removed Iterator usage.

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

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index 2ea1d2f..5d7be8c 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) 2007 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 +43,8 @@ public class ClustalFile
     super.initData();\r
   }\r
 \r
-  public void parse() throws IOException\r
+  public void parse()\r
+      throws IOException\r
   {\r
     int i = 0;\r
     boolean flag = false;\r
@@ -102,7 +98,9 @@ public class ClustalFile
             }\r
           }\r
           else\r
+          {\r
             flag = true;\r
+          }\r
         }\r
       }\r
     }\r
@@ -129,15 +127,8 @@ public class ClustalFile
           }\r
 \r
           Sequence newSeq = parseId(headers.elementAt(i).toString());\r
-          newSeq.setSequence( seqhash.get(headers.elementAt(i).toString()).toString() );\r
-\r
-          if (!isValidProteinSequence(newSeq.getSequence()))\r
-          {\r
-              throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS\r
-                                    + " : " + newSeq.getName()\r
-                                    + " : " + invalidCharacter);\r
-          }\r
-\r
+          newSeq.setSequence(seqhash.get(headers.elementAt(i).toString()).\r
+                             toString());\r
 \r
           seqs.addElement(newSeq);\r
         }\r
@@ -169,9 +160,9 @@ 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
@@ -198,21 +189,21 @@ public class ClustalFile
 \r
       while ( (j < s.length) && (s[j] != null))\r
       {\r
-        out.append(new Format("%-" + maxid + "s").form( printId(s[j]) + " "));\r
+        out.append(new Format("%-" + maxid + "s").form(printId(s[j]) + " "));\r
 \r
         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