From 262c43178b46da173a54111671bc2979a3469f0b Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 31 Jan 2007 14:47:35 +0000
Subject: [PATCH] make new dataset seq if residues deleted

---
 src/jalview/datamodel/Sequence.java |   23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 02fc543..a0a858a 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -20,6 +20,7 @@ package jalview.datamodel;
 
 
 import java.util.*;
+import jalview.analysis.AlignSeq;
 
 
 /**
@@ -568,9 +569,31 @@ public class Sequence implements SequenceI
       System.arraycopy(sequence,j,tmp,i,sequence.length-j);
     }
 
+    if (this.datasetSequence != null)
+    {
+      for (int s = i; s < j; s++)
+      {
+        if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
+        {
+
+          Sequence ds = new Sequence(name,
+                                     AlignSeq.extractGaps(
+                                         jalview.util.Comparison.GapChars,
+                                         this.getSequenceAsString()
+                                     ),
+                                     start,
+                                     end);
+          ds.setDescription(description);
+        }
+        break;
+      }
+    }
+
     sequence = tmp;
+
   }
 
+
   /**
    * DOCUMENT ME!
    *
-- 
1.7.10.2