2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2006 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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26 import jalview.commands.*;
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28 import java.awt.event.*;
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30 import java.io.InputStreamReader;
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31 import java.io.BufferedReader;
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32 import java.net.URL;
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35 public class AlignFrame extends Frame implements ActionListener,
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36 ItemListener, KeyListener, MouseListener
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38 public AlignmentPanel alignPanel;
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39 public AlignViewport viewport;
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40 int DEFAULT_WIDTH = 700;
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41 int DEFAULT_HEIGHT = 500;
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43 String jalviewServletURL;
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46 public AlignFrame(AlignmentI al,
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47 jalview.bin.JalviewLite applet,
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52 jalviewServletURL = applet.getParameter("APPLICATION_URL");
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56 }catch(Exception ex)
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58 ex.printStackTrace();
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61 viewport = new AlignViewport(al, applet);
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62 alignPanel = new AlignmentPanel(this, viewport);
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64 viewport.updateConservation(alignPanel);
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65 viewport.updateConsensus(alignPanel);
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67 annotationPanelMenuItem.setState(viewport.showAnnotation);
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69 seqLimits.setState(viewport.showJVSuffix);
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73 String param = applet.getParameter("sortBy");
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76 if (param.equalsIgnoreCase("Id"))
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77 sortIDMenuItem_actionPerformed();
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78 else if (param.equalsIgnoreCase("Pairwise Identity"))
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79 sortPairwiseMenuItem_actionPerformed();
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82 param = applet.getParameter("wrap");
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85 if (param.equalsIgnoreCase("true"))
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87 wrapMenuItem.setState(true);
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88 wrapMenuItem_actionPerformed();
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94 param = applet.getParameter("windowWidth");
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97 int width = Integer.parseInt(param);
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98 DEFAULT_WIDTH = width;
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100 param = applet.getParameter("windowHeight");
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103 int height = Integer.parseInt(param);
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104 DEFAULT_HEIGHT = height;
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107 catch (Exception ex)
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112 //Some JVMS send keyevents to Top frame or lowest panel,
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113 //Havent worked out why yet. So add to both this frame and seqCanvas for now
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114 this.addKeyListener(this);
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115 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
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116 alignPanel.idPanel.idCanvas.addKeyListener(this);
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117 alignPanel.scalePanel.addKeyListener(this);
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118 alignPanel.annotationPanel.addKeyListener(this);
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127 add(alignPanel, BorderLayout.CENTER);
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128 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
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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, String type)
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153 Hashtable featureLinks = new Hashtable();
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154 boolean featuresFile = false;
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156 featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport.alignment,
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157 alignPanel.seqPanel.seqCanvas.
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158 getFeatureRenderer().featureColours,
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162 catch(Exception ex)
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164 ex.printStackTrace();
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169 if(featureLinks.size()>0)
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170 alignPanel.seqPanel.seqCanvas
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171 .getFeatureRenderer().featureLinks = featureLinks;
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172 viewport.showSequenceFeatures = true;
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173 sequenceFeatures.setState(true);
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174 alignPanel.repaint();
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180 public void keyPressed(KeyEvent evt)
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182 if (viewport.cursorMode
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183 && evt.getKeyCode() >= KeyEvent.VK_0
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184 && evt.getKeyCode() <= KeyEvent.VK_9)
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186 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
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189 switch (evt.getKeyCode())
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191 case 27: // escape key
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192 deselectAllSequenceMenuItem_actionPerformed();
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194 case KeyEvent.VK_X:
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195 if (evt.isControlDown() || evt.isMetaDown())
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197 cut_actionPerformed();
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200 case KeyEvent.VK_C:
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201 if (viewport.cursorMode && !evt.isControlDown())
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203 alignPanel.seqPanel.setCursorColumn();
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205 if (evt.isControlDown() || evt.isMetaDown())
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207 copy_actionPerformed();
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210 case KeyEvent.VK_V:
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211 if (evt.isControlDown())
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213 paste(evt.isShiftDown());
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216 case KeyEvent.VK_A:
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217 if (evt.isControlDown() || evt.isMetaDown())
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219 selectAllSequenceMenuItem_actionPerformed();
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222 case KeyEvent.VK_DOWN:
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223 if(viewport.cursorMode)
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225 alignPanel.seqPanel.moveCursor(0,1);
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228 moveSelectedSequences(false);
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231 case KeyEvent.VK_UP:
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232 if (viewport.cursorMode)
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234 alignPanel.seqPanel.moveCursor(0,-1);
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237 moveSelectedSequences(true);
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240 case KeyEvent.VK_LEFT:
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241 if(viewport.cursorMode)
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243 alignPanel.seqPanel.moveCursor(-1,0);
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247 case KeyEvent.VK_RIGHT:
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248 if (viewport.cursorMode)
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250 alignPanel.seqPanel.moveCursor(1,0);
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253 case KeyEvent.VK_SPACE:
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254 if(viewport.cursorMode)
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256 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
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257 || evt.isShiftDown()
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263 case KeyEvent.VK_DELETE:
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264 case KeyEvent.VK_BACK_SPACE:
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265 if(viewport.cursorMode)
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267 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
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268 || evt.isShiftDown()
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269 || evt.isAltDown());
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273 cut_actionPerformed();
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274 alignPanel.seqPanel.seqCanvas.repaint();
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278 case KeyEvent.VK_S:
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279 if(viewport.cursorMode)
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281 alignPanel.seqPanel.setCursorRow();
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284 case KeyEvent.VK_P:
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285 if(viewport.cursorMode)
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287 alignPanel.seqPanel.setCursorPosition();
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291 case KeyEvent.VK_ENTER:
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292 case KeyEvent.VK_COMMA:
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293 if(viewport.cursorMode)
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295 alignPanel.seqPanel.setCursorRowAndColumn();
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299 case KeyEvent.VK_Q:
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300 if(viewport.cursorMode)
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302 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
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305 case KeyEvent.VK_M:
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306 if(viewport.cursorMode)
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308 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
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312 case KeyEvent.VK_F2:
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313 viewport.cursorMode = ! viewport.cursorMode;
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314 statusBar.setText("Keyboard editing mode is "+
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315 (viewport.cursorMode ? "on" : "off"));
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316 if(viewport.cursorMode)
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318 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
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319 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
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323 case KeyEvent.VK_F:
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324 if (evt.isControlDown())
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326 findMenuItem_actionPerformed();
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330 case KeyEvent.VK_H:
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332 boolean toggleSeqs = !evt.isControlDown();
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333 boolean toggleCols = !evt.isShiftDown();
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334 boolean hide = false;
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335 SequenceGroup sg = viewport.getSelectionGroup();
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339 if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())
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342 viewport.hideAllSelectedSeqs();
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344 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
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345 viewport.showAllHiddenSeqs();
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350 if (viewport.colSel.getSelected().size() > 0)
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352 viewport.hideSelectedColumns();
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354 viewport.selectionGroup = sg;
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357 viewport.showAllHiddenColumns();
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362 case KeyEvent.VK_PAGE_UP:
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363 if (viewport.wrapAlignment)
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364 alignPanel.scrollUp(true);
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366 alignPanel.setScrollValues(viewport.startRes,
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368 - viewport.endSeq + viewport.startSeq);
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371 case KeyEvent.VK_PAGE_DOWN:
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372 if (viewport.wrapAlignment)
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373 alignPanel.scrollUp(false);
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375 alignPanel.setScrollValues(viewport.startRes,
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377 + viewport.endSeq - viewport.startSeq);
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380 case KeyEvent.VK_Z:
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381 if (evt.isControlDown())
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383 undoMenuItem_actionPerformed();
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387 case KeyEvent.VK_Y:
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388 if (evt.isControlDown())
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390 redoMenuItem_actionPerformed();
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394 case KeyEvent.VK_L:
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395 if (evt.isControlDown())
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397 trimAlignment(true);
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401 case KeyEvent.VK_R:
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402 if (evt.isControlDown())
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404 trimAlignment(false);
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408 case KeyEvent.VK_E:
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409 if (evt.isControlDown())
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411 if (evt.isShiftDown())
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412 this.removeAllGapsMenuItem_actionPerformed();
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414 removeGappedColumnMenuItem_actionPerformed();
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417 case KeyEvent.VK_I:
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418 if (evt.isControlDown())
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420 if (evt.isAltDown())
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421 viewport.invertColumnSelection();
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423 this.invertSequenceMenuItem_actionPerformed();
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427 case KeyEvent.VK_U:
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428 if (evt.isControlDown())
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430 this.deleteGroups_actionPerformed();
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436 alignPanel.repaint();
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438 public void keyReleased(KeyEvent evt)
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440 public void keyTyped(KeyEvent evt)
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443 public void itemStateChanged(ItemEvent evt)
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445 if(evt.getSource()==colourTextMenuItem)
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446 colourTextMenuItem_actionPerformed();
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447 else if(evt.getSource()==wrapMenuItem)
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448 wrapMenuItem_actionPerformed();
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449 else if(evt.getSource()==scaleAbove)
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450 scaleAbove_actionPerformed();
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451 else if(evt.getSource()==scaleLeft)
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452 scaleLeft_actionPerformed();
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453 else if(evt.getSource()==scaleRight)
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454 scaleRight_actionPerformed();
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455 else if(evt.getSource()==seqLimits)
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456 seqLimits_itemStateChanged();
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457 else if(evt.getSource()==viewBoxesMenuItem)
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458 viewBoxesMenuItem_actionPerformed();
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459 else if(evt.getSource()==viewTextMenuItem)
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460 viewTextMenuItem_actionPerformed();
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461 else if(evt.getSource()==renderGapsMenuItem)
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462 renderGapsMenuItem_actionPerformed();
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463 else if(evt.getSource()==annotationPanelMenuItem)
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464 annotationPanelMenuItem_actionPerformed();
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465 else if(evt.getSource()==sequenceFeatures)
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467 viewport.showSequenceFeatures(sequenceFeatures.getState());
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468 alignPanel.seqPanel.seqCanvas.repaint();
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470 else if(evt.getSource()==conservationMenuItem)
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471 conservationMenuItem_actionPerformed();
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472 else if(evt.getSource()==abovePIDThreshold)
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473 abovePIDThreshold_actionPerformed();
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474 else if(evt.getSource()==applyToAllGroups)
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475 applyToAllGroups_actionPerformed();
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476 else if(evt.getSource()==autoCalculate)
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477 viewport.autocalculateConsensus = autoCalculate.getState();
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479 public void actionPerformed(ActionEvent evt)
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481 Object source = evt.getSource();
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483 if(source==inputText)
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484 inputText_actionPerformed();
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485 else if(source==loadTree)
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486 loadTree_actionPerformed();
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487 else if(source==loadApplication)
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488 launchFullApplication();
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489 else if(source==closeMenuItem)
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490 closeMenuItem_actionPerformed();
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491 else if(source==copy)
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492 copy_actionPerformed();
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493 else if(source==undoMenuItem)
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494 undoMenuItem_actionPerformed();
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495 else if(source==redoMenuItem)
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496 redoMenuItem_actionPerformed();
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497 else if(source==inputText)
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498 inputText_actionPerformed();
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499 else if(source==closeMenuItem)
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500 closeMenuItem_actionPerformed();
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501 else if(source==undoMenuItem)
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502 undoMenuItem_actionPerformed();
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503 else if(source==redoMenuItem)
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504 redoMenuItem_actionPerformed();
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505 else if(source==copy)
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506 copy_actionPerformed();
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507 else if(source==pasteNew)
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508 pasteNew_actionPerformed();
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509 else if(source==pasteThis)
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510 pasteThis_actionPerformed();
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511 else if(source==cut)
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512 cut_actionPerformed();
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513 else if(source==delete)
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514 delete_actionPerformed();
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515 else if(source==deleteGroups)
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516 deleteGroups_actionPerformed();
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517 else if(source==selectAllSequenceMenuItem)
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518 selectAllSequenceMenuItem_actionPerformed();
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519 else if(source==deselectAllSequenceMenuItem)
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520 deselectAllSequenceMenuItem_actionPerformed();
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521 else if(source==invertSequenceMenuItem)
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522 invertSequenceMenuItem_actionPerformed();
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523 else if(source==invertColSel)
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524 { viewport.invertColumnSelection(); alignPanel.repaint(); }
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525 else if(source==remove2LeftMenuItem)
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526 trimAlignment(true);
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527 else if(source==remove2RightMenuItem)
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528 trimAlignment(false);
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529 else if(source==removeGappedColumnMenuItem)
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530 removeGappedColumnMenuItem_actionPerformed();
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531 else if(source==removeAllGapsMenuItem)
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532 removeAllGapsMenuItem_actionPerformed();
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533 else if(source==findMenuItem)
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534 findMenuItem_actionPerformed();
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535 else if(source==font)
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536 font_actionPerformed();
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537 else if(source==showColumns)
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539 viewport.showAllHiddenColumns(); alignPanel.repaint();
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541 else if(source==showSeqs)
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543 viewport.showAllHiddenSeqs();
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545 else if(source == hideColumns)
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547 viewport.hideSelectedColumns(); alignPanel.repaint();
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549 else if(source == hideSequences && viewport.getSelectionGroup()!=null)
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551 viewport.hideAllSelectedSeqs();
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553 else if(source==featureSettings)
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554 featureSettings_actionPerformed();
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555 else if(source==overviewMenuItem)
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556 overviewMenuItem_actionPerformed();
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557 else if(source==noColourmenuItem)
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558 noColourmenuItem_actionPerformed();
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559 else if(source==clustalColour)
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560 clustalColour_actionPerformed();
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561 else if(source==zappoColour)
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562 zappoColour_actionPerformed();
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563 else if(source==taylorColour)
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564 taylorColour_actionPerformed();
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565 else if(source==hydrophobicityColour)
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566 hydrophobicityColour_actionPerformed();
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567 else if(source==helixColour)
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568 helixColour_actionPerformed();
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569 else if(source==strandColour)
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570 strandColour_actionPerformed();
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571 else if(source==turnColour)
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572 turnColour_actionPerformed();
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573 else if(source==buriedColour)
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574 buriedColour_actionPerformed();
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575 else if(source==nucleotideColour)
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576 nucleotideColour_actionPerformed();
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577 else if(source==modifyPID)
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578 modifyPID_actionPerformed();
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579 else if(source==modifyConservation)
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580 modifyConservation_actionPerformed();
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581 else if(source==userDefinedColour)
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582 userDefinedColour_actionPerformed();
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583 else if(source==PIDColour)
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584 PIDColour_actionPerformed();
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585 else if(source==BLOSUM62Colour)
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586 BLOSUM62Colour_actionPerformed();
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587 else if(source==annotationColour)
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588 new AnnotationColourChooser(viewport, alignPanel);
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589 else if(source==sortPairwiseMenuItem)
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590 sortPairwiseMenuItem_actionPerformed();
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591 else if(source==sortIDMenuItem)
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592 sortIDMenuItem_actionPerformed();
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593 else if(source==sortGroupMenuItem)
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594 sortGroupMenuItem_actionPerformed();
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595 else if(source==removeRedundancyMenuItem)
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596 removeRedundancyMenuItem_actionPerformed();
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597 else if(source==pairwiseAlignmentMenuItem)
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598 pairwiseAlignmentMenuItem_actionPerformed();
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599 else if(source==PCAMenuItem)
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600 PCAMenuItem_actionPerformed();
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601 else if(source==averageDistanceTreeMenuItem)
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602 averageDistanceTreeMenuItem_actionPerformed();
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603 else if(source==neighbourTreeMenuItem)
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604 neighbourTreeMenuItem_actionPerformed();
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605 else if(source==njTreeBlosumMenuItem)
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606 njTreeBlosumMenuItem_actionPerformed();
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607 else if(source==avDistanceTreeBlosumMenuItem)
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608 avTreeBlosumMenuItem_actionPerformed();
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609 else if(source==documentation)
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610 documentation_actionPerformed();
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611 else if(source==about)
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612 about_actionPerformed();
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616 public void inputText_actionPerformed()
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618 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
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619 Frame frame = new Frame();
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621 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
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624 protected void outputText_actionPerformed(ActionEvent e)
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626 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
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627 Frame frame = new Frame();
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629 jalview.bin.JalviewLite.addFrame(frame,
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630 "Alignment output - " + e.getActionCommand(),
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632 cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
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633 viewport.getAlignment().getSequences(),
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634 viewport.showJVSuffix));
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637 void launchFullApplication()
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639 StringBuffer url = new StringBuffer(jalviewServletURL);
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641 url.append("?open="+
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642 appendProtocol( viewport.applet.getParameter("file") ) );
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644 if(viewport.applet.getParameter("features")!=null)
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646 url.append( "&features=" );
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647 url.append( appendProtocol( viewport.applet.getParameter("features") ) );
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650 if(viewport.applet.getParameter("annotations")!=null)
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652 url.append( "&annotations=" );
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653 url.append( appendProtocol( viewport.applet.getParameter("annotations") ) );
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656 if(viewport.applet.getParameter("jnetfile")!=null)
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658 url.append( "&annotations=" );
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659 url.append( appendProtocol( viewport.applet.getParameter("jnetfile") ) );
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662 if(viewport.applet.getParameter("defaultColour")!=null)
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664 url.append("&colour=" +
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665 removeWhiteSpace(viewport.applet.getParameter("defaultColour"))
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669 if(viewport.applet.getParameter("userDefinedColour")!=null)
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671 url.append( "&colour=" +
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672 removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") )
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676 showURL(url.toString(), "FULL_APP");
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680 String removeWhiteSpace(String colour)
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682 StringBuffer sb = new StringBuffer();
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683 for (int i = 0; i < colour.length(); i++)
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685 if (Character.isWhitespace(colour.charAt(i)))
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688 sb.append(colour.charAt(i));
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691 return sb.toString();
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695 String appendProtocol(String url)
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699 }catch(java.net.MalformedURLException ex)
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701 url = viewport.applet.getCodeBase()+url;
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706 public void closeMenuItem_actionPerformed()
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708 PaintRefresher.components.remove(viewport.alignment);
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709 if(PaintRefresher.components.size()==0 && viewport.applet==null)
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719 void updateEditMenuBar()
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722 if (viewport.historyList.size() > 0)
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724 undoMenuItem.setEnabled(true);
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725 CommandI command = (CommandI) viewport.historyList.peek();
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726 undoMenuItem.setLabel("Undo " + command.getDescription());
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730 undoMenuItem.setEnabled(false);
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731 undoMenuItem.setLabel("Undo");
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734 if (viewport.redoList.size() > 0)
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736 redoMenuItem.setEnabled(true);
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738 CommandI command = (CommandI) viewport.redoList.peek();
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739 redoMenuItem.setLabel("Redo " + command.getDescription());
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743 redoMenuItem.setEnabled(false);
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744 redoMenuItem.setLabel("Redo");
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748 public void addHistoryItem(CommandI command)
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750 if(command.getSize()>0)
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752 viewport.historyList.push(command);
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753 viewport.redoList.removeAllElements();
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754 updateEditMenuBar();
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755 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
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762 * @param e DOCUMENT ME!
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764 protected void undoMenuItem_actionPerformed()
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766 if(viewport.historyList.size()<1)
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769 CommandI command = (CommandI)viewport.historyList.pop();
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770 viewport.redoList.push(command);
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771 command.undoCommand();
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773 AlignViewport originalSource = getOriginatingSource(command);
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775 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
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776 updateEditMenuBar();
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777 originalSource.firePropertyChange("alignment", null,null);
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783 * @param e DOCUMENT ME!
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785 protected void redoMenuItem_actionPerformed()
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787 CommandI command = (CommandI) viewport.redoList.pop();
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788 viewport.historyList.push(command);
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789 command.doCommand();
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791 AlignViewport originalSource = getOriginatingSource(command);
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792 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
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794 updateEditMenuBar();
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795 originalSource.firePropertyChange("alignment", null, null);
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798 AlignViewport getOriginatingSource(CommandI command)
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800 AlignViewport originalSource = viewport;
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801 //For sequence removal and addition, we need to fire
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802 //the property change event FROM the viewport where the
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803 //original alignment was altered
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804 if (command instanceof EditCommand)
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806 EditCommand editCommand = (EditCommand) command;
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807 AlignmentI al = editCommand.getAlignment();
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808 Vector comps = (Vector) PaintRefresher.components
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809 .get(viewport.getSequenceSetId());
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810 for (int i = 0; i < comps.size(); i++)
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812 if (comps.elementAt(i) instanceof AlignmentPanel)
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814 if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)
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816 originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
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822 return originalSource;
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825 public void moveSelectedSequences(boolean up)
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827 SequenceGroup sg = viewport.getSelectionGroup();
\r
835 for (int i = 1; i < viewport.alignment.getHeight(); i++)
\r
837 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
838 if (!sg.getSequences(false).contains(seq))
\r
843 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
\r
844 if (sg.getSequences(false).contains(temp))
\r
849 viewport.alignment.getSequences().setElementAt(temp, i);
\r
850 viewport.alignment.getSequences().setElementAt(seq, i - 1);
\r
855 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
\r
857 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
858 if (!sg.getSequences(true).contains(seq))
\r
863 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
\r
864 if (sg.getSequences(true).contains(temp))
\r
869 viewport.alignment.getSequences().setElementAt(temp, i);
\r
870 viewport.alignment.getSequences().setElementAt(seq, i + 1);
\r
874 alignPanel.repaint();
\r
877 static StringBuffer copiedSequences;
\r
878 static Vector copiedHiddenColumns;
\r
879 protected void copy_actionPerformed()
\r
881 if (viewport.getSelectionGroup() == null)
\r
886 SequenceGroup sg = viewport.getSelectionGroup();
\r
887 copiedSequences = new StringBuffer();
\r
888 Hashtable orderedSeqs = new Hashtable();
\r
889 for (int i = 0; i < sg.getSize(false); i++)
\r
891 SequenceI seq = sg.getSequenceAt(i);
\r
892 int index = viewport.alignment.findIndex(seq);
\r
893 orderedSeqs.put(index + "", seq);
\r
896 int index = 0, startRes, endRes;
\r
899 if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
\r
901 copiedHiddenColumns = new Vector();
\r
902 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
\r
903 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();
\r
906 int[] region = (int[])
\r
907 viewport.getColumnSelection().getHiddenColumns().elementAt(i);
\r
909 copiedHiddenColumns.addElement(new int[]
\r
910 {region[0] - hiddenOffset,
\r
911 region[1] - hiddenOffset});
\r
915 copiedHiddenColumns = null;
\r
918 for (int i = 0; i < sg.getSize(false); i++)
\r
920 SequenceI seq = null;
\r
922 while (seq == null)
\r
924 if (orderedSeqs.containsKey(index + ""))
\r
926 seq = (SequenceI) orderedSeqs.get(index + "");
\r
938 //Returns residue following index if gap
\r
939 startRes = seq.findPosition(sg.getStartRes());
\r
942 //Need to find the residue preceeding index if gap
\r
945 for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
\r
947 ch = seq.getCharAt(j);
\r
948 if (!jalview.util.Comparison.isGap( (ch)))
\r
956 endRes += seq.getStart() -1;
\r
959 copiedSequences.append(seq.getName() + "\t" +
\r
962 seq.getSequence(sg.getStartRes(),
\r
963 sg.getEndRes() + 1) + "\n");
\r
968 protected void pasteNew_actionPerformed()
\r
973 protected void pasteThis_actionPerformed()
\r
978 void paste(boolean newAlignment)
\r
983 if (copiedSequences == null)
\r
988 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
989 Vector seqs = new Vector();
\r
990 while (st.hasMoreElements())
\r
992 String name = st.nextToken();
\r
993 int start = Integer.parseInt(st.nextToken());
\r
994 int end = Integer.parseInt(st.nextToken());
\r
995 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
\r
997 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
998 for (int i = 0; i < seqs.size(); i++)
\r
1000 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
1005 String newtitle = new String("Copied sequences");
\r
1006 if (getTitle().startsWith("Copied sequences"))
\r
1008 newtitle = getTitle();
\r
1012 newtitle = newtitle.concat("- from " + getTitle());
\r
1014 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
1018 if (copiedHiddenColumns != null)
\r
1020 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
1022 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
1023 af.viewport.hideColumns(region[0], region[1]);
\r
1028 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
\r
1033 for (int i = 0; i < newSeqs.length; i++)
\r
1035 viewport.alignment.addSequence(newSeqs[i]);
\r
1039 addHistoryItem(new EditCommand(
\r
1041 EditCommand.PASTE,
\r
1044 viewport.alignment.getWidth(),
\r
1045 viewport.alignment)
\r
1048 viewport.setEndSeq(viewport.alignment.getHeight());
\r
1049 viewport.alignment.getWidth();
\r
1050 viewport.firePropertyChange("alignment", null, null);
\r
1054 catch (Exception ex)
\r
1055 {} // could be anything being pasted in here
\r
1059 protected void cut_actionPerformed()
\r
1061 copy_actionPerformed();
\r
1062 delete_actionPerformed();
\r
1065 protected void delete_actionPerformed()
\r
1068 SequenceGroup sg = viewport.getSelectionGroup();
\r
1074 Vector seqs = new Vector();
\r
1076 for (int i = 0; i < sg.getSize(false); i++)
\r
1078 seq = sg.getSequenceAt(i);
\r
1079 seqs.addElement(seq);
\r
1083 // If the cut affects all sequences, remove highlighted columns
\r
1084 if (sg.getSize(false) == viewport.alignment.getHeight())
\r
1086 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
1087 sg.getEndRes() + 1);
\r
1091 SequenceI [] cut = new SequenceI[seqs.size()];
\r
1092 for(int i=0; i<seqs.size(); i++)
\r
1093 cut[i] = (SequenceI)seqs.elementAt(i);
\r
1097 //ADD HISTORY ITEM
\r
1099 addHistoryItem(new EditCommand("Cut Sequences",
\r
1103 sg.getEndRes()-sg.getStartRes()+1,
\r
1104 viewport.alignment));
\r
1107 viewport.setSelectionGroup(null);
\r
1108 viewport.alignment.deleteGroup(sg);
\r
1110 viewport.firePropertyChange("alignment", null,
\r
1111 viewport.getAlignment().getSequences());
\r
1113 if (viewport.getAlignment().getHeight() < 1)
\r
1115 this.setVisible(false);
\r
1119 protected void deleteGroups_actionPerformed()
\r
1121 viewport.alignment.deleteAllGroups();
\r
1122 viewport.sequenceColours=null;
\r
1123 viewport.setSelectionGroup(null);
\r
1125 alignPanel.repaint();
\r
1128 public void selectAllSequenceMenuItem_actionPerformed()
\r
1130 SequenceGroup sg = new SequenceGroup();
\r
1131 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1133 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
1135 sg.setEndRes(viewport.alignment.getWidth()-1);
\r
1136 viewport.setSelectionGroup(sg);
\r
1137 alignPanel.repaint();
\r
1138 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1141 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1143 if(viewport.cursorMode)
\r
1145 alignPanel.seqPanel.keyboardNo1=null;
\r
1146 alignPanel.seqPanel.keyboardNo2=null;
\r
1148 viewport.setSelectionGroup(null);
\r
1149 viewport.getColumnSelection().clear();
\r
1150 viewport.setSelectionGroup(null);
\r
1151 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1152 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1153 alignPanel.repaint();
\r
1154 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1157 public void invertSequenceMenuItem_actionPerformed()
\r
1159 SequenceGroup sg = viewport.getSelectionGroup();
\r
1160 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1162 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1165 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1168 void trimAlignment(boolean trimLeft)
\r
1170 ColumnSelection colSel = viewport.getColumnSelection();
\r
1173 if (colSel.size() > 0)
\r
1176 column = colSel.getMin();
\r
1178 column = colSel.getMax();
\r
1180 SequenceI [] seqs;
\r
1181 if(viewport.getSelectionGroup()!=null)
\r
1182 seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
\r
1184 seqs = viewport.alignment.getSequencesArray();
\r
1187 TrimRegionCommand trimRegion;
\r
1190 trimRegion = new TrimRegionCommand("Remove Left",
\r
1191 TrimRegionCommand.TRIM_LEFT,
\r
1194 viewport.alignment,
\r
1196 viewport.selectionGroup);
\r
1197 viewport.setStartRes(0);
\r
1201 trimRegion = new TrimRegionCommand("Remove Right",
\r
1202 TrimRegionCommand.TRIM_RIGHT,
\r
1205 viewport.alignment,
\r
1207 viewport.selectionGroup);
\r
1210 statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
\r
1213 addHistoryItem(trimRegion);
\r
1215 Vector groups = viewport.alignment.getGroups();
\r
1217 for (int i = 0; i < groups.size(); i++)
\r
1219 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1221 if ( (trimLeft && !sg.adjustForRemoveLeft(column))
\r
1222 || (!trimLeft && !sg.adjustForRemoveRight(column)))
\r
1224 viewport.alignment.deleteGroup(sg);
\r
1228 viewport.firePropertyChange("alignment", null,
\r
1229 viewport.getAlignment().getSequences());
\r
1234 public void removeGappedColumnMenuItem_actionPerformed()
\r
1236 int start = 0, end = viewport.alignment.getWidth()-1;
\r
1239 if (viewport.getSelectionGroup() != null)
\r
1241 seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
\r
1242 start = viewport.getSelectionGroup().getStartRes();
\r
1243 end = viewport.getSelectionGroup().getEndRes();
\r
1246 seqs = viewport.alignment.getSequencesArray();
\r
1249 RemoveGapColCommand removeGapCols =
\r
1250 new RemoveGapColCommand("Remove Gapped Columns",
\r
1253 viewport.getGapCharacter());
\r
1255 addHistoryItem(removeGapCols);
\r
1257 statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");
\r
1259 //This is to maintain viewport position on first residue
\r
1260 //of first sequence
\r
1261 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1262 int startRes = seq.findPosition(viewport.startRes);
\r
1263 // ShiftList shifts;
\r
1264 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
\r
1265 // edit.alColumnChanges=shifts.getInverse();
\r
1266 // if (viewport.hasHiddenColumns)
\r
1267 // viewport.getColumnSelection().compensateForEdits(shifts);
\r
1268 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1269 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1273 public void removeAllGapsMenuItem_actionPerformed()
\r
1275 int start = 0, end = viewport.alignment.getWidth()-1;
\r
1278 if (viewport.getSelectionGroup() != null)
\r
1280 seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
\r
1281 start = viewport.getSelectionGroup().getStartRes();
\r
1282 end = viewport.getSelectionGroup().getEndRes();
\r
1285 seqs = viewport.alignment.getSequencesArray();
\r
1287 //This is to maintain viewport position on first residue
\r
1288 //of first sequence
\r
1289 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1290 int startRes = seq.findPosition(viewport.startRes);
\r
1292 addHistoryItem(new RemoveGapsCommand("Remove Gaps",
\r
1295 viewport.getGapCharacter()));
\r
1297 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1299 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1303 public void findMenuItem_actionPerformed()
\r
1305 new Finder(alignPanel);
\r
1308 public void font_actionPerformed()
\r
1310 new FontChooser(alignPanel);
\r
1314 public void seqLimits_itemStateChanged()
\r
1316 viewport.setShowJVSuffix(seqLimits.getState());
\r
1317 alignPanel.fontChanged();
\r
1318 alignPanel.repaint();
\r
1322 protected void colourTextMenuItem_actionPerformed()
\r
1324 viewport.setColourText(colourTextMenuItem.getState());
\r
1325 alignPanel.repaint();
\r
1328 protected void wrapMenuItem_actionPerformed()
\r
1330 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
1331 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
1332 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
1333 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
1334 scaleRight.setEnabled(wrapMenuItem.getState());
\r
1335 alignPanel.repaint();
\r
1339 protected void scaleAbove_actionPerformed()
\r
1341 viewport.setScaleAboveWrapped(scaleAbove.getState());
\r
1342 alignPanel.repaint();
\r
1345 protected void scaleLeft_actionPerformed()
\r
1347 viewport.setScaleLeftWrapped(scaleLeft.getState());
\r
1348 alignPanel.repaint();
\r
1351 protected void scaleRight_actionPerformed()
\r
1353 viewport.setScaleRightWrapped(scaleRight.getState());
\r
1354 alignPanel.repaint();
\r
1357 public void viewBoxesMenuItem_actionPerformed()
\r
1359 viewport.setShowBoxes(viewBoxesMenuItem.getState());
\r
1360 alignPanel.repaint();
\r
1363 public void viewTextMenuItem_actionPerformed()
\r
1365 viewport.setShowText(viewTextMenuItem.getState());
\r
1366 alignPanel.repaint();
\r
1369 protected void renderGapsMenuItem_actionPerformed()
\r
1371 viewport.setRenderGaps(renderGapsMenuItem.getState());
\r
1372 alignPanel.repaint();
\r
1375 public void annotationPanelMenuItem_actionPerformed()
\r
1377 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
\r
1378 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
\r
1381 public void featureSettings_actionPerformed()
\r
1383 new FeatureSettings(viewport, alignPanel);
\r
1386 public void overviewMenuItem_actionPerformed()
\r
1388 if (alignPanel.overviewPanel != null)
\r
1393 Frame frame = new Frame();
\r
1394 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1395 frame.add(overview);
\r
1396 // +50 must allow for applet frame window
\r
1397 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
1398 overview.preferredSize().width,
\r
1399 overview.preferredSize().height + 50);
\r
1402 frame.addWindowListener(new WindowAdapter()
\r
1404 public void windowClosing(WindowEvent e)
\r
1406 alignPanel.setOverviewPanel(null);
\r
1410 alignPanel.setOverviewPanel(overview);
\r
1414 protected void noColourmenuItem_actionPerformed()
\r
1416 changeColour(null);
\r
1419 public void clustalColour_actionPerformed()
\r
1421 abovePIDThreshold.setState(false);
\r
1422 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
\r
1423 viewport.alignment.getWidth()));
\r
1426 public void zappoColour_actionPerformed()
\r
1428 changeColour(new ZappoColourScheme());
\r
1431 public void taylorColour_actionPerformed()
\r
1433 changeColour(new TaylorColourScheme());
\r
1436 public void hydrophobicityColour_actionPerformed()
\r
1438 changeColour(new HydrophobicColourScheme());
\r
1441 public void helixColour_actionPerformed()
\r
1443 changeColour(new HelixColourScheme());
\r
1446 public void strandColour_actionPerformed()
\r
1448 changeColour(new StrandColourScheme());
\r
1451 public void turnColour_actionPerformed()
\r
1453 changeColour(new TurnColourScheme());
\r
1456 public void buriedColour_actionPerformed()
\r
1458 changeColour(new BuriedColourScheme());
\r
1461 public void nucleotideColour_actionPerformed()
\r
1463 changeColour(new NucleotideColourScheme());
\r
1466 protected void applyToAllGroups_actionPerformed()
\r
1468 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
\r
1471 void changeColour(ColourSchemeI cs)
\r
1473 int threshold = 0;
\r
1477 if (viewport.getAbovePIDThreshold())
\r
1479 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
\r
1481 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1483 viewport.setGlobalColourScheme(cs);
\r
1487 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1490 if (viewport.getConservationSelected())
\r
1493 Alignment al = (Alignment) viewport.alignment;
\r
1494 Conservation c = new Conservation("All",
\r
1495 ResidueProperties.propHash, 3,
\r
1496 al.getSequences(), 0,
\r
1497 al.getWidth() - 1);
\r
1500 c.verdict(false, viewport.ConsPercGaps);
\r
1502 cs.setConservation(c);
\r
1504 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1510 cs.setConservation(null);
\r
1513 cs.setConsensus(viewport.hconsensus);
\r
1516 viewport.setGlobalColourScheme(cs);
\r
1518 if (viewport.getColourAppliesToAllGroups())
\r
1520 Vector groups = viewport.alignment.getGroups();
\r
1521 for (int i = 0; i < groups.size(); i++)
\r
1523 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1530 if (cs instanceof ClustalxColourScheme)
\r
1532 sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth());
\r
1538 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1540 catch (Exception ex)
\r
1542 ex.printStackTrace();
\r
1547 if (viewport.getAbovePIDThreshold()
\r
1548 || cs instanceof PIDColourScheme
\r
1549 || cs instanceof Blosum62ColourScheme)
\r
1551 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1552 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth()));
\r
1555 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1557 if (viewport.getConservationSelected())
\r
1559 Conservation c = new Conservation("Group",
\r
1560 ResidueProperties.propHash, 3,
\r
1561 sg.getSequences(true), 0,
\r
1562 viewport.alignment.getWidth() - 1);
\r
1564 c.verdict(false, viewport.ConsPercGaps);
\r
1565 sg.cs.setConservation(c);
\r
1569 sg.cs.setConservation(null);
\r
1570 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1577 if (alignPanel.getOverviewPanel() != null)
\r
1579 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1582 alignPanel.repaint();
\r
1587 protected void modifyPID_actionPerformed()
\r
1589 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1591 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
1593 SliderPanel.showPIDSlider();
\r
1597 protected void modifyConservation_actionPerformed()
\r
1599 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1601 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
1603 SliderPanel.showConservationSlider();
\r
1607 protected void conservationMenuItem_actionPerformed()
\r
1609 viewport.setConservationSelected(conservationMenuItem.getState());
\r
1611 viewport.setAbovePIDThreshold(false);
\r
1612 abovePIDThreshold.setState(false);
\r
1614 changeColour(viewport.getGlobalColourScheme());
\r
1616 modifyConservation_actionPerformed();
\r
1619 public void abovePIDThreshold_actionPerformed()
\r
1621 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
1623 conservationMenuItem.setState(false);
\r
1624 viewport.setConservationSelected(false);
\r
1626 changeColour(viewport.getGlobalColourScheme());
\r
1628 modifyPID_actionPerformed();
\r
1631 public void userDefinedColour_actionPerformed()
\r
1633 new UserDefinedColours(alignPanel, null);
\r
1636 public void PIDColour_actionPerformed()
\r
1638 changeColour(new PIDColourScheme());
\r
1641 public void BLOSUM62Colour_actionPerformed()
\r
1643 changeColour(new Blosum62ColourScheme());
\r
1646 public void sortPairwiseMenuItem_actionPerformed()
\r
1648 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
\r
1649 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1650 viewport.getAlignment().getSequenceAt(0));
\r
1651 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment));
\r
1652 alignPanel.repaint();
\r
1655 public void sortIDMenuItem_actionPerformed()
\r
1657 // addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1658 // HistoryItem.SORT));
\r
1659 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1660 alignPanel.repaint();
\r
1663 public void sortGroupMenuItem_actionPerformed()
\r
1665 // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1666 // HistoryItem.SORT));
\r
1667 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1668 alignPanel.repaint();
\r
1672 public void removeRedundancyMenuItem_actionPerformed()
\r
1674 new RedundancyPanel(alignPanel);
\r
1677 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
1679 if (viewport.getSelectionGroup()!=null
\r
1680 && viewport.getSelectionGroup().getSize(false) > 1)
\r
1682 Frame frame = new Frame();
\r
1683 frame.add(new PairwiseAlignPanel(alignPanel));
\r
1684 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
1688 public void PCAMenuItem_actionPerformed()
\r
1690 //are the sequences aligned?
\r
1691 if (!viewport.alignment.isAligned())
\r
1693 SequenceI current;
\r
1694 int Width = viewport.getAlignment().getWidth();
\r
1696 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1699 current = viewport.getAlignment().getSequenceAt(i);
\r
1701 if (current.getLength() < Width)
\r
1703 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1706 alignPanel.repaint();
\r
1709 if ( (viewport.getSelectionGroup() != null &&
\r
1710 viewport.getSelectionGroup().getSize(false) < 4 &&
\r
1711 viewport.getSelectionGroup().getSize(false) > 0)
\r
1712 || viewport.getAlignment().getHeight() < 4)
\r
1719 new PCAPanel(viewport);
\r
1721 catch (java.lang.OutOfMemoryError ex)
\r
1727 public void averageDistanceTreeMenuItem_actionPerformed()
\r
1729 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1732 public void neighbourTreeMenuItem_actionPerformed()
\r
1734 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1737 protected void njTreeBlosumMenuItem_actionPerformed()
\r
1739 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1742 protected void avTreeBlosumMenuItem_actionPerformed()
\r
1744 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1747 void NewTreePanel(String type, String pwType, String title)
\r
1749 //are the sequences aligned?
\r
1750 if (!viewport.alignment.isAligned())
\r
1752 SequenceI current;
\r
1753 int Width = viewport.getAlignment().getWidth();
\r
1755 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1758 current = viewport.getAlignment().getSequenceAt(i);
\r
1760 if (current.getLength() < Width)
\r
1762 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1765 alignPanel.repaint();
\r
1769 if ( (viewport.getSelectionGroup() != null &&
\r
1770 viewport.getSelectionGroup().getSize(false) > 1)
\r
1771 || (viewport.getSelectionGroup() == null
\r
1772 && viewport.alignment.getHeight() > 1))
\r
1774 final TreePanel tp = new TreePanel(viewport,
\r
1778 addTreeMenuItem(tp, title);
\r
1780 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
1784 void loadTree_actionPerformed()
\r
1786 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1787 cap.setText("Paste your Newick tree file here.");
\r
1788 cap.treeImport = true;
\r
1789 Frame frame = new Frame();
\r
1791 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
1794 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
1796 TreePanel tp = new TreePanel(viewport,
\r
1800 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
1801 addTreeMenuItem(tp, treeFile);
\r
1804 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1806 final MenuItem item = new MenuItem(title);
\r
1807 sortByTreeMenu.add(item);
\r
1808 item.addActionListener(new java.awt.event.ActionListener()
\r
1810 public void actionPerformed(ActionEvent evt)
\r
1812 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1813 // HistoryItem.SORT));
\r
1814 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1815 alignPanel.repaint();
\r
1819 treePanel.addWindowListener(new WindowAdapter()
\r
1821 public void windowClosing(WindowEvent e)
\r
1823 sortByTreeMenu.remove(item);
\r
1828 protected void documentation_actionPerformed()
\r
1830 showURL("http://www.jalview.org/help.html", "HELP");
\r
1833 protected void about_actionPerformed()
\r
1836 class AboutPanel extends Canvas
\r
1839 public AboutPanel(String version)
\r
1840 { this.version = version; }
\r
1842 public void paint(Graphics g)
\r
1844 g.setColor(Color.white);
\r
1845 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1846 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1847 FontMetrics fm = g.getFontMetrics();
\r
1848 int fh = fm.getHeight();
\r
1850 g.setColor(Color.black);
\r
1851 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
1852 g.drawString("Jalview - Release "+version, 200, y += fh);
\r
1853 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1854 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
1856 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
1859 "For any issues relating to Jalview, email help@jalview.org", x,
\r
1861 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
1862 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
1864 g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh);
\r
1868 String version = "test";
\r
1869 java.net.URL url = getClass().getResource("/.build_properties");
\r
1874 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
1875 url.openStream()));
\r
1877 while ( (line = reader.readLine()) != null)
\r
1879 if (line.indexOf("VERSION") > -1)
\r
1881 version = line.substring(line.indexOf("=") + 1);
\r
1885 catch (Exception ex)
\r
1887 ex.printStackTrace();
\r
1892 Frame frame = new Frame();
\r
1893 frame.add(new AboutPanel(version));
\r
1894 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
\r
1898 public void showURL(String url, String target)
\r
1900 if (viewport.applet == null)
\r
1902 System.out.println("Not running as applet - no browser available.");
\r
1908 System.out.println("Show url: "+url);
\r
1909 viewport.applet.getAppletContext().showDocument(new java.net.URL(url),
\r
1912 catch (Exception ex)
\r
1914 ex.printStackTrace();
\r
1920 //////////////////////////////////////////////////////////////////////////////////
\r
1921 //JBuilder Graphics here
\r
1923 protected MenuBar alignFrameMenuBar = new MenuBar();
\r
1924 protected Menu fileMenu = new Menu("File");
\r
1925 protected MenuItem loadApplication = new MenuItem("View in Full Application");
\r
1926 protected MenuItem loadTree = new MenuItem("Load Associated Tree");
\r
1927 protected MenuItem closeMenuItem = new MenuItem("Close");
\r
1928 protected Menu editMenu = new Menu("Edit");
\r
1929 protected Menu viewMenu = new Menu("View");
\r
1930 protected Menu colourMenu = new Menu("Colour");
\r
1931 protected Menu calculateMenu = new Menu("Calculate");
\r
1932 protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
1933 protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
1934 protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
1935 protected MenuItem remove2LeftMenuItem = new MenuItem();
\r
1936 protected MenuItem remove2RightMenuItem = new MenuItem();
\r
1937 protected MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
1938 protected MenuItem removeAllGapsMenuItem = new MenuItem();
\r
1939 protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
1940 protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
1941 protected MenuItem sortPairwiseMenuItem = new MenuItem();
\r
1942 protected MenuItem sortIDMenuItem = new MenuItem();
\r
1943 protected MenuItem sortGroupMenuItem = new MenuItem();
\r
1944 protected MenuItem removeRedundancyMenuItem = new MenuItem();
\r
1945 protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
1946 protected MenuItem PCAMenuItem = new MenuItem();
\r
1947 protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
1948 protected MenuItem neighbourTreeMenuItem = new MenuItem();
\r
1949 BorderLayout borderLayout1 = new BorderLayout();
\r
1950 public Label statusBar = new Label();
\r
1951 protected Menu outputTextboxMenu = new Menu();
\r
1952 protected MenuItem clustalColour = new MenuItem();
\r
1953 protected MenuItem zappoColour = new MenuItem();
\r
1954 protected MenuItem taylorColour = new MenuItem();
\r
1955 protected MenuItem hydrophobicityColour = new MenuItem();
\r
1956 protected MenuItem helixColour = new MenuItem();
\r
1957 protected MenuItem strandColour = new MenuItem();
\r
1958 protected MenuItem turnColour = new MenuItem();
\r
1959 protected MenuItem buriedColour = new MenuItem();
\r
1960 protected MenuItem userDefinedColour = new MenuItem();
\r
1961 protected MenuItem PIDColour = new MenuItem();
\r
1962 protected MenuItem BLOSUM62Colour = new MenuItem();
\r
1963 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
1964 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
1965 protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
1966 protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
1967 MenuItem overviewMenuItem = new MenuItem();
\r
1968 protected MenuItem undoMenuItem = new MenuItem();
\r
1969 protected MenuItem redoMenuItem = new MenuItem();
\r
1970 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
1971 MenuItem noColourmenuItem = new MenuItem();
\r
1972 protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
1973 protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
1974 MenuItem findMenuItem = new MenuItem();
\r
1975 protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
1976 protected MenuItem nucleotideColour = new MenuItem();
\r
1977 MenuItem deleteGroups = new MenuItem();
\r
1978 MenuItem delete = new MenuItem();
\r
1979 MenuItem copy = new MenuItem();
\r
1980 MenuItem cut = new MenuItem();
\r
1981 Menu pasteMenu = new Menu();
\r
1982 MenuItem pasteNew = new MenuItem();
\r
1983 MenuItem pasteThis = new MenuItem();
\r
1984 protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
1985 protected MenuItem font = new MenuItem();
\r
1986 protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
1987 protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
1988 protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
1989 MenuItem modifyPID = new MenuItem();
\r
1990 MenuItem modifyConservation = new MenuItem();
\r
1991 protected CheckboxMenuItem autoCalculate
\r
1992 = new CheckboxMenuItem("Autocalculate Consensus", true);
\r
1993 protected Menu sortByTreeMenu = new Menu();
\r
1994 Menu sort = new Menu();
\r
1995 Menu calculate = new Menu();
\r
1996 MenuItem inputText = new MenuItem();
\r
1997 Menu helpMenu = new Menu();
\r
1998 MenuItem documentation = new MenuItem();
\r
1999 MenuItem about = new MenuItem();
\r
2000 protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
2001 Panel embeddedMenu;
\r
2002 Label embeddedEdit;
\r
2003 Label embeddedSelect;
\r
2004 Label embeddedView;
\r
2005 Label embeddedFormat;
\r
2006 Label embeddedColour;
\r
2007 Label embeddedFile;
\r
2008 Label embeddedHelp;
\r
2009 Label embeddedCalculate;
\r
2010 FlowLayout flowLayout1;
\r
2012 private void jbInit() throws Exception {
\r
2014 setMenuBar(alignFrameMenuBar);
\r
2018 // dynamically fill save as menu with available formats
\r
2019 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
2022 item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
2024 item.addActionListener(new java.awt.event.ActionListener()
\r
2026 public void actionPerformed(ActionEvent e)
\r
2028 outputText_actionPerformed(e);
\r
2032 outputTextboxMenu.add(item);
\r
2034 closeMenuItem.addActionListener(this);
\r
2035 loadApplication.addActionListener(this);
\r
2037 loadTree.addActionListener(this);
\r
2038 selectAllSequenceMenuItem.addActionListener(this);
\r
2039 deselectAllSequenceMenuItem.addActionListener(this);
\r
2040 invertSequenceMenuItem.addActionListener(this);
\r
2041 remove2LeftMenuItem.setLabel("Remove Left");
\r
2042 remove2LeftMenuItem.addActionListener(this);
\r
2043 remove2RightMenuItem.setLabel("Remove Right");
\r
2044 remove2RightMenuItem.addActionListener(this);
\r
2045 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
2046 removeGappedColumnMenuItem.addActionListener(this);
\r
2047 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
2048 removeAllGapsMenuItem.addActionListener(this);
\r
2049 viewBoxesMenuItem.setLabel("Boxes");
\r
2050 viewBoxesMenuItem.setState(true);
\r
2051 viewBoxesMenuItem.addItemListener(this);
\r
2052 viewTextMenuItem.setLabel("Text");
\r
2053 viewTextMenuItem.setState(true);
\r
2054 viewTextMenuItem.addItemListener(this);
\r
2055 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
2056 sortPairwiseMenuItem.addActionListener(this);
\r
2057 sortIDMenuItem.setLabel("by ID");
\r
2058 sortIDMenuItem.addActionListener(this);
\r
2059 sortGroupMenuItem.setLabel("by Group");
\r
2060 sortGroupMenuItem.addActionListener(this);
\r
2061 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
2062 removeRedundancyMenuItem.addActionListener(this);
\r
2063 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
2064 pairwiseAlignmentMenuItem.addActionListener(this);
\r
2065 PCAMenuItem.setLabel("Principal Component Analysis");
\r
2066 PCAMenuItem.addActionListener(this);
\r
2067 averageDistanceTreeMenuItem.setLabel(
\r
2068 "Average Distance Using % Identity");
\r
2069 averageDistanceTreeMenuItem.addActionListener(this);
\r
2070 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
2071 neighbourTreeMenuItem.addActionListener(this);
\r
2072 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
2073 statusBar.setBackground(Color.white);
\r
2074 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
2075 statusBar.setText("Status bar");
\r
2076 outputTextboxMenu.setLabel("Output to Textbox");
\r
2077 clustalColour.setLabel("Clustalx");
\r
2079 clustalColour.addActionListener(this);
\r
2080 zappoColour.setLabel("Zappo");
\r
2081 zappoColour.addActionListener(this);
\r
2082 taylorColour.setLabel("Taylor");
\r
2083 taylorColour.addActionListener(this);
\r
2084 hydrophobicityColour.setLabel("Hydrophobicity");
\r
2085 hydrophobicityColour.addActionListener(this);
\r
2086 helixColour.setLabel("Helix Propensity");
\r
2087 helixColour.addActionListener(this);
\r
2088 strandColour.setLabel("Strand Propensity");
\r
2089 strandColour.addActionListener(this);
\r
2090 turnColour.setLabel("Turn Propensity");
\r
2091 turnColour.addActionListener(this);
\r
2092 buriedColour.setLabel("Buried Index");
\r
2093 buriedColour.addActionListener(this);
\r
2094 userDefinedColour.setLabel("User Defined...");
\r
2095 userDefinedColour.addActionListener(this);
\r
2096 PIDColour.setLabel("Percentage Identity");
\r
2097 PIDColour.addActionListener(this);
\r
2098 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
2099 BLOSUM62Colour.addActionListener(this);
\r
2100 avDistanceTreeBlosumMenuItem.setLabel(
\r
2101 "Average Distance Using BLOSUM62");
\r
2102 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
2103 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
2104 njTreeBlosumMenuItem.addActionListener(this);
\r
2105 annotationPanelMenuItem.setLabel("Show Annotations");
\r
2106 annotationPanelMenuItem.addItemListener(this);
\r
2107 colourTextMenuItem.setLabel("Colour Text");
\r
2108 colourTextMenuItem.addItemListener(this);
\r
2109 overviewMenuItem.setLabel("Overview Window");
\r
2110 overviewMenuItem.addActionListener(this);
\r
2111 undoMenuItem.setEnabled(false);
\r
2112 undoMenuItem.setLabel("Undo");
\r
2113 undoMenuItem.addActionListener(this);
\r
2114 redoMenuItem.setEnabled(false);
\r
2115 redoMenuItem.setLabel("Redo");
\r
2116 redoMenuItem.addActionListener(this);
\r
2117 conservationMenuItem.setLabel("by Conservation");
\r
2118 conservationMenuItem.addItemListener(this);
\r
2119 noColourmenuItem.setLabel("None");
\r
2120 noColourmenuItem.addActionListener(this);
\r
2121 wrapMenuItem.setLabel("Wrap");
\r
2122 wrapMenuItem.addItemListener(this);
\r
2123 renderGapsMenuItem.setLabel("Show Gaps");
\r
2124 renderGapsMenuItem.setState(true);
\r
2125 renderGapsMenuItem.addItemListener(this);
\r
2126 findMenuItem.setLabel("Find...");
\r
2127 findMenuItem.addActionListener(this);
\r
2128 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
2129 abovePIDThreshold.addItemListener(this);
\r
2130 nucleotideColour.setLabel("Nucleotide");
\r
2131 nucleotideColour.addActionListener(this);
\r
2132 deleteGroups.setLabel("Undefine Groups");
\r
2133 deleteGroups.addActionListener(this);
\r
2134 copy.setLabel("Copy");
\r
2135 copy.addActionListener(this);
\r
2136 cut.setLabel("Cut");
\r
2137 cut.addActionListener(this);
\r
2138 delete.setLabel("Delete");
\r
2139 delete.addActionListener(this);
\r
2140 pasteMenu.setLabel("Paste");
\r
2141 pasteNew.setLabel("To New Alignment");
\r
2142 pasteNew.addActionListener(this);
\r
2143 pasteThis.setLabel("Add To This Alignment");
\r
2144 pasteThis.addActionListener(this);
\r
2145 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
2146 applyToAllGroups.setState(true);
\r
2147 applyToAllGroups.addItemListener(this);
\r
2148 font.setLabel("Font...");
\r
2149 font.addActionListener(this);
\r
2150 scaleAbove.setLabel("Scale Above");
\r
2151 scaleAbove.setState(true);
\r
2152 scaleAbove.setEnabled(false);
\r
2153 scaleAbove.addItemListener(this);
\r
2154 scaleLeft.setEnabled(false);
\r
2155 scaleLeft.setState(true);
\r
2156 scaleLeft.setLabel("Scale Left");
\r
2157 scaleLeft.addItemListener(this);
\r
2158 scaleRight.setEnabled(false);
\r
2159 scaleRight.setState(true);
\r
2160 scaleRight.setLabel("Scale Right");
\r
2161 scaleRight.addItemListener(this);
\r
2162 modifyPID.setLabel("Modify Identity Threshold...");
\r
2163 modifyPID.addActionListener(this);
\r
2164 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
2165 modifyConservation.addActionListener(this);
\r
2166 sortByTreeMenu.setLabel("By Tree Order");
\r
2167 sort.setLabel("Sort");
\r
2168 calculate.setLabel("Calculate Tree");
\r
2169 autoCalculate.addItemListener(this);
\r
2170 inputText.setLabel("Input from textbox");
\r
2171 inputText.addActionListener(this);
\r
2173 helpMenu.setLabel("Help");
\r
2174 documentation.setLabel("Documentation");
\r
2175 documentation.addActionListener(this);
\r
2177 about.setLabel("About...");
\r
2178 about.addActionListener(this);
\r
2179 seqLimits.setState(true);
\r
2180 seqLimits.setLabel("Show Sequence Limits");
\r
2181 seqLimits.addItemListener(this);
\r
2182 featureSettings.setLabel("Feature Settings...");
\r
2183 featureSettings.addActionListener(this);
\r
2184 sequenceFeatures.setLabel("Sequence Features");
\r
2185 sequenceFeatures.addItemListener(this);
\r
2186 sequenceFeatures.setState(false);
\r
2187 annotationColour.setLabel("by Annotation...");
\r
2188 annotationColour.addActionListener(this);
\r
2189 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
2190 invertColSel.setLabel("Invert Column Selection");
\r
2191 menu1.setLabel("Show");
\r
2192 showColumns.setLabel("All Columns ");
\r
2193 showSeqs.setLabel("All Sequences");
\r
2194 menu2.setLabel("Hide");
\r
2195 hideColumns.setLabel("Selected Columns");
\r
2196 hideSequences.setLabel("Selected Sequences");
\r
2197 invertColSel.addActionListener(this);
\r
2198 showColumns.addActionListener(this);
\r
2199 showSeqs.addActionListener(this);
\r
2200 hideColumns.addActionListener(this);
\r
2201 hideSequences.addActionListener(this);
\r
2202 formatMenu.setLabel("Format");
\r
2203 selectMenu.setLabel("Select");
\r
2204 alignFrameMenuBar.add(fileMenu);
\r
2205 alignFrameMenuBar.add(editMenu);
\r
2206 alignFrameMenuBar.add(selectMenu);
\r
2207 alignFrameMenuBar.add(viewMenu);
\r
2208 alignFrameMenuBar.add(formatMenu);
\r
2209 alignFrameMenuBar.add(colourMenu);
\r
2210 alignFrameMenuBar.add(calculateMenu);
\r
2211 alignFrameMenuBar.add(helpMenu);
\r
2212 fileMenu.add(inputText);
\r
2213 fileMenu.add(outputTextboxMenu);
\r
2214 if(jalviewServletURL!=null)
\r
2215 fileMenu.add(loadApplication);
\r
2216 fileMenu.addSeparator();
\r
2217 fileMenu.add(loadTree);
\r
2218 fileMenu.add(closeMenuItem);
\r
2219 editMenu.add(undoMenuItem);
\r
2220 editMenu.add(redoMenuItem);
\r
2221 editMenu.add(cut);
\r
2222 editMenu.add(copy);
\r
2223 editMenu.add(pasteMenu);
\r
2224 editMenu.add(delete);
\r
2225 editMenu.addSeparator();
\r
2226 editMenu.add(remove2LeftMenuItem);
\r
2227 editMenu.add(remove2RightMenuItem);
\r
2228 editMenu.add(removeGappedColumnMenuItem);
\r
2229 editMenu.add(removeAllGapsMenuItem);
\r
2230 editMenu.add(removeRedundancyMenuItem);
\r
2231 viewMenu.add(menu1);
\r
2232 viewMenu.add(menu2);
\r
2233 viewMenu.addSeparator();
\r
2234 viewMenu.add(annotationPanelMenuItem);
\r
2235 viewMenu.addSeparator();
\r
2236 viewMenu.add(sequenceFeatures);
\r
2237 viewMenu.add(featureSettings);
\r
2238 viewMenu.addSeparator();
\r
2239 viewMenu.add(overviewMenuItem);
\r
2240 colourMenu.add(applyToAllGroups);
\r
2241 colourMenu.addSeparator();
\r
2242 colourMenu.add(noColourmenuItem);
\r
2243 colourMenu.add(clustalColour);
\r
2244 colourMenu.add(BLOSUM62Colour);
\r
2245 colourMenu.add(PIDColour);
\r
2246 colourMenu.add(zappoColour);
\r
2247 colourMenu.add(taylorColour);
\r
2248 colourMenu.add(hydrophobicityColour);
\r
2249 colourMenu.add(helixColour);
\r
2250 colourMenu.add(strandColour);
\r
2251 colourMenu.add(turnColour);
\r
2252 colourMenu.add(buriedColour);
\r
2253 colourMenu.add(nucleotideColour);
\r
2254 colourMenu.add(userDefinedColour);
\r
2255 colourMenu.addSeparator();
\r
2256 colourMenu.add(conservationMenuItem);
\r
2257 colourMenu.add(modifyConservation);
\r
2258 colourMenu.add(abovePIDThreshold);
\r
2259 colourMenu.add(modifyPID);
\r
2260 colourMenu.add(annotationColour);
\r
2261 calculateMenu.add(sort);
\r
2262 calculateMenu.add(calculate);
\r
2263 calculateMenu.addSeparator();
\r
2264 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
2265 calculateMenu.add(PCAMenuItem);
\r
2266 calculateMenu.add(autoCalculate);
\r
2267 this.add(statusBar, BorderLayout.SOUTH);
\r
2268 pasteMenu.add(pasteNew);
\r
2269 pasteMenu.add(pasteThis);
\r
2270 sort.add(sortIDMenuItem);
\r
2271 sort.add(sortByTreeMenu);
\r
2272 sort.add(sortGroupMenuItem);
\r
2273 sort.add(sortPairwiseMenuItem);
\r
2274 calculate.add(averageDistanceTreeMenuItem);
\r
2275 calculate.add(neighbourTreeMenuItem);
\r
2276 calculate.add(avDistanceTreeBlosumMenuItem);
\r
2277 calculate.add(njTreeBlosumMenuItem);
\r
2278 helpMenu.add(documentation);
\r
2279 helpMenu.add(about);
\r
2280 menu1.add(showColumns);
\r
2281 menu1.add(showSeqs);
\r
2282 menu2.add(hideColumns);
\r
2283 menu2.add(hideSequences);
\r
2284 formatMenu.add(font);
\r
2285 formatMenu.add(seqLimits);
\r
2286 formatMenu.add(wrapMenuItem);
\r
2287 formatMenu.add(scaleAbove);
\r
2288 formatMenu.add(scaleLeft);
\r
2289 formatMenu.add(scaleRight);
\r
2290 formatMenu.add(viewBoxesMenuItem);
\r
2291 formatMenu.add(viewTextMenuItem);
\r
2292 formatMenu.add(colourTextMenuItem);
\r
2293 formatMenu.add(renderGapsMenuItem);
\r
2294 selectMenu.add(findMenuItem);
\r
2295 selectMenu.addSeparator();
\r
2296 selectMenu.add(selectAllSequenceMenuItem);
\r
2297 selectMenu.add(deselectAllSequenceMenuItem);
\r
2298 selectMenu.add(invertSequenceMenuItem);
\r
2299 selectMenu.add(invertColSel);
\r
2300 selectMenu.add(deleteGroups);
\r
2303 public void setEmbedded()
\r
2306 embeddedMenu = new Panel();
\r
2307 embeddedEdit = new Label("Edit");
\r
2308 embeddedSelect = new Label("Select");
\r
2309 embeddedView = new Label("View");
\r
2310 embeddedFormat = new Label("Format");
\r
2311 embeddedColour = new Label("Colour");
\r
2312 embeddedFile = new Label("File");
\r
2313 embeddedHelp = new Label("Help");
\r
2314 embeddedCalculate = new Label("Calculate");
\r
2315 flowLayout1 = new FlowLayout();
\r
2316 embeddedMenu.setBackground(Color.lightGray);
\r
2317 embeddedMenu.setLayout(flowLayout1);
\r
2318 embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2319 embeddedSelect.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2320 embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2321 embeddedFormat.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2322 embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2323 embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2324 embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2325 embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2326 embeddedMenu.add(embeddedFile);
\r
2327 embeddedMenu.add(embeddedEdit);
\r
2328 embeddedMenu.add(embeddedSelect);
\r
2329 embeddedMenu.add(embeddedView);
\r
2330 embeddedMenu.add(embeddedFormat);
\r
2331 embeddedMenu.add(embeddedColour);
\r
2332 embeddedMenu.add(embeddedCalculate);
\r
2333 embeddedMenu.add(embeddedHelp);
\r
2334 flowLayout1.setAlignment(FlowLayout.LEFT);
\r
2335 flowLayout1.setHgap(2);
\r
2336 flowLayout1.setVgap(0);
\r
2337 embeddedFile.addMouseListener(this);
\r
2338 embeddedEdit.addMouseListener(this);
\r
2339 embeddedSelect.addMouseListener(this);
\r
2340 embeddedView.addMouseListener(this);
\r
2341 embeddedFormat.addMouseListener(this);
\r
2342 embeddedColour.addMouseListener(this);
\r
2343 embeddedCalculate.addMouseListener(this);
\r
2344 embeddedHelp.addMouseListener(this);
\r
2346 // setVisible(false);
\r
2347 fileMenu.remove(closeMenuItem);
\r
2348 fileMenu.remove(3); // Seperator
\r
2350 viewport.applet.setLayout(new BorderLayout());
\r
2351 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
\r
2352 viewport.applet.add(statusBar, BorderLayout.SOUTH);
\r
2353 // viewport.applet.validate();
\r
2355 alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height
\r
2356 - embeddedMenu.HEIGHT - statusBar.HEIGHT);
\r
2358 viewport.applet.add(alignPanel, BorderLayout.CENTER);
\r
2359 viewport.applet.validate();
\r
2365 PopupMenu filePopup, editPopup, searchPopup,
\r
2366 viewPopup, formatPopup, colourPopup, calculatePopup, helpPopup;
\r
2367 MenuItem featureSettings = new MenuItem();
\r
2368 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
2369 MenuItem annotationColour = new MenuItem();
\r
2370 MenuItem invertColSel = new MenuItem();
\r
2371 Menu menu1 = new Menu();
\r
2372 MenuItem showColumns = new MenuItem();
\r
2373 MenuItem showSeqs = new MenuItem();
\r
2374 Menu menu2 = new Menu();
\r
2375 MenuItem hideColumns = new MenuItem();
\r
2376 MenuItem hideSequences = new MenuItem();
\r
2377 Menu formatMenu = new Menu();
\r
2378 Menu selectMenu = new Menu();
\r
2380 public void mousePressed(MouseEvent evt)
\r
2382 PopupMenu popup = null;
\r
2383 Label source = (Label)evt.getSource();
\r
2384 if(source==embeddedFile)
\r
2386 popup = filePopup = genPopupMenu(filePopup, fileMenu);
\r
2388 else if(source==embeddedEdit)
\r
2390 popup = editPopup = genPopupMenu(editPopup, editMenu);
\r
2392 else if(source==embeddedSelect)
\r
2394 popup = searchPopup = genPopupMenu(searchPopup, selectMenu);
\r
2396 else if(source==embeddedView)
\r
2398 popup = viewPopup = genPopupMenu(viewPopup, viewMenu);
\r
2400 else if (source ==embeddedFormat)
\r
2402 popup = formatPopup = genPopupMenu(formatPopup, formatMenu);
\r
2404 else if(source==embeddedColour)
\r
2406 popup = colourPopup = genPopupMenu(colourPopup, colourMenu);
\r
2408 else if(source==embeddedCalculate)
\r
2410 popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);
\r
2412 else if(source==embeddedHelp)
\r
2414 popup = helpPopup = genPopupMenu(helpPopup, helpMenu);
\r
2417 embeddedMenu.add(popup);
\r
2418 popup.show(embeddedMenu,
\r
2419 source.getBounds().x,
\r
2420 source.getBounds().y + source.getBounds().getSize().height);
\r
2423 PopupMenu genPopupMenu(PopupMenu popup, Menu original)
\r
2429 popup = new PopupMenu();
\r
2430 int m, mSize = original.getItemCount();
\r
2431 for(m=0; m<mSize; m++)
\r
2433 popup.add(original.getItem(m));
\r
2440 public void mouseClicked(MouseEvent evt)
\r
2442 public void mouseReleased(MouseEvent evt)
\r
2444 public void mouseEntered(MouseEvent evt)
\r
2446 public void mouseExited(MouseEvent evt)
\r