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Merge branch 'bugs/JAL-2780_JAL-2781_pdbnegativenums' into releases/Release_2_10_4_Branch
[jalview.git]
/
src
/
jalview
/
viewmodel
/
AlignmentViewport.java
diff --git
a/src/jalview/viewmodel/AlignmentViewport.java
b/src/jalview/viewmodel/AlignmentViewport.java
index
3702cd0
..
a0cbff4
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.TreeModel;
import jalview.api.AlignCalcManagerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.AlignCalcManagerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
@@
-33,7
+34,6
@@
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.Annotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.Annotation;
-import jalview.datamodel.CigarArray;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.HiddenSequences;
@@
-80,7
+80,7
@@
import java.util.Map;
public abstract class AlignmentViewport
implements AlignViewportI, CommandListener, VamsasSource
{
public abstract class AlignmentViewport
implements AlignViewportI, CommandListener, VamsasSource
{
- final protected ViewportRanges ranges;
+ protected ViewportRanges ranges;
protected ViewStyleI viewStyle = new ViewStyle();
protected ViewStyleI viewStyle = new ViewStyle();
@@
-948,11
+948,15
@@
public abstract class AlignmentViewport
groupConsensus = null;
groupConservation = null;
hconsensus = null;
groupConsensus = null;
groupConservation = null;
hconsensus = null;
+ hconservation = null;
hcomplementConsensus = null;
hcomplementConsensus = null;
- // colour scheme may hold reference to consensus
- residueShading = null;
- // TODO remove listeners from changeSupport?
+ gapcounts = null;
+ calculator = null;
+ residueShading = null; // may hold a reference to Consensus
changeSupport = null;
changeSupport = null;
+ ranges = null;
+ currentTree = null;
+ selectionGroup = null;
setAlignment(null);
}
setAlignment(null);
}
@@
-1334,7
+1338,10
@@
public abstract class AlignmentViewport
public void removePropertyChangeListener(
java.beans.PropertyChangeListener listener)
{
public void removePropertyChangeListener(
java.beans.PropertyChangeListener listener)
{
- changeSupport.removePropertyChangeListener(listener);
+ if (changeSupport != null)
+ {
+ changeSupport.removePropertyChangeListener(listener);
+ }
}
/**
}
/**
@@
-1673,13
+1680,6
@@
public abstract class AlignmentViewport
}
@Override
}
@Override
- public CigarArray getViewAsCigars(boolean selectedRegionOnly)
- {
- return new CigarArray(alignment, alignment.getHiddenColumns(),
- (selectedRegionOnly ? selectionGroup : null));
- }
-
- @Override
public jalview.datamodel.AlignmentView getAlignmentView(
boolean selectedOnly)
{
public jalview.datamodel.AlignmentView getAlignmentView(
boolean selectedOnly)
{
@@
-2877,6
+2877,8
@@
public abstract class AlignmentViewport
*/
private SearchResultsI searchResults = null;
*/
private SearchResultsI searchResults = null;
+ protected TreeModel currentTree = null;
+
@Override
public boolean hasSearchResults()
{
@Override
public boolean hasSearchResults()
{
@@
-2935,4
+2937,16
@@
public abstract class AlignmentViewport
+ ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
return sq;
}
+ ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
return sq;
}
+
+ @Override
+ public void setCurrentTree(TreeModel tree)
+ {
+ currentTree = tree;
+ }
+
+ @Override
+ public TreeModel getCurrentTree()
+ {
+ return currentTree;
+ }
}
}