import jalview.io.NewickFile;
import jalview.io.ScoreMatrixFile;
import jalview.io.TCoffeeScoreFile;
+import jalview.io.exceptions.ImageOutputException;
import jalview.io.vcf.VCFLoader;
import jalview.jbgui.GAlignFrame;
import jalview.project.Jalview2XML;
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;
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
- htmlSVG.exportHTML(null);
+ try
+ {
+ htmlSVG.exportHTML(null);
+ } catch (ImageOutputException x)
+ {
+ // report problem to console and raise dialog
+ }
}
@Override
public void bioJSMenuItem_actionPerformed(ActionEvent e)
{
BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
- bjs.exportHTML(null);
+ try
+ {
+ bjs.exportHTML(null);
+ } catch (ImageOutputException x)
+ {
+ // report problem to console and raise dialog
+ }
}
public void createImageMap(File file, String image)
{
- alignPanel.makePNGImageMap(file, image);
+ try
+ {
+ alignPanel.makePNGImageMap(file, image);
+ } catch (ImageOutputException x)
+ {
+ // report problem to console and raise dialog
+ }
+ }
+
+ @Override
+ public void createPNG_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ createPNG(null);
+ } catch (ImageOutputException ioex)
+ {
+ // raise dialog, and report via console
+ }
+ }
+
+ @Override
+ public void createEPS_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ createEPS(null);
+ } catch (ImageOutputException ioex)
+ {
+ // raise dialog, and report via console
+ }
+
+ }
+
+ @Override
+ public void createSVG_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ createSVG(null);
+ } catch (ImageOutputException ioex)
+ {
+ // raise dialog, and report via console
+ }
+
}
/**
*
* @param f
*/
- @Override
- public void createPNG(File f)
+ public void createPNG(File f) throws ImageOutputException
{
createPNG(f, null, BitmapImageSizing.nullBitmapImageSizing());
}
public void createPNG(File f, String renderer, BitmapImageSizing userBis)
+ throws ImageOutputException
{
alignPanel.makeAlignmentImage(TYPE.PNG, f, renderer, userBis);
}
*
* @param f
*/
- @Override
- public void createEPS(File f)
+ public void createEPS(File f) throws ImageOutputException
{
createEPS(f, null);
}
- public void createEPS(File f, String renderer)
+ public void createEPS(File f, String renderer) throws ImageOutputException
{
alignPanel.makeAlignmentImage(TYPE.EPS, f, renderer);
}
*
* @param f
*/
- @Override
- public void createSVG(File f)
+ public void createSVG(File f) throws ImageOutputException
{
createSVG(f, null);
}
- public void createSVG(File f, String renderer)
+ public void createSVG(File f, String renderer) throws ImageOutputException
{
alignPanel.makeAlignmentImage(TYPE.SVG, f, renderer);
}
// 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)
+ ContactMatrixI cm = sequences[i]
+ .getContactMatrixFor(sequences[i].getAnnotation()[a]);
+ if (cm != null)
{
- alignment.addContactListFor(sequences[i].getAnnotation()[a], cm);
+ alignment.addContactListFor(sequences[i].getAnnotation()[a],
+ cm);
}
-
+
alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
a);
}
pane = editPane;
}
- JInternalFrame frame = new JInternalFrame();
-
+ JalviewInternalFrame frame = new JalviewInternalFrame();
+ frame.setFrameIcon(null);
frame.getContentPane().add(new JScrollPane(pane));
Desktop.addInternalFrame(frame, MessageManager
{
return alignPanel.overviewPanel;
}
- JInternalFrame frame = new JInternalFrame();
+ JalviewInternalFrame frame = new JalviewInternalFrame();
+ frame.setFrameIcon(null);
final OverviewPanel overview = new OverviewPanel(alignPanel, frame,
showHidden);
frame.setContentPane(overview);
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;
}
else
{
- JInternalFrame frame = new JInternalFrame();
+ JalviewInternalFrame frame = new JalviewInternalFrame();
+ frame.setFrameIcon(null);
frame.setContentPane(new PairwiseAlignPanel(viewport));
Desktop.addInternalFrame(frame,
MessageManager.getString("action.pairwise_alignment"), 600,
return tp;
}
- public void showContactMapTree(AlignmentAnnotation aa,
- ContactMatrixI cm)
+ public void showContactMapTree(AlignmentAnnotation aa, ContactMatrixI cm)
{
int x = 4, y = 5;
int w = 400, h = 500;