import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceGroup;
+import jalview.gui.Preferences;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.ColourSchemeI;
import jalview.util.MessageManager;
oldcs = av.getGlobalColourScheme();
if (av.getAlignment().getGroups() != null)
{
- oldgroupColours = new HashMap<SequenceGroup, ColourSchemeI>();
+ oldgroupColours = new HashMap<>();
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
oldgroupColours.put(sg, sg.getColourScheme());
// TODO remove duplication with gui.AnnotationRowFilter
// TODO add 'per sequence only' option / parameter
- annotationLabels = new HashMap<AlignmentAnnotation, String>();
- Vector<String> list = new Vector<String>();
+ annotationLabels = new HashMap<>();
+ Vector<String> list = new Vector<>();
AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
if (anns == null)
{
private void setDefaultMinMax()
{
minColour.setBackground(av.applet.getDefaultColourParameter(
- "ANNOTATIONCOLOUR_MIN", Color.orange));
+ Preferences.ANNOTATIONCOLOUR_MIN, Color.orange));
maxColour.setBackground(av.applet
- .getDefaultColourParameter("ANNOTATIONCOLOUR_MAX", Color.red));
+ .getDefaultColourParameter(Preferences.ANNOTATIONCOLOUR_MAX, Color.red));
}
else if (evt.getSource() == cancel)
{
reset();
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
frame.setVisible(false);
}
}
currentAnnotation.threshold.value = slider.getValue() / 1000f;
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
}
}
// update colours in linked windows
ap.alignmentChanged();
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
void reset()
sg.setColourScheme(oldgroupColours.get(sg));
}
}
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
@Override
@Override
public void mouseReleased(MouseEvent evt)
{
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
@Override