Examples of org.broad.igv.ui.util.ProgressMonitor

org.broad.igv.ui.util.ProgressMonitor
TODO This class probably shouldn't exist, bet we could use built-in progress monitors instead @author eflakes

        public void run() {


            final boolean runningBatch = igvArgs.getBatchFile() != null;
            BatchRunner.setIsBatchMode(runningBatch);


            final ProgressMonitor monitor = new ProgressMonitor();
            final ProgressBar.ProgressDialog progressDialog = ProgressBar.showProgressDialog(mainFrame, "Initializing...", monitor, false);
            progressDialog.getProgressBar().setIndeterminate(true);
            monitor.fireProgressChange(20);


            mainFrame.setIconImage(getIconImage());
            if (Globals.IS_MAC) {
                setAppleDockIcon();
            }


            final PreferenceManager preferenceManager = PreferenceManager.getInstance();


            try {
                contentPane.getCommandBar().initializeGenomeList(monitor);
            } catch (FileNotFoundException ex) {
                JOptionPane.showMessageDialog(mainFrame, "Error initializing genome list: " + ex.getMessage());
                log.error("Error initializing genome list: ", ex);
            } catch (NoRouteToHostException ex) {
                JOptionPane.showMessageDialog(mainFrame, "Network error initializing genome list: " + ex.getMessage());
                log.error("Network error initializing genome list: ", ex);
            } finally {
                monitor.fireProgressChange(50);
                closeWindow(progressDialog);
            }


            if (igvArgs.getGenomeId() != null) {
                IGV.getInstance().loadGenomeById(igvArgs.getGenomeId());

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                    // If we haven't changed genomes we're done.
                    if (genomeListItem.getId().equalsIgnoreCase(GenomeManager.getInstance().getGenomeId())) {
                        return;
                    }


                    final ProgressMonitor monitor = new ProgressMonitor();
                    final ProgressBar.ProgressDialog progressDialog = ProgressBar.showProgressDialog(IGV.getMainFrame(), "Loading Genome...", monitor, false);


                    try {
                        monitor.fireProgressChange(50);


                        Genome genome;


                        igv.resetSession(null);
                        genome = igv.getGenomeManager().loadGenome(genomeListItem.getLocation(), null);


                        updateChromosFromGenome(genome);
                        monitor.fireProgressChange(25);


                        genomeComboBox.setSelectedItem(genomeListItem);


                        monitor.fireProgressChange(25);


                        FrameManager.getDefaultFrame().setChromosomeName(genome.getHomeChromosome(), true);
                        IGV.getInstance().doRefresh();


                    } catch (GenomeServerException e) {

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        boolean showProgressDialog = dialogsParent != null;
        if (!showProgressDialog) {
            urlDownloader.run();
            return urlDownloader;
        } else {
            ProgressMonitor monitor = new ProgressMonitor();
            urlDownloader.setMonitor(monitor);
            ActionListener buttonListener = new ActionListener() {
                @Override
                public void actionPerformed(ActionEvent e) {
                    urlDownloader.cancel(true);

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        DownsampleOptions downsampleOptions = new DownsampleOptions();


        final AlignmentTrack.BisulfiteContext bisulfiteContext =
                renderOptions != null ? renderOptions.bisulfiteContext : null;


        ProgressMonitor monitor = null;
        //Show cancel button
        if (IGV.hasInstance() && !Globals.isBatch() && !Globals.isHeadless()) {
            ActionListener cancelListener = new ActionListener() {
                @Override
                public void actionPerformed(ActionEvent e) {

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Related Classes of org.broad.igv.ui.util.ProgressMonitor

org.broad.igv.sam.AlignmentDataManager

org.broad.igv.ui.IGV$StartupRunnable

org.broad.igv.ui.IGVCommandBar

org.broad.igv.util.HttpUtils

java.beans.PropertyChangeSupport

java.beans.PropertyChangeEvent

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