import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SeqCigar;
import jalview.viewmodel.ViewportRanges;
import jalview.ws.DBRefFetcher;
import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
+import jalview.ws.datamodel.alphafold.PAEContactMatrix;
import jalview.ws.jws1.Discoverer;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.jabaws2.Jws2Instance;
@Override
public void setProgressBar(String message, long id)
{
- progressBar.setProgressBar(message, id);
+ if (!Platform.isHeadless())
+ progressBar.setProgressBar(message, id);
}
@Override
@Override
public void createPNG(File f)
{
- alignPanel.makeAlignmentImage(TYPE.PNG, f);
+ createPNG(f, null, 0.0f, 0, 0);
+ }
+
+ public void createPNG(File f, String renderer, float bitmapscale,
+ int bitmapwidth, int bitmapheight)
+ {
+ alignPanel.makeAlignmentImage(TYPE.PNG, f, renderer, bitmapscale,
+ bitmapwidth, bitmapheight);
}
/**
@Override
public void createEPS(File f)
{
- alignPanel.makeAlignmentImage(TYPE.EPS, f);
+ createEPS(f, null);
+ }
+
+ public void createEPS(File f, String renderer)
+ {
+ alignPanel.makeAlignmentImage(TYPE.EPS, f, renderer);
}
/**
@Override
public void createSVG(File f)
{
- alignPanel.makeAlignmentImage(TYPE.SVG, f);
+ createSVG(f, null);
+ }
+
+ public void createSVG(File f, String renderer)
+ {
+ alignPanel.makeAlignmentImage(TYPE.SVG, f, renderer);
}
@Override
.intValue();
}
}
- alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
- // was
- // duplicated
- // earlier
+ // annotation was duplicated earlier
+ alignment.addAnnotation(sequences[i].getAnnotation()[a]);
+ // take care of contact matrix too
+ ContactMatrixI cm=sequences[i].getContactMatrixFor(sequences[i].getAnnotation()[a]);
+ if (cm!=null)
+ {
+ alignment.addContactListFor(sequences[i].getAnnotation()[a], cm);
+ }
+
alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
a);
}
{
viewport.invertColumnSelection();
alignPanel.paintAlignment(true, false);
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
viewport.setGatherViewsHere(true);
}
tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
+
return newap;
}
}
/**
- * DOCUMENT ME!
+ * Opens an Overview panel for the alignment, unless one is open already
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void overviewMenuItem_actionPerformed(ActionEvent e)
{
+ boolean showHiddenRegions = Cache
+ .getDefault(Preferences.SHOW_OV_HIDDEN_AT_START, false);
+ openOverviewPanel(showHiddenRegions);
+ }
+
+ public OverviewPanel openOverviewPanel(boolean showHidden)
+ {
if (alignPanel.overviewPanel != null)
{
- return;
+ return alignPanel.overviewPanel;
}
-
JInternalFrame frame = new JInternalFrame();
- final OverviewPanel overview = new OverviewPanel(alignPanel);
+ final OverviewPanel overview = new OverviewPanel(alignPanel, frame,
+ showHidden);
frame.setContentPane(overview);
- Desktop.addInternalFrame(frame, MessageManager
- .formatMessage("label.overview_params", new Object[]
- { this.getTitle() }), 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;
frame.addInternalFrameListener(
new javax.swing.event.InternalFrameAdapter()
{
javax.swing.event.InternalFrameEvent evt)
{
overview.dispose();
- alignPanel.setOverviewPanel(null);
+ thePanel.setOverviewPanel(null);
}
});
if (getKeyListeners().length > 0)
}
alignPanel.setOverviewPanel(overview);
+ alignPanel.setOverviewTitle(this);
+
+ return overview;
}
@Override
return tp;
}
+ public void showContactMapTree(AlignmentAnnotation aa,
+ ContactMatrixI cm)
+ {
+ int x = 4, y = 5;
+ int w = 400, h = 500;
+
+ try
+ {
+ NewickFile fin = new NewickFile(
+ new FileParse(cm.getNewick(), DataSourceType.PASTE));
+ String title = cm.getAnnotLabel() + " " + cm.getTreeMethod() + " tree"
+ + aa.sequenceRef != null
+ ? (" for " + aa.sequenceRef.getDisplayId(false))
+ : "";
+
+ 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)
+ {
+ try
+ {
+ nf.parse();
+ if (nf.getTree() == null)
+ {
+ return null;
+ }
+ TreePanel tp = new TreePanel(alignPanel, nf, aa, title);
+
+ tp.setSize(w, h);
+
+ if (x > 0 && y > 0)
+ {
+ tp.setLocation(x, y);
+ }
+
+ 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;
/**
{
if (index > -1)
{
+ /*
+ * update current Overview window title (if there is one)
+ * 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)
+ */
alignPanel = alignPanels.get(index);
+ alignPanel.setOverviewTitle(this);
+
viewport = alignPanel.av;
avc.setViewportAndAlignmentPanel(viewport, alignPanel);
setMenusFromViewport(viewport);
* update non-sequence-related annotations
*/
@Override
- protected void setAnnotationsVisibility(boolean visible,
+ public void setAnnotationsVisibility(boolean visible,
boolean forSequences, boolean forAlignment)
{
AlignmentAnnotation[] anns = alignPanel.getAlignment()
{
return lastFeatureSettingsBounds;
}
+
}
class PrintThread extends Thread
git://source.jalview.org / jalview.git / blobdiff