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Merge branch 'features/JAL-1738_JAL-345_selectionfromhighlight' into develop
[jalview.git]
/
src
/
jalview
/
viewmodel
/
AlignmentViewport.java
diff --git
a/src/jalview/viewmodel/AlignmentViewport.java
b/src/jalview/viewmodel/AlignmentViewport.java
index
aa7cd12
..
fecccb0
100644
(file)
--- a/
src/jalview/viewmodel/AlignmentViewport.java
+++ b/
src/jalview/viewmodel/AlignmentViewport.java
@@
-36,6
+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.ProfilesI;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceCollectionI;
@@
-700,7
+701,7
@@
public abstract class AlignmentViewport implements AlignViewportI,
/**
* results of alignment consensus analysis for visible portion of view
*/
/**
* results of alignment consensus analysis for visible portion of view
*/
- protected Hashtable[] hconsensus = null;
+ protected ProfilesI hconsensus = null;
/**
* results of cDNA complement consensus visible portion of view
/**
* results of cDNA complement consensus visible portion of view
@@
-734,7
+735,7
@@
public abstract class AlignmentViewport implements AlignViewportI,
}
@Override
}
@Override
- public void setSequenceConsensusHash(Hashtable[] hconsensus)
+ public void setSequenceConsensusHash(ProfilesI hconsensus)
{
this.hconsensus = hconsensus;
}
{
this.hconsensus = hconsensus;
}
@@
-746,7
+747,7
@@
public abstract class AlignmentViewport implements AlignViewportI,
}
@Override
}
@Override
- public Hashtable[] getSequenceConsensusHash()
+ public ProfilesI getSequenceConsensusHash()
{
return hconsensus;
}
{
return hconsensus;
}
@@
-939,7
+940,9
@@
public abstract class AlignmentViewport implements AlignViewportI,
groupConservation = null;
hconsensus = null;
hcomplementConsensus = null;
groupConservation = null;
hconsensus = null;
hcomplementConsensus = null;
- // TODO removed listeners from changeSupport?
+ // colour scheme may hold reference to consensus
+ globalColourScheme = null;
+ // TODO remove listeners from changeSupport?
changeSupport = null;
setAlignment(null);
}
changeSupport = null;
setAlignment(null);
}
@@
-1864,7
+1867,7
@@
public abstract class AlignmentViewport implements AlignViewportI,
cs.setConsensus(hconsensus);
if (cs.conservationApplied())
{
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));
}
alignment.getSequences(), 0, alignment.getWidth(), false,
getConsPercGaps(), false));
}