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JAL-2727 null more fields in AlignmentViewport.dispose(); pull up
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Thu, 14 Sep 2017 09:05:43 +0000
(10:05 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Thu, 14 Sep 2017 09:05:43 +0000
(10:05 +0100)
currentTree
src/jalview/api/AlignViewportI.java
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src/jalview/appletgui/AlignViewport.java
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src/jalview/gui/AlignViewport.java
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src/jalview/gui/Jalview2XML.java
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src/jalview/viewmodel/AlignmentViewport.java
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diff --git
a/src/jalview/api/AlignViewportI.java
b/src/jalview/api/AlignViewportI.java
index
9e6d1c0
..
248bae2
100644
(file)
--- a/
src/jalview/api/AlignViewportI.java
+++ b/
src/jalview/api/AlignViewportI.java
@@
-21,6
+21,7
@@
package jalview.api;
import jalview.analysis.Conservation;
package jalview.api;
import jalview.analysis.Conservation;
+import jalview.analysis.TreeModel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
@@
-494,4
+495,8
@@
public interface AlignViewportI extends ViewStyleI
* @return
*/
void setProteinFontAsCdna(boolean b);
* @return
*/
void setProteinFontAsCdna(boolean b);
+
+ public abstract TreeModel getCurrentTree();
+
+ public abstract void setCurrentTree(TreeModel tree);
}
}
diff --git
a/src/jalview/appletgui/AlignViewport.java
b/src/jalview/appletgui/AlignViewport.java
index
b07666e
..
c83f93f
100644
(file)
--- a/
src/jalview/appletgui/AlignViewport.java
+++ b/
src/jalview/appletgui/AlignViewport.java
@@
-20,7
+20,6
@@
*/
package jalview.appletgui;
*/
package jalview.appletgui;
-import jalview.analysis.TreeModel;
import jalview.api.AlignViewportI;
import jalview.api.FeatureSettingsModelI;
import jalview.bin.JalviewLite;
import jalview.api.AlignViewportI;
import jalview.api.FeatureSettingsModelI;
import jalview.bin.JalviewLite;
@@
-54,8
+53,6
@@
public class AlignViewport extends AlignmentViewport
boolean validCharWidth = true;
boolean validCharWidth = true;
- TreeModel currentTree = null;
-
public jalview.bin.JalviewLite applet;
boolean MAC = false;
public jalview.bin.JalviewLite applet;
boolean MAC = false;
@@
-274,16
+271,6
@@
public class AlignViewport extends AlignmentViewport
ranges.setEndSeq(height / getCharHeight());
}
ranges.setEndSeq(height / getCharHeight());
}
- public void setCurrentTree(TreeModel tree)
- {
- currentTree = tree;
- }
-
- public TreeModel getCurrentTree()
- {
- return currentTree;
- }
-
boolean centreColumnLabels;
public boolean getCentreColumnLabels()
boolean centreColumnLabels;
public boolean getCentreColumnLabels()
diff --git
a/src/jalview/gui/AlignViewport.java
b/src/jalview/gui/AlignViewport.java
index
c22a37d
..
90271c8
100644
(file)
--- a/
src/jalview/gui/AlignViewport.java
+++ b/
src/jalview/gui/AlignViewport.java
@@
-76,8
+76,6
@@
public class AlignViewport extends AlignmentViewport
{
Font font;
{
Font font;
- TreeModel currentTree = null;
-
boolean cursorMode = false;
boolean antiAlias = false;
boolean cursorMode = false;
boolean antiAlias = false;
@@
-448,27
+446,6
@@
public class AlignViewport extends AlignmentViewport
}
/**
}
/**
- * DOCUMENT ME!
- *
- * @param tree
- * DOCUMENT ME!
- */
- public void setCurrentTree(TreeModel tree)
- {
- currentTree = tree;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public TreeModel getCurrentTree()
- {
- return currentTree;
- }
-
- /**
* returns the visible column regions of the alignment
*
* @param selectedRegionOnly
* returns the visible column regions of the alignment
*
* @param selectedRegionOnly
@@
-1110,5
+1087,4
@@
public class AlignViewport extends AlignmentViewport
}
fr.setTransparency(featureSettings.getTransparency());
}
}
fr.setTransparency(featureSettings.getTransparency());
}
-
}
}
diff --git
a/src/jalview/gui/Jalview2XML.java
b/src/jalview/gui/Jalview2XML.java
index
1658f0f
..
4fffe6f
100644
(file)
--- a/
src/jalview/gui/Jalview2XML.java
+++ b/
src/jalview/gui/Jalview2XML.java
@@
-1084,7
+1084,7
@@
public class Jalview2XML
// SAVE TREES
// /////////////////////////////////
// SAVE TREES
// /////////////////////////////////
- if (!storeDS && av.currentTree != null)
+ if (!storeDS && av.getCurrentTree() != null)
{
// FIND ANY ASSOCIATED TREES
// NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
{
// FIND ANY ASSOCIATED TREES
// NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
@@
-1102,7
+1102,7
@@
public class Jalview2XML
{
Tree tree = new Tree();
tree.setTitle(tp.getTitle());
{
Tree tree = new Tree();
tree.setTitle(tp.getTitle());
- tree.setCurrentTree((av.currentTree == tp.getTree()));
+ tree.setCurrentTree((av.getCurrentTree() == tp.getTree()));
tree.setNewick(tp.getTree().print());
tree.setThreshold(tp.treeCanvas.threshold);
tree.setNewick(tp.getTree().print());
tree.setThreshold(tp.treeCanvas.threshold);
diff --git
a/src/jalview/viewmodel/AlignmentViewport.java
b/src/jalview/viewmodel/AlignmentViewport.java
index
a8afe9a
..
8e949a5
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;
@@
-955,6
+956,8
@@
public abstract class AlignmentViewport
residueShading = null; // may hold a reference to Consensus
changeSupport = null;
ranges = null;
residueShading = null; // may hold a reference to Consensus
changeSupport = null;
ranges = null;
+ currentTree = null;
+ selectionGroup = null;
setAlignment(null);
}
setAlignment(null);
}
@@
-2879,6
+2882,8
@@
public abstract class AlignmentViewport
*/
private SearchResultsI searchResults = null;
*/
private SearchResultsI searchResults = null;
+ protected TreeModel currentTree = null;
+
@Override
public boolean hasSearchResults()
{
@Override
public boolean hasSearchResults()
{
@@
-2937,4
+2942,16
@@
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;
+ }
}
}