/*\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
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
\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
\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
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