/*
* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
*/
package jalview.gui;
-import jalview.analysis.*;
-
-import jalview.datamodel.*;
-
-import jalview.io.*;
-
-import jalview.jbgui.*;
-
-import org.jibble.epsgraphics.*;
+import java.beans.*;
+import java.io.*;
+import java.util.*;
+import javax.imageio.*;
import java.awt.*;
import java.awt.event.*;
import java.awt.image.*;
-
-import java.io.*;
-
-import java.util.*;
-
import javax.swing.*;
-import javax.imageio.*;
-
-import java.beans.PropertyChangeEvent;
+import org.jibble.epsgraphics.*;
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.jbgui.*;
/**
* DOCUMENT ME!
* @author $author$
* @version $Revision$
*/
-public class TreePanel extends GTreePanel
+public class TreePanel
+ extends GTreePanel
{
- String type;
- String pwtype;
- TreeCanvas treeCanvas;
- NJTree tree;
- AlignViewport av;
-
- /**
- * Creates a new TreePanel object.
- *
- * @param av DOCUMENT ME!
- * @param seqVector DOCUMENT ME!
- * @param type DOCUMENT ME!
- * @param pwtype DOCUMENT ME!
- * @param s DOCUMENT ME!
- * @param e DOCUMENT ME!
- */
- public TreePanel(AlignmentPanel ap, String type, String pwtype)
+ String type;
+ String pwtype;
+ TreeCanvas treeCanvas;
+ NJTree tree;
+ AlignViewport av;
+
+ /**
+ * Creates a new TreePanel object.
+ *
+ * @param av DOCUMENT ME!
+ * @param seqVector DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ * @param pwtype DOCUMENT ME!
+ * @param s DOCUMENT ME!
+ * @param e DOCUMENT ME!
+ */
+ public TreePanel(AlignmentPanel ap, String type, String pwtype)
+ {
+ super();
+ initTreePanel(ap, type, pwtype, null, null);
+
+ // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
+ // showDistances(true);
+ }
+
+ /**
+ * Creates a new TreePanel object.
+ *
+ * @param av DOCUMENT ME!
+ * @param seqVector DOCUMENT ME!
+ * @param newtree DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ * @param pwtype DOCUMENT ME!
+ */
+ public TreePanel(AlignmentPanel ap,
+ String type,
+ String pwtype,
+ NewickFile newtree)
+ {
+ super();
+ initTreePanel(ap, type, pwtype, newtree, null);
+ }
+
+ public TreePanel(AlignmentPanel av,
+ String type,
+ String pwtype,
+ NewickFile newtree, AlignmentView inputData)
+ {
+ super();
+ initTreePanel(av, type, pwtype, newtree, inputData);
+ }
+
+ public AlignmentI getAlignment()
+ {
+ return treeCanvas.av.getAlignment();
+ }
+
+ public AlignViewport getViewPort()
+ {
+ return treeCanvas.av;
+ }
+
+ void initTreePanel(AlignmentPanel ap, String type, String pwtype,
+ NewickFile newTree, AlignmentView inputData)
+ {
+
+ av = ap.av;
+ this.type = type;
+ this.pwtype = pwtype;
+
+ treeCanvas = new TreeCanvas(this, ap, scrollPane);
+ scrollPane.setViewportView(treeCanvas);
+
+ PaintRefresher.Register(this, ap.av.getSequenceSetId());
+
+ buildAssociatedViewMenu();
+
+ av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
{
- super();
- initTreePanel(ap, type, pwtype, null, null);
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ if (evt.getPropertyName().equals("alignment"))
+ {
+ if (tree == null)
+ {
+ System.out.println("tree is null");
+ }
+ if (evt.getNewValue() == null)
+ {
+ System.out.println("new alignment sequences vector value is null");
+ }
- // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
- // showDistances(true);
- }
+ tree.UpdatePlaceHolders( (Vector) evt.getNewValue());
+ treeCanvas.nameHash.clear(); // reset the mapping between canvas rectangles and leafnodes
+ repaint();
+ }
+ }
+ });
- /**
- * Creates a new TreePanel object.
- *
- * @param av DOCUMENT ME!
- * @param seqVector DOCUMENT ME!
- * @param newtree DOCUMENT ME!
- * @param type DOCUMENT ME!
- * @param pwtype DOCUMENT ME!
- */
- public TreePanel(AlignmentPanel ap,
- String type,
- String pwtype,
- NewickFile newtree)
+ TreeLoader tl = new TreeLoader(newTree);
+ if (inputData != null)
{
- super();
- initTreePanel(ap, type, pwtype, newtree, null);
+ tl.odata = inputData;
}
+ tl.start();
- public TreePanel(AlignmentPanel av,
- String type,
- String pwtype,
- NewickFile newtree, AlignmentView inputData) {
- super();
- initTreePanel(av,type,pwtype,newtree,inputData);
- }
+ }
- public AlignmentI getAlignment()
- {
- return treeCanvas.av.getAlignment();
- }
- public AlignViewport getViewPort() {
- return treeCanvas.av;
- }
+ public void viewMenu_menuSelected()
+ {
+ buildAssociatedViewMenu();
+ }
- void initTreePanel(AlignmentPanel ap, String type, String pwtype,
- NewickFile newTree, AlignmentView inputData)
+ void buildAssociatedViewMenu()
+ {
+ AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av.
+ getSequenceSetId());
+ if (aps.length == 1 && treeCanvas.ap == aps[0])
{
+ associateLeavesMenu.setVisible(false);
+ return;
+ }
- av = ap.av;
- this.type = type;
- this.pwtype = pwtype;
-
- treeCanvas = new TreeCanvas(this, ap, scrollPane);
- scrollPane.setViewportView(treeCanvas);
+ associateLeavesMenu.setVisible(true);
- PaintRefresher.Register(this, ap.av.getSequenceSetId());
+ if ( (viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
+ {
+ viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
+ }
- buildAssociatedViewMenu();
+ associateLeavesMenu.removeAll();
- av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
+ JRadioButtonMenuItem item;
+ ButtonGroup buttonGroup = new ButtonGroup();
+ int i, iSize = aps.length;
+ final TreePanel thisTreePanel = this;
+ for (i = 0; i < iSize; i++)
+ {
+ final AlignmentPanel ap = aps[i];
+ item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
+ buttonGroup.add(item);
+ item.addActionListener(new ActionListener()
{
- public void propertyChange(PropertyChangeEvent evt)
+ public void actionPerformed(ActionEvent evt)
{
- if (evt.getPropertyName().equals("alignment"))
- {
- if(tree==null)
- System.out.println("tree is null");
- if(evt.getNewValue()==null)
- System.out.println("new alignment sequences vector value is null");
-
- tree.UpdatePlaceHolders( (Vector) evt.getNewValue());
- treeCanvas.nameHash.clear(); // reset the mapping between canvas rectangles and leafnodes
- repaint();
- }
+ treeCanvas.applyToAllViews = false;
+ treeCanvas.ap = ap;
+ treeCanvas.av = ap.av;
+ PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
}
});
- TreeLoader tl = new TreeLoader(newTree);
- if (inputData!=null) {
- tl.odata=inputData;
- }
- tl.start();
-
+ associateLeavesMenu.add(item);
}
- public void viewMenu_menuSelected()
+ final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
+ buttonGroup.add(itemf);
+ itemf.setSelected(treeCanvas.applyToAllViews);
+ itemf.addActionListener(new ActionListener()
{
- buildAssociatedViewMenu();
- }
-
-
- void buildAssociatedViewMenu()
- {
- AlignmentPanel [] aps = PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
- if(aps.length==1 && treeCanvas.ap==aps[0])
+ public void actionPerformed(ActionEvent evt)
{
- associateLeavesMenu.setVisible(false);
- return;
+ treeCanvas.applyToAllViews = itemf.isSelected();
}
+ });
+ associateLeavesMenu.add(itemf);
- associateLeavesMenu.setVisible(true);
+ }
- if( (viewMenu.getItem(viewMenu.getItemCount()-2) instanceof JMenuItem))
+ class TreeLoader
+ extends Thread
+ {
+ NewickFile newtree;
+ jalview.datamodel.AlignmentView odata = null;
+ public TreeLoader(NewickFile newtree)
+ {
+ this.newtree = newtree;
+ if (newtree != null)
{
- viewMenu.insertSeparator(viewMenu.getItemCount()-1);
+ // Must be outside run(), as Jalview2XML tries to
+ // update distance/bootstrap visibility at the same time
+ showBootstrap(newtree.HasBootstrap());
+ showDistances(newtree.HasDistances());
}
+ }
- associateLeavesMenu.removeAll();
-
-
- JRadioButtonMenuItem item;
- ButtonGroup buttonGroup = new ButtonGroup();
- int i, iSize = aps.length;
- final TreePanel thisTreePanel = this;
- for(i=0; i<iSize; i++)
- {
- final AlignmentPanel ap = aps[i];
- item = new JRadioButtonMenuItem(ap.av.viewName, ap==treeCanvas.ap );
- buttonGroup.add(item);
- item.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent evt)
- {
- treeCanvas.applyToAllViews = false;
- treeCanvas.ap = ap;
- treeCanvas.av = ap.av;
- PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
- }
- });
-
- associateLeavesMenu.add(item);
- }
+ public void run()
+ {
- final JRadioButtonMenuItem itemf =
- new JRadioButtonMenuItem("All Views", treeCanvas.applyToAllViews);
- buttonGroup.add(itemf);
- itemf.addActionListener(new ActionListener()
+ if (newtree != null)
{
- public void actionPerformed(ActionEvent evt)
+ if (odata == null)
{
- treeCanvas.applyToAllViews = itemf.isSelected();
+ tree = new NJTree(av.alignment.getSequencesArray(),
+ newtree);
}
- });
- associateLeavesMenu.add(itemf);
-
- }
-
- class TreeLoader extends Thread
- {
- NewickFile newtree;
- jalview.datamodel.AlignmentView odata=null;
- public TreeLoader(NewickFile newtree)
- {
- this.newtree = newtree;
- if (newtree != null)
+ else
+ {
+ tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);
+ }
+ if (!tree.hasOriginalSequenceData())
{
- // Must be outside run(), as Jalview2XML tries to
- // update distance/bootstrap visibility at the same time
- showBootstrap(newtree.HasBootstrap());
- showDistances(newtree.HasDistances());
+ allowOriginalSeqData(false);
}
}
-
- public void run()
+ else
{
-
- if(newtree!=null)
+ int start, end;
+ SequenceI[] seqs;
+ AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup() != null);
+ if (av.getSelectionGroup() == null)
{
- if (odata==null) {
- tree = new NJTree(av.alignment.getSequencesArray(),
- newtree);
- } else {
- tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);
- }
- if (!tree.hasOriginalSequenceData())
- allowOriginalSeqData(false);
+ start = 0;
+ end = av.alignment.getWidth();
+ seqs = av.alignment.getSequencesArray();
}
else
{
- int start, end;
- SequenceI [] seqs;
- AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null);
- if(av.getSelectionGroup()==null)
- {
- start = 0;
- end = av.alignment.getWidth();
- seqs = av.alignment.getSequencesArray();
- }
- else
- {
- start = av.getSelectionGroup().getStartRes();
- end = av.getSelectionGroup().getEndRes()+1;
- seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
- }
-
- tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
- showDistances(true);
+ start = av.getSelectionGroup().getStartRes();
+ end = av.getSelectionGroup().getEndRes() + 1;
+ seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
}
+ tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
+ showDistances(true);
+ }
- tree.reCount(tree.getTopNode());
- tree.findHeight(tree.getTopNode());
- treeCanvas.setTree(tree);
- treeCanvas.repaint();
- av.setCurrentTree(tree);
+ tree.reCount(tree.getTopNode());
+ tree.findHeight(tree.getTopNode());
+ treeCanvas.setTree(tree);
+ treeCanvas.repaint();
+ av.setCurrentTree(tree);
- }
}
-
- public void showDistances(boolean b)
+ }
+
+ public void showDistances(boolean b)
+ {
+ treeCanvas.setShowDistances(b);
+ distanceMenu.setSelected(b);
+ }
+
+ public void showBootstrap(boolean b)
+ {
+ treeCanvas.setShowBootstrap(b);
+ bootstrapMenu.setSelected(b);
+ }
+
+ public void showPlaceholders(boolean b)
+ {
+ placeholdersMenu.setState(b);
+ treeCanvas.setMarkPlaceholders(b);
+ }
+
+ private void allowOriginalSeqData(boolean b)
+ {
+ originalSeqData.setVisible(b);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public NJTree getTree()
+ {
+ return tree;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void textbox_actionPerformed(ActionEvent e)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+
+ StringBuffer buffer = new StringBuffer();
+
+ if (type.equals("AV"))
{
- treeCanvas.setShowDistances(b);
- distanceMenu.setSelected(b);
+ buffer.append("Average distance tree using ");
}
-
- public void showBootstrap(boolean b)
+ else
{
- treeCanvas.setShowBootstrap(b);
- bootstrapMenu.setSelected(b);
+ buffer.append("Neighbour joining tree using ");
}
- public void showPlaceholders(boolean b)
+ if (pwtype.equals("BL"))
{
- placeholdersMenu.setState(b);
- treeCanvas.setMarkPlaceholders(b);
+ buffer.append("BLOSUM62");
}
-
- private void allowOriginalSeqData(boolean b) {
- originalSeqData.setVisible(b);
- }
-
-
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public NJTree getTree()
+ else
{
- return tree;
+ buffer.append("PID");
}
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void textbox_actionPerformed(ActionEvent e)
+ Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
+
+ jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
+ cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
+ tree.isHasRootDistance()));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void saveAsNewick_actionPerformed(ActionEvent e)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+ getProperty(
+ "LAST_DIRECTORY"));
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Save tree as newick file");
+ chooser.setToolTipText("Save");
+
+ int value = chooser.showSaveDialog(null);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
{
- CutAndPasteTransfer cap = new CutAndPasteTransfer();
-
- StringBuffer buffer = new StringBuffer();
-
- if (type.equals("AV"))
- {
- buffer.append("Average distance tree using ");
- }
- else
- {
- buffer.append("Neighbour joining tree using ");
- }
-
- if (pwtype.equals("BL"))
- {
- buffer.append("BLOSUM62");
- }
- else
- {
- buffer.append("PID");
- }
-
- Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ chooser.getSelectedFile().getParent());
+ try
+ {
jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
- cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()));
+ String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
+ tree.isHasRootDistance());
+ java.io.PrintWriter out = new java.io.PrintWriter(new java.io.
+ FileWriter(
+ choice));
+ out.println(output);
+ out.close();
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
}
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void saveAsNewick_actionPerformed(ActionEvent e)
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void printMenu_actionPerformed(ActionEvent e)
+ {
+ //Putting in a thread avoids Swing painting problems
+ treeCanvas.startPrinting();
+ }
+
+ public void originalSeqData_actionPerformed(ActionEvent e)
+ {
+ if (!tree.hasOriginalSequenceData())
{
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
- "LAST_DIRECTORY"));
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save tree as newick file");
- chooser.setToolTipText("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());
-
- try
- {
- jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
- String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance());
- java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
- choice));
- out.println(output);
- out.close();
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
+ jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
+ return;
}
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void printMenu_actionPerformed(ActionEvent e)
+ // decide if av alignment is sufficiently different to original data to warrant a new window to be created
+ // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
+ // or create a selection box around columns in alignment view
+ // test Alignment(SeqCigar[])
+ char gc = '-';
+ try {
+ // we try to get the associated view's gap character
+ // but this may fail if the view was closed...
+ gc = av.
+ getGapCharacter();
+ } catch (Exception ex) {};
+ Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
+
+ if (alAndColsel != null && alAndColsel[0] != null)
{
- //Putting in a thread avoids Swing painting problems
- treeCanvas.startPrinting();
- }
-
+ // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
- public void originalSeqData_actionPerformed(ActionEvent e)
- {
- if (!tree.hasOriginalSequenceData())
+ Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]);
+ Alignment dataset = av.getAlignment().getDataset();
+ if (dataset != null)
{
- jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
- return;
+ al.setDataset(dataset);
}
- // decide if av alignment is sufficiently different to original data to warrant a new window to be created
- // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
- // or create a selection box around columns in alignment view
- // test Alignment(SeqCigar[])
- Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.
- getGapCharacter());
-
-
- if (alAndColsel != null && alAndColsel[0]!=null)
- {
- // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
-
- Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
- Alignment dataset = av.getAlignment().getDataset();
- 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
-);
-
- //>>>This is a fix for the moment, until a better solution is found!!<<<
- // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
-
- // af.addSortByOrderMenuItem(ServiceName + " Ordering",
- // msaorder);
-
- Desktop.addInternalFrame(af, "Original Data for " + this.title,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
- }
- }
- }
+ if (true)
+ {
+ // make a new frame!
+ AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1],
+ AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT
+ );
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void fitToWindow_actionPerformed(ActionEvent e)
- {
- treeCanvas.fitToWindow = fitToWindow.isSelected();
- repaint();
- }
+ //>>>This is a fix for the moment, until a better solution is found!!<<<
+ // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void font_actionPerformed(ActionEvent e)
- {
- if (treeCanvas == null)
- {
- return;
- }
+ // af.addSortByOrderMenuItem(ServiceName + " Ordering",
+ // msaorder);
- new FontChooser(this);
+ Desktop.addInternalFrame(af, "Original Data for " + this.title,
+ AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
}
-
- public Font getTreeFont()
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void fitToWindow_actionPerformed(ActionEvent e)
+ {
+ treeCanvas.fitToWindow = fitToWindow.isSelected();
+ repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void font_actionPerformed(ActionEvent e)
+ {
+ if (treeCanvas == null)
{
- return treeCanvas.font;
+ return;
}
- public void setTreeFont(Font font)
- {
- if(treeCanvas!=null)
- treeCanvas.setFont(font);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void distanceMenu_actionPerformed(ActionEvent e)
- {
- treeCanvas.setShowDistances(distanceMenu.isSelected());
- }
+ new FontChooser(this);
+ }
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void bootstrapMenu_actionPerformed(ActionEvent e)
- {
- treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
- }
+ public Font getTreeFont()
+ {
+ return treeCanvas.font;
+ }
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void placeholdersMenu_actionPerformed(ActionEvent e)
+ public void setTreeFont(Font font)
+ {
+ if (treeCanvas != null)
{
- treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
+ treeCanvas.setFont(font);
}
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void epsTree_actionPerformed(ActionEvent e)
- {
- boolean accurateText = true;
-
- String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
- "Prompt each time");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void distanceMenu_actionPerformed(ActionEvent e)
+ {
+ treeCanvas.setShowDistances(distanceMenu.isSelected());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void bootstrapMenu_actionPerformed(ActionEvent e)
+ {
+ treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void placeholdersMenu_actionPerformed(ActionEvent e)
+ {
+ treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void epsTree_actionPerformed(ActionEvent e)
+ {
+ 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("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.equalsIgnoreCase("text"))
+ if (renderStyle == null || eps.cancelled)
{
- accurateText = false;
+ return;
}
- int width = treeCanvas.getWidth();
- int height = treeCanvas.getHeight();
+ }
- try
- {
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
- "LAST_DIRECTORY"), new String[] { "eps" },
- new String[] { "Encapsulated Postscript" },
- "Encapsulated Postscript");
- chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle("Create EPS file from tree");
- chooser.setToolTipText("Save");
+ if (renderStyle.equalsIgnoreCase("text"))
+ {
+ accurateText = false;
+ }
- int value = chooser.showSaveDialog(this);
+ int width = treeCanvas.getWidth();
+ int height = treeCanvas.getHeight();
- if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
- {
- return;
- }
+ try
+ {
+ jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
+ jalview.bin.Cache.getProperty(
+ "LAST_DIRECTORY"), new String[]
+ {"eps"},
+ new String[]
+ {"Encapsulated Postscript"},
+ "Encapsulated Postscript");
+ chooser.setFileView(new jalview.io.JalviewFileView());
+ chooser.setDialogTitle("Create EPS file from tree");
+ chooser.setToolTipText("Save");
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+ {
+ 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());
- 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);
+ pg.setAccurateTextMode(accurateText);
- treeCanvas.draw(pg, width, height);
+ treeCanvas.draw(pg, width, height);
- pg.flush();
- pg.close();
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
+ pg.flush();
+ pg.close();
}
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void pngTree_actionPerformed(ActionEvent e)
+ catch (Exception ex)
{
- int width = treeCanvas.getWidth();
- int height = treeCanvas.getHeight();
-
- try
- {
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
- "LAST_DIRECTORY"), new String[] { "png" },
- new String[] { "Portable network graphics" },
- "Portable network graphics");
+ ex.printStackTrace();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void pngTree_actionPerformed(ActionEvent e)
+ {
+ int width = treeCanvas.getWidth();
+ int height = treeCanvas.getHeight();
+
+ try
+ {
+ jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
+ jalview.bin.Cache.getProperty(
+ "LAST_DIRECTORY"), new String[]
+ {"png"},
+ new String[]
+ {"Portable network graphics"},
+ "Portable network graphics");
- chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle("Create PNG image from tree");
- chooser.setToolTipText("Save");
+ chooser.setFileView(new jalview.io.JalviewFileView());
+ chooser.setDialogTitle("Create PNG image from tree");
+ chooser.setToolTipText("Save");
- int value = chooser.showSaveDialog(this);
+ int value = chooser.showSaveDialog(this);
- if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
- {
- return;
- }
+ if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+ {
+ 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);
- Graphics png = bi.getGraphics();
+ BufferedImage bi = new BufferedImage(width, height,
+ BufferedImage.TYPE_INT_RGB);
+ Graphics png = bi.getGraphics();
- treeCanvas.draw(png, width, height);
+ treeCanvas.draw(png, width, height);
- ImageIO.write(bi, "png", out);
- out.close();
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
+ ImageIO.write(bi, "png", out);
+ out.close();
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
}
+ }
}