import jalview.datamodel.*;
import jalview.schemes.*;
+import jalview.structure.StructureSelectionManager;
/**
* DOCUMENT ME!
{
if (ap != null)
{
- ap.paintAlignment(true);
+ ap.paintAlignment(false);
}
Thread.sleep(200);
}
{
if (ap != null)
{
- ap.paintAlignment(true);
+ ap.paintAlignment(false);
}
Thread.sleep(200);
*/
public void setAlignment(AlignmentI align)
{
+ if (alignment!=null && alignment.getCodonFrames()!=null)
+ {
+ StructureSelectionManager.getStructureSelectionManager().removeMappings(alignment.getCodonFrames());
+ }
this.alignment = align;
+ if (alignment.getCodonFrames()!=null)
+ {
+ StructureSelectionManager.getStructureSelectionManager().addMappings(alignment.getCodonFrames());
+ }
}
/**
}
/**
- * This method returns an array of new SequenceI objects
+ * This method returns an array of new SequenceI objects
* derived from the whole alignment or just the current
* selection with start and end points adjusted
* @note if you need references to the actual SequenceI objects in the alignment or currently selected then use getSequenceSelection()
if (selectionGroup == null)
{
sequences = alignment.getSequencesArray();
- AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
for (int i=0; i<sequences.length; i++)
{
sequences[i] = new Sequence(sequences[i], annots); // construct new sequence with subset of visible annotation