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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27 import jalview.analysis.*;
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28 import jalview.datamodel.*;
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29 import jalview.io.*;
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31 public class TreePanel extends Frame implements ActionListener, ItemListener
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38 TreeCanvas treeCanvas;
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42 public NJTree getTree()
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48 * Creates a new TreePanel object.
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50 * @param av DOCUMENT ME!
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51 * @param seqVector DOCUMENT ME!
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52 * @param type DOCUMENT ME!
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53 * @param pwtype DOCUMENT ME!
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54 * @param s DOCUMENT ME!
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55 * @param e DOCUMENT ME!
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57 public TreePanel(AlignViewport av, String type, String pwtype)
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62 this.setMenuBar(jMenuBar1);
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64 catch (Exception ex)
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66 ex.printStackTrace();
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69 initTreePanel(av, type, pwtype, null);
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73 * Creates a new TreePanel object.
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75 * @param av DOCUMENT ME!
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76 * @param seqVector DOCUMENT ME!
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77 * @param newtree DOCUMENT ME!
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78 * @param type DOCUMENT ME!
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79 * @param pwtype DOCUMENT ME!
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81 public TreePanel(AlignViewport av,
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89 this.setMenuBar(jMenuBar1);
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93 e.printStackTrace();
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96 initTreePanel(av, type, pwtype, newtree);
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100 void initTreePanel(AlignViewport av,
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103 NewickFile newTree)
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108 this.pwtype = pwtype;
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110 treeCanvas = new TreeCanvas(av, scrollPane);
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111 scrollPane.add(treeCanvas);
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114 TreeLoader tl = new TreeLoader(newTree);
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119 void showOriginalData()
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121 // decide if av alignment is sufficiently different to original data to warrant a new window to be created
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122 // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
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123 // or create a selection box around columns in alignment view
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124 // test Alignment(SeqCigar[])
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125 Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.
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126 getGapCharacter());
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128 if (alAndColsel != null && alAndColsel[0]!=null)
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130 Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]);
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131 AlignFrame af = new AlignFrame(al,
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133 "Original Data for Tree",
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136 af.viewport.setHiddenColumns( (ColumnSelection) alAndColsel[1] );
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140 class TreeLoader extends Thread
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142 NewickFile newtree;
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143 jalview.datamodel.AlignmentView odata=null;
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145 public TreeLoader(NewickFile newtree)
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147 this.newtree = newtree;
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155 tree = new NJTree(av.alignment.getSequencesArray(),
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158 tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);
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165 AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null);
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166 if(av.getSelectionGroup()==null)
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169 end = av.alignment.getWidth();
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170 seqs = av.alignment.getSequencesArray();
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174 start = av.getSelectionGroup().getStartRes();
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175 end = av.getSelectionGroup().getEndRes()+1;
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176 seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
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179 tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
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182 tree.reCount(tree.getTopNode());
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183 tree.findHeight(tree.getTopNode());
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184 treeCanvas.setTree(tree);
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187 distanceMenu.setState(newtree.HasDistances());
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188 bootstrapMenu.setState(newtree.HasBootstrap());
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189 treeCanvas.setShowBootstrap(newtree.HasBootstrap());
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190 treeCanvas.setShowDistances(newtree.HasDistances());
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194 treeCanvas.repaint();
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196 av.setCurrentTree(tree);
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201 public void actionPerformed(ActionEvent evt)
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203 if(evt.getSource()==newickOutput)
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204 newickOutput_actionPerformed();
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205 else if(evt.getSource()==fontSize)
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206 fontSize_actionPerformed();
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207 else if(evt.getSource()==inputData)
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208 showOriginalData();
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211 public void itemStateChanged(ItemEvent evt)
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213 if(evt.getSource()==fitToWindow)
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214 treeCanvas.fitToWindow = fitToWindow.getState();
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216 else if(evt.getSource()==distanceMenu)
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217 treeCanvas.setShowDistances(distanceMenu.getState());
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219 else if(evt.getSource()==bootstrapMenu)
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220 treeCanvas.setShowBootstrap(bootstrapMenu.getState());
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222 else if(evt.getSource()==placeholdersMenu)
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223 treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
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225 treeCanvas.repaint();
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229 public void newickOutput_actionPerformed()
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231 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
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232 String output = fout.print(false, true);
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233 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
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234 cap.setText(output);
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235 java.awt.Frame frame = new java.awt.Frame();
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237 jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);
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240 public java.awt.Font getTreeFont()
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242 return treeCanvas.font;
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245 public void setTreeFont(java.awt.Font font)
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247 treeCanvas.font = font;
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248 treeCanvas.repaint();
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251 protected void fontSize_actionPerformed()
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253 if( treeCanvas==null )
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256 new FontChooser(this);
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262 BorderLayout borderLayout1 = new BorderLayout();
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263 protected ScrollPane scrollPane = new ScrollPane();
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264 MenuBar jMenuBar1 = new MenuBar();
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265 Menu jMenu2 = new Menu();
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266 protected MenuItem fontSize = new MenuItem();
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267 protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();
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268 protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();
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269 protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();
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270 protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();
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271 Menu fileMenu = new Menu();
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272 MenuItem newickOutput = new MenuItem();
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273 MenuItem inputData = new MenuItem();
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275 private void jbInit() throws Exception {
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276 setLayout(borderLayout1);
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277 this.setBackground(Color.white);
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278 this.setFont(new java.awt.Font("Verdana", 0, 12));
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279 jMenu2.setLabel("View");
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280 fontSize.setLabel("Font...");
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281 fontSize.addActionListener(this);
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282 bootstrapMenu.setLabel("Show Bootstrap Values");
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283 bootstrapMenu.addItemListener(this);
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284 distanceMenu.setLabel("Show Distances");
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285 distanceMenu.addItemListener(this);
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286 placeholdersMenu.setLabel("Mark Unassociated Leaves");
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287 placeholdersMenu.addItemListener(this);
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288 fitToWindow.setState(true);
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289 fitToWindow.setLabel("Fit To Window");
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290 fitToWindow.addItemListener(this);
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291 fileMenu.setLabel("File");
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292 newickOutput.setLabel("Newick Format");
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293 newickOutput.addActionListener(this);
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294 inputData.setLabel("Input Data...");
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296 add(scrollPane, BorderLayout.CENTER);
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297 jMenuBar1.add(fileMenu);
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298 jMenuBar1.add(jMenu2);
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299 jMenu2.add(fitToWindow);
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300 jMenu2.add(fontSize);
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301 jMenu2.add(distanceMenu);
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302 jMenu2.add(bootstrapMenu);
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303 jMenu2.add(placeholdersMenu);
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304 fileMenu.add(newickOutput);
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305 fileMenu.add(inputData);
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306 inputData.addActionListener(this);
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