X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=ff02d49ec487eef6189d2acba088ca4b4267e9bf;hb=fbec1b33d0fc169d72be059a5d2cf12b248270e1;hp=c45863817185173ab0dda713f701cb6ab826019c;hpb=1026b7a36483fe6fec0a3d90f1496e49dc9b00ad;p=jalview.git diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index c458638..ff02d49 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -1,246 +1,456 @@ +/* + * 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 jalview.util.*; -import javax.swing.*; -import java.awt.print.*; + +import jalview.jbgui.*; + +import org.jibble.epsgraphics.*; + import java.awt.*; +import java.awt.event.*; import java.awt.image.*; -import org.jibble.epsgraphics.*; -import javax.imageio.*; +import java.io.*; +import java.util.*; + +import javax.imageio.*; + +import javax.swing.*; +/** + * 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(); - tree = new NJTree(seq, type, pwtype, start, end); + this.type = type; + this.pwtype = pwtype; - treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName); + start = s; + end = e; - tree.reCount(tree.getTopNode()); - tree.findHeight(tree.getTopNode()); - scrollPane.setViewportView(treeCanvas); + String longestName = ""; + seq = new Sequence[seqVector.size()]; - } - public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree, - String type, String pwtype) - { - super(); - // These are probably only arbitrary strings reflecting source of tree - this.type = type; - this.pwtype = pwtype; - - start = 0; - end = seqVector.size(); - - String longestName = ""; - seq = new Sequence [seqVector.size()]; - for (int i=0;i < seqVector.size();i++) - { - seq[i] = (Sequence) seqVector.elementAt(i); - if(seq[i].getName().length()>longestName.length()) - longestName = seq[i].getName(); - } - // This constructor matches sequence names to treenodes and sets up the tree layouts. - tree = new NJTree(seq, newtree); - - tree.reCount(tree.getTopNode()); - tree.findHeight(tree.getTopNode()); - - treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName); - treeCanvas.setShowBootstrap(newtree.HasBootstrap()); - treeCanvas.setShowDistances(newtree.HasDistances()); - scrollPane.setViewportView(treeCanvas); + for (int i = 0; i < seqVector.size(); i++) + { + seq[i] = (Sequence) seqVector.elementAt(i); + + if (seq[i].getName().length() > longestName.length()) + { + longestName = seq[i].getName(); + } + } + 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); } - public String getText(String format) + /** + * 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) { - return null; + super(); + + // These are probably only arbitrary strings reflecting source of tree + this.type = type; + this.pwtype = pwtype; + + start = 0; + end = seqVector.size(); + + 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()); + + 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 } - public void saveAsNewick_actionPerformed(ActionEvent e) + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public NJTree getTree() { - - 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(); - } - catch (Exception ex) { - ex.printStackTrace(); - } + return tree; } - } - - protected void printMenu_actionPerformed(ActionEvent e) - { - - //Putting in a thread avoids Swing painting problems - treeCanvas.startPrinting(); - } - - protected void fitToWindow_actionPerformed(ActionEvent e) - { - treeCanvas.fitToWindow = fitToWindow.isSelected(); - repaint(); - } + /** + * DOCUMENT ME! + * + * @param tree DOCUMENT ME! + */ + 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); + } - protected void fontSize_actionPerformed(ActionEvent e) - { - if( treeCanvas==null ) - return; - - String size = fontSize.getText().substring( fontSize.getText().indexOf("-")+1); - - 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 tree DOCUMENT ME! + */ + 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(); + } - protected void distanceMenu_actionPerformed(ActionEvent e) - { - treeCanvas.setShowDistances(distanceMenu.isSelected()); - } + /** + * 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); - protected void bootstrapMenu_actionPerformed(ActionEvent e) - { - treeCanvas.setShowBootstrap(bootstrapMenu.isSelected()); - } + jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode()); + cap.setText(fout.print(false, true)); + } + /** + * 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(false, true); // distances only + 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 epsTree_actionPerformed(ActionEvent e) - { - int width = treeCanvas.getWidth(), height=treeCanvas.getHeight(); - try + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void printMenu_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"); + //Putting in a thread avoids Swing painting problems + treeCanvas.startPrinting(); + } - int value = chooser.showSaveDialog(this); - if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION) - return; + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void fitToWindow_actionPerformed(ActionEvent e) + { + treeCanvas.fitToWindow = fitToWindow.isSelected(); + repaint(); + } - 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); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void fontSize_actionPerformed(ActionEvent e) + { + if (treeCanvas == null) + { + return; + } + + String size = fontSize.getText().substring(fontSize.getText().indexOf("-") + + 1); + + 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 distanceMenu_actionPerformed(ActionEvent e) + { + treeCanvas.setShowDistances(distanceMenu.isSelected()); + } - treeCanvas.draw(pg, width, height); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void bootstrapMenu_actionPerformed(ActionEvent e) + { + treeCanvas.setShowBootstrap(bootstrapMenu.isSelected()); + } - pg.flush(); - pg.close(); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void placeholdersMenu_actionPerformed(ActionEvent e) + { + treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected()); } - catch (Exception ex) + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void epsTree_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[] { "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); + + treeCanvas.draw(pg, width, height); + + pg.flush(); + pg.close(); + } + catch (Exception ex) + { + ex.printStackTrace(); + } } - } - protected void pngTree_actionPerformed(ActionEvent e) - { - int width = treeCanvas.getWidth(), height = treeCanvas.getHeight(); - try + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void pngTree_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"); + int width = treeCanvas.getWidth(); + int height = treeCanvas.getHeight(); - chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle("Create PNG image from tree"); - chooser.setToolTipText("Save"); + 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"); - int value = chooser.showSaveDialog(this); - if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION) - return; + chooser.setFileView(new jalview.io.JalviewFileView()); + chooser.setDialogTitle("Create PNG image from tree"); + chooser.setToolTipText("Save"); - jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getParent()); - FileOutputStream out = new FileOutputStream(chooser.getSelectedFile()); + int value = chooser.showSaveDialog(this); - BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB); - Graphics png = bi.getGraphics(); + if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION) + { + return; + } - treeCanvas.draw(png, width, height); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", + chooser.getSelectedFile().getParent()); - ImageIO.write(bi, "png", out); - out.close(); - } - catch (Exception ex) - { - ex.printStackTrace(); - } - } + 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(); + } + } }