/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
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())
{
if (stretchGroup == null)
{
- stretchGroup = av.getAlignment().findGroup(sequence);
- if (stretchGroup != null && res > stretchGroup.getStartRes()
- && res < stretchGroup.getEndRes())
- {
- av.setSelectionGroup(stretchGroup);
- }
- else
- {
- stretchGroup = null;
- }
+ stretchGroup = av.getAlignment().findGroup(sequence, res);
+ av.setSelectionGroup(stretchGroup);
}
- else if (!stretchGroup.getSequences(null).contains(sequence)
+ if (stretchGroup == null
+ || !stretchGroup.getSequences(null).contains(sequence)
|| stretchGroup.getStartRes() > res
|| stretchGroup.getEndRes() < res)
{
if (av.getConservationSelected())
{
- SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
- "Background");
+ SliderPanel.setConservationSlider(ap, av.getViewportColourScheme(),
+ ap.getViewName());
}
if (av.getAbovePIDThreshold())
{
- SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
- "Background");
+ SliderPanel.setPIDSliderSource(ap, av.getViewportColourScheme(),
+ ap.getViewName());
}
}
SliderPanel.setConservationSlider(ap, stretchGroup.cs,
stretchGroup.getName());
}
- else
+ if (stretchGroup.cs.getThreshold() > 0)
{
SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
stretchGroup.getName());