private void updateClickAction() {
String clickAction = getConfig().getParameter(CONFIG_ONCLICK_ACTION);
if (clickAction == null) return;
if ("none".equals(clickAction)) {
geneCanvas.setLocusClickHandler(null);
} else if ("link".equals(clickAction)) {
geneCanvas.setLocusClickHandler(
new LocusClickHandler() {
public void onClick(int x, int y, GenomeRange locus) {
String url = getConfig().getParameter(CONFIG_ONCLICK_URL);
url = resolveURL(url, locus);
Window.open(url, "locus", "");
}
});
} else if ("info".equals(clickAction)) {
geneCanvas.setLocusClickHandler(
new LocusClickHandler() {
public void onClick(int x, int y, GenomeRange locus) {
geneCanvas.displayInfo(x, y, locus);
}
});
} else if ("set".equals(clickAction)) {
geneCanvas.setLocusClickHandler(
new LocusClickHandler() {
public void onClick(int clientX, int clientY, GenomeRange locus) {
String key = getConfig().getParameter(CONFIG_ONCLICK_P_KEY);
if (key == null) return;
// parse name:%q,chr:%chr
String[] actions = key.split(",");
if (actions == null) return;
Properties prop = new Properties();
for (String each : actions) {
String[] keyAndValue = each.split(":");
if (keyAndValue == null || keyAndValue.length != 2) continue;
String value = resolveURL(keyAndValue[1].trim(), locus);
if (value == null) return;
prop.put(keyAndValue[0].trim(), value);
}
getTrackGroup().getPropertyWriter().setProperty(prop);
}
});
}
}
@Override
public void setUp(TrackFrame trackFrame, TrackGroup group) {
geneCanvas.setTrackGroup(group);
update(group.getTrackWindow(), true);
TrackConfig config = getConfig();
config.addConfig("DB Path", new StringType(CONFIG_PATH), "");
config.addConfig("WIG DB Path", new StringType(CONFIG_WIG_PATH), "");
ValueDomain windowFuncitionTypes =
ValueDomain.createNewValueDomain(new String[] {"MAX", "MIN", "MEDIAN", "AVG"});
config.addConfig(
"Window Function", new StringType(CONFIG_GRAPH_WINDOW, windowFuncitionTypes), "MEDIAN");
config.addHiddenConfig(CONFIG_DB_TYPE, "AUTO");
style.setup(config);
ValueDomain actionTypes =
ValueDomain.createNewValueDomain(new String[] {"none", "link", "info", "set"});
config.addConfig("On Click Action", new StringType(CONFIG_ONCLICK_ACTION, actionTypes), "none");
config.addConfig(
"On Click URL", new StringType(CONFIG_ONCLICK_URL), "http://www.google.com/search?q=%q");
config.addConfig(
"On Click Set (key:value, ...)", new StringType(CONFIG_ONCLICK_P_KEY), "read:%q");
config.addConfig("Genome DB Path", new StringType(CONFIG_GENOME_DB_PATH), "");
updateClickAction();
}
@Override
public void onChangeTrackGroupProperty(TrackGroupPropertyChange change) {
if (change.containsOneOf(
new String[] {UTGBProperty.SPECIES, UTGBProperty.REVISION, UTGBProperty.TARGET})) {
geneCanvas.clear();
update(change.getTrackWindow(), false);
}
}
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();
}
});
}