import jalview.datamodel.CigarArray;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenSequences;
-import jalview.datamodel.ProfileI;
-import jalview.datamodel.SearchResults;
+import jalview.datamodel.ProfilesI;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceGroup;
sg.cs = null;
continue;
}
- sg.cs = cs.applyTo(sg, getHiddenRepSequences());
+ sg.cs = cs.getInstance(sg, getHiddenRepSequences());
sg.setConsPercGaps(ConsPercGaps);
if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
|| cs instanceof Blosum62ColourScheme)
/**
* results of alignment consensus analysis for visible portion of view
*/
- protected ProfileI[] hconsensus = null;
+ protected ProfilesI hconsensus = null;
/**
* results of cDNA complement consensus visible portion of view
}
@Override
- public void setSequenceConsensusHash(ProfileI[] hconsensus)
+ public void setSequenceConsensusHash(ProfilesI hconsensus)
{
this.hconsensus = hconsensus;
}
}
@Override
- public ProfileI[] getSequenceConsensusHash()
+ public ProfilesI getSequenceConsensusHash()
{
return hconsensus;
}
cs.setConsensus(hconsensus);
if (cs.conservationApplied())
{
- cs.setConservation(Conservation.calculateConservation("All", 3,
+ cs.setConservation(Conservation.calculateConservation("All",
alignment.getSequences(), 0, alignment.getWidth(), false,
getConsPercGaps(), false));
}
* the SearchResults to add to
* @return the offset (below top of visible region) of the matched sequence
*/
- protected int findComplementScrollTarget(SearchResults sr)
+ protected int findComplementScrollTarget(SearchResultsI sr)
{
final AlignViewportI complement = getCodingComplement();
if (complement == null || !complement.isFollowHighlight())
*/
private boolean selectionIsDefinedGroup = false;
+
@Override
public boolean isSelectionDefinedGroup()
{
return selectionGroup.getContext() == alignment
|| selectionIsDefinedGroup;
}
+
+ /**
+ * null, or currently highlighted results on this view
+ */
+ private SearchResultsI searchResults = null;
+
+ @Override
+ public boolean hasSearchResults()
+ {
+ return searchResults != null;
+ }
+
+ @Override
+ public void setSearchResults(SearchResultsI results)
+ {
+ searchResults = results;
+ }
+
+ @Override
+ public SearchResultsI getSearchResults()
+ {
+ return searchResults;
+ }
}