*/
package jalview.gui;
+import java.util.Locale;
+
import jalview.analysis.AlignmentSorter;
import jalview.analysis.AverageDistanceTree;
import jalview.analysis.NJTree;
SimilarityParamsI similarityParams;
- TreeCanvas treeCanvas;
+ private TreeCanvas treeCanvas;
TreeModel tree;
- AlignViewport av;
+ private AlignViewport av;
/**
* Creates a new TreePanel object.
public AlignmentI getAlignment()
{
- return treeCanvas.av.getAlignment();
+ return getTreeCanvas().getViewport().getAlignment();
}
public AlignmentViewport getViewPort()
{
- return treeCanvas.av;
+ // @Mungo - Why don't we return our own viewport ???
+ return getTreeCanvas().getViewport();
}
void initTreePanel(AlignmentPanel ap, String type, String modelName,
{
av.removePropertyChangeListener(listener);
}
+ releaseReferences();
}
});
}
/**
+ * 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()
{
AlignmentPanel[] aps = PaintRefresher
.getAssociatedPanels(av.getSequenceSetId());
- if (aps.length == 1 && treeCanvas.ap == aps[0])
+ if (aps.length == 1 && getTreeCanvas().getAssociatedPanel() == aps[0])
{
associateLeavesMenu.setVisible(false);
return;
for (i = 0; i < iSize; i++)
{
final AlignmentPanel ap = aps[i];
- item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
+ item = new JRadioButtonMenuItem(ap.av.getViewName(),
+ ap == treeCanvas.getAssociatedPanel());
buttonGroup.add(item);
item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent evt)
{
treeCanvas.applyToAllViews = false;
- treeCanvas.ap = ap;
- treeCanvas.av = ap.av;
+ treeCanvas.setAssociatedPanel(ap);
+ treeCanvas.setViewport(ap.av);
PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
}
});
else
{
ScoreModelI sm = ScoreModels.getInstance()
- .getScoreModel(scoreModelName, treeCanvas.ap);
+ .getScoreModel(scoreModelName,
+ treeCanvas.getAssociatedPanel());
TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
? new NJTree(av, sm, similarityParams)
: new AverageDistanceTree(av, sm, similarityParams);
}
else
{
- treeCanvas.ap.alignFrame
- .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
+ treeCanvas.getAssociatedPanel().alignFrame
+ .addHistoryItem(
+ sortAlignmentIn(treeCanvas.getAssociatedPanel()));
}
}
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));
}
/**
if (sq != null)
{
// search dbrefs, features and annotation
- DBRefEntry[] refs = jalview.util.DBRefUtils
+ List<DBRefEntry> refs = jalview.util.DBRefUtils
.selectRefs(sq.getDBRefs(), new String[]
- { labelClass.toUpperCase() });
+ { labelClass.toUpperCase(Locale.ROOT) });
if (refs != null)
{
- for (int i = 0; i < refs.length; i++)
+ for (int i = 0, ni = refs.size(); i < ni; i++)
{
if (newname == null)
{
- newname = new String(refs[i].getAccessionId());
+ newname = new String(refs.get(i).getAccessionId());
}
else
{
- newname = newname + "; " + refs[i].getAccessionId();
+ newname += "; " + refs.get(i).getAccessionId();
}
}
}
* 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)
/*
* 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;
}
ex.printStackTrace();
}
}
+
+ public AlignViewport getViewport()
+ {
+ return av;
+ }
+
+ public void setViewport(AlignViewport av)
+ {
+ this.av = av;
+ }
+
+ public TreeCanvas getTreeCanvas()
+ {
+ return treeCanvas;
+ }
}