public void run() {
if (main.getBioPAXModel() == null) {
MessageDialog.openError(main.getShell(), "Error!", "Load or query a BioPAX model first!");
return;
}
// open dialog
CompartmentQueryParamWithEntitiesDialog dialog =
new CompartmentQueryParamWithEntitiesDialog(main);
options = dialog.open(options);
if (!options.isCancel()) {
options.setCancel(true);
} else {
return;
}
// Source and target node sets
Set<String> source = new HashSet<String>(dialog.getSourceAddedCompartments());
Set<String> target = new HashSet<String>(dialog.getTargetAddedCompartments());
Set<BioPAXElement> result =
QueryExecuter.runPathsFromTo(
BioPAXUtil.getElementsAtLocations(main.getBioPAXModel(), source),
BioPAXUtil.getElementsAtLocations(main.getBioPAXModel(), target),
main.getBioPAXModel(),
options.getLimitType() ? LimitType.NORMAL : LimitType.SHORTEST_PLUS_K,
options.getLengthLimit());
viewAndHighlightResult(result, options.isCurrentView(), "Query Result");
}
/**
* Create shell for query dialogs
*
* @param opt
*/
protected void createContents(QueryOptionsPack opt) {
shell = new Shell(getParent(), SWT.RESIZE | SWT.DIALOG_TRIM | SWT.APPLICATION_MODAL);
// Information is added as the first thing into each query dialog.
infoLabel = new Label(shell, SWT.NONE);
GridData gridData = new GridData(GridData.FILL, GridData.FILL, false, false);
// Maximum span within all different query dialogs
gridData.horizontalSpan = 8;
gridData.verticalSpan = 6;
infoLabel.setLayoutData(gridData);
if (forSIF) selectedTypes = opt.getSifTypes();
}
/** After clicking execute button, all data in dialog is saved to GoIOptionsPack */
public void storeValuesToOptionsPack(QueryOptionsPack opt) {
// store Length Limit
opt.setLengthLimit(Integer.parseInt(lengthLimit.getText()));
// if currentView is selected
if (currentViewButton.getSelection()) {
opt.setCurrentView(true);
}
// if newView is selected
else {
opt.setCurrentView(false);
}
if (downstreamButton != null) {
// if downstream is selected
if (downstreamButton.getSelection()) {
opt.setDownstream(true);
opt.setUpstream(false);
}
// if upstream is selected
else if (upstreamButton.getSelection()) {
opt.setDownstream(false);
opt.setUpstream(true);
}
// if both is selected
else {
opt.setDownstream(true);
opt.setUpstream(true);
}
}
// store stop distance according to user's selection
if (shortestPlusKButton != null) {
opt.setLimitType(!shortestPlusKButton.getSelection());
opt.setShortestPlusKLimit(Integer.parseInt(shortestPlusK.getText()));
}
// if strict is selected.
if (strictButton != null && strictButton.getSelection()) {
opt.setStrict(true);
} else {
opt.setStrict(false);
}
if (sourceST != null) opt.setSourceList(sourceST.getSymbols());
if (targetST != null) opt.setTargetList(targetST.getSymbols());
if (forSIF) {
opt.setSifTypes(selectedTypes);
}
}
/**
* After creating the dialog box, initial values are assigned to the fields with data in opt
* OptionsPack
*/
public void setInitialValues(QueryOptionsPack opt) {
if (main.getPathwayGraph() == null) {
newViewButton.setSelection(true);
currentViewButton.setSelection(false);
currentViewButton.setEnabled(false);
opt.setCurrentView(false);
}
if (opt.isCurrentView()) {
currentViewButton.setSelection(true);
} else {
newViewButton.setSelection(true);
}
lengthLimit.setText(String.valueOf(opt.getLengthLimit()));
if (sourceST != null && opt.getSourceList() != null) {
sourceST.symbolText.setText(opt.getOneStringSources());
}
if (targetST != null && opt.getTargetList() != null) {
targetST.symbolText.setText(opt.getOneStringTargets());
}
if (downstreamButton != null) {
// Downstream, Upstream or Both
if (opt.isDownstream() && opt.isUpstream() && bothButton != null) {
bothButton.setSelection(true);
} else if (opt.isDownstream()) {
downstreamButton.setSelection(true);
} else if (opt.isUpstream()) {
upstreamButton.setSelection(true);
}
}
if (strictButton != null) {
// Strict
if (opt.isStrict()) {
strictButton.setSelection(true);
}
}
// Set both texts' values
if (shortestPlusK != null) {
shortestPlusK.setText(String.valueOf(opt.getShortestPlusKLimit()));
}
if (shortestPlusKButton != null) {
shortestPlusKButton.setSelection(!opt.getLimitType());
}
}