From 431c2f9d6cdc71c3c8308dada22121bb137376e9 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Mon, 23 May 2005 17:48:35 +0000
Subject: [PATCH] added getSequencesInOrder (part of refactor from AlignPanel
 menu action for cut'n'paste).

---
 src/jalview/datamodel/SequenceGroup.java |   40 +++++++++++++++++++++++++++++-
 1 file changed, 39 insertions(+), 1 deletion(-)

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 7aae434..22b9165 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -209,7 +209,9 @@ public class SequenceGroup
   public int getWidth()
   {
     // MC This needs to get reset when characters are inserted and deleted
-    for (int i = 0; i < sequences.size(); i++)
+    if (sequences.size()>0)
+      width = ((SequenceI) sequences.elementAt(0)).getLength();
+    for (int i = 1; i < sequences.size(); i++)
     {
       SequenceI seq = (SequenceI) sequences.elementAt(i);
       if (seq.getLength() > width)
@@ -227,4 +229,40 @@ public class SequenceGroup
   {
     return outlineColour;
   }
+  /**
+   *
+   * returns the sequences in the group ordered by the ordering given by al
+   *
+   * @param al Alignment
+   * @return SequenceI[]
+   */
+  public SequenceI[] getSequencesInOrder(Alignment al) {
+    int sz;
+    java.util.Hashtable orderedSeqs = new java.util.Hashtable();
+    SequenceI[] seqs=new SequenceI[sz=sequences.size()];
+    for(int i=0; i<sz; i++)
+    {
+      SequenceI seq = (SequenceI) sequences.get(i);
+      int index = al.findIndex(seq);
+      orderedSeqs.put(index+"", seq);
+    }
+
+    int index=0;
+    for(int i=0; i<sz; i++) {
+      SequenceI seq = null;
+      while (seq == null)
+      {
+        if (orderedSeqs.containsKey(index + ""))
+        {
+          seq = (SequenceI) orderedSeqs.get(index + "");
+          index++;
+          break;
+        }
+        else
+          index++;
+      }
+      seqs[index] = seq;
+    }
+    return seqs;
+  }
 }
-- 
1.7.10.2