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JAL-3691 automatic insertion of Locale.ROOT to toUpperCase() and toLowerCase() and...
[jalview.git]
/
src
/
jalview
/
gui
/
TreePanel.java
diff --git
a/src/jalview/gui/TreePanel.java
b/src/jalview/gui/TreePanel.java
index
30604cb
..
b730df4
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;
@@
-159,6
+161,7
@@
public class TreePanel extends GTreePanel
{
av.removePropertyChangeListener(listener);
}
{
av.removePropertyChangeListener(listener);
}
+ releaseReferences();
}
});
}
});
@@
-168,6
+171,17
@@
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()
* @return
*/
protected PropertyChangeListener addAlignmentListener()
@@
-681,7
+695,7
@@
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));
}
/**
}
/**
@@
-709,20
+723,20
@@
public class TreePanel extends GTreePanel
if (sq != null)
{
// search dbrefs, features and annotation
if (sq != null)
{
// search dbrefs, features and annotation
- DBRefEntry[] refs = jalview.util.DBRefUtils
+ List<DBRefEntry> refs = jalview.util.DBRefUtils
.selectRefs(sq.getDBRefs(), new String[]
.selectRefs(sq.getDBRefs(), new String[]
- { labelClass.toUpperCase() });
+ { labelClass.toUpperCase(Locale.ROOT) });
if (refs != null)
{
if (refs != null)
{
- for (int i = 0; i < refs.length; i++)
+ for (int i = 0, ni = refs.size(); i < ni; i++)
{
if (newname == null)
{
{
if (newname == null)
{
- newname = new String(refs[i].getAccessionId());
+ newname = new String(refs.get(i).getAccessionId());
}
else
{
}
else
{
- newname = newname + "; " + refs[i].getAccessionId();
+ newname += "; " + refs.get(i).getAccessionId();
}
}
}
}
}
}
@@
-774,7
+788,7
@@
public class TreePanel extends GTreePanel
* i18n description of Neighbour Joining or Average Distance method
*/
String treecalcnm = MessageManager
* i18n description of Neighbour Joining or Average Distance method
*/
String treecalcnm = MessageManager
- .getString("label.tree_calc_" + treeType.toLowerCase());
+ .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)
@@
-784,7
+798,7
@@
public class TreePanel extends GTreePanel
/*
* put them together as <method> Using <model>
*/
/*
* put them together as <method> Using <model>
*/
- final String ttl = MessageManager.formatMessage("label.treecalc_title",
+ final String ttl = MessageManager.formatMessage("label.calc_title",
treecalcnm, smn);
return ttl;
}
treecalcnm, smn);
return ttl;
}