From 7ce577333808c104a6ea08e024372269bce3eef0 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 12 May 2010 08:46:30 +0000
Subject: [PATCH] fix for JAL-527

---
 src/jalview/analysis/AlignSeq.java |   19 +++++++++++++++----
 1 file changed, 15 insertions(+), 4 deletions(-)

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 15727ef..bf66f30 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -501,12 +501,24 @@ 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;
@@ -525,7 +537,7 @@ 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++)
-- 
1.7.10.2