X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FGrouping.java;h=def5d5a3cbdd8a9a837ad85344ff4b6c0a0fb6f4;hb=5784154b972346e9a3718654d7f875da49b3c167;hp=b01c815db332ac6eb2061af7e9edc2460e4977b9;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git

diff --git a/src/jalview/analysis/Grouping.java b/src/jalview/analysis/Grouping.java
index b01c815..def5d5a 100644
--- a/src/jalview/analysis/Grouping.java
+++ b/src/jalview/analysis/Grouping.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -91,8 +91,8 @@ public class Grouping
     i = 0;
     for (String key : gps.keySet())
     {
-      SequenceGroup group = new SequenceGroup(gps.get(key), "Subseq: "
-              + key, null, true, true, false, 0, width - 1);
+      SequenceGroup group = new SequenceGroup(gps.get(key),
+              "Subseq: " + key, null, true, true, false, 0, width - 1);
 
       groups[i++] = group;
     }
@@ -127,6 +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;
@@ -134,7 +139,7 @@ public class Grouping
     {
       spos[i++] = pos.intValue();
     }
-    ;
+
     for (i = 0; i < sequences.length; i++)
     {
       int slen = sequences[i].getLength();
@@ -173,8 +178,8 @@ public class Grouping
     i = 0;
     for (String key : gps.keySet())
     {
-      SequenceGroup group = new SequenceGroup(gps.get(key), "Subseq: "
-              + key, null, true, true, false, 0, width - 1);
+      SequenceGroup group = new SequenceGroup(gps.get(key),
+              "Subseq: " + key, null, true, true, false, 0, width - 1);
 
       groups[i++] = group;
     }
@@ -264,7 +269,7 @@ public class Grouping
      * seqs.length) { for (int i = 0; i < seqs.length; i++) { if (!hasScore[i])
      * { scores[i] = (max + i); } else { int nf=(feats[i]==null) ? 0
      * :((SequenceFeature[]) feats[i]).length;
-     * System.err.println("Sorting on Score: seq "+seqs[i].getName()+
+     * jalview.bin.Console.errPrintln("Sorting on Score: seq "+seqs[i].getName()+
      * " Feats: "+nf+" Score : "+scores[i]); } } }
      * 
      * jalview.util.QuickSort.sort(scores, seqs); } else if
@@ -275,7 +280,7 @@ public class Grouping
      * (int i=0;i<seqs.length; i++) { double nf; scores[i] =
      * (0.05+fr*i)+(nf=((feats[i]==null) ? 0.0 :1.0*((SequenceFeature[])
      * feats[i]).length));
-     * System.err.println("Sorting on Density: seq "+seqs[i].getName()+
+     * jalview.bin.Console.errPrintln("Sorting on Density: seq "+seqs[i].getName()+
      * " Feats: "+nf+" Score : "+scores[i]); }
      * jalview.util.QuickSort.sort(scores, seqs); } else { if
      * (method==FEATURE_LABEL) { throw new Error("Not yet implemented."); } } if