From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 22 Dec 2005 15:59:21 +0000 (+0000)
Subject: Watch for trim left/right null widths
X-Git-Tag: Root_VamJalview_2_07b+~226
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0fc00d51cd14f722f147ddc451ec157131ce9a3a;p=jalview.git

Watch for trim left/right null widths
---

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 338294b..f0aeed9 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -205,13 +205,23 @@ public class Alignment implements AlignmentI
      */
     public void trimLeft(int i)
     {
-        for (int j = 0; j < getHeight(); j++)
+        int j, jSize = getHeight();
+        for (j = 0; j < jSize; j++)
         {
             SequenceI s = getSequenceAt(j);
             int newstart = s.findPosition(i);
 
-            s.setStart(newstart);
-            s.setSequence(s.getSequence().substring(i));
+            if(i>s.getLength())
+            {
+              sequences.removeElement(s);
+              j--;
+              jSize--;
+            }
+            else
+            {
+              s.setStart(newstart);
+              s.setSequence(s.getSequence().substring(i));
+            }
         }
     }
 
@@ -228,7 +238,8 @@ public class Alignment implements AlignmentI
             int newend = s.findPosition(i);
 
             s.setEnd(newend);
-            s.setSequence(s.getSequence().substring(0, i + 1));
+            if(s.getLength()>i)
+              s.setSequence(s.getSequence().substring(0, i + 1));
         }
     }