{
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);
}
/**
if (cs != null)
{
ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
- // Make sure viewport is up to date w.r.t. any sliders
- if (viewport.getAbovePIDThreshold())
- {
- int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
- "Background");
- viewport.setThreshold(threshold);
- }
-
- if (viewport.getConservationSelected())
- {
- cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
- cs, "Background"));
- }
}
viewport.setGlobalColourScheme(cs);
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Show the PID threshold slider panel
*/
@Override
protected void modifyPID_actionPerformed()
{
- if (viewport.getAbovePIDThreshold()
- && viewport.getGlobalColourScheme() != null)
- {
- SliderPanel.setPIDSliderSource(alignPanel,
- viewport.getGlobalColourScheme(), "Background");
- SliderPanel.showPIDSlider();
- }
+ SliderPanel.setPIDSliderSource(alignPanel,
+ viewport.getViewportColourScheme(), alignPanel.getViewName());
+ SliderPanel.showPIDSlider();
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Show the Conservation slider panel
*/
@Override
protected void modifyConservation_actionPerformed()
{
- if (viewport.getConservationSelected()
- && viewport.getGlobalColourScheme() != null)
- {
- SliderPanel.setConservationSlider(alignPanel,
- viewport.getGlobalColourScheme(), "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);
changeColour(viewport.getGlobalColourScheme());
if (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
colourMenu.add(modifyPID);
colourMenu.add(annotationColour);
- /*
- * select the default colour for the alignment (this may be
- * overridden later)
- */
- boolean nucleotide = viewport.getAlignment().isNucleotide();
- String defaultColourScheme = Cache.getDefault(
- nucleotide ? Preferences.DEFAULT_COLOUR_NUC
- : Preferences.DEFAULT_COLOUR_PROT,
- ResidueColourScheme.NONE);
+ ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
+ String schemeName = colourScheme == null ? null : colourScheme
+ .getSchemeName();
- ColourMenuHelper.setColourSelected(colourMenu, defaultColourScheme);
+ ColourMenuHelper.setColourSelected(colourMenu, schemeName);
}
}