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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
5450102
..
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;
@@
-84,11
+88,11
@@
public class TreePanel extends GTreePanel
SimilarityParamsI similarityParams;
SimilarityParamsI similarityParams;
- TreeCanvas treeCanvas;
+ private TreeCanvas treeCanvas;
TreeModel tree;
TreeModel tree;
- AlignViewport av;
+ private AlignViewport av;
/**
* Creates a new TreePanel object.
/**
* Creates a new TreePanel object.
@@
-120,12
+124,13
@@
public class TreePanel extends GTreePanel
public AlignmentI getAlignment()
{
public AlignmentI getAlignment()
{
- return treeCanvas.av.getAlignment();
+ return getTreeCanvas().getViewport().getAlignment();
}
public AlignmentViewport getViewPort()
{
}
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,
}
void initTreePanel(AlignmentPanel ap, String type, String modelName,
@@
-158,6
+163,7
@@
public class TreePanel extends GTreePanel
{
av.removePropertyChangeListener(listener);
}
{
av.removePropertyChangeListener(listener);
}
+ releaseReferences();
}
});
}
});
@@
-167,17
+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");
@@
-190,12
+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;
}
}
};
}
}
};
@@
-213,7
+233,7
@@
public class TreePanel extends GTreePanel
{
AlignmentPanel[] aps = PaintRefresher
.getAssociatedPanels(av.getSequenceSetId());
{
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;
{
associateLeavesMenu.setVisible(false);
return;
@@
-236,7
+256,8
@@
public class TreePanel extends GTreePanel
for (i = 0; i < iSize; i++)
{
final AlignmentPanel ap = aps[i];
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()
{
buttonGroup.add(item);
item.addActionListener(new ActionListener()
{
@@
-244,8
+265,8
@@
public class TreePanel extends GTreePanel
public void actionPerformed(ActionEvent evt)
{
treeCanvas.applyToAllViews = false;
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());
}
});
PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
}
});
@@
-304,8
+325,8
@@
public class TreePanel extends GTreePanel
}
else
{
}
else
{
- ScoreModelI sm = ScoreModels.getInstance()
- .getScoreModel(scoreModelName, treeCanvas.ap);
+ 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);
@@
-391,7
+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"));
@@
-402,7
+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
@@
-441,7
+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;
}
@@
-571,8
+592,8
@@
public class TreePanel extends GTreePanel
}
else
{
}
else
{
- treeCanvas.ap.alignFrame
- .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
+ treeCanvas.getAssociatedPanel().alignFrame.addHistoryItem(
+ sortAlignmentIn(treeCanvas.getAssociatedPanel()));
}
}
}
}
@@
-677,7
+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));
}
/**
}
/**
@@
-705,20
+727,20
@@
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();
}
}
}
}
}
}
@@
-769,8
+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)
@@
-780,7
+802,7
@@
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;
}
@@
-799,8
+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);
@@
-814,4
+835,19
@@
public class TreePanel extends GTreePanel
ex.printStackTrace();
}
}
ex.printStackTrace();
}
}
+
+ public AlignViewport getViewport()
+ {
+ return av;
+ }
+
+ public void setViewport(AlignViewport av)
+ {
+ this.av = av;
+ }
+
+ public TreeCanvas getTreeCanvas()
+ {
+ return treeCanvas;
+ }
}
}