Examples of org.broad.igv.ui.panel.TrackPanel

org.broad.igv.ui.panel.TrackPanel
@author eflakes


                if (locator != null) {
                    locator.setTrackLine(trackLine);
                    // Alignment tracks must be loaded synchronously
                    if (isAlignmentFile(locator.getPath())) {
                        TrackPanel panel = igv.getPanelFor(locator);
                        panel.addTracks(igv.load(locator));
                    } else {
                        aSync.add(locator);
                    }
                    trackLine = null; // Reset for next time
                    locator = null;

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    private void placeTracksInPanels(List<ResourceLocator> locatorPaths, Map<String, List<Track>> loadedTracks) {
        for (ResourceLocator loc : locatorPaths) {
            //TrackPanel panel = IGV.getInstance().getPanelFor(new ResourceLocator(path));
            // If loading from UCSC use a single panel
            TrackPanel panel = igv.getTrackPanel(IGV.DATA_PANEL_NAME);
            String path = loc.getPath();
            if (loadedTracks.containsKey(path)) {
                panel.addTracks(loadedTracks.get(path));
            }
        }
    }

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        overlayGroups.addActionListener(new ActionListener() {
            @Override
            public void actionPerformed(ActionEvent e) {
                MergedTracks mergedTracks = new MergedTracks(UUID.randomUUID().toString(), "Overlay", dataTrackList);
                Track firstTrack = tracks.iterator().next();
                TrackPanel panel = TrackPanel.getParentPanel(firstTrack);
                panel.addTrack(mergedTracks);
                panel.moveSelectedTracksTo(Arrays.asList(mergedTracks), firstTrack, false);
                panel.removeTracks(tracks);
            }
        });


        int numDataTracks = dataTrackList.size();
        overlayGroups.setEnabled(numDataTracks >= 2 && numDataTracks == tracks.size());
        menu.add(overlayGroups);


        // Enable "separateTracks" menu if selection is a single track, and that track is merged.


        JMenuItem unmergeItem = new JMenuItem("Separate Tracks");
        menu.add(unmergeItem);


        Track firstTrack = tracks.iterator().next();
        if(tracks.size() == 1 && firstTrack instanceof MergedTracks) {


        unmergeItem.addActionListener(new ActionListener() {
            @Override
            public void actionPerformed(ActionEvent e) {
                Track firstTrack = tracks.iterator().next();
                TrackPanel panel = TrackPanel.getParentPanel(firstTrack);
                final MergedTracks mergedTracks = (MergedTracks) firstTrack;
                mergedTracks.setTrackAlphas(255);
                panel.addTracks(mergedTracks.getMemberTracks());
                panel.moveSelectedTracksTo(mergedTracks.getMemberTracks(), mergedTracks, true);
                IGV.getInstance().removeTracks(Arrays.asList(mergedTracks));
            }
        });
        }
        else {

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            for (List<Track> tracks : tmp) {
                for (Track track : tracks) {
                    if (track != geneTrack && track != seqTrack && track.getResourceLocator() != null) {


                        TrackPanel panel = trackPanelCache.get(track.getResourceLocator().getPath());
                        if (panel == null) {
                            panel = IGV.getInstance().getPanelFor(track.getResourceLocator());
                            trackPanelCache.put(track.getResourceLocator().getPath(), panel);
                        }
                        panel.addTrack(track);
                    }
                }
            }


            if(IGV.hasInstance()){

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                DataSourceTrack dataTrack = (DataSourceTrack) track;
                dataTrack.updateTrackReferences(panelTracks);
            }
        }


        TrackPanel panel = IGV.getInstance().getTrackPanel(panelName);
        panel.addTracks(panelTracks);
    }

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Related Classes of org.broad.igv.ui.panel.TrackPanel

org.broad.igv.session.IGVSessionReader

org.broad.igv.session.UCSCSessionReader

org.broad.igv.track.TrackGroup

org.broad.igv.track.TrackMenuUtils

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