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Merge branch 'JAL-3878_ws-overhaul-3' into with_ws_overhaul-3
[jalview.git]
/
src
/
jalview
/
gui
/
TreePanel.java
diff --git
a/src/jalview/gui/TreePanel.java
b/src/jalview/gui/TreePanel.java
index
37b4dac
..
ec4ef7b
100755
(executable)
--- a/
src/jalview/gui/TreePanel.java
+++ b/
src/jalview/gui/TreePanel.java
@@
-20,6
+20,8
@@
*/
package jalview.gui;
*/
package jalview.gui;
+import java.util.Locale;
+
import jalview.analysis.AlignmentSorter;
import jalview.analysis.AverageDistanceTree;
import jalview.analysis.NJTree;
import jalview.analysis.AlignmentSorter;
import jalview.analysis.AverageDistanceTree;
import jalview.analysis.NJTree;
@@
-28,6
+30,8
@@
import jalview.analysis.TreeModel;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
+import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.commands.CommandI;
import jalview.commands.OrderCommand;
import jalview.datamodel.Alignment;
import jalview.commands.CommandI;
import jalview.commands.OrderCommand;
import jalview.datamodel.Alignment;
@@
-159,6
+163,7
@@
public class TreePanel extends GTreePanel
{
av.removePropertyChangeListener(listener);
}
{
av.removePropertyChangeListener(listener);
}
+ releaseReferences();
}
});
}
});
@@
-168,17
+173,29
@@
public class TreePanel extends GTreePanel
}
/**
}
/**
+ * Ensure any potentially large object references are nulled
+ */
+ public void releaseReferences()
+ {
+ this.tree = null;
+ this.treeCanvas.tree = null;
+ this.treeCanvas.nodeHash = null;
+ this.treeCanvas.nameHash = null;
+ }
+
+ /**
* @return
*/
protected PropertyChangeListener addAlignmentListener()
{
final PropertyChangeListener listener = new PropertyChangeListener()
{
* @return
*/
protected PropertyChangeListener addAlignmentListener()
{
final PropertyChangeListener listener = new PropertyChangeListener()
{
+ @SuppressWarnings("unchecked")
@Override
public void propertyChange(PropertyChangeEvent evt)
{
@Override
public void propertyChange(PropertyChangeEvent evt)
{
- if (evt.getPropertyName().equals("alignment"))
- {
+ switch (evt.getPropertyName()) {
+ case AlignmentViewport.PROPERTY_ALIGNMENT:
if (tree == null)
{
System.out.println("tree is null");
if (tree == null)
{
System.out.println("tree is null");
@@
-191,12
+208,14
@@
public class TreePanel extends GTreePanel
{
System.out.println(
"new alignment sequences vector value is null");
{
System.out.println(
"new alignment sequences vector value is null");
+ return;
}
tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
treeCanvas.nameHash.clear(); // reset the mapping between canvas
// rectangles and leafnodes
repaint();
}
tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
treeCanvas.nameHash.clear(); // reset the mapping between canvas
// rectangles and leafnodes
repaint();
+ break;
}
}
};
}
}
};
@@
-306,9
+325,8
@@
public class TreePanel extends GTreePanel
}
else
{
}
else
{
- ScoreModelI sm = ScoreModels.getInstance()
- .getScoreModel(scoreModelName,
- treeCanvas.getAssociatedPanel());
+ ScoreModelI sm = ScoreModels.getInstance().getScoreModel(
+ scoreModelName, treeCanvas.getAssociatedPanel());
TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
? new NJTree(av, sm, similarityParams)
: new AverageDistanceTree(av, sm, similarityParams);
TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
? new NJTree(av, sm, similarityParams)
: new AverageDistanceTree(av, sm, similarityParams);
@@
-394,7
+412,7
@@
public class TreePanel extends GTreePanel
{
// TODO: JAL-3048 save newick file for Jalview-JS
JalviewFileChooser chooser = new JalviewFileChooser(
{
// TODO: JAL-3048 save newick file for Jalview-JS
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.save_tree_as_newick"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.save_tree_as_newick"));
@@
-405,7
+423,7
@@
public class TreePanel extends GTreePanel
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String choice = chooser.getSelectedFile().getPath();
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ Cache.setProperty("LAST_DIRECTORY",
chooser.getSelectedFile().getParent());
try
chooser.getSelectedFile().getParent());
try
@@
-444,7
+462,7
@@
public class TreePanel extends GTreePanel
AlignmentView originalData = tree.getOriginalData();
if (originalData == null)
{
AlignmentView originalData = tree.getOriginalData();
if (originalData == null)
{
- jalview.bin.Cache.log.info(
+ Console.info(
"Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
return;
}
"Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
return;
}
@@
-574,9
+592,8
@@
public class TreePanel extends GTreePanel
}
else
{
}
else
{
- treeCanvas.getAssociatedPanel().alignFrame
- .addHistoryItem(
- sortAlignmentIn(treeCanvas.getAssociatedPanel()));
+ treeCanvas.getAssociatedPanel().alignFrame.addHistoryItem(
+ sortAlignmentIn(treeCanvas.getAssociatedPanel()));
}
}
}
}
@@
-681,7
+698,8
@@
public class TreePanel extends GTreePanel
String tree = MessageManager.getString("label.tree");
ImageExporter exporter = new ImageExporter(writer, null, imageFormat,
tree);
String tree = MessageManager.getString("label.tree");
ImageExporter exporter = new ImageExporter(writer, null, imageFormat,
tree);
- exporter.doExport(null, this, width, height, tree.toLowerCase());
+ exporter.doExport(null, this, width, height,
+ tree.toLowerCase(Locale.ROOT));
}
/**
}
/**
@@
-711,7
+729,7
@@
public class TreePanel extends GTreePanel
// search dbrefs, features and annotation
List<DBRefEntry> refs = jalview.util.DBRefUtils
.selectRefs(sq.getDBRefs(), new String[]
// search dbrefs, features and annotation
List<DBRefEntry> refs = jalview.util.DBRefUtils
.selectRefs(sq.getDBRefs(), new String[]
- { labelClass.toUpperCase() });
+ { labelClass.toUpperCase(Locale.ROOT) });
if (refs != null)
{
for (int i = 0, ni = refs.size(); i < ni; i++)
if (refs != null)
{
for (int i = 0, ni = refs.size(); i < ni; i++)
@@
-773,8
+791,8
@@
public class TreePanel extends GTreePanel
/*
* i18n description of Neighbour Joining or Average Distance method
*/
/*
* i18n description of Neighbour Joining or Average Distance method
*/
- String treecalcnm = MessageManager
- .getString("label.tree_calc_" + treeType.toLowerCase());
+ String treecalcnm = MessageManager.getString(
+ "label.tree_calc_" + treeType.toLowerCase(Locale.ROOT));
/*
* short score model name (long description can be too long)
/*
* short score model name (long description can be too long)
@@
-803,8
+821,7
@@
public class TreePanel extends GTreePanel
int width = treeCanvas.getWidth();
int height = treeCanvas.getHeight();
int width = treeCanvas.getWidth();
int height = treeCanvas.getHeight();
- FileOutputStream out = new FileOutputStream(
- outFile);
+ FileOutputStream out = new FileOutputStream(outFile);
EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
height);
pg.setAccurateTextMode(!textOption);
EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
height);
pg.setAccurateTextMode(!textOption);
@@
-818,7
+835,7
@@
public class TreePanel extends GTreePanel
ex.printStackTrace();
}
}
ex.printStackTrace();
}
}
-
+
public AlignViewport getViewport()
{
return av;
public AlignViewport getViewport()
{
return av;