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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24 import java.awt.event.*;
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26 import jalview.analysis.*;
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27 import jalview.datamodel.*;
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28 import jalview.io.*;
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29 import jalview.jbappletgui.*;
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31 public class TreePanel
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40 TreeCanvas treeCanvas;
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43 public NJTree getTree()
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49 * Creates a new TreePanel object.
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51 * @param av DOCUMENT ME!
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52 * @param seqVector DOCUMENT ME!
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53 * @param type DOCUMENT ME!
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54 * @param pwtype DOCUMENT ME!
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55 * @param s DOCUMENT ME!
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56 * @param e DOCUMENT ME!
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58 public TreePanel(AlignViewport av, Vector seqVector, String type,
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59 String pwtype, int s, int e)
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62 initTreePanel(av, seqVector, type, pwtype, s, e, null);
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64 // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
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65 treeCanvas.setShowDistances(true);
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69 * Creates a new TreePanel object.
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71 * @param av DOCUMENT ME!
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72 * @param seqVector DOCUMENT ME!
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73 * @param newtree DOCUMENT ME!
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74 * @param type DOCUMENT ME!
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75 * @param pwtype DOCUMENT ME!
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77 public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
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78 String type, String pwtype)
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81 initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);
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85 void initTreePanel(AlignViewport av, Vector seqVector, String type,
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86 String pwtype, int s, int e, NewickFile newTree)
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90 this.pwtype = pwtype;
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95 seq = new Sequence[seqVector.size()];
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96 for(int i=0; i<seqVector.size(); i++)
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97 seq[i] = (SequenceI)seqVector.elementAt(i);
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100 treeCanvas = new TreeCanvas(av, scrollPane);
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101 scrollPane.add(treeCanvas);
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104 TreeLoader tl = new TreeLoader(newTree);
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109 class TreeLoader extends Thread
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111 NewickFile newtree;
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113 public TreeLoader(NewickFile newtree)
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115 this.newtree = newtree;
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121 tree = new NJTree(seq, newtree);
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123 tree = new NJTree(seq, type, pwtype, start, end);
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125 tree.reCount(tree.getTopNode());
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126 tree.findHeight(tree.getTopNode());
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127 treeCanvas.setTree(tree);
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130 treeCanvas.setShowBootstrap(newtree.HasBootstrap());
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131 treeCanvas.setShowDistances(newtree.HasDistances());
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135 treeCanvas.repaint();
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140 public String getText(String format)
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145 protected void fitToWindow_actionPerformed(ActionEvent e)
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147 treeCanvas.fitToWindow = fitToWindow.getState();
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151 public void newickOutput_actionPerformed(ActionEvent actionEvent)
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153 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
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154 String output = fout.print(false, true);
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155 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame.applet);
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156 cap.setText(output);
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157 java.awt.Frame frame = new java.awt.Frame();
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159 jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);
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162 protected void fontSize_actionPerformed(ActionEvent e)
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164 /* if( treeCanvas==null )
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167 String size = fontSize.getLabel().substring( fontSize.getLabel().indexOf("-")+1);
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169 Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,
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170 "Select font size",
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172 JOptionPane.QUESTION_MESSAGE,
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173 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
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174 ,"Font Size - "+size);
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175 if(selection!=null)
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177 fontSize.setText("Font Size - " + selection);
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179 int i = Integer.parseInt(selection.toString());
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180 treeCanvas.setFontSize(i);
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182 scrollPane.setViewportView(treeCanvas);
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186 protected void distanceMenu_actionPerformed(ActionEvent e)
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188 treeCanvas.setShowDistances(distanceMenu.getState());
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191 protected void bootstrapMenu_actionPerformed(ActionEvent e)
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193 treeCanvas.setShowBootstrap(bootstrapMenu.getState());
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196 protected void placeholdersMenu_actionPerformed(ActionEvent e)
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198 treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
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