2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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20 package jalview.appletgui;
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22 import jalview.schemes.*;
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23 import jalview.datamodel.*;
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24 import jalview.analysis.*;
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25 import jalview.io.*;
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27 import java.awt.event.*;
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29 import java.io.InputStreamReader;
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30 import java.io.BufferedReader;
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31 import java.net.URL;
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34 public class AlignFrame extends Frame implements ActionListener,
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35 ItemListener, KeyListener, MouseListener
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37 public AlignmentPanel alignPanel;
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38 public AlignViewport viewport;
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39 int NEW_WINDOW_WIDTH = 700;
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40 int NEW_WINDOW_HEIGHT = 500;
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41 jalview.bin.JalviewLite applet;
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44 public AlignFrame(AlignmentI al,
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45 jalview.bin.JalviewLite applet,
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51 }catch(Exception ex)
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53 ex.printStackTrace();
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56 this.applet = applet;
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57 viewport = new AlignViewport(al, applet);
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58 alignPanel = new AlignmentPanel(this, viewport);
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60 annotationPanelMenuItem.setState(viewport.showAnnotation);
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64 String param = applet.getParameter("sortBy");
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67 if (param.equalsIgnoreCase("Id"))
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68 sortIDMenuItem_actionPerformed();
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69 else if (param.equalsIgnoreCase("Pairwise Identity"))
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70 sortPairwiseMenuItem_actionPerformed();
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73 param = applet.getParameter("wrap");
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76 if (param.equalsIgnoreCase("true"))
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78 wrapMenuItem.setState(true);
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79 wrapMenuItem_actionPerformed();
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85 param = applet.getParameter("windowWidth");
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88 int width = Integer.parseInt(param);
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89 NEW_WINDOW_WIDTH = width;
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91 param = applet.getParameter("windowHeight");
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94 int height = Integer.parseInt(param);
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95 NEW_WINDOW_HEIGHT = height;
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98 catch (Exception ex)
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103 //Some JVMS send keyevents to Top frame or lowest panel,
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104 //Havent worked out why yet. So add to both this frame and seqCanvas for now
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105 this.addKeyListener(this);
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106 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
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107 alignPanel.idPanel.idCanvas.addKeyListener(this);
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109 viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
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111 public void propertyChange(java.beans.PropertyChangeEvent evt)
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113 if (evt.getPropertyName().equals("alignment"))
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115 alignmentChanged();
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127 add(alignPanel, BorderLayout.CENTER);
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128 jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH,
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129 NEW_WINDOW_HEIGHT);
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131 alignPanel.validate();
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132 alignPanel.repaint();
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134 public AlignViewport getAlignViewport()
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139 public SeqCanvas getSeqcanvas()
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141 return alignPanel.seqPanel.seqCanvas;
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148 * @param String DOCUMENT ME!
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151 public void parseFeaturesFile(String file)
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153 String line = null;
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156 BufferedReader in = null;
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157 java.io.InputStream is = getClass().getResourceAsStream("/" + file);
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160 in = new BufferedReader(new java.io.InputStreamReader(is));
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164 URL url = new URL(file);
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165 in = new BufferedReader(new InputStreamReader(url.openStream()));
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168 SequenceI seq = null;
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169 String type, desc, token;
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171 int index, start, end;
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172 StringTokenizer st;
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173 SequenceFeature sf;
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174 FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
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176 String featureGroup = null;
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177 while ( (line = in.readLine()) != null)
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180 st = new StringTokenizer(line, "\t");
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181 if (st.countTokens() == 2)
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183 type = st.nextToken();
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184 if(type.equalsIgnoreCase("startgroup"))
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186 featureGroup = st.nextToken();
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188 else if(type.equalsIgnoreCase("endgroup"))
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190 //We should check whether this is the current group,
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191 //but at present theres no way of showing more than 1 group
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193 featureGroup = null;
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197 UserColourScheme ucs = new UserColourScheme(st.nextToken());
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198 fr.setColour(type, ucs.findColour("A"));
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203 while (st.hasMoreElements())
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205 desc = st.nextToken();
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206 token = st.nextToken();
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207 if (!token.equals("ID_NOT_SPECIFIED"))
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209 index = viewport.alignment.findIndex(viewport.alignment.findName(
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215 index = Integer.parseInt(st.nextToken());
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218 start = Integer.parseInt(st.nextToken());
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219 end = Integer.parseInt(st.nextToken());
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221 seq = viewport.alignment.getSequenceAt(index);
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223 type = st.nextToken();
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225 if(fr.getColour(type)==null)
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227 // Probably the old style groups file
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228 UserColourScheme ucs = new UserColourScheme(type);
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229 fr.setColour(type, ucs.findColour("A"));
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232 sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
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234 seq.addSequenceFeature(sf);
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238 viewport.showSequenceFeatures = true;
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239 sequenceFeatures.setState(true);
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241 alignPanel.repaint();
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244 catch (Exception ex)
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246 ex.printStackTrace();
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247 System.out.println("Error parsing groups file: " + ex +"\n"+line);
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251 public void keyPressed(KeyEvent evt)
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253 if (viewport.cursorMode
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254 && evt.getKeyCode() >= KeyEvent.VK_0
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255 && evt.getKeyCode() <= KeyEvent.VK_9)
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257 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
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260 switch (evt.getKeyCode())
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262 case 27: // escape key
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263 deselectAllSequenceMenuItem_actionPerformed();
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265 case KeyEvent.VK_X:
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266 if (evt.isControlDown() || evt.isMetaDown())
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268 cut_actionPerformed();
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271 case KeyEvent.VK_C:
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272 if (viewport.cursorMode)
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274 alignPanel.seqPanel.setCursorColumn();
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276 if (evt.isControlDown() || evt.isMetaDown())
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278 copy_actionPerformed();
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281 case KeyEvent.VK_V:
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282 if (evt.isControlDown() || evt.isMetaDown())
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287 case KeyEvent.VK_A:
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288 if (evt.isControlDown() || evt.isMetaDown())
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290 selectAllSequenceMenuItem_actionPerformed();
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293 case KeyEvent.VK_DOWN:
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294 if(viewport.cursorMode)
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296 alignPanel.seqPanel.moveCursor(0,1);
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299 moveSelectedSequences(false);
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302 case KeyEvent.VK_UP:
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303 if (viewport.cursorMode)
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305 alignPanel.seqPanel.moveCursor(0,-1);
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308 moveSelectedSequences(true);
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311 case KeyEvent.VK_LEFT:
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312 if(viewport.cursorMode)
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314 alignPanel.seqPanel.moveCursor(-1,0);
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318 case KeyEvent.VK_RIGHT:
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319 if (viewport.cursorMode)
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321 alignPanel.seqPanel.moveCursor(1,0);
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324 case KeyEvent.VK_SPACE:
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325 if(viewport.cursorMode)
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327 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown());
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331 case KeyEvent.VK_DELETE:
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332 if(viewport.cursorMode)
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334 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown());
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338 case KeyEvent.VK_BACK_SPACE:
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339 if(!viewport.cursorMode)
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341 cut_actionPerformed();
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342 alignPanel.seqPanel.seqCanvas.repaint();
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346 case KeyEvent.VK_S:
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347 if(viewport.cursorMode)
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349 alignPanel.seqPanel.setCursorRow();
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352 case KeyEvent.VK_P:
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353 if(viewport.cursorMode)
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355 alignPanel.seqPanel.setCursorPosition();
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359 case KeyEvent.VK_ENTER:
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360 case KeyEvent.VK_COMMA:
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361 if(viewport.cursorMode)
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363 alignPanel.seqPanel.setCursorRowAndColumn();
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367 case KeyEvent.VK_Q:
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368 if(viewport.cursorMode)
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370 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
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373 case KeyEvent.VK_M:
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374 if(viewport.cursorMode)
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376 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
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380 case KeyEvent.VK_F2:
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381 viewport.cursorMode = ! viewport.cursorMode;
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382 statusBar.setText("Keyboard editing mode is "+
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383 (viewport.cursorMode ? "on" : "off"));
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384 if(viewport.cursorMode)
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386 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
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387 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
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389 alignPanel.seqPanel.seqCanvas.repaint();
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392 case KeyEvent.VK_F:
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393 if (evt.isControlDown())
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395 findMenuItem_actionPerformed();
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400 public void keyReleased(KeyEvent evt)
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402 public void keyTyped(KeyEvent evt)
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405 public void itemStateChanged(ItemEvent evt)
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407 if(evt.getSource()==colourTextMenuItem)
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408 colourTextMenuItem_actionPerformed();
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409 else if(evt.getSource()==wrapMenuItem)
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410 wrapMenuItem_actionPerformed();
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411 else if(evt.getSource()==scaleAbove)
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412 scaleAbove_actionPerformed();
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413 else if(evt.getSource()==scaleLeft)
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414 scaleLeft_actionPerformed();
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415 else if(evt.getSource()==scaleRight)
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416 scaleRight_actionPerformed();
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417 else if(evt.getSource()==seqLimits)
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418 seqLimits_itemStateChanged();
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419 else if(evt.getSource()==viewBoxesMenuItem)
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420 viewBoxesMenuItem_actionPerformed();
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421 else if(evt.getSource()==viewTextMenuItem)
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422 viewTextMenuItem_actionPerformed();
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423 else if(evt.getSource()==renderGapsMenuItem)
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424 renderGapsMenuItem_actionPerformed();
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425 else if(evt.getSource()==annotationPanelMenuItem)
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426 annotationPanelMenuItem_actionPerformed();
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427 else if(evt.getSource()==sequenceFeatures)
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429 viewport.showSequenceFeatures(sequenceFeatures.getState());
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430 alignPanel.seqPanel.seqCanvas.repaint();
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432 else if(evt.getSource()==conservationMenuItem)
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433 conservationMenuItem_actionPerformed();
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434 else if(evt.getSource()==abovePIDThreshold)
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435 abovePIDThreshold_actionPerformed();
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436 else if(evt.getSource()==applyToAllGroups)
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437 applyToAllGroups_actionPerformed();
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438 else if(evt.getSource()==autoCalculate)
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439 viewport.autocalculateConsensus = autoCalculate.getState();
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441 public void actionPerformed(ActionEvent evt)
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443 if(evt.getSource()==inputText)
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444 inputText_actionPerformed();
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445 else if(evt.getSource()==loadTree)
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446 loadTree_actionPerformed();
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447 else if(evt.getSource()==closeMenuItem)
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448 closeMenuItem_actionPerformed();
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449 else if(evt.getSource()==copy)
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450 copy_actionPerformed();
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451 else if(evt.getSource()==undoMenuItem)
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452 undoMenuItem_actionPerformed();
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453 else if(evt.getSource()==redoMenuItem)
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454 redoMenuItem_actionPerformed();
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455 else if(evt.getSource()==inputText)
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456 inputText_actionPerformed();
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457 else if(evt.getSource()==closeMenuItem)
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458 closeMenuItem_actionPerformed();
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459 else if(evt.getSource()==undoMenuItem)
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460 undoMenuItem_actionPerformed();
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461 else if(evt.getSource()==redoMenuItem)
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462 redoMenuItem_actionPerformed();
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463 else if(evt.getSource()==copy)
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464 copy_actionPerformed();
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465 else if(evt.getSource()==pasteNew)
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466 pasteNew_actionPerformed();
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467 else if(evt.getSource()==pasteThis)
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468 pasteThis_actionPerformed();
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469 else if(evt.getSource()==cut)
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470 cut_actionPerformed();
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471 else if(evt.getSource()==delete)
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472 delete_actionPerformed();
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473 else if(evt.getSource()==deleteGroups)
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474 deleteGroups_actionPerformed();
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475 else if(evt.getSource()==selectAllSequenceMenuItem)
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476 selectAllSequenceMenuItem_actionPerformed();
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477 else if(evt.getSource()==deselectAllSequenceMenuItem)
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478 deselectAllSequenceMenuItem_actionPerformed();
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479 else if(evt.getSource()==invertSequenceMenuItem)
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480 invertSequenceMenuItem_actionPerformed();
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481 else if(evt.getSource()==remove2LeftMenuItem)
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482 remove2LeftMenuItem_actionPerformed();
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483 else if(evt.getSource()==remove2RightMenuItem)
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484 remove2RightMenuItem_actionPerformed();
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485 else if(evt.getSource()==removeGappedColumnMenuItem)
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486 removeGappedColumnMenuItem_actionPerformed();
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487 else if(evt.getSource()==removeAllGapsMenuItem)
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488 removeAllGapsMenuItem_actionPerformed();
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489 else if(evt.getSource()==findMenuItem)
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490 findMenuItem_actionPerformed();
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491 else if(evt.getSource()==font)
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492 font_actionPerformed();
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493 else if(evt.getSource()==featureSettings)
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494 featureSettings_actionPerformed();
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495 else if(evt.getSource()==overviewMenuItem)
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496 overviewMenuItem_actionPerformed();
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497 else if(evt.getSource()==noColourmenuItem)
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498 noColourmenuItem_actionPerformed();
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499 else if(evt.getSource()==clustalColour)
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500 clustalColour_actionPerformed();
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501 else if(evt.getSource()==zappoColour)
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502 zappoColour_actionPerformed();
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503 else if(evt.getSource()==taylorColour)
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504 taylorColour_actionPerformed();
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505 else if(evt.getSource()==hydrophobicityColour)
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506 hydrophobicityColour_actionPerformed();
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507 else if(evt.getSource()==helixColour)
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508 helixColour_actionPerformed();
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509 else if(evt.getSource()==strandColour)
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510 strandColour_actionPerformed();
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511 else if(evt.getSource()==turnColour)
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512 turnColour_actionPerformed();
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513 else if(evt.getSource()==buriedColour)
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514 buriedColour_actionPerformed();
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515 else if(evt.getSource()==nucleotideColour)
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516 nucleotideColour_actionPerformed();
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517 else if(evt.getSource()==modifyPID)
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518 modifyPID_actionPerformed();
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519 else if(evt.getSource()==modifyConservation)
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520 modifyConservation_actionPerformed();
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521 else if(evt.getSource()==userDefinedColour)
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522 userDefinedColour_actionPerformed();
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523 else if(evt.getSource()==PIDColour)
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524 PIDColour_actionPerformed();
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525 else if(evt.getSource()==BLOSUM62Colour)
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526 BLOSUM62Colour_actionPerformed();
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527 else if(evt.getSource()==annotationColour)
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528 new AnnotationColourChooser(viewport, alignPanel);
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529 else if(evt.getSource()==sortPairwiseMenuItem)
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530 sortPairwiseMenuItem_actionPerformed();
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531 else if(evt.getSource()==sortIDMenuItem)
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532 sortIDMenuItem_actionPerformed();
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533 else if(evt.getSource()==sortGroupMenuItem)
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534 sortGroupMenuItem_actionPerformed();
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535 else if(evt.getSource()==removeRedundancyMenuItem)
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536 removeRedundancyMenuItem_actionPerformed();
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537 else if(evt.getSource()==pairwiseAlignmentMenuItem)
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538 pairwiseAlignmentMenuItem_actionPerformed();
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539 else if(evt.getSource()==PCAMenuItem)
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540 PCAMenuItem_actionPerformed();
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541 else if(evt.getSource()==averageDistanceTreeMenuItem)
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542 averageDistanceTreeMenuItem_actionPerformed();
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543 else if(evt.getSource()==neighbourTreeMenuItem)
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544 neighbourTreeMenuItem_actionPerformed();
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545 else if(evt.getSource()==njTreeBlosumMenuItem)
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546 njTreeBlosumMenuItem_actionPerformed();
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547 else if(evt.getSource()==avDistanceTreeBlosumMenuItem)
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548 avTreeBlosumMenuItem_actionPerformed();
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549 else if(evt.getSource()==documentation)
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550 documentation_actionPerformed();
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551 else if(evt.getSource()==about)
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552 about_actionPerformed();
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556 public void inputText_actionPerformed()
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558 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
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559 Frame frame = new Frame();
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561 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
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564 protected void outputText_actionPerformed(ActionEvent e)
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566 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
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567 Frame frame = new Frame();
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569 jalview.bin.JalviewLite.addFrame(frame,
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570 "Alignment output - " + e.getActionCommand(),
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572 cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
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573 viewport.getAlignment().getSequences(),
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574 viewport.showJVSuffix));
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577 public void closeMenuItem_actionPerformed()
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579 PaintRefresher.components.remove(viewport.alignment);
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580 if(PaintRefresher.components.size()==0 && applet==null)
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586 Stack historyList = new Stack();
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587 Stack redoList = new Stack();
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589 void updateEditMenuBar()
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591 if (historyList.size() > 0)
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593 undoMenuItem.setEnabled(true);
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594 HistoryItem hi = (HistoryItem) historyList.peek();
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595 undoMenuItem.setLabel("Undo " + hi.getDescription());
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599 undoMenuItem.setEnabled(false);
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600 undoMenuItem.setLabel("Undo");
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603 if (redoList.size() > 0)
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605 redoMenuItem.setEnabled(true);
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606 HistoryItem hi = (HistoryItem) redoList.peek();
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607 redoMenuItem.setLabel("Redo " + hi.getDescription());
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611 redoMenuItem.setEnabled(false);
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612 redoMenuItem.setLabel("Redo");
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616 public void addHistoryItem(HistoryItem hi)
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618 historyList.push(hi);
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619 updateEditMenuBar();
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622 protected void undoMenuItem_actionPerformed()
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624 HistoryItem hi = (HistoryItem) historyList.pop();
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625 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
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626 HistoryItem.HIDE));
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627 restoreHistoryItem(hi);
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628 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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631 protected void redoMenuItem_actionPerformed()
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633 HistoryItem hi = (HistoryItem) redoList.pop();
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634 restoreHistoryItem(hi);
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635 updateEditMenuBar();
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636 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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639 // used by undo and redo
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640 void restoreHistoryItem(HistoryItem hi)
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644 updateEditMenuBar();
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646 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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649 public void moveSelectedSequences(boolean up)
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651 SequenceGroup sg = viewport.getSelectionGroup();
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659 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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661 SequenceI seq = viewport.alignment.getSequenceAt(i);
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662 if (!sg.sequences.contains(seq))
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667 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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668 if (sg.sequences.contains(temp))
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673 viewport.alignment.getSequences().setElementAt(temp, i);
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674 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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679 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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681 SequenceI seq = viewport.alignment.getSequenceAt(i);
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682 if (!sg.sequences.contains(seq))
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687 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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688 if (sg.sequences.contains(temp))
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693 viewport.alignment.getSequences().setElementAt(temp, i);
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694 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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698 alignPanel.repaint();
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701 StringBuffer copiedSequences;
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702 protected void copy_actionPerformed()
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704 if (viewport.getSelectionGroup() == null)
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709 SequenceGroup sg = viewport.getSelectionGroup();
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710 copiedSequences = new StringBuffer();
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711 Hashtable orderedSeqs = new Hashtable();
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712 for (int i = 0; i < sg.getSize(); i++)
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714 SequenceI seq = sg.getSequenceAt(i);
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715 int index = viewport.alignment.findIndex(seq);
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716 orderedSeqs.put(index + "", seq);
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719 int index = 0, startRes, endRes;
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722 for (int i = 0; i < sg.getSize(); i++)
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724 SequenceI seq = null;
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726 while (seq == null)
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728 if (orderedSeqs.containsKey(index + ""))
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730 seq = (SequenceI) orderedSeqs.get(index + "");
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742 //Returns residue following index if gap
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743 startRes = seq.findPosition(sg.getStartRes());
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746 //Need to find the residue preceeding index if gap
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749 for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
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751 ch = seq.getCharAt(j);
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752 if (!jalview.util.Comparison.isGap( (ch)))
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760 endRes += seq.getStart() -1;
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763 copiedSequences.append(seq.getName() + "\t" +
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766 seq.getSequence(sg.getStartRes(),
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767 sg.getEndRes() + 1) + "\n");
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772 protected void pasteNew_actionPerformed()
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777 protected void pasteThis_actionPerformed()
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779 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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780 HistoryItem.PASTE));
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784 void paste(boolean newAlignment)
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788 if (copiedSequences == null)
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793 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
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794 Vector seqs = new Vector();
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795 while (st.hasMoreElements())
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797 String name = st.nextToken();
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798 int start = Integer.parseInt(st.nextToken());
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799 int end = Integer.parseInt(st.nextToken());
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800 Sequence sequence = new Sequence(name, st.nextToken(), start, end);
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804 viewport.alignment.addSequence(sequence);
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808 seqs.addElement(sequence);
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814 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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815 for (int i = 0; i < seqs.size(); i++)
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817 newSeqs[i] = (SequenceI) seqs.elementAt(i);
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820 String newtitle = new String("Copied sequences");
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821 if (getTitle().startsWith("Copied sequences"))
\r
823 newtitle = getTitle();
\r
827 newtitle = newtitle.concat("- from " + getTitle());
\r
829 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
834 jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
\r
835 NEW_WINDOW_HEIGHT);
\r
839 viewport.setEndSeq(viewport.alignment.getHeight());
\r
840 viewport.alignment.getWidth();
\r
841 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
845 catch (Exception ex)
\r
846 {} // could be anything being pasted in here
\r
850 protected void cut_actionPerformed()
\r
852 copy_actionPerformed();
\r
853 delete_actionPerformed();
\r
856 protected void delete_actionPerformed()
\r
858 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
\r
859 HistoryItem.HIDE));
\r
860 if (viewport.getSelectionGroup() == null)
\r
866 SequenceGroup sg = viewport.getSelectionGroup();
\r
867 boolean allSequences = false;
\r
868 if(sg.sequences.size()==viewport.alignment.getHeight())
\r
869 allSequences = true;
\r
871 for (int i = 0; i < sg.sequences.size(); i++)
\r
873 SequenceI seq = sg.getSequenceAt(i);
\r
874 int index = viewport.getAlignment().findIndex(seq);
\r
875 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
\r
877 // If the cut affects all sequences, remove highlighted columns
\r
880 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
881 sg.getEndRes() + 1);
\r
885 if (seq.getSequence().length() < 1)
\r
887 viewport.getAlignment().deleteSequence(seq);
\r
891 viewport.getAlignment().getSequences().setElementAt(seq, index);
\r
895 viewport.setSelectionGroup(null);
\r
896 viewport.alignment.deleteGroup(sg);
\r
897 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
\r
898 if (viewport.getAlignment().getHeight() < 1)
\r
902 this.setVisible(false);
\r
904 catch (Exception ex)
\r
907 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
911 protected void deleteGroups_actionPerformed()
\r
913 viewport.alignment.deleteAllGroups();
\r
914 viewport.setSelectionGroup(null);
\r
916 alignPanel.repaint();
\r
919 public void selectAllSequenceMenuItem_actionPerformed()
\r
921 SequenceGroup sg = new SequenceGroup();
\r
922 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
924 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
926 sg.setEndRes(viewport.alignment.getWidth()-1);
\r
927 viewport.setSelectionGroup(sg);
\r
928 alignPanel.repaint();
\r
929 PaintRefresher.Refresh(null, viewport.alignment);
\r
932 public void deselectAllSequenceMenuItem_actionPerformed()
\r
934 if(viewport.cursorMode)
\r
936 alignPanel.seqPanel.keyboardNo1=null;
\r
937 alignPanel.seqPanel.keyboardNo2=null;
\r
939 viewport.setSelectionGroup(null);
\r
940 viewport.getColumnSelection().clear();
\r
941 viewport.setSelectionGroup(null);
\r
942 alignPanel.idPanel.idCanvas.searchResults = null;
\r
943 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
944 alignPanel.repaint();
\r
945 PaintRefresher.Refresh(null, viewport.alignment);
\r
948 public void invertSequenceMenuItem_actionPerformed()
\r
950 SequenceGroup sg = viewport.getSelectionGroup();
\r
951 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
953 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
956 PaintRefresher.Refresh(null, viewport.alignment);
\r
959 public void remove2LeftMenuItem_actionPerformed()
\r
961 ColumnSelection colSel = viewport.getColumnSelection();
\r
962 if (colSel.size() > 0)
\r
964 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
\r
965 HistoryItem.HIDE));
\r
966 int min = colSel.getMin();
\r
967 viewport.getAlignment().trimLeft(min);
\r
968 colSel.compensateForEdit(0, min);
\r
970 if (viewport.getSelectionGroup() != null)
\r
972 viewport.getSelectionGroup().adjustForRemoveLeft(min);
\r
975 Vector groups = viewport.alignment.getGroups();
\r
976 for (int i = 0; i < groups.size(); i++)
\r
978 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
979 if (!sg.adjustForRemoveLeft(min))
\r
981 viewport.alignment.deleteGroup(sg);
\r
984 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
988 public void remove2RightMenuItem_actionPerformed()
\r
990 ColumnSelection colSel = viewport.getColumnSelection();
\r
991 if (colSel.size() > 0)
\r
993 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
\r
994 HistoryItem.HIDE));
\r
995 int max = colSel.getMax();
\r
996 viewport.getAlignment().trimRight(max);
\r
997 if (viewport.getSelectionGroup() != null)
\r
999 viewport.getSelectionGroup().adjustForRemoveRight(max);
\r
1002 Vector groups = viewport.alignment.getGroups();
\r
1003 for (int i = 0; i < groups.size(); i++)
\r
1005 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1006 if (!sg.adjustForRemoveRight(max))
\r
1008 viewport.alignment.deleteGroup(sg);
\r
1011 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1016 public void removeGappedColumnMenuItem_actionPerformed()
\r
1018 addHistoryItem(new HistoryItem("Remove Gapped Columns",
\r
1019 viewport.alignment,
\r
1020 HistoryItem.HIDE));
\r
1022 //This is to maintain viewport position on first residue
\r
1023 //of first sequence
\r
1024 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1025 int startRes = seq.findPosition(viewport.startRes);
\r
1027 viewport.getAlignment().removeGaps();
\r
1029 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1031 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1034 public void removeAllGapsMenuItem_actionPerformed()
\r
1036 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
\r
1037 HistoryItem.HIDE));
\r
1039 //This is to maintain viewport position on first residue
\r
1040 //of first sequence
\r
1041 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1042 int startRes = seq.findPosition(viewport.startRes);
\r
1044 SequenceI current;
\r
1049 int start=0, end = viewport.alignment.getWidth();
\r
1051 if (viewport.getSelectionGroup() != null
\r
1052 && viewport.getSelectionGroup().sequences != null
\r
1053 && viewport.getSelectionGroup().sequences.size()>0)
\r
1055 seqs = viewport.getSelectionGroup().sequences;
\r
1056 start = viewport.getSelectionGroup().getStartRes();
\r
1057 end = viewport.getSelectionGroup().getEndRes()+1;
\r
1060 seqs = viewport.alignment.getSequences();
\r
1062 for (int i = 0; i < seqs.size(); i++)
\r
1064 current = (SequenceI) seqs.elementAt(i);
\r
1065 jSize = current.getLength();
\r
1067 // Removing a range is much quicker than removing gaps
\r
1068 // one by one for long sequences
\r
1070 int rangeStart=-1, rangeEnd=-1;
\r
1074 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
\r
1076 if(rangeStart==-1)
\r
1091 current.deleteChars(rangeStart, rangeEnd);
\r
1092 j-=rangeEnd-rangeStart;
\r
1093 jSize-=rangeEnd-rangeStart;
\r
1101 while (j < end && j < jSize);
\r
1104 current.deleteChars(rangeStart, rangeEnd);
\r
1107 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1108 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1111 public void alignmentChanged()
\r
1113 viewport.alignment.padGaps();
\r
1114 if(viewport.autocalculateConsensus)
\r
1116 viewport.updateConsensus();
\r
1117 viewport.updateConservation();
\r
1120 resetAllColourSchemes();
\r
1121 if(alignPanel.overviewPanel!=null)
\r
1122 alignPanel.overviewPanel.updateOverviewImage();
\r
1124 viewport.alignment.adjustSequenceAnnotations();
\r
1125 alignPanel.repaint();
\r
1128 void resetAllColourSchemes()
\r
1130 ColourSchemeI cs = viewport.globalColourScheme;
\r
1133 if (cs instanceof ClustalxColourScheme)
\r
1135 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
\r
1136 resetClustalX(viewport.alignment.getSequences(),
\r
1137 viewport.alignment.getWidth());
\r
1140 cs.setConsensus(viewport.vconsensus);
\r
1141 if (cs.conservationApplied())
\r
1143 Alignment al = (Alignment) viewport.alignment;
\r
1144 Conservation c = new Conservation("All",
\r
1145 ResidueProperties.propHash, 3,
\r
1146 al.getSequences(), 0,
\r
1147 al.getWidth() - 1);
\r
1149 c.verdict(false, viewport.ConsPercGaps);
\r
1151 cs.setConservation(c);
\r
1155 int s, sSize = viewport.alignment.getGroups().size();
\r
1156 for(s=0; s<sSize; s++)
\r
1158 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
\r
1159 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
\r
1161 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
\r
1163 sg.recalcConservation();
\r
1169 public void findMenuItem_actionPerformed()
\r
1171 new Finder(alignPanel);
\r
1174 public void font_actionPerformed()
\r
1176 new FontChooser(alignPanel);
\r
1180 public void seqLimits_itemStateChanged()
\r
1182 viewport.setShowJVSuffix(seqLimits.getState());
\r
1183 alignPanel.fontChanged();
\r
1184 alignPanel.repaint();
\r
1188 protected void colourTextMenuItem_actionPerformed()
\r
1190 viewport.setColourText(colourTextMenuItem.getState());
\r
1191 alignPanel.repaint();
\r
1194 protected void wrapMenuItem_actionPerformed()
\r
1196 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
1197 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
1198 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
1199 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
1200 scaleRight.setEnabled(wrapMenuItem.getState());
\r
1201 alignPanel.repaint();
\r
1204 protected void scaleAbove_actionPerformed()
\r
1206 viewport.setScaleAboveWrapped(scaleAbove.getState());
\r
1207 alignPanel.repaint();
\r
1210 protected void scaleLeft_actionPerformed()
\r
1212 viewport.setScaleLeftWrapped(scaleLeft.getState());
\r
1213 alignPanel.repaint();
\r
1216 protected void scaleRight_actionPerformed()
\r
1218 viewport.setScaleRightWrapped(scaleRight.getState());
\r
1219 alignPanel.repaint();
\r
1222 public void viewBoxesMenuItem_actionPerformed()
\r
1224 viewport.setShowBoxes(viewBoxesMenuItem.getState());
\r
1225 alignPanel.repaint();
\r
1228 public void viewTextMenuItem_actionPerformed()
\r
1230 viewport.setShowText(viewTextMenuItem.getState());
\r
1231 alignPanel.repaint();
\r
1234 protected void renderGapsMenuItem_actionPerformed()
\r
1236 viewport.setRenderGaps(renderGapsMenuItem.getState());
\r
1237 alignPanel.repaint();
\r
1240 public void annotationPanelMenuItem_actionPerformed()
\r
1242 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
\r
1243 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
\r
1246 public void featureSettings_actionPerformed()
\r
1248 new FeatureSettings(viewport, alignPanel);
\r
1251 public void overviewMenuItem_actionPerformed()
\r
1253 if (alignPanel.overviewPanel != null)
\r
1258 Frame frame = new Frame();
\r
1259 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1260 frame.add(overview);
\r
1261 // +50 must allow for applet frame window
\r
1262 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
1263 overview.preferredSize().width,
\r
1264 overview.preferredSize().height + 50);
\r
1267 frame.addWindowListener(new WindowAdapter()
\r
1269 public void windowClosing(WindowEvent e)
\r
1271 alignPanel.setOverviewPanel(null);
\r
1275 alignPanel.setOverviewPanel(overview);
\r
1279 protected void noColourmenuItem_actionPerformed()
\r
1281 changeColour(null);
\r
1284 public void clustalColour_actionPerformed()
\r
1286 abovePIDThreshold.setState(false);
\r
1287 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
\r
1288 viewport.alignment.getWidth()));
\r
1291 public void zappoColour_actionPerformed()
\r
1293 changeColour(new ZappoColourScheme());
\r
1296 public void taylorColour_actionPerformed()
\r
1298 changeColour(new TaylorColourScheme());
\r
1301 public void hydrophobicityColour_actionPerformed()
\r
1303 changeColour(new HydrophobicColourScheme());
\r
1306 public void helixColour_actionPerformed()
\r
1308 changeColour(new HelixColourScheme());
\r
1311 public void strandColour_actionPerformed()
\r
1313 changeColour(new StrandColourScheme());
\r
1316 public void turnColour_actionPerformed()
\r
1318 changeColour(new TurnColourScheme());
\r
1321 public void buriedColour_actionPerformed()
\r
1323 changeColour(new BuriedColourScheme());
\r
1326 public void nucleotideColour_actionPerformed()
\r
1328 changeColour(new NucleotideColourScheme());
\r
1331 protected void applyToAllGroups_actionPerformed()
\r
1333 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
\r
1336 void changeColour(ColourSchemeI cs)
\r
1338 int threshold = 0;
\r
1342 if (viewport.getAbovePIDThreshold())
\r
1344 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
\r
1346 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1348 viewport.setGlobalColourScheme(cs);
\r
1352 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1355 if (viewport.getConservationSelected())
\r
1358 Alignment al = (Alignment) viewport.alignment;
\r
1359 Conservation c = new Conservation("All",
\r
1360 ResidueProperties.propHash, 3,
\r
1361 al.getSequences(), 0,
\r
1362 al.getWidth() - 1);
\r
1365 c.verdict(false, viewport.ConsPercGaps);
\r
1367 cs.setConservation(c);
\r
1369 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1375 cs.setConservation(null);
\r
1378 cs.setConsensus(viewport.vconsensus);
\r
1381 viewport.setGlobalColourScheme(cs);
\r
1383 if (viewport.getColourAppliesToAllGroups())
\r
1385 Vector groups = viewport.alignment.getGroups();
\r
1386 for (int i = 0; i < groups.size(); i++)
\r
1388 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1395 if (cs instanceof ClustalxColourScheme)
\r
1397 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1403 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1405 catch (Exception ex)
\r
1407 ex.printStackTrace();
\r
1412 if (viewport.getAbovePIDThreshold()
\r
1413 || cs instanceof PIDColourScheme
\r
1414 || cs instanceof Blosum62ColourScheme)
\r
1416 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1417 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
1420 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1422 if (viewport.getConservationSelected())
\r
1424 Conservation c = new Conservation("Group",
\r
1425 ResidueProperties.propHash, 3,
\r
1427 viewport.alignment.getWidth() - 1);
\r
1429 c.verdict(false, viewport.ConsPercGaps);
\r
1430 sg.cs.setConservation(c);
\r
1434 sg.cs.setConservation(null);
\r
1435 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1442 if (alignPanel.getOverviewPanel() != null)
\r
1444 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1447 alignPanel.repaint();
\r
1452 protected void modifyPID_actionPerformed()
\r
1454 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1456 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
1458 SliderPanel.showPIDSlider();
\r
1462 protected void modifyConservation_actionPerformed()
\r
1464 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1466 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
1468 SliderPanel.showConservationSlider();
\r
1472 protected void conservationMenuItem_actionPerformed()
\r
1474 viewport.setConservationSelected(conservationMenuItem.getState());
\r
1476 viewport.setAbovePIDThreshold(false);
\r
1477 abovePIDThreshold.setState(false);
\r
1479 changeColour(viewport.getGlobalColourScheme());
\r
1481 modifyConservation_actionPerformed();
\r
1484 public void abovePIDThreshold_actionPerformed()
\r
1486 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
1488 conservationMenuItem.setState(false);
\r
1489 viewport.setConservationSelected(false);
\r
1491 changeColour(viewport.getGlobalColourScheme());
\r
1493 modifyPID_actionPerformed();
\r
1496 public void userDefinedColour_actionPerformed()
\r
1498 new UserDefinedColours(alignPanel, null);
\r
1501 public void PIDColour_actionPerformed()
\r
1503 changeColour(new PIDColourScheme());
\r
1506 public void BLOSUM62Colour_actionPerformed()
\r
1508 changeColour(new Blosum62ColourScheme());
\r
1511 public void sortPairwiseMenuItem_actionPerformed()
\r
1513 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1514 HistoryItem.SORT));
\r
1515 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1516 viewport.getAlignment().getSequenceAt(0));
\r
1517 alignPanel.repaint();
\r
1520 public void sortIDMenuItem_actionPerformed()
\r
1522 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1523 HistoryItem.SORT));
\r
1524 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1525 alignPanel.repaint();
\r
1528 public void sortGroupMenuItem_actionPerformed()
\r
1530 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1531 HistoryItem.SORT));
\r
1532 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1533 alignPanel.repaint();
\r
1537 public void removeRedundancyMenuItem_actionPerformed()
\r
1539 RedundancyPanel sp = new RedundancyPanel(alignPanel);
\r
1540 Frame frame = new Frame();
\r
1542 jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",
\r
1547 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
1549 if (viewport.getSelectionGroup().getSize() > 1)
\r
1551 Frame frame = new Frame();
\r
1552 frame.add(new PairwiseAlignPanel(alignPanel));
\r
1553 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
1557 public void PCAMenuItem_actionPerformed()
\r
1559 //are the sequences aligned?
\r
1560 if (!viewport.alignment.isAligned())
\r
1562 SequenceI current;
\r
1563 int Width = viewport.getAlignment().getWidth();
\r
1565 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1568 current = viewport.getAlignment().getSequenceAt(i);
\r
1570 if (current.getLength() < Width)
\r
1572 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1575 alignPanel.repaint();
\r
1578 if ( (viewport.getSelectionGroup() != null &&
\r
1579 viewport.getSelectionGroup().getSize() < 4 &&
\r
1580 viewport.getSelectionGroup().getSize() > 0)
\r
1581 || viewport.getAlignment().getHeight() < 4)
\r
1588 new PCAPanel(viewport);
\r
1590 catch (java.lang.OutOfMemoryError ex)
\r
1596 public void averageDistanceTreeMenuItem_actionPerformed()
\r
1598 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1601 public void neighbourTreeMenuItem_actionPerformed()
\r
1603 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1606 protected void njTreeBlosumMenuItem_actionPerformed()
\r
1608 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1611 protected void avTreeBlosumMenuItem_actionPerformed()
\r
1613 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1616 void NewTreePanel(String type, String pwType, String title)
\r
1618 //are the sequences aligned?
\r
1619 if (!viewport.alignment.isAligned())
\r
1621 SequenceI current;
\r
1622 int Width = viewport.getAlignment().getWidth();
\r
1624 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1627 current = viewport.getAlignment().getSequenceAt(i);
\r
1629 if (current.getLength() < Width)
\r
1631 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1634 alignPanel.repaint();
\r
1638 final TreePanel tp;
\r
1639 if (viewport.getSelectionGroup() != null &&
\r
1640 viewport.getSelectionGroup().getSize() > 3)
\r
1642 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
\r
1644 0, viewport.alignment.getWidth());
\r
1648 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1649 type, pwType, 0, viewport.alignment.getWidth());
\r
1652 addTreeMenuItem(tp, title);
\r
1654 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
1657 void loadTree_actionPerformed()
\r
1659 TreePanel tp = null;
\r
1661 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1662 cap.setText("Paste your Newick tree file here.");
\r
1663 cap.treeImport = true;
\r
1664 Frame frame = new Frame();
\r
1666 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
1669 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
1671 TreePanel tp = new TreePanel(viewport,
\r
1672 viewport.getAlignment().getSequences(),
\r
1673 tree, "From File - ", treeFile);
\r
1674 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
1675 addTreeMenuItem(tp, treeFile);
\r
1678 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1680 final MenuItem item = new MenuItem(title);
\r
1681 sortByTreeMenu.add(item);
\r
1682 item.addActionListener(new java.awt.event.ActionListener()
\r
1684 public void actionPerformed(ActionEvent evt)
\r
1686 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1687 HistoryItem.SORT));
\r
1688 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1689 alignPanel.repaint();
\r
1693 treePanel.addWindowListener(new WindowAdapter()
\r
1695 public void windowClosing(WindowEvent e)
\r
1697 sortByTreeMenu.remove(item);
\r
1702 protected void documentation_actionPerformed()
\r
1704 showURL("http://www.jalview.org/help.html", "HELP");
\r
1707 protected void about_actionPerformed()
\r
1710 class AboutPanel extends Canvas
\r
1713 public AboutPanel(String version)
\r
1714 { this.version = version; }
\r
1716 public void paint(Graphics g)
\r
1718 g.setColor(Color.white);
\r
1719 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1720 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1721 FontMetrics fm = g.getFontMetrics();
\r
1722 int fh = fm.getHeight();
\r
1724 g.setColor(Color.black);
\r
1725 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
1726 g.drawString("Jalview - Release "+version, 200, y += fh);
\r
1727 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1728 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
1730 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
1733 "For any issues relating to Jalview, email help@jalview.org", x,
\r
1735 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
1736 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
1738 g.drawString("Bioinformatics, 2004 12;426-7.", x, y += fh);
\r
1742 String version = "test";
\r
1743 java.net.URL url = getClass().getResource("/.build_properties");
\r
1748 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
1749 url.openStream()));
\r
1751 while ( (line = reader.readLine()) != null)
\r
1753 if (line.indexOf("VERSION") > -1)
\r
1755 version = line.substring(line.indexOf("=") + 1);
\r
1759 catch (Exception ex)
\r
1761 ex.printStackTrace();
\r
1766 Frame frame = new Frame();
\r
1767 frame.add(new AboutPanel(version));
\r
1768 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
\r
1772 public void showURL(String url, String target)
\r
1774 if (applet == null)
\r
1776 System.out.println("Not running as applet - no browser available.");
\r
1782 applet.getAppletContext().showDocument(new java.net.URL(url),
\r
1785 catch (Exception ex)
\r
1787 ex.printStackTrace();
\r
1793 //////////////////////////////////////////////////////////////////////////////////
\r
1794 //JBuilder Graphics here
\r
1796 protected MenuBar alignFrameMenuBar = new MenuBar();
\r
1797 protected Menu fileMenu = new Menu("File");
\r
1798 protected MenuItem loadTree = new MenuItem("Load Associated Tree");
\r
1799 protected MenuItem closeMenuItem = new MenuItem("Close");
\r
1800 protected Menu editMenu = new Menu("Edit");
\r
1801 protected Menu viewMenu = new Menu("View");
\r
1802 protected Menu colourMenu = new Menu("Colour");
\r
1803 protected Menu calculateMenu = new Menu("Calculate");
\r
1804 protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
1805 protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
1806 protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
1807 protected MenuItem remove2LeftMenuItem = new MenuItem();
\r
1808 protected MenuItem remove2RightMenuItem = new MenuItem();
\r
1809 protected MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
1810 protected MenuItem removeAllGapsMenuItem = new MenuItem();
\r
1811 protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
1812 protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
1813 protected MenuItem sortPairwiseMenuItem = new MenuItem();
\r
1814 protected MenuItem sortIDMenuItem = new MenuItem();
\r
1815 protected MenuItem sortGroupMenuItem = new MenuItem();
\r
1816 protected MenuItem removeRedundancyMenuItem = new MenuItem();
\r
1817 protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
1818 protected MenuItem PCAMenuItem = new MenuItem();
\r
1819 protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
1820 protected MenuItem neighbourTreeMenuItem = new MenuItem();
\r
1821 BorderLayout borderLayout1 = new BorderLayout();
\r
1822 public Label statusBar = new Label();
\r
1823 protected Menu outputTextboxMenu = new Menu();
\r
1824 protected MenuItem clustalColour = new MenuItem();
\r
1825 protected MenuItem zappoColour = new MenuItem();
\r
1826 protected MenuItem taylorColour = new MenuItem();
\r
1827 protected MenuItem hydrophobicityColour = new MenuItem();
\r
1828 protected MenuItem helixColour = new MenuItem();
\r
1829 protected MenuItem strandColour = new MenuItem();
\r
1830 protected MenuItem turnColour = new MenuItem();
\r
1831 protected MenuItem buriedColour = new MenuItem();
\r
1832 protected MenuItem userDefinedColour = new MenuItem();
\r
1833 protected MenuItem PIDColour = new MenuItem();
\r
1834 protected MenuItem BLOSUM62Colour = new MenuItem();
\r
1835 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
1836 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
1837 protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
1838 protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
1839 MenuItem overviewMenuItem = new MenuItem();
\r
1840 protected MenuItem undoMenuItem = new MenuItem();
\r
1841 protected MenuItem redoMenuItem = new MenuItem();
\r
1842 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
1843 MenuItem noColourmenuItem = new MenuItem();
\r
1844 protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
1845 protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
1846 MenuItem findMenuItem = new MenuItem();
\r
1847 Menu searchMenu = new Menu();
\r
1848 protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
1849 protected MenuItem nucleotideColour = new MenuItem();
\r
1850 MenuItem deleteGroups = new MenuItem();
\r
1851 MenuItem delete = new MenuItem();
\r
1852 MenuItem copy = new MenuItem();
\r
1853 MenuItem cut = new MenuItem();
\r
1854 Menu pasteMenu = new Menu();
\r
1855 MenuItem pasteNew = new MenuItem();
\r
1856 MenuItem pasteThis = new MenuItem();
\r
1857 protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
1858 protected MenuItem font = new MenuItem();
\r
1859 protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
1860 protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
1861 protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
1862 MenuItem modifyPID = new MenuItem();
\r
1863 MenuItem modifyConservation = new MenuItem();
\r
1864 protected CheckboxMenuItem autoCalculate
\r
1865 = new CheckboxMenuItem("Autocalculate Consensus", true);
\r
1866 protected Menu sortByTreeMenu = new Menu();
\r
1867 Menu sort = new Menu();
\r
1868 Menu calculate = new Menu();
\r
1869 MenuItem inputText = new MenuItem();
\r
1870 Menu helpMenu = new Menu();
\r
1871 MenuItem documentation = new MenuItem();
\r
1872 MenuItem about = new MenuItem();
\r
1873 protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
1874 Panel embeddedMenu;
\r
1875 Label embeddedEdit;
\r
1876 Label embeddedSearch;
\r
1877 Label embeddedView;
\r
1878 Label embeddedColour;
\r
1879 Label embeddedFile;
\r
1880 Label embeddedHelp;
\r
1881 Label embeddedCalculate;
\r
1882 FlowLayout flowLayout1;
\r
1884 private void jbInit() throws Exception {
\r
1886 setMenuBar(alignFrameMenuBar);
\r
1890 // dynamically fill save as menu with available formats
\r
1891 for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++)
\r
1894 item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.
\r
1897 item.addActionListener(new java.awt.event.ActionListener()
\r
1899 public void actionPerformed(ActionEvent e)
\r
1901 outputText_actionPerformed(e);
\r
1905 outputTextboxMenu.add(item);
\r
1907 closeMenuItem.addActionListener(this);
\r
1909 loadTree.addActionListener(this);
\r
1910 selectAllSequenceMenuItem.addActionListener(this);
\r
1911 deselectAllSequenceMenuItem.addActionListener(this);
\r
1912 invertSequenceMenuItem.addActionListener(this);
\r
1913 remove2LeftMenuItem.setLabel("Remove Left");
\r
1914 remove2LeftMenuItem.addActionListener(this);
\r
1915 remove2RightMenuItem.setLabel("Remove Right");
\r
1916 remove2RightMenuItem.addActionListener(this);
\r
1917 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
1918 removeGappedColumnMenuItem.addActionListener(this);
\r
1919 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
1920 removeAllGapsMenuItem.addActionListener(this);
\r
1921 viewBoxesMenuItem.setLabel("Boxes");
\r
1922 viewBoxesMenuItem.setState(true);
\r
1923 viewBoxesMenuItem.addItemListener(this);
\r
1924 viewTextMenuItem.setLabel("Text");
\r
1925 viewTextMenuItem.setState(true);
\r
1926 viewTextMenuItem.addItemListener(this);
\r
1927 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
1928 sortPairwiseMenuItem.addActionListener(this);
\r
1929 sortIDMenuItem.setLabel("by ID");
\r
1930 sortIDMenuItem.addActionListener(this);
\r
1931 sortGroupMenuItem.setLabel("by Group");
\r
1932 sortGroupMenuItem.addActionListener(this);
\r
1933 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
1934 removeRedundancyMenuItem.addActionListener(this);
\r
1935 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
1936 pairwiseAlignmentMenuItem.addActionListener(this);
\r
1937 PCAMenuItem.setLabel("Principal Component Analysis");
\r
1938 PCAMenuItem.addActionListener(this);
\r
1939 averageDistanceTreeMenuItem.setLabel(
\r
1940 "Average Distance Using % Identity");
\r
1941 averageDistanceTreeMenuItem.addActionListener(this);
\r
1942 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
1943 neighbourTreeMenuItem.addActionListener(this);
\r
1944 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
1945 statusBar.setBackground(Color.white);
\r
1946 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
1947 statusBar.setText("Status bar");
\r
1948 outputTextboxMenu.setLabel("Output to Textbox");
\r
1949 clustalColour.setLabel("Clustalx");
\r
1951 clustalColour.addActionListener(this);
\r
1952 zappoColour.setLabel("Zappo");
\r
1953 zappoColour.addActionListener(this);
\r
1954 taylorColour.setLabel("Taylor");
\r
1955 taylorColour.addActionListener(this);
\r
1956 hydrophobicityColour.setLabel("Hydrophobicity");
\r
1957 hydrophobicityColour.addActionListener(this);
\r
1958 helixColour.setLabel("Helix Propensity");
\r
1959 helixColour.addActionListener(this);
\r
1960 strandColour.setLabel("Strand Propensity");
\r
1961 strandColour.addActionListener(this);
\r
1962 turnColour.setLabel("Turn Propensity");
\r
1963 turnColour.addActionListener(this);
\r
1964 buriedColour.setLabel("Buried Index");
\r
1965 buriedColour.addActionListener(this);
\r
1966 userDefinedColour.setLabel("User Defined...");
\r
1967 userDefinedColour.addActionListener(this);
\r
1968 PIDColour.setLabel("Percentage Identity");
\r
1969 PIDColour.addActionListener(this);
\r
1970 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
1971 BLOSUM62Colour.addActionListener(this);
\r
1972 avDistanceTreeBlosumMenuItem.setLabel(
\r
1973 "Average Distance Using BLOSUM62");
\r
1974 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
1975 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
1976 njTreeBlosumMenuItem.addActionListener(this);
\r
1977 annotationPanelMenuItem.setLabel("Show Annotations");
\r
1978 annotationPanelMenuItem.addItemListener(this);
\r
1979 colourTextMenuItem.setLabel("Colour Text");
\r
1980 colourTextMenuItem.addItemListener(this);
\r
1981 overviewMenuItem.setLabel("Overview Window");
\r
1982 overviewMenuItem.addActionListener(this);
\r
1983 undoMenuItem.setEnabled(false);
\r
1984 undoMenuItem.setLabel("Undo");
\r
1985 undoMenuItem.addActionListener(this);
\r
1986 redoMenuItem.setEnabled(false);
\r
1987 redoMenuItem.setLabel("Redo");
\r
1988 redoMenuItem.addActionListener(this);
\r
1989 conservationMenuItem.setLabel("by Conservation");
\r
1990 conservationMenuItem.addItemListener(this);
\r
1991 noColourmenuItem.setLabel("None");
\r
1992 noColourmenuItem.addActionListener(this);
\r
1993 wrapMenuItem.setLabel("Wrap");
\r
1994 wrapMenuItem.addItemListener(this);
\r
1995 renderGapsMenuItem.setLabel("Show Gaps");
\r
1996 renderGapsMenuItem.setState(true);
\r
1997 renderGapsMenuItem.addItemListener(this);
\r
1998 findMenuItem.setLabel("Find...");
\r
1999 findMenuItem.addActionListener(this);
\r
2000 searchMenu.setLabel("Search");
\r
2002 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
2003 abovePIDThreshold.addItemListener(this);
\r
2004 nucleotideColour.setLabel("Nucleotide");
\r
2005 nucleotideColour.addActionListener(this);
\r
2006 deleteGroups.setLabel("Undefine Groups");
\r
2007 deleteGroups.addActionListener(this);
\r
2008 copy.setLabel("Copy");
\r
2009 copy.addActionListener(this);
\r
2010 cut.setLabel("Cut");
\r
2011 cut.addActionListener(this);
\r
2012 delete.setLabel("Delete");
\r
2013 delete.addActionListener(this);
\r
2014 pasteMenu.setLabel("Paste");
\r
2015 pasteNew.setLabel("To New Alignment");
\r
2016 pasteNew.addActionListener(this);
\r
2017 pasteThis.setLabel("Add To This Alignment");
\r
2018 pasteThis.addActionListener(this);
\r
2019 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
2020 applyToAllGroups.setState(true);
\r
2021 applyToAllGroups.addItemListener(this);
\r
2022 font.setLabel("Font...");
\r
2023 font.addActionListener(this);
\r
2024 scaleAbove.setLabel("Scale Above");
\r
2025 scaleAbove.setState(true);
\r
2026 scaleAbove.setEnabled(false);
\r
2027 scaleAbove.addItemListener(this);
\r
2028 scaleLeft.setEnabled(false);
\r
2029 scaleLeft.setState(true);
\r
2030 scaleLeft.setLabel("Scale Left");
\r
2031 scaleLeft.addItemListener(this);
\r
2032 scaleRight.setEnabled(false);
\r
2033 scaleRight.setState(true);
\r
2034 scaleRight.setLabel("Scale Right");
\r
2035 scaleRight.addItemListener(this);
\r
2036 modifyPID.setLabel("Modify Identity Threshold...");
\r
2037 modifyPID.addActionListener(this);
\r
2038 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
2039 modifyConservation.addActionListener(this);
\r
2040 sortByTreeMenu.setLabel("By Tree Order");
\r
2041 sort.setLabel("Sort");
\r
2042 calculate.setLabel("Calculate Tree");
\r
2043 autoCalculate.addItemListener(this);
\r
2044 inputText.setLabel("Input from textbox");
\r
2045 inputText.addActionListener(this);
\r
2047 helpMenu.setLabel("Help");
\r
2048 documentation.setLabel("Documentation");
\r
2049 documentation.addActionListener(this);
\r
2051 about.setLabel("About...");
\r
2052 about.addActionListener(this);
\r
2053 seqLimits.setState(true);
\r
2054 seqLimits.setLabel("Show Sequence Limits");
\r
2055 seqLimits.addItemListener(this);
\r
2056 featureSettings.setLabel("Feature Settings...");
\r
2057 featureSettings.addActionListener(this);
\r
2058 sequenceFeatures.setLabel("Sequence Features");
\r
2059 sequenceFeatures.addItemListener(this);
\r
2060 sequenceFeatures.setState(false);
\r
2061 annotationColour.setLabel("by Annotation...");
\r
2062 annotationColour.addActionListener(this);
\r
2064 alignFrameMenuBar.add(fileMenu);
\r
2065 alignFrameMenuBar.add(editMenu);
\r
2066 alignFrameMenuBar.add(searchMenu);
\r
2067 alignFrameMenuBar.add(viewMenu);
\r
2068 alignFrameMenuBar.add(colourMenu);
\r
2069 alignFrameMenuBar.add(calculateMenu);
\r
2070 alignFrameMenuBar.add(helpMenu);
\r
2071 fileMenu.add(inputText);
\r
2072 fileMenu.add(outputTextboxMenu);
\r
2073 fileMenu.addSeparator();
\r
2074 fileMenu.add(loadTree);
\r
2075 fileMenu.add(closeMenuItem);
\r
2076 editMenu.add(undoMenuItem);
\r
2077 editMenu.add(redoMenuItem);
\r
2078 editMenu.add(cut);
\r
2079 editMenu.add(copy);
\r
2080 editMenu.add(pasteMenu);
\r
2081 editMenu.add(delete);
\r
2082 editMenu.addSeparator();
\r
2083 editMenu.add(selectAllSequenceMenuItem);
\r
2084 editMenu.add(deselectAllSequenceMenuItem);
\r
2085 editMenu.add(invertSequenceMenuItem);
\r
2086 editMenu.add(deleteGroups);
\r
2087 editMenu.addSeparator();
\r
2088 editMenu.add(remove2LeftMenuItem);
\r
2089 editMenu.add(remove2RightMenuItem);
\r
2090 editMenu.add(removeGappedColumnMenuItem);
\r
2091 editMenu.add(removeAllGapsMenuItem);
\r
2092 editMenu.add(removeRedundancyMenuItem);
\r
2093 searchMenu.add(findMenuItem);
\r
2094 viewMenu.add(font);
\r
2095 viewMenu.addSeparator();
\r
2096 viewMenu.add(seqLimits);
\r
2097 viewMenu.addSeparator();
\r
2098 viewMenu.add(wrapMenuItem);
\r
2099 viewMenu.add(scaleAbove);
\r
2100 viewMenu.add(scaleLeft);
\r
2101 viewMenu.add(scaleRight);
\r
2102 viewMenu.addSeparator();
\r
2103 viewMenu.add(viewBoxesMenuItem);
\r
2104 viewMenu.add(viewTextMenuItem);
\r
2105 viewMenu.add(colourTextMenuItem);
\r
2106 viewMenu.add(renderGapsMenuItem);
\r
2107 viewMenu.add(annotationPanelMenuItem);
\r
2108 viewMenu.addSeparator();
\r
2109 viewMenu.add(sequenceFeatures);
\r
2110 viewMenu.add(featureSettings);
\r
2111 viewMenu.addSeparator();
\r
2112 viewMenu.add(overviewMenuItem);
\r
2113 colourMenu.add(applyToAllGroups);
\r
2114 colourMenu.addSeparator();
\r
2115 colourMenu.add(noColourmenuItem);
\r
2116 colourMenu.add(clustalColour);
\r
2117 colourMenu.add(BLOSUM62Colour);
\r
2118 colourMenu.add(PIDColour);
\r
2119 colourMenu.add(zappoColour);
\r
2120 colourMenu.add(taylorColour);
\r
2121 colourMenu.add(hydrophobicityColour);
\r
2122 colourMenu.add(helixColour);
\r
2123 colourMenu.add(strandColour);
\r
2124 colourMenu.add(turnColour);
\r
2125 colourMenu.add(buriedColour);
\r
2126 colourMenu.add(nucleotideColour);
\r
2127 colourMenu.add(userDefinedColour);
\r
2128 colourMenu.addSeparator();
\r
2129 colourMenu.add(conservationMenuItem);
\r
2130 colourMenu.add(modifyConservation);
\r
2131 colourMenu.add(abovePIDThreshold);
\r
2132 colourMenu.add(modifyPID);
\r
2133 colourMenu.add(annotationColour);
\r
2134 calculateMenu.add(sort);
\r
2135 calculateMenu.add(calculate);
\r
2136 calculateMenu.addSeparator();
\r
2137 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
2138 calculateMenu.add(PCAMenuItem);
\r
2139 calculateMenu.add(autoCalculate);
\r
2140 this.add(statusBar, BorderLayout.SOUTH);
\r
2141 pasteMenu.add(pasteNew);
\r
2142 pasteMenu.add(pasteThis);
\r
2143 sort.add(sortIDMenuItem);
\r
2144 sort.add(sortByTreeMenu);
\r
2145 sort.add(sortGroupMenuItem);
\r
2146 sort.add(sortPairwiseMenuItem);
\r
2147 calculate.add(averageDistanceTreeMenuItem);
\r
2148 calculate.add(neighbourTreeMenuItem);
\r
2149 calculate.add(avDistanceTreeBlosumMenuItem);
\r
2150 calculate.add(njTreeBlosumMenuItem);
\r
2151 helpMenu.add(documentation);
\r
2152 helpMenu.add(about);
\r
2155 public void setEmbedded()
\r
2158 embeddedMenu = new Panel();
\r
2159 embeddedEdit = new Label();
\r
2160 embeddedSearch = new Label();
\r
2161 embeddedView = new Label();
\r
2162 embeddedColour = new Label();
\r
2163 embeddedFile = new Label();
\r
2164 embeddedHelp = new Label();
\r
2165 embeddedCalculate = new Label();
\r
2166 flowLayout1 = new FlowLayout();
\r
2167 embeddedMenu.setBackground(Color.lightGray);
\r
2168 embeddedMenu.setLayout(flowLayout1);
\r
2169 embeddedEdit.setText("Edit");
\r
2170 embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2171 embeddedSearch.setText("Search");
\r
2172 embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2173 embeddedView.setText("View");
\r
2174 embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2175 embeddedColour.setText("Colour");
\r
2176 embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2177 embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2178 embeddedFile.setText("File");
\r
2179 embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2180 embeddedHelp.setText("Help");
\r
2181 embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2182 embeddedCalculate.setText("Calculate");
\r
2183 embeddedMenu.add(embeddedFile);
\r
2184 embeddedMenu.add(embeddedEdit);
\r
2185 embeddedMenu.add(embeddedSearch);
\r
2186 embeddedMenu.add(embeddedView);
\r
2187 embeddedMenu.add(embeddedColour);
\r
2188 embeddedMenu.add(embeddedCalculate);
\r
2189 embeddedMenu.add(embeddedHelp);
\r
2190 flowLayout1.setAlignment(FlowLayout.LEFT);
\r
2191 flowLayout1.setHgap(2);
\r
2192 flowLayout1.setVgap(0);
\r
2193 embeddedFile.addMouseListener(this);
\r
2194 embeddedEdit.addMouseListener(this);
\r
2195 embeddedSearch.addMouseListener(this);
\r
2196 embeddedView.addMouseListener(this);
\r
2197 embeddedColour.addMouseListener(this);
\r
2198 embeddedCalculate.addMouseListener(this);
\r
2199 embeddedHelp.addMouseListener(this);
\r
2201 // setVisible(false);
\r
2202 fileMenu.remove(closeMenuItem);
\r
2203 fileMenu.remove(2); // Seperator
\r
2205 applet.setLayout(new BorderLayout());
\r
2206 applet.add(embeddedMenu, BorderLayout.NORTH);
\r
2207 applet.add(statusBar, BorderLayout.SOUTH);
\r
2208 // applet.validate();
\r
2210 alignPanel.setSize(applet.size().width, applet.size().height
\r
2211 - embeddedMenu.HEIGHT - statusBar.HEIGHT);
\r
2213 applet.add(alignPanel, BorderLayout.CENTER);
\r
2214 applet.validate();
\r
2220 PopupMenu filePopup, editPopup, searchPopup,
\r
2221 viewPopup, colourPopup, calculatePopup, helpPopup;
\r
2222 MenuItem featureSettings = new MenuItem();
\r
2223 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
2224 MenuItem annotationColour = new MenuItem();
\r
2226 public void mousePressed(MouseEvent evt)
\r
2228 PopupMenu popup = null;
\r
2229 Label source = (Label)evt.getSource();
\r
2230 if(source==embeddedFile)
\r
2232 popup = filePopup = genPopupMenu(filePopup, fileMenu);
\r
2234 else if(source==embeddedEdit)
\r
2236 popup = editPopup = genPopupMenu(editPopup, editMenu);
\r
2238 else if(source==embeddedSearch)
\r
2240 popup = searchPopup = genPopupMenu(searchPopup, searchMenu);
\r
2242 else if(source==embeddedView)
\r
2244 popup = viewPopup = genPopupMenu(viewPopup, viewMenu);
\r
2246 else if(source==embeddedColour)
\r
2248 popup = colourPopup = genPopupMenu(colourPopup, colourMenu);
\r
2250 else if(source==embeddedCalculate)
\r
2252 popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);
\r
2254 else if(source==embeddedHelp)
\r
2256 popup = helpPopup = genPopupMenu(helpPopup, helpMenu);
\r
2259 embeddedMenu.add(popup);
\r
2260 popup.show(embeddedMenu,
\r
2261 source.getBounds().x,
\r
2262 source.getBounds().y + source.getBounds().getSize().height);
\r
2265 PopupMenu genPopupMenu(PopupMenu popup, Menu original)
\r
2271 popup = new PopupMenu();
\r
2272 int m, mSize = original.getItemCount();
\r
2273 for(m=0; m<mSize; m++)
\r
2275 popup.add(original.getItem(m));
\r
2282 public void mouseClicked(MouseEvent evt)
\r
2284 public void mouseReleased(MouseEvent evt)
\r
2286 public void mouseEntered(MouseEvent evt)
\r
2288 public void mouseExited(MouseEvent evt)
\r