private void autoscaleGroup(List<Track> trackList) {
List<ReferenceFrame> frames =
FrameManager.isGeneListMode()
? FrameManager.getFrames()
: Arrays.asList(FrameManager.getDefaultFrame());
List<Range> inViewRanges = new ArrayList<Range>();
synchronized (trackList) {
for (Track track : trackList) {
if (track instanceof ScalableTrack) {
for (ReferenceFrame frame : frames) {
Range range = ((ScalableTrack) track).getInViewRange(frame);
if (range != null) {
inViewRanges.add(range);
}
}
}
}
if (inViewRanges.size() > 0) {
Range inter = computeScale(inViewRanges);
for (Track track : trackList) {
DataRange dr = track.getDataRange();
float min = Math.min(0, inter.min);
float base = Math.max(min, dr.getBaseline());
float max = inter.max;
// Pathological case where min ~= max (no data in view)
if (max - min <= (2 * Float.MIN_VALUE)) {
max = min + 1;
}
DataRange newDR = new DataRange(min, base, max, dr.isDrawBaseline());
newDR.setType(dr.getType());
track.setDataRange(newDR);
}
}
}
}
/**
* Process a track element. This should return a single track, but could return multiple tracks
* since the uniqueness of the track id is not enforced.
*
* @param session
* @param element
* @param additionalInformation
* @return
*/
private List<Track> processTrack(
Session session, Element element, HashMap additionalInformation) {
String id = getAttribute(element, SessionAttribute.ID.getText());
// TODo -- put in utility method, extacts attributes from element **Definitely need to do this
HashMap<String, String> tAttributes = new HashMap();
HashMap<String, String> drAttributes = null;
NamedNodeMap tNodeMap = element.getAttributes();
for (int i = 0; i < tNodeMap.getLength(); i++) {
Node node = tNodeMap.item(i);
String value = node.getNodeValue();
if (value != null && value.length() > 0) {
tAttributes.put(node.getNodeName(), value);
}
}
if (element.hasChildNodes()) {
drAttributes = new HashMap();
Node childNode = element.getFirstChild();
Node sibNode = childNode.getNextSibling();
String sibName = sibNode.getNodeName();
if (sibName.equals(SessionElement.DATA_RANGE.getText())) {
NamedNodeMap drNodeMap = sibNode.getAttributes();
for (int i = 0; i < drNodeMap.getLength(); i++) {
Node node = drNodeMap.item(i);
String value = node.getNodeValue();
if (value != null && value.length() > 0) {
drAttributes.put(node.getNodeName(), value);
}
}
}
}
// Get matching tracks.
List<Track> matchedTracks = trackDictionary.get(id);
if (matchedTracks == null) {
log.info("Warning. No tracks were found with id: " + id + " in session file");
} else {
for (final Track track : matchedTracks) {
// Special case for sequence & gene tracks, they need to be removed before being placed.
if (version >= 4 && track == geneTrack || track == seqTrack) {
igv.removeTracks(Arrays.asList(track));
}
track.restorePersistentState(tAttributes);
if (drAttributes != null) {
DataRange dr = track.getDataRange();
dr.restorePersistentState(drAttributes);
track.setDataRange(dr);
}
}
trackDictionary.remove(id);
}
NodeList elements = element.getChildNodes();
process(session, elements, additionalInformation);
return matchedTracks;
}