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IGVSessionReader.java
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IGVSessionReader.java
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/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package org.broad.igv.session;
import org.broad.igv.Globals;
import org.broad.igv.bedpe.InteractionTrack;
import org.broad.igv.data.CombinedDataSource;
import org.broad.igv.feature.Locus;
import org.broad.igv.feature.RegionOfInterest;
import org.broad.igv.feature.basepair.BasePairTrack;
import org.broad.igv.feature.dsi.DSITrack;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.feature.genome.GenomeListItem;
import org.broad.igv.feature.genome.GenomeManager;
import org.broad.igv.feature.sprite.ClusterTrack;
import org.broad.igv.lists.GeneList;
import org.broad.igv.lists.GeneListManager;
import org.broad.igv.logging.LogManager;
import org.broad.igv.logging.Logger;
import org.broad.igv.maf.MultipleAlignmentTrack;
import org.broad.igv.renderer.ColorScale;
import org.broad.igv.renderer.ColorScaleFactory;
import org.broad.igv.renderer.ContinuousColorScale;
import org.broad.igv.renderer.DataRange;
import org.broad.igv.sam.CoverageTrack;
import org.broad.igv.sam.EWigTrack;
import org.broad.igv.sam.SpliceJunctionTrack;
import org.broad.igv.track.*;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.TrackFilter;
import org.broad.igv.ui.TrackFilterElement;
import org.broad.igv.ui.color.ColorUtilities;
import org.broad.igv.ui.commandbar.GenomeListManager;
import org.broad.igv.ui.panel.FrameManager;
import org.broad.igv.ui.panel.ReferenceFrame;
import org.broad.igv.ui.panel.TrackPanel;
import org.broad.igv.ui.panel.TrackPanelScrollPane;
import org.broad.igv.ui.util.MessageUtils;
import org.broad.igv.util.*;
import org.broad.igv.util.FilterElement.BooleanOperator;
import org.broad.igv.util.FilterElement.Operator;
import org.broad.igv.util.collections.CollUtils;
import org.broad.igv.variant.VariantTrack;
import org.w3c.dom.*;
import java.awt.*;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.lang.ref.WeakReference;
import java.util.List;
import java.util.*;
import java.util.stream.Collectors;
/**
* Class to parse an IGV session file
*/
public class IGVSessionReader implements SessionReader {
private static Logger log = LogManager.getLogger(IGVSessionReader.class);
private static Map<String, String> attributeSynonymMap = new HashMap();
private static WeakReference<IGVSessionReader> currentReader;
private IGV igv;
private int version;
private String genomePath;
private Collection<ResourceLocator> dataFiles;
private Collection<ResourceLocator> missingDataFiles;
private boolean panelElementPresent = false; // Flag indicating if "Panel" sections are present
private TrackFilter filter; // There is a single TrackFilter object per session, usually null
/**
* List of combined data source tracks. Processing of combined data sources has to be deferred until all tracks
* are loaded
*/
private final List<Pair<CombinedDataTrack, Element>> combinedDataSourceTracks = new ArrayList<>();
private Set<Track> allocatedToPanel; // List of tracks allocated to panels, if Panel elements are present.
/**
* Map of id -> track, for second pass through when tracks reference each other
*/
private final Map<String, List<Track>> allTracks = Collections.synchronizedMap(new LinkedHashMap<>());
private final Set<String> erroredResources = Collections.synchronizedSet(new HashSet<>());
private boolean hasTrackElments;
static {
attributeSynonymMap.put("DATA FILE", "DATA SET");
attributeSynonymMap.put("TRACK NAME", "NAME");
}
public IGVSessionReader(IGV igv) {
this.igv = igv;
currentReader = new WeakReference<IGVSessionReader>(this);
}
/**
* @param inputStream
* @param session
* @param sessionPath -- path to the session file. This can be null
* @throws RuntimeException
*/
public void loadSession(InputStream inputStream, Session session, String sessionPath) {
Document document;
try {
document = Utilities.createDOMDocumentFromXmlStream(inputStream);
} catch (Exception e) {
log.error("Load session error", e);
throw new RuntimeException(e);
}
NodeList trackElements = document.getElementsByTagName("Track");
hasTrackElments = trackElements.getLength() > 0;
// Find the root node, either "session" or "global
NodeList nodes = document.getElementsByTagName(SessionElement.SESSION);
if (nodes == null || nodes.getLength() == 0) {
nodes = document.getElementsByTagName(SessionElement.GLOBAL);
}
Node rootNode = nodes.item(0);
// Walk tree processing all nodes, starting with the root
processRootNode(session, rootNode, sessionPath);
processCombinedDataSourceTracks();
// Add tracks not explicitly allocated to panels. This can happen if a track resource path changes after
// session created, and session is hand-editted. It can also happen if the annotation paths for a genome change
// after session creation.
if (allocatedToPanel != null) {
List<Track> unallocatedTracks = new ArrayList<>();
for (List<Track> tracks : allTracks.values()) {
for (Track t : tracks) {
if (!allocatedToPanel.contains(t)) {
unallocatedTracks.add(t);
}
}
}
addUnallocatedTracks(unallocatedTracks);
}
if (session.getGroupTracksBy() != null && session.getGroupTracksBy().length() > 0) {
// igv.setGroupByAttribute(session.getGroupTracksBy());
}
igv.getMainPanel().removeEmptyPanels();
igv.resetOverlayTracks();
}
/**
* The main entry point
*
* @param session
* @param node
* @param sessionPath
*/
private void processRootNode(Session session, Node node, String sessionPath) {
if ((node == null) || (session == null)) {
MessageUtils.showMessage("Invalid session file: root node not found");
return;
}
String nodeName = node.getNodeName();
if (!(nodeName.equalsIgnoreCase(SessionElement.GLOBAL) || nodeName.equalsIgnoreCase(SessionElement.SESSION))) {
MessageUtils.showMessage("Session files must begin with a \"Global\" or \"Session\" element. Found: " + nodeName);
return;
}
Element rootElement = (Element) node;
String versionString = getAttribute(rootElement, SessionAttribute.VERSION);
try {
version = Integer.parseInt(versionString);
} catch (NumberFormatException e) {
log.error("Non integer version number in session file: " + versionString);
}
// Load the genome, which can be an ID, or a path or URL to a .genome or indexed fasta file.
String genomeId = getAttribute(rootElement, SessionAttribute.GENOME);
if (genomeId != null && genomeId.length() > 0) {
if (genomeId.equals(GenomeManager.getInstance().getGenomeId())) {
// No genome change
igv.resetSession(sessionPath);
GenomeManager.getInstance().restoreGenomeTracks(GenomeManager.getInstance().getCurrentGenome());
} else {
// New genome
try {
GenomeListItem item = GenomeListManager.getInstance().getGenomeListItem(genomeId);
if (item != null) {
genomePath = item.getPath();
GenomeManager.getInstance().loadGenome(item.getPath());
} else {
genomePath = genomeId;
if (!FileUtils.isRemote(genomePath) && !ParsingUtils.fileExists(genomePath)) {
genomePath = getAbsolutePath(genomeId, sessionPath);
}
GenomeManager.getInstance().loadGenome(genomePath);
}
} catch (IOException e) {
MessageUtils.showErrorMessage("Error loading genome: " + genomeId, e);
log.error("Error loading genome: " + genomeId, e);
}
}
}
session.setLocus(getAttribute(rootElement, SessionAttribute.LOCUS));
session.setGroupTracksBy(getAttribute(rootElement, SessionAttribute.GROUP_TRACKS_BY));
String nextAutoscaleGroup = getAttribute(rootElement, SessionAttribute.NEXT_AUTOSCALE_GROUP);
if (nextAutoscaleGroup != null) {
try {
session.setNextAutoscaleGroup(Integer.parseInt(nextAutoscaleGroup));
} catch (NumberFormatException e) {
log.error("Error setting next autoscale group", e);
}
}
session.setVersion(version);
NodeList elements = rootElement.getChildNodes();
process(session, elements, sessionPath);
}
private void addUnallocatedTracks(List<Track> tracks) {
Map<String, TrackPanel> trackPanelCache = new HashMap();
log.debug("Adding \"leftover\" tracks");
//For resetting track panels later
List<Map<TrackPanelScrollPane, Integer>> trackPanelAttrs = null;
trackPanelAttrs = igv.getTrackPanelAttrs();
for (Track track : tracks) {
if (track.getResourceLocator() != null) {
TrackPanel panel = trackPanelCache.get(track.getResourceLocator().getPath());
if (panel == null) {
panel = igv.getPanelFor(track);
trackPanelCache.put(track.getResourceLocator().getPath(), panel);
}
panel.addTrack(track);
}
}
igv.resetPanelHeights(trackPanelAttrs.get(0), trackPanelAttrs.get(1));
}
/**
* Process a single session element node.
*
* @param session
* @param element
*/
private void process(Session session, Node element, String sessionPath) {
if ((element == null) || (session == null)) {
return;
}
String nodeName = element.getNodeName();
if (nodeName.equalsIgnoreCase(SessionElement.RESOURCES) ||
nodeName.equalsIgnoreCase(SessionElement.FILES)) {
processResources(session, (Element) element, sessionPath);
} else if (nodeName.equalsIgnoreCase(SessionElement.RESOURCE) ||
nodeName.equalsIgnoreCase(SessionElement.DATA_FILE)) {
processResource(session, (Element) element, sessionPath);
} else if (nodeName.equalsIgnoreCase(SessionElement.REGIONS)) {
processRegions(session, (Element) element, sessionPath);
} else if (nodeName.equalsIgnoreCase(SessionElement.REGION)) {
processRegion(session, (Element) element, sessionPath);
} else if (nodeName.equalsIgnoreCase(SessionElement.GENE_LIST)) {
processGeneList(session, (Element) element);
} else if (nodeName.equalsIgnoreCase(SessionElement.FILTER)) {
processFilter(session, (Element) element, sessionPath);
} else if (nodeName.equalsIgnoreCase(SessionElement.FILTER_ELEMENT)) {
processFilterElement(session, (Element) element, sessionPath);
} else if (nodeName.equalsIgnoreCase(SessionElement.COLOR_SCALES)) {
processColorScales(session, (Element) element, sessionPath);
} else if (nodeName.equalsIgnoreCase(SessionElement.COLOR_SCALE)) {
processColorScale(session, (Element) element, sessionPath);
} else if (nodeName.equalsIgnoreCase(SessionElement.PREFERENCES)) {
processPreferences(session, (Element) element);
} else if (nodeName.equalsIgnoreCase(SessionElement.DATA_TRACKS) ||
nodeName.equalsIgnoreCase(SessionElement.FEATURE_TRACKS) ||
nodeName.equalsIgnoreCase(SessionElement.PANEL)) {
processPanel(session, (Element) element, sessionPath);
} else if (nodeName.equalsIgnoreCase(SessionElement.PANEL_LAYOUT)) {
processPanelLayout(session, (Element) element);
} else if (nodeName.equalsIgnoreCase(SessionElement.HIDDEN_ATTRIBUTES)) {
processHiddenAttributes(session, (Element) element);
} else if (nodeName.equalsIgnoreCase(SessionElement.VISIBLE_ATTRIBUTES)) {
processVisibleAttributes(session, (Element) element);
}
}
private void processResources(Session session, Element element, String sessionPath) {
dataFiles = new ArrayList();
missingDataFiles = new ArrayList();
NodeList elements = element.getChildNodes();
process(session, elements, sessionPath);
if (missingDataFiles.size() > 0) {
StringBuffer message = new StringBuffer();
message.append("<html>The following data file(s) could not be located.<ul>");
for (ResourceLocator file : missingDataFiles) {
if (file.getDBUrl() == null) {
message.append("<li>");
message.append(file.getPath());
message.append("</li>");
} else {
message.append("<li>Server: ");
message.append(file.getDBUrl());
message.append(" Path: ");
message.append(file.getPath());
message.append("</li>");
}
}
message.append("</ul>");
message.append("Common reasons for this include: ");
message.append("<ul><li>The session or data files have been moved.</li> ");
message.append("<li>The data files are located on a drive that is not currently accessible.</li></ul>");
message.append("</html>");
MessageUtils.showMessage(message.toString());
}
// Filter data files that are included in genome annotations. This is to work around a bug introduced with
// json genomes where the genome annotation resources were (doubly) included as session
List<ResourceLocator> genomeResources = GenomeManager.getInstance().getCurrentGenome().getAnnotationResources();
Set<String> absoluteGenomeAnnotationPaths = genomeResources == null ? Collections.emptySet() :
genomeResources.stream().map(rl -> rl.getPath()).collect(Collectors.toSet());
if (dataFiles.size() > 0) {
final List<String> errors = new ArrayList<String>();
// Load files concurrently -- TODO, put a limit on # of threads?
List<Thread> threads = new ArrayList(dataFiles.size());
long t0 = System.currentTimeMillis();
List<Runnable> synchronousLoads = new ArrayList<Runnable>();
for (final ResourceLocator locator : dataFiles) {
if (absoluteGenomeAnnotationPaths.contains(FileUtils.getAbsolutePath(locator.getPath(), genomePath))) {
continue;
}
Runnable runnable = () -> {
try {
// igv.load() loads and initializes tracks, but does not allocate them to panels.
List<Track> tracks = igv.load(locator);
for (Track track : tracks) {
if (track == null) {
log.info("Null track for resource " + locator.getPath());
continue;
}
String id = checkTrackId(track.getId());
if (id == null) {
log.info("Null track id for resource " + locator.getPath());
continue;
}
// id is often an absolute file path. Use just the filename if unique
// if (!FileUtils.isRemote(id)) {
// String fn = (new File(id)).getName();
// if (!allTracks.containsKey(fn)) {
// id = fn;
// }
// }
if (!allTracks.containsKey(id)) {
allTracks.put(id, new ArrayList<>());
}
allTracks.get(id).add(track);
}
} catch (Exception e) {
erroredResources.add(locator.getPath());
log.error("Error loading resource " + locator.getPath(), e);
String ms = "<b>" + locator.getPath() + "</b><br> " + e.toString() + "<br>";
errors.add(ms);
}
};
// Run synchronously if in batch mode or if there are no "track" elements
if (Globals.isBatch() || !hasTrackElments) {
synchronousLoads.add(runnable);
} else {
Thread t = new Thread(runnable);
threads.add(t);
t.start();
}
}
// Wait for all threads to complete
for (Thread t : threads) {
try {
t.join();
} catch (InterruptedException ignore) {
log.error(ignore);
}
}
// Now load data that must be loaded synchronously
for (Runnable runnable : synchronousLoads) {
runnable.run();
}
long dt = System.currentTimeMillis() - t0;
log.debug("Total load time = " + dt);
if (errors.size() > 0) {
StringBuffer buf = new StringBuffer();
buf.append("<html>Errors were encountered loading the session:<br>");
for (String msg : errors) {
buf.append(msg);
}
MessageUtils.showMessage(buf.toString());
}
}
dataFiles = null;
}
/**
* Load a single resource.
* <p/>
* Package private for unit testing
*
* @param session
* @param element
*/
void processResource(Session session, Element element, String sessionPath) {
String nodeName = element.getNodeName();
boolean oldSession = nodeName.equals(SessionElement.DATA_FILE);
String label = getAttribute(element, SessionAttribute.LABEL);
String name = getAttribute(element, SessionAttribute.NAME);
String sampleId = getAttribute(element, SessionAttribute.SAMPLE_ID);
String description = getAttribute(element, SessionAttribute.DESCRIPTION);
String type = getAttribute(element, SessionAttribute.TYPE);
String coverage = getAttribute(element, SessionAttribute.COVERAGE);
String mapping = getAttribute(element, SessionAttribute.MAPPING);
String trackLine = getAttribute(element, SessionAttribute.TRACK_LINE);
String colorString = getAttribute(element, SessionAttribute.COLOR);
String index = getAttribute(element, SessionAttribute.INDEX);
// URL to a database or webservice -- this is not common
String serverURL = getAttribute(element, SessionAttribute.SERVER_URL);
String path = getAttribute(element, SessionAttribute.PATH);
// Older sessions used the "name" attribute for the path.
if (oldSession && name != null) {
path = name;
int idx = name.lastIndexOf("/");
if (idx > 0 && idx + 1 < name.length()) {
name = name.substring(idx + 1);
}
}
String absolutePath = (sessionPath == null || ParsingUtils.isDataURL(path)) ?
path :
getAbsolutePath(path, sessionPath);
ResourceLocator resourceLocator = new ResourceLocator(serverURL, absolutePath);
if (index != null) resourceLocator.setIndexPath(index);
if (coverage != null) {
String absoluteCoveragePath = coverage.equals(".") ? coverage : getAbsolutePath(coverage, sessionPath);
resourceLocator.setCoverage(absoluteCoveragePath);
}
if (mapping != null) {
String absoluteMappingPath = mapping.equals(".") ? mapping : getAbsolutePath(mapping, sessionPath);
resourceLocator.setMappingPath(absoluteMappingPath);
}
String url = getAttribute(element, SessionAttribute.URL);
if (url == null) {
url = getAttribute(element, SessionAttribute.FEATURE_URL);
}
resourceLocator.setFeatureInfoURL(url);
String infolink = getAttribute(element, SessionAttribute.HYPERLINK);
if (infolink == null) {
infolink = getAttribute(element, SessionAttribute.INFOLINK);
}
resourceLocator.setTrackInfoURL(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.setFormat(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, sessionPath);
}
private void processRegions(Session session, Element element, String sessionPath) {
session.clearRegionsOfInterest();
NodeList elements = element.getChildNodes();
process(session, elements, sessionPath);
}
private void processRegion(Session session, Element element, String sessionPath) {
String chromosome = getAttribute(element, SessionAttribute.CHROMOSOME);
String start = getAttribute(element, SessionAttribute.START_INDEX);
String end = getAttribute(element, SessionAttribute.END_INDEX);
String description = getAttribute(element, SessionAttribute.DESCRIPTION);
RegionOfInterest region = new RegionOfInterest(chromosome, Integer.parseInt(start), Integer.parseInt(end), description);
igv.addRegionOfInterest(region);
NodeList elements = element.getChildNodes();
process(session, elements, sessionPath);
}
private void processHiddenAttributes(Session session, Element element) {
NodeList elements = element.getChildNodes();
Set<String> attributes = new HashSet();
for (int i = 0; i < elements.getLength(); i++) {
Node childNode = elements.item(i);
if (childNode.getNodeName().equals("Attribute")) {
attributes.add(((Element) childNode).getAttribute(SessionAttribute.NAME));
}
}
session.setHiddenAttributes(attributes);
}
/**
* For backward compatibility
*
* @param session
* @param element
*/
private void processVisibleAttributes(Session session, Element element) {
NodeList elements = element.getChildNodes();
if (elements.getLength() > 0) {
Set<String> visibleAttributes = new HashSet();
for (int i = 0; i < elements.getLength(); i++) {
Node childNode = elements.item(i);
if (childNode.getNodeName().equals(SessionElement.VISIBLE_ATTRIBUTE)) {
visibleAttributes.add(((Element) childNode).getAttribute(SessionAttribute.NAME));
}
}
final List<String> attributeNames = AttributeManager.getInstance().getAttributeNames();
Set<String> hiddenAttributes = new HashSet<String>(attributeNames);
hiddenAttributes.removeAll(visibleAttributes);
session.setHiddenAttributes(hiddenAttributes);
}
}
private void processGeneList(Session session, Element element) {
String name = getAttribute(element, SessionAttribute.NAME);
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)) {
String frameName = getAttribute((Element) childNode, SessionAttribute.NAME);
ReferenceFrame f = frames.get(frameName);
if (f != null) {
reorderedFrames.add(f);
try {
String chr = getAttribute((Element) childNode, SessionAttribute.CHR);
final String startString =
getAttribute((Element) childNode, SessionAttribute.START).replace(",", "");
final String endString =
getAttribute((Element) childNode, SessionAttribute.END).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.resetFrames();
}
/**
* Example <Filter match="all" name="" showTracks="false">
*
* @param session
* @param element
* @param sessionPath
*/
private void processFilter(Session session, Element element, String sessionPath) {
String match = getAttribute(element, SessionAttribute.FILTER_MATCH);
String showAllTracks = getAttribute(element, SessionAttribute.FILTER_SHOW_ALL_TRACKS);
String filterName = getAttribute(element, SessionAttribute.NAME);
filter = new TrackFilter(filterName, null);
NodeList elements = element.getChildNodes();
process(session, elements, sessionPath);
// Save the filter
session.setFilter(filter);
// Update UI elements -- the matchAll and showAll state is kept in the UI, not the Filter object. This seems wrong. TODO
if ("all".equalsIgnoreCase(match)) {
igv.setFilterMatchAll(true);
} else if ("any".equalsIgnoreCase(match)) {
igv.setFilterMatchAll(false);
}
if ("true".equalsIgnoreCase(showAllTracks)) {
igv.setFilterShowAllTracks(true);
} else {
igv.setFilterShowAllTracks(false);
}
}
private void processFilterElement(Session session, Element element,
String sessionPath) {
if (filter == null) {
throw new RuntimeException("Filter elements defined before filter");
}
String item = getAttribute(element, SessionAttribute.ITEM);
String operator = getAttribute(element, SessionAttribute.OPERATOR);
String value = getAttribute(element, SessionAttribute.VALUE);
String booleanOperator = getAttribute(element, SessionAttribute.BOOLEAN_OPERATOR);
Operator opEnum = CollUtils.findValueOf(Operator.class, operator);
BooleanOperator boolEnum = BooleanOperator.valueOf(booleanOperator.toUpperCase());
TrackFilterElement trackFilterElement = new TrackFilterElement(filter, item,
opEnum, value, boolEnum);
filter.add(trackFilterElement);
NodeList elements = element.getChildNodes();
process(session, elements, sessionPath);
}
/**
* A counter to generate unique panel names. Needed for backward-compatibility of old session files.
*/
private int panelCounter = 1;
/**
* @param node
* @return Whether this node is a track
*/
private static boolean nodeIsTrack(Node node) {
return node.getNodeName() != null &&
(node.getNodeName().equalsIgnoreCase(SessionElement.DATA_TRACK) ||
node.getNodeName().equalsIgnoreCase(SessionElement.TRACK));
}
private void processPanel(Session session, Element element, String sessionPath) {
if (panelElementPresent == false) {
panelElementPresent = true;
// First panel to be processed, do this only once.
// Add any tracks loaded as a side effect of loading genome
final List<Track> tmp = igv.getAllTracks();
for (Track track : tmp) {
String id = checkTrackId(track.getId());
if (!allTracks.containsKey(id)) {
allTracks.put(id, new ArrayList<>());
}
allTracks.get(id).add(track);
}
allocatedToPanel = new LinkedHashSet<>();
// Tracks, if any, will be placed back as prescribed by panel elements
removeAllTracksFromPanels();
}
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 (nodeIsTrack(childNode)) {
List<Track> tracks = processTrack(session, (Element) childNode, sessionPath);
if (tracks != null) {
panelTracks.addAll(tracks);
}
} else {
process(session, childNode, sessionPath);
}
}
//We make a second pass through, resolving references to tracks which may have been processed after being referenced.
//For instance if Track 2 referenced Track 4
for (Track track : panelTracks) {
if (track instanceof FeatureTrack) {
FeatureTrack featureTrack = (FeatureTrack) track;
featureTrack.updateTrackReferences(panelTracks);
} else if (track instanceof DataSourceTrack) {
DataSourceTrack dataTrack = (DataSourceTrack) track;
dataTrack.updateTrackReferences(panelTracks);
}
}
TrackPanel panel = igv.getTrackPanel(panelName);
panel.addTracks(panelTracks);
}
private void processPanelLayout(Session session, Element element) {
String nodeName = element.getNodeName();
NamedNodeMap tNodeMap = element.getAttributes();
for (int i = 0; i < tNodeMap.getLength(); i++) {
Node node = tNodeMap.item(i);
String name = node.getNodeName();
if (name.equals("dividerFractions")) {
String value = node.getNodeValue();
String[] tokens = value.split(",");
double[] divs = new double[tokens.length];
try {
for (int j = 0; j < tokens.length; j++) {
divs[j] = Double.parseDouble(tokens[j]);
}
session.setDividerFractions(divs);
} catch (NumberFormatException e) {
log.error("Error parsing divider locations", e);
}
}
}
}
/**
* 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
* @return
*/
private List<Track> processTrack(Session session, Element element, String sessionPath) {
String id = checkTrackId(getAttribute(element, SessionAttribute.ID));
// Find track matching element id, created earlier from "Resource or File" elements, or during genome load.
// Normally this is a single track, but that can't be assumed as uniqueness of "id" is not enforced.
List<Track> matchedTracks = getTracksById(id);
if (matchedTracks == null) {
//Try creating an absolute path for the id
if (id != null) {
matchedTracks = allTracks.get(getAbsolutePath(id, sessionPath));
}
}
if (matchedTracks != null) {
for (final Track track : matchedTracks) {
track.unmarshalXML(element, version);
allocatedToPanel.add(track);
}
} else {
// No match found, element represents either (1) a track from a file that errored during load, for example
// a file that has been deleted, or (2) a track not created from "Resource" or genome load. These include
// reference sequence, combined, and merged tracks.
String className = getAttribute(element, "clazz");
if (resourceIndpendentTracks.stream().anyMatch(c -> className.contains(c))) {
try {
Track track = createTrack(className, element);
if (track != null) {
track.unmarshalXML(element, version);
matchedTracks = Arrays.asList(track);
allTracks.put(checkTrackId(track.getId()), matchedTracks); // Important for second pass
// Special tracks
if (className.contains("CombinedDataTrack")) {
combinedDataSourceTracks.add(new Pair(track, element));
}
if (className.contains("MergedTracks")) {
List<DataTrack> memberTracks = processChildTracks(session, element, sessionPath);
((MergedTracks) track).setMemberTracks(memberTracks);
NodeList nodeList = element.getElementsByTagName("DataRange");
if (nodeList != null && nodeList.getLength() > 0) {
Element dataRangeElement = (Element) nodeList.item(0);
try {
DataRange dataRange = new DataRange(dataRangeElement, version);
track.setDataRange(dataRange);
} catch (Exception e) {
log.error("Unrecognized DataRange");
}
}
}
} else {
log.warn("Warning. No tracks were found with id: " + id + " in session file");
}
} catch (Exception e) {
log.error("Error restoring track: " + element.toString(), e);
MessageUtils.showMessage("Error loading track: " + element.toString());
}
}
}
NodeList elements = element.getChildNodes();
process(session, elements, sessionPath);
return matchedTracks;
}
/**
* Recursively loop through children of {@code element}, and process them as tracks iff they are determined
* to be so
*
* @param session
* @param element
* @param sessionPath
* @return List of processed tracks.
*/
private List<DataTrack> processChildTracks(Session session, Element element, String sessionPath) {
NodeList memberTrackNodes = element.getChildNodes();
List<DataTrack> memberTracks = new ArrayList<>(memberTrackNodes.getLength());
for (int index = 0; index < memberTrackNodes.getLength(); index++) {
Node memberNode = memberTrackNodes.item(index);
if (nodeIsTrack(memberNode)) {
List<Track> addedTracks = processTrack(session, (Element) memberNode, sessionPath);
if (addedTracks != null) {
for (Track t : addedTracks) {
if (t instanceof DataTrack) {
memberTracks.add((DataTrack) t);
} else {
log.error("Unexpected MergedTrack member class: " + t.getClass().getName());
}
}
}
}
}
return memberTracks;
}
/**
* Process combined data tracks, these are tracks composed from dependent tracks by simple arithmetic operations.
*/
private void processCombinedDataSourceTracks() {
Map<CombinedDataTrack, CombinedDataSource> sourceMap = new HashMap<>();
// First pass -- create data sources
for (Pair<CombinedDataTrack, Element> pair : this.combinedDataSourceTracks) {
Element element = pair.getSecond();
CombinedDataTrack combinedTrack = pair.getFirst();
DataTrack track1 = null;
DataTrack track2 = null;
List<Track> tmp = getTracksById(element.getAttribute("track1"));
if (tmp != null && tmp.size() > 0) {
track1 = (DataTrack) tmp.get(0);
}
tmp = getTracksById(element.getAttribute("track2"));
if (tmp != null && tmp.size() > 0) {
track2 = (DataTrack) tmp.get(0);
}
if (track1 == null || track2 == null) {
log.error("Missing track for combined track: " + pair.getFirst().getName());
return;
}
CombinedDataSource.Operation op = CombinedDataSource.Operation.valueOf(element.getAttribute("op"));
CombinedDataSource source = new CombinedDataSource(track1, track2, op);
sourceMap.put(combinedTrack, source);
}
// Now set datasource on tracks. This needs to be deferred as combined data sources can reference other
// combined sources, we need to instantiate the entire tree before using a datasource
for (Map.Entry<CombinedDataTrack, CombinedDataSource> entry : sourceMap.entrySet()) {
entry.getKey().setDatasource(entry.getValue());
}
}
private void processColorScales(Session session, Element element, String sessionPath) {
NodeList elements = element.getChildNodes();
process(session, elements, sessionPath);
}
private void processColorScale(Session session, Element element, String sessionPath) {
String trackType = getAttribute(element, SessionAttribute.TYPE);
String value = getAttribute(element, SessionAttribute.VALUE);
setColorScaleSet(session, trackType, value);
NodeList elements = element.getChildNodes();
process(session, elements, sessionPath);
}
private void processPreferences(Session session, Element element) {