From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 4 Apr 2006 09:37:12 +0000 (+0000)
Subject: Pad gaps removes excess gaps
X-Git-Tag: Release_2_08~76
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=50be9a6af05e540b996aa6de433fd0edfe9155d5;p=jalview.git

Pad gaps removes excess gaps
---

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 00d1be8..b0b04ca 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -810,18 +810,41 @@ public class Alignment implements AlignmentI
 
     public boolean padGaps() {
       boolean modified=false;
-      int Width = getWidth();
+
+      //Remove excess gaps from the end of alignment
+      int maxLength = -1;
+
       SequenceI current;
+      for (int i = 0; i < sequences.size(); i++)
+      {
+        current = getSequenceAt(i);
+        for (int j = current.getLength(); j > maxLength; j--)
+        {
+          if (j > maxLength && !jalview.util.Comparison.isGap(
+              current.getCharAt(j)))
+          {
+            maxLength = j;
+            break;
+          }
+        }
+      }
+
+      maxLength++;
+
       for (int i = 0; i < sequences.size();
            i++)
       {
         current = getSequenceAt(i);
 
-        if (current.getLength() < Width)
+        if (current.getLength() < maxLength)
         {
-          current.insertCharAt(Width - 1, gapCharacter);
+          current.insertCharAt(maxLength - 1, gapCharacter);
           modified=true;
         }
+        else if(current.getLength() > maxLength)
+        {
+          current.deleteChars(maxLength, current.getLength());
+        }
       }
       return modified;
     }