tidied up system.out messages and moved many to stderr.

[jalview.git] / src / jalview / datamodel / Alignment.java

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 2355a20..d953598 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -14,7 +14,6 @@ public class Alignment implements AlignmentI
   protected Vector   superGroup = new Vector();\r
   protected char        gapCharacter = '-';\r
   public AlignmentAnnotation [] annotations;\r
-  public Conservation conservation;\r
 \r
   public boolean featuresAdded = false;\r
 \r
@@ -292,10 +291,10 @@ public class Alignment implements AlignmentI
       len = getHeight()/2;\r
     } else {\r
       len = (getHeight()+1)/2;\r
-      System.out.println("Sort len is odd = " + len);\r
+      System.out.println("DEBUG:Sort len is odd = " + len); // log.\r
     }\r
     for (int i = 0; i < len; i++) {\r
-      System.out.println("Swapping " + seqs[i].getName() + " and " + seqs[getHeight()-i-1].getName());\r
+      System.out.println("DEBUG:Swapping " + seqs[i].getName() + " and " + seqs[getHeight()-i-1].getName()); // log.\r
       SequenceI tmp = seqs[i];\r
       sequences.setElementAt(seqs[getHeight()-i-1],i);\r
       sequences.setElementAt(tmp,getHeight()-i-1);\r