Package org.broad.igv.util

Examples of org.broad.igv.util.NamedRunnable

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    }

    private void zoom() {


        NamedRunnable runnable = new NamedRunnable() {
            public void run() {
                double s = frame.getChromosomePosition(dragStart);
                double e = frame.getChromosomePosition(dragEnd);
                if (e < s) {
                    double tmp = s;
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        item = new JMenuItem("Copy sequence");
        item.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent e) {

                LongRunningTask.submit(new NamedRunnable() {
                    public String getName() {
                        return "Copy sequence";
                    }

                    public void run() {
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     * @return
     */
    WrappedDataSource getSignalSource(final String chr, final int contextStart, final int contextEnd, final int zoom) {
        if (signalSource == null && signalPath != null && !signalSourceLoading) {
            signalSourceLoading = true;
            NamedRunnable runnable = new NamedRunnable() {
                public void run() {
                    signalSource = new WrappedDataSource(new TDFDataSource(TDFReader.getReader(signalPath), 0, "", genome));
                    signalSource.setNormalizeCounts(true, 1.0e9f);
                    signalSource.getSummaryScoresForRange(chr, contextStart, contextEnd, zoom);
                }
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        if (f != null && f instanceof Mutation) {

            final Mutation mut = (Mutation) f;
            final MouseEvent me = te.getMouseEvent();
            System.out.println("Submitting");
            LongRunningTask.submit(new NamedRunnable() {
                public String getName() {
                    return "Call OMA";
                }

                public void run() {
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    void processVariant(final VariantListEntry variant) {

        VariantListNavigator.this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
        VariantListNavigator.this.variantList.setEnabled(false);

        NamedRunnable runnable = new NamedRunnable() {

            public String getName() {
                return "Process variant: " + variant.toString();
            }
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        doBlatQuery(userSeq);
    }

    public static void doBlatQuery(final String userSeq) {
        LongRunningTask.submit(new NamedRunnable() {
            public String getName() {
                return "Blat sequence";
            }

            public void run() {
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            return;
        }
        loadedIntervalCache.setMaxEntries(2 * FrameManager.getFrames().size());
        isLoading = true;

        NamedRunnable runnable = new NamedRunnable() {

            public String getName() {
                return "loadAlignments";
            }

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Related Classes of org.broad.igv.util.NamedRunnable

  • org.broad.igv.lists.VariantListNavigator
  • org.broad.igv.peaks.PeakTrack
  • org.broad.igv.sam.AlignmentDataManager
  • org.broad.igv.track.MutationTrack
  • org.broad.igv.ui.panel.RegionOfInterestPanel
  • org.broad.igv.ui.panel.RulerPanel
  • org.broad.igv.util.blat.BlatClient
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