git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
[jalview.git]
/
src
/
jalview
/
viewmodel
/
AlignmentViewport.java
diff --git
a/src/jalview/viewmodel/AlignmentViewport.java
b/src/jalview/viewmodel/AlignmentViewport.java
index
c1c88c1
..
c01be4e
100644
(file)
--- a/
src/jalview/viewmodel/AlignmentViewport.java
+++ b/
src/jalview/viewmodel/AlignmentViewport.java
@@
-22,6
+22,7
@@
package jalview.viewmodel;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.Conservation;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.Conservation;
+import jalview.analysis.Profile;
import jalview.api.AlignCalcManagerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.AlignCalcManagerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
@@
-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 Profile[] 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(Profile[] hconsensus)
{
this.hconsensus = hconsensus;
}
{
this.hconsensus = hconsensus;
}
@@
-746,7
+747,7
@@
public abstract class AlignmentViewport implements AlignViewportI,
}
@Override
}
@Override
- public Hashtable[] getSequenceConsensusHash()
+ public Profile[] 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);
}