private void delete() {
final ClientParamSet setToDelete = getSelectedParamSet();
if (selectionController.getClientParamSets().size() <= 1) {
Window.alert("Cannot delete all parameter sets - at least one must remain.");
} else {
if (Window.confirm(
"Do you really want to delete parameter set " + setToDelete.getName() + "?")) {
serviceAsync.delete(
new Service.Token(true),
selector.getSelectedParamSet(),
new AsyncCallback<Void>() {
public void onFailure(Throwable throwable) {
handleGlobalError(throwable);
}
public void onSuccess(Void aVoid) {
selectionController.refresh(
new ParamSetSelectionController.Callback() {
public void refreshed() {
final List<ClientParamSet> paramSets =
selectionController.getClientParamSets();
selectionController.select(paramSets.get(0));
}
});
}
});
}
}
}
private void userChanged() {
if (users == null) {
return;
}
ClientUser user = null;
if (users.getSelectedIndex() > 0) {
final String email = users.getValue(users.getSelectedIndex());
if (userInfo.containsKey(email)) {
user = userInfo.get(email);
}
Cookies.setCookie(
"email",
users.getValue(users.getSelectedIndex()),
ParamSetSelectionController.getCookieExpirationDate(),
null,
"/",
false);
}
// Figure out whether this user can edit parameters or not
final boolean editorEnabled = user != null && user.isParameterEditorEnabled();
if (paramsEditor != null) {
paramsEditor.setEditorEnabled(editorEnabled, user);
}
setOutputPathChangeEnabled(user != null && user.isOutputPathChangeEnabled());
}
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());
}
}
});
}
public void setSelectedParamSet(ClientParamSet paramSet) {
selectionController.select(paramSet);
}
public ClientParamSet getSelectedParamSet() {
return selectionController.getSelectedParamSet();
}
public void setParamSetList(ClientParamSetList newList) {
selectionController.setParamSetList(newList);
}