import jalview.analysis.AlignmentSorter;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.NJTree;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
}
if (viewport.getAlignment().isNucleotide())
{
+ conservationMenuItem.setEnabled(false);
+ clustalColour.setEnabled(false);
+ BLOSUM62Colour.setEnabled(false);
+ zappoColour.setEnabled(false);
+ taylorColour.setEnabled(false);
+ hydrophobicityColour.setEnabled(false);
+ helixColour.setEnabled(false);
+ strandColour.setEnabled(false);
+ turnColour.setEnabled(false);
+ buriedColour.setEnabled(false);
viewport.updateStrucConsensus(alignPanel);
if (viewport.getAlignment().hasRNAStructure())
{
@Override
public void changeColour(ColourSchemeI cs)
{
- // FIXME threshold, conservation, increment belong inside
- // AlignmentColourScheme and/or ViewStyleI, not ColourSchemeI
- if (cs != null)
- {
- if (viewport.getAbovePIDThreshold())
- {
- viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
- viewport.getViewportColourScheme(), "Background"));
- }
-
- if (viewport.getConservationSelected())
- {
- // cs.setConservationApplied(true);
- viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
- viewport.getViewportColourScheme(), "Background"));
- }
- // else
- // {
- // cs.setConservationApplied(false);
- // }
- }
viewport.setGlobalColourScheme(cs);
- viewport.getViewportColourScheme().setConservationApplied(
- viewport.getConservationSelected());
alignPanel.paintAlignment(true);
}
&& viewport.getGlobalColourScheme() != null)
{
SliderPanel.setPIDSliderSource(alignPanel,
- viewport.getViewportColourScheme(), "Background");
+ viewport.getResidueShading(), alignPanel.getViewName());
SliderPanel.showPIDSlider();
}
}
&& viewport.getGlobalColourScheme() != null)
{
SliderPanel.setConservationSlider(alignPanel,
- viewport.getViewportColourScheme(), "Background");
+ viewport.getResidueShading(), alignPanel.getViewName());
SliderPanel.showConservationSlider();
}
}
public void averageDistanceTreeMenuItem_actionPerformed()
{
- NewTreePanel("AV", "PID", "Average distance tree using PID");
+ NewTreePanel(NJTree.AVERAGE_DISTANCE, "PID",
+ "Average distance tree using PID");
}
public void neighbourTreeMenuItem_actionPerformed()
{
- NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
+ NewTreePanel(NJTree.NEIGHBOUR_JOINING, "PID",
+ "Neighbour joining tree using PID");
}
protected void njTreeBlosumMenuItem_actionPerformed()
{
- NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
+ NewTreePanel(NJTree.NEIGHBOUR_JOINING, "BL",
+ "Neighbour joining tree using BLOSUM62");
}
protected void avTreeBlosumMenuItem_actionPerformed()
{
- NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
+ NewTreePanel(NJTree.AVERAGE_DISTANCE, "BL",
+ "Average distance tree using BLOSUM62");
}
void NewTreePanel(String type, String pwType, String title)