// MesquiteProject project = MesquiteTrunk.mesquiteTrunk.openFile(
// pFile.getAbsolutePath(),
// CommandRecord.scriptingRecord);
// for Mesquite 2.01
MesquiteProject project = MesquiteTrunk.mesquiteTrunk.openFile(pFile.getAbsolutePath());
if (project == null) {
LOGGER.warn("Mesquite failed to parse the file " + pFile.getAbsolutePath() + "; skipping it");
return;
}
if (LOGGER.isInfoEnabled()) {
LOGGER.info("MesquiteCOnverter: MesquiteProject project=" + project); //$NON-NLS-1$
}
// taxon first:
ListableVector taxas = project.getTaxas();
Taxa t = null;
for (int i = 0; i < taxas.size(); i++) {
// One Taxa represents one TAXA block in a Nexus file.
t = (Taxa) taxas.elementAt(i);