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() || evt.isMetaDown())
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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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274 cut_actionPerformed();
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275 alignPanel.seqPanel.seqCanvas.repaint();
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279 case KeyEvent.VK_S:
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280 if(viewport.cursorMode)
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282 alignPanel.seqPanel.setCursorRow();
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285 case KeyEvent.VK_P:
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286 if(viewport.cursorMode)
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288 alignPanel.seqPanel.setCursorPosition();
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292 case KeyEvent.VK_ENTER:
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293 case KeyEvent.VK_COMMA:
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294 if(viewport.cursorMode)
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296 alignPanel.seqPanel.setCursorRowAndColumn();
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300 case KeyEvent.VK_Q:
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301 if(viewport.cursorMode)
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303 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
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306 case KeyEvent.VK_M:
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307 if(viewport.cursorMode)
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309 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
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313 case KeyEvent.VK_F2:
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314 viewport.cursorMode = ! viewport.cursorMode;
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315 statusBar.setText("Keyboard editing mode is "+
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316 (viewport.cursorMode ? "on" : "off"));
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317 if(viewport.cursorMode)
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319 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
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320 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
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322 alignPanel.seqPanel.seqCanvas.repaint();
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325 case KeyEvent.VK_F:
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326 if (evt.isControlDown())
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328 findMenuItem_actionPerformed();
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331 case KeyEvent.VK_H:
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333 boolean toggleSeqs = !evt.isControlDown();
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334 boolean toggleCols = !evt.isShiftDown();
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335 boolean hide = false;
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336 SequenceGroup sg = viewport.getSelectionGroup();
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340 if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())
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343 viewport.hideAllSelectedSeqs();
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345 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
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346 viewport.showAllHiddenSeqs();
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351 if (viewport.colSel.getSelected().size() > 0)
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353 viewport.hideSelectedColumns();
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355 viewport.selectionGroup = sg;
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358 viewport.showAllHiddenColumns();
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361 alignPanel.repaint();
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364 case KeyEvent.VK_PAGE_UP:
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365 if (viewport.wrapAlignment)
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366 alignPanel.scrollUp(true);
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368 alignPanel.setScrollValues(viewport.startRes,
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370 - viewport.endSeq + viewport.startSeq);
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372 case KeyEvent.VK_PAGE_DOWN:
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373 if (viewport.wrapAlignment)
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374 alignPanel.scrollUp(false);
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376 alignPanel.setScrollValues(viewport.startRes,
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378 + viewport.endSeq - viewport.startSeq);
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382 public void keyReleased(KeyEvent evt)
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384 public void keyTyped(KeyEvent evt)
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387 public void itemStateChanged(ItemEvent evt)
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389 if(evt.getSource()==colourTextMenuItem)
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390 colourTextMenuItem_actionPerformed();
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391 else if(evt.getSource()==wrapMenuItem)
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392 wrapMenuItem_actionPerformed();
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393 else if(evt.getSource()==scaleAbove)
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394 scaleAbove_actionPerformed();
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395 else if(evt.getSource()==scaleLeft)
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396 scaleLeft_actionPerformed();
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397 else if(evt.getSource()==scaleRight)
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398 scaleRight_actionPerformed();
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399 else if(evt.getSource()==seqLimits)
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400 seqLimits_itemStateChanged();
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401 else if(evt.getSource()==viewBoxesMenuItem)
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402 viewBoxesMenuItem_actionPerformed();
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403 else if(evt.getSource()==viewTextMenuItem)
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404 viewTextMenuItem_actionPerformed();
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405 else if(evt.getSource()==renderGapsMenuItem)
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406 renderGapsMenuItem_actionPerformed();
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407 else if(evt.getSource()==annotationPanelMenuItem)
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408 annotationPanelMenuItem_actionPerformed();
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409 else if(evt.getSource()==sequenceFeatures)
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411 viewport.showSequenceFeatures(sequenceFeatures.getState());
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412 alignPanel.seqPanel.seqCanvas.repaint();
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414 else if(evt.getSource()==conservationMenuItem)
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415 conservationMenuItem_actionPerformed();
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416 else if(evt.getSource()==abovePIDThreshold)
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417 abovePIDThreshold_actionPerformed();
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418 else if(evt.getSource()==applyToAllGroups)
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419 applyToAllGroups_actionPerformed();
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420 else if(evt.getSource()==autoCalculate)
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421 viewport.autocalculateConsensus = autoCalculate.getState();
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423 public void actionPerformed(ActionEvent evt)
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425 Object source = evt.getSource();
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427 if(source==inputText)
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428 inputText_actionPerformed();
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429 else if(source==loadTree)
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430 loadTree_actionPerformed();
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431 else if(source==loadApplication)
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432 launchFullApplication();
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433 else if(source==closeMenuItem)
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434 closeMenuItem_actionPerformed();
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435 else if(source==copy)
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436 copy_actionPerformed();
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437 else if(source==undoMenuItem)
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438 undoMenuItem_actionPerformed();
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439 else if(source==redoMenuItem)
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440 redoMenuItem_actionPerformed();
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441 else if(source==inputText)
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442 inputText_actionPerformed();
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443 else if(source==closeMenuItem)
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444 closeMenuItem_actionPerformed();
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445 else if(source==undoMenuItem)
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446 undoMenuItem_actionPerformed();
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447 else if(source==redoMenuItem)
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448 redoMenuItem_actionPerformed();
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449 else if(source==copy)
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450 copy_actionPerformed();
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451 else if(source==pasteNew)
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452 pasteNew_actionPerformed();
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453 else if(source==pasteThis)
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454 pasteThis_actionPerformed();
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455 else if(source==cut)
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456 cut_actionPerformed();
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457 else if(source==delete)
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458 delete_actionPerformed();
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459 else if(source==deleteGroups)
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460 deleteGroups_actionPerformed();
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461 else if(source==selectAllSequenceMenuItem)
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462 selectAllSequenceMenuItem_actionPerformed();
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463 else if(source==deselectAllSequenceMenuItem)
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464 deselectAllSequenceMenuItem_actionPerformed();
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465 else if(source==invertSequenceMenuItem)
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466 invertSequenceMenuItem_actionPerformed();
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467 else if(source==invertColSel)
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468 { viewport.invertColumnSelection(); alignPanel.repaint(); }
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469 else if(source==remove2LeftMenuItem)
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470 trimAlignment(true);
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471 else if(source==remove2RightMenuItem)
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472 trimAlignment(false);
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473 else if(source==removeGappedColumnMenuItem)
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474 removeGappedColumnMenuItem_actionPerformed();
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475 else if(source==removeAllGapsMenuItem)
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476 removeAllGapsMenuItem_actionPerformed();
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477 else if(source==findMenuItem)
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478 findMenuItem_actionPerformed();
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479 else if(source==font)
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480 font_actionPerformed();
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481 else if(source==showColumns)
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483 viewport.showAllHiddenColumns(); alignPanel.repaint();
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485 else if(source==showSeqs)
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487 viewport.showAllHiddenSeqs();
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489 else if(source == hideColumns)
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491 viewport.hideSelectedColumns(); alignPanel.repaint();
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493 else if(source == hideSequences && viewport.getSelectionGroup()!=null)
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495 viewport.hideAllSelectedSeqs();
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497 else if(source==featureSettings)
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498 featureSettings_actionPerformed();
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499 else if(source==overviewMenuItem)
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500 overviewMenuItem_actionPerformed();
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501 else if(source==noColourmenuItem)
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502 noColourmenuItem_actionPerformed();
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503 else if(source==clustalColour)
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504 clustalColour_actionPerformed();
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505 else if(source==zappoColour)
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506 zappoColour_actionPerformed();
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507 else if(source==taylorColour)
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508 taylorColour_actionPerformed();
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509 else if(source==hydrophobicityColour)
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510 hydrophobicityColour_actionPerformed();
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511 else if(source==helixColour)
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512 helixColour_actionPerformed();
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513 else if(source==strandColour)
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514 strandColour_actionPerformed();
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515 else if(source==turnColour)
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516 turnColour_actionPerformed();
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517 else if(source==buriedColour)
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518 buriedColour_actionPerformed();
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519 else if(source==nucleotideColour)
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520 nucleotideColour_actionPerformed();
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521 else if(source==modifyPID)
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522 modifyPID_actionPerformed();
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523 else if(source==modifyConservation)
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524 modifyConservation_actionPerformed();
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525 else if(source==userDefinedColour)
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526 userDefinedColour_actionPerformed();
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527 else if(source==PIDColour)
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528 PIDColour_actionPerformed();
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529 else if(source==BLOSUM62Colour)
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530 BLOSUM62Colour_actionPerformed();
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531 else if(source==annotationColour)
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532 new AnnotationColourChooser(viewport, alignPanel);
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533 else if(source==sortPairwiseMenuItem)
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534 sortPairwiseMenuItem_actionPerformed();
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535 else if(source==sortIDMenuItem)
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536 sortIDMenuItem_actionPerformed();
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537 else if(source==sortGroupMenuItem)
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538 sortGroupMenuItem_actionPerformed();
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539 else if(source==removeRedundancyMenuItem)
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540 removeRedundancyMenuItem_actionPerformed();
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541 else if(source==pairwiseAlignmentMenuItem)
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542 pairwiseAlignmentMenuItem_actionPerformed();
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543 else if(source==PCAMenuItem)
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544 PCAMenuItem_actionPerformed();
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545 else if(source==averageDistanceTreeMenuItem)
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546 averageDistanceTreeMenuItem_actionPerformed();
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547 else if(source==neighbourTreeMenuItem)
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548 neighbourTreeMenuItem_actionPerformed();
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549 else if(source==njTreeBlosumMenuItem)
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550 njTreeBlosumMenuItem_actionPerformed();
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551 else if(source==avDistanceTreeBlosumMenuItem)
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552 avTreeBlosumMenuItem_actionPerformed();
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553 else if(source==documentation)
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554 documentation_actionPerformed();
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555 else if(source==about)
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556 about_actionPerformed();
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560 public void inputText_actionPerformed()
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562 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
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563 Frame frame = new Frame();
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565 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
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568 protected void outputText_actionPerformed(ActionEvent e)
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570 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
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571 Frame frame = new Frame();
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573 jalview.bin.JalviewLite.addFrame(frame,
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574 "Alignment output - " + e.getActionCommand(),
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576 cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
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577 viewport.getAlignment().getSequences(),
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578 viewport.showJVSuffix));
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581 void launchFullApplication()
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583 StringBuffer url = new StringBuffer(jalviewServletURL);
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585 url.append("?open="+
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586 appendProtocol( viewport.applet.getParameter("file") ) );
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588 if(viewport.applet.getParameter("features")!=null)
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590 url.append( "&features=" );
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591 url.append( appendProtocol( viewport.applet.getParameter("features") ) );
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594 if(viewport.applet.getParameter("annotations")!=null)
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596 url.append( "&annotations=" );
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597 url.append( appendProtocol( viewport.applet.getParameter("annotations") ) );
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600 if(viewport.applet.getParameter("jnetfile")!=null)
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602 url.append( "&annotations=" );
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603 url.append( appendProtocol( viewport.applet.getParameter("jnetfile") ) );
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606 if(viewport.applet.getParameter("defaultColour")!=null)
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608 url.append("&colour=" +
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609 removeWhiteSpace(viewport.applet.getParameter("defaultColour"))
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613 if(viewport.applet.getParameter("userDefinedColour")!=null)
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615 url.append( "&colour=" +
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616 removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") )
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620 showURL(url.toString(), "FULL_APP");
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624 String removeWhiteSpace(String colour)
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626 StringBuffer sb = new StringBuffer();
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627 for (int i = 0; i < colour.length(); i++)
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629 if (Character.isWhitespace(colour.charAt(i)))
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632 sb.append(colour.charAt(i));
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635 return sb.toString();
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639 String appendProtocol(String url)
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643 }catch(java.net.MalformedURLException ex)
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645 url = viewport.applet.getCodeBase()+url;
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650 public void closeMenuItem_actionPerformed()
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652 PaintRefresher.components.remove(viewport.alignment);
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653 if(PaintRefresher.components.size()==0 && viewport.applet==null)
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663 void updateEditMenuBar()
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666 if (viewport.historyList.size() > 0)
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668 undoMenuItem.setEnabled(true);
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669 CommandI command = (CommandI) viewport.historyList.peek();
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670 undoMenuItem.setLabel("Undo " + command.getDescription());
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674 undoMenuItem.setEnabled(false);
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675 undoMenuItem.setLabel("Undo");
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678 if (viewport.redoList.size() > 0)
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680 redoMenuItem.setEnabled(true);
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682 CommandI command = (CommandI) viewport.redoList.peek();
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683 redoMenuItem.setLabel("Redo " + command.getDescription());
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687 redoMenuItem.setEnabled(false);
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688 redoMenuItem.setLabel("Redo");
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692 public void addHistoryItem(CommandI command)
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694 if(command.getSize()>0)
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696 viewport.historyList.push(command);
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697 viewport.redoList.removeAllElements();
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698 updateEditMenuBar();
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699 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
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703 protected void undoMenuItem_actionPerformed()
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705 CommandI command = (CommandI)viewport.historyList.pop();
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706 viewport.redoList.push(command);
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707 command.undoCommand();
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709 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
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710 updateEditMenuBar();
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711 viewport.firePropertyChange("alignment", null,
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712 viewport.getAlignment().getSequences());
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715 protected void redoMenuItem_actionPerformed()
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717 CommandI command = (CommandI) viewport.redoList.pop();
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718 viewport.historyList.push(command);
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719 command.doCommand();
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720 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
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722 updateEditMenuBar();
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723 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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727 public void moveSelectedSequences(boolean up)
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729 SequenceGroup sg = viewport.getSelectionGroup();
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737 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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739 SequenceI seq = viewport.alignment.getSequenceAt(i);
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740 if (!sg.getSequences(false).contains(seq))
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745 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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746 if (sg.getSequences(false).contains(temp))
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751 viewport.alignment.getSequences().setElementAt(temp, i);
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752 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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757 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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759 SequenceI seq = viewport.alignment.getSequenceAt(i);
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760 if (!sg.getSequences(true).contains(seq))
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765 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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766 if (sg.getSequences(true).contains(temp))
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771 viewport.alignment.getSequences().setElementAt(temp, i);
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772 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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776 alignPanel.repaint();
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779 static StringBuffer copiedSequences;
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780 static Vector copiedHiddenColumns;
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781 protected void copy_actionPerformed()
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783 if (viewport.getSelectionGroup() == null)
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788 SequenceGroup sg = viewport.getSelectionGroup();
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789 copiedSequences = new StringBuffer();
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790 Hashtable orderedSeqs = new Hashtable();
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791 for (int i = 0; i < sg.getSize(false); i++)
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793 SequenceI seq = sg.getSequenceAt(i);
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794 int index = viewport.alignment.findIndex(seq);
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795 orderedSeqs.put(index + "", seq);
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798 int index = 0, startRes, endRes;
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801 if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
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803 copiedHiddenColumns = new Vector();
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804 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
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805 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();
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808 int[] region = (int[])
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809 viewport.getColumnSelection().getHiddenColumns().elementAt(i);
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811 copiedHiddenColumns.addElement(new int[]
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812 {region[0] - hiddenOffset,
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813 region[1] - hiddenOffset});
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817 copiedHiddenColumns = null;
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820 for (int i = 0; i < sg.getSize(false); i++)
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822 SequenceI seq = null;
\r
824 while (seq == null)
\r
826 if (orderedSeqs.containsKey(index + ""))
\r
828 seq = (SequenceI) orderedSeqs.get(index + "");
\r
840 //Returns residue following index if gap
\r
841 startRes = seq.findPosition(sg.getStartRes());
\r
844 //Need to find the residue preceeding index if gap
\r
847 for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
\r
849 ch = seq.getCharAt(j);
\r
850 if (!jalview.util.Comparison.isGap( (ch)))
\r
858 endRes += seq.getStart() -1;
\r
861 copiedSequences.append(seq.getName() + "\t" +
\r
864 seq.getSequence(sg.getStartRes(),
\r
865 sg.getEndRes() + 1) + "\n");
\r
870 protected void pasteNew_actionPerformed()
\r
875 protected void pasteThis_actionPerformed()
\r
880 void paste(boolean newAlignment)
\r
884 if (copiedSequences == null)
\r
889 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
890 Vector seqs = new Vector();
\r
891 while (st.hasMoreElements())
\r
893 String name = st.nextToken();
\r
894 int start = Integer.parseInt(st.nextToken());
\r
895 int end = Integer.parseInt(st.nextToken());
\r
896 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
\r
898 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
899 for (int i = 0; i < seqs.size(); i++)
\r
901 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
906 String newtitle = new String("Copied sequences");
\r
907 if (getTitle().startsWith("Copied sequences"))
\r
909 newtitle = getTitle();
\r
913 newtitle = newtitle.concat("- from " + getTitle());
\r
915 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
919 if (copiedHiddenColumns != null)
\r
921 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
923 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
924 af.viewport.hideColumns(region[0], region[1]);
\r
929 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
\r
935 addHistoryItem(new EditCommand(
\r
940 viewport.alignment.getWidth(),
\r
941 viewport.alignment)
\r
944 viewport.setEndSeq(viewport.alignment.getHeight());
\r
945 viewport.alignment.getWidth();
\r
946 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
950 catch (Exception ex)
\r
951 {} // could be anything being pasted in here
\r
955 protected void cut_actionPerformed()
\r
957 copy_actionPerformed();
\r
958 delete_actionPerformed();
\r
961 protected void delete_actionPerformed()
\r
964 SequenceGroup sg = viewport.getSelectionGroup();
\r
970 Vector seqs = new Vector();
\r
972 for (int i = 0; i < sg.getSize(false); i++)
\r
974 seq = sg.getSequenceAt(i);
\r
975 seqs.addElement(seq);
\r
979 // If the cut affects all sequences, remove highlighted columns
\r
980 if (sg.getSize(false) == viewport.alignment.getHeight())
\r
982 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
983 sg.getEndRes() + 1);
\r
987 SequenceI [] cut = new SequenceI[seqs.size()];
\r
988 for(int i=0; i<seqs.size(); i++)
\r
989 cut[i] = (SequenceI)seqs.elementAt(i);
\r
995 addHistoryItem(new EditCommand("Cut Sequences",
\r
999 sg.getEndRes()-sg.getStartRes()+1,
\r
1000 viewport.alignment));
\r
1003 viewport.setSelectionGroup(null);
\r
1004 viewport.alignment.deleteGroup(sg);
\r
1006 viewport.firePropertyChange("alignment", null,
\r
1007 viewport.getAlignment().getSequences());
\r
1009 if (viewport.getAlignment().getHeight() < 1)
\r
1011 this.setVisible(false);
\r
1015 protected void deleteGroups_actionPerformed()
\r
1017 viewport.alignment.deleteAllGroups();
\r
1018 viewport.sequenceColours=null;
\r
1019 viewport.setSelectionGroup(null);
\r
1021 alignPanel.repaint();
\r
1024 public void selectAllSequenceMenuItem_actionPerformed()
\r
1026 SequenceGroup sg = new SequenceGroup();
\r
1027 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1029 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
1031 sg.setEndRes(viewport.alignment.getWidth()-1);
\r
1032 viewport.setSelectionGroup(sg);
\r
1033 alignPanel.repaint();
\r
1034 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1037 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1039 if(viewport.cursorMode)
\r
1041 alignPanel.seqPanel.keyboardNo1=null;
\r
1042 alignPanel.seqPanel.keyboardNo2=null;
\r
1044 viewport.setSelectionGroup(null);
\r
1045 viewport.getColumnSelection().clear();
\r
1046 viewport.setSelectionGroup(null);
\r
1047 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1048 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1049 alignPanel.repaint();
\r
1050 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1053 public void invertSequenceMenuItem_actionPerformed()
\r
1055 SequenceGroup sg = viewport.getSelectionGroup();
\r
1056 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1058 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1061 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1064 void trimAlignment(boolean trimLeft)
\r
1066 ColumnSelection colSel = viewport.getColumnSelection();
\r
1069 if (colSel.size() > 0)
\r
1072 column = colSel.getMin();
\r
1074 column = colSel.getMax();
\r
1076 SequenceI [] seqs;
\r
1077 if(viewport.getSelectionGroup()!=null)
\r
1078 seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
\r
1080 seqs = viewport.alignment.getSequencesArray();
\r
1083 TrimRegionCommand trimRegion;
\r
1086 trimRegion = new TrimRegionCommand("Remove Left",
\r
1087 TrimRegionCommand.TRIM_LEFT,
\r
1090 viewport.alignment,
\r
1092 viewport.selectionGroup);
\r
1093 viewport.setStartRes(0);
\r
1097 trimRegion = new TrimRegionCommand("Remove Right",
\r
1098 TrimRegionCommand.TRIM_RIGHT,
\r
1101 viewport.alignment,
\r
1103 viewport.selectionGroup);
\r
1106 statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
\r
1109 addHistoryItem(trimRegion);
\r
1111 Vector groups = viewport.alignment.getGroups();
\r
1113 for (int i = 0; i < groups.size(); i++)
\r
1115 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1117 if ( (trimLeft && !sg.adjustForRemoveLeft(column))
\r
1118 || (!trimLeft && !sg.adjustForRemoveRight(column)))
\r
1120 viewport.alignment.deleteGroup(sg);
\r
1124 viewport.firePropertyChange("alignment", null,
\r
1125 viewport.getAlignment().getSequences());
\r
1130 public void removeGappedColumnMenuItem_actionPerformed()
\r
1132 int start = 0, end = viewport.alignment.getWidth()-1;
\r
1135 if (viewport.getSelectionGroup() != null)
\r
1137 seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
\r
1138 start = viewport.getSelectionGroup().getStartRes();
\r
1139 end = viewport.getSelectionGroup().getEndRes();
\r
1142 seqs = viewport.alignment.getSequencesArray();
\r
1145 RemoveGapColCommand removeGapCols =
\r
1146 new RemoveGapColCommand("Remove Gapped Columns",
\r
1149 viewport.getGapCharacter());
\r
1151 addHistoryItem(removeGapCols);
\r
1153 statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");
\r
1155 //This is to maintain viewport position on first residue
\r
1156 //of first sequence
\r
1157 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1158 int startRes = seq.findPosition(viewport.startRes);
\r
1159 // ShiftList shifts;
\r
1160 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
\r
1161 // edit.alColumnChanges=shifts.getInverse();
\r
1162 // if (viewport.hasHiddenColumns)
\r
1163 // viewport.getColumnSelection().compensateForEdits(shifts);
\r
1164 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1165 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1169 public void removeAllGapsMenuItem_actionPerformed()
\r
1171 int start = 0, end = viewport.alignment.getWidth()-1;
\r
1174 if (viewport.getSelectionGroup() != null)
\r
1176 seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
\r
1177 start = viewport.getSelectionGroup().getStartRes();
\r
1178 end = viewport.getSelectionGroup().getEndRes();
\r
1181 seqs = viewport.alignment.getSequencesArray();
\r
1183 //This is to maintain viewport position on first residue
\r
1184 //of first sequence
\r
1185 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1186 int startRes = seq.findPosition(viewport.startRes);
\r
1188 addHistoryItem(new RemoveGapsCommand("Remove Gaps",
\r
1191 viewport.getGapCharacter()));
\r
1193 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1195 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1199 public void findMenuItem_actionPerformed()
\r
1201 new Finder(alignPanel);
\r
1204 public void font_actionPerformed()
\r
1206 new FontChooser(alignPanel);
\r
1210 public void seqLimits_itemStateChanged()
\r
1212 viewport.setShowJVSuffix(seqLimits.getState());
\r
1213 alignPanel.fontChanged();
\r
1214 alignPanel.repaint();
\r
1218 protected void colourTextMenuItem_actionPerformed()
\r
1220 viewport.setColourText(colourTextMenuItem.getState());
\r
1221 alignPanel.repaint();
\r
1224 protected void wrapMenuItem_actionPerformed()
\r
1226 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
1227 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
1228 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
1229 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
1230 scaleRight.setEnabled(wrapMenuItem.getState());
\r
1231 alignPanel.repaint();
\r
1235 protected void scaleAbove_actionPerformed()
\r
1237 viewport.setScaleAboveWrapped(scaleAbove.getState());
\r
1238 alignPanel.repaint();
\r
1241 protected void scaleLeft_actionPerformed()
\r
1243 viewport.setScaleLeftWrapped(scaleLeft.getState());
\r
1244 alignPanel.repaint();
\r
1247 protected void scaleRight_actionPerformed()
\r
1249 viewport.setScaleRightWrapped(scaleRight.getState());
\r
1250 alignPanel.repaint();
\r
1253 public void viewBoxesMenuItem_actionPerformed()
\r
1255 viewport.setShowBoxes(viewBoxesMenuItem.getState());
\r
1256 alignPanel.repaint();
\r
1259 public void viewTextMenuItem_actionPerformed()
\r
1261 viewport.setShowText(viewTextMenuItem.getState());
\r
1262 alignPanel.repaint();
\r
1265 protected void renderGapsMenuItem_actionPerformed()
\r
1267 viewport.setRenderGaps(renderGapsMenuItem.getState());
\r
1268 alignPanel.repaint();
\r
1271 public void annotationPanelMenuItem_actionPerformed()
\r
1273 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
\r
1274 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
\r
1277 public void featureSettings_actionPerformed()
\r
1279 new FeatureSettings(viewport, alignPanel);
\r
1282 public void overviewMenuItem_actionPerformed()
\r
1284 if (alignPanel.overviewPanel != null)
\r
1289 Frame frame = new Frame();
\r
1290 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1291 frame.add(overview);
\r
1292 // +50 must allow for applet frame window
\r
1293 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
1294 overview.preferredSize().width,
\r
1295 overview.preferredSize().height + 50);
\r
1298 frame.addWindowListener(new WindowAdapter()
\r
1300 public void windowClosing(WindowEvent e)
\r
1302 alignPanel.setOverviewPanel(null);
\r
1306 alignPanel.setOverviewPanel(overview);
\r
1310 protected void noColourmenuItem_actionPerformed()
\r
1312 changeColour(null);
\r
1315 public void clustalColour_actionPerformed()
\r
1317 abovePIDThreshold.setState(false);
\r
1318 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
\r
1319 viewport.alignment.getWidth()));
\r
1322 public void zappoColour_actionPerformed()
\r
1324 changeColour(new ZappoColourScheme());
\r
1327 public void taylorColour_actionPerformed()
\r
1329 changeColour(new TaylorColourScheme());
\r
1332 public void hydrophobicityColour_actionPerformed()
\r
1334 changeColour(new HydrophobicColourScheme());
\r
1337 public void helixColour_actionPerformed()
\r
1339 changeColour(new HelixColourScheme());
\r
1342 public void strandColour_actionPerformed()
\r
1344 changeColour(new StrandColourScheme());
\r
1347 public void turnColour_actionPerformed()
\r
1349 changeColour(new TurnColourScheme());
\r
1352 public void buriedColour_actionPerformed()
\r
1354 changeColour(new BuriedColourScheme());
\r
1357 public void nucleotideColour_actionPerformed()
\r
1359 changeColour(new NucleotideColourScheme());
\r
1362 protected void applyToAllGroups_actionPerformed()
\r
1364 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
\r
1367 void changeColour(ColourSchemeI cs)
\r
1369 int threshold = 0;
\r
1373 if (viewport.getAbovePIDThreshold())
\r
1375 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
\r
1377 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1379 viewport.setGlobalColourScheme(cs);
\r
1383 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1386 if (viewport.getConservationSelected())
\r
1389 Alignment al = (Alignment) viewport.alignment;
\r
1390 Conservation c = new Conservation("All",
\r
1391 ResidueProperties.propHash, 3,
\r
1392 al.getSequences(), 0,
\r
1393 al.getWidth() - 1);
\r
1396 c.verdict(false, viewport.ConsPercGaps);
\r
1398 cs.setConservation(c);
\r
1400 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1406 cs.setConservation(null);
\r
1409 cs.setConsensus(viewport.hconsensus);
\r
1412 viewport.setGlobalColourScheme(cs);
\r
1414 if (viewport.getColourAppliesToAllGroups())
\r
1416 Vector groups = viewport.alignment.getGroups();
\r
1417 for (int i = 0; i < groups.size(); i++)
\r
1419 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1426 if (cs instanceof ClustalxColourScheme)
\r
1428 sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth());
\r
1434 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1436 catch (Exception ex)
\r
1438 ex.printStackTrace();
\r
1443 if (viewport.getAbovePIDThreshold()
\r
1444 || cs instanceof PIDColourScheme
\r
1445 || cs instanceof Blosum62ColourScheme)
\r
1447 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1448 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth()));
\r
1451 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1453 if (viewport.getConservationSelected())
\r
1455 Conservation c = new Conservation("Group",
\r
1456 ResidueProperties.propHash, 3,
\r
1457 sg.getSequences(true), 0,
\r
1458 viewport.alignment.getWidth() - 1);
\r
1460 c.verdict(false, viewport.ConsPercGaps);
\r
1461 sg.cs.setConservation(c);
\r
1465 sg.cs.setConservation(null);
\r
1466 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1473 if (alignPanel.getOverviewPanel() != null)
\r
1475 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1478 alignPanel.repaint();
\r
1483 protected void modifyPID_actionPerformed()
\r
1485 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1487 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
1489 SliderPanel.showPIDSlider();
\r
1493 protected void modifyConservation_actionPerformed()
\r
1495 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1497 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
1499 SliderPanel.showConservationSlider();
\r
1503 protected void conservationMenuItem_actionPerformed()
\r
1505 viewport.setConservationSelected(conservationMenuItem.getState());
\r
1507 viewport.setAbovePIDThreshold(false);
\r
1508 abovePIDThreshold.setState(false);
\r
1510 changeColour(viewport.getGlobalColourScheme());
\r
1512 modifyConservation_actionPerformed();
\r
1515 public void abovePIDThreshold_actionPerformed()
\r
1517 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
1519 conservationMenuItem.setState(false);
\r
1520 viewport.setConservationSelected(false);
\r
1522 changeColour(viewport.getGlobalColourScheme());
\r
1524 modifyPID_actionPerformed();
\r
1527 public void userDefinedColour_actionPerformed()
\r
1529 new UserDefinedColours(alignPanel, null);
\r
1532 public void PIDColour_actionPerformed()
\r
1534 changeColour(new PIDColourScheme());
\r
1537 public void BLOSUM62Colour_actionPerformed()
\r
1539 changeColour(new Blosum62ColourScheme());
\r
1542 public void sortPairwiseMenuItem_actionPerformed()
\r
1544 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
\r
1545 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1546 viewport.getAlignment().getSequenceAt(0));
\r
1547 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment));
\r
1548 alignPanel.repaint();
\r
1551 public void sortIDMenuItem_actionPerformed()
\r
1553 // addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1554 // HistoryItem.SORT));
\r
1555 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1556 alignPanel.repaint();
\r
1559 public void sortGroupMenuItem_actionPerformed()
\r
1561 // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1562 // HistoryItem.SORT));
\r
1563 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1564 alignPanel.repaint();
\r
1568 public void removeRedundancyMenuItem_actionPerformed()
\r
1570 new RedundancyPanel(alignPanel);
\r
1573 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
1575 if (viewport.getSelectionGroup()!=null
\r
1576 && viewport.getSelectionGroup().getSize(false) > 1)
\r
1578 Frame frame = new Frame();
\r
1579 frame.add(new PairwiseAlignPanel(alignPanel));
\r
1580 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
1584 public void PCAMenuItem_actionPerformed()
\r
1586 //are the sequences aligned?
\r
1587 if (!viewport.alignment.isAligned())
\r
1589 SequenceI current;
\r
1590 int Width = viewport.getAlignment().getWidth();
\r
1592 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1595 current = viewport.getAlignment().getSequenceAt(i);
\r
1597 if (current.getLength() < Width)
\r
1599 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1602 alignPanel.repaint();
\r
1605 if ( (viewport.getSelectionGroup() != null &&
\r
1606 viewport.getSelectionGroup().getSize(false) < 4 &&
\r
1607 viewport.getSelectionGroup().getSize(false) > 0)
\r
1608 || viewport.getAlignment().getHeight() < 4)
\r
1615 new PCAPanel(viewport);
\r
1617 catch (java.lang.OutOfMemoryError ex)
\r
1623 public void averageDistanceTreeMenuItem_actionPerformed()
\r
1625 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1628 public void neighbourTreeMenuItem_actionPerformed()
\r
1630 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1633 protected void njTreeBlosumMenuItem_actionPerformed()
\r
1635 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1638 protected void avTreeBlosumMenuItem_actionPerformed()
\r
1640 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1643 void NewTreePanel(String type, String pwType, String title)
\r
1645 //are the sequences aligned?
\r
1646 if (!viewport.alignment.isAligned())
\r
1648 SequenceI current;
\r
1649 int Width = viewport.getAlignment().getWidth();
\r
1651 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1654 current = viewport.getAlignment().getSequenceAt(i);
\r
1656 if (current.getLength() < Width)
\r
1658 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1661 alignPanel.repaint();
\r
1665 if ( (viewport.getSelectionGroup() != null &&
\r
1666 viewport.getSelectionGroup().getSize(false) > 1)
\r
1667 || (viewport.getSelectionGroup() == null
\r
1668 && viewport.alignment.getHeight() > 1))
\r
1670 final TreePanel tp = new TreePanel(viewport,
\r
1674 addTreeMenuItem(tp, title);
\r
1676 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
1680 void loadTree_actionPerformed()
\r
1682 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1683 cap.setText("Paste your Newick tree file here.");
\r
1684 cap.treeImport = true;
\r
1685 Frame frame = new Frame();
\r
1687 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
1690 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
1692 TreePanel tp = new TreePanel(viewport,
\r
1696 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
1697 addTreeMenuItem(tp, treeFile);
\r
1700 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1702 final MenuItem item = new MenuItem(title);
\r
1703 sortByTreeMenu.add(item);
\r
1704 item.addActionListener(new java.awt.event.ActionListener()
\r
1706 public void actionPerformed(ActionEvent evt)
\r
1708 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1709 // HistoryItem.SORT));
\r
1710 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1711 alignPanel.repaint();
\r
1715 treePanel.addWindowListener(new WindowAdapter()
\r
1717 public void windowClosing(WindowEvent e)
\r
1719 sortByTreeMenu.remove(item);
\r
1724 protected void documentation_actionPerformed()
\r
1726 showURL("http://www.jalview.org/help.html", "HELP");
\r
1729 protected void about_actionPerformed()
\r
1732 class AboutPanel extends Canvas
\r
1735 public AboutPanel(String version)
\r
1736 { this.version = version; }
\r
1738 public void paint(Graphics g)
\r
1740 g.setColor(Color.white);
\r
1741 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1742 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1743 FontMetrics fm = g.getFontMetrics();
\r
1744 int fh = fm.getHeight();
\r
1746 g.setColor(Color.black);
\r
1747 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
1748 g.drawString("Jalview - Release "+version, 200, y += fh);
\r
1749 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1750 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
1752 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
1755 "For any issues relating to Jalview, email help@jalview.org", x,
\r
1757 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
1758 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
1760 g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh);
\r
1764 String version = "test";
\r
1765 java.net.URL url = getClass().getResource("/.build_properties");
\r
1770 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
1771 url.openStream()));
\r
1773 while ( (line = reader.readLine()) != null)
\r
1775 if (line.indexOf("VERSION") > -1)
\r
1777 version = line.substring(line.indexOf("=") + 1);
\r
1781 catch (Exception ex)
\r
1783 ex.printStackTrace();
\r
1788 Frame frame = new Frame();
\r
1789 frame.add(new AboutPanel(version));
\r
1790 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
\r
1794 public void showURL(String url, String target)
\r
1796 if (viewport.applet == null)
\r
1798 System.out.println("Not running as applet - no browser available.");
\r
1804 System.out.println("Show url: "+url);
\r
1805 viewport.applet.getAppletContext().showDocument(new java.net.URL(url),
\r
1808 catch (Exception ex)
\r
1810 ex.printStackTrace();
\r
1816 //////////////////////////////////////////////////////////////////////////////////
\r
1817 //JBuilder Graphics here
\r
1819 protected MenuBar alignFrameMenuBar = new MenuBar();
\r
1820 protected Menu fileMenu = new Menu("File");
\r
1821 protected MenuItem loadApplication = new MenuItem("View in Full Application");
\r
1822 protected MenuItem loadTree = new MenuItem("Load Associated Tree");
\r
1823 protected MenuItem closeMenuItem = new MenuItem("Close");
\r
1824 protected Menu editMenu = new Menu("Edit");
\r
1825 protected Menu viewMenu = new Menu("View");
\r
1826 protected Menu colourMenu = new Menu("Colour");
\r
1827 protected Menu calculateMenu = new Menu("Calculate");
\r
1828 protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
1829 protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
1830 protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
1831 protected MenuItem remove2LeftMenuItem = new MenuItem();
\r
1832 protected MenuItem remove2RightMenuItem = new MenuItem();
\r
1833 protected MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
1834 protected MenuItem removeAllGapsMenuItem = new MenuItem();
\r
1835 protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
1836 protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
1837 protected MenuItem sortPairwiseMenuItem = new MenuItem();
\r
1838 protected MenuItem sortIDMenuItem = new MenuItem();
\r
1839 protected MenuItem sortGroupMenuItem = new MenuItem();
\r
1840 protected MenuItem removeRedundancyMenuItem = new MenuItem();
\r
1841 protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
1842 protected MenuItem PCAMenuItem = new MenuItem();
\r
1843 protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
1844 protected MenuItem neighbourTreeMenuItem = new MenuItem();
\r
1845 BorderLayout borderLayout1 = new BorderLayout();
\r
1846 public Label statusBar = new Label();
\r
1847 protected Menu outputTextboxMenu = new Menu();
\r
1848 protected MenuItem clustalColour = new MenuItem();
\r
1849 protected MenuItem zappoColour = new MenuItem();
\r
1850 protected MenuItem taylorColour = new MenuItem();
\r
1851 protected MenuItem hydrophobicityColour = new MenuItem();
\r
1852 protected MenuItem helixColour = new MenuItem();
\r
1853 protected MenuItem strandColour = new MenuItem();
\r
1854 protected MenuItem turnColour = new MenuItem();
\r
1855 protected MenuItem buriedColour = new MenuItem();
\r
1856 protected MenuItem userDefinedColour = new MenuItem();
\r
1857 protected MenuItem PIDColour = new MenuItem();
\r
1858 protected MenuItem BLOSUM62Colour = new MenuItem();
\r
1859 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
1860 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
1861 protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
1862 protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
1863 MenuItem overviewMenuItem = new MenuItem();
\r
1864 protected MenuItem undoMenuItem = new MenuItem();
\r
1865 protected MenuItem redoMenuItem = new MenuItem();
\r
1866 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
1867 MenuItem noColourmenuItem = new MenuItem();
\r
1868 protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
1869 protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
1870 MenuItem findMenuItem = new MenuItem();
\r
1871 protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
1872 protected MenuItem nucleotideColour = new MenuItem();
\r
1873 MenuItem deleteGroups = new MenuItem();
\r
1874 MenuItem delete = new MenuItem();
\r
1875 MenuItem copy = new MenuItem();
\r
1876 MenuItem cut = new MenuItem();
\r
1877 Menu pasteMenu = new Menu();
\r
1878 MenuItem pasteNew = new MenuItem();
\r
1879 MenuItem pasteThis = new MenuItem();
\r
1880 protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
1881 protected MenuItem font = new MenuItem();
\r
1882 protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
1883 protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
1884 protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
1885 MenuItem modifyPID = new MenuItem();
\r
1886 MenuItem modifyConservation = new MenuItem();
\r
1887 protected CheckboxMenuItem autoCalculate
\r
1888 = new CheckboxMenuItem("Autocalculate Consensus", true);
\r
1889 protected Menu sortByTreeMenu = new Menu();
\r
1890 Menu sort = new Menu();
\r
1891 Menu calculate = new Menu();
\r
1892 MenuItem inputText = new MenuItem();
\r
1893 Menu helpMenu = new Menu();
\r
1894 MenuItem documentation = new MenuItem();
\r
1895 MenuItem about = new MenuItem();
\r
1896 protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
1897 Panel embeddedMenu;
\r
1898 Label embeddedEdit;
\r
1899 Label embeddedSelect;
\r
1900 Label embeddedView;
\r
1901 Label embeddedFormat;
\r
1902 Label embeddedColour;
\r
1903 Label embeddedFile;
\r
1904 Label embeddedHelp;
\r
1905 Label embeddedCalculate;
\r
1906 FlowLayout flowLayout1;
\r
1908 private void jbInit() throws Exception {
\r
1910 setMenuBar(alignFrameMenuBar);
\r
1914 // dynamically fill save as menu with available formats
\r
1915 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
1918 item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
1920 item.addActionListener(new java.awt.event.ActionListener()
\r
1922 public void actionPerformed(ActionEvent e)
\r
1924 outputText_actionPerformed(e);
\r
1928 outputTextboxMenu.add(item);
\r
1930 closeMenuItem.addActionListener(this);
\r
1931 loadApplication.addActionListener(this);
\r
1933 loadTree.addActionListener(this);
\r
1934 selectAllSequenceMenuItem.addActionListener(this);
\r
1935 deselectAllSequenceMenuItem.addActionListener(this);
\r
1936 invertSequenceMenuItem.addActionListener(this);
\r
1937 remove2LeftMenuItem.setLabel("Remove Left");
\r
1938 remove2LeftMenuItem.addActionListener(this);
\r
1939 remove2RightMenuItem.setLabel("Remove Right");
\r
1940 remove2RightMenuItem.addActionListener(this);
\r
1941 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
1942 removeGappedColumnMenuItem.addActionListener(this);
\r
1943 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
1944 removeAllGapsMenuItem.addActionListener(this);
\r
1945 viewBoxesMenuItem.setLabel("Boxes");
\r
1946 viewBoxesMenuItem.setState(true);
\r
1947 viewBoxesMenuItem.addItemListener(this);
\r
1948 viewTextMenuItem.setLabel("Text");
\r
1949 viewTextMenuItem.setState(true);
\r
1950 viewTextMenuItem.addItemListener(this);
\r
1951 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
1952 sortPairwiseMenuItem.addActionListener(this);
\r
1953 sortIDMenuItem.setLabel("by ID");
\r
1954 sortIDMenuItem.addActionListener(this);
\r
1955 sortGroupMenuItem.setLabel("by Group");
\r
1956 sortGroupMenuItem.addActionListener(this);
\r
1957 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
1958 removeRedundancyMenuItem.addActionListener(this);
\r
1959 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
1960 pairwiseAlignmentMenuItem.addActionListener(this);
\r
1961 PCAMenuItem.setLabel("Principal Component Analysis");
\r
1962 PCAMenuItem.addActionListener(this);
\r
1963 averageDistanceTreeMenuItem.setLabel(
\r
1964 "Average Distance Using % Identity");
\r
1965 averageDistanceTreeMenuItem.addActionListener(this);
\r
1966 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
1967 neighbourTreeMenuItem.addActionListener(this);
\r
1968 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
1969 statusBar.setBackground(Color.white);
\r
1970 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
1971 statusBar.setText("Status bar");
\r
1972 outputTextboxMenu.setLabel("Output to Textbox");
\r
1973 clustalColour.setLabel("Clustalx");
\r
1975 clustalColour.addActionListener(this);
\r
1976 zappoColour.setLabel("Zappo");
\r
1977 zappoColour.addActionListener(this);
\r
1978 taylorColour.setLabel("Taylor");
\r
1979 taylorColour.addActionListener(this);
\r
1980 hydrophobicityColour.setLabel("Hydrophobicity");
\r
1981 hydrophobicityColour.addActionListener(this);
\r
1982 helixColour.setLabel("Helix Propensity");
\r
1983 helixColour.addActionListener(this);
\r
1984 strandColour.setLabel("Strand Propensity");
\r
1985 strandColour.addActionListener(this);
\r
1986 turnColour.setLabel("Turn Propensity");
\r
1987 turnColour.addActionListener(this);
\r
1988 buriedColour.setLabel("Buried Index");
\r
1989 buriedColour.addActionListener(this);
\r
1990 userDefinedColour.setLabel("User Defined...");
\r
1991 userDefinedColour.addActionListener(this);
\r
1992 PIDColour.setLabel("Percentage Identity");
\r
1993 PIDColour.addActionListener(this);
\r
1994 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
1995 BLOSUM62Colour.addActionListener(this);
\r
1996 avDistanceTreeBlosumMenuItem.setLabel(
\r
1997 "Average Distance Using BLOSUM62");
\r
1998 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
1999 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
2000 njTreeBlosumMenuItem.addActionListener(this);
\r
2001 annotationPanelMenuItem.setLabel("Show Annotations");
\r
2002 annotationPanelMenuItem.addItemListener(this);
\r
2003 colourTextMenuItem.setLabel("Colour Text");
\r
2004 colourTextMenuItem.addItemListener(this);
\r
2005 overviewMenuItem.setLabel("Overview Window");
\r
2006 overviewMenuItem.addActionListener(this);
\r
2007 undoMenuItem.setEnabled(false);
\r
2008 undoMenuItem.setLabel("Undo");
\r
2009 undoMenuItem.addActionListener(this);
\r
2010 redoMenuItem.setEnabled(false);
\r
2011 redoMenuItem.setLabel("Redo");
\r
2012 redoMenuItem.addActionListener(this);
\r
2013 conservationMenuItem.setLabel("by Conservation");
\r
2014 conservationMenuItem.addItemListener(this);
\r
2015 noColourmenuItem.setLabel("None");
\r
2016 noColourmenuItem.addActionListener(this);
\r
2017 wrapMenuItem.setLabel("Wrap");
\r
2018 wrapMenuItem.addItemListener(this);
\r
2019 renderGapsMenuItem.setLabel("Show Gaps");
\r
2020 renderGapsMenuItem.setState(true);
\r
2021 renderGapsMenuItem.addItemListener(this);
\r
2022 findMenuItem.setLabel("Find...");
\r
2023 findMenuItem.addActionListener(this);
\r
2024 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
2025 abovePIDThreshold.addItemListener(this);
\r
2026 nucleotideColour.setLabel("Nucleotide");
\r
2027 nucleotideColour.addActionListener(this);
\r
2028 deleteGroups.setLabel("Undefine Groups");
\r
2029 deleteGroups.addActionListener(this);
\r
2030 copy.setLabel("Copy");
\r
2031 copy.addActionListener(this);
\r
2032 cut.setLabel("Cut");
\r
2033 cut.addActionListener(this);
\r
2034 delete.setLabel("Delete");
\r
2035 delete.addActionListener(this);
\r
2036 pasteMenu.setLabel("Paste");
\r
2037 pasteNew.setLabel("To New Alignment");
\r
2038 pasteNew.addActionListener(this);
\r
2039 pasteThis.setLabel("Add To This Alignment");
\r
2040 pasteThis.addActionListener(this);
\r
2041 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
2042 applyToAllGroups.setState(true);
\r
2043 applyToAllGroups.addItemListener(this);
\r
2044 font.setLabel("Font...");
\r
2045 font.addActionListener(this);
\r
2046 scaleAbove.setLabel("Scale Above");
\r
2047 scaleAbove.setState(true);
\r
2048 scaleAbove.setEnabled(false);
\r
2049 scaleAbove.addItemListener(this);
\r
2050 scaleLeft.setEnabled(false);
\r
2051 scaleLeft.setState(true);
\r
2052 scaleLeft.setLabel("Scale Left");
\r
2053 scaleLeft.addItemListener(this);
\r
2054 scaleRight.setEnabled(false);
\r
2055 scaleRight.setState(true);
\r
2056 scaleRight.setLabel("Scale Right");
\r
2057 scaleRight.addItemListener(this);
\r
2058 modifyPID.setLabel("Modify Identity Threshold...");
\r
2059 modifyPID.addActionListener(this);
\r
2060 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
2061 modifyConservation.addActionListener(this);
\r
2062 sortByTreeMenu.setLabel("By Tree Order");
\r
2063 sort.setLabel("Sort");
\r
2064 calculate.setLabel("Calculate Tree");
\r
2065 autoCalculate.addItemListener(this);
\r
2066 inputText.setLabel("Input from textbox");
\r
2067 inputText.addActionListener(this);
\r
2069 helpMenu.setLabel("Help");
\r
2070 documentation.setLabel("Documentation");
\r
2071 documentation.addActionListener(this);
\r
2073 about.setLabel("About...");
\r
2074 about.addActionListener(this);
\r
2075 seqLimits.setState(true);
\r
2076 seqLimits.setLabel("Show Sequence Limits");
\r
2077 seqLimits.addItemListener(this);
\r
2078 featureSettings.setLabel("Feature Settings...");
\r
2079 featureSettings.addActionListener(this);
\r
2080 sequenceFeatures.setLabel("Sequence Features");
\r
2081 sequenceFeatures.addItemListener(this);
\r
2082 sequenceFeatures.setState(false);
\r
2083 annotationColour.setLabel("by Annotation...");
\r
2084 annotationColour.addActionListener(this);
\r
2085 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
2086 invertColSel.setLabel("Invert Column Selection");
\r
2087 menu1.setLabel("Show");
\r
2088 showColumns.setLabel("All Columns ");
\r
2089 showSeqs.setLabel("All Sequences");
\r
2090 menu2.setLabel("Hide");
\r
2091 hideColumns.setLabel("Selected Columns");
\r
2092 hideSequences.setLabel("Selected Sequences");
\r
2093 invertColSel.addActionListener(this);
\r
2094 showColumns.addActionListener(this);
\r
2095 showSeqs.addActionListener(this);
\r
2096 hideColumns.addActionListener(this);
\r
2097 hideSequences.addActionListener(this);
\r
2098 formatMenu.setLabel("Format");
\r
2099 selectMenu.setLabel("Select");
\r
2100 alignFrameMenuBar.add(fileMenu);
\r
2101 alignFrameMenuBar.add(editMenu);
\r
2102 alignFrameMenuBar.add(selectMenu);
\r
2103 alignFrameMenuBar.add(viewMenu);
\r
2104 alignFrameMenuBar.add(formatMenu);
\r
2105 alignFrameMenuBar.add(colourMenu);
\r
2106 alignFrameMenuBar.add(calculateMenu);
\r
2107 alignFrameMenuBar.add(helpMenu);
\r
2108 fileMenu.add(inputText);
\r
2109 fileMenu.add(outputTextboxMenu);
\r
2110 if(jalviewServletURL!=null)
\r
2111 fileMenu.add(loadApplication);
\r
2112 fileMenu.addSeparator();
\r
2113 fileMenu.add(loadTree);
\r
2114 fileMenu.add(closeMenuItem);
\r
2115 editMenu.add(undoMenuItem);
\r
2116 editMenu.add(redoMenuItem);
\r
2117 editMenu.add(cut);
\r
2118 editMenu.add(copy);
\r
2119 editMenu.add(pasteMenu);
\r
2120 editMenu.add(delete);
\r
2121 editMenu.addSeparator();
\r
2122 editMenu.add(remove2LeftMenuItem);
\r
2123 editMenu.add(remove2RightMenuItem);
\r
2124 editMenu.add(removeGappedColumnMenuItem);
\r
2125 editMenu.add(removeAllGapsMenuItem);
\r
2126 editMenu.add(removeRedundancyMenuItem);
\r
2127 viewMenu.add(menu1);
\r
2128 viewMenu.add(menu2);
\r
2129 viewMenu.addSeparator();
\r
2130 viewMenu.add(annotationPanelMenuItem);
\r
2131 viewMenu.addSeparator();
\r
2132 viewMenu.add(sequenceFeatures);
\r
2133 viewMenu.add(featureSettings);
\r
2134 viewMenu.addSeparator();
\r
2135 viewMenu.add(overviewMenuItem);
\r
2136 colourMenu.add(applyToAllGroups);
\r
2137 colourMenu.addSeparator();
\r
2138 colourMenu.add(noColourmenuItem);
\r
2139 colourMenu.add(clustalColour);
\r
2140 colourMenu.add(BLOSUM62Colour);
\r
2141 colourMenu.add(PIDColour);
\r
2142 colourMenu.add(zappoColour);
\r
2143 colourMenu.add(taylorColour);
\r
2144 colourMenu.add(hydrophobicityColour);
\r
2145 colourMenu.add(helixColour);
\r
2146 colourMenu.add(strandColour);
\r
2147 colourMenu.add(turnColour);
\r
2148 colourMenu.add(buriedColour);
\r
2149 colourMenu.add(nucleotideColour);
\r
2150 colourMenu.add(userDefinedColour);
\r
2151 colourMenu.addSeparator();
\r
2152 colourMenu.add(conservationMenuItem);
\r
2153 colourMenu.add(modifyConservation);
\r
2154 colourMenu.add(abovePIDThreshold);
\r
2155 colourMenu.add(modifyPID);
\r
2156 colourMenu.add(annotationColour);
\r
2157 calculateMenu.add(sort);
\r
2158 calculateMenu.add(calculate);
\r
2159 calculateMenu.addSeparator();
\r
2160 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
2161 calculateMenu.add(PCAMenuItem);
\r
2162 calculateMenu.add(autoCalculate);
\r
2163 this.add(statusBar, BorderLayout.SOUTH);
\r
2164 pasteMenu.add(pasteNew);
\r
2165 pasteMenu.add(pasteThis);
\r
2166 sort.add(sortIDMenuItem);
\r
2167 sort.add(sortByTreeMenu);
\r
2168 sort.add(sortGroupMenuItem);
\r
2169 sort.add(sortPairwiseMenuItem);
\r
2170 calculate.add(averageDistanceTreeMenuItem);
\r
2171 calculate.add(neighbourTreeMenuItem);
\r
2172 calculate.add(avDistanceTreeBlosumMenuItem);
\r
2173 calculate.add(njTreeBlosumMenuItem);
\r
2174 helpMenu.add(documentation);
\r
2175 helpMenu.add(about);
\r
2176 menu1.add(showColumns);
\r
2177 menu1.add(showSeqs);
\r
2178 menu2.add(hideColumns);
\r
2179 menu2.add(hideSequences);
\r
2180 formatMenu.add(font);
\r
2181 formatMenu.add(seqLimits);
\r
2182 formatMenu.add(wrapMenuItem);
\r
2183 formatMenu.add(scaleAbove);
\r
2184 formatMenu.add(scaleLeft);
\r
2185 formatMenu.add(scaleRight);
\r
2186 formatMenu.add(viewBoxesMenuItem);
\r
2187 formatMenu.add(viewTextMenuItem);
\r
2188 formatMenu.add(colourTextMenuItem);
\r
2189 formatMenu.add(renderGapsMenuItem);
\r
2190 selectMenu.add(findMenuItem);
\r
2191 selectMenu.addSeparator();
\r
2192 selectMenu.add(selectAllSequenceMenuItem);
\r
2193 selectMenu.add(deselectAllSequenceMenuItem);
\r
2194 selectMenu.add(invertSequenceMenuItem);
\r
2195 selectMenu.add(invertColSel);
\r
2196 selectMenu.add(deleteGroups);
\r
2199 public void setEmbedded()
\r
2202 embeddedMenu = new Panel();
\r
2203 embeddedEdit = new Label("Edit");
\r
2204 embeddedSelect = new Label("Select");
\r
2205 embeddedView = new Label("View");
\r
2206 embeddedFormat = new Label("Label");
\r
2207 embeddedColour = new Label("Colour");
\r
2208 embeddedFile = new Label("File");
\r
2209 embeddedHelp = new Label("Help");
\r
2210 embeddedCalculate = new Label("Calculate");
\r
2211 flowLayout1 = new FlowLayout();
\r
2212 embeddedMenu.setBackground(Color.lightGray);
\r
2213 embeddedMenu.setLayout(flowLayout1);
\r
2214 embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2215 embeddedSelect.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2216 embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2217 embeddedFormat.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2218 embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2219 embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2220 embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2221 embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2222 embeddedMenu.add(embeddedFile);
\r
2223 embeddedMenu.add(embeddedEdit);
\r
2224 embeddedMenu.add(embeddedSelect);
\r
2225 embeddedMenu.add(embeddedView);
\r
2226 embeddedMenu.add(embeddedFormat);
\r
2227 embeddedMenu.add(embeddedColour);
\r
2228 embeddedMenu.add(embeddedCalculate);
\r
2229 embeddedMenu.add(embeddedHelp);
\r
2230 flowLayout1.setAlignment(FlowLayout.LEFT);
\r
2231 flowLayout1.setHgap(2);
\r
2232 flowLayout1.setVgap(0);
\r
2233 embeddedFile.addMouseListener(this);
\r
2234 embeddedEdit.addMouseListener(this);
\r
2235 embeddedSelect.addMouseListener(this);
\r
2236 embeddedView.addMouseListener(this);
\r
2237 embeddedFormat.addMouseListener(this);
\r
2238 embeddedColour.addMouseListener(this);
\r
2239 embeddedCalculate.addMouseListener(this);
\r
2240 embeddedHelp.addMouseListener(this);
\r
2242 // setVisible(false);
\r
2243 fileMenu.remove(closeMenuItem);
\r
2244 fileMenu.remove(3); // Seperator
\r
2246 viewport.applet.setLayout(new BorderLayout());
\r
2247 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
\r
2248 viewport.applet.add(statusBar, BorderLayout.SOUTH);
\r
2249 // viewport.applet.validate();
\r
2251 alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height
\r
2252 - embeddedMenu.HEIGHT - statusBar.HEIGHT);
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2254 viewport.applet.add(alignPanel, BorderLayout.CENTER);
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2255 viewport.applet.validate();
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2261 PopupMenu filePopup, editPopup, searchPopup,
\r
2262 viewPopup, colourPopup, calculatePopup, helpPopup;
\r
2263 MenuItem featureSettings = new MenuItem();
\r
2264 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
2265 MenuItem annotationColour = new MenuItem();
\r
2266 MenuItem invertColSel = new MenuItem();
\r
2267 Menu menu1 = new Menu();
\r
2268 MenuItem showColumns = new MenuItem();
\r
2269 MenuItem showSeqs = new MenuItem();
\r
2270 Menu menu2 = new Menu();
\r
2271 MenuItem hideColumns = new MenuItem();
\r
2272 MenuItem hideSequences = new MenuItem();
\r
2273 Menu formatMenu = new Menu();
\r
2274 Menu selectMenu = new Menu();
\r
2276 public void mousePressed(MouseEvent evt)
\r
2278 PopupMenu popup = null;
\r
2279 Label source = (Label)evt.getSource();
\r
2280 if(source==embeddedFile)
\r
2282 popup = filePopup = genPopupMenu(filePopup, fileMenu);
\r
2284 else if(source==embeddedEdit)
\r
2286 popup = editPopup = genPopupMenu(editPopup, editMenu);
\r
2288 else if(source==embeddedSelect)
\r
2290 popup = searchPopup = genPopupMenu(searchPopup, selectMenu);
\r
2292 else if(source==embeddedView)
\r
2294 popup = viewPopup = genPopupMenu(viewPopup, viewMenu);
\r
2296 else if (source ==embeddedFormat)
\r
2298 popup = viewPopup = genPopupMenu(viewPopup, formatMenu);
\r
2300 else if(source==embeddedColour)
\r
2302 popup = colourPopup = genPopupMenu(colourPopup, colourMenu);
\r
2304 else if(source==embeddedCalculate)
\r
2306 popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);
\r
2308 else if(source==embeddedHelp)
\r
2310 popup = helpPopup = genPopupMenu(helpPopup, helpMenu);
\r
2313 embeddedMenu.add(popup);
\r
2314 popup.show(embeddedMenu,
\r
2315 source.getBounds().x,
\r
2316 source.getBounds().y + source.getBounds().getSize().height);
\r
2319 PopupMenu genPopupMenu(PopupMenu popup, Menu original)
\r
2325 popup = new PopupMenu();
\r
2326 int m, mSize = original.getItemCount();
\r
2327 for(m=0; m<mSize; m++)
\r
2329 popup.add(original.getItem(m));
\r
2336 public void mouseClicked(MouseEvent evt)
\r
2338 public void mouseReleased(MouseEvent evt)
\r
2340 public void mouseEntered(MouseEvent evt)
\r
2342 public void mouseExited(MouseEvent evt)
\r