}
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())
{
new String[] { (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
{
- alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
- alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+ alignPanel.seqPanel.seqCanvas.cursorX = viewport.getStartRes();
+ alignPanel.seqPanel.seqCanvas.cursorY = viewport.getStartSeq();
}
break;
}
else
{
- alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
- - viewport.endSeq + viewport.startSeq);
+ alignPanel.setScrollValues(viewport.getStartRes(),
+ 2 * viewport.getStartSeq() - viewport.getEndSeq());
}
break;
}
else
{
- alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
- + viewport.endSeq - viewport.startSeq);
+ alignPanel.setScrollValues(viewport.getStartRes(),
+ viewport.getEndSeq());
}
break;
// This is to maintain viewport position on first residue
// of first sequence
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
- int startRes = seq.findPosition(viewport.startRes);
+ int startRes = seq.findPosition(viewport.getStartRes());
// ShiftList shifts;
// viewport.getAlignment().removeGaps(shifts=new ShiftList());
// edit.alColumnChanges=shifts.getInverse();
// This is to maintain viewport position on first residue
// of first sequence
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
- int startRes = seq.findPosition(viewport.startRes);
+ int startRes = seq.findPosition(viewport.getStartRes());
addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
viewport.getAlignment()));
@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();
}
}