From cf8e95cb72c90c73963816ca71856ba1ab7e1d99 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 9 Dec 2010 15:28:45 +0000
Subject: [PATCH] javadoc and additional convenience method for JAL-716

---
 src/jalview/datamodel/SequenceGroup.java |   26 ++++++++++++++++++++------
 1 file changed, 20 insertions(+), 6 deletions(-)

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index be40bce..f045555 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -627,10 +627,9 @@ public class SequenceGroup
   }
 
   /**
-   * DOCUMENT ME!
+   * Set the first column selected by this group. Runs from 0<=i<N_cols
    * 
    * @param i
-   *          DOCUMENT ME!
    */
   public void setStartRes(int i)
   {
@@ -638,10 +637,9 @@ public class SequenceGroup
   }
 
   /**
-   * DOCUMENT ME!
+   * Set the groups last selected column. Runs from 0<=i<N_cols
    * 
    * @param i
-   *          DOCUMENT ME!
    */
   public void setEndRes(int i)
   {
@@ -794,23 +792,39 @@ public class SequenceGroup
    */
   public SequenceI[] getSequencesInOrder(AlignmentI al)
   {
+    return getSequencesInOrder(al, true);
+  }
+  /**
+   * return an array representing the intersection of the group with al, optionally returning an array the size of al.getHeight() 
+   * where nulls mark the non-intersected sequences
+   * @param al
+   * @param trim
+   * @return null or array
+   */
+  public SequenceI[] getSequencesInOrder(AlignmentI al, boolean trim)
+  {
     int sSize = sequences.size();
     int alHeight = al.getHeight();
 
-    SequenceI[] seqs = new SequenceI[sSize];
+    SequenceI[] seqs = new SequenceI[(trim) ? sSize : alHeight];
 
     int index = 0;
     for (int i = 0; i < alHeight && index < sSize; i++)
     {
       if (sequences.contains(al.getSequenceAt(i)))
       {
-        seqs[index++] = al.getSequenceAt(i);
+        seqs[(trim) ? index : i] = al.getSequenceAt(i);
+        index++;
       }
     }
     if (index == 0)
     {
       return null;
     }
+    if (!trim)
+    {
+      return seqs;
+    }
     if (index < seqs.length)
     {
       SequenceI[] dummy = seqs;
-- 
1.7.10.2