private void processPanel(Session session, Element element, HashMap additionalInformation) {
panelElementPresent = true;
String panelName = element.getAttribute("name");
if (panelName == null) {
panelName = "Panel" + panelCounter++;
}
List<Track> panelTracks = new ArrayList();
NodeList elements = element.getChildNodes();
for (int i = 0; i < elements.getLength(); i++) {
Node childNode = elements.item(i);
if (childNode.getNodeName().equalsIgnoreCase(SessionElement.DATA_TRACK.getText())
|| // Is this a track?
childNode.getNodeName().equalsIgnoreCase(SessionElement.TRACK.getText())) {
List<Track> tracks = processTrack(session, (Element) childNode, additionalInformation);
if (tracks != null) {
panelTracks.addAll(tracks);
}
} else {
process(session, childNode, additionalInformation);
}
}
TrackPanel panel = IGV.getInstance().getTrackPanel(panelName);
panel.addTracks(panelTracks);
}
private void addLeftoverTracks(Collection<List<Track>> tmp) {
Map<String, TrackPanel> trackPanelCache = new HashMap();
if (version < 3 || !panelElementPresent) {
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);
}
}
}
}
}