X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FClustalFile.java;h=5d7be8c52a9ba25275a8559fec5799b099cb6b4b;hb=7000ea3223f2f6a390f56341ba26850d2a137ae0;hp=e72e0df32df2db9c21a6f78fbb39d2d7e2f199a3;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index e72e0df..5d7be8c 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) 2007 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
   {
@@ -49,6 +44,7 @@ public class ClustalFile
   }
 
   public void parse()
+      throws IOException
   {
     int i = 0;
     boolean flag = false;
@@ -102,7 +98,9 @@ public class ClustalFile
             }
           }
           else
+          {
             flag = true;
+          }
         }
       }
     }
@@ -129,7 +127,8 @@ public class ClustalFile
           }
 
           Sequence newSeq = parseId(headers.elementAt(i).toString());
-          newSeq.setSequence( seqhash.get(headers.elementAt(i).toString()).toString() );
+          newSeq.setSequence(seqhash.get(headers.elementAt(i).toString()).
+                             toString());
 
           seqs.addElement(newSeq);
         }
@@ -161,9 +160,9 @@ 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)
@@ -190,21 +189,21 @@ public class ClustalFile
 
       while ( (j < s.length) && (s[j] != null))
       {
-        out.append(new Format("%-" + maxid + "s").form( printId(s[j]) + " "));
+        out.append(new Format("%-" + maxid + "s").form(printId(s[j]) + " "));
 
         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));
           }
         }