/*
* 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.track;
import htsjdk.tribble.Feature;
import htsjdk.tribble.TribbleException;
import org.apache.log4j.Logger;
import org.broad.igv.Globals;
import org.broad.igv.cli_plugin.PluginFeatureSource;
import org.broad.igv.cli_plugin.PluginSource;
import org.broad.igv.feature.*;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.feature.genome.GenomeManager;
import org.broad.igv.prefs.Constants;
import org.broad.igv.prefs.PreferencesManager;
import org.broad.igv.renderer.*;
import org.broad.igv.session.IGVSessionReader;
import org.broad.igv.session.SubtlyImportant;
import org.broad.igv.tools.FeatureSearcher;
import org.broad.igv.tools.motiffinder.MotifFinderSource;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.UIConstants;
import org.broad.igv.event.DataLoadedEvent;
import org.broad.igv.event.IGVEventBus;
import org.broad.igv.event.IGVEventObserver;
import org.broad.igv.ui.panel.ReferenceFrame;
import org.broad.igv.ui.util.MessageUtils;
import org.broad.igv.util.BrowserLauncher;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.StringUtils;
import org.broad.igv.variant.VariantTrack;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import javax.xml.bind.JAXBElement;
import javax.xml.bind.JAXBException;
import javax.xml.bind.MarshalException;
import javax.xml.bind.Marshaller;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlSeeAlso;
import javax.xml.bind.annotation.XmlType;
import javax.xml.namespace.QName;
import java.awt.*;
import java.awt.event.MouseEvent;
import java.io.IOException;
import java.util.*;
import java.util.List;
/**
* Track which displays features, typically showing regions of the genome
* in a qualitative way. Features are rendered using the specified FeatureRenderer.
* The gene track is an example of a feature track.
*
* @author jrobinso
*/
@XmlType(factoryMethod = "getNextTrack")
@XmlSeeAlso({VariantTrack.class, PluginFeatureSource.class, MotifFinderSource.class})
public class FeatureTrack extends AbstractTrack implements IGVEventObserver {
private static Logger log = Logger.getLogger(FeatureTrack.class);
//All tracks have label "Track", we need to specify the type sometimes
//but still preserve backwards compatibility
@XmlAttribute
protected Class clazz = FeatureTrack.class;
public static final int MINIMUM_FEATURE_SPACING = 5;
public static final int DEFAULT_MARGIN = 5;
public static final int NO_FEATURE_ROW_SELECTED = -1;
protected static final Color SELECTED_FEATURE_ROW_COLOR = new Color(100, 100, 100, 30);
private static final int DEFAULT_EXPANDED_HEIGHT = 35;
private static final int DEFAULT_SQUISHED_HEIGHT = 12;
private int expandedRowHeight = DEFAULT_EXPANDED_HEIGHT;
private int squishedRowHeight = DEFAULT_SQUISHED_HEIGHT;
boolean fatalLoadError = false;
Track.DisplayMode lastFeatureMode = null; // Keeps track of the feature display mode before an auto-switch to COLLAPSE
protected List<Rectangle> levelRects = new ArrayList();
// TODO -- this is a memory leak, this cache needs cleared when the reference frame collection (gene list) changes
/**
* Map of reference frame name -> packed features
*/
protected Map<String, PackedFeatures<IGVFeature>> packedFeaturesMap = Collections.synchronizedMap(new HashMap<String, PackedFeatures<IGVFeature>>());
private Renderer renderer;
private DataRenderer coverageRenderer;
// true == features, false = coverage
private boolean showFeatures = true;
protected FeatureSource source;
//track which row of the expanded track is selected by the user. Selection goes away if tracks are collpased
protected int selectedFeatureRowIndex = NO_FEATURE_ROW_SELECTED;
//Feature selected by the user. This is repopulated on each handleDataClick() call.
protected IGVFeature selectedFeature = null;
int margin = DEFAULT_MARGIN;
private static boolean drawBorder = true;
private boolean alternateExonColor = false;
private static final String PLUGIN_SOURCE = "PluginSource";
private static final String SEQUENCE_MATCH_SOURCE = "SequenceMatchSource";
String trackLine = null;
// TODO -- there are WAY too many constructors for this class
/**
* Construct with no feature source. Currently this is only used for the SpliceJunctionTrack subclass.
*
* @param id
* @param name
*/
public FeatureTrack(String id, String name) {
super(id, name);
setSortable(false);
}
public FeatureTrack(ResourceLocator locator, String id, String name) {
super(locator, id, name);
setSortable(false);
}
/**
* Constructor with no ResourceLocator. Note: tracks using this constructor will not be recorded in the
* "Resources" section of session files.
*
* @param id
* @param name
* @param source
* @api
*/
public FeatureTrack(String id, String name, FeatureSource source) {
super(id, name);
init(source, null);
setSortable(false);
}
/**
* Constructor specifically for BigWig data source
*
* @param locator
* @param id
* @param name
* @param source
*/
public FeatureTrack(ResourceLocator locator, String id, String name, FeatureSource source) {
super(locator, id, name);
init(source, locator.getPath());
setSortable(false);
}
public FeatureTrack(ResourceLocator locator, FeatureSource source) {
super(locator);
init(source, locator != null ? locator.getPath() : null);
setSortable(false);
}
public FeatureTrack(ResourceLocator locator, String id, FeatureSource source) {
super(locator, id);
init(source, locator.getPath());
}
/**
* Create a new track which is a shallow copy of this one
*
* @param featureTrack
*/
public FeatureTrack(FeatureTrack featureTrack) {
this(featureTrack.getId(), featureTrack.getName(), featureTrack.source);
}
protected void init(FeatureSource source, String path) {
this.source = source;
setMinimumHeight(10);
setColor(Color.blue.darker());
coverageRenderer = new BarChartRenderer();
int sourceFeatureWindowSize = source.getFeatureWindowSize();
if (sourceFeatureWindowSize > 0) { // Only apply a default if the feature source supports visibility window.
int defVisibilityWindow = PreferencesManager.getPreferences().getAsInt(Constants.DEFAULT_VISIBILITY_WINDOW);
if (defVisibilityWindow > 0) {
setVisibilityWindow(defVisibilityWindow * 1000);
} else {
visibilityWindow = sourceFeatureWindowSize;
}
}
this.renderer = path != null && path.endsWith("junctions.bed") ?
new SpliceJunctionRenderer() : new IGVFeatureRenderer();
IGVEventBus.getInstance().subscribe(DataLoadedEvent.class, this);
}
/**
* Called after features are finished loading, which can be asynchronous
*/
public void receiveEvent(Object e) {
if (e instanceof DataLoadedEvent) {
// DataLoadedEvent event = (DataLoadedEvent) e;
// if (IGV.hasInstance()) {
// // TODO -- WHY IS THIS HERE????
// //TODO Assuming this is necessary, there can be many data loaded events in succession,
// //don't want to layout for each one
// IGV.getInstance().layoutMainPanel();
// }
} else {
log.info("Unknown event type: " + e.getClass());
}
}
@Override
public boolean isFilterable() {
return false; // Don't filter "feature" tracks
}
@Override
public int getHeight() {
if (!isVisible()) {
return 0;
}
int rowHeight = getDisplayMode() == DisplayMode.SQUISHED ? squishedRowHeight : expandedRowHeight;
int minHeight = margin + rowHeight * Math.max(1, getNumberOfFeatureLevels());
return Math.max(minHeight, super.getHeight());
}
public int getExpandedRowHeight() {
return expandedRowHeight;
}
public void setExpandedRowHeight(int expandedRowHeight) {
this.expandedRowHeight = expandedRowHeight;
}
public int getSquishedRowHeight() {
return squishedRowHeight;
}
public void setSquishedRowHeight(int squishedRowHeight) {
this.squishedRowHeight = squishedRowHeight;
}
public int getFeatureWindowSize() {
return source.getFeatureWindowSize();
}
public void setRendererClass(Class rc) {
try {
renderer = (Renderer) rc.newInstance();
} catch (Exception ex) {
log.error("Error instatiating renderer ", ex);
}
}
public void setMargin(int margin) {
this.margin = margin;
}
@Override
public void setProperties(TrackProperties trackProperties) {
super.setProperties(trackProperties);
if (trackProperties.getFeatureVisibilityWindow() >= 0) {
setVisibilityWindow(trackProperties.getFeatureVisibilityWindow());
}
alternateExonColor = trackProperties.isAlternateExonColor();
}
public void setWindowFunction(WindowFunction type) {
// Ignored for feature tracks
}
/**
* Return the maximum number of features for any panel in this track. In whole genome view there is a single panel,
* but there are multiple in gene list view (one for each gene list).
*
* @return
*/
public int getNumberOfFeatureLevels() {
if (areFeaturesStacked() && packedFeaturesMap.size() > 0) {
int n = 0;
synchronized (packedFeaturesMap) {
for (PackedFeatures pf : packedFeaturesMap.values()) {
//dhmay adding null check. To my mind this shouldn't be necessary, but we're encountering
//it intermittently. Food for future thought
if (pf != null) {
n = Math.max(n, pf.getRowCount());
}
}
}
return n;
}
return 1;
}
/**
* @return Whether features are displayed stacked on top of one another, rather than overlapping
*/
protected boolean areFeaturesStacked() {
return getDisplayMode() != DisplayMode.COLLAPSED;
}
/**
* Return a score over the interval. This is required by the track interface to support sorting.
*/
public float getRegionScore(String chr, int start, int end, int zoom, RegionScoreType scoreType, String frameName) {
try {
Iterator<Feature> features = source.getFeatures(chr, start, end);
if (features != null) {
if (scoreType == RegionScoreType.MUTATION_COUNT && this.getTrackType() == TrackType.MUTATION) {
int count = 0;
while (features.hasNext()) {
Feature f = features.next();
if (f.getStart() > end) {
break;
}
if (f.getEnd() >= start) {
count++;
}
}
return count;
} else if (scoreType == RegionScoreType.SCORE) {
// Average score of features in region. Note: Should the score be weighted by genomic size?
float regionScore = 0;
int nValues = 0;
while (features.hasNext()) {
Feature f = features.next();
if (f instanceof IGVFeature) {
if ((f.getEnd() >= start) && (f.getStart() <= end)) {
float value = ((IGVFeature) f).getScore();
regionScore += value;
nValues++;
}
}
}
if (nValues == 0) {
// No scores in interval
return -Float.MAX_VALUE;
} else {
return regionScore / nValues;
}
}
}
} catch (IOException e) {
log.error("Error counting features.", e);
}
return -Float.MAX_VALUE;
}
public Renderer getRenderer() {
if (renderer == null) {
setRendererClass(IGVFeatureRenderer.class);
}
return renderer;
}
/**
* Return a string for popup text.
*
* @param chr
* @param position in genomic coordinates
* @param mouseX
* @return
*/
public String getValueStringAt(String chr, double position, int mouseX, int mouseY, ReferenceFrame frame) {
if (showFeatures) {
List<Feature> allFeatures = getAllFeatureAt(position, mouseY, frame);
if (allFeatures == null) {
return null;
}
StringBuffer buf = new StringBuffer();
boolean firstFeature = true;
int maxNumber = 10;
int n = 1;
for (Feature feature : allFeatures) {
if (feature != null && feature instanceof IGVFeature) {
if (!firstFeature) {
buf.append("<hr><br>");
}
IGVFeature igvFeature = (IGVFeature) feature;
String vs = igvFeature.getValueString(position, mouseX, null);
buf.append(vs);
if (IGV.getInstance().isShowDetailsOnClick()) {
// URL
String url = getFeatureURL(igvFeature);
if (url != null) {
buf.append("<br/><a href=\"" + url + "\">" + url + "</a>");
}
}
firstFeature = false;
if (n > maxNumber) {
buf.append("...");
break;
}
}
n++;
}
return buf.toString();
} else {
int zoom = Math.max(0, frame.getZoom());
if (source == null) {
return null;
}
List<LocusScore> scores = source.getCoverageScores(chr, (int) position - 10, (int) position + 10, zoom);
if (scores == null) {
return "";
} else {
// give a +/- 2 pixel buffer, otherwise very narrow features will be missed.
double bpPerPixel = frame.getScale();
int minWidth = (int) (2 * bpPerPixel); /* * */
LocusScore score = (LocusScore) FeatureUtils.getFeatureAt(position, minWidth, scores);
return score == null ? null : "Mean count: " + score.getScore();
}
}
}
private String getFeatureURL(IGVFeature igvFeature) {
String url = igvFeature.getURL();
if (url == null) {
String trackURL = getUrl();
if (trackURL != null && igvFeature.getIdentifier() != null) {
String encodedID = StringUtils.encodeURL(igvFeature.getIdentifier());
url = trackURL.replaceAll("\\$\\$", encodedID);
}
}
return url;
}
/**
* Get all features which overlap the specified locus
*
* @return
*/
public List<Feature> getFeatures(String chr, int start, int end) {
List<Feature> features = new ArrayList<Feature>();
try {
Iterator<Feature> iter = source.getFeatures(chr, start, end);
while (iter.hasNext()) {
features.add(iter.next());
}
} catch (IOException e) {
throw new RuntimeException(e);
}
return features;
}
/**
* @param position in genomic coordinates
* @param y pixel location in panel coordinates. // TODO offset by track origin before getting here?
* @param frame
* @return
*/
protected List<Feature> getAllFeatureAt(double position, int y, ReferenceFrame frame) {
// Determine the level number (for expanded tracks)
int featureRow = getFeatureRow(y);
return getFeaturesAtPositionInFeatureRow(position, featureRow, frame);
}
/**
* Determine which row the user clicked in and return the appropriate feature
*
* @param y
* @return
*/
private int getFeatureRow(int y) {
int rowHeight;
DisplayMode mode = getDisplayMode();
switch (mode) {
case SQUISHED:
rowHeight = getSquishedRowHeight();
break;
case EXPANDED:
rowHeight = getExpandedRowHeight();
break;
default:
rowHeight = getHeight();
}
return Math.max(0, Math.min(levelRects.size() - 1, (int) ((y - this.getY() - this.margin) / rowHeight)));
}
/**
* Knowing the feature row, figure out which feature is at {@code position}. If not expanded,
* featureRow is ignored
*
* @param position
* @param featureRow
* @param frame
* @return
*/
public List<Feature> getFeaturesAtPositionInFeatureRow(double position, int featureRow, ReferenceFrame frame) {
PackedFeatures<IGVFeature> packedFeatures = packedFeaturesMap.get(frame.getName());
if (packedFeatures == null) {
return null;
}
//If features are stacked we look at only the row.
//If they are collapsed on top of each other, we get all features in all rows
int nLevels = areFeaturesStacked() ? packedFeatures.getRowCount() : 1;
List<IGVFeature> possFeatures = null;
if ((nLevels > 1) && (featureRow < nLevels)) {
possFeatures = packedFeatures.getRows().get(featureRow).getFeatures();
} else {
possFeatures = packedFeatures.getFeatures();
}
List<Feature> featureList = null;
if (possFeatures != null) {
// give a minum 2 pixel or 1/2 bp window, otherwise very narrow features will be missed.
double bpPerPixel = frame.getScale();
double minWidth = Math.max(0.5, MINIMUM_FEATURE_SPACING * bpPerPixel);
int maxFeatureLength = packedFeatures.getMaxFeatureLength();
featureList = FeatureUtils.getAllFeaturesAt(position, maxFeatureLength, minWidth, possFeatures);
}
return featureList;
}
public WindowFunction getWindowFunction() {
return WindowFunction.count;
}
@Override
public boolean handleDataClick(TrackClickEvent te) {
MouseEvent e = te.getMouseEvent();
//Selection of an expanded feature row
if (areFeaturesStacked()) {
if (levelRects != null) {
for (int i = 0; i < levelRects.size(); i++) {
Rectangle rect = levelRects.get(i);
if (rect.contains(e.getPoint())) {
if (i == selectedFeatureRowIndex)
setSelectedFeatureRowIndex(FeatureTrack.NO_FEATURE_ROW_SELECTED);
else {
//make this track selected
setSelected(true);
//select the appropriate row
setSelectedFeatureRowIndex(i);
}
IGV.getInstance().doRefresh();
break;
}
}
}
}
//For feature selection
selectedFeature = null;
Feature f = getFeatureAtMousePosition(te);
if (f != null && f instanceof IGVFeature) {
IGVFeature igvFeature = (IGVFeature) f;
if (selectedFeature != null && igvFeature.contains(selectedFeature) && (selectedFeature.contains(igvFeature))) {
//If something already selected, then if it's the same as this feature, deselect, otherwise, select
//this feature.
//todo: contains() might not do everything I want it to.
selectedFeature = null;
} else {
//if nothing already selected, or something else selected,
// select this feature
selectedFeature = igvFeature;
}
if (IGV.getInstance().isShowDetailsOnClick()) {
openTooltipWindow(te);
} else {
String url = getFeatureURL(igvFeature);
if (url != null) {
try {
BrowserLauncher.openURL(url);
} catch (IOException e1) {
log.error("Error launching url: " + url);
}
e.consume();
return true;
}
}
}
return false;
}
public Feature getFeatureAtMousePosition(TrackClickEvent te) {
MouseEvent e = te.getMouseEvent();
final ReferenceFrame referenceFrame = te.getFrame();
if (referenceFrame != null) {
double location = referenceFrame.getChromosomePosition(e.getX());
List<Feature> features = getAllFeatureAt(location, e.getY(), referenceFrame);
return (features != null && features.size() > 0) ? features.get(0) : null;
} else {
return null;
}
}
/**
* Required by the interface, really not applicable to feature tracks
*/
public boolean isLogNormalized() {
return true;
}
public void overlay(RenderContext context, Rectangle rect) {
renderFeatures(context, rect);
}
@Override
public void setDisplayMode(DisplayMode mode) {
// Explicity setting the display mode overrides the automatic switch
lastFeatureMode = null;
super.setDisplayMode(mode);
}
@Override
public boolean isReadyToPaint(ReferenceFrame frame) {
if (!isShowFeatures(frame)) {
return true; // Ready by definition (nothing to paint)
} else {
PackedFeatures packedFeatures = packedFeaturesMap.get(frame.getName());
String chr = frame.getChrName();
int start = (int) frame.getOrigin();
int end = (int) frame.getEnd();
return (packedFeatures != null && packedFeatures.containsInterval(chr, start, end));
}
}
public void load(ReferenceFrame frame) {
loadFeatures(frame.getChrName(), (int) frame.getOrigin(), (int) frame.getEnd(), frame);
}
/**
* Loads and segregates features into rows such that they do not overlap.
*
* @param chr
* @param start
* @param end
*/
protected void loadFeatures(final String chr, final int start, final int end, final ReferenceFrame frame) {
try {
int delta = (end - start) / 2;
int expandedStart = start - delta;
int expandedEnd = end + delta;
//Make sure we are only querying within the chromosome we allow for somewhat pathological cases of start
//being negative and end being outside, but only if directly queried. Our expansion should not
//set start < 0 or end > chromosomeLength
if (start >= 0) {
expandedStart = Math.max(0, expandedStart);
}
Genome genome = GenomeManager.getInstance().getCurrentGenome();
if (genome != null) {
Chromosome c = genome.getChromosome(chr);
if (c != null && end < c.getLength()) expandedEnd = Math.min(c.getLength(), expandedEnd);
}
Iterator<Feature> iter = source.getFeatures(chr, expandedStart, expandedEnd);
if (iter == null) {
PackedFeatures pf = new PackedFeatures(chr, expandedStart, expandedEnd);
packedFeaturesMap.put(frame.getName(), pf);
} else {
PackedFeatures pf = new PackedFeatures(chr, expandedStart, expandedEnd, iter, getName());
packedFeaturesMap.put(frame.getName(), pf);
log.info("Loaded " + chr + " " + expandedStart + "-" + expandedEnd);
}
} catch (Exception e) {
// Mark the interval with an empty feature list to prevent an endless loop of load attempts.
PackedFeatures pf = new PackedFeatures(chr, start, end);
packedFeaturesMap.put(frame.getName(), pf);
String msg = "Error loading features for interval: " + chr + ":" + start + "-" + end + " <br>" + e.toString();
MessageUtils.showMessage(msg);
log.error(msg, e);
}
}
@Override
public void render(RenderContext context, Rectangle rect) {
Rectangle renderRect = new Rectangle(rect);
renderRect.y = renderRect.y + margin;
renderRect.height -= margin;
showFeatures = isShowFeatures(context.getReferenceFrame());
if (showFeatures) {
if (lastFeatureMode != null) {
super.setDisplayMode(lastFeatureMode);
lastFeatureMode = null;
}
renderFeatures(context, renderRect);
} else {
if (getDisplayMode() != DisplayMode.COLLAPSED) {
// An ugly hack, but we want to prevent this for vcf tracks
if (!(this instanceof VariantTrack)) {
lastFeatureMode = getDisplayMode();
super.setDisplayMode(DisplayMode.COLLAPSED);
}
}
renderCoverage(context, renderRect);
}
if (FeatureTrack.drawBorder) {
Graphics2D borderGraphics = context.getGraphic2DForColor(UIConstants.TRACK_BORDER_GRAY);
borderGraphics.drawLine(rect.x, rect.y, rect.x + rect.width, rect.y);
//TODO Fix height for variant track
borderGraphics.drawLine(rect.x, rect.y + rect.height, rect.x + rect.width, rect.y + rect.height);
}
}
protected boolean isShowFeatures(ReferenceFrame frame) {
if (frame.getChrName().equals(Globals.CHR_ALL)) {
return false;
} else {
double windowSize = frame.getEnd() - frame.getOrigin();
int vw = getVisibilityWindow();
return (vw <= 0 || windowSize <= vw);
}
}
protected void renderCoverage(RenderContext context, Rectangle inputRect) {
final String chr = context.getChr();
List<LocusScore> scores = (source != null && chr.equals(Globals.CHR_ALL)) ?
source.getCoverageScores(chr, (int) context.getOrigin(),
(int) context.getEndLocation(), context.getZoom()) :
null;
if (scores == null) {
Graphics2D g = context.getGraphic2DForColor(Color.gray);
Rectangle textRect = new Rectangle(inputRect);
// Keep text near the top of the track rectangle
textRect.height = Math.min(inputRect.height, 20);
String message = getZoomInMessage(chr);
GraphicUtils.drawCenteredText(message, textRect, g);
} else {
float max = getMaxEstimate(scores);
ContinuousColorScale cs = getColorScale();
if (cs != null) {
cs.setPosEnd(max);
}
setDataRange(new DataRange(0, 0, max));
coverageRenderer.render(scores, context, inputRect, this);
}
}
protected String getZoomInMessage(String chr) {
return chr.equals(Globals.CHR_ALL) ? "Zoom in to see features." :
"Zoom in to see features, or right-click to increase Feature Visibility Window.";
}
private float getMaxEstimate(List<LocusScore> scores) {
float max = 0;
int n = Math.min(200, scores.size());
for (int i = 0; i < n; i++) {
max = Math.max(max, scores.get(i).getScore());
}
return max;
}
/**
* Render features in the given input rectangle.
*
* @param context
* @param inputRect
*/
protected void renderFeatures(RenderContext context, Rectangle inputRect) {
if (log.isTraceEnabled()) {
String msg = String.format("renderFeatures: %s frame: %s", getName(), context.getReferenceFrame().getName());
log.trace(msg);
}
PackedFeatures packedFeatures = packedFeaturesMap.get(context.getReferenceFrame().getName());
if (packedFeatures == null || !packedFeatures.overlapsInterval(context.getChr(), (int) context.getOrigin(), (int) context.getEndLocation() + 1)) {
return;
}
try {
renderFeatureImpl(context, inputRect, packedFeatures);
} catch (TribbleException e) {
log.error("Tribble error", e);
//Error loading features. We'll let the user decide if this is "fatal" or not.
if (!fatalLoadError) {
fatalLoadError = true;
boolean unload = MessageUtils.confirm("<html> Error loading features: " + e.getMessage() +
"<br>Unload track " + getName() + "?");
if (unload) {
Collection<Track> tmp = Arrays.asList((Track) this);
IGV.getInstance().removeTracks(tmp);
IGV.getInstance().doRefresh();
} else {
fatalLoadError = false;
}
}
}
}
protected void renderFeatureImpl(RenderContext context, Rectangle inputRect, PackedFeatures packedFeatures) {
Renderer renderer = getRenderer();
if (areFeaturesStacked()) {
List<PackedFeatures.FeatureRow> rows = packedFeatures.getRows();
if (rows != null && rows.size() > 0) {
int nLevels = rows.size();
synchronized (levelRects) {
levelRects.clear();
// Divide rectangle into equal height levels
double h = getDisplayMode() == DisplayMode.SQUISHED ? squishedRowHeight : expandedRowHeight;
Rectangle rect = new Rectangle(inputRect.x, inputRect.y, inputRect.width, (int) h);
int i = 0;
if (renderer instanceof FeatureRenderer) ((FeatureRenderer) renderer).reset();
for (PackedFeatures.FeatureRow row : rows) {
levelRects.add(new Rectangle(rect));
renderer.render(row.features, context, levelRects.get(i), this);
if (selectedFeatureRowIndex == i) {
Graphics2D fontGraphics = context.getGraphic2DForColor(SELECTED_FEATURE_ROW_COLOR);
fontGraphics.fillRect(rect.x, rect.y, rect.width, rect.height);
}
rect.y += h;
i++;
}
}
}
} else {
List<Feature> features = packedFeatures.getFeatures();
if (features != null) {
renderer.render(features, context, inputRect, this);
}
}
}
/**
* Return the nextLine or previous feature relative to the center location.
* TODO -- investigate delegating this method to FeatureSource, where it might be possible to simplify the implementation
*
* @param chr
* @param center
* @param forward
* @return
* @throws IOException
*/
public Feature nextFeature(String chr, double center, boolean forward, ReferenceFrame frame) throws IOException {
Feature f = null;
boolean canScroll = (forward && !frame.windowAtEnd()) || (!forward && frame.getOrigin() > 0);
PackedFeatures packedFeatures = packedFeaturesMap.get(frame.getName());
if (packedFeatures != null && packedFeatures.containsInterval(chr, (int) center - 1, (int) center + 1)) {
if (packedFeatures.getFeatures().size() > 0 && canScroll) {
f = (forward ? FeatureUtils.getFeatureAfter(center + 1, packedFeatures.getFeatures()) :
FeatureUtils.getFeatureBefore(center - 1, packedFeatures.getFeatures()));
}
if (f == null) {
FeatureSource rawSource = source;
if (source instanceof CachingFeatureSource) {
rawSource = ((CachingFeatureSource) source).getSource();
}
if (rawSource instanceof MotifFinderSource || rawSource instanceof PluginFeatureSource) {
FeatureTrackUtils.nextFeatureSearch(source, chr, packedFeatures.getStart(), packedFeatures.getEnd(),
forward, new FeatureSearcher.GotoFeatureHandler());
} else {
f = FeatureTrackUtils.nextFeature(source, chr, packedFeatures.getStart(), packedFeatures.getEnd(), forward);
}
}
}
return f;
}
public void setVisibilityWindow(int windowSize) {
super.setVisibilityWindow(windowSize);
packedFeaturesMap.clear();
source.setFeatureWindowSize(visibilityWindow);
}
public int getSelectedFeatureRowIndex() {
return selectedFeatureRowIndex;
}
public void setSelectedFeatureRowIndex(int selectedFeatureRowIndex) {
this.selectedFeatureRowIndex = selectedFeatureRowIndex;
}
public IGVFeature getSelectedFeature() {
return selectedFeature;
}
public static boolean isDrawBorder() {
return drawBorder;
}
public static void setDrawBorder(boolean drawBorder) {
FeatureTrack.drawBorder = drawBorder;
}
public boolean isAlternateExonColor() {
return alternateExonColor;
}
@SubtlyImportant
private static FeatureTrack getNextTrack() {
FeatureTrack out = (FeatureTrack) IGVSessionReader.getNextTrack();
if (out == null) out = new FeatureTrack((String) null, null);
return out;
}
@Override
public void restorePersistentState(Node node, int version) throws JAXBException {
super.restorePersistentState(node, version);
if (node.hasChildNodes()) {
NodeList childNodes = node.getChildNodes();
for (int ii = 0; ii < childNodes.getLength(); ii++) {
Node child = childNodes.item(ii);
String nodeName = child.getNodeName();
if (nodeName.contains("#text")) continue;
if (nodeName.equalsIgnoreCase(PLUGIN_SOURCE)) {
source = IGVSessionReader.getJAXBContext().createUnmarshaller().unmarshal(child, PluginFeatureSource.class).getValue();
} else if (nodeName.equalsIgnoreCase(SEQUENCE_MATCH_SOURCE)) {
FeatureSource rawSource = IGVSessionReader.getJAXBContext().createUnmarshaller().unmarshal(child, MotifFinderSource.class).getValue();
source = new CachingFeatureSource(rawSource);
} else {
try {
FeatureSource newSource = (FeatureSource) IGVSessionReader.getJAXBContext().createUnmarshaller().unmarshal(child, Class.forName(nodeName)).getValue();
source = newSource;
} catch (Exception e) {
//Lots can go wrong, it just means this isn't a FeatureSource
//Probably not an error
}
}
}
}
}
/**
* @param m
* @param trackElement
* @throws JAXBException
*/
public void marshalSource(Marshaller m, Element trackElement) throws JAXBException {
if (source == null) return;
FeatureSource rawSource = source;
if (rawSource instanceof CachingFeatureSource) {
rawSource = ((CachingFeatureSource) rawSource).getSource();
}
//We apply special treatment for a few classes
if (rawSource instanceof PluginSource) {
JAXBElement element = new JAXBElement<PluginSource>(new QName("", PLUGIN_SOURCE), PluginSource.class,
(PluginSource) rawSource);
m.marshal(element, trackElement);
} else if (rawSource instanceof MotifFinderSource) {
JAXBElement element = new JAXBElement<MotifFinderSource>(new QName("", SEQUENCE_MATCH_SOURCE), MotifFinderSource.class,
(MotifFinderSource) rawSource);
m.marshal(element, trackElement);
} else {
//Users can write their own FeatureSources, we tag with the fully qualified class name
Class<? extends FeatureSource> srcClazz = rawSource.getClass();
JAXBElement element = new JAXBElement(new QName("", srcClazz.getName()), srcClazz, rawSource);
try {
m.marshal(element, trackElement);
} catch (MarshalException e) {
//This happens if the source is not marshallable
//Many of our classes can't, and that's not an error
}
}
}
/**
* This method exists for Plugin tracks. When restoring a session there is no guarantee of track
* order, so arguments referring to other tracks may fail to resolve. We update those references
* here after all tracks have been processed
*
* @param allTracks
*/
public void updateTrackReferences(List<Track> allTracks) {
if (source instanceof PluginSource) {
((PluginSource) source).updateTrackReferences(allTracks);
}
}
/**
* Features are packed upon loading, effectively a cache.
* This clears that cache. Used to force a refresh
*
* @api
*/
public void clearPackedFeatures() {
this.packedFeaturesMap.clear();
}
/**
* Return currently loaded features. Used to export features to a file.
*
* @param frame
* @return
*/
public List<Feature> getVisibleFeatures(ReferenceFrame frame) {
PackedFeatures packedFeatures = packedFeaturesMap.get(frame.getName());
return (packedFeatures == null) ? Collections.emptyList() : packedFeatures.getFeatures();
}
public void setTrackLine(String trackLine) {
this.trackLine = trackLine;
}
/**
* Return "track" line information for exporting features to a file. Default is null, subclasses may override.
*
* @return
*/
public String getExportTrackLine() {
return trackLine;
}
}