Checks on features displayed

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

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index 0ee41b8..92d5414 100755 (executable)
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.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
@@ -44,15 +44,6 @@ public class JPredFile extends AlignFile
     Hashtable Symscores; // indexes of symbol annotation properties in sequenceI vector\r
     private int QuerySeqPosition;\r
 \r
-    /**\r
-     * Creates a new JPredFile object.\r
-     *\r
-     * @param inStr DOCUMENT ME!\r
-     */\r
-    public JPredFile(String inStr)\r
-    {\r
-        super(inStr);\r
-    }\r
 \r
     /**\r
      * Creates a new JPredFile object.\r
@@ -197,8 +188,8 @@ public class JPredFile extends AlignFile
 \r
                     for (int j = 0; j < i; j++)\r
                     {\r
-                        scores.set(j,\r
-                            (Object) ((Float) scores.get(j)).toString());\r
+                        scores.setElementAt(\r
+                            (Object) ((Float) scores.elementAt(j)).toString(), j);\r
                     }\r
 \r
                     scores.addElement((Object) ascore);\r
@@ -220,7 +211,7 @@ public class JPredFile extends AlignFile
 \r
                 for (int i = 0; i < numSymbols; i++)\r
                 {\r
-                    conf.set(i, (Object) symbols.nextToken());\r
+                    conf.setElementAt( symbols.nextToken(), i);\r
                 }\r
             }\r
             else\r
@@ -351,19 +342,19 @@ public class JPredFile extends AlignFile
     int i=0;\r
     int j=seqs.size();\r
     for (; i<QuerySeqPosition; i++)\r
-        annotSeqs.add(seqs.get(i));\r
+        annotSeqs.addElement(seqs.elementAt(i));\r
       // check that no stray annotations have been added at the end.\r
       {\r
-        SequenceI sq = (SequenceI) seqs.get(j-1);\r
+        SequenceI sq = (SequenceI) seqs.elementAt(j-1);\r
         if (sq.getName().toUpperCase().startsWith("JPRED")) {\r
-          annotSeqs.add(sq);\r
-          seqs.remove(--j);\r
+          annotSeqs.addElement(sq);\r
+          seqs.removeElementAt(--j);\r
         }\r
       }\r
     for (; i<j; i++)\r
-        newseqs.add(seqs.get(i));\r
+        newseqs.addElement(seqs.elementAt(i));\r
 \r
-    seqs.clear();\r
+    seqs.removeAllElements();\r
     seqs = newseqs;\r
   }\r
 }\r