Merge branch 'jims/bug/JAL-4298_java_console_causing_hang_at_startup' into develop

[jalview.git] / src / jalview / analysis / Grouping.java

diff --git a/src/jalview/analysis/Grouping.java b/src/jalview/analysis/Grouping.java
index 2ddd015..def5d5a 100644 (file)
--- a/src/jalview/analysis/Grouping.java
+++ b/src/jalview/analysis/Grouping.java
@@ -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;
     }
@@ -178,8 +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;
     }
@@ -269,7 +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
@@ -280,7 +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