X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=7c8fea39fb9b2cb7cec6e0e7ac83e583fbc328e6;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=4727e5e6e733dc3ad9e22e898ce33a28076fd0bf;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 4727e5e..7c8fea3 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -76,8 +76,10 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   public ColourSchemeI cs;
 
+  // start column (base 0)
   int startRes = 0;
 
+  // end column (base 0)
   int endRes = 0;
 
   public Color outlineColour = Color.black;
@@ -611,13 +613,13 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     synchronized (sequences)
     {
-    if (sequences.contains(s))
-    {
-      deleteSequence(s, recalc);
-    }
-    else
-    {
-      addSequence(s, recalc);
+      if (sequences.contains(s))
+      {
+        deleteSequence(s, recalc);
+      }
+      else
+      {
+        addSequence(s, recalc);
       }
     }
   }
@@ -773,8 +775,9 @@ public class SequenceGroup implements AnnotatedCollectionI
     synchronized (sequences)
     {
       // MC This needs to get reset when characters are inserted and deleted
-      boolean first=true;
-      for (SequenceI seq:sequences) {
+      boolean first = true;
+      for (SequenceI seq : sequences)
+      {
         if (first || seq.getLength() > width)
         {
           width = seq.getLength();
@@ -1295,6 +1298,9 @@ public class SequenceGroup implements AnnotatedCollectionI
     return false;
   }
 
+  /**
+   * Remove all sequences from the group (leaving other properties unchanged).
+   */
   public void clear()
   {
     synchronized (sequences)