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.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;
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);
+ try {
bjs.exportHTML(null);
+ } catch (ImageOutputException x) {
+ // report problem to console and raise dialog
+ }
}
public void createImageMap(File file, String 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
+ }
+
+ }
/**
* Creates a PNG image of the alignment and writes it to the given file. If
* the file is null, the user is prompted to choose a file.
*
* @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)
+ 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);
}
.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);
}
}
public void showContactMapTree(AlignmentAnnotation aa,
- PAEContactMatrix cm)
+ ContactMatrixI cm)
{
int x = 4, y = 5;
int w = 400, h = 500;
{
NewickFile fin = new NewickFile(
new FileParse(cm.getNewick(), DataSourceType.PASTE));
- String title = "PAE Matrix Tree for "
- + cm.getReferenceSeq().getDisplayId(false);
+ String title = aa.label + " "
+ + cm.getTreeMethod() + " tree" + (aa.sequenceRef != null
+ ? (" for " + aa.sequenceRef.getDisplayId(false))
+ : "");
showColumnWiseTree(fin, aa, title, w, h, x, y);
} catch (Throwable xx)
{
return null;
}
- TreePanel tp = new TreePanel(alignPanel, nf, aa, title);
+ TreePanel tp = new TreePanel(alignPanel, nf, aa, treeTitle);
tp.setSize(w, h);
tp.setLocation(x, y);
}
- Desktop.addInternalFrame(tp, title, w, h);
+ Desktop.addInternalFrame(tp, treeTitle, w, h);
return tp;
} catch (Throwable xx)
{