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.schemes.*;
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23 import jalview.datamodel.*;
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24 import jalview.analysis.*;
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25 import jalview.io.*;
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27 import java.awt.event.*;
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29 import java.io.InputStreamReader;
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30 import java.io.BufferedReader;
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31 import java.net.URL;
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34 public class AlignFrame extends Frame implements ActionListener,
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35 ItemListener, KeyListener, MouseListener
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37 public AlignmentPanel alignPanel;
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38 public AlignViewport viewport;
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39 int NEW_WINDOW_WIDTH = 700;
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40 int NEW_WINDOW_HEIGHT = 500;
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41 jalview.bin.JalviewLite applet;
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44 public AlignFrame(AlignmentI al,
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45 jalview.bin.JalviewLite applet,
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51 }catch(Exception ex)
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53 ex.printStackTrace();
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56 this.applet = applet;
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57 viewport = new AlignViewport(al, applet);
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58 alignPanel = new AlignmentPanel(this, viewport);
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60 annotationPanelMenuItem.setState(viewport.showAnnotation);
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64 String param = applet.getParameter("sortBy");
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67 if (param.equalsIgnoreCase("Id"))
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68 sortIDMenuItem_actionPerformed();
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69 else if (param.equalsIgnoreCase("Pairwise Identity"))
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70 sortPairwiseMenuItem_actionPerformed();
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73 param = applet.getParameter("wrap");
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76 if (param.equalsIgnoreCase("true"))
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78 wrapMenuItem.setState(true);
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79 wrapMenuItem_actionPerformed();
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85 param = applet.getParameter("windowWidth");
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88 int width = Integer.parseInt(param);
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89 NEW_WINDOW_WIDTH = width;
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91 param = applet.getParameter("windowHeight");
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94 int height = Integer.parseInt(param);
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95 NEW_WINDOW_HEIGHT = height;
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98 catch (Exception ex)
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103 //Some JVMS send keyevents to Top frame or lowest panel,
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104 //Havent worked out why yet. So add to both this frame and seqCanvas for now
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105 this.addKeyListener(this);
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106 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
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107 alignPanel.idPanel.idCanvas.addKeyListener(this);
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109 viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
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111 public void propertyChange(java.beans.PropertyChangeEvent evt)
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113 if (evt.getPropertyName().equals("alignment"))
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115 alignmentChanged();
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127 add(alignPanel, BorderLayout.CENTER);
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128 jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH,
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129 NEW_WINDOW_HEIGHT);
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131 alignPanel.validate();
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132 alignPanel.repaint();
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134 public AlignViewport getAlignViewport()
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139 public SeqCanvas getSeqcanvas()
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141 return alignPanel.seqPanel.seqCanvas;
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148 * @param String DOCUMENT ME!
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151 public void parseFeaturesFile(String file)
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153 String line = null;
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156 BufferedReader in = null;
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157 java.io.InputStream is = getClass().getResourceAsStream("/" + file);
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160 in = new BufferedReader(new java.io.InputStreamReader(is));
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164 URL url = new URL(file);
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165 in = new BufferedReader(new InputStreamReader(url.openStream()));
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168 SequenceI seq = null;
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169 String type, desc, token;
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171 int index, start, end;
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172 StringTokenizer st;
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173 SequenceFeature sf;
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174 FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
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176 String featureGroup = null;
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177 while ( (line = in.readLine()) != null)
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180 st = new StringTokenizer(line, "\t");
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181 if (st.countTokens() == 2)
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183 type = st.nextToken();
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184 if(type.equalsIgnoreCase("startgroup"))
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186 featureGroup = st.nextToken();
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188 else if(type.equalsIgnoreCase("endgroup"))
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190 //We should check whether this is the current group,
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191 //but at present theres no way of showing more than 1 group
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193 featureGroup = null;
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197 UserColourScheme ucs = new UserColourScheme(st.nextToken());
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198 fr.setColour(type, ucs.findColour("A"));
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203 while (st.hasMoreElements())
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205 desc = st.nextToken();
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206 token = st.nextToken();
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207 if (!token.equals("ID_NOT_SPECIFIED"))
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209 index = viewport.alignment.findIndex(viewport.alignment.findName(
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215 index = Integer.parseInt(st.nextToken());
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218 start = Integer.parseInt(st.nextToken());
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219 end = Integer.parseInt(st.nextToken());
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221 seq = viewport.alignment.getSequenceAt(index);
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223 type = st.nextToken();
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225 if(fr.getColour(type)==null)
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227 // Probably the old style groups file
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228 UserColourScheme ucs = new UserColourScheme(type);
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229 fr.setColour(type, ucs.findColour("A"));
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232 sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
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234 seq.addSequenceFeature(sf);
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238 viewport.showSequenceFeatures = true;
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239 sequenceFeatures.setState(true);
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241 alignPanel.repaint();
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244 catch (Exception ex)
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246 ex.printStackTrace();
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247 System.out.println("Error parsing groups file: " + ex +"\n"+line);
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251 public void keyPressed(KeyEvent evt)
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253 switch (evt.getKeyCode())
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255 case 27: // escape key
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256 deselectAllSequenceMenuItem_actionPerformed();
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258 case KeyEvent.VK_X:
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259 if (evt.isControlDown() || evt.isMetaDown())
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261 cut_actionPerformed();
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264 case KeyEvent.VK_C:
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265 if (evt.isControlDown() || evt.isMetaDown())
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267 copy_actionPerformed();
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270 case KeyEvent.VK_V:
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271 if (evt.isControlDown() || evt.isMetaDown())
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276 case KeyEvent.VK_A:
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277 if (evt.isControlDown() || evt.isMetaDown())
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279 selectAllSequenceMenuItem_actionPerformed();
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282 case KeyEvent.VK_DOWN:
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283 moveSelectedSequences(false);
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285 case KeyEvent.VK_UP:
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286 moveSelectedSequences(true);
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288 case KeyEvent.VK_F:
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289 if (evt.isControlDown())
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291 findMenuItem_actionPerformed();
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294 case KeyEvent.VK_BACK_SPACE:
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295 case KeyEvent.VK_DELETE:
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296 cut_actionPerformed();
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300 public void keyReleased(KeyEvent evt)
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302 public void keyTyped(KeyEvent evt)
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305 public void itemStateChanged(ItemEvent evt)
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307 if(evt.getSource()==colourTextMenuItem)
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308 colourTextMenuItem_actionPerformed();
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309 else if(evt.getSource()==wrapMenuItem)
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310 wrapMenuItem_actionPerformed();
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311 else if(evt.getSource()==scaleAbove)
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312 scaleAbove_actionPerformed();
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313 else if(evt.getSource()==scaleLeft)
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314 scaleLeft_actionPerformed();
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315 else if(evt.getSource()==scaleRight)
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316 scaleRight_actionPerformed();
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317 else if(evt.getSource()==seqLimits)
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318 seqLimits_itemStateChanged();
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319 else if(evt.getSource()==viewBoxesMenuItem)
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320 viewBoxesMenuItem_actionPerformed();
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321 else if(evt.getSource()==viewTextMenuItem)
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322 viewTextMenuItem_actionPerformed();
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323 else if(evt.getSource()==renderGapsMenuItem)
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324 renderGapsMenuItem_actionPerformed();
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325 else if(evt.getSource()==annotationPanelMenuItem)
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326 annotationPanelMenuItem_actionPerformed();
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327 else if(evt.getSource()==sequenceFeatures)
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329 viewport.showSequenceFeatures(sequenceFeatures.getState());
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330 alignPanel.seqPanel.seqCanvas.repaint();
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332 else if(evt.getSource()==conservationMenuItem)
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333 conservationMenuItem_actionPerformed();
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334 else if(evt.getSource()==abovePIDThreshold)
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335 abovePIDThreshold_actionPerformed();
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336 else if(evt.getSource()==applyToAllGroups)
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337 applyToAllGroups_actionPerformed();
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339 public void actionPerformed(ActionEvent evt)
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341 if(evt.getSource()==inputText)
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342 inputText_actionPerformed();
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343 else if(evt.getSource()==loadTree)
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344 loadTree_actionPerformed();
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345 else if(evt.getSource()==closeMenuItem)
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346 closeMenuItem_actionPerformed();
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347 else if(evt.getSource()==copy)
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348 copy_actionPerformed();
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349 else if(evt.getSource()==undoMenuItem)
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350 undoMenuItem_actionPerformed();
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351 else if(evt.getSource()==redoMenuItem)
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352 redoMenuItem_actionPerformed();
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353 else if(evt.getSource()==inputText)
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354 inputText_actionPerformed();
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355 else if(evt.getSource()==closeMenuItem)
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356 closeMenuItem_actionPerformed();
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357 else if(evt.getSource()==undoMenuItem)
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358 undoMenuItem_actionPerformed();
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359 else if(evt.getSource()==redoMenuItem)
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360 redoMenuItem_actionPerformed();
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361 else if(evt.getSource()==copy)
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362 copy_actionPerformed();
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363 else if(evt.getSource()==pasteNew)
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364 pasteNew_actionPerformed();
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365 else if(evt.getSource()==pasteThis)
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366 pasteThis_actionPerformed();
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367 else if(evt.getSource()==cut)
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368 cut_actionPerformed();
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369 else if(evt.getSource()==delete)
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370 delete_actionPerformed();
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371 else if(evt.getSource()==deleteGroups)
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372 deleteGroups_actionPerformed();
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373 else if(evt.getSource()==selectAllSequenceMenuItem)
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374 selectAllSequenceMenuItem_actionPerformed();
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375 else if(evt.getSource()==deselectAllSequenceMenuItem)
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376 deselectAllSequenceMenuItem_actionPerformed();
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377 else if(evt.getSource()==invertSequenceMenuItem)
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378 invertSequenceMenuItem_actionPerformed();
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379 else if(evt.getSource()==remove2LeftMenuItem)
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380 remove2LeftMenuItem_actionPerformed();
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381 else if(evt.getSource()==remove2RightMenuItem)
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382 remove2RightMenuItem_actionPerformed();
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383 else if(evt.getSource()==removeGappedColumnMenuItem)
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384 removeGappedColumnMenuItem_actionPerformed();
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385 else if(evt.getSource()==removeAllGapsMenuItem)
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386 removeAllGapsMenuItem_actionPerformed();
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387 else if(evt.getSource()==findMenuItem)
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388 findMenuItem_actionPerformed();
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389 else if(evt.getSource()==font)
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390 font_actionPerformed();
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391 else if(evt.getSource()==featureSettings)
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392 featureSettings_actionPerformed();
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393 else if(evt.getSource()==overviewMenuItem)
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394 overviewMenuItem_actionPerformed();
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395 else if(evt.getSource()==noColourmenuItem)
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396 noColourmenuItem_actionPerformed();
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397 else if(evt.getSource()==clustalColour)
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398 clustalColour_actionPerformed();
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399 else if(evt.getSource()==zappoColour)
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400 zappoColour_actionPerformed();
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401 else if(evt.getSource()==taylorColour)
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402 taylorColour_actionPerformed();
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403 else if(evt.getSource()==hydrophobicityColour)
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404 hydrophobicityColour_actionPerformed();
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405 else if(evt.getSource()==helixColour)
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406 helixColour_actionPerformed();
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407 else if(evt.getSource()==strandColour)
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408 strandColour_actionPerformed();
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409 else if(evt.getSource()==turnColour)
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410 turnColour_actionPerformed();
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411 else if(evt.getSource()==buriedColour)
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412 buriedColour_actionPerformed();
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413 else if(evt.getSource()==nucleotideColour)
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414 nucleotideColour_actionPerformed();
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415 else if(evt.getSource()==modifyPID)
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416 modifyPID_actionPerformed();
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417 else if(evt.getSource()==modifyConservation)
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418 modifyConservation_actionPerformed();
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419 else if(evt.getSource()==userDefinedColour)
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420 userDefinedColour_actionPerformed();
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421 else if(evt.getSource()==PIDColour)
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422 PIDColour_actionPerformed();
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423 else if(evt.getSource()==BLOSUM62Colour)
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424 BLOSUM62Colour_actionPerformed();
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425 else if(evt.getSource()==annotationColour)
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426 new AnnotationColourChooser(viewport, alignPanel);
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427 else if(evt.getSource()==sortPairwiseMenuItem)
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428 sortPairwiseMenuItem_actionPerformed();
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429 else if(evt.getSource()==sortIDMenuItem)
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430 sortIDMenuItem_actionPerformed();
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431 else if(evt.getSource()==sortGroupMenuItem)
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432 sortGroupMenuItem_actionPerformed();
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433 else if(evt.getSource()==removeRedundancyMenuItem)
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434 removeRedundancyMenuItem_actionPerformed();
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435 else if(evt.getSource()==pairwiseAlignmentMenuItem)
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436 pairwiseAlignmentMenuItem_actionPerformed();
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437 else if(evt.getSource()==PCAMenuItem)
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438 PCAMenuItem_actionPerformed();
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439 else if(evt.getSource()==averageDistanceTreeMenuItem)
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440 averageDistanceTreeMenuItem_actionPerformed();
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441 else if(evt.getSource()==neighbourTreeMenuItem)
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442 neighbourTreeMenuItem_actionPerformed();
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443 else if(evt.getSource()==njTreeBlosumMenuItem)
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444 njTreeBlosumMenuItem_actionPerformed();
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445 else if(evt.getSource()==avDistanceTreeBlosumMenuItem)
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446 avTreeBlosumMenuItem_actionPerformed();
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447 else if(evt.getSource()==documentation)
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448 documentation_actionPerformed();
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449 else if(evt.getSource()==about)
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450 about_actionPerformed();
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454 public void inputText_actionPerformed()
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456 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
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457 Frame frame = new Frame();
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459 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
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462 protected void outputText_actionPerformed(ActionEvent e)
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464 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
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465 Frame frame = new Frame();
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467 jalview.bin.JalviewLite.addFrame(frame,
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468 "Alignment output - " + e.getActionCommand(),
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470 cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
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471 viewport.getAlignment().getSequences(),
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472 viewport.showJVSuffix));
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475 public void closeMenuItem_actionPerformed()
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477 PaintRefresher.components.remove(viewport.alignment);
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478 if(PaintRefresher.components.size()==0 && applet==null)
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484 Stack historyList = new Stack();
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485 Stack redoList = new Stack();
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487 void updateEditMenuBar()
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489 if (historyList.size() > 0)
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491 undoMenuItem.setEnabled(true);
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492 HistoryItem hi = (HistoryItem) historyList.peek();
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493 undoMenuItem.setLabel("Undo " + hi.getDescription());
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497 undoMenuItem.setEnabled(false);
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498 undoMenuItem.setLabel("Undo");
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501 if (redoList.size() > 0)
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503 redoMenuItem.setEnabled(true);
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504 HistoryItem hi = (HistoryItem) redoList.peek();
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505 redoMenuItem.setLabel("Redo " + hi.getDescription());
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509 redoMenuItem.setEnabled(false);
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510 redoMenuItem.setLabel("Redo");
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514 public void addHistoryItem(HistoryItem hi)
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516 historyList.push(hi);
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517 updateEditMenuBar();
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520 protected void undoMenuItem_actionPerformed()
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522 HistoryItem hi = (HistoryItem) historyList.pop();
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523 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
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524 HistoryItem.HIDE));
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525 restoreHistoryItem(hi);
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526 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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529 protected void redoMenuItem_actionPerformed()
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531 HistoryItem hi = (HistoryItem) redoList.pop();
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532 restoreHistoryItem(hi);
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533 updateEditMenuBar();
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534 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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537 // used by undo and redo
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538 void restoreHistoryItem(HistoryItem hi)
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542 updateEditMenuBar();
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544 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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547 public void moveSelectedSequences(boolean up)
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549 SequenceGroup sg = viewport.getSelectionGroup();
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557 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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559 SequenceI seq = viewport.alignment.getSequenceAt(i);
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560 if (!sg.sequences.contains(seq))
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565 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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566 if (sg.sequences.contains(temp))
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571 viewport.alignment.getSequences().setElementAt(temp, i);
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572 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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577 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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579 SequenceI seq = viewport.alignment.getSequenceAt(i);
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580 if (!sg.sequences.contains(seq))
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585 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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586 if (sg.sequences.contains(temp))
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591 viewport.alignment.getSequences().setElementAt(temp, i);
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592 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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596 alignPanel.repaint();
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599 StringBuffer copiedSequences;
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600 protected void copy_actionPerformed()
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602 if (viewport.getSelectionGroup() == null)
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607 SequenceGroup sg = viewport.getSelectionGroup();
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608 copiedSequences = new StringBuffer();
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609 Hashtable orderedSeqs = new Hashtable();
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610 for (int i = 0; i < sg.getSize(); i++)
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612 SequenceI seq = sg.getSequenceAt(i);
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613 int index = viewport.alignment.findIndex(seq);
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614 orderedSeqs.put(index + "", seq);
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617 int index = 0, startRes, endRes;
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620 for (int i = 0; i < sg.getSize(); i++)
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622 SequenceI seq = null;
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624 while (seq == null)
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626 if (orderedSeqs.containsKey(index + ""))
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628 seq = (SequenceI) orderedSeqs.get(index + "");
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640 //Returns residue following index if gap
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641 startRes = seq.findPosition(sg.getStartRes());
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644 //Need to find the residue preceeding index if gap
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647 for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
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649 ch = seq.getCharAt(j);
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650 if (!jalview.util.Comparison.isGap( (ch)))
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658 endRes += seq.getStart() -1;
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661 copiedSequences.append(seq.getName() + "\t" +
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664 seq.getSequence(sg.getStartRes(),
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665 sg.getEndRes() + 1) + "\n");
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670 protected void pasteNew_actionPerformed()
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675 protected void pasteThis_actionPerformed()
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677 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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678 HistoryItem.PASTE));
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682 void paste(boolean newAlignment)
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686 if (copiedSequences == null)
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691 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
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692 Vector seqs = new Vector();
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693 while (st.hasMoreElements())
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695 String name = st.nextToken();
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696 int start = Integer.parseInt(st.nextToken());
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697 int end = Integer.parseInt(st.nextToken());
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698 Sequence sequence = new Sequence(name, st.nextToken(), start, end);
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702 viewport.alignment.addSequence(sequence);
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706 seqs.addElement(sequence);
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712 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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713 for (int i = 0; i < seqs.size(); i++)
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715 newSeqs[i] = (SequenceI) seqs.elementAt(i);
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718 String newtitle = new String("Copied sequences");
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719 if (getTitle().startsWith("Copied sequences"))
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721 newtitle = getTitle();
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725 newtitle = newtitle.concat("- from " + getTitle());
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727 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
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732 jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
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733 NEW_WINDOW_HEIGHT);
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737 viewport.setEndSeq(viewport.alignment.getHeight());
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738 viewport.alignment.getWidth();
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739 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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743 catch (Exception ex)
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744 {} // could be anything being pasted in here
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748 protected void cut_actionPerformed()
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750 copy_actionPerformed();
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751 delete_actionPerformed();
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754 protected void delete_actionPerformed()
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756 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
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757 HistoryItem.HIDE));
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758 if (viewport.getSelectionGroup() == null)
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764 SequenceGroup sg = viewport.getSelectionGroup();
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765 boolean allSequences = false;
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766 if(sg.sequences.size()==viewport.alignment.getHeight())
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767 allSequences = true;
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769 for (int i = 0; i < sg.sequences.size(); i++)
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771 SequenceI seq = sg.getSequenceAt(i);
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772 int index = viewport.getAlignment().findIndex(seq);
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773 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
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775 // If the cut affects all sequences, remove highlighted columns
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778 viewport.getColumnSelection().removeElements(sg.getStartRes(),
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779 sg.getEndRes() + 1);
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783 if (seq.getSequence().length() < 1)
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785 viewport.getAlignment().deleteSequence(seq);
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789 viewport.getAlignment().getSequences().setElementAt(seq, index);
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793 viewport.setSelectionGroup(null);
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794 viewport.alignment.deleteGroup(sg);
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795 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
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796 if (viewport.getAlignment().getHeight() < 1)
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800 this.setVisible(false);
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802 catch (Exception ex)
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805 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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809 protected void deleteGroups_actionPerformed()
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811 viewport.alignment.deleteAllGroups();
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812 viewport.setSelectionGroup(null);
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814 alignPanel.repaint();
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817 public void selectAllSequenceMenuItem_actionPerformed()
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819 SequenceGroup sg = new SequenceGroup();
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820 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
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822 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
824 sg.setEndRes(viewport.alignment.getWidth()-1);
\r
825 viewport.setSelectionGroup(sg);
\r
826 alignPanel.repaint();
\r
827 PaintRefresher.Refresh(null, viewport.alignment);
\r
830 public void deselectAllSequenceMenuItem_actionPerformed()
\r
832 viewport.setSelectionGroup(null);
\r
833 viewport.getColumnSelection().clear();
\r
834 viewport.setSelectionGroup(null);
\r
835 alignPanel.idPanel.idCanvas.searchResults = null;
\r
836 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
837 alignPanel.repaint();
\r
838 PaintRefresher.Refresh(null, viewport.alignment);
\r
841 public void invertSequenceMenuItem_actionPerformed()
\r
843 SequenceGroup sg = viewport.getSelectionGroup();
\r
844 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
846 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
849 PaintRefresher.Refresh(null, viewport.alignment);
\r
852 public void remove2LeftMenuItem_actionPerformed()
\r
854 ColumnSelection colSel = viewport.getColumnSelection();
\r
855 if (colSel.size() > 0)
\r
857 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
\r
858 HistoryItem.HIDE));
\r
859 int min = colSel.getMin();
\r
860 viewport.getAlignment().trimLeft(min);
\r
861 colSel.compensateForEdit(0, min);
\r
863 if (viewport.getSelectionGroup() != null)
\r
865 viewport.getSelectionGroup().adjustForRemoveLeft(min);
\r
868 Vector groups = viewport.alignment.getGroups();
\r
869 for (int i = 0; i < groups.size(); i++)
\r
871 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
872 if (!sg.adjustForRemoveLeft(min))
\r
874 viewport.alignment.deleteGroup(sg);
\r
877 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
881 public void remove2RightMenuItem_actionPerformed()
\r
883 ColumnSelection colSel = viewport.getColumnSelection();
\r
884 if (colSel.size() > 0)
\r
886 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
\r
887 HistoryItem.HIDE));
\r
888 int max = colSel.getMax();
\r
889 viewport.getAlignment().trimRight(max);
\r
890 if (viewport.getSelectionGroup() != null)
\r
892 viewport.getSelectionGroup().adjustForRemoveRight(max);
\r
895 Vector groups = viewport.alignment.getGroups();
\r
896 for (int i = 0; i < groups.size(); i++)
\r
898 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
899 if (!sg.adjustForRemoveRight(max))
\r
901 viewport.alignment.deleteGroup(sg);
\r
904 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
909 public void removeGappedColumnMenuItem_actionPerformed()
\r
911 addHistoryItem(new HistoryItem("Remove Gapped Columns",
\r
912 viewport.alignment,
\r
913 HistoryItem.HIDE));
\r
915 //This is to maintain viewport position on first residue
\r
916 //of first sequence
\r
917 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
918 int startRes = seq.findPosition(viewport.startRes);
\r
920 viewport.getAlignment().removeGaps();
\r
922 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
924 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
927 public void removeAllGapsMenuItem_actionPerformed()
\r
929 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
\r
930 HistoryItem.HIDE));
\r
932 //This is to maintain viewport position on first residue
\r
933 //of first sequence
\r
934 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
935 int startRes = seq.findPosition(viewport.startRes);
\r
942 int start=0, end = viewport.alignment.getWidth();
\r
944 if (viewport.getSelectionGroup() != null
\r
945 && viewport.getSelectionGroup().sequences != null
\r
946 && viewport.getSelectionGroup().sequences.size()>0)
\r
948 seqs = viewport.getSelectionGroup().sequences;
\r
949 start = viewport.getSelectionGroup().getStartRes();
\r
950 end = viewport.getSelectionGroup().getEndRes()+1;
\r
953 seqs = viewport.alignment.getSequences();
\r
955 for (int i = 0; i < seqs.size(); i++)
\r
957 current = (SequenceI) seqs.elementAt(i);
\r
958 jSize = current.getLength();
\r
960 // Removing a range is much quicker than removing gaps
\r
961 // one by one for long sequences
\r
963 int rangeStart=-1, rangeEnd=-1;
\r
967 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
\r
984 current.deleteChars(rangeStart, rangeEnd);
\r
985 j-=rangeEnd-rangeStart;
\r
986 jSize-=rangeEnd-rangeStart;
\r
994 while (j < end && j < jSize);
\r
997 current.deleteChars(rangeStart, rangeEnd);
\r
1000 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1001 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1004 public void alignmentChanged()
\r
1006 viewport.updateConsensus();
\r
1007 viewport.updateConservation ();
\r
1008 resetAllColourSchemes();
\r
1009 if(alignPanel.overviewPanel!=null)
\r
1010 alignPanel.overviewPanel.updateOverviewImage();
\r
1012 viewport.alignment.adjustSequenceAnnotations();
\r
1013 alignPanel.repaint();
\r
1016 void resetAllColourSchemes()
\r
1018 ColourSchemeI cs = viewport.globalColourScheme;
\r
1021 if (cs instanceof ClustalxColourScheme)
\r
1023 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
\r
1024 resetClustalX(viewport.alignment.getSequences(),
\r
1025 viewport.alignment.getWidth());
\r
1028 cs.setConsensus(viewport.vconsensus);
\r
1029 if (cs.conservationApplied())
\r
1031 Alignment al = (Alignment) viewport.alignment;
\r
1032 Conservation c = new Conservation("All",
\r
1033 ResidueProperties.propHash, 3,
\r
1034 al.getSequences(), 0,
\r
1035 al.getWidth() - 1);
\r
1037 c.verdict(false, viewport.ConsPercGaps);
\r
1039 cs.setConservation(c);
\r
1043 int s, sSize = viewport.alignment.getGroups().size();
\r
1044 for(s=0; s<sSize; s++)
\r
1046 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
\r
1047 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
\r
1049 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
\r
1051 sg.recalcConservation();
\r
1057 public void findMenuItem_actionPerformed()
\r
1059 new Finder(alignPanel);
\r
1062 public void font_actionPerformed()
\r
1064 new FontChooser(alignPanel);
\r
1068 public void seqLimits_itemStateChanged()
\r
1070 viewport.setShowJVSuffix(seqLimits.getState());
\r
1071 alignPanel.fontChanged();
\r
1072 alignPanel.repaint();
\r
1076 protected void colourTextMenuItem_actionPerformed()
\r
1078 viewport.setColourText(colourTextMenuItem.getState());
\r
1079 alignPanel.repaint();
\r
1082 protected void wrapMenuItem_actionPerformed()
\r
1084 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
1085 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
1086 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
1087 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
1088 scaleRight.setEnabled(wrapMenuItem.getState());
\r
1089 alignPanel.repaint();
\r
1092 protected void scaleAbove_actionPerformed()
\r
1094 viewport.setScaleAboveWrapped(scaleAbove.getState());
\r
1095 alignPanel.repaint();
\r
1098 protected void scaleLeft_actionPerformed()
\r
1100 viewport.setScaleLeftWrapped(scaleLeft.getState());
\r
1101 alignPanel.repaint();
\r
1104 protected void scaleRight_actionPerformed()
\r
1106 viewport.setScaleRightWrapped(scaleRight.getState());
\r
1107 alignPanel.repaint();
\r
1110 public void viewBoxesMenuItem_actionPerformed()
\r
1112 viewport.setShowBoxes(viewBoxesMenuItem.getState());
\r
1113 alignPanel.repaint();
\r
1116 public void viewTextMenuItem_actionPerformed()
\r
1118 viewport.setShowText(viewTextMenuItem.getState());
\r
1119 alignPanel.repaint();
\r
1122 protected void renderGapsMenuItem_actionPerformed()
\r
1124 viewport.setRenderGaps(renderGapsMenuItem.getState());
\r
1125 alignPanel.repaint();
\r
1128 public void annotationPanelMenuItem_actionPerformed()
\r
1130 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
\r
1131 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
\r
1134 public void featureSettings_actionPerformed()
\r
1136 new FeatureSettings(viewport, alignPanel);
\r
1139 public void overviewMenuItem_actionPerformed()
\r
1141 if (alignPanel.overviewPanel != null)
\r
1146 Frame frame = new Frame();
\r
1147 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1148 frame.add(overview);
\r
1149 // +50 must allow for applet frame window
\r
1150 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
1151 overview.preferredSize().width,
\r
1152 overview.preferredSize().height + 50);
\r
1155 frame.addWindowListener(new WindowAdapter()
\r
1157 public void windowClosing(WindowEvent e)
\r
1159 alignPanel.setOverviewPanel(null);
\r
1163 alignPanel.setOverviewPanel(overview);
\r
1167 protected void noColourmenuItem_actionPerformed()
\r
1169 changeColour(null);
\r
1172 public void clustalColour_actionPerformed()
\r
1174 abovePIDThreshold.setState(false);
\r
1175 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
\r
1176 viewport.alignment.getWidth()));
\r
1179 public void zappoColour_actionPerformed()
\r
1181 changeColour(new ZappoColourScheme());
\r
1184 public void taylorColour_actionPerformed()
\r
1186 changeColour(new TaylorColourScheme());
\r
1189 public void hydrophobicityColour_actionPerformed()
\r
1191 changeColour(new HydrophobicColourScheme());
\r
1194 public void helixColour_actionPerformed()
\r
1196 changeColour(new HelixColourScheme());
\r
1199 public void strandColour_actionPerformed()
\r
1201 changeColour(new StrandColourScheme());
\r
1204 public void turnColour_actionPerformed()
\r
1206 changeColour(new TurnColourScheme());
\r
1209 public void buriedColour_actionPerformed()
\r
1211 changeColour(new BuriedColourScheme());
\r
1214 public void nucleotideColour_actionPerformed()
\r
1216 changeColour(new NucleotideColourScheme());
\r
1219 protected void applyToAllGroups_actionPerformed()
\r
1221 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
\r
1224 void changeColour(ColourSchemeI cs)
\r
1226 int threshold = 0;
\r
1230 if (viewport.getAbovePIDThreshold())
\r
1232 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
\r
1234 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1236 viewport.setGlobalColourScheme(cs);
\r
1240 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1243 if (viewport.getConservationSelected())
\r
1246 Alignment al = (Alignment) viewport.alignment;
\r
1247 Conservation c = new Conservation("All",
\r
1248 ResidueProperties.propHash, 3,
\r
1249 al.getSequences(), 0,
\r
1250 al.getWidth() - 1);
\r
1253 c.verdict(false, viewport.ConsPercGaps);
\r
1255 cs.setConservation(c);
\r
1257 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1263 cs.setConservation(null);
\r
1266 cs.setConsensus(viewport.vconsensus);
\r
1269 viewport.setGlobalColourScheme(cs);
\r
1271 if (viewport.getColourAppliesToAllGroups())
\r
1273 Vector groups = viewport.alignment.getGroups();
\r
1274 for (int i = 0; i < groups.size(); i++)
\r
1276 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1283 if (cs instanceof ClustalxColourScheme)
\r
1285 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1291 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1293 catch (Exception ex)
\r
1295 ex.printStackTrace();
\r
1300 if (viewport.getAbovePIDThreshold()
\r
1301 || cs instanceof PIDColourScheme
\r
1302 || cs instanceof Blosum62ColourScheme)
\r
1304 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1305 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
1308 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1310 if (viewport.getConservationSelected())
\r
1312 Conservation c = new Conservation("Group",
\r
1313 ResidueProperties.propHash, 3,
\r
1315 viewport.alignment.getWidth() - 1);
\r
1317 c.verdict(false, viewport.ConsPercGaps);
\r
1318 sg.cs.setConservation(c);
\r
1322 sg.cs.setConservation(null);
\r
1323 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1330 if (alignPanel.getOverviewPanel() != null)
\r
1332 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1335 alignPanel.repaint();
\r
1340 protected void modifyPID_actionPerformed()
\r
1342 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1344 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
1346 SliderPanel.showPIDSlider();
\r
1350 protected void modifyConservation_actionPerformed()
\r
1352 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1354 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
1356 SliderPanel.showConservationSlider();
\r
1360 protected void conservationMenuItem_actionPerformed()
\r
1362 viewport.setConservationSelected(conservationMenuItem.getState());
\r
1364 viewport.setAbovePIDThreshold(false);
\r
1365 abovePIDThreshold.setState(false);
\r
1367 changeColour(viewport.getGlobalColourScheme());
\r
1369 modifyConservation_actionPerformed();
\r
1372 public void abovePIDThreshold_actionPerformed()
\r
1374 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
1376 conservationMenuItem.setState(false);
\r
1377 viewport.setConservationSelected(false);
\r
1379 changeColour(viewport.getGlobalColourScheme());
\r
1381 modifyPID_actionPerformed();
\r
1384 public void userDefinedColour_actionPerformed()
\r
1386 new UserDefinedColours(alignPanel, null);
\r
1389 public void PIDColour_actionPerformed()
\r
1391 changeColour(new PIDColourScheme());
\r
1394 public void BLOSUM62Colour_actionPerformed()
\r
1396 changeColour(new Blosum62ColourScheme());
\r
1399 public void sortPairwiseMenuItem_actionPerformed()
\r
1401 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1402 HistoryItem.SORT));
\r
1403 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1404 viewport.getAlignment().getSequenceAt(0));
\r
1405 alignPanel.repaint();
\r
1408 public void sortIDMenuItem_actionPerformed()
\r
1410 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1411 HistoryItem.SORT));
\r
1412 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1413 alignPanel.repaint();
\r
1416 public void sortGroupMenuItem_actionPerformed()
\r
1418 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1419 HistoryItem.SORT));
\r
1420 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1421 alignPanel.repaint();
\r
1425 public void removeRedundancyMenuItem_actionPerformed()
\r
1427 RedundancyPanel sp = new RedundancyPanel(alignPanel);
\r
1428 Frame frame = new Frame();
\r
1430 jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",
\r
1435 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
1437 if (viewport.getSelectionGroup().getSize() > 1)
\r
1439 Frame frame = new Frame();
\r
1440 frame.add(new PairwiseAlignPanel(alignPanel));
\r
1441 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
1445 public void PCAMenuItem_actionPerformed()
\r
1447 //are the sequences aligned?
\r
1448 if (!viewport.alignment.isAligned())
\r
1450 SequenceI current;
\r
1451 int Width = viewport.getAlignment().getWidth();
\r
1453 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1456 current = viewport.getAlignment().getSequenceAt(i);
\r
1458 if (current.getLength() < Width)
\r
1460 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1463 alignPanel.repaint();
\r
1466 if ( (viewport.getSelectionGroup() != null &&
\r
1467 viewport.getSelectionGroup().getSize() < 4 &&
\r
1468 viewport.getSelectionGroup().getSize() > 0)
\r
1469 || viewport.getAlignment().getHeight() < 4)
\r
1476 new PCAPanel(viewport);
\r
1478 catch (java.lang.OutOfMemoryError ex)
\r
1484 public void averageDistanceTreeMenuItem_actionPerformed()
\r
1486 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1489 public void neighbourTreeMenuItem_actionPerformed()
\r
1491 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1494 protected void njTreeBlosumMenuItem_actionPerformed()
\r
1496 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1499 protected void avTreeBlosumMenuItem_actionPerformed()
\r
1501 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1504 void NewTreePanel(String type, String pwType, String title)
\r
1506 //are the sequences aligned?
\r
1507 if (!viewport.alignment.isAligned())
\r
1509 SequenceI current;
\r
1510 int Width = viewport.getAlignment().getWidth();
\r
1512 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1515 current = viewport.getAlignment().getSequenceAt(i);
\r
1517 if (current.getLength() < Width)
\r
1519 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1522 alignPanel.repaint();
\r
1526 final TreePanel tp;
\r
1527 if (viewport.getSelectionGroup() != null &&
\r
1528 viewport.getSelectionGroup().getSize() > 3)
\r
1530 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
\r
1532 0, viewport.alignment.getWidth());
\r
1536 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1537 type, pwType, 0, viewport.alignment.getWidth());
\r
1540 addTreeMenuItem(tp, title);
\r
1542 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
1545 void loadTree_actionPerformed()
\r
1547 TreePanel tp = null;
\r
1549 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1550 cap.setText("Paste your Newick tree file here.");
\r
1551 cap.treeImport = true;
\r
1552 Frame frame = new Frame();
\r
1554 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
1557 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
1559 TreePanel tp = new TreePanel(viewport,
\r
1560 viewport.getAlignment().getSequences(),
\r
1561 tree, "From File - ", treeFile);
\r
1562 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
1563 addTreeMenuItem(tp, treeFile);
\r
1566 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1568 final MenuItem item = new MenuItem(title);
\r
1569 sortByTreeMenu.add(item);
\r
1570 item.addActionListener(new java.awt.event.ActionListener()
\r
1572 public void actionPerformed(ActionEvent evt)
\r
1574 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1575 HistoryItem.SORT));
\r
1576 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1577 alignPanel.repaint();
\r
1581 treePanel.addWindowListener(new WindowAdapter()
\r
1583 public void windowClosing(WindowEvent e)
\r
1585 sortByTreeMenu.remove(item);
\r
1590 protected void documentation_actionPerformed()
\r
1592 showURL("http://www.jalview.org/help.html", "HELP");
\r
1595 protected void about_actionPerformed()
\r
1598 class AboutPanel extends Canvas
\r
1601 public AboutPanel(String version)
\r
1602 { this.version = version; }
\r
1604 public void paint(Graphics g)
\r
1606 g.setColor(Color.white);
\r
1607 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1608 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1609 FontMetrics fm = g.getFontMetrics();
\r
1610 int fh = fm.getHeight();
\r
1612 g.setColor(Color.black);
\r
1613 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
1614 g.drawString("Jalview - Release "+version, 200, y += fh);
\r
1615 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1616 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
1618 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
1621 "For any issues relating to Jalview, email help@jalview.org", x,
\r
1623 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
1624 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
1626 g.drawString("Bioinformatics, 2004 12;426-7.", x, y += fh);
\r
1630 String version = "test";
\r
1631 java.net.URL url = getClass().getResource("/.build_properties");
\r
1636 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
1637 url.openStream()));
\r
1639 while ( (line = reader.readLine()) != null)
\r
1641 if (line.indexOf("VERSION") > -1)
\r
1643 version = line.substring(line.indexOf("=") + 1);
\r
1647 catch (Exception ex)
\r
1649 ex.printStackTrace();
\r
1654 Frame frame = new Frame();
\r
1655 frame.add(new AboutPanel(version));
\r
1656 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
\r
1660 public void showURL(String url, String target)
\r
1662 if (applet == null)
\r
1664 System.out.println("Not running as applet - no browser available.");
\r
1670 applet.getAppletContext().showDocument(new java.net.URL(url),
\r
1673 catch (Exception ex)
\r
1675 ex.printStackTrace();
\r
1681 //////////////////////////////////////////////////////////////////////////////////
\r
1682 //JBuilder Graphics here
\r
1684 protected MenuBar alignFrameMenuBar = new MenuBar();
\r
1685 protected Menu fileMenu = new Menu("File");
\r
1686 protected MenuItem loadTree = new MenuItem("Load Associated Tree");
\r
1687 protected MenuItem closeMenuItem = new MenuItem("Close");
\r
1688 protected Menu editMenu = new Menu("Edit");
\r
1689 protected Menu viewMenu = new Menu("View");
\r
1690 protected Menu colourMenu = new Menu("Colour");
\r
1691 protected Menu calculateMenu = new Menu("Calculate");
\r
1692 protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
1693 protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
1694 protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
1695 protected MenuItem remove2LeftMenuItem = new MenuItem();
\r
1696 protected MenuItem remove2RightMenuItem = new MenuItem();
\r
1697 protected MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
1698 protected MenuItem removeAllGapsMenuItem = new MenuItem();
\r
1699 protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
1700 protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
1701 protected MenuItem sortPairwiseMenuItem = new MenuItem();
\r
1702 protected MenuItem sortIDMenuItem = new MenuItem();
\r
1703 protected MenuItem sortGroupMenuItem = new MenuItem();
\r
1704 protected MenuItem removeRedundancyMenuItem = new MenuItem();
\r
1705 protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
1706 protected MenuItem PCAMenuItem = new MenuItem();
\r
1707 protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
1708 protected MenuItem neighbourTreeMenuItem = new MenuItem();
\r
1709 BorderLayout borderLayout1 = new BorderLayout();
\r
1710 public Label statusBar = new Label();
\r
1711 protected Menu outputTextboxMenu = new Menu();
\r
1712 protected MenuItem clustalColour = new MenuItem();
\r
1713 protected MenuItem zappoColour = new MenuItem();
\r
1714 protected MenuItem taylorColour = new MenuItem();
\r
1715 protected MenuItem hydrophobicityColour = new MenuItem();
\r
1716 protected MenuItem helixColour = new MenuItem();
\r
1717 protected MenuItem strandColour = new MenuItem();
\r
1718 protected MenuItem turnColour = new MenuItem();
\r
1719 protected MenuItem buriedColour = new MenuItem();
\r
1720 protected MenuItem userDefinedColour = new MenuItem();
\r
1721 protected MenuItem PIDColour = new MenuItem();
\r
1722 protected MenuItem BLOSUM62Colour = new MenuItem();
\r
1723 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
1724 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
1725 protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
1726 protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
1727 MenuItem overviewMenuItem = new MenuItem();
\r
1728 protected MenuItem undoMenuItem = new MenuItem();
\r
1729 protected MenuItem redoMenuItem = new MenuItem();
\r
1730 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
1731 MenuItem noColourmenuItem = new MenuItem();
\r
1732 protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
1733 protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
1734 MenuItem findMenuItem = new MenuItem();
\r
1735 Menu searchMenu = new Menu();
\r
1736 protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
1737 protected MenuItem nucleotideColour = new MenuItem();
\r
1738 MenuItem deleteGroups = new MenuItem();
\r
1739 MenuItem delete = new MenuItem();
\r
1740 MenuItem copy = new MenuItem();
\r
1741 MenuItem cut = new MenuItem();
\r
1742 Menu pasteMenu = new Menu();
\r
1743 MenuItem pasteNew = new MenuItem();
\r
1744 MenuItem pasteThis = new MenuItem();
\r
1745 protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
1746 protected MenuItem font = new MenuItem();
\r
1747 protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
1748 protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
1749 protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
1750 MenuItem modifyPID = new MenuItem();
\r
1751 MenuItem modifyConservation = new MenuItem();
\r
1752 protected Menu sortByTreeMenu = new Menu();
\r
1753 Menu sort = new Menu();
\r
1754 Menu calculate = new Menu();
\r
1755 MenuItem inputText = new MenuItem();
\r
1756 Menu helpMenu = new Menu();
\r
1757 MenuItem documentation = new MenuItem();
\r
1758 MenuItem about = new MenuItem();
\r
1759 protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
1760 Panel embeddedMenu;
\r
1761 Label embeddedEdit;
\r
1762 Label embeddedSearch;
\r
1763 Label embeddedView;
\r
1764 Label embeddedColour;
\r
1765 Label embeddedFile;
\r
1766 Label embeddedHelp;
\r
1767 Label embeddedCalculate;
\r
1768 FlowLayout flowLayout1;
\r
1770 private void jbInit() throws Exception {
\r
1772 setMenuBar(alignFrameMenuBar);
\r
1776 // dynamically fill save as menu with available formats
\r
1777 for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++)
\r
1780 item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.
\r
1783 item.addActionListener(new java.awt.event.ActionListener()
\r
1785 public void actionPerformed(ActionEvent e)
\r
1787 outputText_actionPerformed(e);
\r
1791 outputTextboxMenu.add(item);
\r
1793 closeMenuItem.addActionListener(this);
\r
1795 loadTree.addActionListener(this);
\r
1796 selectAllSequenceMenuItem.addActionListener(this);
\r
1797 deselectAllSequenceMenuItem.addActionListener(this);
\r
1798 invertSequenceMenuItem.addActionListener(this);
\r
1799 remove2LeftMenuItem.setLabel("Remove Left");
\r
1800 remove2LeftMenuItem.addActionListener(this);
\r
1801 remove2RightMenuItem.setLabel("Remove Right");
\r
1802 remove2RightMenuItem.addActionListener(this);
\r
1803 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
1804 removeGappedColumnMenuItem.addActionListener(this);
\r
1805 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
1806 removeAllGapsMenuItem.addActionListener(this);
\r
1807 viewBoxesMenuItem.setLabel("Boxes");
\r
1808 viewBoxesMenuItem.setState(true);
\r
1809 viewBoxesMenuItem.addItemListener(this);
\r
1810 viewTextMenuItem.setLabel("Text");
\r
1811 viewTextMenuItem.setState(true);
\r
1812 viewTextMenuItem.addItemListener(this);
\r
1813 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
1814 sortPairwiseMenuItem.addActionListener(this);
\r
1815 sortIDMenuItem.setLabel("by ID");
\r
1816 sortIDMenuItem.addActionListener(this);
\r
1817 sortGroupMenuItem.setLabel("by Group");
\r
1818 sortGroupMenuItem.addActionListener(this);
\r
1819 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
1820 removeRedundancyMenuItem.addActionListener(this);
\r
1821 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
1822 pairwiseAlignmentMenuItem.addActionListener(this);
\r
1823 PCAMenuItem.setLabel("Principal Component Analysis");
\r
1824 PCAMenuItem.addActionListener(this);
\r
1825 averageDistanceTreeMenuItem.setLabel(
\r
1826 "Average Distance Using % Identity");
\r
1827 averageDistanceTreeMenuItem.addActionListener(this);
\r
1828 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
1829 neighbourTreeMenuItem.addActionListener(this);
\r
1830 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
1831 statusBar.setBackground(Color.white);
\r
1832 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
1833 statusBar.setText("Status bar");
\r
1834 outputTextboxMenu.setLabel("Output to Textbox");
\r
1835 clustalColour.setLabel("Clustalx");
\r
1837 clustalColour.addActionListener(this);
\r
1838 zappoColour.setLabel("Zappo");
\r
1839 zappoColour.addActionListener(this);
\r
1840 taylorColour.setLabel("Taylor");
\r
1841 taylorColour.addActionListener(this);
\r
1842 hydrophobicityColour.setLabel("Hydrophobicity");
\r
1843 hydrophobicityColour.addActionListener(this);
\r
1844 helixColour.setLabel("Helix Propensity");
\r
1845 helixColour.addActionListener(this);
\r
1846 strandColour.setLabel("Strand Propensity");
\r
1847 strandColour.addActionListener(this);
\r
1848 turnColour.setLabel("Turn Propensity");
\r
1849 turnColour.addActionListener(this);
\r
1850 buriedColour.setLabel("Buried Index");
\r
1851 buriedColour.addActionListener(this);
\r
1852 userDefinedColour.setLabel("User Defined...");
\r
1853 userDefinedColour.addActionListener(this);
\r
1854 PIDColour.setLabel("Percentage Identity");
\r
1855 PIDColour.addActionListener(this);
\r
1856 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
1857 BLOSUM62Colour.addActionListener(this);
\r
1858 avDistanceTreeBlosumMenuItem.setLabel(
\r
1859 "Average Distance Using BLOSUM62");
\r
1860 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
1861 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
1862 njTreeBlosumMenuItem.addActionListener(this);
\r
1863 annotationPanelMenuItem.setLabel("Show Annotations");
\r
1864 annotationPanelMenuItem.addItemListener(this);
\r
1865 colourTextMenuItem.setLabel("Colour Text");
\r
1866 colourTextMenuItem.addItemListener(this);
\r
1867 overviewMenuItem.setLabel("Overview Window");
\r
1868 overviewMenuItem.addActionListener(this);
\r
1869 undoMenuItem.setEnabled(false);
\r
1870 undoMenuItem.setLabel("Undo");
\r
1871 undoMenuItem.addActionListener(this);
\r
1872 redoMenuItem.setEnabled(false);
\r
1873 redoMenuItem.setLabel("Redo");
\r
1874 redoMenuItem.addActionListener(this);
\r
1875 conservationMenuItem.setLabel("by Conservation");
\r
1876 conservationMenuItem.addItemListener(this);
\r
1877 noColourmenuItem.setLabel("None");
\r
1878 noColourmenuItem.addActionListener(this);
\r
1879 wrapMenuItem.setLabel("Wrap");
\r
1880 wrapMenuItem.addItemListener(this);
\r
1881 renderGapsMenuItem.setLabel("Show Gaps");
\r
1882 renderGapsMenuItem.setState(true);
\r
1883 renderGapsMenuItem.addItemListener(this);
\r
1884 findMenuItem.setLabel("Find...");
\r
1885 findMenuItem.addActionListener(this);
\r
1886 searchMenu.setLabel("Search");
\r
1888 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
1889 abovePIDThreshold.addItemListener(this);
\r
1890 nucleotideColour.setLabel("Nucleotide");
\r
1891 nucleotideColour.addActionListener(this);
\r
1892 deleteGroups.setLabel("Undefine Groups");
\r
1893 deleteGroups.addActionListener(this);
\r
1894 copy.setLabel("Copy");
\r
1895 copy.addActionListener(this);
\r
1896 cut.setLabel("Cut");
\r
1897 cut.addActionListener(this);
\r
1898 delete.setLabel("Delete");
\r
1899 delete.addActionListener(this);
\r
1900 pasteMenu.setLabel("Paste");
\r
1901 pasteNew.setLabel("To New Alignment");
\r
1902 pasteNew.addActionListener(this);
\r
1903 pasteThis.setLabel("Add To This Alignment");
\r
1904 pasteThis.addActionListener(this);
\r
1905 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
1906 applyToAllGroups.setState(true);
\r
1907 applyToAllGroups.addItemListener(this);
\r
1908 font.setLabel("Font...");
\r
1909 font.addActionListener(this);
\r
1910 scaleAbove.setLabel("Scale Above");
\r
1911 scaleAbove.setState(true);
\r
1912 scaleAbove.setEnabled(false);
\r
1913 scaleAbove.addItemListener(this);
\r
1914 scaleLeft.setEnabled(false);
\r
1915 scaleLeft.setState(true);
\r
1916 scaleLeft.setLabel("Scale Left");
\r
1917 scaleLeft.addItemListener(this);
\r
1918 scaleRight.setEnabled(false);
\r
1919 scaleRight.setState(true);
\r
1920 scaleRight.setLabel("Scale Right");
\r
1921 scaleRight.addItemListener(this);
\r
1922 modifyPID.setLabel("Modify Identity Threshold...");
\r
1923 modifyPID.addActionListener(this);
\r
1924 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
1925 modifyConservation.addActionListener(this);
\r
1926 sortByTreeMenu.setLabel("By Tree Order");
\r
1927 sort.setLabel("Sort");
\r
1928 calculate.setLabel("Calculate Tree");
\r
1929 inputText.setLabel("Input from textbox");
\r
1930 inputText.addActionListener(this);
\r
1932 helpMenu.setLabel("Help");
\r
1933 documentation.setLabel("Documentation");
\r
1934 documentation.addActionListener(this);
\r
1936 about.setLabel("About...");
\r
1937 about.addActionListener(this);
\r
1938 seqLimits.setState(true);
\r
1939 seqLimits.setLabel("Show Sequence Limits");
\r
1940 seqLimits.addItemListener(this);
\r
1941 featureSettings.setLabel("Feature Settings...");
\r
1942 featureSettings.addActionListener(this);
\r
1943 sequenceFeatures.setLabel("Sequence Features");
\r
1944 sequenceFeatures.addItemListener(this);
\r
1945 sequenceFeatures.setState(false);
\r
1946 annotationColour.setLabel("by Annotation...");
\r
1947 annotationColour.addActionListener(this);
\r
1949 alignFrameMenuBar.add(fileMenu);
\r
1950 alignFrameMenuBar.add(editMenu);
\r
1951 alignFrameMenuBar.add(searchMenu);
\r
1952 alignFrameMenuBar.add(viewMenu);
\r
1953 alignFrameMenuBar.add(colourMenu);
\r
1954 alignFrameMenuBar.add(calculateMenu);
\r
1955 alignFrameMenuBar.add(helpMenu);
\r
1956 fileMenu.add(inputText);
\r
1957 fileMenu.add(outputTextboxMenu);
\r
1958 fileMenu.addSeparator();
\r
1959 fileMenu.add(loadTree);
\r
1960 fileMenu.add(closeMenuItem);
\r
1961 editMenu.add(undoMenuItem);
\r
1962 editMenu.add(redoMenuItem);
\r
1963 editMenu.add(cut);
\r
1964 editMenu.add(copy);
\r
1965 editMenu.add(pasteMenu);
\r
1966 editMenu.add(delete);
\r
1967 editMenu.addSeparator();
\r
1968 editMenu.add(selectAllSequenceMenuItem);
\r
1969 editMenu.add(deselectAllSequenceMenuItem);
\r
1970 editMenu.add(invertSequenceMenuItem);
\r
1971 editMenu.add(deleteGroups);
\r
1972 editMenu.addSeparator();
\r
1973 editMenu.add(remove2LeftMenuItem);
\r
1974 editMenu.add(remove2RightMenuItem);
\r
1975 editMenu.add(removeGappedColumnMenuItem);
\r
1976 editMenu.add(removeAllGapsMenuItem);
\r
1977 editMenu.add(removeRedundancyMenuItem);
\r
1978 searchMenu.add(findMenuItem);
\r
1979 viewMenu.add(font);
\r
1980 viewMenu.addSeparator();
\r
1981 viewMenu.add(seqLimits);
\r
1982 viewMenu.addSeparator();
\r
1983 viewMenu.add(wrapMenuItem);
\r
1984 viewMenu.add(scaleAbove);
\r
1985 viewMenu.add(scaleLeft);
\r
1986 viewMenu.add(scaleRight);
\r
1987 viewMenu.addSeparator();
\r
1988 viewMenu.add(viewBoxesMenuItem);
\r
1989 viewMenu.add(viewTextMenuItem);
\r
1990 viewMenu.add(colourTextMenuItem);
\r
1991 viewMenu.add(renderGapsMenuItem);
\r
1992 viewMenu.add(annotationPanelMenuItem);
\r
1993 viewMenu.addSeparator();
\r
1994 viewMenu.add(sequenceFeatures);
\r
1995 viewMenu.add(featureSettings);
\r
1996 viewMenu.addSeparator();
\r
1997 viewMenu.add(overviewMenuItem);
\r
1998 colourMenu.add(applyToAllGroups);
\r
1999 colourMenu.addSeparator();
\r
2000 colourMenu.add(noColourmenuItem);
\r
2001 colourMenu.add(clustalColour);
\r
2002 colourMenu.add(BLOSUM62Colour);
\r
2003 colourMenu.add(PIDColour);
\r
2004 colourMenu.add(zappoColour);
\r
2005 colourMenu.add(taylorColour);
\r
2006 colourMenu.add(hydrophobicityColour);
\r
2007 colourMenu.add(helixColour);
\r
2008 colourMenu.add(strandColour);
\r
2009 colourMenu.add(turnColour);
\r
2010 colourMenu.add(buriedColour);
\r
2011 colourMenu.add(nucleotideColour);
\r
2012 colourMenu.add(userDefinedColour);
\r
2013 colourMenu.addSeparator();
\r
2014 colourMenu.add(conservationMenuItem);
\r
2015 colourMenu.add(modifyConservation);
\r
2016 colourMenu.add(abovePIDThreshold);
\r
2017 colourMenu.add(modifyPID);
\r
2018 colourMenu.add(annotationColour);
\r
2019 calculateMenu.add(sort);
\r
2020 calculateMenu.add(calculate);
\r
2021 calculateMenu.addSeparator();
\r
2022 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
2023 calculateMenu.add(PCAMenuItem);
\r
2024 this.add(statusBar, BorderLayout.SOUTH);
\r
2025 pasteMenu.add(pasteNew);
\r
2026 pasteMenu.add(pasteThis);
\r
2027 sort.add(sortIDMenuItem);
\r
2028 sort.add(sortByTreeMenu);
\r
2029 sort.add(sortGroupMenuItem);
\r
2030 sort.add(sortPairwiseMenuItem);
\r
2031 calculate.add(averageDistanceTreeMenuItem);
\r
2032 calculate.add(neighbourTreeMenuItem);
\r
2033 calculate.add(avDistanceTreeBlosumMenuItem);
\r
2034 calculate.add(njTreeBlosumMenuItem);
\r
2035 helpMenu.add(documentation);
\r
2036 helpMenu.add(about);
\r
2039 public void setEmbedded()
\r
2042 embeddedMenu = new Panel();
\r
2043 embeddedEdit = new Label();
\r
2044 embeddedSearch = new Label();
\r
2045 embeddedView = new Label();
\r
2046 embeddedColour = new Label();
\r
2047 embeddedFile = new Label();
\r
2048 embeddedHelp = new Label();
\r
2049 embeddedCalculate = new Label();
\r
2050 flowLayout1 = new FlowLayout();
\r
2051 embeddedMenu.setBackground(Color.lightGray);
\r
2052 embeddedMenu.setLayout(flowLayout1);
\r
2053 embeddedEdit.setText("Edit");
\r
2054 embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2055 embeddedSearch.setText("Search");
\r
2056 embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2057 embeddedView.setText("View");
\r
2058 embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2059 embeddedColour.setText("Colour");
\r
2060 embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2061 embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2062 embeddedFile.setText("File");
\r
2063 embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2064 embeddedHelp.setText("Help");
\r
2065 embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2066 embeddedCalculate.setText("Calculate");
\r
2067 embeddedMenu.add(embeddedFile);
\r
2068 embeddedMenu.add(embeddedEdit);
\r
2069 embeddedMenu.add(embeddedSearch);
\r
2070 embeddedMenu.add(embeddedView);
\r
2071 embeddedMenu.add(embeddedColour);
\r
2072 embeddedMenu.add(embeddedCalculate);
\r
2073 embeddedMenu.add(embeddedHelp);
\r
2074 flowLayout1.setAlignment(FlowLayout.LEFT);
\r
2075 flowLayout1.setHgap(2);
\r
2076 flowLayout1.setVgap(0);
\r
2077 embeddedFile.addMouseListener(this);
\r
2078 embeddedEdit.addMouseListener(this);
\r
2079 embeddedSearch.addMouseListener(this);
\r
2080 embeddedView.addMouseListener(this);
\r
2081 embeddedColour.addMouseListener(this);
\r
2082 embeddedCalculate.addMouseListener(this);
\r
2083 embeddedHelp.addMouseListener(this);
\r
2085 // setVisible(false);
\r
2086 fileMenu.remove(closeMenuItem);
\r
2087 fileMenu.remove(2); // Seperator
\r
2089 applet.setLayout(new BorderLayout());
\r
2090 applet.add(embeddedMenu, BorderLayout.NORTH);
\r
2091 applet.add(statusBar, BorderLayout.SOUTH);
\r
2092 // applet.validate();
\r
2094 alignPanel.setSize(applet.size().width, applet.size().height
\r
2095 - embeddedMenu.HEIGHT - statusBar.HEIGHT);
\r
2097 applet.add(alignPanel, BorderLayout.CENTER);
\r
2098 applet.validate();
\r
2104 PopupMenu filePopup, editPopup, searchPopup,
\r
2105 viewPopup, colourPopup, calculatePopup, helpPopup;
\r
2106 MenuItem featureSettings = new MenuItem();
\r
2107 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
2108 MenuItem annotationColour = new MenuItem();
\r
2110 public void mousePressed(MouseEvent evt)
\r
2112 PopupMenu popup = null;
\r
2113 Label source = (Label)evt.getSource();
\r
2114 if(source==embeddedFile)
\r
2116 popup = filePopup = genPopupMenu(filePopup, fileMenu);
\r
2118 else if(source==embeddedEdit)
\r
2120 popup = editPopup = genPopupMenu(editPopup, editMenu);
\r
2122 else if(source==embeddedSearch)
\r
2124 popup = searchPopup = genPopupMenu(searchPopup, searchMenu);
\r
2126 else if(source==embeddedView)
\r
2128 popup = viewPopup = genPopupMenu(viewPopup, viewMenu);
\r
2130 else if(source==embeddedColour)
\r
2132 popup = colourPopup = genPopupMenu(colourPopup, colourMenu);
\r
2134 else if(source==embeddedCalculate)
\r
2136 popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);
\r
2138 else if(source==embeddedHelp)
\r
2140 popup = helpPopup = genPopupMenu(helpPopup, helpMenu);
\r
2143 embeddedMenu.add(popup);
\r
2144 popup.show(embeddedMenu,
\r
2145 source.getBounds().x,
\r
2146 source.getBounds().y + source.getBounds().getSize().height);
\r
2149 PopupMenu genPopupMenu(PopupMenu popup, Menu original)
\r
2155 popup = new PopupMenu();
\r
2156 int m, mSize = original.getItemCount();
\r
2157 for(m=0; m<mSize; m++)
\r
2159 popup.add(original.getItem(m));
\r
2166 public void mouseClicked(MouseEvent evt)
\r
2168 public void mouseReleased(MouseEvent evt)
\r
2170 public void mouseEntered(MouseEvent evt)
\r
2172 public void mouseExited(MouseEvent evt)
\r