From 555416956c6668d4f49d0cbf5a1e784e20636afa Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 31 Oct 2005 15:53:08 +0000
Subject: [PATCH] equalsIgnoreCase CLUSTAL

---
 src/jalview/io/ClustalFile.java |   14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index 981e3c9..e72e0df 100755
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -55,8 +55,9 @@ public class ClustalFile
 
     Vector headers = new Vector();
     Hashtable seqhash = new Hashtable();
-
-    String line;
+    StringBuffer tempseq;
+    String line, id;
+    StringTokenizer str;
 
     try
     {
@@ -64,14 +65,13 @@ public class ClustalFile
       {
         if (line.indexOf(" ") != 0)
         {
-          StringTokenizer str = new StringTokenizer(line, " ");
-          String id = "";
+          str = new StringTokenizer(line, " ");
 
           if (str.hasMoreTokens())
           {
             id = str.nextToken();
 
-            if (id.equals("CLUSTAL"))
+            if (id.equalsIgnoreCase("CLUSTAL"))
             {
               flag = true;
             }
@@ -79,8 +79,6 @@ public class ClustalFile
             {
               if (flag)
               {
-                StringBuffer tempseq;
-
                 if (seqhash.containsKey(id))
                 {
                   tempseq = (StringBuffer) seqhash.get(id);
@@ -103,6 +101,8 @@ public class ClustalFile
               }
             }
           }
+          else
+            flag = true;
         }
       }
     }
-- 
1.7.10.2