import jalview.io.JalviewFileView;
import jalview.io.JnetAnnotationMaker;
import jalview.io.NewickFile;
+import jalview.io.StructureFile;
import jalview.io.TCoffeeScoreFile;
import jalview.jbgui.GAlignFrame;
import jalview.schemes.Blosum62ColourScheme;
toggleHiddenRegions(toggleSeqs, toggleCols);
break;
}
+ case KeyEvent.VK_B:
+ {
+ boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
+ boolean modifyExisting = true; // always modify, don't clear
+ // evt.isShiftDown();
+ boolean invertHighlighted = evt.isAltDown();
+ avc.markHighlightedColumns(invertHighlighted, modifyExisting,
+ toggleSel);
+ break;
+ }
case KeyEvent.VK_PAGE_UP:
if (viewport.getWrapAlignment())
{
@Override
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
- new HtmlSvgOutput(null, alignPanel);
+ HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
+ htmlSVG.exportHTML(null);
}
@Override
public void bioJSMenuItem_actionPerformed(ActionEvent e)
{
- BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
- bjs.exportJalviewAlignmentAsBioJsHtmlFile();
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
+ bjs.exportHTML(null);
}
public void createImageMap(File file, String image)
viewport.setFollowHighlight(state);
if (state)
{
- alignPanel.scrollToPosition(
- alignPanel.getSeqPanel().seqCanvas.searchResults, false);
+ alignPanel.scrollToPosition(viewport.getSearchResults(), false);
}
}
}
if (type != null)
{
- if (type.equalsIgnoreCase("PDB"))
+ if (StructureFile.isStructureFile(type))
{
filesmatched.add(new Object[] { file, protocol, mtch });
continue;
this,
MessageManager
.formatMessage(
- "label.automatically_associate_pdb_files_with_sequences_same_name",
+ "label.automatically_associate_structure_files_with_sequences_same_name",
new Object[] { Integer
.valueOf(
filesmatched
.size())
.toString() }),
MessageManager
- .getString("label.automatically_associate_pdb_files_by_name"),
+ .getString("label.automatically_associate_structure_files_by_name"),
JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
{
}
return false;
}
+
+ @Override
+ protected void selectHighlightedColumns_actionPerformed(
+ ActionEvent actionEvent)
+ {
+ // include key modifier check in case user selects from menu
+ avc.markHighlightedColumns(
+ (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
+ true,
+ (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
+ }
}
class PrintThread extends Thread