formatting

[jalview.git] / src / jalview / io / ClustalFile.java

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