{
ascore = symbols.nextToken();
- Float score = new Float(ascore);
+ Float score = Float.valueOf(ascore);
scores.addElement(score);
}
for (int j = 0; j < i; j++)
{
- scores.setElementAt(
- ((Float) scores.elementAt(j)).toString(), j);
+ scores.setElementAt(((Float) scores.elementAt(j)).toString(),
+ j);
}
scores.addElement(ascore);
seq_entries.addElement(newseq.toString());
ids.addElement(id);
- Symscores.put(id, new Integer(ids.size() - 1));
+ Symscores.put(id, Integer.valueOf(ids.size() - 1));
}
}
}
{
// Add all sequence like objects
Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
- seq_entries.elementAt(i).toString(), 1, seq_entries
- .elementAt(i).toString().length());
+ seq_entries.elementAt(i).toString(), 1,
+ seq_entries.elementAt(i).toString().length());
if (maxLength != seq_entries.elementAt(i).toString().length())
{
- throw new IOException(
- MessageManager
- .formatMessage(
- "exception.jpredconcide_entry_has_unexpected_number_of_columns",
- new String[] { ids.elementAt(i).toString() }));
+ throw new IOException(MessageManager.formatMessage(
+ "exception.jpredconcide_entry_has_unexpected_number_of_columns",
+ new String[]
+ { ids.elementAt(i).toString() }));
}
- if ((newSeq.getName().startsWith("QUERY") || newSeq.getName()
- .startsWith("align;")) && (QuerySeqPosition == -1))
+ if ((newSeq.getName().startsWith("QUERY")
+ || newSeq.getName().startsWith("align;"))
+ && (QuerySeqPosition == -1))
{
QuerySeqPosition = seqs.size();
}
} catch (Exception e)
{
tal = null;
- IOException ex = new IOException(
- MessageManager
- .formatMessage(
- "exception.couldnt_parse_concise_annotation_for_prediction",
- new String[] { e.getMessage() }));
+ IOException ex = new IOException(MessageManager.formatMessage(
+ "exception.couldnt_parse_concise_annotation_for_prediction",
+ new String[]
+ { e.getMessage() }));
e.printStackTrace(); // java 1.1 does not have :
// ex.setStackTrace(e.getStackTrace());
throw ex;
* @return String
*/
@Override
- public String print()
+ public String print(SequenceI[] sqs, boolean jvsuffix)
{
return "Not Supported";
}