*/
package jalview.gui;
+import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
/**
* list of alignment panels to use for superposition
*/
- protected Vector<AlignmentPanel> _alignwith = new Vector<>();
+ protected Vector<AlignmentViewPanel> _alignwith = new Vector<>();
/**
* list of alignment panels that are used for colouring structures by aligned
* sequences
*/
- protected Vector<AlignmentPanel> _colourwith = new Vector<>();
+ protected Vector<AlignmentViewPanel> _colourwith = new Vector<>();
private String viewId = null;
return (_alignwith != null) && _alignwith.contains(ap2);
}
- public boolean isUsedforcolourby(AlignmentPanel ap2)
+ @Override
+ public boolean isUsedforcolourby(AlignmentViewPanel avp)
{
- return (_colourwith != null) && _colourwith.contains(ap2);
+ return (_colourwith != null) && _colourwith.contains(avp);
}
/**
{
AlignmentI al = getAlignmentPanel().av.getAlignment();
ColourSchemeI cs = ColourSchemes.getInstance()
- .getColourScheme(colourSchemeName, al, null);
+ .getColourScheme(colourSchemeName, getAlignmentPanel().av, al,
+ null);
getBinding().setJalviewColourScheme(cs);
}
});
viewMenu.add(seqColourBy);
+ showAlignmentOnly = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_alignment_only"));
+ showAlignmentOnly.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideHiddenRegions.setEnabled(showAlignmentOnly.isSelected());
+ getBinding().setShowAlignmentOnly(showAlignmentOnly.isSelected());
+ getBinding().showStructures(getAlignmentPanel().getAlignViewport(),
+ true);
+ }
+ });
+ viewMenu.add(showAlignmentOnly);
+
+ hideHiddenRegions = new JCheckBoxMenuItem(
+ MessageManager.getString("label.hide_hidden_regions"));
+ hideHiddenRegions.setEnabled(false);
+ hideHiddenRegions.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ getBinding().setHideHiddenRegions(hideHiddenRegions.isSelected());
+ getBinding().showStructures(getAlignmentPanel().getAlignViewport(),
+ false);
+ }
+ });
+ viewMenu.add(hideHiddenRegions);
+
final ItemListener handler = new ItemListener()
{
@Override
int[] alm = new int[_alignwith.size()];
int a = 0;
- for (AlignmentPanel alignPanel : _alignwith)
+ for (AlignmentViewPanel alignPanel : _alignwith)
{
- als[a] = alignPanel.av.getAlignment();
+ AlignViewportI av = alignPanel.getAlignViewport();
+ als[a] = av.getAlignment();
alm[a] = -1;
- alc[a++] = alignPanel.av.getAlignment().getHiddenColumns();
+ alc[a++] = av.getAlignment().getHiddenColumns();
}
reply = getBinding().superposeStructures(als, alm, alc);
if (reply != null)
} catch (Exception e)
{
StringBuffer sp = new StringBuffer();
- for (AlignmentPanel alignPanel : _alignwith)
+ for (AlignmentViewPanel avp : _alignwith)
{
- sp.append("'" + alignPanel.alignFrame.getTitle() + "' ");
+ sp.append(
+ "'" + ((AlignmentPanel) avp).alignFrame.getTitle() + "' ");
}
Cache.log.info("Couldn't align structures with the " + sp.toString()
+ "associated alignment panels.", e);
}
}
// Set the colour using the current view for the associated alignframe
- for (AlignmentPanel alignPanel : _colourwith)
+ for (AlignmentViewPanel avp : _colourwith)
{
- binding.colourBySequence(alignPanel);
+ binding.colourBySequence(avp);
}
seqColoursApplied = true;
}
}
@Override
- public void toFront()
+ public void raiseViewer()
{
toFront();
}