X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=9c1e42eab6030bc279679da282b096d2acd97c68;hb=0705a85fe0a3d391e5aba360340a0c342c898366;hp=a574795993971bceaf17bedec4459eaddfd9e7a6;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index a574795..9c1e42e 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -1,310 +1,477 @@ /* -* 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 -*/ - + * 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.datamodel.*; import jalview.analysis.*; -import jalview.jbgui.GTreePanel; + +import jalview.datamodel.*; + import jalview.io.*; -import java.awt.event.*; -import java.util.*; -import java.io.*; -import javax.swing.*; + +import jalview.jbgui.*; + +import org.jibble.epsgraphics.*; + import java.awt.*; +import java.awt.event.*; import java.awt.image.*; -import org.jibble.epsgraphics.*; + +import java.io.*; + +import java.util.*; + import javax.imageio.*; +import java.beans.PropertyChangeEvent; +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ public class TreePanel extends GTreePanel { - SequenceI[] seq; - String type; - String pwtype; - AlignViewport av; - int start; - int end; - TreeCanvas treeCanvas; - NJTree tree; - - public NJTree getTree() - { - return tree; - } - - public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e) - { - super(); - - this.type = type; - this.pwtype = pwtype; - - start = s; - end = e; - - String longestName = ""; - seq = new Sequence [seqVector.size()]; - for (int i=0;i < seqVector.size();i++) + SequenceI[] seq; + String type; + String pwtype; + int start; + int end; + TreeCanvas treeCanvas; + NJTree tree; + + /** + * 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, Vector seqVector, String type, + String pwtype, int s, int e) { - seq[i] = (Sequence) seqVector.elementAt(i); - if(seq[i].getName().length()>longestName.length()) - longestName = seq[i].getName(); + super(); + initTreePanel(av, seqVector, type, pwtype, s, e, null); + + // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default + showDistances(true); } - tree = new NJTree(seq, type, pwtype, start, end); - - treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName); - treeCanvas.setShowDistances(true); // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default - setViewStateFromTreeCanvas(treeCanvas); - tree.reCount(tree.getTopNode()); - tree.findHeight(tree.getTopNode()); - scrollPane.setViewportView(treeCanvas); - - } - private void setViewStateFromTreeCanvas(TreeCanvas tree) { - // update view menu state from treeCanvas render state - distanceMenu.setSelected(tree.showDistances); - bootstrapMenu.setSelected(tree.showBootstrap); - placeholdersMenu.setSelected(tree.markPlaceholders); - } - - private void setTreeCanvasFromViewState(TreeCanvas tree) { - // update view menu state from treeCanvas render state - tree.showDistances = distanceMenu.isSelected(); - tree.showBootstrap = bootstrapMenu.isSelected(); - tree.markPlaceholders = placeholdersMenu.isSelected(); + /** + * 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, Vector seqVector, NewickFile newtree, + String type, String pwtype) + { + super(); + initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree); } + public AlignmentI getAlignment() + { + return treeCanvas.av.getAlignment(); + } - public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree, - String type, String pwtype) + + void initTreePanel(AlignViewport av, Vector seqVector, String type, + String pwtype, int s, int e, NewickFile newTree) { - super(); - // These are probably only arbitrary strings reflecting source of tree + this.type = type; this.pwtype = pwtype; - start = 0; - end = seqVector.size(); + start = s; + end = e; - String longestName = ""; - seq = new Sequence [seqVector.size()]; - for (int i=0;i < seqVector.size();i++) - { - seq[i] = (Sequence) seqVector.elementAt(i); - } - // This constructor matches sequence names to treenodes and sets up the tree layouts. - tree = new NJTree(seq, newtree); - // Now have to calculate longest name based on the leaves - Vector leaves = tree.findLeaves(tree.getTopNode(),new Vector()); - boolean has_placeholders = false; - for (int i=0;i < leaves.size();i++) { - SequenceNode lf = (SequenceNode) leaves.elementAt(i); - if (lf.isPlaceholder()) - has_placeholders = true; - if (longestName.length()<((Sequence) lf.element()).getName().length()) - longestName = TreeCanvas.PLACEHOLDER+((Sequence) lf.element()).getName(); - } - tree.reCount(tree.getTopNode()); - tree.findHeight(tree.getTopNode()); + seq = new Sequence[seqVector.size()]; + seqVector.toArray(seq); - treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName); - treeCanvas.setShowBootstrap(newtree.HasBootstrap()); - treeCanvas.setShowDistances(newtree.HasDistances()); - scrollPane.setViewportView(treeCanvas); - treeCanvas.setMarkPlaceholders(has_placeholders); - setViewStateFromTreeCanvas(treeCanvas); - // JBPNote TODO: preference for always marking placeholders in new associated tree - } + treeCanvas = new TreeCanvas(av, scrollPane); + scrollPane.setViewportView(treeCanvas); - public void textbox_actionPerformed(ActionEvent e) - { - CutAndPasteTransfer cap = new CutAndPasteTransfer(); + 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"); - StringBuffer buffer = new StringBuffer(); + tree.UpdatePlaceHolders( (Vector) evt.getNewValue()); - if(type.equals("AV")) - buffer.append("Average distance tree using "); - else - buffer.append("Neighbour joining tree using "); + repaint(); + } + } + }); - 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(false,true) ); + TreeLoader tl = new TreeLoader(newTree); + tl.start(); } - - public void saveAsNewick_actionPerformed(ActionEvent e) + class TreeLoader extends Thread { + NewickFile newtree; - 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(false,true); // distances only - java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) ); - out.println(output); - out.close(); + 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()); + } } - catch (Exception ex) { - ex.printStackTrace(); + + public void run() + { + if(newtree!=null) + tree = new NJTree(seq, newtree); + else + tree = new NJTree(seq, type, pwtype, start, end); + + tree.reCount(tree.getTopNode()); + tree.findHeight(tree.getTopNode()); + treeCanvas.setTree(tree); + + treeCanvas.repaint(); + } } - } - protected void printMenu_actionPerformed(ActionEvent e) - { + public void showDistances(boolean b) + { + treeCanvas.setShowDistances(b); + distanceMenu.setSelected(b); + } + + public void showBootstrap(boolean b) + { + treeCanvas.setShowBootstrap(b); + bootstrapMenu.setSelected(b); + } - //Putting in a thread avoids Swing painting problems - treeCanvas.startPrinting(); - } + public void showPlaceholders(boolean b) + { + placeholdersMenu.setState(b); + treeCanvas.setMarkPlaceholders(b); + } - protected void fitToWindow_actionPerformed(ActionEvent e) - { - treeCanvas.fitToWindow = fitToWindow.isSelected(); - repaint(); - } - protected void fontSize_actionPerformed(ActionEvent e) - { - if( treeCanvas==null ) - return; - String size = fontSize.getText().substring( fontSize.getText().indexOf("-")+1); + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public NJTree getTree() + { + return tree; + } - Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop, - "Select font size", - "Font size", - JOptionPane.QUESTION_MESSAGE, - null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"} - ,"Font Size - "+size); - if(selection!=null) - { - fontSize.setText("Font Size - " + selection); - int i = Integer.parseInt(selection.toString()); - treeCanvas.setFontSize(i); - } - scrollPane.setViewportView(treeCanvas); + /** + * 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())); + } - protected void distanceMenu_actionPerformed(ActionEvent e) - { - treeCanvas.setShowDistances(distanceMenu.isSelected()); - } + /** + * 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(); + } + } + } - protected void bootstrapMenu_actionPerformed(ActionEvent e) - { - treeCanvas.setShowBootstrap(bootstrapMenu.isSelected()); - } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void printMenu_actionPerformed(ActionEvent e) + { + //Putting in a thread avoids Swing painting problems + treeCanvas.startPrinting(); + } - protected void placeholdersMenu_actionPerformed(ActionEvent e) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void fitToWindow_actionPerformed(ActionEvent e) { - treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected()); - } + treeCanvas.fitToWindow = fitToWindow.isSelected(); + repaint(); + } - protected void epsTree_actionPerformed(ActionEvent e) - { - int width = treeCanvas.getWidth(), height=treeCanvas.getHeight(); - try + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void font_actionPerformed(ActionEvent e) { - 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 (treeCanvas == null) + { + return; + } - int value = chooser.showSaveDialog(this); - if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION) - return; + new FontChooser(this); + } - 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); + public Font getTreeFont() + { + return treeCanvas.font; + } + public void setTreeFont(Font font) + { + if(treeCanvas!=null) + treeCanvas.setFont(font); + } - treeCanvas.draw(pg, width, height); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void distanceMenu_actionPerformed(ActionEvent e) + { + treeCanvas.setShowDistances(distanceMenu.isSelected()); + } - pg.flush(); - pg.close(); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void bootstrapMenu_actionPerformed(ActionEvent e) + { + treeCanvas.setShowBootstrap(bootstrapMenu.isSelected()); } - catch (Exception ex) + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void placeholdersMenu_actionPerformed(ActionEvent e) { - ex.printStackTrace(); + treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected()); } - } - protected void pngTree_actionPerformed(ActionEvent e) - { - int width = treeCanvas.getWidth(), height = treeCanvas.getHeight(); - try + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void epsTree_actionPerformed(ActionEvent e) { - 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"); + boolean accurateText = true; - chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle("Create PNG image from tree"); - chooser.setToolTipText("Save"); + String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING", + "Prompt each time"); - int value = chooser.showSaveDialog(this); - if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION) - return; + // 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()); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", + chooser.getSelectedFile().getParent()); - BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB); - Graphics png = bi.getGraphics(); + FileOutputStream out = new FileOutputStream(chooser.getSelectedFile()); + EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, + height); - treeCanvas.draw(png, width, height); + pg.setAccurateTextMode(accurateText); - ImageIO.write(bi, "png", out); - out.close(); + treeCanvas.draw(pg, width, height); + + pg.flush(); + pg.close(); + } + catch (Exception ex) + { + ex.printStackTrace(); + } } - catch (Exception ex) + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void pngTree_actionPerformed(ActionEvent e) { - ex.printStackTrace(); - } - } + 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(); + } + } }