{
FileFormatI format = fileFormat;
cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
- .formatSequences(format,
- exportData.getAlignment(),
+ .formatSequences(format, exportData.getAlignment(),
exportData.getOmitHidden(),
exportData.getStartEndPostions(),
viewport.getColumnSelection()));
}
String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
- seqs,
- omitHidden, null);
+ seqs, omitHidden, null);
StringSelection ss = new StringSelection(output);
* colour scheme to all groups. If unchecked, groups may have their own
* independent colour schemes.
*
+ * @param selected
*/
@Override
- protected void applyToAllGroups_actionPerformed()
+ public void applyToAllGroups_actionPerformed(boolean selected)
{
- viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
+ viewport.setColourAppliesToAllGroups(selected);
}
/**
@Override
protected void modifyPID_actionPerformed()
{
- if (viewport.getAbovePIDThreshold())
- {
- SliderPanel.setPIDSliderSource(alignPanel,
- viewport.getViewportColourScheme(), "Background");
- SliderPanel.showPIDSlider();
- }
+ SliderPanel.setPIDSliderSource(alignPanel,
+ viewport.getViewportColourScheme(), alignPanel.getViewName());
+ SliderPanel.showPIDSlider();
}
/**
@Override
protected void modifyConservation_actionPerformed()
{
- if (viewport.getConservationSelected()
- && viewport.getGlobalColourScheme() != null)
- {
- SliderPanel.setConservationSlider(alignPanel,
- viewport.getViewportColourScheme(), "Background");
- SliderPanel.showConservationSlider();
- }
+ SliderPanel.setConservationSlider(alignPanel,
+ viewport.getViewportColourScheme(), alignPanel.getViewName());
+ SliderPanel.showConservationSlider();
}
/**
* Action on selecting or deselecting (Colour) By Conservation
*/
@Override
- protected void conservationMenuItem_actionPerformed()
+ public void conservationMenuItem_actionPerformed(boolean selected)
{
- boolean selected = conservationMenuItem.isSelected();
modifyConservation.setEnabled(selected);
viewport.setConservationSelected(selected);
viewport.getViewportColourScheme().setConservationApplied(selected);
* Action on selecting or deselecting (Colour) Above PID Threshold
*/
@Override
- public void abovePIDThreshold_actionPerformed()
+ public void abovePIDThreshold_actionPerformed(boolean selected)
{
- boolean selected = abovePIDThreshold.isSelected();
modifyPID.setEnabled(selected);
viewport.setAbovePIDThreshold(selected);
+ if (!selected)
+ {
+ viewport.getViewportColourScheme().setThreshold(0,
+ viewport.isIgnoreGapsConsensus());
+ }
changeColour(viewport.getGlobalColourScheme());
if (selected)
}
if (FileFormat.Jnet.equals(format))
{
- JPredFile predictions = new JPredFile(
- file, sourceType);
+ JPredFile predictions = new JPredFile(file, sourceType);
new JnetAnnotationMaker();
JnetAnnotationMaker.add_annotation(predictions,
viewport.getAlignment(), 0, false);
}
/*
+ * 'focus' any colour slider that is open to the selected viewport
+ */
+ if (viewport.getConservationSelected())
+ {
+ SliderPanel.setConservationSlider(alignPanel,
+ viewport.getViewportColourScheme(), alignPanel.getViewName());
+ }
+ else
+ {
+ SliderPanel.hideConservationSlider();
+ }
+ if (viewport.getAbovePIDThreshold())
+ {
+ SliderPanel.setPIDSliderSource(alignPanel,
+ viewport.getViewportColourScheme(), alignPanel.getViewName());
+ }
+ else
+ {
+ SliderPanel.hidePIDSlider();
+ }
+
+ /*
* If there is a frame linked to this one in a SplitPane, switch it to the
* same view tab index. No infinite recursion of calls should happen, since
* tabSelectionChanged() should not get invoked on setting the selected