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");
}
/**
* 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());
}
}