X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJPredFile.java;h=0734ccd1de228f665d2c95e6d78baf7004caf9f4;hb=ce63216585308bf40dd3f8370c3af13e098a7a3b;hp=0ee41b8c64a811653ecc74a395b3458ede94aedf;hpb=a853fae4d9d4dbc80e877741c017fca7ee80c59e;p=jalview.git

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index 0ee41b8..0734ccd 100755
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -197,8 +197,8 @@ 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 +220,7 @@ 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 +351,19 @@ 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;
   }
 }