From 02a310e8406f7cfbb5cf7a6d56b0bcec43761b08 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 31 Oct 2005 15:52:49 +0000
Subject: [PATCH] Catch numberformatexceptions

---
 src/jalview/io/AlignFile.java |   27 +++++++++++++++++----------
 1 file changed, 17 insertions(+), 10 deletions(-)

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 3a05402..5b94eb8 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -199,20 +199,27 @@ public abstract class AlignFile extends FileParse
       if (id.indexOf("/") > 0)
       {
         st = new StringTokenizer(id, "/");
+        String limits=null;
+        try{
+          if (st.countTokens() == 2)
+          {
+            id = st.nextToken();
 
-        if (st.countTokens() == 2)
-        {
-          id = st.nextToken();
-
-          String tmp = st.nextToken();
+            limits = st.nextToken();
 
-          st = new StringTokenizer(tmp, "-");
+            st = new StringTokenizer(limits, "-");
 
-          if (st.countTokens() == 2)
-          {
-            seq.setStart( Integer.valueOf(st.nextToken()).intValue() );
-            seq.setEnd( Integer.valueOf(st.nextToken()).intValue() );
+            if (st.countTokens() == 2)
+            {
+              seq.setStart(Integer.valueOf(st.nextToken()).intValue());
+              seq.setEnd(Integer.valueOf(st.nextToken()).intValue());
+            }
           }
+        }catch(NumberFormatException ex)
+        {
+            // Problem parsing sequence limits. Just add it back to the
+          // Id so we dont lose this info
+          id += "/" + limits;
         }
       }
       seq.setName(id);
-- 
1.7.10.2