/*
* 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.maf;
import org.apache.log4j.Logger;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.renderer.ContinuousColorScale;
import org.broad.igv.renderer.GraphicUtils;
import org.broad.igv.track.*;
import org.broad.igv.ui.FontManager;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.panel.IGVPopupMenu;
import org.broad.igv.ui.panel.ReferenceFrame;
import org.broad.igv.util.ResourceLocator;
import javax.swing.*;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.MouseEvent;
import java.io.IOException;
import java.util.*;
import java.util.List;
/**
* @author jrobinso
*/
public class MultipleAlignmentTrack extends AbstractTrack {
public static final int margin = 5;
private static Logger log = Logger.getLogger(MultipleAlignmentTrack.class);
private static int EXPANDED_HEIGHT = 14;
private static int GAPS_HEIGHT = 25;
Genome genome;
private String refId;
private List<String> selectedSpecies;
//private Map<String, String> speciesNames;
MAFRenderer renderer = new MAFRenderer();
Rectangle visibleNameRect;
private int tileSize = 500;
//MafChunk currentChunk
MAFReader reader;
MAFCache loadedAlignments;
/**
* Map of chr alias -> "true" chromosome names.
*/
private HashMap<String, String> chrMappings;
public MultipleAlignmentTrack(final ResourceLocator locator, Genome genome) throws IOException {
super(locator);
this.genome = genome;
if (locator.getPath().endsWith(".maf.dict")) {
reader = new MAFListReader(locator.getPath());
// speciesNames.put(genome.getId(), genome.getDisplayName());
} else {
MAFParser parser = new MAFParser(locator.getPath()); // new MAFLocalReader(locator.getPath());
String trackName = parser.getTrackName();
if (trackName != null) {
setName(trackName);
}
reader = parser;
}
refId = reader.getRefId();
Collection<String> mafChrNames = getChrNames();
if (mafChrNames != null) {
chrMappings = new HashMap();
for (String mafChr : mafChrNames) {
String chr = genome.getCanonicalChrName(mafChr);
chrMappings.put(chr, mafChr);
}
}
selectedSpecies = new ArrayList<String>();
selectedSpecies.addAll(reader.getSpecies());
}
public List<String> getSelectedSpecies() {
return selectedSpecies;
}
/**
* @param selectedSpecies the selectedSpecies to set
*/
public void setSelectedSpecies(List<String> selectedSpecies) {
this.selectedSpecies = selectedSpecies;
}
public String getSpeciesName(String speciesId) {
String name = reader.getSpeciesName(speciesId);
return name == null ? speciesId : name;
}
@Override
public int getHeight() {
return GAPS_HEIGHT + (getSelectedSpecies().size() + 1) * EXPANDED_HEIGHT;
}
@Override
public void renderName(Graphics2D g2D, Rectangle trackRectangle, Rectangle visibleRectangle) {
this.visibleNameRect = trackRectangle;
if (isSelected()) {
g2D.setBackground(Color.LIGHT_GRAY);
} else {
g2D.setBackground(Color.WHITE);
}
Rectangle rect = new Rectangle(trackRectangle);
g2D.clearRect(rect.x, rect.y, rect.width, rect.height);
Font font = FontManager.getFont(fontSize);
g2D.setFont(font);
int y = trackRectangle.y;
rect.height = GAPS_HEIGHT;
rect.y = y;
//text, rect.x + rect.width - margin, yPos, g2D
GraphicUtils.drawVerticallyCenteredText("Gaps", margin, rect, g2D, true);
rect.y += rect.height;
rect.height = EXPANDED_HEIGHT;
for (String sp : getSelectedSpecies()) {
String name = getSpeciesName(sp);
if (name == null) {
name = sp;
}
if (visibleRectangle.intersects(rect)) {
GraphicUtils.drawVerticallyCenteredText(name, margin, rect, g2D, true);
}
rect.y += rect.height;
}
}
public void setColorScale(ContinuousColorScale colorScale) {
//To change body of implemented methods use File | Settings | File Templates.
}
@Override
public boolean isReadyToPaint(ReferenceFrame frame) {
if (frame.getScale() > 1) return true; // Zoomed out, nothing to pain
String chr = frame.getChrName();
int start = (int) frame.getOrigin();
int end = (int) frame.getEnd();
return loadedAlignments != null && loadedAlignments.contains(chr, start, end);
}
@Override
public void load(ReferenceFrame frame) {
String chr = frame.getChrName();
double origin = frame.getOrigin();
double w = frame.getEnd() - origin;
// Get some buffer (+/- 1/2 screen)
String mafChr = chrMappings == null ? chr : chrMappings.get(chr);
int start = (int) Math.max(0, origin - w);
int end = (int) (origin + 2 * w);
List<MultipleAlignmentBlock> alignments = null;
try {
alignments = reader.loadAlignments(mafChr, start, end);
} catch (IOException e) {
log.error(e);
throw new RuntimeException(e);
}
loadedAlignments = new MAFCache(chr, start, end, alignments);
}
public void render(RenderContext context, Rectangle rect) {
double locScale = context.getScale();
if (locScale > 1) {
Rectangle r = new Rectangle(rect);
if (visibleNameRect != null) {
r.y = visibleNameRect.y;
r.height = visibleNameRect.height;
}
Graphics2D g = context.getGraphic2DForColor(Color.black);
GraphicUtils.drawCenteredText("Zoom in to see alignments.", r, g);
return;
}
ReferenceFrame frame = context.getReferenceFrame();
String chr = frame.getChrName();
int start = (int) frame.getOrigin();
int end = (int) frame.getEnd();
List<MultipleAlignmentBlock> alignments = null;
if (loadedAlignments != null && loadedAlignments.contains(chr, start, end)) {
alignments = loadedAlignments.getAlignments();
if (alignments != null) {
for (MultipleAlignmentBlock ma : alignments) {
renderAlignment(context, rect, ma);
}
}
}
}
private void renderAlignment(RenderContext context, Rectangle trackRectangle, MultipleAlignmentBlock ma) {
int y = trackRectangle.y;
MultipleAlignmentBlock.Sequence reference = ma.getRefSequence();
if (reference == null) {
return;
}
Rectangle rect = new Rectangle(trackRectangle);
rect.height = GAPS_HEIGHT;
rect.y = y;
renderer.renderGaps(ma.getGaps(), context, rect);
rect.y += rect.height;
rect.height = EXPANDED_HEIGHT;
for (String sp : getSelectedSpecies()) {
MultipleAlignmentBlock.Sequence seq = ma.getSequence(sp);
if (seq != null) {
renderer.renderSequence(ma, seq, reference, ma.getGaps(), context, rect, this);
}
rect.y += rect.height;
}
}
public boolean isLogNormalized() {
return false;
}
public String getValueStringAt(String chr, double position, int mouseX, int mouseY, ReferenceFrame frame) {
return "Multiple alignments";
}
public float getRegionScore(String chr, int start, int end, int zoom,
RegionScoreType type, String frameName) {
return 0;
}
/**
* Override to return a specialized popup menu
*
* @return
*/
@Override
public IGVPopupMenu getPopupMenu(TrackClickEvent te) {
IGVPopupMenu menu = new IGVPopupMenu();
if (getId().endsWith("hg18.maf.dict") || getId().endsWith("hg19.maf.dict")) {
menu.addSeparator();
JMenuItem configTrack = new JMenuItem("Configure track...");
configTrack.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent actionEvent) {
configureTrack();
}
});
menu.add(configTrack);
menu.addSeparator();
}
List<Track> selfAsList = Arrays.asList((Track) this);
return menu;
}
@Override
public boolean handleDataClick(TrackClickEvent te) {
MouseEvent e = te.getMouseEvent();
if (e.isPopupTrigger()) {
configureTrack();
} else {
if (IGV.getInstance().isShowDetailsOnClick()) {
openTooltipWindow(te);
}
}
return true;
}
private void configureTrack() {
AbstractMultipleAlignmentDialog dialog;
if (getId().endsWith("hg18.maf.dict") || getId().endsWith("hg19.maf.dict")) {
dialog = new Multiz44ConfigurationDialog(IGV.getMainFrame(), true, this);
} else {
dialog = null;
}
dialog.setLocationRelativeTo(IGV.getMainFrame());
dialog.addWindowListener(new java.awt.event.WindowAdapter() {
public void windowClosing(java.awt.event.WindowEvent e) {
System.exit(0);
}
});
dialog.setVisible(true);
if (dialog.isCancelled()) {
} else {
List<String> selectedSpecies = dialog.getSelectedSpecies();
setSelectedSpecies(selectedSpecies);
IGV.getInstance().repaint();
}
}
public Collection<String> getChrNames() {
return reader.getChrNames();
}
static String getKey(String chr, int tileNo) {
return chr + tileNo;
}
static class MAFCache {
String chr;
int start;
int end;
List<MultipleAlignmentBlock> alignments;
MAFCache(String chr, int start, int end, List<MultipleAlignmentBlock> alignments) {
this.chr = chr;
this.start = start;
this.end = end;
this.alignments = alignments;
}
boolean contains(String chr, int start, int end) {
return this.start <= start && this.end >= end && this.chr.equals(chr);
}
public List<MultipleAlignmentBlock> getAlignments() {
return alignments;
}
}
}