X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=34392487f7e101c6a1e75e9d9ae6a00994b53eb6;hb=f27f81a74bbe1be141d23df8aba578515e3179a2;hp=dec4fa433dac9c8d4562233b568650944049b414;hpb=25aaaa87042b3f507ad4348120df7dd073182759;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index dec4fa4..3439248 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 2.8.2b1)
- * Copyright (C) 2014 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.
  * 
@@ -20,11 +20,6 @@
  */
 package jalview.datamodel;
 
-import jalview.analysis.AAFrequency;
-import jalview.analysis.Conservation;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ResidueProperties;
-
 import java.awt.Color;
 import java.util.ArrayList;
 import java.util.Hashtable;
@@ -32,6 +27,11 @@ import java.util.List;
 import java.util.Map;
 import java.util.Vector;
 
+import jalview.analysis.AAFrequency;
+import jalview.analysis.Conservation;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
+
 /**
  * Collects a set contiguous ranges on a set of sequences
  * 
@@ -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;
@@ -1295,6 +1297,9 @@ public class SequenceGroup implements AnnotatedCollectionI
     return false;
   }
 
+  /**
+   * Remove all sequences from the group (leaving other properties unchanged).
+   */
   public void clear()
   {
     synchronized (sequences)