X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=c0b0c689b1bb2235fa7acb811ea26324ab8bd3d4;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=bde218ca639c8b6e01fa1024a4734c4f1b9024f9;hpb=d187567c926fed31f9cd9bda0dc112bc4d1b1261;p=jalview.git
diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index bde218c..c0b0c68 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -1,519 +1,888 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 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
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-package jalview.gui;
-
-import jalview.analysis.*;
-
-import jalview.datamodel.*;
-
-import jalview.io.*;
-
-import jalview.jbgui.*;
-
-import org.jibble.epsgraphics.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-
-import java.io.*;
-
-import java.util.*;
-
-import javax.imageio.*;
-
-import java.beans.PropertyChangeEvent;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-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(AlignViewport av, String type, String pwtype)
- {
- super();
- initTreePanel(av, type, pwtype, 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(AlignViewport av,
- String type,
- String pwtype,
- NewickFile newtree)
- {
- super();
- initTreePanel(av, type, pwtype, newtree);
- }
-
- public AlignmentI getAlignment()
- {
- return treeCanvas.av.getAlignment();
- }
-
-
- void initTreePanel(AlignViewport av, String type, String pwtype,
- NewickFile newTree)
- {
-
- this.type = type;
- this.pwtype = pwtype;
-
- treeCanvas = new TreeCanvas(av, scrollPane);
- scrollPane.setViewportView(treeCanvas);
-
- av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
- {
- 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 value is null");
-
- tree.UpdatePlaceHolders( (Vector) evt.getNewValue());
-
- repaint();
- }
- }
- });
-
- this.av = av;
-
-
- TreeLoader tl = new TreeLoader(newTree);
- tl.start();
-
- }
-
- class TreeLoader extends Thread
- {
- NewickFile newtree;
- jalview.datamodel.CigarArray odata=null;
- public TreeLoader(NewickFile newtree)
- {
- this.newtree = newtree;
- if (newtree != null)
- {
- // Must be outside run(), as Jalview2XML tries to
- // update distance/bootstrap visibility at the same time
- showBootstrap(newtree.HasBootstrap());
- showDistances(newtree.HasDistances());
- }
- }
-
- public void run()
- {
-
- if(newtree!=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);
- }
- else
- {
- int start, end;
- SequenceI [] seqs;
- CigarArray seqStrings = av.getViewAsCigars(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);
- }
-
-
- tree.reCount(tree.getTopNode());
- tree.findHeight(tree.getTopNode());
- treeCanvas.setTree(tree);
- treeCanvas.repaint();
- av.setCurrentTree(tree);
-
- }
- }
-
- 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"))
- {
- 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);
-
- 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)
- {
- 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();
- }
- }
- }
-
- /**
- * 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)
- {
- String originalData = tree.printOriginalSequenceData(av.getGapCharacter());
- if (originalData!=null) {
- CutAndPasteTransfer cap = new CutAndPasteTransfer();
- cap.setText(originalData);
- Desktop.addInternalFrame(cap, "Original Data",
- 400, 400);
- } else {
- System.err.println("IMPLEMENTATION BUG! originalSeqData is not available.");
- }
-
- }
-
-
- /**
- * 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;
- }
-
- new FontChooser(this);
- }
-
- public Font getTreeFont()
- {
- return treeCanvas.font;
- }
-
- 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());
- }
-
- /**
- * 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("text"))
- {
- accurateText = false;
- }
-
- 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");
-
- 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());
- EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
- height);
-
- pg.setAccurateTextMode(accurateText);
-
- treeCanvas.draw(pg, width, height);
-
- pg.flush();
- pg.close();
- }
- catch (Exception ex)
- {
- 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");
-
- 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();
-
- treeCanvas.draw(png, width, height);
-
- ImageIO.write(bi, "png", out);
- out.close();
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.analysis.AlignmentSorter;
+import jalview.analysis.NJTree;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.ViewBasedAnalysisI;
+import jalview.bin.Cache;
+import jalview.commands.CommandI;
+import jalview.commands.OrderCommand;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.BinaryNode;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.NodeTransformI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.io.NewickFile;
+import jalview.jbgui.GTreePanel;
+import jalview.schemes.ResidueProperties;
+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.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 org.jibble.epsgraphics.EpsGraphics2D;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+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)
+ {
+ 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 AlignmentViewport 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()
+ {
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ if (evt.getPropertyName().equals("alignment"))
+ {
+ if (tree == null)
+ {
+ System.out.println("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.
+ return;
+ }
+ if (evt.getNewValue() == null)
+ {
+ System.out
+ .println("new alignment sequences vector value is null");
+ }
+
+ tree.UpdatePlaceHolders((List) evt.getNewValue());
+ treeCanvas.nameHash.clear(); // reset the mapping between canvas
+ // rectangles and leafnodes
+ repaint();
+ }
+ }
+ });
+
+ TreeLoader tl = new TreeLoader(newTree);
+ if (inputData != null)
+ {
+ tl.odata = inputData;
+ }
+ tl.start();
+
+ }
+
+ public void viewMenu_menuSelected()
+ {
+ buildAssociatedViewMenu();
+ }
+
+ void buildAssociatedViewMenu()
+ {
+ AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
+ .getSequenceSetId());
+ if (aps.length == 1 && treeCanvas.ap == aps[0])
+ {
+ associateLeavesMenu.setVisible(false);
+ return;
+ }
+
+ associateLeavesMenu.setVisible(true);
+
+ if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
+ {
+ viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
+ }
+
+ 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);
+ }
+
+ final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
+ MessageManager.getString("label.all_views"));
+ buttonGroup.add(itemf);
+ itemf.setSelected(treeCanvas.applyToAllViews);
+ itemf.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ treeCanvas.applyToAllViews = itemf.isSelected();
+ }
+ });
+ associateLeavesMenu.add(itemf);
+
+ }
+
+ class TreeLoader extends Thread
+ {
+ NewickFile newtree;
+
+ jalview.datamodel.AlignmentView odata = null;
+
+ public TreeLoader(NewickFile newtree)
+ {
+ this.newtree = newtree;
+ if (newtree != null)
+ {
+ // Must be outside run(), as Jalview2XML tries to
+ // update distance/bootstrap visibility at the same time
+ showBootstrap(newtree.HasBootstrap());
+ showDistances(newtree.HasDistances());
+ }
+ }
+
+ public void run()
+ {
+
+ if (newtree != null)
+ {
+ if (odata == null)
+ {
+ tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
+ }
+ else
+ {
+ tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
+ newtree);
+ }
+ if (!tree.hasOriginalSequenceData())
+ {
+ allowOriginalSeqData(false);
+ }
+ }
+ else
+ {
+ int start, end;
+ SequenceI[] seqs;
+ boolean selview = av.getSelectionGroup() != null
+ && av.getSelectionGroup().getSize() > 1;
+ AlignmentView seqStrings = av.getAlignmentView(selview);
+ if (!selview)
+ {
+ start = 0;
+ end = av.getAlignment().getWidth();
+ seqs = av.getAlignment().getSequencesArray();
+ }
+ else
+ {
+ start = av.getSelectionGroup().getStartRes();
+ end = av.getSelectionGroup().getEndRes() + 1;
+ seqs = av.getSelectionGroup().getSequencesInOrder(
+ av.getAlignment());
+ }
+ ScoreModelI sm = ResidueProperties.getScoreModel(pwtype);
+ if (sm instanceof ViewBasedAnalysisI)
+ {
+ try
+ {
+ sm = sm.getClass().newInstance();
+ ((ViewBasedAnalysisI) sm)
+ .configureFromAlignmentView(treeCanvas.ap);
+ } catch (Exception q)
+ {
+ Cache.log.error("Couldn't create a scoremodel instance for "
+ + sm.getName());
+ }
+ tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
+ }
+ else
+ {
+ tree = new NJTree(seqs, seqStrings, type, pwtype, null, start,
+ end);
+ }
+ showDistances(true);
+ }
+
+ tree.reCount(tree.getTopNode());
+ tree.findHeight(tree.getTopNode());
+ treeCanvas.setTree(tree);
+ treeCanvas.repaint();
+ av.setCurrentTree(tree);
+ if (av.getSortByTree())
+ {
+ sortByTree_actionPerformed();
+ }
+ }
+ }
+
+ 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"))
+ {
+ buffer.append("Average distance tree using ");
+ }
+ else
+ {
+ buffer.append("Neighbour joining tree using ");
+ }
+
+ if (pwtype.equals("BL"))
+ {
+ buffer.append("BLOSUM62");
+ }
+ else
+ {
+ buffer.append("PID");
+ }
+
+ jalview.io.NewickFile fout = new jalview.io.NewickFile(
+ tree.getTopNode());
+ try
+ {
+ cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
+ tree.isHasRootDistance()));
+ Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("generating newick tree file", oom);
+ cap.dispose();
+ }
+
+ }
+
+ /**
+ * 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(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());
+
+ 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();
+ }
+ }
+ }
+
+ /**
+ * 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())
+ {
+ 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
+ // 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)
+ {
+ // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
+
+ Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
+ Alignment 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);
+
+ // >>>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, MessageManager.formatMessage(
+ "label.original_data_for_params",
+ new Object[] { this.title }), AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void fitToWindow_actionPerformed(ActionEvent e)
+ {
+ treeCanvas.fitToWindow = fitToWindow.isSelected();
+ repaint();
+ }
+
+ /**
+ * sort the associated alignment view by the current tree.
+ *
+ * @param e
+ */
+ @Override
+ public void sortByTree_actionPerformed()
+ {
+
+ if (treeCanvas.applyToAllViews)
+ {
+ final ArrayList commands = new ArrayList();
+ for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
+ .getSequenceSetId()))
+ {
+ commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
+ }
+ av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
+ {
+
+ @Override
+ public void undoCommand(AlignmentI[] views)
+ {
+ for (CommandI tsort : commands)
+ {
+ tsort.undoCommand(views);
+ }
+ }
+
+ @Override
+ public int getSize()
+ {
+ return commands.size();
+ }
+
+ @Override
+ public String getDescription()
+ {
+ return "Tree Sort (many views)";
+ }
+
+ @Override
+ public void doCommand(AlignmentI[] views)
+ {
+
+ for (CommandI tsort : commands)
+ {
+ tsort.doCommand(views);
+ }
+ }
+ });
+ for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
+ .getSequenceSetId()))
+ {
+ // ensure all the alignFrames refresh their GI after adding an undo item
+ ap.alignFrame.updateEditMenuBar();
+ }
+ }
+ else
+ {
+ treeCanvas.ap.alignFrame
+ .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
+ }
+
+ }
+
+ public CommandI sortAlignmentIn(AlignmentPanel ap)
+ {
+ AlignmentViewport av = ap.av;
+ SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByTree(av.getAlignment(), tree);
+ CommandI undo;
+ undo = new OrderCommand("Tree Sort", oldOrder, av.getAlignment());
+
+ ap.paintAlignment(true);
+ return undo;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void font_actionPerformed(ActionEvent e)
+ {
+ if (treeCanvas == null)
+ {
+ return;
+ }
+
+ new FontChooser(this);
+ }
+
+ public Font getTreeFont()
+ {
+ return treeCanvas.font;
+ }
+
+ 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());
+ }
+
+ /**
+ * 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("text"))
+ {
+ accurateText = false;
+ }
+
+ 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(MessageManager
+ .getString("label.create_eps_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());
+ EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
+
+ pg.setAccurateTextMode(accurateText);
+
+ treeCanvas.draw(pg, width, height);
+
+ pg.flush();
+ pg.close();
+ } catch (Exception ex)
+ {
+ 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(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();
+
+ treeCanvas.draw(png, width, height);
+
+ ImageIO.write(bi, "png", out);
+ out.close();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ /**
+ * change node labels to the annotation referred to by labelClass TODO:
+ * promote to a datamodel modification that can be undone TODO: make argument
+ * one case of a generic transformation function ie { undoStep = apply(Tree,
+ * TransformFunction)};
+ *
+ * @param labelClass
+ */
+ public void changeNames(final String labelClass)
+ {
+ tree.applyToNodes(new NodeTransformI()
+ {
+
+ public void transform(BinaryNode node)
+ {
+ if (node instanceof SequenceNode
+ && !((SequenceNode) node).isPlaceholder()
+ && !((SequenceNode) node).isDummy())
+ {
+ String newname = null;
+ SequenceI sq = (SequenceI) ((SequenceNode) node).element();
+ if (sq != null)
+ {
+ // search dbrefs, features and annotation
+ DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
+ sq.getDBRef(),
+ new String[] { labelClass.toUpperCase() });
+ if (refs != null)
+ {
+ for (int i = 0; i < refs.length; i++)
+ {
+ if (newname == null)
+ {
+ newname = new String(refs[i].getAccessionId());
+ }
+ else
+ {
+ newname = newname + "; " + refs[i].getAccessionId();
+ }
+ }
+ }
+ if (newname == null)
+ {
+ SequenceFeature sf[] = sq.getSequenceFeatures();
+ for (int i = 0; sf != null && i < sf.length; i++)
+ {
+ if (sf[i].getType().equals(labelClass))
+ {
+ if (newname == null)
+ {
+ newname = new String(sf[i].getDescription());
+ }
+ else
+ {
+ newname = newname + "; " + sf[i].getDescription();
+ }
+ }
+ }
+ }
+ }
+ if (newname != null)
+ {
+ String oldname = ((SequenceNode) node).getName();
+ // TODO : save in the undo object for this modification.
+ ((SequenceNode) node).setName(newname);
+ }
+ }
+ }
+ });
+ }
+}