X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=2a8c9b44ae5a1d0d5d4601b29336bf838109d6e1;hb=1d6ae39a6442c455d362b933f1da89b0a481e5f5;hp=87c4d1491ebcfbb10b27a3cd58ee3e944b79f98b;hpb=d6110253d39dee5570f3357b4c87b89eadcb8aeb;p=jalview.git diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index 87c4d14..2a8c9b4 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -1,24 +1,40 @@ +/* + * 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.io.*; -import java.awt.event.*; -import java.util.*; import java.io.*; -import jalview.util.*; -import javax.swing.*; -import java.awt.print.*; -import java.awt.*; -import java.awt.image.*; -import org.jibble.epsgraphics.*; +import java.util.*; import javax.imageio.*; +import java.awt.*; +import java.awt.event.*; +import java.awt.image.*; +import javax.swing.*; +import org.jibble.epsgraphics.*; +import jalview.analysis.*; +import jalview.datamodel.*; +import jalview.io.*; +import jalview.jbgui.*; - -public class TreePanel extends GTreePanel +public class TreePanel + extends GTreePanel { SequenceI[] seq; String type; @@ -29,12 +45,8 @@ public class TreePanel extends GTreePanel TreeCanvas treeCanvas; NJTree tree; - public NJTree getTree() - { - return tree; - } - - public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e) + public TreePanel(AlignViewport av, Vector seqVector, String type, + String pwtype, int s, int e) { super(); @@ -45,80 +57,165 @@ public class TreePanel extends GTreePanel end = e; String longestName = ""; - seq = new Sequence [seqVector.size()]; - for (int i=0;i < seqVector.size();i++) + 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()) + + 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 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); + } + + // 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++) { - super(); - // These are probably only arbitrary strings reflecting source of tree - this.type = type; - this.pwtype = pwtype; + SequenceNode lf = (SequenceNode) leaves.elementAt(i); - start = 0; - end = seqVector.size(); + if (lf.isPlaceholder()) + { + has_placeholders = true; + } - String longestName = ""; - seq = new Sequence [seqVector.size()]; - for (int i=0;i < seqVector.size();i++) + if (longestName.length() < ( (Sequence) lf.element()).getName() + .length()) { - seq[i] = (Sequence) seqVector.elementAt(i); - if(seq[i].getName().length()>longestName.length()) - longestName = seq[i].getName(); + longestName = TreeCanvas.PLACEHOLDER + + ( (Sequence) lf.element()).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()); + 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 = 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 String getText(String format) + public NJTree getTree() + { + return tree; + } + + 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(); + } + + 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 { - return null; + buffer.append("Neighbour joining tree using "); } - public void saveAsNewick_actionPerformed(ActionEvent e) + if (pwtype.equals("BL")) { + buffer.append("BLOSUM62"); + } + else + { + buffer.append("PID"); + } + + Desktop.addInternalFrame(cap, buffer.toString(), 500, 100); - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. - getProperty("LAST_DIRECTORY")); + jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode()); + cap.setText(fout.print(false, true)); + } + + 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", choice); - try{ + + 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 ) ); + 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) { + catch (Exception ex) + { ex.printStackTrace(); } } @@ -126,7 +223,6 @@ public class TreePanel extends GTreePanel protected void printMenu_actionPerformed(ActionEvent e) { - //Putting in a thread avoids Swing painting problems treeCanvas.startPrinting(); } @@ -137,29 +233,33 @@ public class TreePanel extends GTreePanel repaint(); } - 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); + 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); } protected void distanceMenu_actionPerformed(ActionEvent e) @@ -172,31 +272,47 @@ public class TreePanel extends GTreePanel treeCanvas.setShowBootstrap(bootstrapMenu.isSelected()); } + protected void placeholdersMenu_actionPerformed(ActionEvent e) + { + treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected()); + } protected void epsTree_actionPerformed(ActionEvent e) { - int width = treeCanvas.getWidth(), height=treeCanvas.getHeight(); + 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"}, "Encapsulated Postscript"); + 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().getPath()); - FileOutputStream out = new FileOutputStream(chooser.getSelectedFile()); - EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height); + 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(); + pg.flush(); + pg.close(); } catch (Exception ex) { @@ -205,35 +321,48 @@ public class TreePanel extends GTreePanel } protected void pngTree_actionPerformed(ActionEvent e) - { - int width = treeCanvas.getWidth(), height = treeCanvas.getHeight(); + { + 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"}, "Portable network graphics"); + 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()); - jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath()); FileOutputStream out = new FileOutputStream(chooser.getSelectedFile()); - BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB); + 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(); + ImageIO.write(bi, "png", out); + out.close(); } catch (Exception ex) { ex.printStackTrace(); } } - }