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, jalview.bin.JalviewLite applet, String title)
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48 }catch(Exception ex)
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50 ex.printStackTrace();
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53 this.applet = applet;
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54 viewport = new AlignViewport(al, applet);
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55 alignPanel = new AlignmentPanel(this, viewport);
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57 annotationPanelMenuItem.setState(viewport.showAnnotation);
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61 String param = applet.getParameter("sortBy");
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64 if (param.equalsIgnoreCase("Id"))
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65 sortIDMenuItem_actionPerformed();
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66 else if (param.equalsIgnoreCase("Pairwise Identity"))
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67 sortPairwiseMenuItem_actionPerformed();
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70 param = applet.getParameter("wrap");
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73 if (param.equalsIgnoreCase("true"))
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75 wrapMenuItem.setState(true);
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76 wrapMenuItem_actionPerformed();
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82 param = applet.getParameter("windowWidth");
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85 int width = Integer.parseInt(param);
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86 NEW_WINDOW_WIDTH = width;
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88 param = applet.getParameter("windowHeight");
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91 int height = Integer.parseInt(param);
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92 NEW_WINDOW_HEIGHT = height;
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95 catch (Exception ex)
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100 //Some JVMS send keyevents to Top frame or lowest panel,
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101 //Havent worked out why yet. So add to both this frame and seqCanvas for now
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102 this.addKeyListener(this);
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103 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
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104 alignPanel.idPanel.idCanvas.addKeyListener(this);
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106 viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
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108 public void propertyChange(java.beans.PropertyChangeEvent evt)
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110 if (evt.getPropertyName().equals("alignment"))
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112 alignmentChanged();
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118 add(alignPanel, BorderLayout.CENTER);
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119 jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
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121 alignPanel.validate();
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122 alignPanel.repaint();
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124 public AlignViewport getAlignViewport()
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129 public SeqCanvas getSeqcanvas()
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131 return alignPanel.seqPanel.seqCanvas;
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138 * @param String DOCUMENT ME!
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141 public void parseFeaturesFile(String file)
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143 String line = null;
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146 URL url = new URL(file);
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148 BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));
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149 SequenceI seq = null;
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150 String type, desc, token;
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152 int index, start, end;
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153 StringTokenizer st;
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154 SequenceFeature sf;
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155 FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
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157 String featureGroup = null;
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158 while ( (line = in.readLine()) != null)
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161 st = new StringTokenizer(line, "\t");
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162 if (st.countTokens() == 2)
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164 type = st.nextToken();
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165 if(type.equalsIgnoreCase("startgroup"))
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167 featureGroup = st.nextToken();
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169 else if(type.equalsIgnoreCase("endgroup"))
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171 //We should check whether this is the current group,
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172 //but at present theres no way of showing more than 1 group
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174 featureGroup = null;
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178 UserColourScheme ucs = new UserColourScheme(st.nextToken());
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179 fr.setColour(type, ucs.findColour("A"));
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184 while (st.hasMoreElements())
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186 desc = st.nextToken();
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187 token = st.nextToken();
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188 if (!token.equals("ID_NOT_SPECIFIED"))
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190 index = viewport.alignment.findIndex(viewport.alignment.findName(
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196 index = Integer.parseInt(st.nextToken());
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199 start = Integer.parseInt(st.nextToken());
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200 end = Integer.parseInt(st.nextToken());
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202 seq = viewport.alignment.getSequenceAt(index);
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204 type = st.nextToken();
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206 if(fr.getColour(type)==null)
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208 // Probably the old style groups file
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209 UserColourScheme ucs = new UserColourScheme(type);
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210 fr.setColour(type, ucs.findColour("A"));
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213 sf = new SequenceFeature(type, desc, "", start, end);
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214 sf.setFeatureGroup(featureGroup);
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216 seq.addSequenceFeature(sf);
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220 viewport.showSequenceFeatures = true;
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221 viewMenu.addSeparator();
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222 viewMenu.add(sequenceFeatures);
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223 viewMenu.add(featureSettings);
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226 alignPanel.repaint();
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229 catch (Exception ex)
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231 ex.printStackTrace();
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232 System.out.println("Error parsing groups file: " + ex +"\n"+line);
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236 public void keyPressed(KeyEvent evt)
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238 switch (evt.getKeyCode())
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240 case 27: // escape key
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241 deselectAllSequenceMenuItem_actionPerformed();
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243 case KeyEvent.VK_X:
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244 if (evt.isControlDown() || evt.isMetaDown())
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246 cut_actionPerformed();
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249 case KeyEvent.VK_C:
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250 if (evt.isControlDown() || evt.isMetaDown())
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252 copy_actionPerformed();
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255 case KeyEvent.VK_V:
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256 if (evt.isControlDown() || evt.isMetaDown())
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261 case KeyEvent.VK_A:
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262 if (evt.isControlDown() || evt.isMetaDown())
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264 selectAllSequenceMenuItem_actionPerformed();
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267 case KeyEvent.VK_DOWN:
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268 moveSelectedSequences(false);
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270 case KeyEvent.VK_UP:
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271 moveSelectedSequences(true);
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273 case KeyEvent.VK_F:
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274 if (evt.isControlDown())
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276 findMenuItem_actionPerformed();
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279 case KeyEvent.VK_BACK_SPACE:
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280 case KeyEvent.VK_DELETE:
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281 cut_actionPerformed();
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285 public void keyReleased(KeyEvent evt)
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287 public void keyTyped(KeyEvent evt)
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290 public void itemStateChanged(ItemEvent evt)
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292 if(evt.getSource()==colourTextMenuItem)
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293 colourTextMenuItem_actionPerformed();
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294 else if(evt.getSource()==wrapMenuItem)
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295 wrapMenuItem_actionPerformed();
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296 else if(evt.getSource()==scaleAbove)
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297 scaleAbove_actionPerformed();
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298 else if(evt.getSource()==scaleLeft)
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299 scaleLeft_actionPerformed();
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300 else if(evt.getSource()==scaleRight)
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301 scaleRight_actionPerformed();
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302 else if(evt.getSource()==seqLimits)
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303 seqLimits_itemStateChanged();
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304 else if(evt.getSource()==viewBoxesMenuItem)
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305 viewBoxesMenuItem_actionPerformed();
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306 else if(evt.getSource()==viewTextMenuItem)
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307 viewTextMenuItem_actionPerformed();
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308 else if(evt.getSource()==renderGapsMenuItem)
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309 renderGapsMenuItem_actionPerformed();
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310 else if(evt.getSource()==annotationPanelMenuItem)
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311 annotationPanelMenuItem_actionPerformed();
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312 else if(evt.getSource()==sequenceFeatures)
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313 { viewport.showSequenceFeatures(sequenceFeatures.getState());
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314 alignPanel.seqPanel.seqCanvas.repaint();
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316 else if(evt.getSource()==conservationMenuItem)
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317 conservationMenuItem_actionPerformed();
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318 else if(evt.getSource()==abovePIDThreshold)
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319 abovePIDThreshold_actionPerformed();
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320 else if(evt.getSource()==applyToAllGroups)
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321 applyToAllGroups_actionPerformed();
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323 public void actionPerformed(ActionEvent evt)
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325 if(evt.getSource()==inputText)
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326 inputText_actionPerformed();
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327 else if(evt.getSource()==closeMenuItem)
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328 closeMenuItem_actionPerformed();
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329 else if(evt.getSource()==copy)
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330 copy_actionPerformed();
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331 else if(evt.getSource()==undoMenuItem)
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332 undoMenuItem_actionPerformed();
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333 else if(evt.getSource()==redoMenuItem)
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334 redoMenuItem_actionPerformed();
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335 else if(evt.getSource()==inputText)
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336 inputText_actionPerformed();
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337 else if(evt.getSource()==closeMenuItem)
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338 closeMenuItem_actionPerformed();
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339 else if(evt.getSource()==undoMenuItem)
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340 undoMenuItem_actionPerformed();
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341 else if(evt.getSource()==redoMenuItem)
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342 redoMenuItem_actionPerformed();
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343 else if(evt.getSource()==copy)
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344 copy_actionPerformed();
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345 else if(evt.getSource()==pasteNew)
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346 pasteNew_actionPerformed();
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347 else if(evt.getSource()==pasteThis)
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348 pasteThis_actionPerformed();
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349 else if(evt.getSource()==cut)
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350 cut_actionPerformed();
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351 else if(evt.getSource()==delete)
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352 delete_actionPerformed();
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353 else if(evt.getSource()==deleteGroups)
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354 deleteGroups_actionPerformed();
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355 else if(evt.getSource()==selectAllSequenceMenuItem)
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356 selectAllSequenceMenuItem_actionPerformed();
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357 else if(evt.getSource()==deselectAllSequenceMenuItem)
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358 deselectAllSequenceMenuItem_actionPerformed();
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359 else if(evt.getSource()==invertSequenceMenuItem)
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360 invertSequenceMenuItem_actionPerformed();
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361 else if(evt.getSource()==remove2LeftMenuItem)
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362 remove2LeftMenuItem_actionPerformed();
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363 else if(evt.getSource()==remove2RightMenuItem)
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364 remove2RightMenuItem_actionPerformed();
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365 else if(evt.getSource()==removeGappedColumnMenuItem)
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366 removeGappedColumnMenuItem_actionPerformed();
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367 else if(evt.getSource()==removeAllGapsMenuItem)
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368 removeAllGapsMenuItem_actionPerformed();
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369 else if(evt.getSource()==findMenuItem)
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370 findMenuItem_actionPerformed();
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371 else if(evt.getSource()==font)
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372 font_actionPerformed();
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373 else if(evt.getSource()==featureSettings)
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374 featureSettings_actionPerformed();
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375 else if(evt.getSource()==overviewMenuItem)
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376 overviewMenuItem_actionPerformed();
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377 else if(evt.getSource()==noColourmenuItem)
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378 noColourmenuItem_actionPerformed();
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379 else if(evt.getSource()==clustalColour)
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380 clustalColour_actionPerformed();
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381 else if(evt.getSource()==zappoColour)
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382 zappoColour_actionPerformed();
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383 else if(evt.getSource()==taylorColour)
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384 taylorColour_actionPerformed();
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385 else if(evt.getSource()==hydrophobicityColour)
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386 hydrophobicityColour_actionPerformed();
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387 else if(evt.getSource()==helixColour)
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388 helixColour_actionPerformed();
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389 else if(evt.getSource()==strandColour)
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390 strandColour_actionPerformed();
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391 else if(evt.getSource()==turnColour)
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392 turnColour_actionPerformed();
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393 else if(evt.getSource()==buriedColour)
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394 buriedColour_actionPerformed();
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395 else if(evt.getSource()==nucleotideColour)
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396 nucleotideColour_actionPerformed();
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397 else if(evt.getSource()==modifyPID)
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398 modifyPID_actionPerformed();
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399 else if(evt.getSource()==modifyConservation)
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400 modifyConservation_actionPerformed();
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401 else if(evt.getSource()==userDefinedColour)
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402 userDefinedColour_actionPerformed();
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403 else if(evt.getSource()==PIDColour)
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404 PIDColour_actionPerformed();
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405 else if(evt.getSource()==BLOSUM62Colour)
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406 BLOSUM62Colour_actionPerformed();
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407 else if(evt.getSource()==sortPairwiseMenuItem)
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408 sortPairwiseMenuItem_actionPerformed();
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409 else if(evt.getSource()==sortIDMenuItem)
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410 sortIDMenuItem_actionPerformed();
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411 else if(evt.getSource()==sortGroupMenuItem)
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412 sortGroupMenuItem_actionPerformed();
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413 else if(evt.getSource()==removeRedundancyMenuItem)
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414 removeRedundancyMenuItem_actionPerformed();
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415 else if(evt.getSource()==pairwiseAlignmentMenuItem)
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416 pairwiseAlignmentMenuItem_actionPerformed();
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417 else if(evt.getSource()==PCAMenuItem)
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418 PCAMenuItem_actionPerformed();
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419 else if(evt.getSource()==averageDistanceTreeMenuItem)
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420 averageDistanceTreeMenuItem_actionPerformed();
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421 else if(evt.getSource()==neighbourTreeMenuItem)
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422 neighbourTreeMenuItem_actionPerformed();
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423 else if(evt.getSource()==njTreeBlosumMenuItem)
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424 njTreeBlosumMenuItem_actionPerformed();
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425 else if(evt.getSource()==avDistanceTreeBlosumMenuItem)
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426 avTreeBlosumMenuItem_actionPerformed();
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427 else if(evt.getSource()==documentation)
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428 documentation_actionPerformed();
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429 else if(evt.getSource()==about)
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430 about_actionPerformed();
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434 public void inputText_actionPerformed()
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436 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);
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437 Frame frame = new Frame();
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439 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
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442 protected void outputText_actionPerformed(ActionEvent e)
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444 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet);
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445 Frame frame = new Frame();
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447 jalview.bin.JalviewLite.addFrame(frame,
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448 "Alignment output - " + e.getActionCommand(),
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450 cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
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451 viewport.getAlignment().getSequences(),
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452 viewport.showJVSuffix));
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455 public void closeMenuItem_actionPerformed()
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457 PaintRefresher.components.remove(viewport.alignment);
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458 if(PaintRefresher.components.size()==0 && applet==null)
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464 Stack historyList = new Stack();
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465 Stack redoList = new Stack();
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467 void updateEditMenuBar()
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469 if (historyList.size() > 0)
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471 undoMenuItem.setEnabled(true);
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472 HistoryItem hi = (HistoryItem) historyList.peek();
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473 undoMenuItem.setLabel("Undo " + hi.getDescription());
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477 undoMenuItem.setEnabled(false);
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478 undoMenuItem.setLabel("Undo");
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481 if (redoList.size() > 0)
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483 redoMenuItem.setEnabled(true);
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484 HistoryItem hi = (HistoryItem) redoList.peek();
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485 redoMenuItem.setLabel("Redo " + hi.getDescription());
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489 redoMenuItem.setEnabled(false);
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490 redoMenuItem.setLabel("Redo");
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494 public void addHistoryItem(HistoryItem hi)
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496 historyList.push(hi);
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497 updateEditMenuBar();
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500 protected void undoMenuItem_actionPerformed()
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502 HistoryItem hi = (HistoryItem) historyList.pop();
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503 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
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504 HistoryItem.HIDE));
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505 restoreHistoryItem(hi);
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506 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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509 protected void redoMenuItem_actionPerformed()
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511 HistoryItem hi = (HistoryItem) redoList.pop();
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512 restoreHistoryItem(hi);
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513 updateEditMenuBar();
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514 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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517 // used by undo and redo
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518 void restoreHistoryItem(HistoryItem hi)
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520 if (hi.getType() == HistoryItem.SORT)
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522 for (int i = 0; i < hi.getSequences().size(); i++)
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524 viewport.alignment.getSequences().setElementAt(hi.getSequences().
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530 for (int i = 0; i < hi.getSequences().size(); i++)
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532 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
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533 if (restore.getLength() == 0)
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535 // log.System.out.println(hi.getHidden().elementAt(i));
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536 restore.setSequence(hi.getHidden().elementAt(i).toString());
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537 viewport.alignment.getSequences().insertElementAt(
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539 hi.getAlignIndex(i));
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543 restore.setSequence(hi.getHidden().elementAt(i).toString());
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546 if (hi.getType() == HistoryItem.PASTE)
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548 for (int i = viewport.alignment.getHeight() - 1;
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549 i > hi.getSequences().size() - 1; i--)
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551 viewport.alignment.deleteSequence(i);
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556 updateEditMenuBar();
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558 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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561 public void moveSelectedSequences(boolean up)
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563 SequenceGroup sg = viewport.getSelectionGroup();
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571 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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573 SequenceI seq = viewport.alignment.getSequenceAt(i);
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574 if (!sg.sequences.contains(seq))
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579 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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580 if (sg.sequences.contains(temp))
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585 viewport.alignment.getSequences().setElementAt(temp, i);
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586 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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591 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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593 SequenceI seq = viewport.alignment.getSequenceAt(i);
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594 if (!sg.sequences.contains(seq))
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599 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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600 if (sg.sequences.contains(temp))
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605 viewport.alignment.getSequences().setElementAt(temp, i);
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606 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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610 alignPanel.repaint();
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613 StringBuffer copiedSequences;
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614 protected void copy_actionPerformed()
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616 if (viewport.getSelectionGroup() == null)
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621 SequenceGroup sg = viewport.getSelectionGroup();
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622 copiedSequences = new StringBuffer();
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623 Hashtable orderedSeqs = new Hashtable();
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624 for (int i = 0; i < sg.getSize(); i++)
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626 SequenceI seq = sg.getSequenceAt(i);
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627 int index = viewport.alignment.findIndex(seq);
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628 orderedSeqs.put(index + "", seq);
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631 int index = 0, startRes, endRes;
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634 for (int i = 0; i < sg.getSize(); i++)
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636 SequenceI seq = null;
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638 while (seq == null)
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640 if (orderedSeqs.containsKey(index + ""))
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642 seq = (SequenceI) orderedSeqs.get(index + "");
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654 //Returns residue following index if gap
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655 startRes = seq.findPosition(sg.getStartRes());
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658 //Need to find the residue preceeding index if gap
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661 for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
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663 ch = seq.getCharAt(j);
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664 if (!jalview.util.Comparison.isGap( (ch)))
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672 endRes += seq.getStart() -1;
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675 copiedSequences.append(seq.getName() + "\t" +
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678 seq.getSequence(sg.getStartRes(),
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679 sg.getEndRes() + 1) + "\n");
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684 protected void pasteNew_actionPerformed()
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689 protected void pasteThis_actionPerformed()
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691 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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692 HistoryItem.PASTE));
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696 void paste(boolean newAlignment)
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700 if (copiedSequences == null)
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705 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
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706 Vector seqs = new Vector();
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707 while (st.hasMoreElements())
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709 String name = st.nextToken();
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710 int start = Integer.parseInt(st.nextToken());
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711 int end = Integer.parseInt(st.nextToken());
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712 Sequence sequence = new Sequence(name, st.nextToken(), start, end);
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716 viewport.alignment.addSequence(sequence);
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720 seqs.addElement(sequence);
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726 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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727 for (int i = 0; i < seqs.size(); i++)
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729 newSeqs[i] = (SequenceI) seqs.elementAt(i);
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732 String newtitle = new String("Copied sequences");
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733 if (getTitle().startsWith("Copied sequences"))
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735 newtitle = getTitle();
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739 newtitle = newtitle.concat("- from " + getTitle());
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741 AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet, newtitle);
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743 jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
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744 NEW_WINDOW_HEIGHT);
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748 viewport.setEndSeq(viewport.alignment.getHeight());
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749 viewport.alignment.getWidth();
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750 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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754 catch (Exception ex)
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755 {} // could be anything being pasted in here
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759 protected void cut_actionPerformed()
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761 copy_actionPerformed();
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762 delete_actionPerformed();
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765 protected void delete_actionPerformed()
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767 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
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768 HistoryItem.HIDE));
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769 if (viewport.getSelectionGroup() == null)
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775 SequenceGroup sg = viewport.getSelectionGroup();
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776 boolean allSequences = false;
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777 if(sg.sequences.size()==viewport.alignment.getHeight())
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778 allSequences = true;
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780 for (int i = 0; i < sg.sequences.size(); i++)
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782 SequenceI seq = sg.getSequenceAt(i);
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783 int index = viewport.getAlignment().findIndex(seq);
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784 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
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786 // If the cut affects all sequences, remove highlighted columns
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789 viewport.getColumnSelection().removeElements(sg.getStartRes(),
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790 sg.getEndRes() + 1);
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794 if (seq.getSequence().length() < 1)
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796 viewport.getAlignment().deleteSequence(seq);
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800 viewport.getAlignment().getSequences().setElementAt(seq, index);
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804 viewport.setSelectionGroup(null);
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805 viewport.alignment.deleteGroup(sg);
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806 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
\r
807 if (viewport.getAlignment().getHeight() < 1)
\r
811 this.setVisible(false);
\r
813 catch (Exception ex)
\r
816 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
820 protected void deleteGroups_actionPerformed()
\r
822 viewport.alignment.deleteAllGroups();
\r
823 viewport.setSelectionGroup(null);
\r
825 alignPanel.repaint();
\r
828 public void selectAllSequenceMenuItem_actionPerformed()
\r
830 SequenceGroup sg = new SequenceGroup();
\r
831 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
833 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
835 sg.setEndRes(viewport.alignment.getWidth()-1);
\r
836 viewport.setSelectionGroup(sg);
\r
837 alignPanel.repaint();
\r
838 PaintRefresher.Refresh(null, viewport.alignment);
\r
841 public void deselectAllSequenceMenuItem_actionPerformed()
\r
843 viewport.setSelectionGroup(null);
\r
844 viewport.getColumnSelection().clear();
\r
845 viewport.setSelectionGroup(null);
\r
846 alignPanel.idPanel.idCanvas.searchResults = null;
\r
847 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
848 alignPanel.repaint();
\r
849 PaintRefresher.Refresh(null, viewport.alignment);
\r
852 public void invertSequenceMenuItem_actionPerformed()
\r
854 SequenceGroup sg = viewport.getSelectionGroup();
\r
855 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
857 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
860 PaintRefresher.Refresh(null, viewport.alignment);
\r
863 public void remove2LeftMenuItem_actionPerformed()
\r
865 ColumnSelection colSel = viewport.getColumnSelection();
\r
866 if (colSel.size() > 0)
\r
868 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
\r
869 HistoryItem.HIDE));
\r
870 int min = colSel.getMin();
\r
871 viewport.getAlignment().trimLeft(min);
\r
872 colSel.compensateForEdit(0, min);
\r
874 if (viewport.getSelectionGroup() != null)
\r
876 viewport.getSelectionGroup().adjustForRemoveLeft(min);
\r
879 Vector groups = viewport.alignment.getGroups();
\r
880 for (int i = 0; i < groups.size(); i++)
\r
882 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
883 if (!sg.adjustForRemoveLeft(min))
\r
885 viewport.alignment.deleteGroup(sg);
\r
888 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
892 public void remove2RightMenuItem_actionPerformed()
\r
894 ColumnSelection colSel = viewport.getColumnSelection();
\r
895 if (colSel.size() > 0)
\r
897 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
\r
898 HistoryItem.HIDE));
\r
899 int max = colSel.getMax();
\r
900 viewport.getAlignment().trimRight(max);
\r
901 if (viewport.getSelectionGroup() != null)
\r
903 viewport.getSelectionGroup().adjustForRemoveRight(max);
\r
906 Vector groups = viewport.alignment.getGroups();
\r
907 for (int i = 0; i < groups.size(); i++)
\r
909 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
910 if (!sg.adjustForRemoveRight(max))
\r
912 viewport.alignment.deleteGroup(sg);
\r
915 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
920 public void removeGappedColumnMenuItem_actionPerformed()
\r
922 addHistoryItem(new HistoryItem("Remove Gapped Columns",
\r
923 viewport.alignment,
\r
924 HistoryItem.HIDE));
\r
926 //This is to maintain viewport position on first residue
\r
927 //of first sequence
\r
928 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
929 int startRes = seq.findPosition(viewport.startRes);
\r
931 viewport.getAlignment().removeGaps();
\r
933 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
935 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
938 public void removeAllGapsMenuItem_actionPerformed()
\r
940 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
\r
941 HistoryItem.HIDE));
\r
943 //This is to maintain viewport position on first residue
\r
944 //of first sequence
\r
945 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
946 int startRes = seq.findPosition(viewport.startRes);
\r
953 int start=0, end = viewport.alignment.getWidth();
\r
955 if (viewport.getSelectionGroup() != null
\r
956 && viewport.getSelectionGroup().sequences != null
\r
957 && viewport.getSelectionGroup().sequences.size()>0)
\r
959 seqs = viewport.getSelectionGroup().sequences;
\r
960 start = viewport.getSelectionGroup().getStartRes();
\r
961 end = viewport.getSelectionGroup().getEndRes()+1;
\r
964 seqs = viewport.alignment.getSequences();
\r
966 for (int i = 0; i < seqs.size(); i++)
\r
968 current = (SequenceI) seqs.elementAt(i);
\r
969 jSize = current.getLength();
\r
971 // Removing a range is much quicker than removing gaps
\r
972 // one by one for long sequences
\r
974 int rangeStart=-1, rangeEnd=-1;
\r
978 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
\r
995 current.deleteChars(rangeStart, rangeEnd);
\r
996 j-=rangeEnd-rangeStart;
\r
997 jSize-=rangeEnd-rangeStart;
\r
1005 while (j < end && j < jSize);
\r
1008 current.deleteChars(rangeStart, rangeEnd);
\r
1011 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1012 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1015 public void alignmentChanged()
\r
1017 viewport.updateConsensus();
\r
1018 viewport.updateConservation ();
\r
1019 resetAllColourSchemes();
\r
1020 if(alignPanel.overviewPanel!=null)
\r
1021 alignPanel.overviewPanel.updateOverviewImage();
\r
1023 viewport.alignment.adjustSequenceAnnotations();
\r
1024 alignPanel.repaint();
\r
1027 void resetAllColourSchemes()
\r
1029 ColourSchemeI cs = viewport.globalColourScheme;
\r
1032 if (cs instanceof ClustalxColourScheme)
\r
1034 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
\r
1035 resetClustalX(viewport.alignment.getSequences(),
\r
1036 viewport.alignment.getWidth());
\r
1039 cs.setConsensus(viewport.vconsensus);
\r
1040 if (cs.conservationApplied())
\r
1042 Alignment al = (Alignment) viewport.alignment;
\r
1043 Conservation c = new Conservation("All",
\r
1044 ResidueProperties.propHash, 3,
\r
1045 al.getSequences(), 0,
\r
1046 al.getWidth() - 1);
\r
1048 c.verdict(false, viewport.ConsPercGaps);
\r
1050 cs.setConservation(c);
\r
1054 int s, sSize = viewport.alignment.getGroups().size();
\r
1055 for(s=0; s<sSize; s++)
\r
1057 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
\r
1058 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
\r
1060 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
\r
1062 sg.recalcConservation();
\r
1068 public void findMenuItem_actionPerformed()
\r
1070 new Finder(alignPanel);
\r
1073 public void font_actionPerformed()
\r
1075 new FontChooser(alignPanel);
\r
1079 public void seqLimits_itemStateChanged()
\r
1081 viewport.setShowJVSuffix(seqLimits.getState());
\r
1082 alignPanel.fontChanged();
\r
1083 alignPanel.repaint();
\r
1087 protected void colourTextMenuItem_actionPerformed()
\r
1089 viewport.setColourText(colourTextMenuItem.getState());
\r
1090 alignPanel.repaint();
\r
1093 protected void wrapMenuItem_actionPerformed()
\r
1095 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
1096 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
1097 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
1098 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
1099 scaleRight.setEnabled(wrapMenuItem.getState());
\r
1100 alignPanel.repaint();
\r
1103 protected void scaleAbove_actionPerformed()
\r
1105 viewport.setScaleAboveWrapped(scaleAbove.getState());
\r
1106 alignPanel.repaint();
\r
1109 protected void scaleLeft_actionPerformed()
\r
1111 viewport.setScaleLeftWrapped(scaleLeft.getState());
\r
1112 alignPanel.repaint();
\r
1115 protected void scaleRight_actionPerformed()
\r
1117 viewport.setScaleRightWrapped(scaleRight.getState());
\r
1118 alignPanel.repaint();
\r
1121 public void viewBoxesMenuItem_actionPerformed()
\r
1123 viewport.setShowBoxes(viewBoxesMenuItem.getState());
\r
1124 alignPanel.repaint();
\r
1127 public void viewTextMenuItem_actionPerformed()
\r
1129 viewport.setShowText(viewTextMenuItem.getState());
\r
1130 alignPanel.repaint();
\r
1133 protected void renderGapsMenuItem_actionPerformed()
\r
1135 viewport.setRenderGaps(renderGapsMenuItem.getState());
\r
1136 alignPanel.repaint();
\r
1139 public void annotationPanelMenuItem_actionPerformed()
\r
1141 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
\r
1142 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
\r
1145 public void featureSettings_actionPerformed()
\r
1147 new FeatureSettings(viewport, alignPanel);
\r
1150 public void overviewMenuItem_actionPerformed()
\r
1152 if (alignPanel.overviewPanel != null)
\r
1157 Frame frame = new Frame();
\r
1158 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1159 frame.add(overview);
\r
1160 // +50 must allow for applet frame window
\r
1161 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
1162 overview.preferredSize().width,
\r
1163 overview.preferredSize().height + 50);
\r
1166 frame.addWindowListener(new WindowAdapter()
\r
1168 public void windowClosing(WindowEvent e)
\r
1170 alignPanel.setOverviewPanel(null);
\r
1174 alignPanel.setOverviewPanel(overview);
\r
1178 protected void noColourmenuItem_actionPerformed()
\r
1180 changeColour(null);
\r
1183 public void clustalColour_actionPerformed()
\r
1185 abovePIDThreshold.setState(false);
\r
1186 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
\r
1187 viewport.alignment.getWidth()));
\r
1190 public void zappoColour_actionPerformed()
\r
1192 changeColour(new ZappoColourScheme());
\r
1195 public void taylorColour_actionPerformed()
\r
1197 changeColour(new TaylorColourScheme());
\r
1200 public void hydrophobicityColour_actionPerformed()
\r
1202 changeColour(new HydrophobicColourScheme());
\r
1205 public void helixColour_actionPerformed()
\r
1207 changeColour(new HelixColourScheme());
\r
1210 public void strandColour_actionPerformed()
\r
1212 changeColour(new StrandColourScheme());
\r
1215 public void turnColour_actionPerformed()
\r
1217 changeColour(new TurnColourScheme());
\r
1220 public void buriedColour_actionPerformed()
\r
1222 changeColour(new BuriedColourScheme());
\r
1225 public void nucleotideColour_actionPerformed()
\r
1227 changeColour(new NucleotideColourScheme());
\r
1230 protected void applyToAllGroups_actionPerformed()
\r
1232 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
\r
1235 void changeColour(ColourSchemeI cs)
\r
1237 int threshold = 0;
\r
1241 if (viewport.getAbovePIDThreshold())
\r
1243 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
\r
1245 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1247 viewport.setGlobalColourScheme(cs);
\r
1251 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1254 if (viewport.getConservationSelected())
\r
1257 Alignment al = (Alignment) viewport.alignment;
\r
1258 Conservation c = new Conservation("All",
\r
1259 ResidueProperties.propHash, 3,
\r
1260 al.getSequences(), 0,
\r
1261 al.getWidth() - 1);
\r
1264 c.verdict(false, viewport.ConsPercGaps);
\r
1266 cs.setConservation(c);
\r
1268 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1274 cs.setConservation(null);
\r
1277 cs.setConsensus(viewport.vconsensus);
\r
1280 viewport.setGlobalColourScheme(cs);
\r
1282 if (viewport.getColourAppliesToAllGroups())
\r
1284 Vector groups = viewport.alignment.getGroups();
\r
1285 for (int i = 0; i < groups.size(); i++)
\r
1287 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1294 if (cs instanceof ClustalxColourScheme)
\r
1296 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1302 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1304 catch (Exception ex)
\r
1306 ex.printStackTrace();
\r
1311 if (viewport.getAbovePIDThreshold()
\r
1312 || cs instanceof PIDColourScheme
\r
1313 || cs instanceof Blosum62ColourScheme)
\r
1315 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1316 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
1319 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1321 if (viewport.getConservationSelected())
\r
1323 Conservation c = new Conservation("Group",
\r
1324 ResidueProperties.propHash, 3,
\r
1326 viewport.alignment.getWidth() - 1);
\r
1328 c.verdict(false, viewport.ConsPercGaps);
\r
1329 sg.cs.setConservation(c);
\r
1333 sg.cs.setConservation(null);
\r
1334 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1341 if (alignPanel.getOverviewPanel() != null)
\r
1343 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1346 alignPanel.repaint();
\r
1351 protected void modifyPID_actionPerformed()
\r
1353 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1355 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
1357 SliderPanel.showPIDSlider();
\r
1361 protected void modifyConservation_actionPerformed()
\r
1363 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1365 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
1367 SliderPanel.showConservationSlider();
\r
1371 protected void conservationMenuItem_actionPerformed()
\r
1373 viewport.setConservationSelected(conservationMenuItem.getState());
\r
1375 viewport.setAbovePIDThreshold(false);
\r
1376 abovePIDThreshold.setState(false);
\r
1378 changeColour(viewport.getGlobalColourScheme());
\r
1380 modifyConservation_actionPerformed();
\r
1383 public void abovePIDThreshold_actionPerformed()
\r
1385 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
1387 conservationMenuItem.setState(false);
\r
1388 viewport.setConservationSelected(false);
\r
1390 changeColour(viewport.getGlobalColourScheme());
\r
1392 modifyPID_actionPerformed();
\r
1395 public void userDefinedColour_actionPerformed()
\r
1397 new UserDefinedColours(alignPanel, null);
\r
1400 public void PIDColour_actionPerformed()
\r
1402 changeColour(new PIDColourScheme());
\r
1405 public void BLOSUM62Colour_actionPerformed()
\r
1407 changeColour(new Blosum62ColourScheme());
\r
1410 public void sortPairwiseMenuItem_actionPerformed()
\r
1412 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1413 HistoryItem.SORT));
\r
1414 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1415 viewport.getAlignment().getSequenceAt(0));
\r
1416 alignPanel.repaint();
\r
1419 public void sortIDMenuItem_actionPerformed()
\r
1421 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1422 HistoryItem.SORT));
\r
1423 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1424 alignPanel.repaint();
\r
1427 public void sortGroupMenuItem_actionPerformed()
\r
1429 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1430 HistoryItem.SORT));
\r
1431 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1432 alignPanel.repaint();
\r
1436 public void removeRedundancyMenuItem_actionPerformed()
\r
1438 RedundancyPanel sp = new RedundancyPanel(alignPanel);
\r
1439 Frame frame = new Frame();
\r
1441 jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",
\r
1446 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
1448 if (viewport.getSelectionGroup().getSize() > 1)
\r
1450 Frame frame = new Frame();
\r
1451 frame.add(new PairwiseAlignPanel(alignPanel));
\r
1452 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
1456 public void PCAMenuItem_actionPerformed()
\r
1458 //are the sequences aligned?
\r
1459 if (!viewport.alignment.isAligned())
\r
1461 SequenceI current;
\r
1462 int Width = viewport.getAlignment().getWidth();
\r
1464 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1467 current = viewport.getAlignment().getSequenceAt(i);
\r
1469 if (current.getLength() < Width)
\r
1471 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1474 alignPanel.repaint();
\r
1477 if ( (viewport.getSelectionGroup() != null &&
\r
1478 viewport.getSelectionGroup().getSize() < 4 &&
\r
1479 viewport.getSelectionGroup().getSize() > 0)
\r
1480 || viewport.getAlignment().getHeight() < 4)
\r
1487 new PCAPanel(viewport);
\r
1489 catch (java.lang.OutOfMemoryError ex)
\r
1495 public void averageDistanceTreeMenuItem_actionPerformed()
\r
1497 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1500 public void neighbourTreeMenuItem_actionPerformed()
\r
1502 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1505 protected void njTreeBlosumMenuItem_actionPerformed()
\r
1507 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1510 protected void avTreeBlosumMenuItem_actionPerformed()
\r
1512 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1515 void NewTreePanel(String type, String pwType, String title)
\r
1517 //are the sequences aligned?
\r
1518 if (!viewport.alignment.isAligned())
\r
1520 SequenceI current;
\r
1521 int Width = viewport.getAlignment().getWidth();
\r
1523 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1526 current = viewport.getAlignment().getSequenceAt(i);
\r
1528 if (current.getLength() < Width)
\r
1530 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1533 alignPanel.repaint();
\r
1537 final TreePanel tp;
\r
1538 if (viewport.getSelectionGroup() != null &&
\r
1539 viewport.getSelectionGroup().getSize() > 3)
\r
1541 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
\r
1543 0, viewport.alignment.getWidth());
\r
1547 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1548 type, pwType, 0, viewport.alignment.getWidth());
\r
1551 addTreeMenuItem(tp, title);
\r
1553 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
1556 public void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1558 final MenuItem item = new MenuItem(title);
\r
1559 sortByTreeMenu.add(item);
\r
1560 item.addActionListener(new java.awt.event.ActionListener()
\r
1562 public void actionPerformed(ActionEvent evt)
\r
1564 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1565 HistoryItem.SORT));
\r
1566 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1567 alignPanel.repaint();
\r
1571 treePanel.addWindowListener(new WindowAdapter()
\r
1573 public void windowClosing(WindowEvent e)
\r
1575 sortByTreeMenu.remove(item);
\r
1580 protected void documentation_actionPerformed()
\r
1582 showURL("http://www.jalview.org/help.html", "HELP");
\r
1585 protected void about_actionPerformed()
\r
1588 class AboutPanel extends Canvas
\r
1591 public AboutPanel(String version)
\r
1592 { this.version = version; }
\r
1594 public void paint(Graphics g)
\r
1596 g.setColor(Color.white);
\r
1597 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1598 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1599 FontMetrics fm = g.getFontMetrics();
\r
1600 int fh = fm.getHeight();
\r
1602 g.setColor(Color.black);
\r
1603 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
1604 g.drawString("Jalview - Release "+version, 200, y += fh);
\r
1605 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1606 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
1608 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
1611 "For any issues relating to Jalview, email help@jalview.org", x,
\r
1613 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
1614 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
1616 g.drawString("Bioinformatics, 2004 12;426-7.", x, y += fh);
\r
1620 String version = "test";
\r
1621 java.net.URL url = getClass().getResource("/.build_properties");
\r
1626 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
1627 url.openStream()));
\r
1629 while ( (line = reader.readLine()) != null)
\r
1631 if (line.indexOf("VERSION") > -1)
\r
1633 version = line.substring(line.indexOf("=") + 1);
\r
1637 catch (Exception ex)
\r
1639 ex.printStackTrace();
\r
1644 Frame frame = new Frame();
\r
1645 frame.add(new AboutPanel(version));
\r
1646 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
\r
1650 public void showURL(String url, String target)
\r
1652 if (applet == null)
\r
1654 System.out.println("Not running as applet - no browser available.");
\r
1660 applet.getAppletContext().showDocument(new java.net.URL(url),
\r
1663 catch (Exception ex)
\r
1665 ex.printStackTrace();
\r
1671 //////////////////////////////////////////////////////////////////////////////////
\r
1672 //JBuilder Graphics here
\r
1674 protected MenuBar alignFrameMenuBar = new MenuBar();
\r
1675 protected Menu fileMenu = new Menu();
\r
1676 protected MenuItem closeMenuItem = new MenuItem();
\r
1677 protected Menu editMenu = new Menu();
\r
1678 protected Menu viewMenu = new Menu();
\r
1679 protected Menu colourMenu = new Menu();
\r
1680 protected Menu calculateMenu = new Menu();
\r
1681 protected MenuItem selectAllSequenceMenuItem = new MenuItem();
\r
1682 protected MenuItem deselectAllSequenceMenuItem = new MenuItem();
\r
1683 protected MenuItem invertSequenceMenuItem = new MenuItem();
\r
1684 protected MenuItem remove2LeftMenuItem = new MenuItem();
\r
1685 protected MenuItem remove2RightMenuItem = new MenuItem();
\r
1686 protected MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
1687 protected MenuItem removeAllGapsMenuItem = new MenuItem();
\r
1688 protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
1689 protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
1690 protected MenuItem sortPairwiseMenuItem = new MenuItem();
\r
1691 protected MenuItem sortIDMenuItem = new MenuItem();
\r
1692 protected MenuItem sortGroupMenuItem = new MenuItem();
\r
1693 protected MenuItem removeRedundancyMenuItem = new MenuItem();
\r
1694 protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
1695 protected MenuItem PCAMenuItem = new MenuItem();
\r
1696 protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
1697 protected MenuItem neighbourTreeMenuItem = new MenuItem();
\r
1698 BorderLayout borderLayout1 = new BorderLayout();
\r
1699 public Label statusBar = new Label();
\r
1700 protected Menu outputTextboxMenu = new Menu();
\r
1701 protected MenuItem clustalColour = new MenuItem();
\r
1702 protected MenuItem zappoColour = new MenuItem();
\r
1703 protected MenuItem taylorColour = new MenuItem();
\r
1704 protected MenuItem hydrophobicityColour = new MenuItem();
\r
1705 protected MenuItem helixColour = new MenuItem();
\r
1706 protected MenuItem strandColour = new MenuItem();
\r
1707 protected MenuItem turnColour = new MenuItem();
\r
1708 protected MenuItem buriedColour = new MenuItem();
\r
1709 protected MenuItem userDefinedColour = new MenuItem();
\r
1710 protected MenuItem PIDColour = new MenuItem();
\r
1711 protected MenuItem BLOSUM62Colour = new MenuItem();
\r
1712 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
1713 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
1714 protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
1715 protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
1716 MenuItem overviewMenuItem = new MenuItem();
\r
1717 protected MenuItem undoMenuItem = new MenuItem();
\r
1718 protected MenuItem redoMenuItem = new MenuItem();
\r
1719 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
1720 MenuItem noColourmenuItem = new MenuItem();
\r
1721 protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
1722 protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
1723 MenuItem findMenuItem = new MenuItem();
\r
1724 Menu searchMenu = new Menu();
\r
1725 protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
1726 protected MenuItem nucleotideColour = new MenuItem();
\r
1727 MenuItem deleteGroups = new MenuItem();
\r
1728 MenuItem delete = new MenuItem();
\r
1729 MenuItem copy = new MenuItem();
\r
1730 MenuItem cut = new MenuItem();
\r
1731 Menu pasteMenu = new Menu();
\r
1732 MenuItem pasteNew = new MenuItem();
\r
1733 MenuItem pasteThis = new MenuItem();
\r
1734 protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
1735 protected MenuItem font = new MenuItem();
\r
1736 protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
1737 protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
1738 protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
1739 MenuItem modifyPID = new MenuItem();
\r
1740 MenuItem modifyConservation = new MenuItem();
\r
1741 protected Menu sortByTreeMenu = new Menu();
\r
1742 Menu sort = new Menu();
\r
1743 Menu calculate = new Menu();
\r
1744 MenuItem inputText = new MenuItem();
\r
1745 Menu helpMenu = new Menu();
\r
1746 MenuItem documentation = new MenuItem();
\r
1747 MenuItem about = new MenuItem();
\r
1748 protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
1749 Panel embeddedMenu;
\r
1750 Label embeddedEdit;
\r
1751 Label embeddedSearch;
\r
1752 Label embeddedView;
\r
1753 Label embeddedColour;
\r
1754 Label embeddedFile;
\r
1755 Label embeddedHelp;
\r
1756 Label embeddedCalculate;
\r
1757 FlowLayout flowLayout1;
\r
1759 private void jbInit() throws Exception {
\r
1761 setMenuBar(alignFrameMenuBar);
\r
1765 // dynamically fill save as menu with available formats
\r
1766 for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++)
\r
1769 item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.
\r
1772 item.addActionListener(new java.awt.event.ActionListener()
\r
1774 public void actionPerformed(ActionEvent e)
\r
1776 outputText_actionPerformed(e);
\r
1780 outputTextboxMenu.add(item);
\r
1783 fileMenu.setLabel("File");
\r
1784 closeMenuItem.setLabel("Close");
\r
1785 closeMenuItem.addActionListener(this);
\r
1786 editMenu.setLabel("Edit");
\r
1787 viewMenu.setLabel("View");
\r
1788 colourMenu.setLabel("Colour");
\r
1789 calculateMenu.setLabel("Calculate");
\r
1790 selectAllSequenceMenuItem.setLabel("Select all");
\r
1791 selectAllSequenceMenuItem.addActionListener(this);
\r
1792 deselectAllSequenceMenuItem.setLabel("Deselect All");
\r
1793 deselectAllSequenceMenuItem.addActionListener(this);
\r
1794 invertSequenceMenuItem.setLabel("Invert Selection");
\r
1795 invertSequenceMenuItem.addActionListener(this);
\r
1796 remove2LeftMenuItem.setLabel("Remove Left");
\r
1797 remove2LeftMenuItem.addActionListener(this);
\r
1798 remove2RightMenuItem.setLabel("Remove Right");
\r
1799 remove2RightMenuItem.addActionListener(this);
\r
1800 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
1801 removeGappedColumnMenuItem.addActionListener(this);
\r
1802 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
1803 removeAllGapsMenuItem.addActionListener(this);
\r
1804 viewBoxesMenuItem.setLabel("Boxes");
\r
1805 viewBoxesMenuItem.setState(true);
\r
1806 viewBoxesMenuItem.addItemListener(this);
\r
1807 viewTextMenuItem.setLabel("Text");
\r
1808 viewTextMenuItem.setState(true);
\r
1809 viewTextMenuItem.addItemListener(this);
\r
1810 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
1811 sortPairwiseMenuItem.addActionListener(this);
\r
1812 sortIDMenuItem.setLabel("by ID");
\r
1813 sortIDMenuItem.addActionListener(this);
\r
1814 sortGroupMenuItem.setLabel("by Group");
\r
1815 sortGroupMenuItem.addActionListener(this);
\r
1816 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
1817 removeRedundancyMenuItem.addActionListener(this);
\r
1818 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
1819 pairwiseAlignmentMenuItem.addActionListener(this);
\r
1820 PCAMenuItem.setLabel("Principal Component Analysis");
\r
1821 PCAMenuItem.addActionListener(this);
\r
1822 averageDistanceTreeMenuItem.setLabel(
\r
1823 "Average Distance Using % Identity");
\r
1824 averageDistanceTreeMenuItem.addActionListener(this);
\r
1825 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
1826 neighbourTreeMenuItem.addActionListener(this);
\r
1827 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
1828 statusBar.setBackground(Color.white);
\r
1829 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
1830 statusBar.setText("Status bar");
\r
1831 outputTextboxMenu.setLabel("Output to Textbox");
\r
1832 clustalColour.setLabel("Clustalx");
\r
1834 clustalColour.addActionListener(this);
\r
1835 zappoColour.setLabel("Zappo");
\r
1836 zappoColour.addActionListener(this);
\r
1837 taylorColour.setLabel("Taylor");
\r
1838 taylorColour.addActionListener(this);
\r
1839 hydrophobicityColour.setLabel("Hydrophobicity");
\r
1840 hydrophobicityColour.addActionListener(this);
\r
1841 helixColour.setLabel("Helix Propensity");
\r
1842 helixColour.addActionListener(this);
\r
1843 strandColour.setLabel("Strand Propensity");
\r
1844 strandColour.addActionListener(this);
\r
1845 turnColour.setLabel("Turn Propensity");
\r
1846 turnColour.addActionListener(this);
\r
1847 buriedColour.setLabel("Buried Index");
\r
1848 buriedColour.addActionListener(this);
\r
1849 userDefinedColour.setLabel("User Defined...");
\r
1850 userDefinedColour.addActionListener(this);
\r
1851 PIDColour.setLabel("Percentage Identity");
\r
1852 PIDColour.addActionListener(this);
\r
1853 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
1854 BLOSUM62Colour.addActionListener(this);
\r
1855 avDistanceTreeBlosumMenuItem.setLabel(
\r
1856 "Average Distance Using BLOSUM62");
\r
1857 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
1858 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
1859 njTreeBlosumMenuItem.addActionListener(this);
\r
1860 annotationPanelMenuItem.setLabel("Show Annotations");
\r
1861 annotationPanelMenuItem.addItemListener(this);
\r
1862 colourTextMenuItem.setLabel("Colour Text");
\r
1863 colourTextMenuItem.addItemListener(this);
\r
1864 overviewMenuItem.setLabel("Overview Window");
\r
1865 overviewMenuItem.addActionListener(this);
\r
1866 undoMenuItem.setEnabled(false);
\r
1867 undoMenuItem.setLabel("Undo");
\r
1868 undoMenuItem.addActionListener(this);
\r
1869 redoMenuItem.setEnabled(false);
\r
1870 redoMenuItem.setLabel("Redo");
\r
1871 redoMenuItem.addActionListener(this);
\r
1872 conservationMenuItem.setLabel("by Conservation");
\r
1873 conservationMenuItem.addItemListener(this);
\r
1874 noColourmenuItem.setLabel("None");
\r
1875 noColourmenuItem.addActionListener(this);
\r
1876 wrapMenuItem.setLabel("Wrap");
\r
1877 wrapMenuItem.addItemListener(this);
\r
1878 renderGapsMenuItem.setLabel("Show Gaps");
\r
1879 renderGapsMenuItem.setState(true);
\r
1880 renderGapsMenuItem.addItemListener(this);
\r
1881 findMenuItem.setLabel("Find...");
\r
1882 findMenuItem.addActionListener(this);
\r
1883 searchMenu.setLabel("Search");
\r
1885 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
1886 abovePIDThreshold.addItemListener(this);
\r
1887 nucleotideColour.setLabel("Nucleotide");
\r
1888 nucleotideColour.addActionListener(this);
\r
1889 deleteGroups.setLabel("Undefine Groups");
\r
1890 deleteGroups.addActionListener(this);
\r
1891 copy.setLabel("Copy");
\r
1892 copy.addActionListener(this);
\r
1893 cut.setLabel("Cut");
\r
1894 cut.addActionListener(this);
\r
1895 delete.setLabel("Delete");
\r
1896 delete.addActionListener(this);
\r
1897 pasteMenu.setLabel("Paste");
\r
1898 pasteNew.setLabel("To New Alignment");
\r
1899 pasteNew.addActionListener(this);
\r
1900 pasteThis.setLabel("Add To This Alignment");
\r
1901 pasteThis.addActionListener(this);
\r
1902 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
1903 applyToAllGroups.setState(true);
\r
1904 applyToAllGroups.addItemListener(this);
\r
1905 font.setLabel("Font...");
\r
1906 font.addActionListener(this);
\r
1907 scaleAbove.setLabel("Scale Above");
\r
1908 scaleAbove.setState(true);
\r
1909 scaleAbove.setEnabled(false);
\r
1910 scaleAbove.addItemListener(this);
\r
1911 scaleLeft.setEnabled(false);
\r
1912 scaleLeft.setState(true);
\r
1913 scaleLeft.setLabel("Scale Left");
\r
1914 scaleLeft.addItemListener(this);
\r
1915 scaleRight.setEnabled(false);
\r
1916 scaleRight.setState(true);
\r
1917 scaleRight.setLabel("Scale Right");
\r
1918 scaleRight.addItemListener(this);
\r
1919 modifyPID.setLabel("Modify Identity Threshold...");
\r
1920 modifyPID.addActionListener(this);
\r
1921 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
1922 modifyConservation.addActionListener(this);
\r
1923 sortByTreeMenu.setLabel("By Tree Order");
\r
1924 sort.setLabel("Sort");
\r
1925 calculate.setLabel("Calculate Tree");
\r
1926 inputText.setLabel("Input from textbox");
\r
1927 inputText.addActionListener(this);
\r
1929 helpMenu.setLabel("Help");
\r
1930 documentation.setLabel("Documentation");
\r
1931 documentation.addActionListener(this);
\r
1933 about.setLabel("About...");
\r
1934 about.addActionListener(this);
\r
1935 seqLimits.setState(true);
\r
1936 seqLimits.setLabel("Show Sequence Limits");
\r
1937 seqLimits.addItemListener(this);
\r
1938 featureSettings.setLabel("Feature Settings...");
\r
1939 featureSettings.addActionListener(this);
\r
1940 sequenceFeatures.setLabel("Sequence Features");
\r
1941 sequenceFeatures.addItemListener(this);
\r
1942 sequenceFeatures.setState(true);
\r
1944 alignFrameMenuBar.add(fileMenu);
\r
1945 alignFrameMenuBar.add(editMenu);
\r
1946 alignFrameMenuBar.add(searchMenu);
\r
1947 alignFrameMenuBar.add(viewMenu);
\r
1948 alignFrameMenuBar.add(colourMenu);
\r
1949 alignFrameMenuBar.add(calculateMenu);
\r
1950 alignFrameMenuBar.add(helpMenu);
\r
1951 fileMenu.add(inputText);
\r
1952 fileMenu.add(outputTextboxMenu);
\r
1953 fileMenu.addSeparator();
\r
1954 fileMenu.add(closeMenuItem);
\r
1955 editMenu.add(undoMenuItem);
\r
1956 editMenu.add(redoMenuItem);
\r
1957 editMenu.add(cut);
\r
1958 editMenu.add(copy);
\r
1959 editMenu.add(pasteMenu);
\r
1960 editMenu.add(delete);
\r
1961 editMenu.addSeparator();
\r
1962 editMenu.add(selectAllSequenceMenuItem);
\r
1963 editMenu.add(deselectAllSequenceMenuItem);
\r
1964 editMenu.add(invertSequenceMenuItem);
\r
1965 editMenu.add(deleteGroups);
\r
1966 editMenu.addSeparator();
\r
1967 editMenu.add(remove2LeftMenuItem);
\r
1968 editMenu.add(remove2RightMenuItem);
\r
1969 editMenu.add(removeGappedColumnMenuItem);
\r
1970 editMenu.add(removeAllGapsMenuItem);
\r
1971 editMenu.add(removeRedundancyMenuItem);
\r
1972 searchMenu.add(findMenuItem);
\r
1973 viewMenu.add(font);
\r
1974 viewMenu.addSeparator();
\r
1975 viewMenu.add(seqLimits);
\r
1976 viewMenu.addSeparator();
\r
1977 viewMenu.add(wrapMenuItem);
\r
1978 viewMenu.add(scaleAbove);
\r
1979 viewMenu.add(scaleLeft);
\r
1980 viewMenu.add(scaleRight);
\r
1981 viewMenu.addSeparator();
\r
1982 viewMenu.add(viewBoxesMenuItem);
\r
1983 viewMenu.add(viewTextMenuItem);
\r
1984 viewMenu.add(colourTextMenuItem);
\r
1985 viewMenu.add(renderGapsMenuItem);
\r
1986 viewMenu.add(annotationPanelMenuItem);
\r
1987 viewMenu.addSeparator();
\r
1988 viewMenu.add(overviewMenuItem);
\r
1989 colourMenu.add(applyToAllGroups);
\r
1990 colourMenu.addSeparator();
\r
1991 colourMenu.add(noColourmenuItem);
\r
1992 colourMenu.add(clustalColour);
\r
1993 colourMenu.add(BLOSUM62Colour);
\r
1994 colourMenu.add(PIDColour);
\r
1995 colourMenu.add(zappoColour);
\r
1996 colourMenu.add(taylorColour);
\r
1997 colourMenu.add(hydrophobicityColour);
\r
1998 colourMenu.add(helixColour);
\r
1999 colourMenu.add(strandColour);
\r
2000 colourMenu.add(turnColour);
\r
2001 colourMenu.add(buriedColour);
\r
2002 colourMenu.add(nucleotideColour);
\r
2003 colourMenu.add(userDefinedColour);
\r
2004 colourMenu.addSeparator();
\r
2005 colourMenu.add(conservationMenuItem);
\r
2006 colourMenu.add(modifyConservation);
\r
2007 colourMenu.add(abovePIDThreshold);
\r
2008 colourMenu.add(modifyPID);
\r
2009 calculateMenu.add(sort);
\r
2010 calculateMenu.add(calculate);
\r
2011 calculateMenu.addSeparator();
\r
2012 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
2013 calculateMenu.add(PCAMenuItem);
\r
2014 this.add(statusBar, BorderLayout.SOUTH);
\r
2015 pasteMenu.add(pasteNew);
\r
2016 pasteMenu.add(pasteThis);
\r
2017 sort.add(sortIDMenuItem);
\r
2018 sort.add(sortByTreeMenu);
\r
2019 sort.add(sortGroupMenuItem);
\r
2020 sort.add(sortPairwiseMenuItem);
\r
2021 calculate.add(averageDistanceTreeMenuItem);
\r
2022 calculate.add(neighbourTreeMenuItem);
\r
2023 calculate.add(avDistanceTreeBlosumMenuItem);
\r
2024 calculate.add(njTreeBlosumMenuItem);
\r
2025 helpMenu.add(documentation);
\r
2026 helpMenu.add(about);
\r
2029 public void setEmbedded()
\r
2032 embeddedMenu = new Panel();
\r
2033 embeddedEdit = new Label();
\r
2034 embeddedSearch = new Label();
\r
2035 embeddedView = new Label();
\r
2036 embeddedColour = new Label();
\r
2037 embeddedFile = new Label();
\r
2038 embeddedHelp = new Label();
\r
2039 embeddedCalculate = new Label();
\r
2040 flowLayout1 = new FlowLayout();
\r
2041 embeddedMenu.setBackground(Color.lightGray);
\r
2042 embeddedMenu.setLayout(flowLayout1);
\r
2043 embeddedEdit.setText("Edit");
\r
2044 embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2045 embeddedSearch.setText("Search");
\r
2046 embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2047 embeddedView.setText("View");
\r
2048 embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2049 embeddedColour.setText("Colour");
\r
2050 embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2051 embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2052 embeddedFile.setText("File");
\r
2053 embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2054 embeddedHelp.setText("Help");
\r
2055 embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2056 embeddedCalculate.setText("Calculate");
\r
2057 embeddedMenu.add(embeddedFile);
\r
2058 embeddedMenu.add(embeddedEdit);
\r
2059 embeddedMenu.add(embeddedSearch);
\r
2060 embeddedMenu.add(embeddedView);
\r
2061 embeddedMenu.add(embeddedColour);
\r
2062 embeddedMenu.add(embeddedCalculate);
\r
2063 embeddedMenu.add(embeddedHelp);
\r
2064 flowLayout1.setAlignment(FlowLayout.LEFT);
\r
2065 flowLayout1.setHgap(2);
\r
2066 flowLayout1.setVgap(0);
\r
2067 embeddedFile.addMouseListener(this);
\r
2068 embeddedEdit.addMouseListener(this);
\r
2069 embeddedSearch.addMouseListener(this);
\r
2070 embeddedView.addMouseListener(this);
\r
2071 embeddedColour.addMouseListener(this);
\r
2072 embeddedCalculate.addMouseListener(this);
\r
2073 embeddedHelp.addMouseListener(this);
\r
2075 setVisible(false);
\r
2076 fileMenu.remove(closeMenuItem);
\r
2077 fileMenu.remove(2); // Seperator
\r
2079 applet.setLayout(new BorderLayout());
\r
2080 applet.add(embeddedMenu, BorderLayout.NORTH);
\r
2081 applet.add(statusBar, BorderLayout.SOUTH);
\r
2082 applet.validate();
\r
2085 alignPanel.setSize(applet.size().width, applet.size().height
\r
2086 - embeddedMenu.HEIGHT - statusBar.HEIGHT);
\r
2088 applet.add(alignPanel, BorderLayout.CENTER);
\r
2089 applet.validate();
\r
2094 PopupMenu filePopup, editPopup, searchPopup,
\r
2095 viewPopup, colourPopup, calculatePopup, helpPopup;
\r
2096 MenuItem featureSettings = new MenuItem();
\r
2097 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
2099 public void mousePressed(MouseEvent evt)
\r
2101 PopupMenu popup = null;
\r
2102 Label source = (Label)evt.getSource();
\r
2103 if(source==embeddedFile)
\r
2105 popup = filePopup = genPopupMenu(filePopup, fileMenu);
\r
2107 else if(source==embeddedEdit)
\r
2109 popup = editPopup = genPopupMenu(editPopup, editMenu);
\r
2111 else if(source==embeddedSearch)
\r
2113 popup = searchPopup = genPopupMenu(searchPopup, searchMenu);
\r
2115 else if(source==embeddedView)
\r
2117 popup = viewPopup = genPopupMenu(viewPopup, viewMenu);
\r
2119 else if(source==embeddedColour)
\r
2121 popup = colourPopup = genPopupMenu(colourPopup, colourMenu);
\r
2123 else if(source==embeddedCalculate)
\r
2125 popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);
\r
2127 else if(source==embeddedHelp)
\r
2129 popup = helpPopup = genPopupMenu(helpPopup, helpMenu);
\r
2132 embeddedMenu.add(popup);
\r
2133 popup.show(embeddedMenu,
\r
2134 source.getBounds().x,
\r
2135 source.getBounds().y + source.getBounds().getSize().height);
\r
2138 PopupMenu genPopupMenu(PopupMenu popup, Menu original)
\r
2144 popup = new PopupMenu();
\r
2145 int m, mSize = original.getItemCount();
\r
2146 for(m=0; m<mSize; m++)
\r
2148 popup.add(original.getItem(m));
\r
2155 public void mouseClicked(MouseEvent evt)
\r
2157 public void mouseReleased(MouseEvent evt)
\r
2159 public void mouseEntered(MouseEvent evt)
\r
2161 public void mouseExited(MouseEvent evt)
\r