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JAL-966 JAL-1738 JAL-345 interfaces for SearchResults and SearchResults.Match
[jalview.git]
/
src
/
jalview
/
viewmodel
/
AlignmentViewport.java
diff --git
a/src/jalview/viewmodel/AlignmentViewport.java
b/src/jalview/viewmodel/AlignmentViewport.java
index
3f93637
..
2f733ed
100644
(file)
--- a/
src/jalview/viewmodel/AlignmentViewport.java
+++ b/
src/jalview/viewmodel/AlignmentViewport.java
@@
-1,6
+1,6
@@
/*
/*
- * 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.
*
*
* This file is part of Jalview.
*
@@
-36,7
+36,7
@@
import jalview.datamodel.Annotation;
import jalview.datamodel.CigarArray;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.CigarArray;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenSequences;
-import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceGroup;
@@
-612,7
+612,7
@@
public abstract class AlignmentViewport implements AlignViewportI,
boolean recalc = false;
if (cs != null)
{
boolean recalc = false;
if (cs != null)
{
- cs.setConservationApplied(recalc = getConservationSelected());
+ recalc = getConservationSelected();
if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
|| cs instanceof Blosum62ColourScheme)
{
if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
|| cs instanceof Blosum62ColourScheme)
{
@@
-629,6
+629,7
@@
public abstract class AlignmentViewport implements AlignViewportI,
cs.setConsensus(hconsensus);
cs.setConservation(hconservation);
}
cs.setConsensus(hconsensus);
cs.setConservation(hconservation);
}
+ cs.setConservationApplied(getConservationSelected());
cs.alignmentChanged(alignment, hiddenRepSequences);
}
if (getColourAppliesToAllGroups())
cs.alignmentChanged(alignment, hiddenRepSequences);
}
if (getColourAppliesToAllGroups())
@@
-2714,7
+2715,7
@@
public abstract class AlignmentViewport implements AlignViewportI,
* the SearchResults to add to
* @return the offset (below top of visible region) of the matched sequence
*/
* 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())
{
final AlignViewportI complement = getCodingComplement();
if (complement == null || !complement.isFollowHighlight())