\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
{\r
for (int j = 0; j < width; j++)\r
{\r
- float value = Float.parseFloat(preds[i].getCharAt(\r
- j) + "");\r
+ float value = new Float(preds[i].getCharAt(\r
+ j) + "").floatValue();\r
annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(\r
j) + "", "", preds[i].getCharAt(j),\r
value);\r