import java.util.List;
import java.util.Locale;
import java.util.Vector;
-import java.util.concurrent.Callable;
import javax.swing.ButtonGroup;
import javax.swing.JCheckBoxMenuItem;
import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.util.imagemaker.BitmapImageSizing;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.ViewportRanges;
import jalview.ws.DBRefFetcher;
@Override
public void setProgressBar(String message, long id)
{
- if (!Platform.isHeadless())
+ if (!Platform.isHeadless() && progressBar != null)
progressBar.setProgressBar(message, id);
}
public void registerHandler(final long id,
final IProgressIndicatorHandler handler)
{
- progressBar.registerHandler(id, handler);
+ if (progressBar != null)
+ progressBar.registerHandler(id, handler);
}
/**
@Override
public boolean operationInProgress()
{
- return progressBar.operationInProgress();
+ return progressBar == null ? false : progressBar.operationInProgress();
}
/**
}
AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
- Callable<Void> cancelAction = () -> {
+ Runnable cancelAction = () -> {
lastSaveSuccessful = false;
- return null;
};
- Callable<Void> outputAction = () -> {
+ Runnable outputAction = () -> {
// todo defer this to inside formatSequences (or later)
AlignmentExportData exportData = viewport.getAlignExportData(options);
String output = new FormatAdapter(alignPanel, options)
AlignFrame.this.getViewport().setSavedUpToDate(true);
}
}
- return null;
};
/*
{
try
{
- outputAction.call();
+ outputAction.run();
} catch (Exception e)
{
// TODO Auto-generated catch block
FileFormatI fileFormat = FileFormats.getInstance()
.forName(fileFormatName);
AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
- Callable<Void> outputAction = () -> {
+ Runnable outputAction = () -> {
// todo defer this to inside formatSequences (or later)
AlignmentExportData exportData = viewport.getAlignExportData(options);
CutAndPasteTransfer cap = new CutAndPasteTransfer();
oom);
cap.dispose();
}
- return null;
};
/*
{
try
{
- outputAction.call();
+ outputAction.run();
} catch (Exception e)
{
e.printStackTrace();
@Override
public void createPNG(File f)
{
- alignPanel.makeAlignmentImage(TYPE.PNG, f);
+ createPNG(f, null, BitmapImageSizing.nullBitmapImageSizing());
+ }
+
+ public void createPNG(File f, String renderer, BitmapImageSizing userBis)
+ {
+ alignPanel.makeAlignmentImage(TYPE.PNG, f, renderer, userBis);
}
/**
@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
String choice = chooser.getSelectedFile().getPath();
Cache.setProperty("LAST_DIRECTORY", choice);
loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
- return null;
});
chooser.showOpenDialog(this);
return;
}
- Callable okAction = () -> {
+ Runnable okAction = () -> {
SequenceI[] cut = sg.getSequences()
.toArray(new SequenceI[sg.getSize()]);
{
}
}
- return null;
};
/*
{
try
{
- okAction.call();
+ okAction.run();
} catch (Exception e)
{
e.printStackTrace();
{
viewport.invertColumnSelection();
alignPanel.paintAlignment(true, false);
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
@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;
}
.getString("label.possible_problem_with_tree_file"),
JvOptionPane.WARNING_MESSAGE);
}
- return null;
});
chooser.showOpenDialog(this);
}
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(
- new FileParse(cm.getNewickString(), DataSourceType.PASTE));
- fin.parse();
- if (fin.getTree() == null)
- {
- return;
- }
+ new FileParse(cm.getNewick(), DataSourceType.PASTE));
String title = "PAE Matrix Tree for "
+ cm.getReferenceSeq().getDisplayId(false);
- TreePanel tp = new TreePanel(alignPanel, fin, aa, title);
+
+ 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);
}
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)
* update non-sequence-related annotations
*/
@Override
- protected void setAnnotationsVisibility(boolean visible,
+ public void setAnnotationsVisibility(boolean visible,
boolean forSequences, boolean forAlignment)
{
AlignmentAnnotation[] anns = alignPanel.getAlignment()
Cache.setProperty("LAST_DIRECTORY", choice);
SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
new VCFLoader(choice).loadVCF(seqs, us);
- return null;
});
chooser.showOpenDialog(null);
git://source.jalview.org / jalview.git / blobdiff