@Override
public void overviewMenuItem_actionPerformed(ActionEvent e)
{
- boolean showHiddenRegions = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START,
- false);
+ boolean showHiddenRegions = Cache
+ .getDefault(Preferences.SHOW_OV_HIDDEN_AT_START, false);
openOverviewPanel(showHiddenRegions);
}
return alignPanel.overviewPanel;
}
JInternalFrame frame = new JInternalFrame();
- final OverviewPanel overview = new OverviewPanel(alignPanel, frame, showHidden);
+ final OverviewPanel overview = new OverviewPanel(alignPanel, frame,
+ showHidden);
frame.setContentPane(overview);
- Desktop.addInternalFrame(frame, "", true, frame.getWidth(), frame.getHeight(),
- true, true);
+ Desktop.addInternalFrame(frame, "", true, frame.getWidth(),
+ frame.getHeight(), true, true);
frame.setFrameIcon(null);
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
- final AlignmentPanel thePanel = this.alignPanel;
+ final AlignmentPanel thePanel = this.alignPanel;
frame.addInternalFrameListener(
new javax.swing.event.InternalFrameAdapter()
{
alignPanel.setOverviewPanel(overview);
alignPanel.setOverviewTitle(this);
-
+
return overview;
}
return showNewickTree(nf, treeTitle, null, w, h, x, y);
}
-
/**
* Add a treeviewer for the tree extracted from a Newick file object to the
* current alignment view
return tp;
}
-
public void showContactMapTree(AlignmentAnnotation aa,
PAEContactMatrix cm)
{
int x = 4, y = 5;
int w = 400, h = 500;
-
+
try
{
NewickFile fin = new NewickFile(
String title = "PAE Matrix Tree for "
+ cm.getReferenceSeq().getDisplayId(false);
- showColumnWiseTree(fin, aa, title, w,h, x,y);
+ showColumnWiseTree(fin, aa, title, w, h, x, y);
} catch (Throwable xx)
{
Console.error("Unexpected exception showing tree for contact matrix",
xx);
}
}
- public TreePanel showColumnWiseTree(NewickFile nf, AlignmentAnnotation aa, String treeTitle,
- int w, int h, int x, int y)
+
+ public TreePanel showColumnWiseTree(NewickFile nf, AlignmentAnnotation aa,
+ String treeTitle, int w, int h, int x, int y)
{
- try
+ try
+ {
+ nf.parse();
+ if (nf.getTree() == null)
{
- nf.parse();
- if (nf.getTree() == null)
- {
- return null;
- }
- TreePanel tp = new TreePanel(alignPanel, nf, aa, title);
-
- tp.setSize(w, h);
+ return null;
+ }
+ TreePanel tp = new TreePanel(alignPanel, nf, aa, title);
- if (x > 0 && y > 0)
- {
- tp.setLocation(x, y);
- }
+ tp.setSize(w, h);
- Desktop.addInternalFrame(tp, title, w, h);
- return tp;
- } catch (Throwable xx)
+ if (x > 0 && y > 0)
{
- Console.error("Unexpected exception showing tree for contact matrix",
- xx);
+ tp.setLocation(x, y);
}
- return null;
+
+ Desktop.addInternalFrame(tp, title, w, h);
+ return tp;
+ } catch (Throwable xx)
+ {
+ Console.error("Unexpected exception showing tree for contact matrix",
+ xx);
+ }
+ return null;
}
-
+
private boolean buildingMenu = false;
/**
* to add view name "Original" if necessary
*/
alignPanel.setOverviewTitle(this);
-
+
/*
* switch panels and set Overview title (if there is one
* because it was opened automatically)