X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FClustalFile.java;h=90c22f98b43f4211b87d80322f851e3f4268569b;hb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;hp=e72e0df32df2db9c21a6f78fbb39d2d7e2f199a3;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index e72e0df..90c22f9 100755
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -32,11 +32,6 @@ public class ClustalFile
   {
   }
 
-  public ClustalFile(String inStr)
-  {
-    super(inStr);
-  }
-
   public ClustalFile(String inFile, String type)
       throws IOException
   {
@@ -48,7 +43,7 @@ public class ClustalFile
     super.initData();
   }
 
-  public void parse()
+  public void parse() throws IOException
   {
     int i = 0;
     boolean flag = false;
@@ -161,9 +156,9 @@ public class ClustalFile
     {
       String tmp = printId(s[i]);
 
-      if (s[i].getSequence().length() > max)
+      if (s[i].getSequence().length > max)
       {
-        max = s[i].getSequence().length();
+        max = s[i].getSequence().length;
       }
 
       if (tmp.length() > maxid)
@@ -195,16 +190,16 @@ public class ClustalFile
         int start = i * len;
         int end = start + len;
 
-        if ( (end < s[j].getSequence().length()) &&
-            (start < s[j].getSequence().length()))
+        if ( (end < s[j].getSequence().length) &&
+            (start < s[j].getSequence().length))
         {
-          out.append(s[j].getSequence().substring(start, end));
+          out.append(s[j].getSequenceAsString(start, end));
         }
         else
         {
-          if (start < s[j].getSequence().length())
+          if (start < s[j].getSequence().length)
           {
-            out.append(s[j].getSequence().substring(start));
+            out.append(s[j].getSequenceAsString().substring(start));
           }
         }