X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=a27c51bc71763c716df8a84769c682630227b6c7;hb=d83c0095dae033f5b4b7c81eb1493083b5cbe346;hp=bf66f30e02b2d59781cb6df06fdb722c155cd51e;hpb=34f1207ac30761e3aac6ede40075446f7fec9900;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index bf66f30..a27c51b 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -143,7 +143,7 @@ public class AlignSeq
   public AlignSeq(SequenceI s1, String string1, SequenceI s2,
           String string2, String type)
   {
-    SeqInit(s1, string1, s2, string2, type);
+    SeqInit(s1, string1.toUpperCase(), s2, string2.toUpperCase(), type);
   }
 
   /**
@@ -501,22 +501,23 @@ public class AlignSeq
     // TODO: Use original sequence characters rather than re-translated
     // characters in output
     // Find the biggest id length for formatting purposes
-    String s1id=s1.getName(),s2id=s2.getName();
+    String s1id = s1.getName(), s2id = s2.getName();
     int maxid = s1.getName().length();
     if (s2.getName().length() > maxid)
     {
       maxid = s2.getName().length();
     }
-    if (maxid>30) {
+    if (maxid > 30)
+    {
       maxid = 30;
       // JAL-527 - truncate the sequence ids
-      if (s1.getName().length()>maxid)
+      if (s1.getName().length() > maxid)
       {
-        s1id = s1.getName().substring(0,30);
+        s1id = s1.getName().substring(0, 30);
       }
-      if (s2.getName().length()>maxid)
+      if (s2.getName().length() > maxid)
       {
-        s2id = s2.getName().substring(0,30);
+        s2id = s2.getName().substring(0, 30);
       }
     }
     int len = 72 - maxid - 1;
@@ -537,8 +538,7 @@ public class AlignSeq
     for (int j = 0; j < nochunks; j++)
     {
       // Print the first aligned sequence
-      output.append(new Format("%" + (maxid) + "s").form(s1id)
-              + " ");
+      output.append(new Format("%" + (maxid) + "s").form(s1id) + " ");
 
       for (int i = 0; i < len; i++)
       {