@Override
public void activateActions() {
getChooser().setFileSelectionMode(JFileChooser.FILES_ONLY);
final File f = getFile(showOpenDialog());
if (f != null) {
final SpinningDialWaitIndicator indicator =
new SpinningDialWaitIndicator(MainView.getInstance());
indicator.setText("importing genes and proteins from " + f.getName());
Thread t =
new Thread(
new Runnable() {
@Override
public void run() {
load(indicator, f);
}
});
t.setName("ENA-XML-IMPORT");
t.start();
}
}
private void load(final SpinningDialWaitIndicator indicator, File f) {
try {
ENAXMLReader reader =
new ENAXMLReader(DefaultEntityFactory.getInstance(), new FileInputStream(f));
List<GeneProduct> products = reader.getProducts();
ReconstructionManager manager = DefaultReconstructionManager.getInstance();
Reconstruction recon = manager.active();
for (GeneProduct p : products) {
recon.addProduct(p);
}
// bit of a hack for now - add a single chromosome
Chromosome c =
recon.genome().createChromosome(1, new ChromosomeSequence(reader.getGenomeString()));
List<Gene> genes = reader.getGeneMap();
for (Gene gene : genes) {
c.add(gene);
}
for (Map.Entry<Gene, GeneProduct> e : reader.associations()) {
recon.associate(e.getKey(), e.getValue());
}
for (String warning : reader.getWarnings()) {
MainView.getInstance().addWarningMessage(warning);
}
} catch (FileNotFoundException ex) {
MainView.getInstance()
.getMessageManager()
.addReport(new ErrorMessage("File not found " + ex.getMessage()));
} catch (XMLStreamException ex) {
MainView.getInstance().getMessageManager().addReport(new ErrorMessage(ex.getMessage()));
} finally {
SwingUtilities.invokeLater(
new Runnable() {
@Override
public void run() {
MainView.getInstance().update();
}
});
indicator.dispose();
}
}