private void processFilter(Session session, Element element, HashMap additionalInformation) {
String match = getAttribute(element, SessionAttribute.FILTER_MATCH.getText());
String showAllTracks = getAttribute(element, SessionAttribute.FILTER_SHOW_ALL_TRACKS.getText());
String filterName = getAttribute(element, SessionAttribute.NAME.getText());
TrackFilter filter = new TrackFilter(filterName, null);
additionalInformation.put(SessionElement.FILTER, filter);
NodeList elements = element.getChildNodes();
process(session, elements, additionalInformation);
// Save the filter
session.setFilter(filter);
// Set filter properties
if ("all".equalsIgnoreCase(match)) {
IGV.getInstance().setFilterMatchAll(true);
} else if ("any".equalsIgnoreCase(match)) {
IGV.getInstance().setFilterMatchAll(false);
}
if ("true".equalsIgnoreCase(showAllTracks)) {
IGV.getInstance().setFilterShowAllTracks(true);
} else {
IGV.getInstance().setFilterShowAllTracks(false);
}
}
private void processPreferences(Session session, Element element, HashMap additionalInformation) {
NodeList elements = element.getChildNodes();
for (int i = 0; i < elements.getLength(); i++) {
Node child = elements.item(i);
if (child.getNodeName().equalsIgnoreCase(SessionElement.PROPERTY.getText())) {
Element childNode = (Element) child;
String name = getAttribute(childNode, SessionAttribute.NAME.getText());
String value = getAttribute(childNode, SessionAttribute.VALUE.getText());
session.setPreference(name, value);
}
}
}
private void processGeneList(Session session, Element element, HashMap additionalInformation) {
String name = getAttribute(element, SessionAttribute.NAME.getText());
String txt = element.getTextContent();
String[] genes = txt.trim().split("\\s+");
GeneList gl = new GeneList(name, Arrays.asList(genes));
GeneListManager.getInstance().addGeneList(gl);
session.setCurrentGeneList(gl);
// Adjust frames
processFrames(element);
}
private void processFrames(Element element) {
NodeList elements = element.getChildNodes();
if (elements.getLength() > 0) {
Map<String, ReferenceFrame> frames = new HashMap();
for (ReferenceFrame f : FrameManager.getFrames()) {
frames.put(f.getName(), f);
}
List<ReferenceFrame> reorderedFrames = new ArrayList();
for (int i = 0; i < elements.getLength(); i++) {
Node childNode = elements.item(i);
if (childNode.getNodeName().equalsIgnoreCase(SessionElement.FRAME.getText())) {
String frameName = getAttribute((Element) childNode, SessionAttribute.NAME.getText());
ReferenceFrame f = frames.get(frameName);
if (f != null) {
reorderedFrames.add(f);
try {
String chr = getAttribute((Element) childNode, SessionAttribute.CHR.getText());
final String startString =
getAttribute((Element) childNode, SessionAttribute.START.getText())
.replace(",", "");
final String endString =
getAttribute((Element) childNode, SessionAttribute.END.getText())
.replace(",", "");
int start = ParsingUtils.parseInt(startString);
int end = ParsingUtils.parseInt(endString);
org.broad.igv.feature.Locus locus = new Locus(chr, start, end);
f.jumpTo(locus);
} catch (NumberFormatException e) {
e.printStackTrace(); // To change body of catch statement use File | Settings |
// File Templates.
}
}
}
}
if (reorderedFrames.size() > 0) {
FrameManager.setFrames(reorderedFrames);
}
}
IGV.getInstance().resetFrames();
}
private void processResource(Session session, Element element, HashMap additionalInformation) {
String nodeName = element.getNodeName();
boolean oldSession = nodeName.equals(SessionElement.DATA_FILE.getText());
String label = getAttribute(element, SessionAttribute.LABEL.getText());
String name = getAttribute(element, SessionAttribute.NAME.getText());
String sampleId = getAttribute(element, SessionAttribute.SAMPLE_ID.getText());
String description = getAttribute(element, SessionAttribute.DESCRIPTION.getText());
String type = getAttribute(element, SessionAttribute.TYPE.getText());
String coverage = getAttribute(element, SessionAttribute.COVERAGE.getText());
String trackLine = getAttribute(element, SessionAttribute.TRACK_LINE.getText());
String colorString = getAttribute(element, SessionAttribute.COLOR.getText());
String relPathValue = getAttribute(element, SessionAttribute.RELATIVE_PATH.getText());
boolean isRelativePath = ((relPathValue != null) && relPathValue.equalsIgnoreCase("true"));
String serverURL = getAttribute(element, SessionAttribute.SERVER_URL.getText());
// Older sessions used the "name" attribute for the path.
String path = getAttribute(element, SessionAttribute.PATH.getText());
if (oldSession && name != null) {
path = name;
int idx = name.lastIndexOf("/");
if (idx > 0 && idx + 1 < name.length()) {
name = name.substring(idx + 1);
}
}
ResourceLocator resourceLocator;
if (isRelativePath) {
final String sessionPath = session.getPath();
String absolutePath;
if (sessionPath == null) {
log.error("Null session path -- this is not expected");
MessageUtils.showMessage("Unexpected error loading session: null session path");
return;
}
absolutePath = FileUtils.getAbsolutePath(path, sessionPath);
fullToRelPathMap.put(absolutePath, path);
resourceLocator = new ResourceLocator(serverURL, absolutePath);
// If the resourceLocator is relative, we assume coverage is as well
if (coverage != null) {
String absoluteCoveragePath = FileUtils.getAbsolutePath(coverage, sessionPath);
resourceLocator.setCoverage(absoluteCoveragePath);
}
} else {
resourceLocator = new ResourceLocator(serverURL, path);
resourceLocator.setCoverage(coverage);
}
String url = getAttribute(element, SessionAttribute.URL.getText());
if (url == null) {
url = getAttribute(element, SessionAttribute.FEATURE_URL.getText());
}
resourceLocator.setUrl(url);
String infolink = getAttribute(element, SessionAttribute.HYPERLINK.getText());
if (infolink == null) {
infolink = getAttribute(element, SessionAttribute.INFOLINK.getText());
}
resourceLocator.setInfolink(infolink);
// Label is deprecated in favor of name.
if (name != null) {
resourceLocator.setName(name);
} else {
resourceLocator.setName(label);
}
resourceLocator.setSampleId(sampleId);
resourceLocator.setDescription(description);
// This test added to get around earlier bug in the writer
if (type != null && !type.equals("local")) {
resourceLocator.setType(type);
}
resourceLocator.setCoverage(coverage);
resourceLocator.setTrackLine(trackLine);
if (colorString != null) {
try {
Color c = ColorUtilities.stringToColor(colorString);
resourceLocator.setColor(c);
} catch (Exception e) {
log.error("Error setting color: ", e);
}
}
dataFiles.add(resourceLocator);
NodeList elements = element.getChildNodes();
process(session, elements, additionalInformation);
}