2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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20 package jalview.appletgui;
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22 import jalview.datamodel.*;
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23 import jalview.io.NewickFile;
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24 import jalview.analysis.*;
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25 import jalview.jbappletgui.GTreePanel;
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26 import java.awt.event.*;
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28 import jalview.io.NewickFile;
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31 public class TreePanel extends GTreePanel
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39 TreeCanvas treeCanvas;
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42 public NJTree getTree()
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47 public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e)
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52 this.pwtype = pwtype;
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57 String longestName = "";
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58 seq = new Sequence [seqVector.size()];
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59 for (int i=0;i < seqVector.size();i++)
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61 seq[i] = (Sequence) seqVector.elementAt(i);
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62 if(seq[i].getName().length()>longestName.length())
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63 longestName = seq[i].getName();
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66 tree = new NJTree(seq, type, pwtype, start, end);
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68 treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
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70 tree.reCount(tree.getTopNode());
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71 tree.findHeight(tree.getTopNode());
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72 scrollPane.add(treeCanvas);
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75 public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
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76 String type, String pwtype)
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79 // These are probably only arbitrary strings reflecting source of tree
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81 this.pwtype = pwtype;
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84 end = seqVector.size();
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86 String longestName = "";
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87 seq = new Sequence [seqVector.size()];
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88 for (int i=0;i < seqVector.size();i++)
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90 seq[i] = (Sequence) seqVector.elementAt(i);
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92 // This constructor matches sequence names to treenodes and sets up the tree layouts.
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93 tree = new NJTree(seq, newtree);
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94 // Now have to calculate longest name based on the leaves
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95 Vector leaves = tree.findLeaves(tree.getTopNode(),new Vector());
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97 for (int i=0;i < leaves.size();i++)
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98 if (longestName.length()<((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName().length())
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99 longestName = TreeCanvas.PLACEHOLDER+((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName();
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101 tree.reCount(tree.getTopNode());
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102 tree.findHeight(tree.getTopNode());
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104 treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
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105 treeCanvas.setShowBootstrap(newtree.HasBootstrap());
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106 treeCanvas.setShowDistances(newtree.HasDistances());
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107 distanceMenu.setState(newtree.HasDistances());
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108 bootstrapMenu.setState(newtree.HasBootstrap());
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109 if (true) // JBPNote TODO: preference for always marking placeholders in new associated tree
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110 placeholdersMenu.setState(treeCanvas.markPlaceholders);
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111 scrollPane.add(treeCanvas);
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115 public String getText(String format) {
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119 protected void fitToWindow_actionPerformed(ActionEvent e)
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121 treeCanvas.fitToWindow = fitToWindow.getState();
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125 public void newickOutput_actionPerformed(ActionEvent actionEvent)
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127 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
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128 String output = fout.print(false, true);
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129 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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130 cap.setText(output);
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131 java.awt.Frame frame = new java.awt.Frame();
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133 jalview.bin.JalviewLite.addFrame(frame, type+" "+pwtype, 500,100);
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138 protected void fontSize_actionPerformed(ActionEvent e)
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140 /* if( treeCanvas==null )
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143 String size = fontSize.getLabel().substring( fontSize.getLabel().indexOf("-")+1);
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145 Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,
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146 "Select font size",
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148 JOptionPane.QUESTION_MESSAGE,
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149 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
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150 ,"Font Size - "+size);
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151 if(selection!=null)
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153 fontSize.setText("Font Size - " + selection);
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155 int i = Integer.parseInt(selection.toString());
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156 treeCanvas.setFontSize(i);
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158 scrollPane.setViewportView(treeCanvas);
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162 protected void distanceMenu_actionPerformed(ActionEvent e)
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164 treeCanvas.setShowDistances(distanceMenu.getState());
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167 protected void bootstrapMenu_actionPerformed(ActionEvent e)
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169 treeCanvas.setShowBootstrap(bootstrapMenu.getState());
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172 protected void placeholdersMenu_actionPerformed(ActionEvent e)
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174 treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
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