import jalview.analysis.scoremodels.ScoreModels;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
-import jalview.bin.Cache;
import jalview.commands.CommandI;
import jalview.commands.OrderCommand;
import jalview.datamodel.Alignment;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceNode;
+import jalview.gui.ImageExporter.ImageWriterI;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.io.NewickFile;
import jalview.jbgui.GTreePanel;
-import jalview.util.ImageMaker;
+import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
-import jalview.util.dialogrunner.RunResponse;
import jalview.viewmodel.AlignmentViewport;
import java.awt.Font;
import java.awt.Graphics;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import java.awt.image.BufferedImage;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.io.File;
import java.io.FileOutputStream;
import java.util.ArrayList;
import java.util.List;
-import java.util.concurrent.atomic.AtomicBoolean;
-import javax.imageio.ImageIO;
import javax.swing.ButtonGroup;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
import javax.swing.JRadioButtonMenuItem;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
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()));
}
}
}
/**
- * Outputs the Tree in EPS format. The user is prompted for the file to save
- * to, and (unless a preference is already set) for the choice of Text or
- * Lineart for character rendering.
- */
- @Override
- public void epsTree_actionPerformed()
- {
- JalviewFileChooser chooser = new JalviewFileChooser(
- ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION);
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(
- MessageManager.getString("label.create_eps_from_tree"));
- chooser.setToolTipText(MessageManager.getString("action.save"));
-
- int value = chooser.showSaveDialog(this);
-
- if (value != JalviewFileChooser.APPROVE_OPTION)
- {
- return;
- }
- File outFile = chooser.getSelectedFile();
- Cache.setProperty("LAST_DIRECTORY", outFile.getParent());
-
- String renderStyle = Cache.getDefault("EPS_RENDERING",
- "Prompt each time");
- AtomicBoolean textOption = new AtomicBoolean(
- !"Lineart".equals(renderStyle));
-
- /*
- * configure the export action to run on OK in the dialog
- */
- RunResponse okAction = new RunResponse(JOptionPane.OK_OPTION)
- {
- @Override
- public void run()
- {
- writeEpsFile(outFile, textOption.get());
- }
- };
-
- /*
- * Prompt for character rendering style if preference is not set
- */
- if (renderStyle.equalsIgnoreCase("Prompt each time")
- && !(System.getProperty("java.awt.headless") != null && System
- .getProperty("java.awt.headless").equals("true")))
- {
- LineartOptions eps = new LineartOptions("EPS_RENDERING", "EPS",
- textOption);
- eps.setResponseAction(okAction);
- eps.showDialog();
- /* no code here - JalviewJS won't execute it */
- }
- else
- {
- /*
- * if preference set, just run the export action
- */
- writeEpsFile(outFile, textOption.get());
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Outputs the Tree in image format (currently EPS or PNG). The user is
+ * prompted for the file to save to, and for EPS (unless a preference is
+ * already set) for the choice of Text or Lineart for character rendering.
*/
@Override
- public void pngTree_actionPerformed(ActionEvent e)
+ public void writeTreeImage(TYPE imageFormat)
{
int width = treeCanvas.getWidth();
int height = treeCanvas.getHeight();
-
- try
+ ImageWriterI writer = new ImageWriterI()
{
- JalviewFileChooser chooser = new JalviewFileChooser(
- ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION);
-
- chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(
- MessageManager.getString("label.create_png_from_tree"));
- chooser.setToolTipText(MessageManager.getString("action.save"));
-
- int value = chooser.showSaveDialog(this);
-
- if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+ @Override
+ public void exportImage(Graphics g) throws Exception
{
- return;
+ treeCanvas.draw(g, width, height);
}
-
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
- chooser.getSelectedFile().getParent());
-
- FileOutputStream out = new FileOutputStream(
- chooser.getSelectedFile());
-
- BufferedImage bi = new BufferedImage(width, height,
- BufferedImage.TYPE_INT_RGB);
- Graphics png = bi.getGraphics();
-
- treeCanvas.draw(png, width, height);
-
- ImageIO.write(bi, "png", out);
- out.close();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
+ };
+ String tree = MessageManager.getString("label.tree");
+ ImageExporter exporter = new ImageExporter(writer, null, imageFormat,
+ tree);
+ exporter.doExport(null, this, width, height, tree.toLowerCase());
}
/**
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() });
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();
}
}
}
/*
* 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;
+ }
}