private void finalizeFileTableInit() {
files = new FileTable();
final RootPanel filePanel = RootPanel.get("fileTable");
filePanel.add(files);
connectOutputLocationAndFileTable();
connectTitleAndFileTable();
}
private void finalizeSpectrumQa(final List<SpectrumQaParamFileInfo> list) {
if (list == null || list.isEmpty()) {
DOM.setStyleAttribute(DOM.getElementById("spectrumQaRow"), "display", "none");
} else {
DOM.setStyleAttribute(DOM.getElementById("spectrumQaRow"), "display", "");
spectrumQaSetupPanel = new SpectrumQaSetupPanel(list);
final RootPanel rootSpectrumQaPanel = RootPanel.get("spectrumQa");
rootSpectrumQaPanel.add(spectrumQaSetupPanel);
}
showPageContentsAfterLoad();
}
private void initEditorToggle() {
final RootPanel togglePanel = RootPanel.get("paramsToggleButton");
editorToggle =
new ToggleButton(new Image("images/triright.png"), new Image("images/tridown.png"));
editorToggle.setDown(false);
editorToggle.addStyleName("toggle-button");
togglePanel.add(editorToggle);
editorToggle.addClickHandler(
new ClickHandler() {
@Override
public void onClick(final ClickEvent event) {
paramsEditor.setEditorExpanded(editorToggle.isDown());
}
});
}
private void initTitleEditor() {
final RootPanel titlePanel = RootPanel.get("title");
title.setVisibleLength(60);
titlePanel.add(title);
title.addKeyUpHandler(
new KeyUpHandler() {
@Override
public void onKeyUp(final KeyUpEvent event) {
userEditedTitle = true;
updateOutputLocation();
}
});
titleChangeListener = new TitleChangeListener();
title.addChangeHandler(titleChangeListener);
}
private void initRunButton() {
// Run Button ////////////////////////////////////////////
runButton = new PushButton();
RootPanel.get("runButton").add(runButton);
runButton.setEnabled(false);
runButton.addClickHandler(new RunClickHandler());
}
private void initAddFilesButton() {
// Add files button produces a dialog
addFileButton =
new PushButton(
"",
new ClickHandler() {
@Override
public void onClick(final ClickEvent event) {
final int clientWidth = Window.getClientWidth();
final int clientHeight = Window.getClientHeight();
final int popupWidth = clientWidth * 3 / 4;
final int popupHeight = clientHeight * 3 / 4;
final int posX = (clientWidth - popupWidth) / 2;
final int posY = (clientHeight - popupHeight) / 2;
final FileTreeDialog dialog = new FileTreeDialog(popupWidth, popupHeight);
dialog.setPopupPosition(posX, posY);
dialog.setSelectedFilesListener(
new SelectedFilesListener() {
@Override
public void selectedFiles(final FileInfo[] info) {
files.addFiles(info);
}
});
dialog.show();
}
});
addFileButton.setEnabled(false);
RootPanel.get("addFileButton").add(addFileButton);
}
private void initOutputLocation() {
// currently, the save location is populated deterministically by the combination of
// the users's input
final RootPanel outputPanel = RootPanel.get("output");
output = new TextBox();
output.setVisibleLength(150);
output.addChangeHandler(
new ChangeHandler() {
@Override
public void onChange(final ChangeEvent event) {
outputPathUserSpecified = true;
updateOutputLocation();
}
});
outputPanel.add(output);
final RootPanel outputWarning = RootPanel.get("outputWarning");
outputValidationPanel = new ValidationPanel(2);
outputWarning.add(outputValidationPanel);
connectOutputLocationAndFileTable();
// Fire userChanged to get the output location updated
userChanged();
updateOutputLocation();
}
private void initUserList(final ClientUser[] list) {
// The user listing is downloaded by an async call.
final RootPanel userPanel = RootPanel.get("email");
userPanel.add(users);
users.addChangeHandler(
new ChangeHandler() {
@Override
public void onChange(final ChangeEvent event) {
userChanged();
}
});
users.addItem(SELECT_USER_STRING, "");
userInfo.clear();
for (final ClientUser user : list) {
users.addItem(user.getName(), user.getEmail());
userInfo.put(user.getEmail(), user);
}
// Select the user according to the cookie stored
final String userEmail = Cookies.getCookie("email");
selectUser(userEmail);
}
private void finalizeInitReport(
final Boolean reportEnabled, List<ClientSearchEngine> searchEngines) {
boolean quameterEnabled = false;
for (ClientSearchEngine engine : searchEngines) {
if ("QUAMETER".equals(engine.getEngineConfig().getCode())) {
quameterEnabled = true;
}
}
if (reportEnabled || quameterEnabled) {
DOM.setStyleAttribute(DOM.getElementById("reportingRow"), "display", "");
final RootPanel rootPanel = RootPanel.get("report");
if (quameterEnabled) {
quameterCategorySelector = new QuameterCategorySelector(this, this);
rootPanel.add(quameterCategorySelector);
}
if (reportEnabled) {
reportSetupPanel = new ReportSetupPanel(quameterCategorySelector);
rootPanel.add(reportSetupPanel);
}
} else {
DOM.setStyleAttribute(DOM.getElementById("reportingRow"), "display", "none");
}
}
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());
}
}
});
}
private void initMessage(final String message) {
final RootPanel messagePanel = RootPanel.get("messagePlaceholder");
messageDisplay.setVisible(false);
messagePanel.add(messageDisplay);
displayMessage(message);
}
private void initAdditionalSettings() {
additionalSettingsPanel = new AdditionalSettingsPanel();
final RootPanel panel = RootPanel.get("publicResults");
panel.add(additionalSettingsPanel);
}
