public boolean savePathway() {
Pathway pathway = engine.getActivePathway();
boolean result = true;
// Overwrite the existing xml file.
// If the target file is read-only, let the user select a new pathway
if (pathway.getSourceFile() != null && pathway.getSourceFile().canWrite()) {
try {
engine.savePathway(pathway.getSourceFile());
} catch (ConverterException e) {
handleConverterException(e.getMessage(), null, e);
}
} else {
result = savePathwayAs();
}
return result;
}
/**
* Creates the list of interaction partners displayed in the top part of the {@link RegIntTab}
*
* @param parent The {@link JScrollPane} containing either the regulators or the targets of the
* selected element
* @param map The map of interaction partners, either regulators or targets, also found in results
* @param results The entire {@link ResultsObj}. Must have map as either its regulator or target
* map
* @param builder The {@link PanelBuilder} that will include this pathway
* @return the list of interaction partners (in pathway form for expression visualization)
*/
private VPathwaySwing createPathway(
JScrollPane parent, Map<Xref, Interaction> map, ResultsObj results, PanelBuilder builder) {
VPathwaySwing vPathwaySwing = new VPathwaySwing(parent);
VPathway vPathway = vPathwaySwing.createVPathway();
vPathway.setEditMode(false);
Pathway sourcePw = new Pathway();
Map<Xref, Interaction> sorted = sortXrefs(map);
x = 0;
for (Xref xref : sorted.keySet()) {
PathwayElement pwe = createPathwayELement(xref);
sourcePw.add(pwe);
JLabel linkout = new JLabel(icon);
JPanel linkoutPane = new JPanel();
linkout.addMouseListener(new InfoButtonListener(xref, results, plugin));
linkoutPane.add(linkout);
linkoutPane.setCursor(new Cursor(Cursor.HAND_CURSOR));
linkoutPane.setVisible(true);
List<File> uniqueFiles = new ArrayList<File>();
for (File intFile : sorted.get(xref).getFiles()) {
if (!uniqueFiles.contains(intFile)
&& RegIntPreferences.getPreferences().getSelectedIntFiles().contains(intFile)) {
uniqueFiles.add(intFile);
}
}
builder.addLabel(
uniqueFiles.size()
+ "/"
+ RegIntPreferences.getPreferences().getSelectedIntFiles().size(),
cc.xy(6, y));
builder.add(linkoutPane, cc.xy(4, y));
y = y + 2;
x++;
}
vPathway.fromModel(sourcePw);
vPathway.setSelectionEnabled(false);
vPathway.addVPathwayListener(plugin.getDesktop().getVisualizationManager());
return vPathwaySwing;
}
/**
* Call this when the user is about to perform an action that could lead to discarding the current
* pathway. (For example when creating a new pathway)
*
* <p>Checks if there are any unsaved changes, and asks the user if they want to save those
* changes.
*
* @return true if the user allows discarding the pathway, possibly after saving.
*/
public boolean canDiscardPathway() {
Pathway pathway = engine.getActivePathway();
// checking not necessary if there is no pathway or if pathway is not changed.
if (pathway == null || !pathway.hasChanged()) return true;
int result =
JOptionPane.showConfirmDialog(
frame,
"Save changes?",
"Your pathway has changed. Do you want to save?",
JOptionPane.YES_NO_CANCEL_OPTION,
JOptionPane.QUESTION_MESSAGE);
if (result == JOptionPane.CANCEL_OPTION) // cancel
{
return false;
} else if (result == JOptionPane.YES_OPTION) // yes
{
// return false if save is cancelled.
return (savePathway());
}
// yes or no
return true;
}