@Override
public void handleEvent(FormatEvent event) {
switch (event.getType()) {
case PROGRESS:
progressBar.setValue((int) (event.getProgress() * 100.0));
if (event.getSubTask() != null) {
statusLabel.setText(event.getSubTask());
}
break;
case COMPLETED:
setVisible(false);
if (GenomeController.getInstance().isGenomeLoaded()) {
if (formatter instanceof BAMToCoverage) {
// For coverage tracks, we report success, but don't offer to open the track.
DialogUtils.displayMessage(
"Format Successful",
String.format(
"<HTML>Format successful.<BR>Coverage will be available the next time you open <i>%s</i>.</HTML>",
formatter.getInputFile().getName()));
} else {
if (toLoadTrack
|| DialogUtils.askYesNo("Format Successful", "Format successful. Open track now?")
== DialogUtils.YES) {
try {
FrameController.getInstance()
.addTrackFromPath(formatter.getOutputFile().getAbsolutePath(), null, null);
} catch (Exception ex) {
}
}
}
} else {
DialogUtils.displayMessage(
"Format Successful",
"<HTML>Format successful. <BR>A genome must be loaded before you can open this track.</HTML>");
}
break;
case FAILED:
setVisible(false);
SavantFileFormatter.reportFormattingError(event.getError(), formatter.getInputFile());
break;
}
}
/**
* Add a listener to monitor changes in the reference genome.
*
* @param l the listener to be added
*/
public static void addGenomeChangedListener(Listener<GenomeChangedEvent> l) {
genomeController.addListener(l);
}
/**
* Set the current genome.
*
* @param genome the genome to set
*/
public static void setGenome(GenomeAdapter genome) {
genomeController.setGenome((Genome) genome);
}
/**
* Get the loaded genome.
*
* @return the loaded genome
*/
public static GenomeAdapter getGenome() {
return genomeController.getGenome();
}
/**
* Tell whether Savant has loaded a genome yet.
*
* @return true if a genome is loaded
*/
public static boolean isGenomeLoaded() {
return genomeController.isGenomeLoaded();
}
/**
* Utility methods for dealing with Savant genomes.
*
* @author tarkvara
*/
public class GenomeUtils {
private static GenomeController genomeController = GenomeController.getInstance();
/**
* Tell whether Savant has loaded a genome yet.
*
* @return true if a genome is loaded
*/
public static boolean isGenomeLoaded() {
return genomeController.isGenomeLoaded();
}
/**
* Get the loaded genome.
*
* @return the loaded genome
*/
public static GenomeAdapter getGenome() {
return genomeController.getGenome();
}
/**
* Set the current genome.
*
* @param genome the genome to set
*/
public static void setGenome(GenomeAdapter genome) {
genomeController.setGenome((Genome) genome);
}
/** Create a placeholder genome with the given name and length. */
public static GenomeAdapter createGenome(String name, int length) {
return new Genome(name, length);
}
/**
* Create a new genome from the given track full of sequence data.
*
* @param seqTrack a track containing sequence information
* @return a genome object for the given sequence
*/
public static GenomeAdapter createGenome(TrackAdapter seqTrack) {
return Genome.createFromTrack((Track) seqTrack);
}
/**
* Create a new genome from the given file full of sequence data.
*
* @param f a file containing sequence information
* @return a genome object for the given sequence
*/
public static GenomeAdapter createGenome(File f) throws Throwable {
return createGenome(TrackUtils.createTrack(f)[0]);
}
/**
* Add a listener to monitor changes in the reference genome.
*
* @param l the listener to be added
*/
public static void addGenomeChangedListener(Listener<GenomeChangedEvent> l) {
genomeController.addListener(l);
}
/**
* Remove a genome change listener.
*
* @param l the listener to be removed
*/
public static void removeGenomeChangedListener(Listener<GenomeChangedEvent> l) {
genomeController.removeListener(l);
}
}
/**
* Remove a genome change listener.
*
* @param l the listener to be removed
*/
public static void removeGenomeChangedListener(Listener<GenomeChangedEvent> l) {
genomeController.removeListener(l);
}