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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175 String featureGroup = null, groupLink = null;
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176 Hashtable typeLink = new Hashtable();
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178 while ( (line = in.readLine()) != null)
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180 st = new StringTokenizer(line, "\t");
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181 if(!st.hasMoreTokens())
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184 if (st.countTokens() < 4)
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186 type = st.nextToken();
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187 if(type.equalsIgnoreCase("startgroup"))
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189 featureGroup = st.nextToken();
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190 if (st.hasMoreElements())
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192 groupLink = st.nextToken();
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193 fr.addFeatureLink(featureGroup, groupLink);
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196 else if(type.equalsIgnoreCase("endgroup"))
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198 //We should check whether this is the current group,
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199 //but at present theres no way of showing more than 1 group
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201 featureGroup = null;
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206 UserColourScheme ucs = new UserColourScheme(st.nextToken());
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207 fr.setColour(type, ucs.findColour("A"));
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208 if (st.hasMoreElements())
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210 String link = st.nextToken();
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211 typeLink.put(type, link);
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212 fr.addFeatureLink(type, link);
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219 while (st.hasMoreElements())
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221 desc = st.nextToken();
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223 token = st.nextToken();
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224 if (!token.equals("ID_NOT_SPECIFIED"))
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226 index = viewport.alignment.findIndex(viewport.alignment.findName(
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232 index = Integer.parseInt(st.nextToken());
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235 start = Integer.parseInt(st.nextToken());
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236 end = Integer.parseInt(st.nextToken());
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238 seq = viewport.alignment.getSequenceAt(index);
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240 type = st.nextToken();
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242 if(fr.getColour(type)==null)
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244 // Probably the old style groups file
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245 UserColourScheme ucs = new UserColourScheme(type);
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246 fr.setColour(type, ucs.findColour("A"));
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249 sf = new SequenceFeature(type, desc, start, end, 0f, featureGroup);
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250 seq.addSequenceFeature(sf);
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252 if(groupLink!=null)
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254 sf.addLink(groupLink);
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255 sf.description += "%LINK%";
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257 if(typeLink.containsKey(type))
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259 sf.addLink(typeLink.get(type).toString());
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260 sf.description += "%LINK%";
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263 parseDescriptionHTML(sf);
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267 viewport.showSequenceFeatures = true;
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268 sequenceFeatures.setState(true);
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270 alignPanel.repaint();
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273 catch (Exception ex)
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275 ex.printStackTrace();
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276 System.out.println("Error parsing groups file: " + ex +"\n"+line);
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280 void parseDescriptionHTML(SequenceFeature sf)
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282 StringBuffer sb = new StringBuffer();
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283 StringTokenizer st = new StringTokenizer(sf.getDescription(), "<");
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284 String token, link;
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285 while(st.hasMoreElements())
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287 token = st.nextToken("<>");
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288 if(token.equalsIgnoreCase("html") || token.startsWith("/"))
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291 if(token.startsWith("a href="))
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293 link = token.substring(token.indexOf("\"")+1, token.length()-1);
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294 String label = st.nextToken("<>");
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295 sf.addLink(label+"|"+link);
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296 sb.append(label+"%LINK%");
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298 else if(token.equalsIgnoreCase("br"))
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304 sf.description = sb.toString();
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307 public void keyPressed(KeyEvent evt)
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309 if (viewport.cursorMode
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310 && evt.getKeyCode() >= KeyEvent.VK_0
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311 && evt.getKeyCode() <= KeyEvent.VK_9)
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313 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
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316 switch (evt.getKeyCode())
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318 case 27: // escape key
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319 deselectAllSequenceMenuItem_actionPerformed();
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321 case KeyEvent.VK_X:
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322 if (evt.isControlDown() || evt.isMetaDown())
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324 cut_actionPerformed();
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327 case KeyEvent.VK_C:
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328 if (viewport.cursorMode)
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330 alignPanel.seqPanel.setCursorColumn();
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332 if (evt.isControlDown() || evt.isMetaDown())
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334 copy_actionPerformed();
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337 case KeyEvent.VK_V:
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338 if (evt.isControlDown() || evt.isMetaDown())
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343 case KeyEvent.VK_A:
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344 if (evt.isControlDown() || evt.isMetaDown())
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346 selectAllSequenceMenuItem_actionPerformed();
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349 case KeyEvent.VK_DOWN:
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350 if(viewport.cursorMode)
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352 alignPanel.seqPanel.moveCursor(0,1);
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355 moveSelectedSequences(false);
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358 case KeyEvent.VK_UP:
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359 if (viewport.cursorMode)
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361 alignPanel.seqPanel.moveCursor(0,-1);
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364 moveSelectedSequences(true);
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367 case KeyEvent.VK_LEFT:
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368 if(viewport.cursorMode)
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370 alignPanel.seqPanel.moveCursor(-1,0);
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374 case KeyEvent.VK_RIGHT:
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375 if (viewport.cursorMode)
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377 alignPanel.seqPanel.moveCursor(1,0);
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380 case KeyEvent.VK_SPACE:
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381 if(viewport.cursorMode)
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383 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown());
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387 case KeyEvent.VK_DELETE:
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388 case KeyEvent.VK_BACK_SPACE:
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389 if(viewport.cursorMode)
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391 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown());
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395 cut_actionPerformed();
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396 alignPanel.seqPanel.seqCanvas.repaint();
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400 case KeyEvent.VK_S:
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401 if(viewport.cursorMode)
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403 alignPanel.seqPanel.setCursorRow();
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406 case KeyEvent.VK_P:
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407 if(viewport.cursorMode)
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409 alignPanel.seqPanel.setCursorPosition();
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413 case KeyEvent.VK_ENTER:
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414 case KeyEvent.VK_COMMA:
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415 if(viewport.cursorMode)
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417 alignPanel.seqPanel.setCursorRowAndColumn();
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421 case KeyEvent.VK_Q:
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422 if(viewport.cursorMode)
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424 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
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427 case KeyEvent.VK_M:
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428 if(viewport.cursorMode)
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430 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
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434 case KeyEvent.VK_F2:
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435 viewport.cursorMode = ! viewport.cursorMode;
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436 statusBar.setText("Keyboard editing mode is "+
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437 (viewport.cursorMode ? "on" : "off"));
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438 if(viewport.cursorMode)
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440 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
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441 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
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443 alignPanel.seqPanel.seqCanvas.repaint();
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446 case KeyEvent.VK_F:
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447 if (evt.isControlDown())
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449 findMenuItem_actionPerformed();
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454 public void keyReleased(KeyEvent evt)
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456 public void keyTyped(KeyEvent evt)
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459 public void itemStateChanged(ItemEvent evt)
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461 if(evt.getSource()==colourTextMenuItem)
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462 colourTextMenuItem_actionPerformed();
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463 else if(evt.getSource()==wrapMenuItem)
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464 wrapMenuItem_actionPerformed();
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465 else if(evt.getSource()==scaleAbove)
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466 scaleAbove_actionPerformed();
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467 else if(evt.getSource()==scaleLeft)
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468 scaleLeft_actionPerformed();
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469 else if(evt.getSource()==scaleRight)
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470 scaleRight_actionPerformed();
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471 else if(evt.getSource()==seqLimits)
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472 seqLimits_itemStateChanged();
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473 else if(evt.getSource()==viewBoxesMenuItem)
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474 viewBoxesMenuItem_actionPerformed();
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475 else if(evt.getSource()==viewTextMenuItem)
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476 viewTextMenuItem_actionPerformed();
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477 else if(evt.getSource()==renderGapsMenuItem)
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478 renderGapsMenuItem_actionPerformed();
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479 else if(evt.getSource()==annotationPanelMenuItem)
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480 annotationPanelMenuItem_actionPerformed();
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481 else if(evt.getSource()==sequenceFeatures)
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483 viewport.showSequenceFeatures(sequenceFeatures.getState());
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484 alignPanel.seqPanel.seqCanvas.repaint();
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486 else if(evt.getSource()==conservationMenuItem)
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487 conservationMenuItem_actionPerformed();
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488 else if(evt.getSource()==abovePIDThreshold)
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489 abovePIDThreshold_actionPerformed();
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490 else if(evt.getSource()==applyToAllGroups)
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491 applyToAllGroups_actionPerformed();
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492 else if(evt.getSource()==autoCalculate)
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493 viewport.autocalculateConsensus = autoCalculate.getState();
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495 public void actionPerformed(ActionEvent evt)
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497 if(evt.getSource()==inputText)
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498 inputText_actionPerformed();
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499 else if(evt.getSource()==loadTree)
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500 loadTree_actionPerformed();
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501 else if(evt.getSource()==closeMenuItem)
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502 closeMenuItem_actionPerformed();
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503 else if(evt.getSource()==copy)
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504 copy_actionPerformed();
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505 else if(evt.getSource()==undoMenuItem)
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506 undoMenuItem_actionPerformed();
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507 else if(evt.getSource()==redoMenuItem)
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508 redoMenuItem_actionPerformed();
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509 else if(evt.getSource()==inputText)
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510 inputText_actionPerformed();
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511 else if(evt.getSource()==closeMenuItem)
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512 closeMenuItem_actionPerformed();
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513 else if(evt.getSource()==undoMenuItem)
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514 undoMenuItem_actionPerformed();
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515 else if(evt.getSource()==redoMenuItem)
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516 redoMenuItem_actionPerformed();
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517 else if(evt.getSource()==copy)
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518 copy_actionPerformed();
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519 else if(evt.getSource()==pasteNew)
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520 pasteNew_actionPerformed();
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521 else if(evt.getSource()==pasteThis)
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522 pasteThis_actionPerformed();
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523 else if(evt.getSource()==cut)
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524 cut_actionPerformed();
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525 else if(evt.getSource()==delete)
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526 delete_actionPerformed();
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527 else if(evt.getSource()==deleteGroups)
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528 deleteGroups_actionPerformed();
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529 else if(evt.getSource()==selectAllSequenceMenuItem)
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530 selectAllSequenceMenuItem_actionPerformed();
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531 else if(evt.getSource()==deselectAllSequenceMenuItem)
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532 deselectAllSequenceMenuItem_actionPerformed();
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533 else if(evt.getSource()==invertSequenceMenuItem)
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534 invertSequenceMenuItem_actionPerformed();
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535 else if(evt.getSource()==remove2LeftMenuItem)
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536 remove2LeftMenuItem_actionPerformed();
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537 else if(evt.getSource()==remove2RightMenuItem)
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538 remove2RightMenuItem_actionPerformed();
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539 else if(evt.getSource()==removeGappedColumnMenuItem)
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540 removeGappedColumnMenuItem_actionPerformed();
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541 else if(evt.getSource()==removeAllGapsMenuItem)
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542 removeAllGapsMenuItem_actionPerformed();
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543 else if(evt.getSource()==findMenuItem)
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544 findMenuItem_actionPerformed();
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545 else if(evt.getSource()==font)
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546 font_actionPerformed();
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547 else if(evt.getSource()==featureSettings)
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548 featureSettings_actionPerformed();
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549 else if(evt.getSource()==overviewMenuItem)
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550 overviewMenuItem_actionPerformed();
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551 else if(evt.getSource()==noColourmenuItem)
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552 noColourmenuItem_actionPerformed();
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553 else if(evt.getSource()==clustalColour)
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554 clustalColour_actionPerformed();
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555 else if(evt.getSource()==zappoColour)
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556 zappoColour_actionPerformed();
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557 else if(evt.getSource()==taylorColour)
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558 taylorColour_actionPerformed();
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559 else if(evt.getSource()==hydrophobicityColour)
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560 hydrophobicityColour_actionPerformed();
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561 else if(evt.getSource()==helixColour)
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562 helixColour_actionPerformed();
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563 else if(evt.getSource()==strandColour)
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564 strandColour_actionPerformed();
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565 else if(evt.getSource()==turnColour)
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566 turnColour_actionPerformed();
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567 else if(evt.getSource()==buriedColour)
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568 buriedColour_actionPerformed();
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569 else if(evt.getSource()==nucleotideColour)
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570 nucleotideColour_actionPerformed();
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571 else if(evt.getSource()==modifyPID)
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572 modifyPID_actionPerformed();
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573 else if(evt.getSource()==modifyConservation)
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574 modifyConservation_actionPerformed();
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575 else if(evt.getSource()==userDefinedColour)
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576 userDefinedColour_actionPerformed();
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577 else if(evt.getSource()==PIDColour)
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578 PIDColour_actionPerformed();
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579 else if(evt.getSource()==BLOSUM62Colour)
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580 BLOSUM62Colour_actionPerformed();
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581 else if(evt.getSource()==annotationColour)
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582 new AnnotationColourChooser(viewport, alignPanel);
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583 else if(evt.getSource()==sortPairwiseMenuItem)
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584 sortPairwiseMenuItem_actionPerformed();
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585 else if(evt.getSource()==sortIDMenuItem)
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586 sortIDMenuItem_actionPerformed();
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587 else if(evt.getSource()==sortGroupMenuItem)
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588 sortGroupMenuItem_actionPerformed();
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589 else if(evt.getSource()==removeRedundancyMenuItem)
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590 removeRedundancyMenuItem_actionPerformed();
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591 else if(evt.getSource()==pairwiseAlignmentMenuItem)
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592 pairwiseAlignmentMenuItem_actionPerformed();
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593 else if(evt.getSource()==PCAMenuItem)
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594 PCAMenuItem_actionPerformed();
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595 else if(evt.getSource()==averageDistanceTreeMenuItem)
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596 averageDistanceTreeMenuItem_actionPerformed();
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597 else if(evt.getSource()==neighbourTreeMenuItem)
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598 neighbourTreeMenuItem_actionPerformed();
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599 else if(evt.getSource()==njTreeBlosumMenuItem)
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600 njTreeBlosumMenuItem_actionPerformed();
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601 else if(evt.getSource()==avDistanceTreeBlosumMenuItem)
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602 avTreeBlosumMenuItem_actionPerformed();
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603 else if(evt.getSource()==documentation)
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604 documentation_actionPerformed();
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605 else if(evt.getSource()==about)
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606 about_actionPerformed();
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610 public void inputText_actionPerformed()
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612 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
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613 Frame frame = new Frame();
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615 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
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618 protected void outputText_actionPerformed(ActionEvent e)
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620 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
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621 Frame frame = new Frame();
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623 jalview.bin.JalviewLite.addFrame(frame,
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624 "Alignment output - " + e.getActionCommand(),
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626 cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
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627 viewport.getAlignment().getSequences(),
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628 viewport.showJVSuffix));
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631 public void closeMenuItem_actionPerformed()
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633 PaintRefresher.components.remove(viewport.alignment);
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634 if(PaintRefresher.components.size()==0 && applet==null)
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640 Stack historyList = new Stack();
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641 Stack redoList = new Stack();
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643 void updateEditMenuBar()
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645 if (historyList.size() > 0)
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647 undoMenuItem.setEnabled(true);
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648 HistoryItem hi = (HistoryItem) historyList.peek();
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649 undoMenuItem.setLabel("Undo " + hi.getDescription());
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653 undoMenuItem.setEnabled(false);
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654 undoMenuItem.setLabel("Undo");
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657 if (redoList.size() > 0)
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659 redoMenuItem.setEnabled(true);
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660 HistoryItem hi = (HistoryItem) redoList.peek();
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661 redoMenuItem.setLabel("Redo " + hi.getDescription());
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665 redoMenuItem.setEnabled(false);
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666 redoMenuItem.setLabel("Redo");
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670 public void addHistoryItem(HistoryItem hi)
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672 historyList.push(hi);
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673 updateEditMenuBar();
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676 protected void undoMenuItem_actionPerformed()
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678 HistoryItem hi = (HistoryItem) historyList.pop();
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679 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
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680 HistoryItem.HIDE));
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681 restoreHistoryItem(hi);
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682 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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685 protected void redoMenuItem_actionPerformed()
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687 HistoryItem hi = (HistoryItem) redoList.pop();
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688 restoreHistoryItem(hi);
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689 updateEditMenuBar();
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690 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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693 // used by undo and redo
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694 void restoreHistoryItem(HistoryItem hi)
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698 updateEditMenuBar();
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700 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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703 public void moveSelectedSequences(boolean up)
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705 SequenceGroup sg = viewport.getSelectionGroup();
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713 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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715 SequenceI seq = viewport.alignment.getSequenceAt(i);
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716 if (!sg.sequences.contains(seq))
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721 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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722 if (sg.sequences.contains(temp))
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727 viewport.alignment.getSequences().setElementAt(temp, i);
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728 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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733 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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735 SequenceI seq = viewport.alignment.getSequenceAt(i);
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736 if (!sg.sequences.contains(seq))
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741 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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742 if (sg.sequences.contains(temp))
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747 viewport.alignment.getSequences().setElementAt(temp, i);
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748 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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752 alignPanel.repaint();
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755 StringBuffer copiedSequences;
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756 protected void copy_actionPerformed()
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758 if (viewport.getSelectionGroup() == null)
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763 SequenceGroup sg = viewport.getSelectionGroup();
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764 copiedSequences = new StringBuffer();
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765 Hashtable orderedSeqs = new Hashtable();
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766 for (int i = 0; i < sg.getSize(); i++)
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768 SequenceI seq = sg.getSequenceAt(i);
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769 int index = viewport.alignment.findIndex(seq);
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770 orderedSeqs.put(index + "", seq);
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773 int index = 0, startRes, endRes;
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776 for (int i = 0; i < sg.getSize(); i++)
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778 SequenceI seq = null;
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780 while (seq == null)
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782 if (orderedSeqs.containsKey(index + ""))
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784 seq = (SequenceI) orderedSeqs.get(index + "");
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796 //Returns residue following index if gap
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797 startRes = seq.findPosition(sg.getStartRes());
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800 //Need to find the residue preceeding index if gap
\r
803 for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
\r
805 ch = seq.getCharAt(j);
\r
806 if (!jalview.util.Comparison.isGap( (ch)))
\r
814 endRes += seq.getStart() -1;
\r
817 copiedSequences.append(seq.getName() + "\t" +
\r
820 seq.getSequence(sg.getStartRes(),
\r
821 sg.getEndRes() + 1) + "\n");
\r
826 protected void pasteNew_actionPerformed()
\r
831 protected void pasteThis_actionPerformed()
\r
833 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
\r
834 HistoryItem.PASTE));
\r
838 void paste(boolean newAlignment)
\r
842 if (copiedSequences == null)
\r
847 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
848 Vector seqs = new Vector();
\r
849 while (st.hasMoreElements())
\r
851 String name = st.nextToken();
\r
852 int start = Integer.parseInt(st.nextToken());
\r
853 int end = Integer.parseInt(st.nextToken());
\r
854 Sequence sequence = new Sequence(name, st.nextToken(), start, end);
\r
858 viewport.alignment.addSequence(sequence);
\r
862 seqs.addElement(sequence);
\r
868 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
869 for (int i = 0; i < seqs.size(); i++)
\r
871 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
874 String newtitle = new String("Copied sequences");
\r
875 if (getTitle().startsWith("Copied sequences"))
\r
877 newtitle = getTitle();
\r
881 newtitle = newtitle.concat("- from " + getTitle());
\r
883 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
888 jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
\r
889 NEW_WINDOW_HEIGHT);
\r
893 viewport.setEndSeq(viewport.alignment.getHeight());
\r
894 viewport.alignment.getWidth();
\r
895 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
899 catch (Exception ex)
\r
900 {} // could be anything being pasted in here
\r
904 protected void cut_actionPerformed()
\r
906 copy_actionPerformed();
\r
907 delete_actionPerformed();
\r
910 protected void delete_actionPerformed()
\r
912 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
\r
913 HistoryItem.HIDE));
\r
914 if (viewport.getSelectionGroup() == null)
\r
920 SequenceGroup sg = viewport.getSelectionGroup();
\r
921 boolean allSequences = false;
\r
922 if(sg.sequences.size()==viewport.alignment.getHeight())
\r
923 allSequences = true;
\r
925 for (int i = 0; i < sg.sequences.size(); i++)
\r
927 SequenceI seq = sg.getSequenceAt(i);
\r
928 int index = viewport.getAlignment().findIndex(seq);
\r
929 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
\r
931 // If the cut affects all sequences, remove highlighted columns
\r
934 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
935 sg.getEndRes() + 1);
\r
939 if (seq.getSequence().length() < 1)
\r
941 viewport.getAlignment().deleteSequence(seq);
\r
945 viewport.getAlignment().getSequences().setElementAt(seq, index);
\r
949 viewport.setSelectionGroup(null);
\r
950 viewport.alignment.deleteGroup(sg);
\r
951 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
\r
952 if (viewport.getAlignment().getHeight() < 1)
\r
956 this.setVisible(false);
\r
958 catch (Exception ex)
\r
961 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
965 protected void deleteGroups_actionPerformed()
\r
967 viewport.alignment.deleteAllGroups();
\r
968 viewport.setSelectionGroup(null);
\r
970 alignPanel.repaint();
\r
973 public void selectAllSequenceMenuItem_actionPerformed()
\r
975 SequenceGroup sg = new SequenceGroup();
\r
976 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
978 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
980 sg.setEndRes(viewport.alignment.getWidth()-1);
\r
981 viewport.setSelectionGroup(sg);
\r
982 alignPanel.repaint();
\r
983 PaintRefresher.Refresh(null, viewport.alignment);
\r
986 public void deselectAllSequenceMenuItem_actionPerformed()
\r
988 if(viewport.cursorMode)
\r
990 alignPanel.seqPanel.keyboardNo1=null;
\r
991 alignPanel.seqPanel.keyboardNo2=null;
\r
993 viewport.setSelectionGroup(null);
\r
994 viewport.getColumnSelection().clear();
\r
995 viewport.setSelectionGroup(null);
\r
996 alignPanel.idPanel.idCanvas.searchResults = null;
\r
997 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
998 alignPanel.repaint();
\r
999 PaintRefresher.Refresh(null, viewport.alignment);
\r
1002 public void invertSequenceMenuItem_actionPerformed()
\r
1004 SequenceGroup sg = viewport.getSelectionGroup();
\r
1005 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1007 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1010 PaintRefresher.Refresh(null, viewport.alignment);
\r
1013 public void remove2LeftMenuItem_actionPerformed()
\r
1015 ColumnSelection colSel = viewport.getColumnSelection();
\r
1016 if (colSel.size() > 0)
\r
1018 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
\r
1019 HistoryItem.HIDE));
\r
1020 int min = colSel.getMin();
\r
1021 viewport.getAlignment().trimLeft(min);
\r
1022 colSel.compensateForEdit(0, min);
\r
1024 if (viewport.getSelectionGroup() != null)
\r
1026 viewport.getSelectionGroup().adjustForRemoveLeft(min);
\r
1029 Vector groups = viewport.alignment.getGroups();
\r
1030 for (int i = 0; i < groups.size(); i++)
\r
1032 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1033 if (!sg.adjustForRemoveLeft(min))
\r
1035 viewport.alignment.deleteGroup(sg);
\r
1038 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1042 public void remove2RightMenuItem_actionPerformed()
\r
1044 ColumnSelection colSel = viewport.getColumnSelection();
\r
1045 if (colSel.size() > 0)
\r
1047 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
\r
1048 HistoryItem.HIDE));
\r
1049 int max = colSel.getMax();
\r
1050 viewport.getAlignment().trimRight(max);
\r
1051 if (viewport.getSelectionGroup() != null)
\r
1053 viewport.getSelectionGroup().adjustForRemoveRight(max);
\r
1056 Vector groups = viewport.alignment.getGroups();
\r
1057 for (int i = 0; i < groups.size(); i++)
\r
1059 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1060 if (!sg.adjustForRemoveRight(max))
\r
1062 viewport.alignment.deleteGroup(sg);
\r
1065 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1070 public void removeGappedColumnMenuItem_actionPerformed()
\r
1072 addHistoryItem(new HistoryItem("Remove Gapped Columns",
\r
1073 viewport.alignment,
\r
1074 HistoryItem.HIDE));
\r
1076 //This is to maintain viewport position on first residue
\r
1077 //of first sequence
\r
1078 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1079 int startRes = seq.findPosition(viewport.startRes);
\r
1081 viewport.getAlignment().removeGaps();
\r
1083 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1085 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1088 public void removeAllGapsMenuItem_actionPerformed()
\r
1090 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
\r
1091 HistoryItem.HIDE));
\r
1093 //This is to maintain viewport position on first residue
\r
1094 //of first sequence
\r
1095 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1096 int startRes = seq.findPosition(viewport.startRes);
\r
1098 SequenceI current;
\r
1103 int start=0, end = viewport.alignment.getWidth();
\r
1105 if (viewport.getSelectionGroup() != null
\r
1106 && viewport.getSelectionGroup().sequences != null
\r
1107 && viewport.getSelectionGroup().sequences.size()>0)
\r
1109 seqs = viewport.getSelectionGroup().sequences;
\r
1110 start = viewport.getSelectionGroup().getStartRes();
\r
1111 end = viewport.getSelectionGroup().getEndRes()+1;
\r
1114 seqs = viewport.alignment.getSequences();
\r
1116 for (int i = 0; i < seqs.size(); i++)
\r
1118 current = (SequenceI) seqs.elementAt(i);
\r
1119 jSize = current.getLength();
\r
1121 // Removing a range is much quicker than removing gaps
\r
1122 // one by one for long sequences
\r
1124 int rangeStart=-1, rangeEnd=-1;
\r
1128 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
\r
1130 if(rangeStart==-1)
\r
1145 current.deleteChars(rangeStart, rangeEnd);
\r
1146 j-=rangeEnd-rangeStart;
\r
1147 jSize-=rangeEnd-rangeStart;
\r
1155 while (j < end && j < jSize);
\r
1158 current.deleteChars(rangeStart, rangeEnd);
\r
1161 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1162 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1165 public void alignmentChanged()
\r
1167 viewport.alignment.padGaps();
\r
1168 if(viewport.autocalculateConsensus)
\r
1170 viewport.updateConsensus();
\r
1171 viewport.updateConservation();
\r
1174 resetAllColourSchemes();
\r
1175 if(alignPanel.overviewPanel!=null)
\r
1176 alignPanel.overviewPanel.updateOverviewImage();
\r
1178 viewport.alignment.adjustSequenceAnnotations();
\r
1179 alignPanel.repaint();
\r
1182 void resetAllColourSchemes()
\r
1184 ColourSchemeI cs = viewport.globalColourScheme;
\r
1187 if (cs instanceof ClustalxColourScheme)
\r
1189 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
\r
1190 resetClustalX(viewport.alignment.getSequences(),
\r
1191 viewport.alignment.getWidth());
\r
1194 cs.setConsensus(viewport.vconsensus);
\r
1195 if (cs.conservationApplied())
\r
1197 Alignment al = (Alignment) viewport.alignment;
\r
1198 Conservation c = new Conservation("All",
\r
1199 ResidueProperties.propHash, 3,
\r
1200 al.getSequences(), 0,
\r
1201 al.getWidth() - 1);
\r
1203 c.verdict(false, viewport.ConsPercGaps);
\r
1205 cs.setConservation(c);
\r
1209 int s, sSize = viewport.alignment.getGroups().size();
\r
1210 for(s=0; s<sSize; s++)
\r
1212 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
\r
1213 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
\r
1215 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
\r
1217 sg.recalcConservation();
\r
1223 public void findMenuItem_actionPerformed()
\r
1225 new Finder(alignPanel);
\r
1228 public void font_actionPerformed()
\r
1230 new FontChooser(alignPanel);
\r
1234 public void seqLimits_itemStateChanged()
\r
1236 viewport.setShowJVSuffix(seqLimits.getState());
\r
1237 alignPanel.fontChanged();
\r
1238 alignPanel.repaint();
\r
1242 protected void colourTextMenuItem_actionPerformed()
\r
1244 viewport.setColourText(colourTextMenuItem.getState());
\r
1245 alignPanel.repaint();
\r
1248 protected void wrapMenuItem_actionPerformed()
\r
1250 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
1251 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
1252 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
1253 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
1254 scaleRight.setEnabled(wrapMenuItem.getState());
\r
1255 alignPanel.repaint();
\r
1258 protected void scaleAbove_actionPerformed()
\r
1260 viewport.setScaleAboveWrapped(scaleAbove.getState());
\r
1261 alignPanel.repaint();
\r
1264 protected void scaleLeft_actionPerformed()
\r
1266 viewport.setScaleLeftWrapped(scaleLeft.getState());
\r
1267 alignPanel.repaint();
\r
1270 protected void scaleRight_actionPerformed()
\r
1272 viewport.setScaleRightWrapped(scaleRight.getState());
\r
1273 alignPanel.repaint();
\r
1276 public void viewBoxesMenuItem_actionPerformed()
\r
1278 viewport.setShowBoxes(viewBoxesMenuItem.getState());
\r
1279 alignPanel.repaint();
\r
1282 public void viewTextMenuItem_actionPerformed()
\r
1284 viewport.setShowText(viewTextMenuItem.getState());
\r
1285 alignPanel.repaint();
\r
1288 protected void renderGapsMenuItem_actionPerformed()
\r
1290 viewport.setRenderGaps(renderGapsMenuItem.getState());
\r
1291 alignPanel.repaint();
\r
1294 public void annotationPanelMenuItem_actionPerformed()
\r
1296 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
\r
1297 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
\r
1300 public void featureSettings_actionPerformed()
\r
1302 new FeatureSettings(viewport, alignPanel);
\r
1305 public void overviewMenuItem_actionPerformed()
\r
1307 if (alignPanel.overviewPanel != null)
\r
1312 Frame frame = new Frame();
\r
1313 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1314 frame.add(overview);
\r
1315 // +50 must allow for applet frame window
\r
1316 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
1317 overview.preferredSize().width,
\r
1318 overview.preferredSize().height + 50);
\r
1321 frame.addWindowListener(new WindowAdapter()
\r
1323 public void windowClosing(WindowEvent e)
\r
1325 alignPanel.setOverviewPanel(null);
\r
1329 alignPanel.setOverviewPanel(overview);
\r
1333 protected void noColourmenuItem_actionPerformed()
\r
1335 changeColour(null);
\r
1338 public void clustalColour_actionPerformed()
\r
1340 abovePIDThreshold.setState(false);
\r
1341 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
\r
1342 viewport.alignment.getWidth()));
\r
1345 public void zappoColour_actionPerformed()
\r
1347 changeColour(new ZappoColourScheme());
\r
1350 public void taylorColour_actionPerformed()
\r
1352 changeColour(new TaylorColourScheme());
\r
1355 public void hydrophobicityColour_actionPerformed()
\r
1357 changeColour(new HydrophobicColourScheme());
\r
1360 public void helixColour_actionPerformed()
\r
1362 changeColour(new HelixColourScheme());
\r
1365 public void strandColour_actionPerformed()
\r
1367 changeColour(new StrandColourScheme());
\r
1370 public void turnColour_actionPerformed()
\r
1372 changeColour(new TurnColourScheme());
\r
1375 public void buriedColour_actionPerformed()
\r
1377 changeColour(new BuriedColourScheme());
\r
1380 public void nucleotideColour_actionPerformed()
\r
1382 changeColour(new NucleotideColourScheme());
\r
1385 protected void applyToAllGroups_actionPerformed()
\r
1387 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
\r
1390 void changeColour(ColourSchemeI cs)
\r
1392 int threshold = 0;
\r
1396 if (viewport.getAbovePIDThreshold())
\r
1398 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
\r
1400 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1402 viewport.setGlobalColourScheme(cs);
\r
1406 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1409 if (viewport.getConservationSelected())
\r
1412 Alignment al = (Alignment) viewport.alignment;
\r
1413 Conservation c = new Conservation("All",
\r
1414 ResidueProperties.propHash, 3,
\r
1415 al.getSequences(), 0,
\r
1416 al.getWidth() - 1);
\r
1419 c.verdict(false, viewport.ConsPercGaps);
\r
1421 cs.setConservation(c);
\r
1423 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1429 cs.setConservation(null);
\r
1432 cs.setConsensus(viewport.vconsensus);
\r
1435 viewport.setGlobalColourScheme(cs);
\r
1437 if (viewport.getColourAppliesToAllGroups())
\r
1439 Vector groups = viewport.alignment.getGroups();
\r
1440 for (int i = 0; i < groups.size(); i++)
\r
1442 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1449 if (cs instanceof ClustalxColourScheme)
\r
1451 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1457 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1459 catch (Exception ex)
\r
1461 ex.printStackTrace();
\r
1466 if (viewport.getAbovePIDThreshold()
\r
1467 || cs instanceof PIDColourScheme
\r
1468 || cs instanceof Blosum62ColourScheme)
\r
1470 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1471 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
1474 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1476 if (viewport.getConservationSelected())
\r
1478 Conservation c = new Conservation("Group",
\r
1479 ResidueProperties.propHash, 3,
\r
1481 viewport.alignment.getWidth() - 1);
\r
1483 c.verdict(false, viewport.ConsPercGaps);
\r
1484 sg.cs.setConservation(c);
\r
1488 sg.cs.setConservation(null);
\r
1489 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1496 if (alignPanel.getOverviewPanel() != null)
\r
1498 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1501 alignPanel.repaint();
\r
1506 protected void modifyPID_actionPerformed()
\r
1508 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1510 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
1512 SliderPanel.showPIDSlider();
\r
1516 protected void modifyConservation_actionPerformed()
\r
1518 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1520 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
1522 SliderPanel.showConservationSlider();
\r
1526 protected void conservationMenuItem_actionPerformed()
\r
1528 viewport.setConservationSelected(conservationMenuItem.getState());
\r
1530 viewport.setAbovePIDThreshold(false);
\r
1531 abovePIDThreshold.setState(false);
\r
1533 changeColour(viewport.getGlobalColourScheme());
\r
1535 modifyConservation_actionPerformed();
\r
1538 public void abovePIDThreshold_actionPerformed()
\r
1540 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
1542 conservationMenuItem.setState(false);
\r
1543 viewport.setConservationSelected(false);
\r
1545 changeColour(viewport.getGlobalColourScheme());
\r
1547 modifyPID_actionPerformed();
\r
1550 public void userDefinedColour_actionPerformed()
\r
1552 new UserDefinedColours(alignPanel, null);
\r
1555 public void PIDColour_actionPerformed()
\r
1557 changeColour(new PIDColourScheme());
\r
1560 public void BLOSUM62Colour_actionPerformed()
\r
1562 changeColour(new Blosum62ColourScheme());
\r
1565 public void sortPairwiseMenuItem_actionPerformed()
\r
1567 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1568 HistoryItem.SORT));
\r
1569 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1570 viewport.getAlignment().getSequenceAt(0));
\r
1571 alignPanel.repaint();
\r
1574 public void sortIDMenuItem_actionPerformed()
\r
1576 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1577 HistoryItem.SORT));
\r
1578 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1579 alignPanel.repaint();
\r
1582 public void sortGroupMenuItem_actionPerformed()
\r
1584 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1585 HistoryItem.SORT));
\r
1586 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1587 alignPanel.repaint();
\r
1591 public void removeRedundancyMenuItem_actionPerformed()
\r
1593 RedundancyPanel sp = new RedundancyPanel(alignPanel);
\r
1594 Frame frame = new Frame();
\r
1596 jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",
\r
1601 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
1603 if (viewport.getSelectionGroup().getSize() > 1)
\r
1605 Frame frame = new Frame();
\r
1606 frame.add(new PairwiseAlignPanel(alignPanel));
\r
1607 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
1611 public void PCAMenuItem_actionPerformed()
\r
1613 //are the sequences aligned?
\r
1614 if (!viewport.alignment.isAligned())
\r
1616 SequenceI current;
\r
1617 int Width = viewport.getAlignment().getWidth();
\r
1619 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1622 current = viewport.getAlignment().getSequenceAt(i);
\r
1624 if (current.getLength() < Width)
\r
1626 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1629 alignPanel.repaint();
\r
1632 if ( (viewport.getSelectionGroup() != null &&
\r
1633 viewport.getSelectionGroup().getSize() < 4 &&
\r
1634 viewport.getSelectionGroup().getSize() > 0)
\r
1635 || viewport.getAlignment().getHeight() < 4)
\r
1642 new PCAPanel(viewport);
\r
1644 catch (java.lang.OutOfMemoryError ex)
\r
1650 public void averageDistanceTreeMenuItem_actionPerformed()
\r
1652 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1655 public void neighbourTreeMenuItem_actionPerformed()
\r
1657 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1660 protected void njTreeBlosumMenuItem_actionPerformed()
\r
1662 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1665 protected void avTreeBlosumMenuItem_actionPerformed()
\r
1667 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1670 void NewTreePanel(String type, String pwType, String title)
\r
1672 //are the sequences aligned?
\r
1673 if (!viewport.alignment.isAligned())
\r
1675 SequenceI current;
\r
1676 int Width = viewport.getAlignment().getWidth();
\r
1678 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1681 current = viewport.getAlignment().getSequenceAt(i);
\r
1683 if (current.getLength() < Width)
\r
1685 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1688 alignPanel.repaint();
\r
1692 final TreePanel tp;
\r
1693 if (viewport.getSelectionGroup() != null &&
\r
1694 viewport.getSelectionGroup().getSize() > 3)
\r
1696 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
\r
1698 0, viewport.alignment.getWidth());
\r
1702 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1703 type, pwType, 0, viewport.alignment.getWidth());
\r
1706 addTreeMenuItem(tp, title);
\r
1708 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
1711 void loadTree_actionPerformed()
\r
1713 TreePanel tp = null;
\r
1715 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1716 cap.setText("Paste your Newick tree file here.");
\r
1717 cap.treeImport = true;
\r
1718 Frame frame = new Frame();
\r
1720 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
1723 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
1725 TreePanel tp = new TreePanel(viewport,
\r
1726 viewport.getAlignment().getSequences(),
\r
1727 tree, "From File - ", treeFile);
\r
1728 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
1729 addTreeMenuItem(tp, treeFile);
\r
1732 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1734 final MenuItem item = new MenuItem(title);
\r
1735 sortByTreeMenu.add(item);
\r
1736 item.addActionListener(new java.awt.event.ActionListener()
\r
1738 public void actionPerformed(ActionEvent evt)
\r
1740 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1741 HistoryItem.SORT));
\r
1742 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1743 alignPanel.repaint();
\r
1747 treePanel.addWindowListener(new WindowAdapter()
\r
1749 public void windowClosing(WindowEvent e)
\r
1751 sortByTreeMenu.remove(item);
\r
1756 protected void documentation_actionPerformed()
\r
1758 showURL("http://www.jalview.org/help.html", "HELP");
\r
1761 protected void about_actionPerformed()
\r
1764 class AboutPanel extends Canvas
\r
1767 public AboutPanel(String version)
\r
1768 { this.version = version; }
\r
1770 public void paint(Graphics g)
\r
1772 g.setColor(Color.white);
\r
1773 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1774 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1775 FontMetrics fm = g.getFontMetrics();
\r
1776 int fh = fm.getHeight();
\r
1778 g.setColor(Color.black);
\r
1779 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
1780 g.drawString("Jalview - Release "+version, 200, y += fh);
\r
1781 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1782 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
1784 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
1787 "For any issues relating to Jalview, email help@jalview.org", x,
\r
1789 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
1790 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
1792 g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh);
\r
1796 String version = "test";
\r
1797 java.net.URL url = getClass().getResource("/.build_properties");
\r
1802 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
1803 url.openStream()));
\r
1805 while ( (line = reader.readLine()) != null)
\r
1807 if (line.indexOf("VERSION") > -1)
\r
1809 version = line.substring(line.indexOf("=") + 1);
\r
1813 catch (Exception ex)
\r
1815 ex.printStackTrace();
\r
1820 Frame frame = new Frame();
\r
1821 frame.add(new AboutPanel(version));
\r
1822 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
\r
1826 public void showURL(String url, String target)
\r
1828 if (applet == null)
\r
1830 System.out.println("Not running as applet - no browser available.");
\r
1836 applet.getAppletContext().showDocument(new java.net.URL(url),
\r
1839 catch (Exception ex)
\r
1841 ex.printStackTrace();
\r
1847 //////////////////////////////////////////////////////////////////////////////////
\r
1848 //JBuilder Graphics here
\r
1850 protected MenuBar alignFrameMenuBar = new MenuBar();
\r
1851 protected Menu fileMenu = new Menu("File");
\r
1852 protected MenuItem loadTree = new MenuItem("Load Associated Tree");
\r
1853 protected MenuItem closeMenuItem = new MenuItem("Close");
\r
1854 protected Menu editMenu = new Menu("Edit");
\r
1855 protected Menu viewMenu = new Menu("View");
\r
1856 protected Menu colourMenu = new Menu("Colour");
\r
1857 protected Menu calculateMenu = new Menu("Calculate");
\r
1858 protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
1859 protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
1860 protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
1861 protected MenuItem remove2LeftMenuItem = new MenuItem();
\r
1862 protected MenuItem remove2RightMenuItem = new MenuItem();
\r
1863 protected MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
1864 protected MenuItem removeAllGapsMenuItem = new MenuItem();
\r
1865 protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
1866 protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
1867 protected MenuItem sortPairwiseMenuItem = new MenuItem();
\r
1868 protected MenuItem sortIDMenuItem = new MenuItem();
\r
1869 protected MenuItem sortGroupMenuItem = new MenuItem();
\r
1870 protected MenuItem removeRedundancyMenuItem = new MenuItem();
\r
1871 protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
1872 protected MenuItem PCAMenuItem = new MenuItem();
\r
1873 protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
1874 protected MenuItem neighbourTreeMenuItem = new MenuItem();
\r
1875 BorderLayout borderLayout1 = new BorderLayout();
\r
1876 public Label statusBar = new Label();
\r
1877 protected Menu outputTextboxMenu = new Menu();
\r
1878 protected MenuItem clustalColour = new MenuItem();
\r
1879 protected MenuItem zappoColour = new MenuItem();
\r
1880 protected MenuItem taylorColour = new MenuItem();
\r
1881 protected MenuItem hydrophobicityColour = new MenuItem();
\r
1882 protected MenuItem helixColour = new MenuItem();
\r
1883 protected MenuItem strandColour = new MenuItem();
\r
1884 protected MenuItem turnColour = new MenuItem();
\r
1885 protected MenuItem buriedColour = new MenuItem();
\r
1886 protected MenuItem userDefinedColour = new MenuItem();
\r
1887 protected MenuItem PIDColour = new MenuItem();
\r
1888 protected MenuItem BLOSUM62Colour = new MenuItem();
\r
1889 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
1890 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
1891 protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
1892 protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
1893 MenuItem overviewMenuItem = new MenuItem();
\r
1894 protected MenuItem undoMenuItem = new MenuItem();
\r
1895 protected MenuItem redoMenuItem = new MenuItem();
\r
1896 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
1897 MenuItem noColourmenuItem = new MenuItem();
\r
1898 protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
1899 protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
1900 MenuItem findMenuItem = new MenuItem();
\r
1901 Menu searchMenu = new Menu();
\r
1902 protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
1903 protected MenuItem nucleotideColour = new MenuItem();
\r
1904 MenuItem deleteGroups = new MenuItem();
\r
1905 MenuItem delete = new MenuItem();
\r
1906 MenuItem copy = new MenuItem();
\r
1907 MenuItem cut = new MenuItem();
\r
1908 Menu pasteMenu = new Menu();
\r
1909 MenuItem pasteNew = new MenuItem();
\r
1910 MenuItem pasteThis = new MenuItem();
\r
1911 protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
1912 protected MenuItem font = new MenuItem();
\r
1913 protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
1914 protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
1915 protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
1916 MenuItem modifyPID = new MenuItem();
\r
1917 MenuItem modifyConservation = new MenuItem();
\r
1918 protected CheckboxMenuItem autoCalculate
\r
1919 = new CheckboxMenuItem("Autocalculate Consensus", true);
\r
1920 protected Menu sortByTreeMenu = new Menu();
\r
1921 Menu sort = new Menu();
\r
1922 Menu calculate = new Menu();
\r
1923 MenuItem inputText = new MenuItem();
\r
1924 Menu helpMenu = new Menu();
\r
1925 MenuItem documentation = new MenuItem();
\r
1926 MenuItem about = new MenuItem();
\r
1927 protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
1928 Panel embeddedMenu;
\r
1929 Label embeddedEdit;
\r
1930 Label embeddedSearch;
\r
1931 Label embeddedView;
\r
1932 Label embeddedColour;
\r
1933 Label embeddedFile;
\r
1934 Label embeddedHelp;
\r
1935 Label embeddedCalculate;
\r
1936 FlowLayout flowLayout1;
\r
1938 private void jbInit() throws Exception {
\r
1940 setMenuBar(alignFrameMenuBar);
\r
1944 // dynamically fill save as menu with available formats
\r
1945 for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++)
\r
1948 item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.
\r
1951 item.addActionListener(new java.awt.event.ActionListener()
\r
1953 public void actionPerformed(ActionEvent e)
\r
1955 outputText_actionPerformed(e);
\r
1959 outputTextboxMenu.add(item);
\r
1961 closeMenuItem.addActionListener(this);
\r
1963 loadTree.addActionListener(this);
\r
1964 selectAllSequenceMenuItem.addActionListener(this);
\r
1965 deselectAllSequenceMenuItem.addActionListener(this);
\r
1966 invertSequenceMenuItem.addActionListener(this);
\r
1967 remove2LeftMenuItem.setLabel("Remove Left");
\r
1968 remove2LeftMenuItem.addActionListener(this);
\r
1969 remove2RightMenuItem.setLabel("Remove Right");
\r
1970 remove2RightMenuItem.addActionListener(this);
\r
1971 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
1972 removeGappedColumnMenuItem.addActionListener(this);
\r
1973 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
1974 removeAllGapsMenuItem.addActionListener(this);
\r
1975 viewBoxesMenuItem.setLabel("Boxes");
\r
1976 viewBoxesMenuItem.setState(true);
\r
1977 viewBoxesMenuItem.addItemListener(this);
\r
1978 viewTextMenuItem.setLabel("Text");
\r
1979 viewTextMenuItem.setState(true);
\r
1980 viewTextMenuItem.addItemListener(this);
\r
1981 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
1982 sortPairwiseMenuItem.addActionListener(this);
\r
1983 sortIDMenuItem.setLabel("by ID");
\r
1984 sortIDMenuItem.addActionListener(this);
\r
1985 sortGroupMenuItem.setLabel("by Group");
\r
1986 sortGroupMenuItem.addActionListener(this);
\r
1987 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
1988 removeRedundancyMenuItem.addActionListener(this);
\r
1989 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
1990 pairwiseAlignmentMenuItem.addActionListener(this);
\r
1991 PCAMenuItem.setLabel("Principal Component Analysis");
\r
1992 PCAMenuItem.addActionListener(this);
\r
1993 averageDistanceTreeMenuItem.setLabel(
\r
1994 "Average Distance Using % Identity");
\r
1995 averageDistanceTreeMenuItem.addActionListener(this);
\r
1996 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
1997 neighbourTreeMenuItem.addActionListener(this);
\r
1998 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
1999 statusBar.setBackground(Color.white);
\r
2000 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
2001 statusBar.setText("Status bar");
\r
2002 outputTextboxMenu.setLabel("Output to Textbox");
\r
2003 clustalColour.setLabel("Clustalx");
\r
2005 clustalColour.addActionListener(this);
\r
2006 zappoColour.setLabel("Zappo");
\r
2007 zappoColour.addActionListener(this);
\r
2008 taylorColour.setLabel("Taylor");
\r
2009 taylorColour.addActionListener(this);
\r
2010 hydrophobicityColour.setLabel("Hydrophobicity");
\r
2011 hydrophobicityColour.addActionListener(this);
\r
2012 helixColour.setLabel("Helix Propensity");
\r
2013 helixColour.addActionListener(this);
\r
2014 strandColour.setLabel("Strand Propensity");
\r
2015 strandColour.addActionListener(this);
\r
2016 turnColour.setLabel("Turn Propensity");
\r
2017 turnColour.addActionListener(this);
\r
2018 buriedColour.setLabel("Buried Index");
\r
2019 buriedColour.addActionListener(this);
\r
2020 userDefinedColour.setLabel("User Defined...");
\r
2021 userDefinedColour.addActionListener(this);
\r
2022 PIDColour.setLabel("Percentage Identity");
\r
2023 PIDColour.addActionListener(this);
\r
2024 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
2025 BLOSUM62Colour.addActionListener(this);
\r
2026 avDistanceTreeBlosumMenuItem.setLabel(
\r
2027 "Average Distance Using BLOSUM62");
\r
2028 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
2029 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
2030 njTreeBlosumMenuItem.addActionListener(this);
\r
2031 annotationPanelMenuItem.setLabel("Show Annotations");
\r
2032 annotationPanelMenuItem.addItemListener(this);
\r
2033 colourTextMenuItem.setLabel("Colour Text");
\r
2034 colourTextMenuItem.addItemListener(this);
\r
2035 overviewMenuItem.setLabel("Overview Window");
\r
2036 overviewMenuItem.addActionListener(this);
\r
2037 undoMenuItem.setEnabled(false);
\r
2038 undoMenuItem.setLabel("Undo");
\r
2039 undoMenuItem.addActionListener(this);
\r
2040 redoMenuItem.setEnabled(false);
\r
2041 redoMenuItem.setLabel("Redo");
\r
2042 redoMenuItem.addActionListener(this);
\r
2043 conservationMenuItem.setLabel("by Conservation");
\r
2044 conservationMenuItem.addItemListener(this);
\r
2045 noColourmenuItem.setLabel("None");
\r
2046 noColourmenuItem.addActionListener(this);
\r
2047 wrapMenuItem.setLabel("Wrap");
\r
2048 wrapMenuItem.addItemListener(this);
\r
2049 renderGapsMenuItem.setLabel("Show Gaps");
\r
2050 renderGapsMenuItem.setState(true);
\r
2051 renderGapsMenuItem.addItemListener(this);
\r
2052 findMenuItem.setLabel("Find...");
\r
2053 findMenuItem.addActionListener(this);
\r
2054 searchMenu.setLabel("Search");
\r
2056 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
2057 abovePIDThreshold.addItemListener(this);
\r
2058 nucleotideColour.setLabel("Nucleotide");
\r
2059 nucleotideColour.addActionListener(this);
\r
2060 deleteGroups.setLabel("Undefine Groups");
\r
2061 deleteGroups.addActionListener(this);
\r
2062 copy.setLabel("Copy");
\r
2063 copy.addActionListener(this);
\r
2064 cut.setLabel("Cut");
\r
2065 cut.addActionListener(this);
\r
2066 delete.setLabel("Delete");
\r
2067 delete.addActionListener(this);
\r
2068 pasteMenu.setLabel("Paste");
\r
2069 pasteNew.setLabel("To New Alignment");
\r
2070 pasteNew.addActionListener(this);
\r
2071 pasteThis.setLabel("Add To This Alignment");
\r
2072 pasteThis.addActionListener(this);
\r
2073 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
2074 applyToAllGroups.setState(true);
\r
2075 applyToAllGroups.addItemListener(this);
\r
2076 font.setLabel("Font...");
\r
2077 font.addActionListener(this);
\r
2078 scaleAbove.setLabel("Scale Above");
\r
2079 scaleAbove.setState(true);
\r
2080 scaleAbove.setEnabled(false);
\r
2081 scaleAbove.addItemListener(this);
\r
2082 scaleLeft.setEnabled(false);
\r
2083 scaleLeft.setState(true);
\r
2084 scaleLeft.setLabel("Scale Left");
\r
2085 scaleLeft.addItemListener(this);
\r
2086 scaleRight.setEnabled(false);
\r
2087 scaleRight.setState(true);
\r
2088 scaleRight.setLabel("Scale Right");
\r
2089 scaleRight.addItemListener(this);
\r
2090 modifyPID.setLabel("Modify Identity Threshold...");
\r
2091 modifyPID.addActionListener(this);
\r
2092 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
2093 modifyConservation.addActionListener(this);
\r
2094 sortByTreeMenu.setLabel("By Tree Order");
\r
2095 sort.setLabel("Sort");
\r
2096 calculate.setLabel("Calculate Tree");
\r
2097 autoCalculate.addItemListener(this);
\r
2098 inputText.setLabel("Input from textbox");
\r
2099 inputText.addActionListener(this);
\r
2101 helpMenu.setLabel("Help");
\r
2102 documentation.setLabel("Documentation");
\r
2103 documentation.addActionListener(this);
\r
2105 about.setLabel("About...");
\r
2106 about.addActionListener(this);
\r
2107 seqLimits.setState(true);
\r
2108 seqLimits.setLabel("Show Sequence Limits");
\r
2109 seqLimits.addItemListener(this);
\r
2110 featureSettings.setLabel("Feature Settings...");
\r
2111 featureSettings.addActionListener(this);
\r
2112 sequenceFeatures.setLabel("Sequence Features");
\r
2113 sequenceFeatures.addItemListener(this);
\r
2114 sequenceFeatures.setState(false);
\r
2115 annotationColour.setLabel("by Annotation...");
\r
2116 annotationColour.addActionListener(this);
\r
2118 alignFrameMenuBar.add(fileMenu);
\r
2119 alignFrameMenuBar.add(editMenu);
\r
2120 alignFrameMenuBar.add(searchMenu);
\r
2121 alignFrameMenuBar.add(viewMenu);
\r
2122 alignFrameMenuBar.add(colourMenu);
\r
2123 alignFrameMenuBar.add(calculateMenu);
\r
2124 alignFrameMenuBar.add(helpMenu);
\r
2125 fileMenu.add(inputText);
\r
2126 fileMenu.add(outputTextboxMenu);
\r
2127 fileMenu.addSeparator();
\r
2128 fileMenu.add(loadTree);
\r
2129 fileMenu.add(closeMenuItem);
\r
2130 editMenu.add(undoMenuItem);
\r
2131 editMenu.add(redoMenuItem);
\r
2132 editMenu.add(cut);
\r
2133 editMenu.add(copy);
\r
2134 editMenu.add(pasteMenu);
\r
2135 editMenu.add(delete);
\r
2136 editMenu.addSeparator();
\r
2137 editMenu.add(selectAllSequenceMenuItem);
\r
2138 editMenu.add(deselectAllSequenceMenuItem);
\r
2139 editMenu.add(invertSequenceMenuItem);
\r
2140 editMenu.add(deleteGroups);
\r
2141 editMenu.addSeparator();
\r
2142 editMenu.add(remove2LeftMenuItem);
\r
2143 editMenu.add(remove2RightMenuItem);
\r
2144 editMenu.add(removeGappedColumnMenuItem);
\r
2145 editMenu.add(removeAllGapsMenuItem);
\r
2146 editMenu.add(removeRedundancyMenuItem);
\r
2147 searchMenu.add(findMenuItem);
\r
2148 viewMenu.add(font);
\r
2149 viewMenu.addSeparator();
\r
2150 viewMenu.add(seqLimits);
\r
2151 viewMenu.addSeparator();
\r
2152 viewMenu.add(wrapMenuItem);
\r
2153 viewMenu.add(scaleAbove);
\r
2154 viewMenu.add(scaleLeft);
\r
2155 viewMenu.add(scaleRight);
\r
2156 viewMenu.addSeparator();
\r
2157 viewMenu.add(viewBoxesMenuItem);
\r
2158 viewMenu.add(viewTextMenuItem);
\r
2159 viewMenu.add(colourTextMenuItem);
\r
2160 viewMenu.add(renderGapsMenuItem);
\r
2161 viewMenu.add(annotationPanelMenuItem);
\r
2162 viewMenu.addSeparator();
\r
2163 viewMenu.add(sequenceFeatures);
\r
2164 viewMenu.add(featureSettings);
\r
2165 viewMenu.addSeparator();
\r
2166 viewMenu.add(overviewMenuItem);
\r
2167 colourMenu.add(applyToAllGroups);
\r
2168 colourMenu.addSeparator();
\r
2169 colourMenu.add(noColourmenuItem);
\r
2170 colourMenu.add(clustalColour);
\r
2171 colourMenu.add(BLOSUM62Colour);
\r
2172 colourMenu.add(PIDColour);
\r
2173 colourMenu.add(zappoColour);
\r
2174 colourMenu.add(taylorColour);
\r
2175 colourMenu.add(hydrophobicityColour);
\r
2176 colourMenu.add(helixColour);
\r
2177 colourMenu.add(strandColour);
\r
2178 colourMenu.add(turnColour);
\r
2179 colourMenu.add(buriedColour);
\r
2180 colourMenu.add(nucleotideColour);
\r
2181 colourMenu.add(userDefinedColour);
\r
2182 colourMenu.addSeparator();
\r
2183 colourMenu.add(conservationMenuItem);
\r
2184 colourMenu.add(modifyConservation);
\r
2185 colourMenu.add(abovePIDThreshold);
\r
2186 colourMenu.add(modifyPID);
\r
2187 colourMenu.add(annotationColour);
\r
2188 calculateMenu.add(sort);
\r
2189 calculateMenu.add(calculate);
\r
2190 calculateMenu.addSeparator();
\r
2191 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
2192 calculateMenu.add(PCAMenuItem);
\r
2193 calculateMenu.add(autoCalculate);
\r
2194 this.add(statusBar, BorderLayout.SOUTH);
\r
2195 pasteMenu.add(pasteNew);
\r
2196 pasteMenu.add(pasteThis);
\r
2197 sort.add(sortIDMenuItem);
\r
2198 sort.add(sortByTreeMenu);
\r
2199 sort.add(sortGroupMenuItem);
\r
2200 sort.add(sortPairwiseMenuItem);
\r
2201 calculate.add(averageDistanceTreeMenuItem);
\r
2202 calculate.add(neighbourTreeMenuItem);
\r
2203 calculate.add(avDistanceTreeBlosumMenuItem);
\r
2204 calculate.add(njTreeBlosumMenuItem);
\r
2205 helpMenu.add(documentation);
\r
2206 helpMenu.add(about);
\r
2209 public void setEmbedded()
\r
2212 embeddedMenu = new Panel();
\r
2213 embeddedEdit = new Label();
\r
2214 embeddedSearch = new Label();
\r
2215 embeddedView = new Label();
\r
2216 embeddedColour = new Label();
\r
2217 embeddedFile = new Label();
\r
2218 embeddedHelp = new Label();
\r
2219 embeddedCalculate = new Label();
\r
2220 flowLayout1 = new FlowLayout();
\r
2221 embeddedMenu.setBackground(Color.lightGray);
\r
2222 embeddedMenu.setLayout(flowLayout1);
\r
2223 embeddedEdit.setText("Edit");
\r
2224 embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2225 embeddedSearch.setText("Search");
\r
2226 embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2227 embeddedView.setText("View");
\r
2228 embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2229 embeddedColour.setText("Colour");
\r
2230 embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2231 embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2232 embeddedFile.setText("File");
\r
2233 embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2234 embeddedHelp.setText("Help");
\r
2235 embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2236 embeddedCalculate.setText("Calculate");
\r
2237 embeddedMenu.add(embeddedFile);
\r
2238 embeddedMenu.add(embeddedEdit);
\r
2239 embeddedMenu.add(embeddedSearch);
\r
2240 embeddedMenu.add(embeddedView);
\r
2241 embeddedMenu.add(embeddedColour);
\r
2242 embeddedMenu.add(embeddedCalculate);
\r
2243 embeddedMenu.add(embeddedHelp);
\r
2244 flowLayout1.setAlignment(FlowLayout.LEFT);
\r
2245 flowLayout1.setHgap(2);
\r
2246 flowLayout1.setVgap(0);
\r
2247 embeddedFile.addMouseListener(this);
\r
2248 embeddedEdit.addMouseListener(this);
\r
2249 embeddedSearch.addMouseListener(this);
\r
2250 embeddedView.addMouseListener(this);
\r
2251 embeddedColour.addMouseListener(this);
\r
2252 embeddedCalculate.addMouseListener(this);
\r
2253 embeddedHelp.addMouseListener(this);
\r
2255 // setVisible(false);
\r
2256 fileMenu.remove(closeMenuItem);
\r
2257 fileMenu.remove(2); // Seperator
\r
2259 applet.setLayout(new BorderLayout());
\r
2260 applet.add(embeddedMenu, BorderLayout.NORTH);
\r
2261 applet.add(statusBar, BorderLayout.SOUTH);
\r
2262 // applet.validate();
\r
2264 alignPanel.setSize(applet.size().width, applet.size().height
\r
2265 - embeddedMenu.HEIGHT - statusBar.HEIGHT);
\r
2267 applet.add(alignPanel, BorderLayout.CENTER);
\r
2268 applet.validate();
\r
2274 PopupMenu filePopup, editPopup, searchPopup,
\r
2275 viewPopup, colourPopup, calculatePopup, helpPopup;
\r
2276 MenuItem featureSettings = new MenuItem();
\r
2277 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
2278 MenuItem annotationColour = new MenuItem();
\r
2280 public void mousePressed(MouseEvent evt)
\r
2282 PopupMenu popup = null;
\r
2283 Label source = (Label)evt.getSource();
\r
2284 if(source==embeddedFile)
\r
2286 popup = filePopup = genPopupMenu(filePopup, fileMenu);
\r
2288 else if(source==embeddedEdit)
\r
2290 popup = editPopup = genPopupMenu(editPopup, editMenu);
\r
2292 else if(source==embeddedSearch)
\r
2294 popup = searchPopup = genPopupMenu(searchPopup, searchMenu);
\r
2296 else if(source==embeddedView)
\r
2298 popup = viewPopup = genPopupMenu(viewPopup, viewMenu);
\r
2300 else if(source==embeddedColour)
\r
2302 popup = colourPopup = genPopupMenu(colourPopup, colourMenu);
\r
2304 else if(source==embeddedCalculate)
\r
2306 popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);
\r
2308 else if(source==embeddedHelp)
\r
2310 popup = helpPopup = genPopupMenu(helpPopup, helpMenu);
\r
2313 embeddedMenu.add(popup);
\r
2314 popup.show(embeddedMenu,
\r
2315 source.getBounds().x,
\r
2316 source.getBounds().y + source.getBounds().getSize().height);
\r
2319 PopupMenu genPopupMenu(PopupMenu popup, Menu original)
\r
2325 popup = new PopupMenu();
\r
2326 int m, mSize = original.getItemCount();
\r
2327 for(m=0; m<mSize; m++)
\r
2329 popup.add(original.getItem(m));
\r
2336 public void mouseClicked(MouseEvent evt)
\r
2338 public void mouseReleased(MouseEvent evt)
\r
2340 public void mouseEntered(MouseEvent evt)
\r
2342 public void mouseExited(MouseEvent evt)
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