/**
* 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;
}
/**
* Sorts the list of interaction partners. Alphabetical sorting is the default, but can be set to
* sort by number of occurrences in {@link PreferenceDialog}.
*
* @param map The interactions to sort
* @return The sorted interactions
*/
private Map<Xref, Interaction> sortXrefs(Map<Xref, Interaction> map) {
Map<Xref, Interaction> sorted = new LinkedHashMap<Xref, Interaction>();
if (RegIntPreferences.getPreferences().getSort()
== RegIntPreferences.BY_NUMBER_OF_OCCURRENCES) {
List<ObjectsToSort> list = new ArrayList<ObjectsToSort>();
for (Xref xref : map.keySet()) {
ObjectsToSort obj = new ObjectsToSort(xref, map.get(xref).getFiles().size());
list.add(obj);
}
Collections.sort(list);
for (ObjectsToSort obj : list) {
sorted.put(obj.getXref(), map.get(obj.getXref()));
}
} else {
sorted = new TreeMap<Xref, Interaction>(map); // alphabetical sorting
// as default
}
return sorted;
}