X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=28c62831ab6e3d78e21cc543115a2e1dd565a815;hb=bd37829796d6d9f9b8340967eea49eb0d98f70a7;hp=15727ef31efa3ea88f74bc25ca3466abcfb85074;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 15727ef..28c6283 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.
@@ -501,12 +501,25 @@ 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();
     int maxid = s1.getName().length();
     if (s2.getName().length() > maxid)
     {
       maxid = s2.getName().length();
     }
-
+    if (maxid > 30)
+    {
+      maxid = 30;
+      // JAL-527 - truncate the sequence ids
+      if (s1.getName().length() > maxid)
+      {
+        s1id = s1.getName().substring(0, 30);
+      }
+      if (s2.getName().length() > maxid)
+      {
+        s2id = s2.getName().substring(0, 30);
+      }
+    }
     int len = 72 - maxid - 1;
     int nochunks = ((aseq1.length - count) / len) + 1;
     pid = 0;
@@ -525,8 +538,7 @@ public class AlignSeq
     for (int j = 0; j < nochunks; j++)
     {
       // Print the first aligned sequence
-      output.append(new Format("%" + (maxid) + "s").form(s1.getName())
-              + " ");
+      output.append(new Format("%" + (maxid) + "s").form(s1id) + " ");
 
       for (int i = 0; i < len; i++)
       {
@@ -572,8 +584,7 @@ public class AlignSeq
 
       // Now print the second aligned sequence
       output = output.append("\n");
-      output = output.append(new Format("%" + (maxid) + "s").form(s2
-              .getName())
+      output = output.append(new Format("%" + (maxid) + "s").form(s2id)
               + " ");
 
       for (int i = 0; i < len; i++)