else if (MessageManager.getString(REPORTING_CUTOFF_KEY)
.equals(name))
{
- if (CUTOFF_EVALUE.equals(arg.getValue()))
+ if (MessageManager.getString(CUTOFF_EVALUE)
+ .equals(arg.getValue()))
{
useEvalueCutoff = true;
}
- else if (CUTOFF_SCORE.equals(arg.getValue()))
+ else if (MessageManager.getString(CUTOFF_SCORE)
+ .equals(arg.getValue()))
{
useScoreCutoff = true;
}
}
else if (MessageManager.getString(DATABASE_KEY).equals(name))
{
- dbFound = true;
- dbPath = arg.getValue();
- if (!MessageManager.getString(THIS_ALIGNMENT_KEY)
- .equals(dbPath))
+ databaseFile = new File(arg.getValue());
+ if (!arg.getValue().isEmpty())
{
- int pos = dbPath.lastIndexOf(File.separator);
- databaseName = dbPath.substring(pos + 1);
- databaseFile = new File(dbPath);
+ searchAlignment = false;
}
- searchAlignment = false;
}
else if (MessageManager.getString(RETURN_N_NEW_SEQ).equals(name))
{
AlignmentI copy = new Alignment(al);
deleteHmmSequences(copy);
- sequencesHash = stashSequences(copy.getSequencesArray());
+ if (searchAlignment)
+ {
+ sequencesHash = stashSequences(copy.getSequencesArray());
+ }
exportStockholm(copy.getSequencesArray(), databaseFile, null);