*/
package jalview.gui;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+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.Locale;
+
+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;
+
import jalview.analysis.AlignmentSorter;
import jalview.analysis.AverageDistanceTree;
import jalview.analysis.NJTree;
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.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.BinaryNode;
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.io.exceptions.ImageOutputException;
import jalview.jbgui.GTreePanel;
-import jalview.util.ImageMaker;
+import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
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.FileOutputStream;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.imageio.ImageIO;
-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;
-
/**
* DOCUMENT ME!
*
SimilarityParamsI options)
{
super();
+ this.setFrameIcon(null);
this.similarityParams = options;
initTreePanel(ap, type, modelName, null, null);
String theTitle, AlignmentView inputData)
{
super();
+ this.setFrameIcon(null);
this.treeTitle = theTitle;
initTreePanel(alignPanel, null, null, newtree, inputData);
}
+ /**
+ * columnwise tree associated with positions in aa
+ *
+ * @param alignPanel
+ * @param fin
+ * @param title
+ * @param aa
+ */
+ public TreePanel(AlignmentPanel alignPanel, NewickFile fin,
+ AlignmentAnnotation aa, String title)
+ {
+ super();
+ columnWise = true;
+ assocAnnotation = aa;
+ this.setFrameIcon(null);
+ this.treeTitle = title;
+ initTreePanel(alignPanel, null, null, fin, null);
+ }
+
+ boolean columnWise = false;
+
+ AlignmentAnnotation assocAnnotation = null;
+
+ public boolean isColumnWise()
+ {
+ return columnWise;
+ }
+
+ public AlignmentAnnotation getAssocAnnotation()
+ {
+ return assocAnnotation;
+ }
+
public AlignmentI getAlignment()
{
return getTreeCanvas().getViewport().getAlignment();
public AlignmentViewport getViewPort()
{
+ // @Mungo - Why don't we return our own viewport ???
return getTreeCanvas().getViewport();
}
NewickFile newTree, AlignmentView inputData)
{
- setViewport(ap.av);
+ av = ap.av;
this.treeType = type;
this.scoreModelName = modelName;
treeCanvas = new TreeCanvas(this, ap, scrollPane);
- scrollPane.setViewportView(getTreeCanvas());
+ scrollPane.setViewportView(treeCanvas);
+
+ if (columnWise)
+ {
+ bootstrapMenu.setVisible(false);
+ placeholdersMenu.setState(false);
+ placeholdersMenu.setVisible(false);
+ fitToWindow.setState(false);
+ sortAssocViews.setVisible(false);
+ }
+ addKeyListener(new KeyAdapter()
+ {
+ @Override
+ public void keyPressed(KeyEvent e)
+ {
+ switch (e.getKeyCode())
+ {
+ case 27: // escape
+ treeCanvas.clearSelectedLeaves();
+ e.consume();
+ break;
+
+ }
+
+ }
+ });
PaintRefresher.Register(this, ap.av.getSequenceSetId());
buildAssociatedViewMenu();
@Override
public void internalFrameClosed(InternalFrameEvent evt)
{
- if (getViewport() != null)
+ if (av != null)
{
- getViewport().removePropertyChangeListener(listener);
+ av.removePropertyChangeListener(listener);
}
releaseReferences();
}
{
if (tree == null)
{
- System.out.println("tree is null");
+ jalview.bin.Console.outPrintln("tree is null");
// TODO: deal with case when a change event is received whilst a
// tree is still being calculated - should save reference for
// processing message later.
}
if (evt.getNewValue() == null)
{
- System.out.println(
+ jalview.bin.Console.outPrintln(
"new alignment sequences vector value is null");
}
tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
- getTreeCanvas().nameHash.clear(); // reset the mapping between canvas
+ treeCanvas.nameHash.clear(); // reset the mapping between canvas
// rectangles and leafnodes
repaint();
}
}
};
- getViewport().addPropertyChangeListener(listener);
+ av.addPropertyChangeListener(listener);
return listener;
}
void buildAssociatedViewMenu()
{
AlignmentPanel[] aps = PaintRefresher
- .getAssociatedPanels(getViewport().getSequenceSetId());
+ .getAssociatedPanels(av.getSequenceSetId());
if (aps.length == 1 && getTreeCanvas().getAssociatedPanel() == aps[0])
{
associateLeavesMenu.setVisible(false);
for (i = 0; i < iSize; i++)
{
final AlignmentPanel ap = aps[i];
- item = new JRadioButtonMenuItem(ap.av.getViewName(), ap == getTreeCanvas().getAssociatedPanel());
+ item = new JRadioButtonMenuItem(ap.av.getViewName(),
+ ap == treeCanvas.getAssociatedPanel());
buttonGroup.add(item);
item.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent evt)
{
- getTreeCanvas().applyToAllViews = false;
- getTreeCanvas().setAssociatedPanel(ap);
- getTreeCanvas().setViewport(ap.av);
+ treeCanvas.applyToAllViews = false;
+ treeCanvas.setAssociatedPanel(ap);
+ treeCanvas.setViewport(ap.av);
PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
}
});
final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
MessageManager.getString("label.all_views"));
buttonGroup.add(itemf);
- itemf.setSelected(getTreeCanvas().applyToAllViews);
+ itemf.setSelected(treeCanvas.applyToAllViews);
itemf.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent evt)
{
- getTreeCanvas().applyToAllViews = itemf.isSelected();
+ treeCanvas.applyToAllViews = itemf.isSelected();
}
});
associateLeavesMenu.add(itemf);
if (newtree != null)
{
- tree = new TreeModel(getViewport().getAlignment().getSequencesArray(), odata,
+ tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
newtree);
if (tree.getOriginalData() == null)
{
}
else
{
- ScoreModelI sm = ScoreModels.getInstance()
- .getScoreModel(scoreModelName, getTreeCanvas().getAssociatedPanel());
+ ScoreModelI sm = ScoreModels.getInstance().getScoreModel(
+ scoreModelName, treeCanvas.getAssociatedPanel());
TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
- ? new NJTree(getViewport(), sm, similarityParams)
- : new AverageDistanceTree(getViewport(), sm, similarityParams);
+ ? new NJTree(av, sm, similarityParams)
+ : new AverageDistanceTree(av, sm, similarityParams);
tree = new TreeModel(njtree);
- showDistances(true);
+ // don't display distances for columnwise trees
}
-
+ showDistances(!columnWise);
tree.reCount(tree.getTopNode());
tree.findHeight(tree.getTopNode());
- getTreeCanvas().setTree(tree);
- getTreeCanvas().repaint();
- getViewport().setCurrentTree(tree);
- if (getViewport().getSortByTree())
+ treeCanvas.setTree(tree);
+ treeCanvas.repaint();
+ av.setCurrentTree(tree);
+ if (av.getSortByTree())
{
sortByTree_actionPerformed();
}
public void showDistances(boolean b)
{
- getTreeCanvas().setShowDistances(b);
+ treeCanvas.setShowDistances(b);
distanceMenu.setSelected(b);
}
public void showBootstrap(boolean b)
{
- getTreeCanvas().setShowBootstrap(b);
+ treeCanvas.setShowBootstrap(b);
bootstrapMenu.setSelected(b);
}
public void showPlaceholders(boolean b)
{
placeholdersMenu.setState(b);
- getTreeCanvas().setMarkPlaceholders(b);
+ treeCanvas.setMarkPlaceholders(b);
}
/**
@Override
public void saveAsNewick_actionPerformed(ActionEvent e)
{
+ // 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"));
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ Cache.setProperty("LAST_DIRECTORY",
chooser.getSelectedFile().getParent());
try
public void printMenu_actionPerformed(ActionEvent e)
{
// Putting in a thread avoids Swing painting problems
- getTreeCanvas().startPrinting();
+ treeCanvas.startPrinting();
}
@Override
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;
}
{
// we try to get the associated view's gap character
// but this may fail if the view was closed...
- gc = getViewport().getGapCharacter();
+ gc = av.getGapCharacter();
} catch (Exception ex)
{
// AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
- AlignmentI dataset = (getViewport() != null && getViewport().getAlignment() != null)
- ? getViewport().getAlignment().getDataset()
+ AlignmentI dataset = (av != null && av.getAlignment() != null)
+ ? av.getAlignment().getDataset()
: null;
if (dataset != null)
{
@Override
public void fitToWindow_actionPerformed(ActionEvent e)
{
- getTreeCanvas().fitToWindow = fitToWindow.isSelected();
+ treeCanvas.fitToWindow = fitToWindow.isSelected();
repaint();
}
public void sortByTree_actionPerformed()
{
- if (getTreeCanvas().applyToAllViews)
+ if (treeCanvas.applyToAllViews)
{
final ArrayList<CommandI> commands = new ArrayList<>();
for (AlignmentPanel ap : PaintRefresher
- .getAssociatedPanels(getViewport().getSequenceSetId()))
+ .getAssociatedPanels(av.getSequenceSetId()))
{
commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
}
- getViewport().getAlignPanel().alignFrame.addHistoryItem(new CommandI()
+ av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
{
@Override
}
});
for (AlignmentPanel ap : PaintRefresher
- .getAssociatedPanels(getViewport().getSequenceSetId()))
+ .getAssociatedPanels(av.getSequenceSetId()))
{
// ensure all the alignFrames refresh their GI after adding an undo item
ap.alignFrame.updateEditMenuBar();
}
else
{
- getTreeCanvas().getAssociatedPanel().alignFrame
- .addHistoryItem(sortAlignmentIn(getTreeCanvas().getAssociatedPanel()));
+ treeCanvas.getAssociatedPanel().alignFrame.addHistoryItem(
+ sortAlignmentIn(treeCanvas.getAssociatedPanel()));
}
}
@Override
public void font_actionPerformed(ActionEvent e)
{
- if (getTreeCanvas() == null)
+ if (treeCanvas == null)
{
return;
}
public Font getTreeFont()
{
- return getTreeCanvas().font;
+ return treeCanvas.font;
}
public void setTreeFont(Font f)
{
- if (getTreeCanvas() != null)
+ if (treeCanvas != null)
{
- getTreeCanvas().setFont(f);
+ treeCanvas.setFont(f);
}
}
@Override
public void distanceMenu_actionPerformed(ActionEvent e)
{
- getTreeCanvas().setShowDistances(distanceMenu.isSelected());
+ treeCanvas.setShowDistances(distanceMenu.isSelected());
}
/**
@Override
public void bootstrapMenu_actionPerformed(ActionEvent e)
{
- getTreeCanvas().setShowBootstrap(bootstrapMenu.isSelected());
+ treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
}
/**
@Override
public void placeholdersMenu_actionPerformed(ActionEvent e)
{
- getTreeCanvas().setMarkPlaceholders(placeholdersMenu.isSelected());
+ treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
}
/**
- * 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 epsTree_actionPerformed(ActionEvent e)
+ public void writeTreeImage(TYPE imageFormat)
{
- boolean accurateText = true;
-
- String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
- "Prompt each time");
-
- // If we need to prompt, and if the GUI is visible then
- // Prompt for EPS rendering style
- if (renderStyle.equalsIgnoreCase("Prompt each time")
- && !(System.getProperty("java.awt.headless") != null && System
- .getProperty("java.awt.headless").equals("true")))
- {
- EPSOptions eps = new EPSOptions();
- renderStyle = eps.getValue();
-
- if (renderStyle == null || eps.cancelled)
- {
- return;
- }
-
- }
-
- if (renderStyle.equalsIgnoreCase("text"))
- {
- accurateText = false;
- }
-
- int width = getTreeCanvas().getWidth();
- int height = getTreeCanvas().getHeight();
-
- try
+ int width = treeCanvas.getWidth();
+ int height = treeCanvas.getHeight();
+ ImageWriterI writer = new ImageWriterI()
{
- 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)
+ @Override
+ public void exportImage(Graphics g) throws Exception
{
- return;
+ treeCanvas.draw(g, width, height);
}
-
- Cache.setProperty("LAST_DIRECTORY",
- chooser.getSelectedFile().getParent());
-
- FileOutputStream out = new FileOutputStream(
- chooser.getSelectedFile());
- EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
- height);
-
- pg.setAccurateTextMode(accurateText);
-
- getTreeCanvas().draw(pg, width, height);
-
- pg.flush();
- pg.close();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void pngTree_actionPerformed(ActionEvent e)
- {
- int width = getTreeCanvas().getWidth();
- int height = getTreeCanvas().getHeight();
-
+ };
+ String tree = MessageManager.getString("label.tree");
+ ImageExporter exporter = new ImageExporter(writer, null, imageFormat,
+ tree);
try
{
- 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)
- {
- return;
- }
-
- 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();
-
- getTreeCanvas().draw(png, width, height);
-
- ImageIO.write(bi, "png", out);
- out.close();
- } catch (Exception ex)
+ exporter.doExport(null, this, width, height,
+ tree.toLowerCase(Locale.ROOT));
+ } catch (ImageOutputException ioex)
{
- ex.printStackTrace();
+ Console.error(
+ "Unexpected error whilst writing " + imageFormat.toString(),
+ ioex);
}
}
&& !((SequenceNode) node).isDummy())
{
String newname = null;
- SequenceI sq = (SequenceI) ((SequenceNode) node).element();
+ SequenceI sq = (SequenceI) ((BinaryNode) node).element();
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();
}
}
}
{
// String oldname = ((SequenceNode) node).getName();
// TODO : save oldname in the undo object for this modification.
- ((SequenceNode) node).setName(newname);
+ ((BinaryNode) node).setName(newname);
}
}
}
/*
* 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)
return ttl;
}
+ /**
+ * Builds an EPS image and writes it to the specified file.
+ *
+ * @param outFile
+ * @param textOption
+ * true for Text character rendering, false for Lineart
+ */
+ protected void writeEpsFile(File outFile, boolean textOption)
+ {
+ try
+ {
+ int width = treeCanvas.getWidth();
+ int height = treeCanvas.getHeight();
+
+ FileOutputStream out = new FileOutputStream(outFile);
+ EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
+ height);
+ pg.setAccurateTextMode(!textOption);
+ treeCanvas.draw(pg, width, height);
+
+ pg.flush();
+ pg.close();
+ } catch (Exception ex)
+ {
+ jalview.bin.Console.errPrintln("Error writing tree as EPS");
+ ex.printStackTrace();
+ }
+ }
+
public AlignViewport getViewport()
{
return av;
git://source.jalview.org / jalview.git / blobdiff