*/
package jalview.gui;
-import jalview.analysis.AlignSeq;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.RnaViewerModel;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.ext.varna.RnaModel;
-import jalview.structure.SecondaryStructureListener;
-import jalview.structure.SelectionListener;
-import jalview.structure.SelectionSource;
-import jalview.structure.StructureSelectionManager;
-import jalview.structure.VamsasSource;
-import jalview.util.Comparison;
-import jalview.util.MessageManager;
-import jalview.util.ShiftList;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.util.Collection;
import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation;
import fr.orsay.lri.varna.models.rna.ModeleBase;
import fr.orsay.lri.varna.models.rna.RNA;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.RnaViewerModel;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.ext.varna.RnaModel;
+import jalview.structure.SecondaryStructureListener;
+import jalview.structure.SelectionListener;
+import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+import jalview.util.ShiftList;
public class AppVarna extends JInternalFrame
implements SelectionListener, SecondaryStructureListener,
}
}
+ /**
+ * highlight a region from start to end (inclusive) on rna
+ *
+ * @param rna
+ * @param start
+ * - first base pair index (from 0)
+ * @param end
+ * - last base pair index (from 0)
+ */
public void highlightRegion(RNA rna, int start, int end)
{
clearLastSelection();
*/
protected AppVarna(AlignmentPanel ap)
{
+ this.setFrameIcon(null);
this.ap = ap;
this.viewId = System.currentTimeMillis() + "." + this.hashCode();
vab = new AppVarnaBinding();
RnaModel rnaModel = models.get(rna);
if (rnaModel.seq == sequence)
{
- int highlightPos = rnaModel.gapped ? index : position - 1;
+ int highlightPos = rnaModel.gapped ? index
+ : position - sequence.getStart();
mouseOverHighlighter.highlightRegion(rna, highlightPos, highlightPos);
vab.updateSelectedRNA(rna);
}
{
return;
}
- if (seqsel != null && seqsel.getSize() > 0)
+
+ RnaModel rnaModel = models.get(rna);
+
+ if (seqsel != null && seqsel.getSize() > 0
+ && seqsel.contains(rnaModel.seq))
{
int start = seqsel.getStartRes(), end = seqsel.getEndRes();
- ShiftList shift = offsets.get(rna);
- if (shift != null)
+ if (rnaModel.gapped)
{
- start = shift.shift(start);
- end = shift.shift(end);
+ ShiftList shift = offsets.get(rna);
+ if (shift != null)
+ {
+ start = shift.shift(start);
+ end = shift.shift(end);
+ }
}
+ else
+ {
+ start = rnaModel.seq.findPosition(start) - rnaModel.seq.getStart();
+ end = rnaModel.seq.findPosition(end) - rnaModel.seq.getStart();
+ }
+
selectionHighlighter.highlightRegion(rna, start, end);
selectionHighlighter.getLastHighlight()
.setOutlineColor(seqsel.getOutlineColour());