args.add("-A");
args.add(getFilePath(hitsAlignmentFile, true));
- boolean dbFound = false;
- String dbPath = "";
File databaseFile = null;
boolean useEvalueCutoff = false;
}
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;
}
}
}
deleteHmmSequences(copy);
- sequencesHash = stashSequences(copy.getSequencesArray());
+ if (searchAlignment)
+ {
+ sequencesHash = stashSequences(copy.getSequencesArray());
+ }
exportStockholm(copy.getSequencesArray(), databaseFile, null);
}