public void setTrackWindow(TrackWindow window, int newPixelX) {
TrackWindow prev = this.window;
this.window = window;
if (!prev.hasSameScaleWith(window)) {
Style.scaleXwithAnimation(
canvas, (double) window.getPixelWidth() / prev.getPixelWidth(), newPixelX, 0.5);
} else {
Style.scaleX(canvas, 1);
}
}
@Override
public void draw() {
String path = getConfig().getString(CONFIG_GENOME_DB_PATH, "");
String trackBaseURL = "utgb-core/Sequence.txt?path=" + path + "&%q";
String newURL = getTrackURL(trackBaseURL);
// replace track group properties
TrackWindow w = getTrackWindow();
final int startSeq = w.getStartOnGenome();
final RequestBuilder rb = new RequestBuilder(RequestBuilder.GET, newURL);
try {
rb.sendRequest(
null,
new RequestCallback() {
public void onResponseReceived(Request request, Response response) {
String strSeqarr = response.getText();
geneCanvas.setSequencetxt(strSeqarr);
geneCanvas.setStartSeq(startSeq);
char[] chrSeqarr = strSeqarr.toCharArray();
if (!chrSeqarr.equals(null)) {
geneCanvas.setSequencetxt(chrSeqarr);
geneCanvas.setReadStyle(style);
geneCanvas.draw();
getFrame().loadingDone();
}
}
public void onError(Request request, Throwable exception) {
// NOTE: we should output an error message to user
}
});
} catch (Exception e) {
//
}
}
protected void update(TrackWindow newWindow, boolean forceReload) {
current = newWindow;
if (!forceReload && geneCanvas.hasCacheCovering(newWindow)) {
if (!needUpdateForGraphicRefinement) {
geneCanvas.setTrackWindow(newWindow, false);
refresh();
return;
}
}
geneCanvas.setTrackWindow(newWindow, true);
// retrieve gene data from the API
TrackWindow prefetchWindow = geneCanvas.getPrefetchWindow();
String chr = getTrackGroupProperty(UTGBProperty.TARGET);
ReadQueryConfig queryConfig =
new ReadQueryConfig(
prefetchWindow.getPixelWidth(),
BrowserInfo.isCanvasSupported(),
Layout.valueOf(Layout.class, style.layout.toUpperCase()),
style.numReadsMax,
getWIGPath());
queryConfig.window =
GraphWindow.valueOf(
GraphWindow.class, getConfig().getString(CONFIG_GRAPH_WINDOW, "MEDIAN"));
getFrame().setNowLoading();
getBrowserService()
.getOnGenomeData(
getGenomeDB(),
new ChrLoc(chr, prefetchWindow.getStartOnGenome(), prefetchWindow.getEndOnGenome()),
queryConfig,
new AsyncCallback<List<GenomeRange>>() {
public void onFailure(Throwable e) {
GWT.log("failed to retrieve gene data", e);
UTGBEntryPointBase.showErrorMessage(
"read data retrieval failed: " + e.getMessage());
needUpdateForGraphicRefinement = true;
getFrame().loadingDone();
}
public void onSuccess(List<GenomeRange> dataSet) {
if ("pileup".equals(style.layout)
&& dataSet.size() > 0
&& DataChecker.isReadCoverage(dataSet.get(0))) {
needUpdateForGraphicRefinement = true;
// narrow down the prefetch range
float prefetchFactor = geneCanvas.getPrefetchFactor();
prefetchFactor /= 2.0;
geneCanvas.setPrefetchFactor(prefetchFactor);
} else {
float newPrefetchFactor = geneCanvas.getPrefetchFactor() * 2.0f;
if (newPrefetchFactor > 1.0f) newPrefetchFactor = 1.0f;
// broaden the prefetch range upon successful read data retrieval
geneCanvas.setPrefetchFactor(newPrefetchFactor);
needUpdateForGraphicRefinement = false;
}
geneCanvas.resetData(dataSet);
refresh();
}
});
}
private void setPixelWidth(int width, int height) {
int pixelWidthWithSpan =
window.convertToPixelLength(window.getSequenceLength() + this.span - 2);
canvas.setPixelSize(pixelWidthWithSpan, height);
canvas.setCoordSize(pixelWidthWithSpan, height);
}
public BarGraphCanvas(TrackWindow window, int windowHeight) {
this.window = window;
// Style.border(canvas, 1, "solid", "gray");
initWidget(canvas);
setPixelSize(window.getPixelWidth(), windowHeight);
}
public void draw(List<CompactWIGData> graphData, GraphStyle style) {
for (CompactWIGData each : graphData) {
if (each.getSpan() > span) {
this.span = each.getSpan();
}
}
setPixelWidth(window.getPixelWidth(), style.windowHeight);
scale.updateStyle(style);
for (CompactWIGData data : graphData) {
// get graph color
Color graphColor = new Color(DEFAULT_COLOR);
if (style.color.isDefined()) {
graphColor = new Color(style.color.get());
} else if (data.getTrack().containsKey("color")) {
String colorStr = data.getTrack().get("color");
String c[] = colorStr.split(",");
if (c.length == 3)
graphColor =
new Color(Integer.valueOf(c[0]), Integer.valueOf(c[1]), Integer.valueOf(c[2]));
}
// draw graph
canvas.saveContext();
canvas.setLineWidth(1.0f);
canvas.setStrokeStyle(graphColor);
min = scale.getMin();
max = scale.getMax();
float y2 = scale.getYPosition(0.0f);
// draw data graph
final boolean isReverse = window.isReverseStrand();
final int pixelWidth = data.getData().length;
for (int i = 0; i < pixelWidth; ++i) {
float value = data.getData()[i];
float y1;
if (value == 0.0f) {
if (!style.drawZeroValue) continue;
else {
y1 = y2 + ((min < max) ? -0.5f : 0.5f);
}
} else {
y1 = scale.getYPosition(value);
}
int x = i;
if (isReverse) {
x = pixelWidth - x - 1;
}
canvas.saveContext();
canvas.beginPath();
canvas.translate(x + 0.5f, 0);
canvas.moveTo(0, y1);
canvas.lineTo(0, y2);
canvas.stroke();
canvas.restoreContext();
}
canvas.restoreContext();
}
}