import jalview.commands.EditCommand.Action;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResults;
-import jalview.datamodel.SearchResults.Match;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
* @param results
* @return true if results were matched, false if not
*/
- private boolean setStatusMessage(SearchResults results)
+ private boolean setStatusMessage(SearchResultsI results)
{
AlignmentI al = this.av.getAlignment();
int sequenceIndex = al.findIndex(results);
return false;
}
SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
- for (Match m : results.getResults())
+ for (SearchResultMatchI m : results.getResults())
{
SequenceI seq = m.getSequence();
if (seq.getDatasetSequence() != null)
if (features != null && features.length > 0)
{
- SearchResults highlight = new SearchResults();
+ SearchResultsI highlight = new SearchResults();
highlight.addResult(sequence, features[0].getBegin(),
features[0].getEnd());
seqCanvas.highlightSearchResults(highlight);
}
@Override
- public void highlightSequence(SearchResults results)
+ public void highlightSequence(SearchResultsI results)
{
if (av.isFollowHighlight())
{
stretchGroup = av.getSelectionGroup();
- if (stretchGroup == null)
+ if (stretchGroup == null || !stretchGroup.contains(sequence, res))
{
- stretchGroup = av.getAlignment().findGroup(sequence);
- if (stretchGroup != null && res > stretchGroup.getStartRes()
- && res < stretchGroup.getEndRes())
+ stretchGroup = av.getAlignment().findGroup(sequence, res);
+ if (stretchGroup != null)
{
+ // only update the current selection if the popup menu has a group to
+ // focus on
av.setSelectionGroup(stretchGroup);
}
- else
- {
- stretchGroup = null;
- }
- }
-
- else if (!stretchGroup.getSequences(null).contains(sequence)
- || stretchGroup.getStartRes() > res
- || stretchGroup.getEndRes() < res)
- {
- stretchGroup = null;
-
- SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence);
-
- if (allGroups != null)
- {
- for (int i = 0; i < allGroups.length; i++)
- {
- if (allGroups[i].getStartRes() <= res
- && allGroups[i].getEndRes() >= res)
- {
- stretchGroup = allGroups[i];
- break;
- }
- }
- }
- av.setSelectionGroup(stretchGroup);
}
// DETECT RIGHT MOUSE BUTTON IN AWT
if (av.getConservationSelected())
{
- SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
- "Background");
+ SliderPanel.setConservationSlider(ap, av.getResidueShading(),
+ ap.getViewName());
}
if (av.getAbovePIDThreshold())
{
- SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
- "Background");
+ SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
+ ap.getViewName());
}
}
SliderPanel.setConservationSlider(ap, stretchGroup.cs,
stretchGroup.getName());
}
- else
+ if (stretchGroup.cs.getThreshold() > 0)
{
SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
stretchGroup.getName());
}
PaintRefresher.Refresh(ap, av.getSequenceSetId());
ap.paintAlignment(needOverviewUpdate);
- needOverviewUpdate =false;
+ needOverviewUpdate = false;
changeEndRes = false;
changeStartRes = false;
stretchGroup = null;