public RegIntTab(RegIntPlugin plugin) {
super(JSplitPane.VERTICAL_SPLIT);
tab = this;
this.plugin = plugin;
pathwayPanel.setLayout(new BorderLayout());
backpagePanel.setLayout(new BoxLayout(backpagePanel, BoxLayout.PAGE_AXIS));
swingEngine = plugin.getDesktop().getSwingEngine();
JScrollPane pathwayScroll = new JScrollPane(pathwayPanel);
pathwayScroll.getVerticalScrollBar().setUnitIncrement(20);
JScrollPane backpageScroll = new JScrollPane(backpagePanel);
backpageScroll.getVerticalScrollBar().setUnitIncrement(20);
setTopComponent(pathwayScroll);
setBottomComponent(backpageScroll);
setOneTouchExpandable(true);
setDividerLocation(400);
}
/**
* Updates the bottom part of the {@link RegIntTab} with information about the Xref selected in
* the top part of RIPTab and its interaction
*
* @param xref one of the interaction partners (displayed in the top part of the RIPTAB) of the
* Xref selected in the main pathway
* @param results the results object from updating the top part of the RIPTab by selecting an Xref
* in the main pathway
*/
public void updateBackpagePanel(Xref xref, ResultsObj results) {
backpagePanel.removeAll();
backpagePanel.setLayout(new BoxLayout(backpagePanel, BoxLayout.PAGE_AXIS));
PathwayElement e = PathwayElement.createPathwayElement(ObjectType.DATANODE);
e.setDataSource(xref.getDataSource());
e.setElementID(xref.getId());
BackpageTextProvider bpt = new BackpageTextProvider();
bpt.addBackpageHook(new BackpageInfo(swingEngine.getGdbManager().getCurrentGdb(), results));
// TODO: fix file table, doesn't always show files
bpt.addBackpageHook(new BackpageFileTable(results, plugin));
bpt.addBackpageHook(new BackpagePMID(results));
// TODO: change this to use multiple BridgeDb databases?
bpt.addBackpageHook(
new BackpageTextProvider.BackpageXrefs(swingEngine.getGdbManager().getCurrentGdb()));
bpt.addBackpageHook(new BackpageExpression(plugin.getDesktop().getGexManager()));
bpt.addBackpageHook(new BackpageMiscInfo(results));
BackpagePane bpp = new BackpagePane(bpt, swingEngine.getEngine());
bpp.setInput(e);
bpp.addHyperlinkListener(
new HyperlinkListener() {
@Override
public void hyperlinkUpdate(HyperlinkEvent e) {
if (e.getEventType().equals(HyperlinkEvent.EventType.ACTIVATED)) {
try {
Desktop.getDesktop().browse(e.getURL().toURI());
} catch (IOException e1) {
e1.printStackTrace();
} catch (URISyntaxException e1) {
e1.printStackTrace();
}
}
}
});
backpagePanel.add(bpp);
backpagePanel.revalidate();
backpagePanel.repaint();
}
/**
* 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;
}
/**
* Updates the top part of the {@link RegIntTab} with a list of interaction partners of the
* selected Xref
*
* @param xref The {@link Xref} from the selected pathway element
*/
public void updatePathwayPanel(PathwayElement elm) {
Xref xref = elm.getXref();
backpagePanel.removeAll();
JLabel loading = new JLabel("<html><br> Loading...</html>", JLabel.LEFT);
loading.setVerticalAlignment(JLabel.TOP);
pathwayPanel.removeAll();
pathwayPanel.setLayout(new BorderLayout());
pathwayPanel.setBackground(Color.WHITE);
pathwayPanel.add(loading, BorderLayout.CENTER);
pathwayPanel.revalidate();
try {
ResultsObj results = plugin.findInteractions(xref);
if (results != null) {
FormLayout layout =
new FormLayout(
"5dlu, 123px, 3dlu, pref, 3dlu, pref, 5dlu",
tab.getRowLayout(results.getRegulatorMap().size(), results.getTargetMap().size()));
PanelBuilder builder = new PanelBuilder(layout);
builder.setDefaultDialogBorder();
CellConstraints cc = new CellConstraints();
builder.addSeparator("", cc.xyw(1, 1, 7));
y = 2;
int y2 = y;
if (results.getRegulatorMap().size() > 0) {
builder.addLabel("Regulators:", cc.xy(2, y));
y = y + 2;
y2 = y;
JScrollPane sourceScroll =
new JScrollPane(
ScrollPaneConstants.VERTICAL_SCROLLBAR_NEVER,
ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER);
sourceScroll.setMinimumSize(new Dimension(50, 50));
VPathwaySwing vPathwaySwing =
createPathway(sourceScroll, results.getRegulatorMap(), results, builder);
sourceScroll.add(vPathwaySwing);
builder.add(sourceScroll, cc.xywh(2, y2, 1, (2 * results.getRegulatorMap().size())));
}
if (results.getTargetMap().size() > 0) {
y++;
builder.addLabel("Targets:", cc.xy(2, y));
y = y + 2;
y2 = y;
JScrollPane targetScroll =
new JScrollPane(
ScrollPaneConstants.VERTICAL_SCROLLBAR_NEVER,
ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER);
targetScroll.setMinimumSize(new Dimension(50, 50));
VPathwaySwing vPathwaySwing =
createPathway(targetScroll, results.getTargetMap(), results, builder);
targetScroll.add(vPathwaySwing);
builder.add(targetScroll, cc.xywh(2, y2, 1, (2 * results.getTargetMap().size())));
}
JPanel panel = builder.getPanel();
pathwayPanel.removeAll();
JLabel selectedLabel =
new JLabel(
"<html><br /> <B>Selected: "
+ elm.getTextLabel()
+ " ("
+ xref.getDataSource().getSystemCode()
+ ": "
+ xref.getId()
+ ")</B></html>");
pathwayPanel.setLayout(new BorderLayout());
pathwayPanel.add(selectedLabel, BorderLayout.NORTH);
pathwayPanel.add(panel, BorderLayout.CENTER);
pathwayPanel.setBackground(Color.WHITE);
pathwayPanel.revalidate();
pathwayPanel.repaint();
} else {
setPathwayPanelText("<html><br> No results found.</html>");
}
} catch (Exception e) {
e.printStackTrace();
}
}