@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();
}
});
}