package jalview.gui;
import jalview.analysis.AnnotationSorter;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
public void paintAlignment(boolean updateOverview,
boolean updateStructures)
{
- final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
- av.isShowAutocalculatedAbove());
- sorter.sort(getAlignment().getAlignmentAnnotation(),
- av.getSortAnnotationsBy());
repaint();
if (updateStructures)
}
/**
+ * Sorts annotations according to currently selected preferences. Does nothing
+ * if currently set to 'Custom' (manual) ordering.
+ */
+ @Override
+ public void sortAnnotations(boolean autoCalcOnly)
+ {
+ SequenceAnnotationOrder sortBy = av.getSortAnnotationsBy();
+ if (sortBy != SequenceAnnotationOrder.CUSTOM)
+ {
+ final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
+ av.isShowAutocalculatedAbove(), autoCalcOnly);
+ sorter.sort(getAlignment().getAlignmentAnnotation(), sortBy);
+ }
+ }
+
+ /**
* DOCUMENT ME!
*
* @param g