting column selection
---

diff --git a/src/jalview/analysis/Grouping.java b/src/jalview/analysis/Grouping.java
index ddf483b..2ddd015 100644
--- a/src/jalview/analysis/Grouping.java
+++ b/src/jalview/analysis/Grouping.java
@@ -25,7 +25,6 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -128,6 +127,11 @@ public class Grouping
         }
       }
     }
+
+    /*
+     * get selected columns (in the order they were selected);
+     * note this could include right-to-left ranges
+     */
     int[] spos = new int[cs.getSelected().size()];
     int width = -1;
     int i = 0;
@@ -136,11 +140,6 @@ public class Grouping
       spos[i++] = pos.intValue();
     }
 
-    /*
-     * ensure column selection is in ascending order
-     */
-    Arrays.sort(spos);
-
     for (i = 0; i < sequences.length; i++)
     {
       int slen = sequences[i].getLength();
diff --git a/test/jalview/analysis/GroupingTest.java b/test/jalview/analysis/GroupingTest.java
index 3afa6e5..df39b81 100644
--- a/test/jalview/analysis/GroupingTest.java
+++ b/test/jalview/analysis/GroupingTest.java
@@ -53,10 +53,15 @@ public class GroupingTest
   AlignmentI alignment = new Alignment(
           new SequenceI[] { s1, s2, s3, s4, s5 });
 
+  /*
+   * test for the case where column selections are not added in
+   * left to right order
+   */
+  int[] positions = new int[] { 7, 9, 1 };
+
   @Test(groups = { "Functional" })
   public void testMakeGroupsWithBoth()
   {
-    int[] positions = new int[] { 1, 7, 9 };
     String[] str = new String[alignment.getHeight()];
     int seq = 0;
     for (SequenceI s : alignment.getSequences())
@@ -72,11 +77,6 @@ public class GroupingTest
             alignment.getSequencesArray(), str,
             Arrays.asList(new SequenceGroup[] { sg_12, sg_345 }));
 
-    /*
-     * test for the case where column selections are not added in
-     * left to right order
-     */
-    positions = new int[] { 7, 9, 1 };
     ColumnSelection cs = new ColumnSelection();
     for (int p : positions)
     {