import jalview.analysis.NJTree;
import jalview.analysis.TreeBuilder;
import jalview.analysis.TreeModel;
+import jalview.analysis.scoremodels.ScoreModels;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
-import jalview.api.analysis.ViewBasedAnalysisI;
import jalview.bin.Cache;
import jalview.commands.CommandI;
import jalview.commands.OrderCommand;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.BinaryNode;
-import jalview.datamodel.ColumnSelection;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.NodeTransformI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import java.awt.event.ActionListener;
import java.awt.image.BufferedImage;
import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
import java.io.FileOutputStream;
import java.util.ArrayList;
import java.util.List;
import javax.swing.ButtonGroup;
import javax.swing.JMenuItem;
import javax.swing.JRadioButtonMenuItem;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
import org.jibble.epsgraphics.EpsGraphics2D;
{
String treeType;
- ScoreModelI scoreModel; // if tree computed
+ String scoreModelName; // if tree computed
String treeTitle; // if tree loaded
*
* @param ap
* @param type
- * @param sm
+ * @param modelName
* @param options
*/
- public TreePanel(AlignmentPanel ap, String type, ScoreModelI sm,
+ public TreePanel(AlignmentPanel ap, String type, String modelName,
SimilarityParamsI options)
{
super();
this.similarityParams = options;
- initTreePanel(ap, type, sm, null, null);
+ initTreePanel(ap, type, modelName, null, null);
// We know this tree has distances. JBPNote TODO: prolly should add this as
// a userdefined default
return treeCanvas.av;
}
- void initTreePanel(AlignmentPanel ap, String type, ScoreModelI sm,
+ void initTreePanel(AlignmentPanel ap, String type, String modelName,
NewickFile newTree, AlignmentView inputData)
{
av = ap.av;
this.treeType = type;
- this.scoreModel = sm;
+ this.scoreModelName = modelName;
treeCanvas = new TreeCanvas(this, ap, scrollPane);
scrollPane.setViewportView(treeCanvas);
buildAssociatedViewMenu();
- av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
+ final PropertyChangeListener listener = addAlignmentListener();
+
+ /*
+ * remove listener when window is closed, so that this
+ * panel can be garbage collected
+ */
+ addInternalFrameListener(new InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosed(InternalFrameEvent evt)
+ {
+ if (av != null)
+ {
+ av.removePropertyChangeListener(listener);
+ }
+ }
+ });
+
+ TreeLoader tl = new TreeLoader(newTree, inputData);
+ tl.start();
+
+ }
+
+ /**
+ * @return
+ */
+ protected PropertyChangeListener addAlignmentListener()
+ {
+ final PropertyChangeListener listener = new PropertyChangeListener()
{
@Override
public void propertyChange(PropertyChangeEvent evt)
}
if (evt.getNewValue() == null)
{
- System.out
- .println("new alignment sequences vector value is null");
+ System.out.println(
+ "new alignment sequences vector value is null");
}
tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
repaint();
}
}
- });
-
- TreeLoader tl = new TreeLoader(newTree, inputData);
- tl.start();
-
+ };
+ av.addPropertyChangeListener(listener);
+ return listener;
}
@Override
void buildAssociatedViewMenu()
{
- AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
- .getSequenceSetId());
+ AlignmentPanel[] aps = PaintRefresher
+ .getAssociatedPanels(av.getSequenceSetId());
if (aps.length == 1 && treeCanvas.ap == aps[0])
{
associateLeavesMenu.setVisible(false);
associateLeavesMenu.setVisible(true);
- if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
+ if ((viewMenu
+ .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
{
viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
}
}
else
{
- ScoreModelI sm = configureScoreModel();
- TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING) ? new NJTree(
- av, sm, similarityParams) : new AverageDistanceTree(av, sm,
- similarityParams);
+ ScoreModelI sm = ScoreModels.getInstance()
+ .getScoreModel(scoreModelName, treeCanvas.ap);
+ TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
+ ? new NJTree(av, sm, similarityParams)
+ : new AverageDistanceTree(av, sm, similarityParams);
tree = new TreeModel(njtree);
showDistances(true);
}
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.save_tree_as_newick"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.save_tree_as_newick"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(null);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
- .getSelectedFile().getParent());
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ chooser.getSelectedFile().getParent());
try
{
jalview.io.NewickFile fout = new jalview.io.NewickFile(
tree.getTopNode());
- String output = fout.print(tree.hasBootstrap(),
- tree.hasDistances(), tree.hasRootDistance());
+ String output = fout.print(tree.hasBootstrap(), tree.hasDistances(),
+ tree.hasRootDistance());
java.io.PrintWriter out = new java.io.PrintWriter(
new java.io.FileWriter(choice));
out.println(output);
AlignmentView originalData = tree.getOriginalData();
if (originalData == null)
{
- jalview.bin.Cache.log
- .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
+ jalview.bin.Cache.log.info(
+ "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
return;
}
// decide if av alignment is sufficiently different to original data to
{
}
- Object[] alAndColsel = originalData
- .getAlignmentAndColumnSelection(gc);
+ Object[] alAndColsel = originalData.getAlignmentAndHiddenColumns(gc);
if (alAndColsel != null && alAndColsel[0] != null)
{
// AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
- AlignmentI dataset = (av != null && av.getAlignment() != null) ? av
- .getAlignment().getDataset() : null;
+ AlignmentI dataset = (av != null && av.getAlignment() != null)
+ ? av.getAlignment().getDataset()
+ : null;
if (dataset != null)
{
al.setDataset(dataset);
if (true)
{
// make a new frame!
- AlignFrame af = new AlignFrame(al,
- (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
// >>>This is a fix for the moment, until a better solution is
// found!!<<<
// msaorder);
Desktop.addInternalFrame(af, MessageManager.formatMessage(
- "label.original_data_for_params",
- new Object[] { this.title }), AlignFrame.DEFAULT_WIDTH,
+ "label.original_data_for_params", new Object[]
+ { this.title }), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
}
}
if (treeCanvas.applyToAllViews)
{
- final ArrayList<CommandI> commands = new ArrayList<CommandI>();
- for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
- .getSequenceSetId()))
+ final ArrayList<CommandI> commands = new ArrayList<>();
+ for (AlignmentPanel ap : PaintRefresher
+ .getAssociatedPanels(av.getSequenceSetId()))
{
commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
}
}
}
});
- for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
- .getSequenceSetId()))
+ for (AlignmentPanel ap : PaintRefresher
+ .getAssociatedPanels(av.getSequenceSetId()))
{
// ensure all the alignFrames refresh their GI after adding an undo item
ap.alignFrame.updateEditMenuBar();
public CommandI sortAlignmentIn(AlignmentPanel ap)
{
+ // TODO: move to alignment view controller
AlignmentViewport viewport = ap.av;
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
CommandI undo;
undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
- ap.paintAlignment(true);
+ ap.paintAlignment(true, false);
return undo;
}
JalviewFileChooser chooser = new JalviewFileChooser(
ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION);
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.create_eps_from_tree"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.create_eps_from_tree"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
return;
}
- Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile()
- .getParent());
+ Cache.setProperty("LAST_DIRECTORY",
+ chooser.getSelectedFile().getParent());
- FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
- EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
+ FileOutputStream out = new FileOutputStream(
+ chooser.getSelectedFile());
+ EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
+ height);
pg.setAccurateTextMode(accurateText);
ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION);
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.create_png_from_tree"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.create_png_from_tree"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
return;
}
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
- .getSelectedFile().getParent());
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ chooser.getSelectedFile().getParent());
- FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+ FileOutputStream out = new FileOutputStream(
+ chooser.getSelectedFile());
BufferedImage bi = new BufferedImage(width, height,
BufferedImage.TYPE_INT_RGB);
if (sq != null)
{
// search dbrefs, features and annotation
- DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
- sq.getDBRefs(),
- new String[] { labelClass.toUpperCase() });
+ DBRefEntry[] refs = jalview.util.DBRefUtils
+ .selectRefs(sq.getDBRefs(), new String[]
+ { labelClass.toUpperCase() });
if (refs != null)
{
for (int i = 0; i < refs.length; i++)
}
if (newname == null)
{
- SequenceFeature sf[] = sq.getSequenceFeatures();
- for (int i = 0; sf != null && i < sf.length; i++)
+ List<SequenceFeature> features = sq.getFeatures()
+ .getPositionalFeatures(labelClass);
+ for (SequenceFeature feature : features)
{
- if (sf[i].getType().equals(labelClass))
+ if (newname == null)
{
- if (newname == null)
- {
- newname = new String(sf[i].getDescription());
- }
- else
- {
- newname = newname + "; " + sf[i].getDescription();
- }
+ newname = feature.getDescription();
+ }
+ else
+ {
+ newname = newname + "; " + feature.getDescription();
}
}
}
* Neighbour Joining Using BLOSUM62
* <p>
* For a tree loaded from file, just uses the file name
+ *
* @return
*/
public String getPanelTitle()
/*
* 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());
/*
* short score model name (long description can be too long)
*/
- String smn = scoreModel.getName();
+ String smn = scoreModelName;
/*
* put them together as <method> Using <model>
treecalcnm, smn);
return ttl;
}
-
- /**
- * If the score model is one that requires to get state data from the current
- * view, create and configure a new instance of it
- *
- * @return
- */
- protected ScoreModelI configureScoreModel()
- {
- if (scoreModel instanceof ViewBasedAnalysisI)
- {
- try
- {
- scoreModel = scoreModel.getClass().newInstance();
- ((ViewBasedAnalysisI) scoreModel)
- .configureFromAlignmentView(treeCanvas.ap);
- } catch (Exception q)
- {
- Cache.log.error("Couldn't create a scoremodel instance for "
- + scoreModel.getName());
- }
- }
- return scoreModel;
- }
}