*/
package jalview.appletgui;
-import jalview.analysis.AnnotationSorter;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.JalviewLite;
// this value is set false when selection area being dragged
boolean fastPaint = true;
- @Override
- public void finalize() throws Throwable
- {
- alignFrame = null;
- av = null;
- vpRanges = null;
- seqPanel = null;
- seqPanelHolder = null;
- sequenceHolderPanel = null;
- scalePanel = null;
- scalePanelHolder = null;
- annotationPanel = null;
- annotationPanelHolder = null;
- annotationSpaceFillerHolder = null;
- super.finalize();
- }
-
public AlignmentPanel(AlignFrame af, final AlignViewport av)
{
try
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))
}
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;
public void paintAlignment(boolean updateOverview,
boolean updateStructures)
{
- final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
- av.isShowAutocalculatedAbove());
- sorter.sort(getAlignment().getAlignmentAnnotation(),
- av.getSortAnnotationsBy());
repaint();
if (updateStructures)
}
+ @Override
+ public void sortAnnotations(boolean autocalcOnly)
+ {
+ }
+
}