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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62 seqLimits.setState(viewport.showJVSuffix);
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66 String param = applet.getParameter("sortBy");
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69 if (param.equalsIgnoreCase("Id"))
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70 sortIDMenuItem_actionPerformed();
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71 else if (param.equalsIgnoreCase("Pairwise Identity"))
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72 sortPairwiseMenuItem_actionPerformed();
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75 param = applet.getParameter("wrap");
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78 if (param.equalsIgnoreCase("true"))
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80 wrapMenuItem.setState(true);
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81 wrapMenuItem_actionPerformed();
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87 param = applet.getParameter("windowWidth");
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90 int width = Integer.parseInt(param);
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91 NEW_WINDOW_WIDTH = width;
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93 param = applet.getParameter("windowHeight");
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96 int height = Integer.parseInt(param);
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97 NEW_WINDOW_HEIGHT = height;
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100 catch (Exception ex)
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105 //Some JVMS send keyevents to Top frame or lowest panel,
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106 //Havent worked out why yet. So add to both this frame and seqCanvas for now
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107 this.addKeyListener(this);
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108 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
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109 alignPanel.idPanel.idCanvas.addKeyListener(this);
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111 viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
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113 public void propertyChange(java.beans.PropertyChangeEvent evt)
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115 if (evt.getPropertyName().equals("alignment"))
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117 alignmentChanged();
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129 add(alignPanel, BorderLayout.CENTER);
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130 jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH,
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131 NEW_WINDOW_HEIGHT);
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133 alignPanel.validate();
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134 alignPanel.repaint();
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136 public AlignViewport getAlignViewport()
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141 public SeqCanvas getSeqcanvas()
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143 return alignPanel.seqPanel.seqCanvas;
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150 * @param String DOCUMENT ME!
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153 public void parseFeaturesFile(String file, String type)
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155 Hashtable featureLinks = new Hashtable();
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156 boolean featuresFile = false;
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158 featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport.alignment,
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159 alignPanel.seqPanel.seqCanvas.
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160 getFeatureRenderer().featureColours,
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164 catch(Exception ex)
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166 ex.printStackTrace();
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171 if(featureLinks.size()>0)
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172 alignPanel.seqPanel.seqCanvas
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173 .getFeatureRenderer().featureLinks = featureLinks;
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174 viewport.showSequenceFeatures = true;
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175 sequenceFeatures.setState(true);
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176 alignPanel.repaint();
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182 public void keyPressed(KeyEvent evt)
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184 if (viewport.cursorMode
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185 && evt.getKeyCode() >= KeyEvent.VK_0
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186 && evt.getKeyCode() <= KeyEvent.VK_9)
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188 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
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191 switch (evt.getKeyCode())
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193 case 27: // escape key
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194 deselectAllSequenceMenuItem_actionPerformed();
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196 case KeyEvent.VK_X:
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197 if (evt.isControlDown() || evt.isMetaDown())
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199 cut_actionPerformed();
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202 case KeyEvent.VK_C:
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203 if (viewport.cursorMode && !evt.isControlDown())
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205 alignPanel.seqPanel.setCursorColumn();
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207 if (evt.isControlDown() || evt.isMetaDown())
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209 copy_actionPerformed();
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212 case KeyEvent.VK_V:
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213 if (evt.isControlDown() || evt.isMetaDown())
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218 case KeyEvent.VK_A:
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219 if (evt.isControlDown() || evt.isMetaDown())
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221 selectAllSequenceMenuItem_actionPerformed();
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224 case KeyEvent.VK_DOWN:
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225 if(viewport.cursorMode)
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227 alignPanel.seqPanel.moveCursor(0,1);
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230 moveSelectedSequences(false);
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233 case KeyEvent.VK_UP:
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234 if (viewport.cursorMode)
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236 alignPanel.seqPanel.moveCursor(0,-1);
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239 moveSelectedSequences(true);
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242 case KeyEvent.VK_LEFT:
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243 if(viewport.cursorMode)
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245 alignPanel.seqPanel.moveCursor(-1,0);
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249 case KeyEvent.VK_RIGHT:
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250 if (viewport.cursorMode)
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252 alignPanel.seqPanel.moveCursor(1,0);
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255 case KeyEvent.VK_SPACE:
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256 if(viewport.cursorMode)
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258 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown());
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262 case KeyEvent.VK_DELETE:
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263 case KeyEvent.VK_BACK_SPACE:
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264 if(viewport.cursorMode)
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266 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown());
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270 cut_actionPerformed();
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271 alignPanel.seqPanel.seqCanvas.repaint();
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275 case KeyEvent.VK_S:
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276 if(viewport.cursorMode)
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278 alignPanel.seqPanel.setCursorRow();
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281 case KeyEvent.VK_P:
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282 if(viewport.cursorMode)
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284 alignPanel.seqPanel.setCursorPosition();
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288 case KeyEvent.VK_ENTER:
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289 case KeyEvent.VK_COMMA:
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290 if(viewport.cursorMode)
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292 alignPanel.seqPanel.setCursorRowAndColumn();
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296 case KeyEvent.VK_Q:
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297 if(viewport.cursorMode)
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299 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
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302 case KeyEvent.VK_M:
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303 if(viewport.cursorMode)
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305 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
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309 case KeyEvent.VK_F2:
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310 viewport.cursorMode = ! viewport.cursorMode;
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311 statusBar.setText("Keyboard editing mode is "+
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312 (viewport.cursorMode ? "on" : "off"));
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313 if(viewport.cursorMode)
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315 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
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316 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
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318 alignPanel.seqPanel.seqCanvas.repaint();
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321 case KeyEvent.VK_F:
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322 if (evt.isControlDown())
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324 findMenuItem_actionPerformed();
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329 public void keyReleased(KeyEvent evt)
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331 public void keyTyped(KeyEvent evt)
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334 public void itemStateChanged(ItemEvent evt)
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336 if(evt.getSource()==colourTextMenuItem)
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337 colourTextMenuItem_actionPerformed();
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338 else if(evt.getSource()==wrapMenuItem)
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339 wrapMenuItem_actionPerformed();
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340 else if(evt.getSource()==scaleAbove)
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341 scaleAbove_actionPerformed();
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342 else if(evt.getSource()==scaleLeft)
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343 scaleLeft_actionPerformed();
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344 else if(evt.getSource()==scaleRight)
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345 scaleRight_actionPerformed();
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346 else if(evt.getSource()==seqLimits)
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347 seqLimits_itemStateChanged();
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348 else if(evt.getSource()==viewBoxesMenuItem)
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349 viewBoxesMenuItem_actionPerformed();
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350 else if(evt.getSource()==viewTextMenuItem)
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351 viewTextMenuItem_actionPerformed();
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352 else if(evt.getSource()==renderGapsMenuItem)
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353 renderGapsMenuItem_actionPerformed();
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354 else if(evt.getSource()==annotationPanelMenuItem)
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355 annotationPanelMenuItem_actionPerformed();
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356 else if(evt.getSource()==sequenceFeatures)
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358 viewport.showSequenceFeatures(sequenceFeatures.getState());
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359 alignPanel.seqPanel.seqCanvas.repaint();
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361 else if(evt.getSource()==conservationMenuItem)
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362 conservationMenuItem_actionPerformed();
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363 else if(evt.getSource()==abovePIDThreshold)
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364 abovePIDThreshold_actionPerformed();
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365 else if(evt.getSource()==applyToAllGroups)
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366 applyToAllGroups_actionPerformed();
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367 else if(evt.getSource()==autoCalculate)
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368 viewport.autocalculateConsensus = autoCalculate.getState();
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370 public void actionPerformed(ActionEvent evt)
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372 if(evt.getSource()==inputText)
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373 inputText_actionPerformed();
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374 else if(evt.getSource()==loadTree)
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375 loadTree_actionPerformed();
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376 else if(evt.getSource()==loadApplication)
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377 launchFullApplication();
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378 else if(evt.getSource()==closeMenuItem)
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379 closeMenuItem_actionPerformed();
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380 else if(evt.getSource()==copy)
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381 copy_actionPerformed();
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382 else if(evt.getSource()==undoMenuItem)
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383 undoMenuItem_actionPerformed();
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384 else if(evt.getSource()==redoMenuItem)
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385 redoMenuItem_actionPerformed();
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386 else if(evt.getSource()==inputText)
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387 inputText_actionPerformed();
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388 else if(evt.getSource()==closeMenuItem)
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389 closeMenuItem_actionPerformed();
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390 else if(evt.getSource()==undoMenuItem)
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391 undoMenuItem_actionPerformed();
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392 else if(evt.getSource()==redoMenuItem)
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393 redoMenuItem_actionPerformed();
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394 else if(evt.getSource()==copy)
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395 copy_actionPerformed();
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396 else if(evt.getSource()==pasteNew)
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397 pasteNew_actionPerformed();
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398 else if(evt.getSource()==pasteThis)
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399 pasteThis_actionPerformed();
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400 else if(evt.getSource()==cut)
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401 cut_actionPerformed();
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402 else if(evt.getSource()==delete)
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403 delete_actionPerformed();
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404 else if(evt.getSource()==deleteGroups)
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405 deleteGroups_actionPerformed();
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406 else if(evt.getSource()==selectAllSequenceMenuItem)
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407 selectAllSequenceMenuItem_actionPerformed();
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408 else if(evt.getSource()==deselectAllSequenceMenuItem)
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409 deselectAllSequenceMenuItem_actionPerformed();
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410 else if(evt.getSource()==invertSequenceMenuItem)
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411 invertSequenceMenuItem_actionPerformed();
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412 else if(evt.getSource()==remove2LeftMenuItem)
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413 remove2LeftMenuItem_actionPerformed();
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414 else if(evt.getSource()==remove2RightMenuItem)
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415 remove2RightMenuItem_actionPerformed();
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416 else if(evt.getSource()==removeGappedColumnMenuItem)
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417 removeGappedColumnMenuItem_actionPerformed();
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418 else if(evt.getSource()==removeAllGapsMenuItem)
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419 removeAllGapsMenuItem_actionPerformed();
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420 else if(evt.getSource()==findMenuItem)
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421 findMenuItem_actionPerformed();
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422 else if(evt.getSource()==font)
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423 font_actionPerformed();
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424 else if(evt.getSource()==featureSettings)
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425 featureSettings_actionPerformed();
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426 else if(evt.getSource()==overviewMenuItem)
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427 overviewMenuItem_actionPerformed();
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428 else if(evt.getSource()==noColourmenuItem)
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429 noColourmenuItem_actionPerformed();
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430 else if(evt.getSource()==clustalColour)
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431 clustalColour_actionPerformed();
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432 else if(evt.getSource()==zappoColour)
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433 zappoColour_actionPerformed();
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434 else if(evt.getSource()==taylorColour)
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435 taylorColour_actionPerformed();
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436 else if(evt.getSource()==hydrophobicityColour)
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437 hydrophobicityColour_actionPerformed();
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438 else if(evt.getSource()==helixColour)
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439 helixColour_actionPerformed();
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440 else if(evt.getSource()==strandColour)
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441 strandColour_actionPerformed();
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442 else if(evt.getSource()==turnColour)
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443 turnColour_actionPerformed();
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444 else if(evt.getSource()==buriedColour)
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445 buriedColour_actionPerformed();
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446 else if(evt.getSource()==nucleotideColour)
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447 nucleotideColour_actionPerformed();
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448 else if(evt.getSource()==modifyPID)
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449 modifyPID_actionPerformed();
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450 else if(evt.getSource()==modifyConservation)
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451 modifyConservation_actionPerformed();
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452 else if(evt.getSource()==userDefinedColour)
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453 userDefinedColour_actionPerformed();
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454 else if(evt.getSource()==PIDColour)
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455 PIDColour_actionPerformed();
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456 else if(evt.getSource()==BLOSUM62Colour)
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457 BLOSUM62Colour_actionPerformed();
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458 else if(evt.getSource()==annotationColour)
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459 new AnnotationColourChooser(viewport, alignPanel);
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460 else if(evt.getSource()==sortPairwiseMenuItem)
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461 sortPairwiseMenuItem_actionPerformed();
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462 else if(evt.getSource()==sortIDMenuItem)
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463 sortIDMenuItem_actionPerformed();
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464 else if(evt.getSource()==sortGroupMenuItem)
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465 sortGroupMenuItem_actionPerformed();
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466 else if(evt.getSource()==removeRedundancyMenuItem)
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467 removeRedundancyMenuItem_actionPerformed();
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468 else if(evt.getSource()==pairwiseAlignmentMenuItem)
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469 pairwiseAlignmentMenuItem_actionPerformed();
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470 else if(evt.getSource()==PCAMenuItem)
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471 PCAMenuItem_actionPerformed();
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472 else if(evt.getSource()==averageDistanceTreeMenuItem)
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473 averageDistanceTreeMenuItem_actionPerformed();
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474 else if(evt.getSource()==neighbourTreeMenuItem)
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475 neighbourTreeMenuItem_actionPerformed();
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476 else if(evt.getSource()==njTreeBlosumMenuItem)
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477 njTreeBlosumMenuItem_actionPerformed();
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478 else if(evt.getSource()==avDistanceTreeBlosumMenuItem)
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479 avTreeBlosumMenuItem_actionPerformed();
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480 else if(evt.getSource()==documentation)
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481 documentation_actionPerformed();
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482 else if(evt.getSource()==about)
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483 about_actionPerformed();
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487 public void inputText_actionPerformed()
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489 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
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490 Frame frame = new Frame();
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492 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
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495 protected void outputText_actionPerformed(ActionEvent e)
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497 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
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498 Frame frame = new Frame();
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500 jalview.bin.JalviewLite.addFrame(frame,
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501 "Alignment output - " + e.getActionCommand(),
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503 cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
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504 viewport.getAlignment().getSequences(),
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505 viewport.showJVSuffix));
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508 void launchFullApplication()
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510 StringBuffer url = new StringBuffer("http://bug.compbio.dundee.ac.uk:8080/Jalview/jalview?");
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512 url.append("open="+
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513 appendProtocol( applet.getParameter("file") ) );
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515 if(applet.getParameter("features")!=null)
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517 url.append( "&features=" );
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518 url.append( appendProtocol( applet.getParameter("features") ) );
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521 if(applet.getParameter("defaultColour")!=null)
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523 url.append("&colour=" +
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524 removeWhiteSpace(applet.getParameter("defaultColour"))
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528 if(applet.getParameter("userDefinedColour")!=null)
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530 url.append( "&colour=" +
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531 removeWhiteSpace( applet.getParameter("userDefinedColour") )
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535 showURL(url.toString(), "FULL_APP");
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539 String removeWhiteSpace(String colour)
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541 StringBuffer sb = new StringBuffer();
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542 for (int i = 0; i < colour.length(); i++)
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544 if (Character.isWhitespace(colour.charAt(i)))
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547 sb.append(colour.charAt(i));
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550 return sb.toString();
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554 String appendProtocol(String url)
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558 }catch(java.net.MalformedURLException ex)
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560 url = applet.getCodeBase()+url;
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565 public void closeMenuItem_actionPerformed()
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567 PaintRefresher.components.remove(viewport.alignment);
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568 if(PaintRefresher.components.size()==0 && applet==null)
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574 Stack historyList = new Stack();
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575 Stack redoList = new Stack();
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577 void updateEditMenuBar()
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579 if (historyList.size() > 0)
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581 undoMenuItem.setEnabled(true);
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582 HistoryItem hi = (HistoryItem) historyList.peek();
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583 undoMenuItem.setLabel("Undo " + hi.getDescription());
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587 undoMenuItem.setEnabled(false);
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588 undoMenuItem.setLabel("Undo");
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591 if (redoList.size() > 0)
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593 redoMenuItem.setEnabled(true);
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594 HistoryItem hi = (HistoryItem) redoList.peek();
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595 redoMenuItem.setLabel("Redo " + hi.getDescription());
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599 redoMenuItem.setEnabled(false);
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600 redoMenuItem.setLabel("Redo");
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604 public void addHistoryItem(HistoryItem hi)
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606 historyList.push(hi);
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607 updateEditMenuBar();
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610 protected void undoMenuItem_actionPerformed()
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612 HistoryItem hi = (HistoryItem) historyList.pop();
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613 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
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614 HistoryItem.HIDE));
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615 restoreHistoryItem(hi);
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616 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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619 protected void redoMenuItem_actionPerformed()
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621 HistoryItem hi = (HistoryItem) redoList.pop();
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622 restoreHistoryItem(hi);
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623 updateEditMenuBar();
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624 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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627 // used by undo and redo
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628 void restoreHistoryItem(HistoryItem hi)
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632 updateEditMenuBar();
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634 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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637 public void moveSelectedSequences(boolean up)
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639 SequenceGroup sg = viewport.getSelectionGroup();
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647 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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649 SequenceI seq = viewport.alignment.getSequenceAt(i);
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650 if (!sg.sequences.contains(seq))
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655 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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656 if (sg.sequences.contains(temp))
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661 viewport.alignment.getSequences().setElementAt(temp, i);
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662 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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667 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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669 SequenceI seq = viewport.alignment.getSequenceAt(i);
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670 if (!sg.sequences.contains(seq))
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675 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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676 if (sg.sequences.contains(temp))
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681 viewport.alignment.getSequences().setElementAt(temp, i);
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682 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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686 alignPanel.repaint();
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689 StringBuffer copiedSequences;
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690 protected void copy_actionPerformed()
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692 if (viewport.getSelectionGroup() == null)
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697 SequenceGroup sg = viewport.getSelectionGroup();
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698 copiedSequences = new StringBuffer();
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699 Hashtable orderedSeqs = new Hashtable();
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700 for (int i = 0; i < sg.getSize(); i++)
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702 SequenceI seq = sg.getSequenceAt(i);
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703 int index = viewport.alignment.findIndex(seq);
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704 orderedSeqs.put(index + "", seq);
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707 int index = 0, startRes, endRes;
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710 for (int i = 0; i < sg.getSize(); i++)
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712 SequenceI seq = null;
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714 while (seq == null)
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716 if (orderedSeqs.containsKey(index + ""))
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718 seq = (SequenceI) orderedSeqs.get(index + "");
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730 //Returns residue following index if gap
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731 startRes = seq.findPosition(sg.getStartRes());
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734 //Need to find the residue preceeding index if gap
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737 for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
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739 ch = seq.getCharAt(j);
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740 if (!jalview.util.Comparison.isGap( (ch)))
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748 endRes += seq.getStart() -1;
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751 copiedSequences.append(seq.getName() + "\t" +
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754 seq.getSequence(sg.getStartRes(),
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755 sg.getEndRes() + 1) + "\n");
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760 protected void pasteNew_actionPerformed()
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765 protected void pasteThis_actionPerformed()
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767 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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768 HistoryItem.PASTE));
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772 void paste(boolean newAlignment)
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776 if (copiedSequences == null)
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781 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
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782 Vector seqs = new Vector();
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783 while (st.hasMoreElements())
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785 String name = st.nextToken();
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786 int start = Integer.parseInt(st.nextToken());
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787 int end = Integer.parseInt(st.nextToken());
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788 Sequence sequence = new Sequence(name, st.nextToken(), start, end);
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792 viewport.alignment.addSequence(sequence);
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796 seqs.addElement(sequence);
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802 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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803 for (int i = 0; i < seqs.size(); i++)
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805 newSeqs[i] = (SequenceI) seqs.elementAt(i);
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808 String newtitle = new String("Copied sequences");
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809 if (getTitle().startsWith("Copied sequences"))
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811 newtitle = getTitle();
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815 newtitle = newtitle.concat("- from " + getTitle());
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817 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
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822 jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
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823 NEW_WINDOW_HEIGHT);
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827 viewport.setEndSeq(viewport.alignment.getHeight());
\r
828 viewport.alignment.getWidth();
\r
829 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
833 catch (Exception ex)
\r
834 {} // could be anything being pasted in here
\r
838 protected void cut_actionPerformed()
\r
840 copy_actionPerformed();
\r
841 delete_actionPerformed();
\r
844 protected void delete_actionPerformed()
\r
846 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
\r
847 HistoryItem.HIDE));
\r
848 if (viewport.getSelectionGroup() == null)
\r
854 SequenceGroup sg = viewport.getSelectionGroup();
\r
855 boolean allSequences = false;
\r
856 if(sg.sequences.size()==viewport.alignment.getHeight())
\r
857 allSequences = true;
\r
859 for (int i = 0; i < sg.sequences.size(); i++)
\r
861 SequenceI seq = sg.getSequenceAt(i);
\r
862 int index = viewport.getAlignment().findIndex(seq);
\r
863 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
\r
865 // If the cut affects all sequences, remove highlighted columns
\r
868 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
869 sg.getEndRes() + 1);
\r
873 if (seq.getSequence().length() < 1)
\r
875 viewport.getAlignment().deleteSequence(seq);
\r
879 viewport.getAlignment().getSequences().setElementAt(seq, index);
\r
883 viewport.setSelectionGroup(null);
\r
884 viewport.alignment.deleteGroup(sg);
\r
885 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
\r
886 if (viewport.getAlignment().getHeight() < 1)
\r
890 this.setVisible(false);
\r
892 catch (Exception ex)
\r
895 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
899 protected void deleteGroups_actionPerformed()
\r
901 viewport.alignment.deleteAllGroups();
\r
902 viewport.setSelectionGroup(null);
\r
904 alignPanel.repaint();
\r
907 public void selectAllSequenceMenuItem_actionPerformed()
\r
909 SequenceGroup sg = new SequenceGroup();
\r
910 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
912 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
914 sg.setEndRes(viewport.alignment.getWidth()-1);
\r
915 viewport.setSelectionGroup(sg);
\r
916 alignPanel.repaint();
\r
917 PaintRefresher.Refresh(null, viewport.alignment);
\r
920 public void deselectAllSequenceMenuItem_actionPerformed()
\r
922 if(viewport.cursorMode)
\r
924 alignPanel.seqPanel.keyboardNo1=null;
\r
925 alignPanel.seqPanel.keyboardNo2=null;
\r
927 viewport.setSelectionGroup(null);
\r
928 viewport.getColumnSelection().clear();
\r
929 viewport.setSelectionGroup(null);
\r
930 alignPanel.idPanel.idCanvas.searchResults = null;
\r
931 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
932 alignPanel.repaint();
\r
933 PaintRefresher.Refresh(null, viewport.alignment);
\r
936 public void invertSequenceMenuItem_actionPerformed()
\r
938 SequenceGroup sg = viewport.getSelectionGroup();
\r
939 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
941 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
944 PaintRefresher.Refresh(null, viewport.alignment);
\r
947 public void remove2LeftMenuItem_actionPerformed()
\r
949 ColumnSelection colSel = viewport.getColumnSelection();
\r
950 if (colSel.size() > 0)
\r
952 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
\r
953 HistoryItem.HIDE));
\r
954 int min = colSel.getMin();
\r
955 viewport.getAlignment().trimLeft(min);
\r
956 colSel.compensateForEdit(0, min);
\r
958 if (viewport.getSelectionGroup() != null)
\r
960 viewport.getSelectionGroup().adjustForRemoveLeft(min);
\r
963 Vector groups = viewport.alignment.getGroups();
\r
964 for (int i = 0; i < groups.size(); i++)
\r
966 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
967 if (!sg.adjustForRemoveLeft(min))
\r
969 viewport.alignment.deleteGroup(sg);
\r
972 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
976 public void remove2RightMenuItem_actionPerformed()
\r
978 ColumnSelection colSel = viewport.getColumnSelection();
\r
979 if (colSel.size() > 0)
\r
981 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
\r
982 HistoryItem.HIDE));
\r
983 int max = colSel.getMax();
\r
984 viewport.getAlignment().trimRight(max);
\r
985 if (viewport.getSelectionGroup() != null)
\r
987 viewport.getSelectionGroup().adjustForRemoveRight(max);
\r
990 Vector groups = viewport.alignment.getGroups();
\r
991 for (int i = 0; i < groups.size(); i++)
\r
993 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
994 if (!sg.adjustForRemoveRight(max))
\r
996 viewport.alignment.deleteGroup(sg);
\r
999 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1004 public void removeGappedColumnMenuItem_actionPerformed()
\r
1006 addHistoryItem(new HistoryItem("Remove Gapped Columns",
\r
1007 viewport.alignment,
\r
1008 HistoryItem.HIDE));
\r
1010 //This is to maintain viewport position on first residue
\r
1011 //of first sequence
\r
1012 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1013 int startRes = seq.findPosition(viewport.startRes);
\r
1015 viewport.getAlignment().removeGaps();
\r
1017 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1019 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1022 public void removeAllGapsMenuItem_actionPerformed()
\r
1024 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
\r
1025 HistoryItem.HIDE));
\r
1027 //This is to maintain viewport position on first residue
\r
1028 //of first sequence
\r
1029 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1030 int startRes = seq.findPosition(viewport.startRes);
\r
1032 SequenceI current;
\r
1037 int start=0, end = viewport.alignment.getWidth();
\r
1039 if (viewport.getSelectionGroup() != null
\r
1040 && viewport.getSelectionGroup().sequences != null
\r
1041 && viewport.getSelectionGroup().sequences.size()>0)
\r
1043 seqs = viewport.getSelectionGroup().sequences;
\r
1044 start = viewport.getSelectionGroup().getStartRes();
\r
1045 end = viewport.getSelectionGroup().getEndRes()+1;
\r
1048 seqs = viewport.alignment.getSequences();
\r
1050 for (int i = 0; i < seqs.size(); i++)
\r
1052 current = (SequenceI) seqs.elementAt(i);
\r
1053 jSize = current.getLength();
\r
1055 // Removing a range is much quicker than removing gaps
\r
1056 // one by one for long sequences
\r
1058 int rangeStart=-1, rangeEnd=-1;
\r
1062 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
\r
1064 if(rangeStart==-1)
\r
1079 current.deleteChars(rangeStart, rangeEnd);
\r
1080 j-=rangeEnd-rangeStart;
\r
1081 jSize-=rangeEnd-rangeStart;
\r
1089 while (j < end && j < jSize);
\r
1092 current.deleteChars(rangeStart, rangeEnd);
\r
1095 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1096 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1099 public void alignmentChanged()
\r
1101 viewport.alignment.padGaps();
\r
1102 if(viewport.autocalculateConsensus)
\r
1104 viewport.updateConsensus();
\r
1105 viewport.updateConservation();
\r
1108 resetAllColourSchemes();
\r
1109 if(alignPanel.overviewPanel!=null)
\r
1110 alignPanel.overviewPanel.updateOverviewImage();
\r
1112 viewport.alignment.adjustSequenceAnnotations();
\r
1113 alignPanel.repaint();
\r
1116 void resetAllColourSchemes()
\r
1118 ColourSchemeI cs = viewport.globalColourScheme;
\r
1121 if (cs instanceof ClustalxColourScheme)
\r
1123 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
\r
1124 resetClustalX(viewport.alignment.getSequences(),
\r
1125 viewport.alignment.getWidth());
\r
1128 cs.setConsensus(viewport.vconsensus);
\r
1129 if (cs.conservationApplied())
\r
1131 Alignment al = (Alignment) viewport.alignment;
\r
1132 Conservation c = new Conservation("All",
\r
1133 ResidueProperties.propHash, 3,
\r
1134 al.getSequences(), 0,
\r
1135 al.getWidth() - 1);
\r
1137 c.verdict(false, viewport.ConsPercGaps);
\r
1139 cs.setConservation(c);
\r
1143 int s, sSize = viewport.alignment.getGroups().size();
\r
1144 for(s=0; s<sSize; s++)
\r
1146 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
\r
1147 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
\r
1149 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
\r
1151 sg.recalcConservation();
\r
1157 public void findMenuItem_actionPerformed()
\r
1159 new Finder(alignPanel);
\r
1162 public void font_actionPerformed()
\r
1164 new FontChooser(alignPanel);
\r
1168 public void seqLimits_itemStateChanged()
\r
1170 viewport.setShowJVSuffix(seqLimits.getState());
\r
1171 alignPanel.fontChanged();
\r
1172 alignPanel.repaint();
\r
1176 protected void colourTextMenuItem_actionPerformed()
\r
1178 viewport.setColourText(colourTextMenuItem.getState());
\r
1179 alignPanel.repaint();
\r
1182 protected void wrapMenuItem_actionPerformed()
\r
1184 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
1185 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
1186 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
1187 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
1188 scaleRight.setEnabled(wrapMenuItem.getState());
\r
1189 alignPanel.repaint();
\r
1192 protected void scaleAbove_actionPerformed()
\r
1194 viewport.setScaleAboveWrapped(scaleAbove.getState());
\r
1195 alignPanel.repaint();
\r
1198 protected void scaleLeft_actionPerformed()
\r
1200 viewport.setScaleLeftWrapped(scaleLeft.getState());
\r
1201 alignPanel.repaint();
\r
1204 protected void scaleRight_actionPerformed()
\r
1206 viewport.setScaleRightWrapped(scaleRight.getState());
\r
1207 alignPanel.repaint();
\r
1210 public void viewBoxesMenuItem_actionPerformed()
\r
1212 viewport.setShowBoxes(viewBoxesMenuItem.getState());
\r
1213 alignPanel.repaint();
\r
1216 public void viewTextMenuItem_actionPerformed()
\r
1218 viewport.setShowText(viewTextMenuItem.getState());
\r
1219 alignPanel.repaint();
\r
1222 protected void renderGapsMenuItem_actionPerformed()
\r
1224 viewport.setRenderGaps(renderGapsMenuItem.getState());
\r
1225 alignPanel.repaint();
\r
1228 public void annotationPanelMenuItem_actionPerformed()
\r
1230 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
\r
1231 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
\r
1234 public void featureSettings_actionPerformed()
\r
1236 new FeatureSettings(viewport, alignPanel);
\r
1239 public void overviewMenuItem_actionPerformed()
\r
1241 if (alignPanel.overviewPanel != null)
\r
1246 Frame frame = new Frame();
\r
1247 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1248 frame.add(overview);
\r
1249 // +50 must allow for applet frame window
\r
1250 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
1251 overview.preferredSize().width,
\r
1252 overview.preferredSize().height + 50);
\r
1255 frame.addWindowListener(new WindowAdapter()
\r
1257 public void windowClosing(WindowEvent e)
\r
1259 alignPanel.setOverviewPanel(null);
\r
1263 alignPanel.setOverviewPanel(overview);
\r
1267 protected void noColourmenuItem_actionPerformed()
\r
1269 changeColour(null);
\r
1272 public void clustalColour_actionPerformed()
\r
1274 abovePIDThreshold.setState(false);
\r
1275 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
\r
1276 viewport.alignment.getWidth()));
\r
1279 public void zappoColour_actionPerformed()
\r
1281 changeColour(new ZappoColourScheme());
\r
1284 public void taylorColour_actionPerformed()
\r
1286 changeColour(new TaylorColourScheme());
\r
1289 public void hydrophobicityColour_actionPerformed()
\r
1291 changeColour(new HydrophobicColourScheme());
\r
1294 public void helixColour_actionPerformed()
\r
1296 changeColour(new HelixColourScheme());
\r
1299 public void strandColour_actionPerformed()
\r
1301 changeColour(new StrandColourScheme());
\r
1304 public void turnColour_actionPerformed()
\r
1306 changeColour(new TurnColourScheme());
\r
1309 public void buriedColour_actionPerformed()
\r
1311 changeColour(new BuriedColourScheme());
\r
1314 public void nucleotideColour_actionPerformed()
\r
1316 changeColour(new NucleotideColourScheme());
\r
1319 protected void applyToAllGroups_actionPerformed()
\r
1321 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
\r
1324 void changeColour(ColourSchemeI cs)
\r
1326 int threshold = 0;
\r
1330 if (viewport.getAbovePIDThreshold())
\r
1332 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
\r
1334 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1336 viewport.setGlobalColourScheme(cs);
\r
1340 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1343 if (viewport.getConservationSelected())
\r
1346 Alignment al = (Alignment) viewport.alignment;
\r
1347 Conservation c = new Conservation("All",
\r
1348 ResidueProperties.propHash, 3,
\r
1349 al.getSequences(), 0,
\r
1350 al.getWidth() - 1);
\r
1353 c.verdict(false, viewport.ConsPercGaps);
\r
1355 cs.setConservation(c);
\r
1357 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1363 cs.setConservation(null);
\r
1366 cs.setConsensus(viewport.vconsensus);
\r
1369 viewport.setGlobalColourScheme(cs);
\r
1371 if (viewport.getColourAppliesToAllGroups())
\r
1373 Vector groups = viewport.alignment.getGroups();
\r
1374 for (int i = 0; i < groups.size(); i++)
\r
1376 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1383 if (cs instanceof ClustalxColourScheme)
\r
1385 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1391 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1393 catch (Exception ex)
\r
1395 ex.printStackTrace();
\r
1400 if (viewport.getAbovePIDThreshold()
\r
1401 || cs instanceof PIDColourScheme
\r
1402 || cs instanceof Blosum62ColourScheme)
\r
1404 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1405 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
1408 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1410 if (viewport.getConservationSelected())
\r
1412 Conservation c = new Conservation("Group",
\r
1413 ResidueProperties.propHash, 3,
\r
1415 viewport.alignment.getWidth() - 1);
\r
1417 c.verdict(false, viewport.ConsPercGaps);
\r
1418 sg.cs.setConservation(c);
\r
1422 sg.cs.setConservation(null);
\r
1423 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1430 if (alignPanel.getOverviewPanel() != null)
\r
1432 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1435 alignPanel.repaint();
\r
1440 protected void modifyPID_actionPerformed()
\r
1442 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1444 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
1446 SliderPanel.showPIDSlider();
\r
1450 protected void modifyConservation_actionPerformed()
\r
1452 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1454 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
1456 SliderPanel.showConservationSlider();
\r
1460 protected void conservationMenuItem_actionPerformed()
\r
1462 viewport.setConservationSelected(conservationMenuItem.getState());
\r
1464 viewport.setAbovePIDThreshold(false);
\r
1465 abovePIDThreshold.setState(false);
\r
1467 changeColour(viewport.getGlobalColourScheme());
\r
1469 modifyConservation_actionPerformed();
\r
1472 public void abovePIDThreshold_actionPerformed()
\r
1474 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
1476 conservationMenuItem.setState(false);
\r
1477 viewport.setConservationSelected(false);
\r
1479 changeColour(viewport.getGlobalColourScheme());
\r
1481 modifyPID_actionPerformed();
\r
1484 public void userDefinedColour_actionPerformed()
\r
1486 new UserDefinedColours(alignPanel, null);
\r
1489 public void PIDColour_actionPerformed()
\r
1491 changeColour(new PIDColourScheme());
\r
1494 public void BLOSUM62Colour_actionPerformed()
\r
1496 changeColour(new Blosum62ColourScheme());
\r
1499 public void sortPairwiseMenuItem_actionPerformed()
\r
1501 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1502 HistoryItem.SORT));
\r
1503 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1504 viewport.getAlignment().getSequenceAt(0));
\r
1505 alignPanel.repaint();
\r
1508 public void sortIDMenuItem_actionPerformed()
\r
1510 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1511 HistoryItem.SORT));
\r
1512 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1513 alignPanel.repaint();
\r
1516 public void sortGroupMenuItem_actionPerformed()
\r
1518 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1519 HistoryItem.SORT));
\r
1520 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1521 alignPanel.repaint();
\r
1525 public void removeRedundancyMenuItem_actionPerformed()
\r
1527 new RedundancyPanel(alignPanel);
\r
1530 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
1532 if (viewport.getSelectionGroup().getSize() > 1)
\r
1534 Frame frame = new Frame();
\r
1535 frame.add(new PairwiseAlignPanel(alignPanel));
\r
1536 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
1540 public void PCAMenuItem_actionPerformed()
\r
1542 //are the sequences aligned?
\r
1543 if (!viewport.alignment.isAligned())
\r
1545 SequenceI current;
\r
1546 int Width = viewport.getAlignment().getWidth();
\r
1548 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1551 current = viewport.getAlignment().getSequenceAt(i);
\r
1553 if (current.getLength() < Width)
\r
1555 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1558 alignPanel.repaint();
\r
1561 if ( (viewport.getSelectionGroup() != null &&
\r
1562 viewport.getSelectionGroup().getSize() < 4 &&
\r
1563 viewport.getSelectionGroup().getSize() > 0)
\r
1564 || viewport.getAlignment().getHeight() < 4)
\r
1571 new PCAPanel(viewport);
\r
1573 catch (java.lang.OutOfMemoryError ex)
\r
1579 public void averageDistanceTreeMenuItem_actionPerformed()
\r
1581 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1584 public void neighbourTreeMenuItem_actionPerformed()
\r
1586 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1589 protected void njTreeBlosumMenuItem_actionPerformed()
\r
1591 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1594 protected void avTreeBlosumMenuItem_actionPerformed()
\r
1596 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1599 void NewTreePanel(String type, String pwType, String title)
\r
1601 //are the sequences aligned?
\r
1602 if (!viewport.alignment.isAligned())
\r
1604 SequenceI current;
\r
1605 int Width = viewport.getAlignment().getWidth();
\r
1607 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1610 current = viewport.getAlignment().getSequenceAt(i);
\r
1612 if (current.getLength() < Width)
\r
1614 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1617 alignPanel.repaint();
\r
1621 final TreePanel tp;
\r
1622 if (viewport.getSelectionGroup() != null &&
\r
1623 viewport.getSelectionGroup().getSize() > 3)
\r
1625 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
\r
1627 0, viewport.alignment.getWidth());
\r
1631 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1632 type, pwType, 0, viewport.alignment.getWidth());
\r
1635 addTreeMenuItem(tp, title);
\r
1637 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
1640 void loadTree_actionPerformed()
\r
1642 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1643 cap.setText("Paste your Newick tree file here.");
\r
1644 cap.treeImport = true;
\r
1645 Frame frame = new Frame();
\r
1647 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
1650 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
1652 TreePanel tp = new TreePanel(viewport,
\r
1653 viewport.getAlignment().getSequences(),
\r
1654 tree, "From File - ", treeFile);
\r
1655 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
1656 addTreeMenuItem(tp, treeFile);
\r
1659 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1661 final MenuItem item = new MenuItem(title);
\r
1662 sortByTreeMenu.add(item);
\r
1663 item.addActionListener(new java.awt.event.ActionListener()
\r
1665 public void actionPerformed(ActionEvent evt)
\r
1667 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1668 HistoryItem.SORT));
\r
1669 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1670 alignPanel.repaint();
\r
1674 treePanel.addWindowListener(new WindowAdapter()
\r
1676 public void windowClosing(WindowEvent e)
\r
1678 sortByTreeMenu.remove(item);
\r
1683 protected void documentation_actionPerformed()
\r
1685 showURL("http://www.jalview.org/help.html", "HELP");
\r
1688 protected void about_actionPerformed()
\r
1691 class AboutPanel extends Canvas
\r
1694 public AboutPanel(String version)
\r
1695 { this.version = version; }
\r
1697 public void paint(Graphics g)
\r
1699 g.setColor(Color.white);
\r
1700 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1701 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1702 FontMetrics fm = g.getFontMetrics();
\r
1703 int fh = fm.getHeight();
\r
1705 g.setColor(Color.black);
\r
1706 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
1707 g.drawString("Jalview - Release "+version, 200, y += fh);
\r
1708 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1709 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
1711 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
1714 "For any issues relating to Jalview, email help@jalview.org", x,
\r
1716 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
1717 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
1719 g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh);
\r
1723 String version = "test";
\r
1724 java.net.URL url = getClass().getResource("/.build_properties");
\r
1729 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
1730 url.openStream()));
\r
1732 while ( (line = reader.readLine()) != null)
\r
1734 if (line.indexOf("VERSION") > -1)
\r
1736 version = line.substring(line.indexOf("=") + 1);
\r
1740 catch (Exception ex)
\r
1742 ex.printStackTrace();
\r
1747 Frame frame = new Frame();
\r
1748 frame.add(new AboutPanel(version));
\r
1749 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
\r
1753 public void showURL(String url, String target)
\r
1755 if (applet == null)
\r
1757 System.out.println("Not running as applet - no browser available.");
\r
1763 System.out.println("Show url: "+url);
\r
1764 applet.getAppletContext().showDocument(new java.net.URL(url),
\r
1767 catch (Exception ex)
\r
1769 ex.printStackTrace();
\r
1775 //////////////////////////////////////////////////////////////////////////////////
\r
1776 //JBuilder Graphics here
\r
1778 protected MenuBar alignFrameMenuBar = new MenuBar();
\r
1779 protected Menu fileMenu = new Menu("File");
\r
1780 protected MenuItem loadApplication = new MenuItem("View in Full Application");
\r
1781 protected MenuItem loadTree = new MenuItem("Load Associated Tree");
\r
1782 protected MenuItem closeMenuItem = new MenuItem("Close");
\r
1783 protected Menu editMenu = new Menu("Edit");
\r
1784 protected Menu viewMenu = new Menu("View");
\r
1785 protected Menu colourMenu = new Menu("Colour");
\r
1786 protected Menu calculateMenu = new Menu("Calculate");
\r
1787 protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
1788 protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
1789 protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
1790 protected MenuItem remove2LeftMenuItem = new MenuItem();
\r
1791 protected MenuItem remove2RightMenuItem = new MenuItem();
\r
1792 protected MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
1793 protected MenuItem removeAllGapsMenuItem = new MenuItem();
\r
1794 protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
1795 protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
1796 protected MenuItem sortPairwiseMenuItem = new MenuItem();
\r
1797 protected MenuItem sortIDMenuItem = new MenuItem();
\r
1798 protected MenuItem sortGroupMenuItem = new MenuItem();
\r
1799 protected MenuItem removeRedundancyMenuItem = new MenuItem();
\r
1800 protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
1801 protected MenuItem PCAMenuItem = new MenuItem();
\r
1802 protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
1803 protected MenuItem neighbourTreeMenuItem = new MenuItem();
\r
1804 BorderLayout borderLayout1 = new BorderLayout();
\r
1805 public Label statusBar = new Label();
\r
1806 protected Menu outputTextboxMenu = new Menu();
\r
1807 protected MenuItem clustalColour = new MenuItem();
\r
1808 protected MenuItem zappoColour = new MenuItem();
\r
1809 protected MenuItem taylorColour = new MenuItem();
\r
1810 protected MenuItem hydrophobicityColour = new MenuItem();
\r
1811 protected MenuItem helixColour = new MenuItem();
\r
1812 protected MenuItem strandColour = new MenuItem();
\r
1813 protected MenuItem turnColour = new MenuItem();
\r
1814 protected MenuItem buriedColour = new MenuItem();
\r
1815 protected MenuItem userDefinedColour = new MenuItem();
\r
1816 protected MenuItem PIDColour = new MenuItem();
\r
1817 protected MenuItem BLOSUM62Colour = new MenuItem();
\r
1818 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
1819 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
1820 protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
1821 protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
1822 MenuItem overviewMenuItem = new MenuItem();
\r
1823 protected MenuItem undoMenuItem = new MenuItem();
\r
1824 protected MenuItem redoMenuItem = new MenuItem();
\r
1825 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
1826 MenuItem noColourmenuItem = new MenuItem();
\r
1827 protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
1828 protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
1829 MenuItem findMenuItem = new MenuItem();
\r
1830 Menu searchMenu = new Menu();
\r
1831 protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
1832 protected MenuItem nucleotideColour = new MenuItem();
\r
1833 MenuItem deleteGroups = new MenuItem();
\r
1834 MenuItem delete = new MenuItem();
\r
1835 MenuItem copy = new MenuItem();
\r
1836 MenuItem cut = new MenuItem();
\r
1837 Menu pasteMenu = new Menu();
\r
1838 MenuItem pasteNew = new MenuItem();
\r
1839 MenuItem pasteThis = new MenuItem();
\r
1840 protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
1841 protected MenuItem font = new MenuItem();
\r
1842 protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
1843 protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
1844 protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
1845 MenuItem modifyPID = new MenuItem();
\r
1846 MenuItem modifyConservation = new MenuItem();
\r
1847 protected CheckboxMenuItem autoCalculate
\r
1848 = new CheckboxMenuItem("Autocalculate Consensus", true);
\r
1849 protected Menu sortByTreeMenu = new Menu();
\r
1850 Menu sort = new Menu();
\r
1851 Menu calculate = new Menu();
\r
1852 MenuItem inputText = new MenuItem();
\r
1853 Menu helpMenu = new Menu();
\r
1854 MenuItem documentation = new MenuItem();
\r
1855 MenuItem about = new MenuItem();
\r
1856 protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
1857 Panel embeddedMenu;
\r
1858 Label embeddedEdit;
\r
1859 Label embeddedSearch;
\r
1860 Label embeddedView;
\r
1861 Label embeddedColour;
\r
1862 Label embeddedFile;
\r
1863 Label embeddedHelp;
\r
1864 Label embeddedCalculate;
\r
1865 FlowLayout flowLayout1;
\r
1867 private void jbInit() throws Exception {
\r
1869 setMenuBar(alignFrameMenuBar);
\r
1873 // dynamically fill save as menu with available formats
\r
1874 for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++)
\r
1877 item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.
\r
1880 item.addActionListener(new java.awt.event.ActionListener()
\r
1882 public void actionPerformed(ActionEvent e)
\r
1884 outputText_actionPerformed(e);
\r
1888 outputTextboxMenu.add(item);
\r
1890 closeMenuItem.addActionListener(this);
\r
1891 loadApplication.addActionListener(this);
\r
1893 loadTree.addActionListener(this);
\r
1894 selectAllSequenceMenuItem.addActionListener(this);
\r
1895 deselectAllSequenceMenuItem.addActionListener(this);
\r
1896 invertSequenceMenuItem.addActionListener(this);
\r
1897 remove2LeftMenuItem.setLabel("Remove Left");
\r
1898 remove2LeftMenuItem.addActionListener(this);
\r
1899 remove2RightMenuItem.setLabel("Remove Right");
\r
1900 remove2RightMenuItem.addActionListener(this);
\r
1901 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
1902 removeGappedColumnMenuItem.addActionListener(this);
\r
1903 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
1904 removeAllGapsMenuItem.addActionListener(this);
\r
1905 viewBoxesMenuItem.setLabel("Boxes");
\r
1906 viewBoxesMenuItem.setState(true);
\r
1907 viewBoxesMenuItem.addItemListener(this);
\r
1908 viewTextMenuItem.setLabel("Text");
\r
1909 viewTextMenuItem.setState(true);
\r
1910 viewTextMenuItem.addItemListener(this);
\r
1911 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
1912 sortPairwiseMenuItem.addActionListener(this);
\r
1913 sortIDMenuItem.setLabel("by ID");
\r
1914 sortIDMenuItem.addActionListener(this);
\r
1915 sortGroupMenuItem.setLabel("by Group");
\r
1916 sortGroupMenuItem.addActionListener(this);
\r
1917 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
1918 removeRedundancyMenuItem.addActionListener(this);
\r
1919 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
1920 pairwiseAlignmentMenuItem.addActionListener(this);
\r
1921 PCAMenuItem.setLabel("Principal Component Analysis");
\r
1922 PCAMenuItem.addActionListener(this);
\r
1923 averageDistanceTreeMenuItem.setLabel(
\r
1924 "Average Distance Using % Identity");
\r
1925 averageDistanceTreeMenuItem.addActionListener(this);
\r
1926 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
1927 neighbourTreeMenuItem.addActionListener(this);
\r
1928 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
1929 statusBar.setBackground(Color.white);
\r
1930 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
1931 statusBar.setText("Status bar");
\r
1932 outputTextboxMenu.setLabel("Output to Textbox");
\r
1933 clustalColour.setLabel("Clustalx");
\r
1935 clustalColour.addActionListener(this);
\r
1936 zappoColour.setLabel("Zappo");
\r
1937 zappoColour.addActionListener(this);
\r
1938 taylorColour.setLabel("Taylor");
\r
1939 taylorColour.addActionListener(this);
\r
1940 hydrophobicityColour.setLabel("Hydrophobicity");
\r
1941 hydrophobicityColour.addActionListener(this);
\r
1942 helixColour.setLabel("Helix Propensity");
\r
1943 helixColour.addActionListener(this);
\r
1944 strandColour.setLabel("Strand Propensity");
\r
1945 strandColour.addActionListener(this);
\r
1946 turnColour.setLabel("Turn Propensity");
\r
1947 turnColour.addActionListener(this);
\r
1948 buriedColour.setLabel("Buried Index");
\r
1949 buriedColour.addActionListener(this);
\r
1950 userDefinedColour.setLabel("User Defined...");
\r
1951 userDefinedColour.addActionListener(this);
\r
1952 PIDColour.setLabel("Percentage Identity");
\r
1953 PIDColour.addActionListener(this);
\r
1954 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
1955 BLOSUM62Colour.addActionListener(this);
\r
1956 avDistanceTreeBlosumMenuItem.setLabel(
\r
1957 "Average Distance Using BLOSUM62");
\r
1958 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
1959 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
1960 njTreeBlosumMenuItem.addActionListener(this);
\r
1961 annotationPanelMenuItem.setLabel("Show Annotations");
\r
1962 annotationPanelMenuItem.addItemListener(this);
\r
1963 colourTextMenuItem.setLabel("Colour Text");
\r
1964 colourTextMenuItem.addItemListener(this);
\r
1965 overviewMenuItem.setLabel("Overview Window");
\r
1966 overviewMenuItem.addActionListener(this);
\r
1967 undoMenuItem.setEnabled(false);
\r
1968 undoMenuItem.setLabel("Undo");
\r
1969 undoMenuItem.addActionListener(this);
\r
1970 redoMenuItem.setEnabled(false);
\r
1971 redoMenuItem.setLabel("Redo");
\r
1972 redoMenuItem.addActionListener(this);
\r
1973 conservationMenuItem.setLabel("by Conservation");
\r
1974 conservationMenuItem.addItemListener(this);
\r
1975 noColourmenuItem.setLabel("None");
\r
1976 noColourmenuItem.addActionListener(this);
\r
1977 wrapMenuItem.setLabel("Wrap");
\r
1978 wrapMenuItem.addItemListener(this);
\r
1979 renderGapsMenuItem.setLabel("Show Gaps");
\r
1980 renderGapsMenuItem.setState(true);
\r
1981 renderGapsMenuItem.addItemListener(this);
\r
1982 findMenuItem.setLabel("Find...");
\r
1983 findMenuItem.addActionListener(this);
\r
1984 searchMenu.setLabel("Search");
\r
1986 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
1987 abovePIDThreshold.addItemListener(this);
\r
1988 nucleotideColour.setLabel("Nucleotide");
\r
1989 nucleotideColour.addActionListener(this);
\r
1990 deleteGroups.setLabel("Undefine Groups");
\r
1991 deleteGroups.addActionListener(this);
\r
1992 copy.setLabel("Copy");
\r
1993 copy.addActionListener(this);
\r
1994 cut.setLabel("Cut");
\r
1995 cut.addActionListener(this);
\r
1996 delete.setLabel("Delete");
\r
1997 delete.addActionListener(this);
\r
1998 pasteMenu.setLabel("Paste");
\r
1999 pasteNew.setLabel("To New Alignment");
\r
2000 pasteNew.addActionListener(this);
\r
2001 pasteThis.setLabel("Add To This Alignment");
\r
2002 pasteThis.addActionListener(this);
\r
2003 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
2004 applyToAllGroups.setState(true);
\r
2005 applyToAllGroups.addItemListener(this);
\r
2006 font.setLabel("Font...");
\r
2007 font.addActionListener(this);
\r
2008 scaleAbove.setLabel("Scale Above");
\r
2009 scaleAbove.setState(true);
\r
2010 scaleAbove.setEnabled(false);
\r
2011 scaleAbove.addItemListener(this);
\r
2012 scaleLeft.setEnabled(false);
\r
2013 scaleLeft.setState(true);
\r
2014 scaleLeft.setLabel("Scale Left");
\r
2015 scaleLeft.addItemListener(this);
\r
2016 scaleRight.setEnabled(false);
\r
2017 scaleRight.setState(true);
\r
2018 scaleRight.setLabel("Scale Right");
\r
2019 scaleRight.addItemListener(this);
\r
2020 modifyPID.setLabel("Modify Identity Threshold...");
\r
2021 modifyPID.addActionListener(this);
\r
2022 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
2023 modifyConservation.addActionListener(this);
\r
2024 sortByTreeMenu.setLabel("By Tree Order");
\r
2025 sort.setLabel("Sort");
\r
2026 calculate.setLabel("Calculate Tree");
\r
2027 autoCalculate.addItemListener(this);
\r
2028 inputText.setLabel("Input from textbox");
\r
2029 inputText.addActionListener(this);
\r
2031 helpMenu.setLabel("Help");
\r
2032 documentation.setLabel("Documentation");
\r
2033 documentation.addActionListener(this);
\r
2035 about.setLabel("About...");
\r
2036 about.addActionListener(this);
\r
2037 seqLimits.setState(true);
\r
2038 seqLimits.setLabel("Show Sequence Limits");
\r
2039 seqLimits.addItemListener(this);
\r
2040 featureSettings.setLabel("Feature Settings...");
\r
2041 featureSettings.addActionListener(this);
\r
2042 sequenceFeatures.setLabel("Sequence Features");
\r
2043 sequenceFeatures.addItemListener(this);
\r
2044 sequenceFeatures.setState(false);
\r
2045 annotationColour.setLabel("by Annotation...");
\r
2046 annotationColour.addActionListener(this);
\r
2048 alignFrameMenuBar.add(fileMenu);
\r
2049 alignFrameMenuBar.add(editMenu);
\r
2050 alignFrameMenuBar.add(searchMenu);
\r
2051 alignFrameMenuBar.add(viewMenu);
\r
2052 alignFrameMenuBar.add(colourMenu);
\r
2053 alignFrameMenuBar.add(calculateMenu);
\r
2054 alignFrameMenuBar.add(helpMenu);
\r
2055 fileMenu.add(inputText);
\r
2056 fileMenu.add(outputTextboxMenu);
\r
2057 // fileMenu.add(loadApplication);
\r
2058 fileMenu.addSeparator();
\r
2059 fileMenu.add(loadTree);
\r
2060 fileMenu.add(closeMenuItem);
\r
2061 editMenu.add(undoMenuItem);
\r
2062 editMenu.add(redoMenuItem);
\r
2063 editMenu.add(cut);
\r
2064 editMenu.add(copy);
\r
2065 editMenu.add(pasteMenu);
\r
2066 editMenu.add(delete);
\r
2067 editMenu.addSeparator();
\r
2068 editMenu.add(selectAllSequenceMenuItem);
\r
2069 editMenu.add(deselectAllSequenceMenuItem);
\r
2070 editMenu.add(invertSequenceMenuItem);
\r
2071 editMenu.add(deleteGroups);
\r
2072 editMenu.addSeparator();
\r
2073 editMenu.add(remove2LeftMenuItem);
\r
2074 editMenu.add(remove2RightMenuItem);
\r
2075 editMenu.add(removeGappedColumnMenuItem);
\r
2076 editMenu.add(removeAllGapsMenuItem);
\r
2077 editMenu.add(removeRedundancyMenuItem);
\r
2078 searchMenu.add(findMenuItem);
\r
2079 viewMenu.add(font);
\r
2080 viewMenu.addSeparator();
\r
2081 viewMenu.add(seqLimits);
\r
2082 viewMenu.addSeparator();
\r
2083 viewMenu.add(wrapMenuItem);
\r
2084 viewMenu.add(scaleAbove);
\r
2085 viewMenu.add(scaleLeft);
\r
2086 viewMenu.add(scaleRight);
\r
2087 viewMenu.addSeparator();
\r
2088 viewMenu.add(viewBoxesMenuItem);
\r
2089 viewMenu.add(viewTextMenuItem);
\r
2090 viewMenu.add(colourTextMenuItem);
\r
2091 viewMenu.add(renderGapsMenuItem);
\r
2092 viewMenu.add(annotationPanelMenuItem);
\r
2093 viewMenu.addSeparator();
\r
2094 viewMenu.add(sequenceFeatures);
\r
2095 viewMenu.add(featureSettings);
\r
2096 viewMenu.addSeparator();
\r
2097 viewMenu.add(overviewMenuItem);
\r
2098 colourMenu.add(applyToAllGroups);
\r
2099 colourMenu.addSeparator();
\r
2100 colourMenu.add(noColourmenuItem);
\r
2101 colourMenu.add(clustalColour);
\r
2102 colourMenu.add(BLOSUM62Colour);
\r
2103 colourMenu.add(PIDColour);
\r
2104 colourMenu.add(zappoColour);
\r
2105 colourMenu.add(taylorColour);
\r
2106 colourMenu.add(hydrophobicityColour);
\r
2107 colourMenu.add(helixColour);
\r
2108 colourMenu.add(strandColour);
\r
2109 colourMenu.add(turnColour);
\r
2110 colourMenu.add(buriedColour);
\r
2111 colourMenu.add(nucleotideColour);
\r
2112 colourMenu.add(userDefinedColour);
\r
2113 colourMenu.addSeparator();
\r
2114 colourMenu.add(conservationMenuItem);
\r
2115 colourMenu.add(modifyConservation);
\r
2116 colourMenu.add(abovePIDThreshold);
\r
2117 colourMenu.add(modifyPID);
\r
2118 colourMenu.add(annotationColour);
\r
2119 calculateMenu.add(sort);
\r
2120 calculateMenu.add(calculate);
\r
2121 calculateMenu.addSeparator();
\r
2122 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
2123 calculateMenu.add(PCAMenuItem);
\r
2124 calculateMenu.add(autoCalculate);
\r
2125 this.add(statusBar, BorderLayout.SOUTH);
\r
2126 pasteMenu.add(pasteNew);
\r
2127 pasteMenu.add(pasteThis);
\r
2128 sort.add(sortIDMenuItem);
\r
2129 sort.add(sortByTreeMenu);
\r
2130 sort.add(sortGroupMenuItem);
\r
2131 sort.add(sortPairwiseMenuItem);
\r
2132 calculate.add(averageDistanceTreeMenuItem);
\r
2133 calculate.add(neighbourTreeMenuItem);
\r
2134 calculate.add(avDistanceTreeBlosumMenuItem);
\r
2135 calculate.add(njTreeBlosumMenuItem);
\r
2136 helpMenu.add(documentation);
\r
2137 helpMenu.add(about);
\r
2140 public void setEmbedded()
\r
2143 embeddedMenu = new Panel();
\r
2144 embeddedEdit = new Label();
\r
2145 embeddedSearch = new Label();
\r
2146 embeddedView = new Label();
\r
2147 embeddedColour = new Label();
\r
2148 embeddedFile = new Label();
\r
2149 embeddedHelp = new Label();
\r
2150 embeddedCalculate = new Label();
\r
2151 flowLayout1 = new FlowLayout();
\r
2152 embeddedMenu.setBackground(Color.lightGray);
\r
2153 embeddedMenu.setLayout(flowLayout1);
\r
2154 embeddedEdit.setText("Edit");
\r
2155 embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2156 embeddedSearch.setText("Search");
\r
2157 embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2158 embeddedView.setText("View");
\r
2159 embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2160 embeddedColour.setText("Colour");
\r
2161 embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2162 embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2163 embeddedFile.setText("File");
\r
2164 embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2165 embeddedHelp.setText("Help");
\r
2166 embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2167 embeddedCalculate.setText("Calculate");
\r
2168 embeddedMenu.add(embeddedFile);
\r
2169 embeddedMenu.add(embeddedEdit);
\r
2170 embeddedMenu.add(embeddedSearch);
\r
2171 embeddedMenu.add(embeddedView);
\r
2172 embeddedMenu.add(embeddedColour);
\r
2173 embeddedMenu.add(embeddedCalculate);
\r
2174 embeddedMenu.add(embeddedHelp);
\r
2175 flowLayout1.setAlignment(FlowLayout.LEFT);
\r
2176 flowLayout1.setHgap(2);
\r
2177 flowLayout1.setVgap(0);
\r
2178 embeddedFile.addMouseListener(this);
\r
2179 embeddedEdit.addMouseListener(this);
\r
2180 embeddedSearch.addMouseListener(this);
\r
2181 embeddedView.addMouseListener(this);
\r
2182 embeddedColour.addMouseListener(this);
\r
2183 embeddedCalculate.addMouseListener(this);
\r
2184 embeddedHelp.addMouseListener(this);
\r
2186 // setVisible(false);
\r
2187 fileMenu.remove(closeMenuItem);
\r
2188 fileMenu.remove(3); // Seperator
\r
2190 applet.setLayout(new BorderLayout());
\r
2191 applet.add(embeddedMenu, BorderLayout.NORTH);
\r
2192 applet.add(statusBar, BorderLayout.SOUTH);
\r
2193 // applet.validate();
\r
2195 alignPanel.setSize(applet.size().width, applet.size().height
\r
2196 - embeddedMenu.HEIGHT - statusBar.HEIGHT);
\r
2198 applet.add(alignPanel, BorderLayout.CENTER);
\r
2199 applet.validate();
\r
2205 PopupMenu filePopup, editPopup, searchPopup,
\r
2206 viewPopup, colourPopup, calculatePopup, helpPopup;
\r
2207 MenuItem featureSettings = new MenuItem();
\r
2208 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
2209 MenuItem annotationColour = new MenuItem();
\r
2211 public void mousePressed(MouseEvent evt)
\r
2213 PopupMenu popup = null;
\r
2214 Label source = (Label)evt.getSource();
\r
2215 if(source==embeddedFile)
\r
2217 popup = filePopup = genPopupMenu(filePopup, fileMenu);
\r
2219 else if(source==embeddedEdit)
\r
2221 popup = editPopup = genPopupMenu(editPopup, editMenu);
\r
2223 else if(source==embeddedSearch)
\r
2225 popup = searchPopup = genPopupMenu(searchPopup, searchMenu);
\r
2227 else if(source==embeddedView)
\r
2229 popup = viewPopup = genPopupMenu(viewPopup, viewMenu);
\r
2231 else if(source==embeddedColour)
\r
2233 popup = colourPopup = genPopupMenu(colourPopup, colourMenu);
\r
2235 else if(source==embeddedCalculate)
\r
2237 popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);
\r
2239 else if(source==embeddedHelp)
\r
2241 popup = helpPopup = genPopupMenu(helpPopup, helpMenu);
\r
2244 embeddedMenu.add(popup);
\r
2245 popup.show(embeddedMenu,
\r
2246 source.getBounds().x,
\r
2247 source.getBounds().y + source.getBounds().getSize().height);
\r
2250 PopupMenu genPopupMenu(PopupMenu popup, Menu original)
\r
2256 popup = new PopupMenu();
\r
2257 int m, mSize = original.getItemCount();
\r
2258 for(m=0; m<mSize; m++)
\r
2260 popup.add(original.getItem(m));
\r
2267 public void mouseClicked(MouseEvent evt)
\r
2269 public void mouseReleased(MouseEvent evt)
\r
2271 public void mouseEntered(MouseEvent evt)
\r
2273 public void mouseExited(MouseEvent evt)
\r