@Override
public void init_createInput() {
// int alignment_id=properties.getInputID("alignment");
int alignment_id = properties.getInputID("alignment");
alignment = new Alignment(alignment_id);
alignment.outputFastaWithSequenceID(infile);
// --Remove dir if found
if (Util.DirExists("infile-1")) {
Util.deleteDir("infile-1");
}
}
@Override
public void post_parseOutput() {
if (properties.getBoolean("AlignmentInfo")) {
Results results = new Results(outfile);
results.setName(
"BAli-phy results for " + alignment.getName() + " at " + Util.returnCurrentDateAndTime());
results.setNote("Created at " + Util.returnCurrentDateAndTime());
results.saveToDatabase();
properties.put("output_results_id", results.getId());
}
Util.deleteFile(infile);
Util.deleteFile(outfile);
}