Exemple #1
0
  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);
            }
          });
    }
  }
Exemple #2
0
  @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();
  }
Exemple #3
0
  @Override
  public void onChangeTrackGroupProperty(TrackGroupPropertyChange change) {

    if (change.containsOneOf(
        new String[] {UTGBProperty.SPECIES, UTGBProperty.REVISION, UTGBProperty.TARGET})) {
      geneCanvas.clear();
      update(change.getTrackWindow(), false);
    }
  }
Exemple #4
0
  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();
              }
            });
  }