*/
package jalview.appletgui;
-import jalview.analysis.AnnotationSorter;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.JalviewLite;
if (av.hasHiddenColumns())
{
AlignmentI al = av.getAlignment();
- start = al.getHiddenColumns().findColumnPosition(ostart);
- end = al.getHiddenColumns().findColumnPosition(end);
+ start = al.getHiddenColumns().absoluteToVisibleColumn(ostart);
+ end = al.getHiddenColumns().absoluteToVisibleColumn(end);
if (start == end)
{
if (!scrollToNearest && !al.getHiddenColumns().isVisible(ostart))
vpRanges.scrollToWrappedVisible(start);
}
- paintAlignment(redrawOverview);
+ paintAlignment(redrawOverview, false);
return true;
}
apvscroll.addNotify();
hscroll.addNotify();
validate();
- paintAlignment(true);
+ paintAlignment(true, false);
}
/**
}
else
{
- int width = av.getAlignment().getWidth();
+ int width = av.getAlignment().getVisibleWidth();
int height = av.getAlignment().getHeight();
- if (av.hasHiddenColumns())
- {
- width = av.getAlignment().getHiddenColumns()
- .findColumnPosition(width);
- }
if (x < 0)
{
x = 0;
* Repaint the alignment and annotations, and, optionally, any overview window
*/
@Override
- public void paintAlignment(boolean updateOverview)
+ public void paintAlignment(boolean updateOverview,
+ boolean updateStructures)
{
- final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
- av.isShowAutocalculatedAbove());
- sorter.sort(getAlignment().getAlignmentAnnotation(),
- av.getSortAnnotationsBy());
repaint();
- if (updateOverview)
+ if (updateStructures)
{
- // TODO: determine if this paintAlignment changed structure colours
jalview.structure.StructureSelectionManager
.getStructureSelectionManager(av.applet)
.sequenceColoursChanged(this);
-
+ }
+ if (updateOverview)
+ {
if (overviewPanel != null)
{
overviewPanel.updateOverviewImage();
}
+ @Override
+ public void sortAnnotations(boolean autocalcOnly)
+ {
+ }
+
}