import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.io.SequenceAnnotationReport;
+import jalview.renderer.ResidueShaderI;
import jalview.schemes.ResidueProperties;
import jalview.structure.SelectionListener;
import jalview.structure.SelectionSource;
import java.util.ArrayList;
import java.util.List;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.SwingUtilities;
import javax.swing.ToolTipManager;
if (stretchGroup == null)
{
- stretchGroup = av.getAlignment().findGroup(sequence);
-
- if ((stretchGroup != null) && (res > stretchGroup.getStartRes())
- && (res < stretchGroup.getEndRes()))
- {
- av.setSelectionGroup(stretchGroup);
- }
- else
- {
- stretchGroup = null;
- }
+ stretchGroup = av.getAlignment().findGroup(sequence, res);
+ av.setSelectionGroup(stretchGroup);
}
- else if (!stretchGroup.getSequences(null).contains(sequence)
+ if (stretchGroup == null
+ || !stretchGroup.getSequences(null).contains(sequence)
|| (stretchGroup.getStartRes() > res)
|| (stretchGroup.getEndRes() < res))
{
if (av.getConservationSelected())
{
- SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
- "Background");
+ SliderPanel.setConservationSlider(ap, av.getViewportColourScheme(),
+ ap.getViewName());
}
if (av.getAbovePIDThreshold())
{
- SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
- "Background");
+ SliderPanel.setPIDSliderSource(ap, av.getViewportColourScheme(),
+ ap.getViewName());
}
if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
{
stretchGroup.cs.alignmentChanged(stretchGroup,
av.getHiddenRepSequences());
+ ResidueShaderI groupColourScheme = stretchGroup.getGroupColourScheme();
+ String name = stretchGroup.getName();
if (stretchGroup.cs.conservationApplied())
{
- SliderPanel.setConservationSlider(ap, stretchGroup.cs,
- stretchGroup.getName());
+ SliderPanel.setConservationSlider(ap, groupColourScheme, name);
}
- else
+ if (stretchGroup.cs.getThreshold() > 0)
{
- SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
- stretchGroup.getName());
+ SliderPanel.setPIDSliderSource(ap, groupColourScheme, name);
}
}
PaintRefresher.Refresh(this, av.getSequenceSetId());