{
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"));
- }
+ // ? not needed as handled by SliderPanel.valueChanged?
+// if (viewport.getAbovePIDThreshold())
+// {
+ // int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
+// "Background");
+ //todo is threshold held in viewport style or in colour scheme?
+// viewport.setThreshold(threshold);
+ // }
+ //
+ // if (viewport.getConservationSelected())
+ // {
+ // cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
+ // cs, "Background"));
+ // }
}
viewport.setGlobalColourScheme(cs);
+ if (viewport.getConservationSelected())
+ {
+ int conservationInc = SliderPanel.getConservationValue();
+ viewport.getViewportColourScheme()
+ .setConservationInc(conservationInc);
+ }
alignPanel.paintAlignment(true);
}
@Override
protected void modifyPID_actionPerformed()
{
- if (viewport.getAbovePIDThreshold()
- && viewport.getGlobalColourScheme() != null)
+ if (viewport.getAbovePIDThreshold())
{
SliderPanel.setPIDSliderSource(alignPanel,
- viewport.getGlobalColourScheme(), "Background");
+ viewport.getViewportColourScheme(), "Background");
SliderPanel.showPIDSlider();
}
}
&& viewport.getGlobalColourScheme() != null)
{
SliderPanel.setConservationSlider(alignPanel,
- viewport.getGlobalColourScheme(), "Background");
+ viewport.getViewportColourScheme(), "Background");
SliderPanel.showConservationSlider();
}
}
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);
}
}