X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJPredFile.java;h=92d5414a6a7e4b6d82520e9c17d4cf955c713a8e;hb=d587f1aa61946dc14f6f089cf1dc2a3116cfb773;hp=0ee41b8c64a811653ecc74a395b3458ede94aedf;hpb=a853fae4d9d4dbc80e877741c017fca7ee80c59e;p=jalview.git

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