@Override
public void setInSlot(Object slot, IsWidget content) {
if (slot == DetailsPresenter.IMAGE) {
img.clear();
img.add(content);
}
}
@Override
public void show(Detail detail) {
ImageResource res = detail.imageResource();
if (res.getWidth() > IMG_MAX_WIDTH || res.getHeight() > IMG_MAX_HEIGHT) {
setInSlot(
DetailsPresenter.IMAGE,
new FitImage(res.getSafeUri().asString(), IMG_MAX_WIDTH, IMG_MAX_HEIGHT));
} else {
setInSlot(DetailsPresenter.IMAGE, new Image(res));
}
main.clear();
main.add(detail.main());
side.clear();
side.add(detail.side());
title.setText(detail.title());
}
private void onMetricsTabSelected() {
testsMetricsPanel.showWidget(1);
mainTabPanel.forceLayout();
for (String plotId : chosenPlots.keySet()) {
if (plotPanel.getElementById(plotId) == null) {
renderPlots(plotPanel, chosenPlots.get(plotId), plotId);
scrollPanelMetrics.scrollToBottom();
}
}
}
private void onTrendsTabSelected() {
testsMetricsPanel.showWidget(0);
mainTabPanel.forceLayout();
if (!chosenMetrics.isEmpty() && hasChanged) {
plotTrendsPanel.clear();
for (Map.Entry<String, MetricDto> entry : chosenMetrics.entrySet()) {
renderPlots(
plotTrendsPanel,
Arrays.asList(entry.getValue().getPlotSeriesDto()),
entry.getKey(),
entry.getValue().getPlotSeriesDto().getYAxisMin(),
true);
}
scrollPanelTrends.scrollToBottom();
hasChanged = false;
}
}
private void renderPlots(
HTMLPanel panel,
List<PlotSeriesDto> plotSeriesDtoList,
String id,
double yMinimum,
boolean isMetric) {
panel.add(loadIndicator);
SimplePlot redrawingPlot = null;
VerticalPanel plotGroupPanel = new VerticalPanel();
plotGroupPanel.setWidth("100%");
plotGroupPanel.getElement().setId(id);
for (PlotSeriesDto plotSeriesDto : plotSeriesDtoList) {
Markings markings = null;
if (plotSeriesDto.getMarkingSeries() != null) {
markings = new Markings();
for (MarkingDto plotDatasetDto : plotSeriesDto.getMarkingSeries()) {
double x = plotDatasetDto.getValue();
markings.addMarking(
new Marking()
.setX(new Range(x, x))
.setLineWidth(1)
.setColor(plotDatasetDto.getColor()));
}
markingsMap.put(id, new TreeSet<MarkingDto>(plotSeriesDto.getMarkingSeries()));
}
final SimplePlot plot =
createPlot(id, markings, plotSeriesDto.getXAxisLabel(), yMinimum, isMetric);
redrawingPlot = plot;
PlotModel plotModel = plot.getModel();
for (PlotDatasetDto plotDatasetDto : plotSeriesDto.getPlotSeries()) {
SeriesHandler handler =
plotModel.addSeries(plotDatasetDto.getLegend(), plotDatasetDto.getColor());
// Populate plot with data
for (PointDto pointDto : plotDatasetDto.getPlotData()) {
handler.add(new DataPoint(pointDto.getX(), pointDto.getY()));
}
}
// Add X axis label
Label xLabel = new Label(plotSeriesDto.getXAxisLabel());
xLabel.addStyleName(getResources().css().xAxisLabel());
Label plotHeader = new Label(plotSeriesDto.getPlotHeader());
plotHeader.addStyleName(getResources().css().plotHeader());
Label plotLegend = new Label("PLOT LEGEND");
plotLegend.addStyleName(getResources().css().plotLegend());
VerticalPanel vp = new VerticalPanel();
vp.setWidth("100%");
Label panLeftLabel = new Label();
panLeftLabel.addStyleName(getResources().css().panLabel());
panLeftLabel.getElement().appendChild(new Image(getResources().getArrowLeft()).getElement());
panLeftLabel.addClickHandler(
new ClickHandler() {
@Override
public void onClick(ClickEvent event) {
plot.pan(new Pan().setLeft(-100));
}
});
Label panRightLabel = new Label();
panRightLabel.addStyleName(getResources().css().panLabel());
panRightLabel
.getElement()
.appendChild(new Image(getResources().getArrowRight()).getElement());
panRightLabel.addClickHandler(
new ClickHandler() {
@Override
public void onClick(ClickEvent event) {
plot.pan(new Pan().setLeft(100));
}
});
Label zoomInLabel = new Label("Zoom In");
zoomInLabel.addStyleName(getResources().css().zoomLabel());
zoomInLabel.addClickHandler(
new ClickHandler() {
@Override
public void onClick(ClickEvent event) {
plot.zoom();
}
});
Label zoomOutLabel = new Label("Zoom Out");
zoomOutLabel.addStyleName(getResources().css().zoomLabel());
zoomOutLabel.addClickHandler(
new ClickHandler() {
@Override
public void onClick(ClickEvent event) {
plot.zoomOut();
}
});
FlowPanel zoomPanel = new FlowPanel();
zoomPanel.addStyleName(getResources().css().zoomPanel());
zoomPanel.add(panLeftLabel);
zoomPanel.add(panRightLabel);
zoomPanel.add(zoomInLabel);
zoomPanel.add(zoomOutLabel);
vp.add(plotHeader);
vp.add(zoomPanel);
vp.add(plot);
vp.add(xLabel);
// Will be added if there is need it
// vp.add(plotLegend);
plotGroupPanel.add(vp);
}
int loadingId = panel.getWidgetCount() - 1;
panel.remove(loadingId);
panel.add(plotGroupPanel);
// Redraw plot
if (redrawingPlot != null) {
redrawingPlot.redraw();
}
}
private boolean isMaxPlotCountReached() {
return plotPanel.getWidgetCount() >= MAX_PLOT_COUNT;
}
public SimpleParamsEditorPanel(
final ServiceAsync serviceAsync,
final HidesPageContentsWhileLoading contentsHiding,
Map<String, ClientUser> userInfo) {
this.serviceAsync = serviceAsync;
this.userInfo = userInfo;
selectionController = new ParamSetSelectionController(serviceAsync);
selectionController.setContentsHiding(contentsHiding);
validationController = new ValidationController(serviceAsync, selectionController);
validationController.setContentsHiding(contentsHiding);
editorElements = new ArrayList();
contentsHiding.hidePageContentsWhileLoading();
serviceAsync.login(
"",
"",
new AsyncCallback<Boolean>() { // TODO: real login
public void onFailure(Throwable caught) {
contentsHiding.showPageContents();
handleGlobalError(caught);
}
public void onSuccess(Boolean result) {
contentsHiding.showPageContentsAfterLoad();
}
});
HorizontalPanel hp = new HorizontalPanel();
RootPanel paramsSelectorPanel = RootPanel.get("paramsSelector");
paramsSelectorPanel.add(hp);
selector = new ParamsSelector();
selectionController.setSelector(selector);
selectionController.refresh();
hp.add(selector);
// save buttons //////////////////////////////////////////////////////////
PushButton button;
hp.add(saveButton = new PushButton("Save..."));
saveButton.addStyleName(ACTION_LINK);
saveButton.addStyleName(SPACE_AFTER);
saveButton.addClickListener(
new ClickListener() {
public void onClick(Widget widget) {
save();
}
});
saveButton.setVisible(editorVisible);
buttons.add(saveButton);
hp.add(button = new PushButton("Preview..."));
button.addStyleName(ACTION_LINK);
button.addStyleName(SPACE_AFTER);
button.addClickListener(
new ClickListener() {
public void onClick(Widget widget) {
preview();
}
});
buttons.add(button);
hp.add(deleteButton = new PushButton("Delete..."));
deleteButton.addStyleName(ACTION_LINK);
deleteButton.addStyleName(SPACE_AFTER);
deleteButton.addClickListener(
new ClickListener() {
public void onClick(Widget widget) {
delete();
}
});
buttons.add(deleteButton);
// description, initially hidden /////////////////////////////////////////////
HTMLPanel description;
paramsSelectorPanel.add(
description = new HTMLPanel("<I>This is a description of the ParameterSet.</I>"));
description.setSize("500px", "50px");
description.setStyleName("dottedBorder");
description.setVisible(false);
/// Existing DOM //////////////////////////////////////////////////////////////
// Grab the existing DOM for the parameter rows.
ExistingDOMPanel edp = new ExistingDOMPanel("paramRow");
/// database ///////////////////////////////////////////
{
ExistingDOMPanel dbrow = new ExistingDOMPanel("paramDbRow");
Label label = new Label("Database:");
label.setHorizontalAlignment(HasHorizontalAlignment.ALIGN_RIGHT);
label.setStyleName(PARAMS_LABEL);
editorElements.add(dbrow.append("database", "paramDbLabel", label, editorVisible));
final ValidationPanel vp = new ValidationPanel(2);
dlb = new DatabaseListBox("sequence.database", userInfo);
final HorizontalPanel p = new HorizontalPanel();
p.add(dlb);
// dlb.setStyleName("spaceAfter");
PushButton pb = new PushButton("Add or Review Database...");
pb.addStyleName(ACTION_LINK);
pb.setTitle(
"Click here to review the selected database and potentially modify it for your own needs.");
pb.addClickListener(
new ClickListener() {
public void onClick(Widget widget) {
popupDbCurator();
}
});
validationController.add(dlb, "sequence.database", vp);
p.add(pb);
// Add undeployer link if enabled.
serviceAsync.isDatabaseUndeployerEnabled(
new AsyncCallback<Boolean>() {
public void onFailure(Throwable caught) {
// Do nothing, do not add undeploy link.
throw new RuntimeException(
"Can not determine if database undeployer is enabled", caught);
}
public void onSuccess(Boolean result) {
if (result.booleanValue()) {
PushButton du = new PushButton("Undeploy Database");
du.addStyleName(ACTION_LINK);
du.setTitle("Click here to undeploy database from search engines.");
du.addClickListener(new DatabaseUndeploymentAction(serviceAsync, dlb));
p.add(du);
}
}
});
editorElements.add(dbrow.append("database", "paramDbEntry", p, editorVisible));
editorElements.add(dbrow.append("database", "paramDbValidation", vp, editorVisible));
}
/// enzyme /////////////////////////////////////////////
{
Label label = new Label("Protease:");
label.setHorizontalAlignment(HasHorizontalAlignment.ALIGN_RIGHT);
label.setStyleName(PARAMS_LABEL);
editorElements.add(edp.append("enzyme", LABEL1, label, editorVisible));
ValidationPanel vp = new ValidationPanel(2);
ProteaseListBox tb;
validationController.add(tb = new ProteaseListBox("sequence.enzyme"), "sequence.enzyme", vp);
editorElements.add(edp.append("enzyme", ENTRY1, tb, editorVisible));
Label label1 = new Label("Missed Cleavages:");
label1.setStyleName(PARAMS_LABEL);
label1.setHorizontalAlignment(HasHorizontalAlignment.ALIGN_RIGHT);
ValidatableTextBox tdb =
new ValidatableTextBox("sequence.missed_cleavages") {
protected ClientValue getValueFromString(String value) {
if ((value == null) || (value.length() == 0)) {
return null;
}
try {
return new ClientInteger(value);
} catch (NumberFormatException ignore) {
ClientValidationList list = new ClientValidationList();
final ClientValidation cv =
new ClientValidation(
"Not a number: " + value,
"sequence.missed_cleavages",
ClientValidation.SEVERITY_ERROR);
list.add(cv);
validationController.update("sequence.missed_cleavages", list);
return null;
}
}
protected String setValueAsString(ClientValue object) {
return object.toString();
}
public void setAllowedValues(List<? extends ClientValue> values) {
// unused.
}
public String getAllowedValuesParam() {
return null; // no allowed values.
}
};
tdb.setVisibleLength(5);
editorElements.add(edp.append("enzyme", LABEL2, label1, editorVisible));
editorElements.add(edp.append("enzyme", ENTRY2, tdb, editorVisible));
validationController.add(tdb, "sequence.missed_cleavages", vp);
editorElements.add(edp.append("enzyme", VALIDATION, vp, editorVisible));
}
/// modifications /////////////////////////////////////////
{
ValidationPanel vp = new ValidationPanel(2);
Label label = new Label("Fixed Modifications:");
label.setStyleName(PARAMS_LABEL);
label.setHorizontalAlignment(HasHorizontalAlignment.ALIGN_RIGHT);
editorElements.add(edp.append(MODIFICATIONS, LABEL1, label, editorVisible));
// fixed mods label
fixedMods =
new ModificationsLabel(
ModificationSelectionEditor.FIXED_PARAM_NAME,
ModificationSelectionEditor.FIXED_PARAM_NAME);
ModificationSelectionEditor fixedModsEditor =
new ModificationSelectionEditor(
ModificationSelectionEditor.FIXED_PARAM_NAME,
ModificationSelectionEditor.FIXED_MOD_TYPE);
fixedMods.setEditor(fixedModsEditor);
validationController.add(fixedMods, ModificationSelectionEditor.FIXED_PARAM_NAME, vp);
editorElements.add(edp.append(MODIFICATIONS, ENTRY1, fixedMods, editorVisible));
// variable mods label
varMods =
new ModificationsLabel(
ModificationSelectionEditor.VARIABLE_PARAM_NAME,
ModificationSelectionEditor.VARIABLE_PARAM_NAME);
ModificationSelectionEditor varModsEditor =
new ModificationSelectionEditor(
ModificationSelectionEditor.VARIABLE_PARAM_NAME,
ModificationSelectionEditor.VARIABLE_MOD_TYPE);
varMods.setEditor(varModsEditor);
validationController.add(varMods, ModificationSelectionEditor.VARIABLE_PARAM_NAME, vp);
Label label1 = new Label("Variable Modifications:");
label1.setStyleName(PARAMS_LABEL);
label1.setHorizontalAlignment(HasHorizontalAlignment.ALIGN_RIGHT);
editorElements.add(edp.append(MODIFICATIONS, LABEL2, label1, editorVisible));
editorElements.add(edp.append(MODIFICATIONS, ENTRY2, varMods, editorVisible));
editorElements.add(edp.append(MODIFICATIONS, VALIDATION, vp, editorVisible));
}
/// tolerances /////////////////////////////////////////
{
Label label = new Label("Peptide Tolerance:");
label.setStyleName(PARAMS_LABEL);
label.setHorizontalAlignment(HasHorizontalAlignment.ALIGN_RIGHT);
editorElements.add(edp.append(TOLERANCES, LABEL1, label, editorVisible));
ValidationPanel vp = new ValidationPanel(2);
ToleranceBox peptideTolerance;
validationController.add(
peptideTolerance = new ToleranceBox("tolerance.peptide"), "tolerance.peptide", vp);
editorElements.add(edp.append(TOLERANCES, ENTRY1, peptideTolerance, editorVisible));
Label label1 = new Label("Fragment Tolerance:");
editorElements.add(edp.append(TOLERANCES, LABEL2, label1, editorVisible));
label1.setHorizontalAlignment(HasHorizontalAlignment.ALIGN_RIGHT);
label1.setStyleName(PARAMS_LABEL);
ToleranceBox fragmentTolerance;
validationController.add(
fragmentTolerance = new ToleranceBox("tolerance.fragment"), "tolerance.fragment", vp);
editorElements.add(edp.append(TOLERANCES, ENTRY2, fragmentTolerance, editorVisible));
editorElements.add(edp.append(TOLERANCES, VALIDATION, vp, editorVisible));
}
/// instrument /////////////////////////////////////////
ValidationPanel instrumentVp;
{
Label label = new Label("Instrument:");
editorElements.add(edp.append(INSTRUMENT, LABEL1, label, editorVisible));
label.setHorizontalAlignment(HasHorizontalAlignment.ALIGN_RIGHT);
label.setStyleName(PARAMS_LABEL);
instrumentVp = new ValidationPanel(2);
InstrumentListBox lb;
validationController.add(lb = new InstrumentListBox(INSTRUMENT), INSTRUMENT, instrumentVp);
editorElements.add(edp.append(INSTRUMENT, ENTRY1, lb, editorVisible));
editorElements.add(edp.append(INSTRUMENT, VALIDATION, instrumentVp, editorVisible));
}
/// spectrum extraction params /////////////////////////////////////////
{
Label label = new Label("Spectrum extraction:");
editorElements.add(edp.append(INSTRUMENT, LABEL2, label, editorVisible));
label.setHorizontalAlignment(HasHorizontalAlignment.ALIGN_RIGHT);
label.setStyleName(PARAMS_LABEL);
SpectrumExtractionEditor ed = new SpectrumExtractionEditor();
validationController.add(ed, "extractMsnSettings", instrumentVp);
editorElements.add(edp.append(INSTRUMENT, ENTRY2, ed, editorVisible));
}
/// scaffold params /////////////////////////////////////////
{
ExistingDOMPanel row = new ExistingDOMPanel("scaffoldRow");
Label label = new Label("Scaffold:");
editorElements.add(row.append(SCAFFOLD_SETTINGS, "scaffoldLabel", label, editorVisible));
label.setHorizontalAlignment(HasHorizontalAlignment.ALIGN_RIGHT);
label.setStyleName(PARAMS_LABEL);
ValidationPanel vp = new ValidationPanel(2);
ScaffoldSettingsEditor ed = new ScaffoldSettingsEditor();
validationController.add(ed, SCAFFOLD_SETTINGS, vp);
editorElements.add(row.append(SCAFFOLD_SETTINGS, "scaffoldEntry", ed, editorVisible));
editorElements.add(row.append(SCAFFOLD_SETTINGS, "scaffoldValidation", vp, editorVisible));
}
validationController.setEnabled(false);
selectionController.refresh();
validationController.addChangeListener(
new ChangeListener() {
public void onChange(Widget widget) {
for (PushButton button : buttons) {
button.setEnabled(isValid());
}
}
});
}
