/
GWTGenomeCanvas.java
executable file
·1410 lines (1149 loc) · 37.6 KB
/
GWTGenomeCanvas.java
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/*--------------------------------------------------------------------------
* Copyright 2008 utgenome.org
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*--------------------------------------------------------------------------*/
//--------------------------------------
// utgb-core Project
//
// GWTGenomeCanvas.java
// Since: Jul 8, 2008
//
//--------------------------------------
package org.utgenome.gwt.utgb.client.canvas;
import com.google.gwt.core.client.GWT;
import com.google.gwt.dom.client.ImageElement;
import com.google.gwt.user.client.DOM;
import com.google.gwt.user.client.Event;
import com.google.gwt.user.client.Timer;
import com.google.gwt.user.client.Window;
import com.google.gwt.user.client.ui.*;
import com.google.gwt.widgetideas.graphics.client.Color;
import com.google.gwt.widgetideas.graphics.client.GWTCanvas;
import com.google.gwt.widgetideas.graphics.client.ImageLoader;
import com.google.gwt.widgetideas.graphics.client.ImageLoader.CallBack;
import org.utgenome.gwt.ipad.client.TouchableComposite;
import org.utgenome.gwt.ipad.event.*;
import org.utgenome.gwt.utgb.client.UTGBClientException;
import org.utgenome.gwt.utgb.client.bio.*;
import org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas.GraphStyle;
import org.utgenome.gwt.utgb.client.canvas.IntervalLayout.IntervalRetriever;
import org.utgenome.gwt.utgb.client.canvas.IntervalLayout.LocusLayout;
import org.utgenome.gwt.utgb.client.track.TrackGroup;
import org.utgenome.gwt.utgb.client.track.TrackWindow;
import org.utgenome.gwt.utgb.client.ui.FixedWidthLabel;
import org.utgenome.gwt.utgb.client.ui.RoundCornerFrame;
import org.utgenome.gwt.utgb.client.util.Optional;
import org.utgenome.gwt.widget.client.Style;
import java.util.ArrayList;
import java.util.List;
/**
* Browser-side graphic canvas for drawing gene objects
*
* @author leo
*
*/
public class GWTGenomeCanvas extends TouchableComposite {
private ReadDisplayStyle style = new ReadDisplayStyle();
// private int defaultGeneHeight = 12;
// private int defaultMinGeneHeight = 2;
private int geneHeight = style.readHeight;
private int geneMargin = 2;
private boolean reverse = false;
// widget
private GWTCanvas canvas = new GWTCanvas();
private AbsolutePanel basePanel = new AbsolutePanel();
private AbsolutePanel panel = new AbsolutePanel();
private static PopupInfo popupLabel = new PopupInfo();
private LocusClickHandler clickHandler = null;
private IntervalLayout intervalLayout = new IntervalLayout();
private TrackWindow trackWindow;
public static enum CoverageStyle {
DEFAULT, SMOOTH
};
private CoverageStyle coverageStyle = CoverageStyle.DEFAULT;
private List<Widget> readLabels = new ArrayList<Widget>();
private TrackGroup trackGroup;
public GWTGenomeCanvas() {
initWidget();
}
static class PopupInfo extends PopupPanel {
GenomeRange locus;
private FlexTable infoTable = new FlexTable();
public PopupInfo() {
super(true);
RoundCornerFrame infoFrame = new RoundCornerFrame("336699", 0.7f, 4);
infoFrame.setWidgetPanel(infoTable);
this.setWidget(infoFrame);
}
public void setLocus(GenomeRange g) {
if (this.locus == g)
return;
this.locus = g;
}
public void update() {
if (locus == null)
return;
InfoSilkGenerator silk = new InfoSilkGenerator();
locus.accept(silk);
infoTable.clear();
final int numRowsInCol = 15;
final List<String> lines = silk.getLines();
final int cols = lines.size() / numRowsInCol + (lines.size() % numRowsInCol != 0 ? 1 : 0);
for (int col = 0; col < cols; col++) {
VerticalPanel p = new VerticalPanel();
Style.padding(p, Style.LEFT | Style.RIGHT, 5);
Style.fontColor(p, "white");
Style.fontSize(p, 14);
Style.margin(p, 0);
Style.preserveWhiteSpace(p);
for (int i = 0; i < numRowsInCol; i++) {
int index = numRowsInCol * col + i;
if (index >= lines.size())
break;
p.add(new Label(lines.get(index)));
}
infoTable.setWidget(0, col, p);
}
}
}
public void setLocusClickHandler(LocusClickHandler handler) {
this.clickHandler = handler;
}
@Override
public void onBrowserEvent(Event event) {
super.onBrowserEvent(event);
int type = DOM.eventGetType(event);
switch (type) {
case Event.ONMOUSEOVER:
break;
case Event.ONMOUSEMOVE: {
moveDrag(event);
break;
}
case Event.ONMOUSEOUT: {
resetDrag(event);
break;
}
case Event.ONMOUSEDOWN: {
// invoke a click event
startDrag(event);
break;
}
case Event.ONMOUSEUP: {
resetDrag(event);
break;
}
}
}
private void startDrag(Event event) {
if (startDrag(getXOnCanvas(event), getYOnCanvas(event))) {
event.preventDefault();
}
else {
Event.setCapture(this.getElement());
}
}
private boolean startDrag(int clientX, int clientY) {
GenomeRange g = overlappedInterval(clientX, clientY, 2);
if (g != null) {
if (clickHandler != null)
clickHandler.onClick(clientX, clientY, g);
return true;
}
else {
dragStartPoint.set(new DragPoint(clientX, clientY));
Style.cursor(canvas, Style.CURSOR_RESIZE_E);
}
return false;
}
private void moveDrag(Event e) {
moveDrag(getXOnCanvas(e), getYOnCanvas(e));
}
private void moveDrag(int clientX, int clientY) {
// show readLabels
GenomeRange g = overlappedInterval(clientX, clientY, 2);
if (g != null) {
if (popupLabel.locus != g) {
Style.cursor(canvas, Style.CURSOR_POINTER);
displayInfo(clientX, clientY, g);
}
}
else {
if (dragStartPoint.isDefined() && trackWindow != null) {
DragPoint p = dragStartPoint.get();
final int x_origin = trackWindow.convertToGenomePosition(p.x);
int startDiff = trackWindow.convertToGenomePosition(clientX) - x_origin;
if (startDiff != 0) {
int newStart = trackWindow.getStartOnGenome() - startDiff;
if (newStart < 1)
newStart = 1;
int newEnd = newStart + trackWindow.getSequenceLength();
TrackWindow newWindow = trackWindow.newWindow(newStart, newEnd);
if (trackGroup != null)
trackGroup.setTrackWindow(newWindow);
dragStartPoint.set(new DragPoint(clientX, p.y));
}
}
else {
Style.cursor(canvas, Style.CURSOR_AUTO);
popupLabel.setLocus(null);
}
}
}
private void resetDrag(Event event) {
resetDrag(getXOnCanvas(event), getYOnCanvas(event));
DOM.releaseCapture(this.getElement());
event.preventDefault();
}
private void resetDrag(int clientX, int clientY) {
if (dragStartPoint.isDefined() && trackWindow != null) {
DragPoint p = dragStartPoint.get();
final int x_origin = trackWindow.convertToGenomePosition(p.x);
int startDiff = trackWindow.convertToGenomePosition(clientX) - x_origin;
if (startDiff != 0) {
int newStart = trackWindow.getStartOnGenome() - startDiff;
if (newStart < 1)
newStart = 1;
int newEnd = newStart + trackWindow.getSequenceLength();
TrackWindow newWindow = trackWindow.newWindow(newStart, newEnd);
if (trackGroup != null)
trackGroup.setTrackWindow(newWindow);
}
}
dragStartPoint.reset();
Style.cursor(canvas, Style.CURSOR_AUTO);
}
public static class DragPoint {
public final int x;
public final int y;
public DragPoint(int x, int y) {
this.x = x;
this.y = y;
}
}
private Optional<DragPoint> dragStartPoint = new Optional<DragPoint>();
public void displayInfo(final int clientX, final int clientY, final GenomeRange g) {
if (popupLabel == null)
popupLabel = new PopupInfo();
popupLabel.setLocus(g);
Timer timer = new Timer() {
@Override
public void run() {
popupLabel.removeFromParent();
if (popupLabel.locus == g) {
int x = clientX + 10 + getAbsoluteLeft();
int y = clientY + 3 + getAbsoluteTop();
final int w = Window.getClientWidth();
final int h = Window.getClientHeight();
final int xMax = w - 300;
//final int yMax = Math.max(h - 200 + Window.getScrollTop(), Window.getScrollTop());
if (x > xMax)
x = xMax;
// if (y > yMax)
// y = yMax;
popupLabel.setPopupPosition(x, y);
popupLabel.update();
popupLabel.show();
}
}
};
timer.schedule(100);
}
public void setAllowOverlapPairedReads(boolean allow) {
}
/**
* compute the overlapped intervals for the mouse over event
*
* @param event
* @param xBorder
* @return
*/
private GenomeRange overlappedInterval(Event event, int xBorder) {
return overlappedInterval(getXOnCanvas(event), getYOnCanvas(event), xBorder);
}
private GenomeRange overlappedInterval(int clientX, int clientY, int xBorder) {
int h = getReadHeight();
int x = drawPosition(clientX);
int y = clientY;
GenomeRange g = intervalLayout.overlappedInterval(x, y, xBorder, h);
return g;
}
public int getXOnCanvas(Event event) {
return getXOnCanvas(DOM.eventGetClientX(event));
}
public int getXOnCanvas(int clientX) {
return clientX + Window.getScrollLeft() - basePanel.getAbsoluteLeft();
}
public int getYOnCanvas(int clientY) {
return clientY + Window.getScrollTop() - basePanel.getAbsoluteTop();
}
public int getYOnCanvas(Event event) {
return getYOnCanvas(DOM.eventGetClientY(event));
}
private void initWidget() {
super.initWidget(basePanel);
panel.add(canvas, 0, 0);
basePanel.add(panel, 0, 0);
sinkEvents(Event.ONMOUSEMOVE | Event.ONMOUSEOVER | Event.ONMOUSEDOWN | Event.ONMOUSEUP | Event.ONMOUSEOUT);
// add touch handler for iPad
this.addTouchStartHandler(new TouchStartHandler() {
public void onTouchStart(TouchStartEvent event) {
Touch touch = event.touches().get(0);
event.preventDefault();
startDrag(touch.getClientX(), touch.getClientY());
DOM.setCapture(GWTGenomeCanvas.this.getElement());
}
});
this.addTouchMoveHandler(new TouchMoveHandler() {
public void onTouchMove(TouchMoveEvent event) {
event.preventDefault();
Touch touch = event.touches().get(0);
moveDrag(touch.getClientX(), touch.getClientY());
}
});
this.addTouchEndHandler(new TouchEndHandler() {
public void onTouchEnd(TouchEndEvent event) {
Touch touch = event.touches().get(0);
resetDrag(touch.getClientX(), touch.getClientY());
DOM.releaseCapture(GWTGenomeCanvas.this.getElement());
//event.preventDefault();
}
});
this.addTouchCancelHandler(new TouchCancelHandler() {
public void onTouchCancel(TouchCancelEvent event) {
Touch touch = event.touches().get(0);
resetDrag(touch.getClientX(), touch.getClientY());
DOM.releaseCapture(GWTGenomeCanvas.this.getElement());
//event.preventDefault();
}
});
}
private boolean hasCache = false;
private TrackWindow prefetchWindow;
public boolean hasCacheCovering(TrackWindow newWindow) {
return prefetchWindow != null && hasCache && prefetchWindow.contains(newWindow);
}
public TrackWindow getPrefetchWindow() {
return prefetchWindow;
}
private float DEFAULT_PREFETCH_FACTOR = 1.0f;
private float PREFETCH_FACTOR = DEFAULT_PREFETCH_FACTOR;
public void resetPrefetchFactor() {
this.PREFETCH_FACTOR = DEFAULT_PREFETCH_FACTOR;
}
public float getPrefetchFactor() {
return this.PREFETCH_FACTOR;
}
public void setPrefetchFactor(float factor) {
if (factor <= 0.3f)
factor = 0.3f;
this.PREFETCH_FACTOR = factor;
}
/**
* @param newWindow
*/
public void setTrackWindow(TrackWindow newWindow, boolean resetPrefetchWindow) {
if (resetPrefetchWindow || !hasCacheCovering(newWindow)) { // when need to prefetch the data
int prefetchStart = newWindow.getStartOnGenome() - (int) (newWindow.getSequenceLength() * PREFETCH_FACTOR);
int prefetchEnd = newWindow.getEndOnGenome() + (int) (newWindow.getSequenceLength() * PREFETCH_FACTOR);
if (prefetchStart <= 0) {
prefetchStart = 1;
prefetchEnd = newWindow.getEndOnGenome() + (int) (newWindow.getSequenceLength() * PREFETCH_FACTOR * 2);
}
int prefetchPixelSize = (int) (newWindow.getPixelWidth() * (1 + PREFETCH_FACTOR * 2));
prefetchWindow = new TrackWindow(prefetchPixelSize, prefetchStart, prefetchEnd);
hasCache = false;
}
if (trackWindow != null) {
int newX = newWindow.convertToPixelX(trackWindow.getStartOnGenome());
if (!trackWindow.hasSameScaleWith(newWindow)) {
int newPixelWidth = newWindow.convertToPixelLength(trackWindow.getSequenceLength());
Style.scaleXwithAnimation(canvas, (double) newPixelWidth / trackWindow.getPixelWidth(), newX, 0.5);
imageACGT = null;
}
else {
Style.scrollX(canvas, newX, 0.5);
}
}
this.trackWindow = newWindow;
reverse = newWindow.isReverseStrand();
intervalLayout.setTrackWindow(newWindow);
}
public void setTrackGroup(TrackGroup trackGroup) {
this.trackGroup = trackGroup;
}
public int pixelPositionOnWindow(int indexOnGenome) {
return trackWindow.convertToPixelX(indexOnGenome);
}
public void clearWidgets() {
canvas.clear();
//imageACGT = null;
if (popupLabel != null)
popupLabel.removeFromParent();
scale.removeFromParent();
for (Widget w : readLabels) {
w.removeFromParent();
}
readLabels.clear();
Style.scaleXwithAnimation(canvas, 1, 0.0);
panel.setWidgetPosition(canvas, 0, 0);
basePanel.setWidgetPosition(panel, 0, 0);
}
public void clear() {
clearWidgets();
prefetchWindow = null;
hasCache = false;
intervalLayout.clear();
}
public static int width(int x1, int x2) {
return (x1 < x2) ? x2 - x1 : x1 - x2;
}
private final int FONT_WIDTH = 7;
private static final String DEFAULT_COLOR_A = "#50B6E8";
private static final String DEFAULT_COLOR_C = "#E7846E";
private static final String DEFAULT_COLOR_G = "#84AB51";
private static final String DEFAULT_COLOR_T = "#FFA930";
private static final String DEFAULT_COLOR_N = "#999999";
private static final float repeatColorAlpha = 0.3f;
private static final Color[] colors = {
getColor(DEFAULT_COLOR_A, 1.0f),
getColor(DEFAULT_COLOR_C, 1.0f),
getColor(DEFAULT_COLOR_G, 1.0f),
getColor(DEFAULT_COLOR_T, 1.0f),
getColor(DEFAULT_COLOR_A, repeatColorAlpha),
getColor(DEFAULT_COLOR_C, repeatColorAlpha),
getColor(DEFAULT_COLOR_G, repeatColorAlpha),
getColor(DEFAULT_COLOR_T, repeatColorAlpha),
getColor(DEFAULT_COLOR_N, 1.0f)
};
private int getReadHeight() {
return geneHeight + geneMargin;
}
/**
* A class for drawing OnGenome objects on a canvas
*
* @author leo
*
*/
class ReadPainter extends GenomeRangeVisitorBase {
private LocusLayout gl;
private int h = getReadHeight();
private char[] seqtxt;
public void setLayoutInfo(LocusLayout layout) {
this.gl = layout;
}
public void setSeqtxt(char[] sequence) {
this.seqtxt = sequence;
}
public int getYPos() {
return gl.scaledHeight(h);
}
public int getYPos(int y) {
return LocusLayout.scaledHeight(y, h);
}
@Override
public void visitGene(Gene g) {
int gx1 = pixelPositionOnWindow(g.getStart());
int gx2 = pixelPositionOnWindow(g.getEnd());
int geneWidth = gx2 - gx1;
if (geneWidth <= 10) {
draw(g, getYPos());
}
else {
CDS cds = g.getCDS().size() > 0 ? g.getCDS().get(0) : null;
draw(g, g.getExon(), cds, getYPos());
}
drawLabel(g);
}
public void drawBases(int startOnGenome, int y, String seq, String qual) {
char[] seqarr = chrSeq;
int startSeq = intStartSeq;
int pixelWidthOfBase = (int) (trackWindow.getPixelLengthPerBase() + 0.1d);
if (imageACGT == null) {
GWT.log("font image is not loaded");
return;
}
for (int i = 0; i < seq.length(); i++) {
int baseIndex = 8;
switch (seq.charAt(i)) {
case 'A':
baseIndex = 0;
break;
case 'C':
baseIndex = 1;
break;
case 'G':
baseIndex = 2;
break;
case 'T':
baseIndex = 3;
break;
case 'a':
baseIndex = 4;
break;
case 'c':
baseIndex = 5;
break;
case 'g':
baseIndex = 6;
break;
case 't':
baseIndex = 7;
break;
case 'N':
baseIndex = 8;
break;
default:
continue;
}
if (style.unmatchHighlight) {
if (i + startOnGenome >= startSeq && i + (startOnGenome - startSeq) < seqarr.length) {
if (seqarr[i + startOnGenome - startSeq] == seq.charAt(i)) {
baseIndex = 9;
}
else if (baseIndex > 3 && baseIndex < 8) {
baseIndex = 10;
}
}
}
final double x1 = trackWindow.convertToPixelXDouble(startOnGenome + i);
final double x2 = trackWindow.convertToPixelXDouble(startOnGenome + i + 1);
final int actualBaseWidth = (int)x2 - (int)x1;
int h = imageACGT.getHeight();
if (h >= geneHeight)
h = geneHeight;
if (qual == null || h < 5 || !style.showBaseQuality) {
canvas.drawImage(imageACGT, pixelWidthOfBase * baseIndex, 0, pixelWidthOfBase, h, (int) x1, y, pixelWidthOfBase, h);
if(actualBaseWidth != pixelWidthOfBase) {
canvas.drawImage(imageACGT, pixelWidthOfBase * baseIndex, 0, 1, h, (int)x2 - 1, y, 1, h);
}
}
else {
canvas.saveContext();
final int threshold = 40;
if (i < qual.length()) {
int qv = qual.charAt(i) - 33;
if (qv > threshold)
qv = threshold;
if (qv < 0)
qv = 0;
float ratio = (float) qv / threshold;
canvas.setFillStyle(colors[baseIndex]);
canvas.fillRect((int)x1, y, actualBaseWidth, geneHeight);
canvas.setFillStyle(new Color(255, 255, 255, 0.7f));
canvas.fillRect((int)x1, y, actualBaseWidth, h * (1 - ratio));
canvas.drawImage(imageACGT, pixelWidthOfBase * baseIndex, h, pixelWidthOfBase, h, (int)x1, y, pixelWidthOfBase, h);
if(actualBaseWidth != pixelWidthOfBase) {
canvas.drawImage(imageACGT, pixelWidthOfBase * baseIndex, h, 1, h, (int)x2 - 1, y, 1, h);
}
}
canvas.restoreContext();
}
}
}
private void drawLabel(GenomeRange r, int y) {
if (!intervalLayout.hasEnoughHeightForLabels())
return;
IntervalRetriever ir = new IntervalRetriever();
ir.allowPEOverlap = style.overlapPairedReads;
r.accept(ir);
int gx1 = pixelPositionOnWindow(ir.start);
int gx2 = pixelPositionOnWindow(ir.end);
String n = r.getName();
if (n != null) {
int textWidth = IntervalLayout.estimiateLabelWidth(r, geneHeight);
Widget label = new FixedWidthLabel(n, textWidth);
Style.fontSize(label, geneHeight);
Style.fontColor(label, getExonColorText(r));
Style.verticalAlign(label, "middle");
int yPos = y - 1;
if (gx1 - textWidth < 0) {
if (reverse) {
Style.textAlign(label, "right");
panel.add(label, drawPosition(gx2) - textWidth - 1, yPos);
}
else {
Style.textAlign(label, "left");
panel.add(label, drawPosition(gx2) + 1, yPos);
}
}
else {
if (reverse) {
Style.textAlign(label, "left");
panel.add(label, drawPosition(gx1) + 1, yPos);
}
else {
Style.textAlign(label, "right");
panel.add(label, drawPosition(gx1) - textWidth - 1, yPos);
}
}
readLabels.add(label);
}
}
@Override
public void visitGap(Gap p) {
drawPadding(pixelPositionOnWindow(p.getStart()), pixelPositionOnWindow(p.getEnd()), getYPos(), getColor("#666666", 1.0f), true);
}
private void drawLabel(GenomeRange r) {
drawLabel(r, getYPos());
}
@Override
public void visitInterval(Interval interval) {
draw(interval, getYPos());
}
@Override
public void visitRead(Read r) {
draw(r, getYPos());
drawLabel(r);
}
@Override
public void visitSAMReadPair(SAMReadPair pair) {
SAMReadLight first = pair.getFirst();
SAMReadLight second = pair.getSecond();
int y1 = getYPos();
int y2 = y1;
if (!style.overlapPairedReads && first.unclippedSequenceHasOverlapWith(second)) {
if (first.unclippedStart > second.unclippedStart) {
SAMReadLight tmp = first;
first = second;
second = tmp;
}
y2 = getYPos(gl.getYOffset() + 1);
}
else {
visitGap(pair.getGap());
}
drawLabel(pair);
drawSAMRead(first, y1, false);
drawSAMRead(second, y2, false);
}
@Override
public void visitSAMReadPairFragment(SAMReadPairFragment fragment) {
drawLabel(fragment);
visitGap(fragment.getGap());
drawSAMRead(fragment.oneEnd, getYPos(), false);
}
@Override
public void visitSAMReadLight(SAMReadLight r) {
drawSAMRead(r, getYPos(), true);
}
class PostponedInsertion {
final int pixelX;
final String subseq;
public PostponedInsertion(int pixelX, String subseq) {
this.pixelX = pixelX;
this.subseq = subseq;
}
}
public void drawSAMRead(SAMReadLight r, int y, boolean drawLabel) {
try {
int cx1 = pixelPositionOnWindow(r.unclippedStart);
int cx2 = pixelPositionOnWindow(r.unclippedEnd);
int gx1 = pixelPositionOnWindow(r.getStart());
int gx2 = pixelPositionOnWindow(r.getEnd());
int width = gx2 - gx1;
if ((cx2 - cx1) <= 5) {
// when the pixel range is narrow, draw a rectangle only
draw(r, y);
}
else {
boolean drawBase = trackWindow.getSequenceLength() <= (trackWindow.getPixelWidth() / FONT_WIDTH);
CIGAR cigar = new CIGAR(r.cigar);
int readStart = r.getStart();
int seqIndex = 0;
// Drawing insertions should be postponed after all of he read bases are painted.
List<PostponedInsertion> postponed = new ArrayList<PostponedInsertion>();
for (int cigarIndex = 0; cigarIndex < cigar.size(); cigarIndex++) {
CIGAR.Element e = cigar.get(cigarIndex);
int readEnd = readStart + e.length;
int x1 = pixelPositionOnWindow(readStart);
switch (e.type) {
case Deletions:
// ref : AAAAAA
// read: ---AAA
// cigar: 3D3M
drawPadding(x1, pixelPositionOnWindow(readEnd), y, style.getSAMReadColor(r), true);
break;
case Insertions:
// ref : ---AAA
// read: AAAAAA
// cigar: 3I3M
if (r.getSequence() != null)
postponed.add(new PostponedInsertion(x1, r.getSequence().substring(seqIndex, seqIndex + e.length)));
readEnd = readStart;
seqIndex += e.length;
break;
case Padding:
// ref : AAAAAA
// read: ---AAA
// cigar: 3P3M
readEnd = readStart;
drawPadding(x1, pixelPositionOnWindow(readStart) + 1, y, style.getPaddingColor(), false);
break;
case Matches: {
int x2 = pixelPositionOnWindow(readEnd);
if (drawBase && r.getSequence() != null) {
//drawGeneRect(x1, x2, y, getCDSColor(r, 0.3f), true);
drawBases(readStart, y, r.getSequence().substring(seqIndex, seqIndex + e.length),
r.getQV() != null ? r.getQV().substring(seqIndex, seqIndex + e.length) : null);
}
else {
drawGeneRect(x1, x2, y, style.getSAMReadColor(r), style.drawShadow);
}
seqIndex += e.length;
}
break;
case SkippedRegion:
drawPadding(x1, pixelPositionOnWindow(readEnd), y, style.getReadColor(r), true);
break;
case SoftClip: {
int softclipStart = cigarIndex == 0 ? readStart - e.length : readStart;
int softclipEnd = cigarIndex == 0 ? readStart : readStart + e.length;
readEnd = softclipEnd;
int x0 = pixelPositionOnWindow(softclipStart);
x1 = pixelPositionOnWindow(softclipEnd);
if (drawBase && r.getSequence() != null) {
drawBases(softclipStart, y, r.getSequence().substring(seqIndex, seqIndex + e.length).toLowerCase(), r.getQV() != null ? r
.getQV().substring(seqIndex, seqIndex + e.length) : null);
}
else {
drawGeneRect(x0, x1, y, style.getClippedReadColor(r), style.drawShadow);
}
seqIndex += e.length;
}
break;
case HardClip:
readEnd -= e.length;
break;
}
readStart = readEnd;
}
for (PostponedInsertion each : postponed) {
drawGeneRect(each.pixelX, each.pixelX + 1, y, getColor("#111111", 1.0f), true);
}
}
}
catch (UTGBClientException e) {
// when parsing CIGAR string fails, simply draw a rectangle
draw(r, y);
}
if (drawLabel)
drawLabel(r, y);
}
@Override
public void visitSequence(ReferenceSequence referenceSequence) {
// TODO Auto-generated method stub
}
@Override
public void visitReadCoverage(ReadCoverage readCoverage) {
drawBlock(readCoverage);
}
@Override
public void visitGraph(GraphData graph) {
// TODO Auto-generated method stub
}
@Override
public void visitReadList(ReadList readList) {
// TODO Auto-generated method stub
}
};
private class FindMaximumHeight extends GenomeRangeVisitorBase {
int maxHeight = 1;
@Override
public void visitReadCoverage(ReadCoverage readCoverage) {
if (readCoverage.coverage == null)
return;
int startPosOfCoverageOnGenome = readCoverage.getStart();
int viewStartOnGenome = trackWindow.getStartOnGenome();
int viewEndOnGenome = trackWindow.getEndOnGenome();
TrackWindow w = new TrackWindow(readCoverage.pixelWidth, readCoverage.getStart(), readCoverage.getEnd());
int startPosInCoveragePixel = w.convertToPixelX(viewStartOnGenome);
int endPosInCoveragePixel = w.convertToPixelX(viewEndOnGenome);
if (endPosInCoveragePixel > readCoverage.pixelWidth)
endPosInCoveragePixel = readCoverage.pixelWidth;
// set canvas size
for (int i = startPosInCoveragePixel; i < endPosInCoveragePixel; ++i) {
int height = readCoverage.coverage[i];
if (height > maxHeight)
maxHeight = height;
}
}
}
private class CoveragePainter extends GenomeRangeVisitorBase {
private int heigtOfRead = 1;
private float scalingFactor = 1.0f;
public CoveragePainter(int heightOfRead, float scalingFactor) {
this.heigtOfRead = heightOfRead;
this.scalingFactor = scalingFactor;
}
@Override
public void visitReadCoverage(ReadCoverage readCoverage) {
canvas.saveContext();
canvas.setStrokeStyle(getColor("#FFFFFF", 0.0f));
canvas.setFillStyle(getColor("#6699CC", 0.6f));
canvas.setLineWidth(0.1f);
canvas.setLineCap("round");
int x1 = pixelPositionOnWindow(trackWindow.getStartOnGenome());
int x2 = pixelPositionOnWindow(trackWindow.getEndOnGenome());
if (x1 < 0)
x1 = 0;
if (x2 > readCoverage.pixelWidth)
x2 = readCoverage.pixelWidth;
int w = x2 - x1;
canvas.scale(trackWindow.getPixelWidth() / (double) w, 1.0f);
canvas.saveContext();
canvas.beginPath();
canvas.moveTo(-0.5f, -1.0f);
for (int x = x1; x < x2; ++x) {
int h = readCoverage.coverage[x];
if (h <= 0) {
canvas.lineTo(x - x1 + 0.5f, -1.0f);
continue;
}
int y = (int) ((h * heigtOfRead) * scalingFactor);
canvas.lineTo(x - x1 + 0.5f, y + 0.5f);
canvas.stroke();
}
canvas.moveTo(readCoverage.pixelWidth + 0.5f, -1.0f);
canvas.fill();
canvas.restoreContext();
canvas.restoreContext();
}
}
private class RoughCoveragePainter extends GenomeRangeVisitorBase {
private int heigtOfRead = 1;
private float scalingFactor = 1.0f;