2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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20 package jalview.appletgui;
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22 import jalview.schemes.*;
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23 import jalview.datamodel.*;
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24 import jalview.analysis.*;
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25 import jalview.io.*;
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27 import java.awt.event.*;
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29 import java.io.InputStreamReader;
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30 import java.io.BufferedReader;
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31 import java.net.URL;
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34 public class AlignFrame extends Frame implements ActionListener,
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35 ItemListener, KeyListener, MouseListener
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37 public AlignmentPanel alignPanel;
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38 public AlignViewport viewport;
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39 int NEW_WINDOW_WIDTH = 700;
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40 int NEW_WINDOW_HEIGHT = 500;
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42 String jalviewServletURL;
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45 public AlignFrame(AlignmentI al,
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46 jalview.bin.JalviewLite applet,
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51 jalviewServletURL = applet.getParameter("APPLICATION_URL");
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55 }catch(Exception ex)
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57 ex.printStackTrace();
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60 viewport = new AlignViewport(al, applet);
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61 alignPanel = new AlignmentPanel(this, viewport);
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63 annotationPanelMenuItem.setState(viewport.showAnnotation);
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65 seqLimits.setState(viewport.showJVSuffix);
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69 String param = applet.getParameter("sortBy");
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72 if (param.equalsIgnoreCase("Id"))
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73 sortIDMenuItem_actionPerformed();
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74 else if (param.equalsIgnoreCase("Pairwise Identity"))
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75 sortPairwiseMenuItem_actionPerformed();
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78 param = applet.getParameter("wrap");
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81 if (param.equalsIgnoreCase("true"))
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83 wrapMenuItem.setState(true);
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84 wrapMenuItem_actionPerformed();
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90 param = applet.getParameter("windowWidth");
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93 int width = Integer.parseInt(param);
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94 NEW_WINDOW_WIDTH = width;
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96 param = applet.getParameter("windowHeight");
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99 int height = Integer.parseInt(param);
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100 NEW_WINDOW_HEIGHT = height;
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103 catch (Exception ex)
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108 //Some JVMS send keyevents to Top frame or lowest panel,
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109 //Havent worked out why yet. So add to both this frame and seqCanvas for now
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110 this.addKeyListener(this);
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111 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
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112 alignPanel.idPanel.idCanvas.addKeyListener(this);
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113 alignPanel.scalePanel.addKeyListener(this);
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114 alignPanel.annotationPanel.addKeyListener(this);
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116 viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
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118 public void propertyChange(java.beans.PropertyChangeEvent evt)
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120 if (evt.getPropertyName().equals("alignment"))
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122 alignmentChanged();
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134 add(alignPanel, BorderLayout.CENTER);
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135 jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH,
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136 NEW_WINDOW_HEIGHT);
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138 alignPanel.validate();
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139 alignPanel.repaint();
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141 public AlignViewport getAlignViewport()
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146 public SeqCanvas getSeqcanvas()
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148 return alignPanel.seqPanel.seqCanvas;
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155 * @param String DOCUMENT ME!
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158 public void parseFeaturesFile(String file, String type)
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160 Hashtable featureLinks = new Hashtable();
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161 boolean featuresFile = false;
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163 featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport.alignment,
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164 alignPanel.seqPanel.seqCanvas.
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165 getFeatureRenderer().featureColours,
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169 catch(Exception ex)
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171 ex.printStackTrace();
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176 if(featureLinks.size()>0)
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177 alignPanel.seqPanel.seqCanvas
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178 .getFeatureRenderer().featureLinks = featureLinks;
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179 viewport.showSequenceFeatures = true;
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180 sequenceFeatures.setState(true);
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181 alignPanel.repaint();
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187 public void keyPressed(KeyEvent evt)
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189 if (viewport.cursorMode
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190 && evt.getKeyCode() >= KeyEvent.VK_0
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191 && evt.getKeyCode() <= KeyEvent.VK_9)
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193 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
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196 switch (evt.getKeyCode())
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198 case 27: // escape key
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199 deselectAllSequenceMenuItem_actionPerformed();
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201 case KeyEvent.VK_X:
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202 if (evt.isControlDown() || evt.isMetaDown())
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204 cut_actionPerformed();
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207 case KeyEvent.VK_C:
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208 if (viewport.cursorMode && !evt.isControlDown())
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210 alignPanel.seqPanel.setCursorColumn();
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212 if (evt.isControlDown() || evt.isMetaDown())
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214 copy_actionPerformed();
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217 case KeyEvent.VK_V:
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218 if (evt.isControlDown() || evt.isMetaDown())
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223 case KeyEvent.VK_A:
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224 if (evt.isControlDown() || evt.isMetaDown())
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226 selectAllSequenceMenuItem_actionPerformed();
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229 case KeyEvent.VK_DOWN:
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230 if(viewport.cursorMode)
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232 alignPanel.seqPanel.moveCursor(0,1);
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235 moveSelectedSequences(false);
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238 case KeyEvent.VK_UP:
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239 if (viewport.cursorMode)
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241 alignPanel.seqPanel.moveCursor(0,-1);
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244 moveSelectedSequences(true);
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247 case KeyEvent.VK_LEFT:
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248 if(viewport.cursorMode)
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250 alignPanel.seqPanel.moveCursor(-1,0);
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254 case KeyEvent.VK_RIGHT:
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255 if (viewport.cursorMode)
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257 alignPanel.seqPanel.moveCursor(1,0);
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260 case KeyEvent.VK_SPACE:
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261 if(viewport.cursorMode)
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263 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown());
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267 case KeyEvent.VK_DELETE:
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268 case KeyEvent.VK_BACK_SPACE:
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269 if(viewport.cursorMode)
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271 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown());
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275 cut_actionPerformed();
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276 alignPanel.seqPanel.seqCanvas.repaint();
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280 case KeyEvent.VK_S:
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281 if(viewport.cursorMode)
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283 alignPanel.seqPanel.setCursorRow();
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286 case KeyEvent.VK_P:
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287 if(viewport.cursorMode)
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289 alignPanel.seqPanel.setCursorPosition();
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293 case KeyEvent.VK_ENTER:
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294 case KeyEvent.VK_COMMA:
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295 if(viewport.cursorMode)
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297 alignPanel.seqPanel.setCursorRowAndColumn();
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301 case KeyEvent.VK_Q:
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302 if(viewport.cursorMode)
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304 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
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307 case KeyEvent.VK_M:
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308 if(viewport.cursorMode)
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310 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
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314 case KeyEvent.VK_F2:
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315 viewport.cursorMode = ! viewport.cursorMode;
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316 statusBar.setText("Keyboard editing mode is "+
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317 (viewport.cursorMode ? "on" : "off"));
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318 if(viewport.cursorMode)
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320 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
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321 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
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323 alignPanel.seqPanel.seqCanvas.repaint();
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326 case KeyEvent.VK_F:
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327 if (evt.isControlDown())
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329 findMenuItem_actionPerformed();
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332 case KeyEvent.VK_H:
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334 SequenceGroup sg = viewport.getSelectionGroup();
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335 boolean hide = false;
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336 if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())
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339 viewport.hideAllSelectedSeqs();
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341 else if (viewport.colSel.getSelected().size() < 1)
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342 viewport.showAllHiddenSeqs();
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344 if (viewport.colSel.getSelected().size() > 0)
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345 viewport.hideSelectedColumns();
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347 viewport.showAllHiddenColumns();
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349 alignPanel.repaint();
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355 public void keyReleased(KeyEvent evt)
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357 public void keyTyped(KeyEvent evt)
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360 public void itemStateChanged(ItemEvent evt)
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362 if(evt.getSource()==colourTextMenuItem)
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363 colourTextMenuItem_actionPerformed();
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364 else if(evt.getSource()==wrapMenuItem)
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365 wrapMenuItem_actionPerformed();
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366 else if(evt.getSource()==scaleAbove)
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367 scaleAbove_actionPerformed();
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368 else if(evt.getSource()==scaleLeft)
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369 scaleLeft_actionPerformed();
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370 else if(evt.getSource()==scaleRight)
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371 scaleRight_actionPerformed();
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372 else if(evt.getSource()==seqLimits)
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373 seqLimits_itemStateChanged();
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374 else if(evt.getSource()==viewBoxesMenuItem)
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375 viewBoxesMenuItem_actionPerformed();
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376 else if(evt.getSource()==viewTextMenuItem)
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377 viewTextMenuItem_actionPerformed();
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378 else if(evt.getSource()==renderGapsMenuItem)
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379 renderGapsMenuItem_actionPerformed();
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380 else if(evt.getSource()==annotationPanelMenuItem)
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381 annotationPanelMenuItem_actionPerformed();
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382 else if(evt.getSource()==sequenceFeatures)
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384 viewport.showSequenceFeatures(sequenceFeatures.getState());
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385 alignPanel.seqPanel.seqCanvas.repaint();
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387 else if(evt.getSource()==conservationMenuItem)
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388 conservationMenuItem_actionPerformed();
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389 else if(evt.getSource()==abovePIDThreshold)
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390 abovePIDThreshold_actionPerformed();
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391 else if(evt.getSource()==applyToAllGroups)
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392 applyToAllGroups_actionPerformed();
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393 else if(evt.getSource()==autoCalculate)
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394 viewport.autocalculateConsensus = autoCalculate.getState();
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396 public void actionPerformed(ActionEvent evt)
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398 Object source = evt.getSource();
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400 if(source==inputText)
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401 inputText_actionPerformed();
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402 else if(source==loadTree)
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403 loadTree_actionPerformed();
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404 else if(source==loadApplication)
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405 launchFullApplication();
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406 else if(source==closeMenuItem)
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407 closeMenuItem_actionPerformed();
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408 else if(source==copy)
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409 copy_actionPerformed();
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410 else if(source==undoMenuItem)
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411 undoMenuItem_actionPerformed();
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412 else if(source==redoMenuItem)
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413 redoMenuItem_actionPerformed();
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414 else if(source==inputText)
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415 inputText_actionPerformed();
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416 else if(source==closeMenuItem)
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417 closeMenuItem_actionPerformed();
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418 else if(source==undoMenuItem)
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419 undoMenuItem_actionPerformed();
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420 else if(source==redoMenuItem)
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421 redoMenuItem_actionPerformed();
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422 else if(source==copy)
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423 copy_actionPerformed();
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424 else if(source==pasteNew)
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425 pasteNew_actionPerformed();
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426 else if(source==pasteThis)
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427 pasteThis_actionPerformed();
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428 else if(source==cut)
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429 cut_actionPerformed();
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430 else if(source==delete)
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431 delete_actionPerformed();
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432 else if(source==deleteGroups)
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433 deleteGroups_actionPerformed();
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434 else if(source==selectAllSequenceMenuItem)
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435 selectAllSequenceMenuItem_actionPerformed();
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436 else if(source==deselectAllSequenceMenuItem)
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437 deselectAllSequenceMenuItem_actionPerformed();
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438 else if(source==invertSequenceMenuItem)
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439 invertSequenceMenuItem_actionPerformed();
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440 else if(source==invertColSel)
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441 { viewport.invertColumnSelection(); alignPanel.repaint(); }
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442 else if(source==remove2LeftMenuItem)
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443 remove2LeftMenuItem_actionPerformed();
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444 else if(source==remove2RightMenuItem)
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445 remove2RightMenuItem_actionPerformed();
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446 else if(source==removeGappedColumnMenuItem)
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447 removeGappedColumnMenuItem_actionPerformed();
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448 else if(source==removeAllGapsMenuItem)
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449 removeAllGapsMenuItem_actionPerformed();
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450 else if(source==findMenuItem)
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451 findMenuItem_actionPerformed();
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452 else if(source==font)
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453 font_actionPerformed();
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454 else if(source==showColumns)
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456 viewport.showAllHiddenColumns(); alignPanel.repaint();
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458 else if(source==showSeqs)
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460 viewport.showAllHiddenSeqs();
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462 else if(source == hideColumns)
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464 viewport.hideSelectedColumns(); alignPanel.repaint();
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466 else if(source == hideSequences && viewport.getSelectionGroup()!=null)
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468 viewport.hideAllSelectedSeqs();
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470 else if(source==featureSettings)
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471 featureSettings_actionPerformed();
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472 else if(source==overviewMenuItem)
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473 overviewMenuItem_actionPerformed();
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474 else if(source==noColourmenuItem)
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475 noColourmenuItem_actionPerformed();
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476 else if(source==clustalColour)
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477 clustalColour_actionPerformed();
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478 else if(source==zappoColour)
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479 zappoColour_actionPerformed();
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480 else if(source==taylorColour)
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481 taylorColour_actionPerformed();
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482 else if(source==hydrophobicityColour)
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483 hydrophobicityColour_actionPerformed();
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484 else if(source==helixColour)
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485 helixColour_actionPerformed();
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486 else if(source==strandColour)
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487 strandColour_actionPerformed();
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488 else if(source==turnColour)
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489 turnColour_actionPerformed();
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490 else if(source==buriedColour)
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491 buriedColour_actionPerformed();
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492 else if(source==nucleotideColour)
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493 nucleotideColour_actionPerformed();
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494 else if(source==modifyPID)
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495 modifyPID_actionPerformed();
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496 else if(source==modifyConservation)
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497 modifyConservation_actionPerformed();
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498 else if(source==userDefinedColour)
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499 userDefinedColour_actionPerformed();
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500 else if(source==PIDColour)
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501 PIDColour_actionPerformed();
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502 else if(source==BLOSUM62Colour)
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503 BLOSUM62Colour_actionPerformed();
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504 else if(source==annotationColour)
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505 new AnnotationColourChooser(viewport, alignPanel);
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506 else if(source==sortPairwiseMenuItem)
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507 sortPairwiseMenuItem_actionPerformed();
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508 else if(source==sortIDMenuItem)
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509 sortIDMenuItem_actionPerformed();
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510 else if(source==sortGroupMenuItem)
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511 sortGroupMenuItem_actionPerformed();
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512 else if(source==removeRedundancyMenuItem)
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513 removeRedundancyMenuItem_actionPerformed();
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514 else if(source==pairwiseAlignmentMenuItem)
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515 pairwiseAlignmentMenuItem_actionPerformed();
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516 else if(source==PCAMenuItem)
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517 PCAMenuItem_actionPerformed();
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518 else if(source==averageDistanceTreeMenuItem)
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519 averageDistanceTreeMenuItem_actionPerformed();
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520 else if(source==neighbourTreeMenuItem)
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521 neighbourTreeMenuItem_actionPerformed();
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522 else if(source==njTreeBlosumMenuItem)
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523 njTreeBlosumMenuItem_actionPerformed();
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524 else if(source==avDistanceTreeBlosumMenuItem)
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525 avTreeBlosumMenuItem_actionPerformed();
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526 else if(source==documentation)
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527 documentation_actionPerformed();
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528 else if(source==about)
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529 about_actionPerformed();
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533 public void inputText_actionPerformed()
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535 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
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536 Frame frame = new Frame();
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538 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
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541 protected void outputText_actionPerformed(ActionEvent e)
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543 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
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544 Frame frame = new Frame();
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546 jalview.bin.JalviewLite.addFrame(frame,
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547 "Alignment output - " + e.getActionCommand(),
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549 cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
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550 viewport.getAlignment().getSequences(),
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551 viewport.showJVSuffix));
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554 void launchFullApplication()
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556 StringBuffer url = new StringBuffer(jalviewServletURL);
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558 url.append("?open="+
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559 appendProtocol( viewport.applet.getParameter("file") ) );
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561 if(viewport.applet.getParameter("features")!=null)
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563 url.append( "&features=" );
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564 url.append( appendProtocol( viewport.applet.getParameter("features") ) );
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567 if(viewport.applet.getParameter("annotations")!=null)
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569 url.append( "&annotations=" );
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570 url.append( appendProtocol( viewport.applet.getParameter("annotations") ) );
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573 if(viewport.applet.getParameter("defaultColour")!=null)
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575 url.append("&colour=" +
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576 removeWhiteSpace(viewport.applet.getParameter("defaultColour"))
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580 if(viewport.applet.getParameter("userDefinedColour")!=null)
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582 url.append( "&colour=" +
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583 removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") )
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587 showURL(url.toString(), "FULL_APP");
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591 String removeWhiteSpace(String colour)
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593 StringBuffer sb = new StringBuffer();
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594 for (int i = 0; i < colour.length(); i++)
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596 if (Character.isWhitespace(colour.charAt(i)))
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599 sb.append(colour.charAt(i));
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602 return sb.toString();
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606 String appendProtocol(String url)
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610 }catch(java.net.MalformedURLException ex)
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612 url = viewport.applet.getCodeBase()+url;
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617 public void closeMenuItem_actionPerformed()
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619 PaintRefresher.components.remove(viewport.alignment);
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620 if(PaintRefresher.components.size()==0 && viewport.applet==null)
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626 Stack historyList = new Stack();
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627 Stack redoList = new Stack();
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629 void updateEditMenuBar()
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631 if (historyList.size() > 0)
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633 undoMenuItem.setEnabled(true);
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634 HistoryItem hi = (HistoryItem) historyList.peek();
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635 undoMenuItem.setLabel("Undo " + hi.getDescription());
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639 undoMenuItem.setEnabled(false);
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640 undoMenuItem.setLabel("Undo");
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643 if (redoList.size() > 0)
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645 redoMenuItem.setEnabled(true);
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646 HistoryItem hi = (HistoryItem) redoList.peek();
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647 redoMenuItem.setLabel("Redo " + hi.getDescription());
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651 redoMenuItem.setEnabled(false);
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652 redoMenuItem.setLabel("Redo");
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656 public void addHistoryItem(HistoryItem hi)
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658 historyList.push(hi);
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659 updateEditMenuBar();
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662 protected void undoMenuItem_actionPerformed()
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664 HistoryItem hi = (HistoryItem) historyList.pop();
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665 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
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666 HistoryItem.HIDE));
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667 restoreHistoryItem(hi);
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668 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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671 protected void redoMenuItem_actionPerformed()
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673 HistoryItem hi = (HistoryItem) redoList.pop();
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674 restoreHistoryItem(hi);
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675 updateEditMenuBar();
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676 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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679 // used by undo and redo
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680 void restoreHistoryItem(HistoryItem hi)
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684 updateEditMenuBar();
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686 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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689 public void moveSelectedSequences(boolean up)
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691 SequenceGroup sg = viewport.getSelectionGroup();
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699 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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701 SequenceI seq = viewport.alignment.getSequenceAt(i);
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702 if (!sg.getSequences(false).contains(seq))
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707 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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708 if (sg.getSequences(false).contains(temp))
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713 viewport.alignment.getSequences().setElementAt(temp, i);
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714 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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719 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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721 SequenceI seq = viewport.alignment.getSequenceAt(i);
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722 if (!sg.getSequences(true).contains(seq))
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727 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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728 if (sg.getSequences(true).contains(temp))
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733 viewport.alignment.getSequences().setElementAt(temp, i);
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734 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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738 alignPanel.repaint();
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741 static StringBuffer copiedSequences;
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742 static Vector copiedHiddenColumns;
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743 protected void copy_actionPerformed()
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745 if (viewport.getSelectionGroup() == null)
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750 SequenceGroup sg = viewport.getSelectionGroup();
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751 copiedSequences = new StringBuffer();
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752 Hashtable orderedSeqs = new Hashtable();
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753 for (int i = 0; i < sg.getSize(false); i++)
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755 SequenceI seq = sg.getSequenceAt(i);
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756 int index = viewport.alignment.findIndex(seq);
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757 orderedSeqs.put(index + "", seq);
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760 int index = 0, startRes, endRes;
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763 if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
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765 copiedHiddenColumns = new Vector();
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766 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
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767 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();
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770 int[] region = (int[])
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771 viewport.getColumnSelection().getHiddenColumns().elementAt(i);
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773 copiedHiddenColumns.addElement(new int[]
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774 {region[0] - hiddenOffset,
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775 region[1] - hiddenOffset});
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779 copiedHiddenColumns = null;
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782 for (int i = 0; i < sg.getSize(false); i++)
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784 SequenceI seq = null;
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786 while (seq == null)
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788 if (orderedSeqs.containsKey(index + ""))
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790 seq = (SequenceI) orderedSeqs.get(index + "");
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802 //Returns residue following index if gap
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803 startRes = seq.findPosition(sg.getStartRes());
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806 //Need to find the residue preceeding index if gap
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809 for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
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811 ch = seq.getCharAt(j);
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812 if (!jalview.util.Comparison.isGap( (ch)))
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820 endRes += seq.getStart() -1;
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823 copiedSequences.append(seq.getName() + "\t" +
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826 seq.getSequence(sg.getStartRes(),
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827 sg.getEndRes() + 1) + "\n");
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832 protected void pasteNew_actionPerformed()
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837 protected void pasteThis_actionPerformed()
\r
839 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
\r
840 HistoryItem.PASTE));
\r
844 void paste(boolean newAlignment)
\r
848 if (copiedSequences == null)
\r
853 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
854 Vector seqs = new Vector();
\r
855 while (st.hasMoreElements())
\r
857 String name = st.nextToken();
\r
858 int start = Integer.parseInt(st.nextToken());
\r
859 int end = Integer.parseInt(st.nextToken());
\r
860 Sequence sequence = new Sequence(name, st.nextToken(), start, end);
\r
864 viewport.alignment.addSequence(sequence);
\r
868 seqs.addElement(sequence);
\r
874 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
875 for (int i = 0; i < seqs.size(); i++)
\r
877 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
880 String newtitle = new String("Copied sequences");
\r
881 if (getTitle().startsWith("Copied sequences"))
\r
883 newtitle = getTitle();
\r
887 newtitle = newtitle.concat("- from " + getTitle());
\r
889 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
893 if (copiedHiddenColumns != null)
\r
895 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
897 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
898 af.viewport.hideColumns(region[0], region[1]);
\r
903 jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
\r
904 NEW_WINDOW_HEIGHT);
\r
908 viewport.setEndSeq(viewport.alignment.getHeight());
\r
909 viewport.alignment.getWidth();
\r
910 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
914 catch (Exception ex)
\r
915 {} // could be anything being pasted in here
\r
919 protected void cut_actionPerformed()
\r
921 copy_actionPerformed();
\r
922 delete_actionPerformed();
\r
925 protected void delete_actionPerformed()
\r
927 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
\r
928 HistoryItem.HIDE));
\r
929 if (viewport.getSelectionGroup() == null)
\r
935 SequenceGroup sg = viewport.getSelectionGroup();
\r
936 boolean allSequences = false;
\r
937 if(sg.getSize(false)==viewport.alignment.getHeight())
\r
938 allSequences = true;
\r
940 for (int i = 0; i < sg.getSize(false); i++)
\r
942 SequenceI seq = sg.getSequenceAt(i);
\r
943 int index = viewport.getAlignment().findIndex(seq);
\r
944 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
\r
946 // If the cut affects all sequences, remove highlighted columns
\r
949 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
950 sg.getEndRes() + 1);
\r
954 if (seq.getSequence().length() < 1)
\r
956 viewport.getAlignment().deleteSequence(seq);
\r
960 viewport.getAlignment().getSequences().setElementAt(seq, index);
\r
964 viewport.setSelectionGroup(null);
\r
965 viewport.alignment.deleteGroup(sg);
\r
966 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
\r
967 if (viewport.getAlignment().getHeight() < 1)
\r
971 this.setVisible(false);
\r
973 catch (Exception ex)
\r
976 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
980 protected void deleteGroups_actionPerformed()
\r
982 viewport.alignment.deleteAllGroups();
\r
983 viewport.setSelectionGroup(null);
\r
985 alignPanel.repaint();
\r
988 public void selectAllSequenceMenuItem_actionPerformed()
\r
990 SequenceGroup sg = new SequenceGroup();
\r
991 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
993 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
995 sg.setEndRes(viewport.alignment.getWidth()-1);
\r
996 viewport.setSelectionGroup(sg);
\r
997 alignPanel.repaint();
\r
998 PaintRefresher.Refresh(null, viewport.alignment);
\r
1001 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1003 if(viewport.cursorMode)
\r
1005 alignPanel.seqPanel.keyboardNo1=null;
\r
1006 alignPanel.seqPanel.keyboardNo2=null;
\r
1008 viewport.setSelectionGroup(null);
\r
1009 viewport.getColumnSelection().clear();
\r
1010 viewport.setSelectionGroup(null);
\r
1011 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1012 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1013 alignPanel.repaint();
\r
1014 PaintRefresher.Refresh(null, viewport.alignment);
\r
1017 public void invertSequenceMenuItem_actionPerformed()
\r
1019 SequenceGroup sg = viewport.getSelectionGroup();
\r
1020 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1022 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1025 PaintRefresher.Refresh(null, viewport.alignment);
\r
1028 public void remove2LeftMenuItem_actionPerformed()
\r
1030 ColumnSelection colSel = viewport.getColumnSelection();
\r
1031 if (colSel.size() > 0)
\r
1033 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
\r
1034 HistoryItem.HIDE));
\r
1035 int min = colSel.getMin();
\r
1036 viewport.getAlignment().trimLeft(min);
\r
1037 colSel.compensateForEdit(0, min);
\r
1039 if (viewport.getSelectionGroup() != null)
\r
1041 viewport.getSelectionGroup().adjustForRemoveLeft(min);
\r
1044 Vector groups = viewport.alignment.getGroups();
\r
1045 for (int i = 0; i < groups.size(); i++)
\r
1047 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1048 if (!sg.adjustForRemoveLeft(min))
\r
1050 viewport.alignment.deleteGroup(sg);
\r
1053 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1057 public void remove2RightMenuItem_actionPerformed()
\r
1059 ColumnSelection colSel = viewport.getColumnSelection();
\r
1060 if (colSel.size() > 0)
\r
1062 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
\r
1063 HistoryItem.HIDE));
\r
1064 int max = colSel.getMax();
\r
1065 viewport.getAlignment().trimRight(max);
\r
1066 if (viewport.getSelectionGroup() != null)
\r
1068 viewport.getSelectionGroup().adjustForRemoveRight(max);
\r
1071 Vector groups = viewport.alignment.getGroups();
\r
1072 for (int i = 0; i < groups.size(); i++)
\r
1074 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1075 if (!sg.adjustForRemoveRight(max))
\r
1077 viewport.alignment.deleteGroup(sg);
\r
1080 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1085 public void removeGappedColumnMenuItem_actionPerformed()
\r
1087 addHistoryItem(new HistoryItem("Remove Gapped Columns",
\r
1088 viewport.alignment,
\r
1089 HistoryItem.HIDE));
\r
1091 //This is to maintain viewport position on first residue
\r
1092 //of first sequence
\r
1093 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1094 int startRes = seq.findPosition(viewport.startRes);
\r
1096 viewport.getAlignment().removeGaps();
\r
1098 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1100 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1103 public void removeAllGapsMenuItem_actionPerformed()
\r
1105 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
\r
1106 HistoryItem.HIDE));
\r
1108 //This is to maintain viewport position on first residue
\r
1109 //of first sequence
\r
1110 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1111 int startRes = seq.findPosition(viewport.startRes);
\r
1113 SequenceI current;
\r
1118 int start=0, end = viewport.alignment.getWidth();
\r
1120 if (viewport.getSelectionGroup() != null
\r
1121 && viewport.getSelectionGroup().getSequences(false) != null
\r
1122 && viewport.getSelectionGroup().getSize(false)>0)
\r
1124 seqs = viewport.getSelectionGroup().getSequences(true);
\r
1125 start = viewport.getSelectionGroup().getStartRes();
\r
1126 end = viewport.getSelectionGroup().getEndRes()+1;
\r
1129 seqs = viewport.alignment.getSequences();
\r
1131 for (int i = 0; i < seqs.size(); i++)
\r
1133 current = (SequenceI) seqs.elementAt(i);
\r
1134 jSize = current.getLength();
\r
1136 // Removing a range is much quicker than removing gaps
\r
1137 // one by one for long sequences
\r
1139 int rangeStart=-1, rangeEnd=-1;
\r
1143 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
\r
1145 if(rangeStart==-1)
\r
1160 current.deleteChars(rangeStart, rangeEnd);
\r
1161 j-=rangeEnd-rangeStart;
\r
1162 jSize-=rangeEnd-rangeStart;
\r
1170 while (j < end && j < jSize);
\r
1173 current.deleteChars(rangeStart, rangeEnd);
\r
1176 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1177 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1180 public void alignmentChanged()
\r
1182 viewport.alignment.padGaps();
\r
1183 if(viewport.autocalculateConsensus)
\r
1185 viewport.updateConsensus();
\r
1186 viewport.updateConservation();
\r
1189 resetAllColourSchemes();
\r
1190 if(alignPanel.overviewPanel!=null)
\r
1191 alignPanel.overviewPanel.updateOverviewImage();
\r
1193 viewport.alignment.adjustSequenceAnnotations();
\r
1194 alignPanel.repaint();
\r
1197 void resetAllColourSchemes()
\r
1199 ColourSchemeI cs = viewport.globalColourScheme;
\r
1202 if (cs instanceof ClustalxColourScheme)
\r
1204 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
\r
1205 resetClustalX(viewport.alignment.getSequences(),
\r
1206 viewport.alignment.getWidth());
\r
1209 cs.setConsensus(viewport.vconsensus);
\r
1210 if (cs.conservationApplied())
\r
1212 Alignment al = (Alignment) viewport.alignment;
\r
1213 Conservation c = new Conservation("All",
\r
1214 ResidueProperties.propHash, 3,
\r
1215 al.getSequences(), 0,
\r
1216 al.getWidth() - 1);
\r
1218 c.verdict(false, viewport.ConsPercGaps);
\r
1220 cs.setConservation(c);
\r
1224 int s, sSize = viewport.alignment.getGroups().size();
\r
1225 for(s=0; s<sSize; s++)
\r
1227 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
\r
1228 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
\r
1230 ((ClustalxColourScheme)sg.cs).resetClustalX(
\r
1231 sg.getSequences(true), sg.getWidth());
\r
1233 sg.recalcConservation();
\r
1239 public void findMenuItem_actionPerformed()
\r
1241 new Finder(alignPanel);
\r
1244 public void font_actionPerformed()
\r
1246 new FontChooser(alignPanel);
\r
1250 public void seqLimits_itemStateChanged()
\r
1252 viewport.setShowJVSuffix(seqLimits.getState());
\r
1253 alignPanel.fontChanged();
\r
1254 alignPanel.repaint();
\r
1258 protected void colourTextMenuItem_actionPerformed()
\r
1260 viewport.setColourText(colourTextMenuItem.getState());
\r
1261 alignPanel.repaint();
\r
1264 protected void wrapMenuItem_actionPerformed()
\r
1266 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
1267 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
1268 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
1269 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
1270 scaleRight.setEnabled(wrapMenuItem.getState());
\r
1271 alignPanel.repaint();
\r
1275 protected void scaleAbove_actionPerformed()
\r
1277 viewport.setScaleAboveWrapped(scaleAbove.getState());
\r
1278 alignPanel.repaint();
\r
1281 protected void scaleLeft_actionPerformed()
\r
1283 viewport.setScaleLeftWrapped(scaleLeft.getState());
\r
1284 alignPanel.repaint();
\r
1287 protected void scaleRight_actionPerformed()
\r
1289 viewport.setScaleRightWrapped(scaleRight.getState());
\r
1290 alignPanel.repaint();
\r
1293 public void viewBoxesMenuItem_actionPerformed()
\r
1295 viewport.setShowBoxes(viewBoxesMenuItem.getState());
\r
1296 alignPanel.repaint();
\r
1299 public void viewTextMenuItem_actionPerformed()
\r
1301 viewport.setShowText(viewTextMenuItem.getState());
\r
1302 alignPanel.repaint();
\r
1305 protected void renderGapsMenuItem_actionPerformed()
\r
1307 viewport.setRenderGaps(renderGapsMenuItem.getState());
\r
1308 alignPanel.repaint();
\r
1311 public void annotationPanelMenuItem_actionPerformed()
\r
1313 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
\r
1314 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
\r
1317 public void featureSettings_actionPerformed()
\r
1319 new FeatureSettings(viewport, alignPanel);
\r
1322 public void overviewMenuItem_actionPerformed()
\r
1324 if (alignPanel.overviewPanel != null)
\r
1329 Frame frame = new Frame();
\r
1330 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1331 frame.add(overview);
\r
1332 // +50 must allow for applet frame window
\r
1333 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
1334 overview.preferredSize().width,
\r
1335 overview.preferredSize().height + 50);
\r
1338 frame.addWindowListener(new WindowAdapter()
\r
1340 public void windowClosing(WindowEvent e)
\r
1342 alignPanel.setOverviewPanel(null);
\r
1346 alignPanel.setOverviewPanel(overview);
\r
1350 protected void noColourmenuItem_actionPerformed()
\r
1352 changeColour(null);
\r
1355 public void clustalColour_actionPerformed()
\r
1357 abovePIDThreshold.setState(false);
\r
1358 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
\r
1359 viewport.alignment.getWidth()));
\r
1362 public void zappoColour_actionPerformed()
\r
1364 changeColour(new ZappoColourScheme());
\r
1367 public void taylorColour_actionPerformed()
\r
1369 changeColour(new TaylorColourScheme());
\r
1372 public void hydrophobicityColour_actionPerformed()
\r
1374 changeColour(new HydrophobicColourScheme());
\r
1377 public void helixColour_actionPerformed()
\r
1379 changeColour(new HelixColourScheme());
\r
1382 public void strandColour_actionPerformed()
\r
1384 changeColour(new StrandColourScheme());
\r
1387 public void turnColour_actionPerformed()
\r
1389 changeColour(new TurnColourScheme());
\r
1392 public void buriedColour_actionPerformed()
\r
1394 changeColour(new BuriedColourScheme());
\r
1397 public void nucleotideColour_actionPerformed()
\r
1399 changeColour(new NucleotideColourScheme());
\r
1402 protected void applyToAllGroups_actionPerformed()
\r
1404 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
\r
1407 void changeColour(ColourSchemeI cs)
\r
1409 int threshold = 0;
\r
1413 if (viewport.getAbovePIDThreshold())
\r
1415 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
\r
1417 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1419 viewport.setGlobalColourScheme(cs);
\r
1423 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1426 if (viewport.getConservationSelected())
\r
1429 Alignment al = (Alignment) viewport.alignment;
\r
1430 Conservation c = new Conservation("All",
\r
1431 ResidueProperties.propHash, 3,
\r
1432 al.getSequences(), 0,
\r
1433 al.getWidth() - 1);
\r
1436 c.verdict(false, viewport.ConsPercGaps);
\r
1438 cs.setConservation(c);
\r
1440 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1446 cs.setConservation(null);
\r
1449 cs.setConsensus(viewport.vconsensus);
\r
1452 viewport.setGlobalColourScheme(cs);
\r
1454 if (viewport.getColourAppliesToAllGroups())
\r
1456 Vector groups = viewport.alignment.getGroups();
\r
1457 for (int i = 0; i < groups.size(); i++)
\r
1459 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1466 if (cs instanceof ClustalxColourScheme)
\r
1468 sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth());
\r
1474 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1476 catch (Exception ex)
\r
1478 ex.printStackTrace();
\r
1483 if (viewport.getAbovePIDThreshold()
\r
1484 || cs instanceof PIDColourScheme
\r
1485 || cs instanceof Blosum62ColourScheme)
\r
1487 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1488 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth()));
\r
1491 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1493 if (viewport.getConservationSelected())
\r
1495 Conservation c = new Conservation("Group",
\r
1496 ResidueProperties.propHash, 3,
\r
1497 sg.getSequences(true), 0,
\r
1498 viewport.alignment.getWidth() - 1);
\r
1500 c.verdict(false, viewport.ConsPercGaps);
\r
1501 sg.cs.setConservation(c);
\r
1505 sg.cs.setConservation(null);
\r
1506 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1513 if (alignPanel.getOverviewPanel() != null)
\r
1515 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1518 alignPanel.repaint();
\r
1523 protected void modifyPID_actionPerformed()
\r
1525 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1527 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
1529 SliderPanel.showPIDSlider();
\r
1533 protected void modifyConservation_actionPerformed()
\r
1535 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1537 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
1539 SliderPanel.showConservationSlider();
\r
1543 protected void conservationMenuItem_actionPerformed()
\r
1545 viewport.setConservationSelected(conservationMenuItem.getState());
\r
1547 viewport.setAbovePIDThreshold(false);
\r
1548 abovePIDThreshold.setState(false);
\r
1550 changeColour(viewport.getGlobalColourScheme());
\r
1552 modifyConservation_actionPerformed();
\r
1555 public void abovePIDThreshold_actionPerformed()
\r
1557 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
1559 conservationMenuItem.setState(false);
\r
1560 viewport.setConservationSelected(false);
\r
1562 changeColour(viewport.getGlobalColourScheme());
\r
1564 modifyPID_actionPerformed();
\r
1567 public void userDefinedColour_actionPerformed()
\r
1569 new UserDefinedColours(alignPanel, null);
\r
1572 public void PIDColour_actionPerformed()
\r
1574 changeColour(new PIDColourScheme());
\r
1577 public void BLOSUM62Colour_actionPerformed()
\r
1579 changeColour(new Blosum62ColourScheme());
\r
1582 public void sortPairwiseMenuItem_actionPerformed()
\r
1584 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1585 HistoryItem.SORT));
\r
1586 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1587 viewport.getAlignment().getSequenceAt(0));
\r
1588 alignPanel.repaint();
\r
1591 public void sortIDMenuItem_actionPerformed()
\r
1593 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1594 HistoryItem.SORT));
\r
1595 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1596 alignPanel.repaint();
\r
1599 public void sortGroupMenuItem_actionPerformed()
\r
1601 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1602 HistoryItem.SORT));
\r
1603 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1604 alignPanel.repaint();
\r
1608 public void removeRedundancyMenuItem_actionPerformed()
\r
1610 new RedundancyPanel(alignPanel);
\r
1613 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
1615 if (viewport.getSelectionGroup()!=null
\r
1616 && viewport.getSelectionGroup().getSize(false) > 1)
\r
1618 Frame frame = new Frame();
\r
1619 frame.add(new PairwiseAlignPanel(alignPanel));
\r
1620 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
1624 public void PCAMenuItem_actionPerformed()
\r
1626 //are the sequences aligned?
\r
1627 if (!viewport.alignment.isAligned())
\r
1629 SequenceI current;
\r
1630 int Width = viewport.getAlignment().getWidth();
\r
1632 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1635 current = viewport.getAlignment().getSequenceAt(i);
\r
1637 if (current.getLength() < Width)
\r
1639 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1642 alignPanel.repaint();
\r
1645 if ( (viewport.getSelectionGroup() != null &&
\r
1646 viewport.getSelectionGroup().getSize(false) < 4 &&
\r
1647 viewport.getSelectionGroup().getSize(false) > 0)
\r
1648 || viewport.getAlignment().getHeight() < 4)
\r
1655 new PCAPanel(viewport);
\r
1657 catch (java.lang.OutOfMemoryError ex)
\r
1663 public void averageDistanceTreeMenuItem_actionPerformed()
\r
1665 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1668 public void neighbourTreeMenuItem_actionPerformed()
\r
1670 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1673 protected void njTreeBlosumMenuItem_actionPerformed()
\r
1675 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1678 protected void avTreeBlosumMenuItem_actionPerformed()
\r
1680 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1683 void NewTreePanel(String type, String pwType, String title)
\r
1685 //are the sequences aligned?
\r
1686 if (!viewport.alignment.isAligned())
\r
1688 SequenceI current;
\r
1689 int Width = viewport.getAlignment().getWidth();
\r
1691 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1694 current = viewport.getAlignment().getSequenceAt(i);
\r
1696 if (current.getLength() < Width)
\r
1698 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1701 alignPanel.repaint();
\r
1705 if ( (viewport.getSelectionGroup() != null &&
\r
1706 viewport.getSelectionGroup().getSize(false) > 1)
\r
1707 || (viewport.getSelectionGroup() == null
\r
1708 && viewport.alignment.getHeight() > 1))
\r
1710 final TreePanel tp = new TreePanel(viewport,
\r
1714 addTreeMenuItem(tp, title);
\r
1716 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
1720 void loadTree_actionPerformed()
\r
1722 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1723 cap.setText("Paste your Newick tree file here.");
\r
1724 cap.treeImport = true;
\r
1725 Frame frame = new Frame();
\r
1727 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
1730 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
1732 TreePanel tp = new TreePanel(viewport,
\r
1736 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
1737 addTreeMenuItem(tp, treeFile);
\r
1740 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1742 final MenuItem item = new MenuItem(title);
\r
1743 sortByTreeMenu.add(item);
\r
1744 item.addActionListener(new java.awt.event.ActionListener()
\r
1746 public void actionPerformed(ActionEvent evt)
\r
1748 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1749 HistoryItem.SORT));
\r
1750 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1751 alignPanel.repaint();
\r
1755 treePanel.addWindowListener(new WindowAdapter()
\r
1757 public void windowClosing(WindowEvent e)
\r
1759 sortByTreeMenu.remove(item);
\r
1764 protected void documentation_actionPerformed()
\r
1766 showURL("http://www.jalview.org/help.html", "HELP");
\r
1769 protected void about_actionPerformed()
\r
1772 class AboutPanel extends Canvas
\r
1775 public AboutPanel(String version)
\r
1776 { this.version = version; }
\r
1778 public void paint(Graphics g)
\r
1780 g.setColor(Color.white);
\r
1781 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1782 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1783 FontMetrics fm = g.getFontMetrics();
\r
1784 int fh = fm.getHeight();
\r
1786 g.setColor(Color.black);
\r
1787 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
1788 g.drawString("Jalview - Release "+version, 200, y += fh);
\r
1789 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1790 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
1792 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
1795 "For any issues relating to Jalview, email help@jalview.org", x,
\r
1797 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
1798 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
1800 g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh);
\r
1804 String version = "test";
\r
1805 java.net.URL url = getClass().getResource("/.build_properties");
\r
1810 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
1811 url.openStream()));
\r
1813 while ( (line = reader.readLine()) != null)
\r
1815 if (line.indexOf("VERSION") > -1)
\r
1817 version = line.substring(line.indexOf("=") + 1);
\r
1821 catch (Exception ex)
\r
1823 ex.printStackTrace();
\r
1828 Frame frame = new Frame();
\r
1829 frame.add(new AboutPanel(version));
\r
1830 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
\r
1834 public void showURL(String url, String target)
\r
1836 if (viewport.applet == null)
\r
1838 System.out.println("Not running as applet - no browser available.");
\r
1844 System.out.println("Show url: "+url);
\r
1845 viewport.applet.getAppletContext().showDocument(new java.net.URL(url),
\r
1848 catch (Exception ex)
\r
1850 ex.printStackTrace();
\r
1856 //////////////////////////////////////////////////////////////////////////////////
\r
1857 //JBuilder Graphics here
\r
1859 protected MenuBar alignFrameMenuBar = new MenuBar();
\r
1860 protected Menu fileMenu = new Menu("File");
\r
1861 protected MenuItem loadApplication = new MenuItem("View in Full Application");
\r
1862 protected MenuItem loadTree = new MenuItem("Load Associated Tree");
\r
1863 protected MenuItem closeMenuItem = new MenuItem("Close");
\r
1864 protected Menu editMenu = new Menu("Edit");
\r
1865 protected Menu viewMenu = new Menu("View");
\r
1866 protected Menu colourMenu = new Menu("Colour");
\r
1867 protected Menu calculateMenu = new Menu("Calculate");
\r
1868 protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
1869 protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
1870 protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
1871 protected MenuItem remove2LeftMenuItem = new MenuItem();
\r
1872 protected MenuItem remove2RightMenuItem = new MenuItem();
\r
1873 protected MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
1874 protected MenuItem removeAllGapsMenuItem = new MenuItem();
\r
1875 protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
1876 protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
1877 protected MenuItem sortPairwiseMenuItem = new MenuItem();
\r
1878 protected MenuItem sortIDMenuItem = new MenuItem();
\r
1879 protected MenuItem sortGroupMenuItem = new MenuItem();
\r
1880 protected MenuItem removeRedundancyMenuItem = new MenuItem();
\r
1881 protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
1882 protected MenuItem PCAMenuItem = new MenuItem();
\r
1883 protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
1884 protected MenuItem neighbourTreeMenuItem = new MenuItem();
\r
1885 BorderLayout borderLayout1 = new BorderLayout();
\r
1886 public Label statusBar = new Label();
\r
1887 protected Menu outputTextboxMenu = new Menu();
\r
1888 protected MenuItem clustalColour = new MenuItem();
\r
1889 protected MenuItem zappoColour = new MenuItem();
\r
1890 protected MenuItem taylorColour = new MenuItem();
\r
1891 protected MenuItem hydrophobicityColour = new MenuItem();
\r
1892 protected MenuItem helixColour = new MenuItem();
\r
1893 protected MenuItem strandColour = new MenuItem();
\r
1894 protected MenuItem turnColour = new MenuItem();
\r
1895 protected MenuItem buriedColour = new MenuItem();
\r
1896 protected MenuItem userDefinedColour = new MenuItem();
\r
1897 protected MenuItem PIDColour = new MenuItem();
\r
1898 protected MenuItem BLOSUM62Colour = new MenuItem();
\r
1899 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
1900 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
1901 protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
1902 protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
1903 MenuItem overviewMenuItem = new MenuItem();
\r
1904 protected MenuItem undoMenuItem = new MenuItem();
\r
1905 protected MenuItem redoMenuItem = new MenuItem();
\r
1906 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
1907 MenuItem noColourmenuItem = new MenuItem();
\r
1908 protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
1909 protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
1910 MenuItem findMenuItem = new MenuItem();
\r
1911 Menu searchMenu = new Menu();
\r
1912 protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
1913 protected MenuItem nucleotideColour = new MenuItem();
\r
1914 MenuItem deleteGroups = new MenuItem();
\r
1915 MenuItem delete = new MenuItem();
\r
1916 MenuItem copy = new MenuItem();
\r
1917 MenuItem cut = new MenuItem();
\r
1918 Menu pasteMenu = new Menu();
\r
1919 MenuItem pasteNew = new MenuItem();
\r
1920 MenuItem pasteThis = new MenuItem();
\r
1921 protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
1922 protected MenuItem font = new MenuItem();
\r
1923 protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
1924 protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
1925 protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
1926 MenuItem modifyPID = new MenuItem();
\r
1927 MenuItem modifyConservation = new MenuItem();
\r
1928 protected CheckboxMenuItem autoCalculate
\r
1929 = new CheckboxMenuItem("Autocalculate Consensus", true);
\r
1930 protected Menu sortByTreeMenu = new Menu();
\r
1931 Menu sort = new Menu();
\r
1932 Menu calculate = new Menu();
\r
1933 MenuItem inputText = new MenuItem();
\r
1934 Menu helpMenu = new Menu();
\r
1935 MenuItem documentation = new MenuItem();
\r
1936 MenuItem about = new MenuItem();
\r
1937 protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
1938 Panel embeddedMenu;
\r
1939 Label embeddedEdit;
\r
1940 Label embeddedSearch;
\r
1941 Label embeddedView;
\r
1942 Label embeddedColour;
\r
1943 Label embeddedFile;
\r
1944 Label embeddedHelp;
\r
1945 Label embeddedCalculate;
\r
1946 FlowLayout flowLayout1;
\r
1948 private void jbInit() throws Exception {
\r
1950 setMenuBar(alignFrameMenuBar);
\r
1954 // dynamically fill save as menu with available formats
\r
1955 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
1958 item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
1960 item.addActionListener(new java.awt.event.ActionListener()
\r
1962 public void actionPerformed(ActionEvent e)
\r
1964 outputText_actionPerformed(e);
\r
1968 outputTextboxMenu.add(item);
\r
1970 closeMenuItem.addActionListener(this);
\r
1971 loadApplication.addActionListener(this);
\r
1973 loadTree.addActionListener(this);
\r
1974 selectAllSequenceMenuItem.addActionListener(this);
\r
1975 deselectAllSequenceMenuItem.addActionListener(this);
\r
1976 invertSequenceMenuItem.addActionListener(this);
\r
1977 remove2LeftMenuItem.setLabel("Remove Left");
\r
1978 remove2LeftMenuItem.addActionListener(this);
\r
1979 remove2RightMenuItem.setLabel("Remove Right");
\r
1980 remove2RightMenuItem.addActionListener(this);
\r
1981 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
1982 removeGappedColumnMenuItem.addActionListener(this);
\r
1983 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
1984 removeAllGapsMenuItem.addActionListener(this);
\r
1985 viewBoxesMenuItem.setLabel("Boxes");
\r
1986 viewBoxesMenuItem.setState(true);
\r
1987 viewBoxesMenuItem.addItemListener(this);
\r
1988 viewTextMenuItem.setLabel("Text");
\r
1989 viewTextMenuItem.setState(true);
\r
1990 viewTextMenuItem.addItemListener(this);
\r
1991 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
1992 sortPairwiseMenuItem.addActionListener(this);
\r
1993 sortIDMenuItem.setLabel("by ID");
\r
1994 sortIDMenuItem.addActionListener(this);
\r
1995 sortGroupMenuItem.setLabel("by Group");
\r
1996 sortGroupMenuItem.addActionListener(this);
\r
1997 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
1998 removeRedundancyMenuItem.addActionListener(this);
\r
1999 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
2000 pairwiseAlignmentMenuItem.addActionListener(this);
\r
2001 PCAMenuItem.setLabel("Principal Component Analysis");
\r
2002 PCAMenuItem.addActionListener(this);
\r
2003 averageDistanceTreeMenuItem.setLabel(
\r
2004 "Average Distance Using % Identity");
\r
2005 averageDistanceTreeMenuItem.addActionListener(this);
\r
2006 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
2007 neighbourTreeMenuItem.addActionListener(this);
\r
2008 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
2009 statusBar.setBackground(Color.white);
\r
2010 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
2011 statusBar.setText("Status bar");
\r
2012 outputTextboxMenu.setLabel("Output to Textbox");
\r
2013 clustalColour.setLabel("Clustalx");
\r
2015 clustalColour.addActionListener(this);
\r
2016 zappoColour.setLabel("Zappo");
\r
2017 zappoColour.addActionListener(this);
\r
2018 taylorColour.setLabel("Taylor");
\r
2019 taylorColour.addActionListener(this);
\r
2020 hydrophobicityColour.setLabel("Hydrophobicity");
\r
2021 hydrophobicityColour.addActionListener(this);
\r
2022 helixColour.setLabel("Helix Propensity");
\r
2023 helixColour.addActionListener(this);
\r
2024 strandColour.setLabel("Strand Propensity");
\r
2025 strandColour.addActionListener(this);
\r
2026 turnColour.setLabel("Turn Propensity");
\r
2027 turnColour.addActionListener(this);
\r
2028 buriedColour.setLabel("Buried Index");
\r
2029 buriedColour.addActionListener(this);
\r
2030 userDefinedColour.setLabel("User Defined...");
\r
2031 userDefinedColour.addActionListener(this);
\r
2032 PIDColour.setLabel("Percentage Identity");
\r
2033 PIDColour.addActionListener(this);
\r
2034 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
2035 BLOSUM62Colour.addActionListener(this);
\r
2036 avDistanceTreeBlosumMenuItem.setLabel(
\r
2037 "Average Distance Using BLOSUM62");
\r
2038 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
2039 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
2040 njTreeBlosumMenuItem.addActionListener(this);
\r
2041 annotationPanelMenuItem.setLabel("Show Annotations");
\r
2042 annotationPanelMenuItem.addItemListener(this);
\r
2043 colourTextMenuItem.setLabel("Colour Text");
\r
2044 colourTextMenuItem.addItemListener(this);
\r
2045 overviewMenuItem.setLabel("Overview Window");
\r
2046 overviewMenuItem.addActionListener(this);
\r
2047 undoMenuItem.setEnabled(false);
\r
2048 undoMenuItem.setLabel("Undo");
\r
2049 undoMenuItem.addActionListener(this);
\r
2050 redoMenuItem.setEnabled(false);
\r
2051 redoMenuItem.setLabel("Redo");
\r
2052 redoMenuItem.addActionListener(this);
\r
2053 conservationMenuItem.setLabel("by Conservation");
\r
2054 conservationMenuItem.addItemListener(this);
\r
2055 noColourmenuItem.setLabel("None");
\r
2056 noColourmenuItem.addActionListener(this);
\r
2057 wrapMenuItem.setLabel("Wrap");
\r
2058 wrapMenuItem.addItemListener(this);
\r
2059 renderGapsMenuItem.setLabel("Show Gaps");
\r
2060 renderGapsMenuItem.setState(true);
\r
2061 renderGapsMenuItem.addItemListener(this);
\r
2062 findMenuItem.setLabel("Find...");
\r
2063 findMenuItem.addActionListener(this);
\r
2064 searchMenu.setLabel("Search");
\r
2066 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
2067 abovePIDThreshold.addItemListener(this);
\r
2068 nucleotideColour.setLabel("Nucleotide");
\r
2069 nucleotideColour.addActionListener(this);
\r
2070 deleteGroups.setLabel("Undefine Groups");
\r
2071 deleteGroups.addActionListener(this);
\r
2072 copy.setLabel("Copy");
\r
2073 copy.addActionListener(this);
\r
2074 cut.setLabel("Cut");
\r
2075 cut.addActionListener(this);
\r
2076 delete.setLabel("Delete");
\r
2077 delete.addActionListener(this);
\r
2078 pasteMenu.setLabel("Paste");
\r
2079 pasteNew.setLabel("To New Alignment");
\r
2080 pasteNew.addActionListener(this);
\r
2081 pasteThis.setLabel("Add To This Alignment");
\r
2082 pasteThis.addActionListener(this);
\r
2083 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
2084 applyToAllGroups.setState(true);
\r
2085 applyToAllGroups.addItemListener(this);
\r
2086 font.setLabel("Font...");
\r
2087 font.addActionListener(this);
\r
2088 scaleAbove.setLabel("Scale Above");
\r
2089 scaleAbove.setState(true);
\r
2090 scaleAbove.setEnabled(false);
\r
2091 scaleAbove.addItemListener(this);
\r
2092 scaleLeft.setEnabled(false);
\r
2093 scaleLeft.setState(true);
\r
2094 scaleLeft.setLabel("Scale Left");
\r
2095 scaleLeft.addItemListener(this);
\r
2096 scaleRight.setEnabled(false);
\r
2097 scaleRight.setState(true);
\r
2098 scaleRight.setLabel("Scale Right");
\r
2099 scaleRight.addItemListener(this);
\r
2100 modifyPID.setLabel("Modify Identity Threshold...");
\r
2101 modifyPID.addActionListener(this);
\r
2102 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
2103 modifyConservation.addActionListener(this);
\r
2104 sortByTreeMenu.setLabel("By Tree Order");
\r
2105 sort.setLabel("Sort");
\r
2106 calculate.setLabel("Calculate Tree");
\r
2107 autoCalculate.addItemListener(this);
\r
2108 inputText.setLabel("Input from textbox");
\r
2109 inputText.addActionListener(this);
\r
2111 helpMenu.setLabel("Help");
\r
2112 documentation.setLabel("Documentation");
\r
2113 documentation.addActionListener(this);
\r
2115 about.setLabel("About...");
\r
2116 about.addActionListener(this);
\r
2117 seqLimits.setState(true);
\r
2118 seqLimits.setLabel("Show Sequence Limits");
\r
2119 seqLimits.addItemListener(this);
\r
2120 featureSettings.setLabel("Feature Settings...");
\r
2121 featureSettings.addActionListener(this);
\r
2122 sequenceFeatures.setLabel("Sequence Features");
\r
2123 sequenceFeatures.addItemListener(this);
\r
2124 sequenceFeatures.setState(false);
\r
2125 annotationColour.setLabel("by Annotation...");
\r
2126 annotationColour.addActionListener(this);
\r
2127 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
2128 invertColSel.setLabel("Invert Column Selection");
\r
2129 menu1.setLabel("Show");
\r
2130 showColumns.setLabel("All Columns ");
\r
2131 showSeqs.setLabel("All Sequences");
\r
2132 menu2.setLabel("Hide");
\r
2133 hideColumns.setLabel("Selected Columns");
\r
2134 hideSequences.setLabel("Selected Sequences");
\r
2135 invertColSel.addActionListener(this);
\r
2136 showColumns.addActionListener(this);
\r
2137 showSeqs.addActionListener(this);
\r
2138 hideColumns.addActionListener(this);
\r
2139 hideSequences.addActionListener(this);
\r
2142 alignFrameMenuBar.add(fileMenu);
\r
2143 alignFrameMenuBar.add(editMenu);
\r
2144 alignFrameMenuBar.add(searchMenu);
\r
2145 alignFrameMenuBar.add(viewMenu);
\r
2146 alignFrameMenuBar.add(colourMenu);
\r
2147 alignFrameMenuBar.add(calculateMenu);
\r
2148 alignFrameMenuBar.add(helpMenu);
\r
2149 fileMenu.add(inputText);
\r
2150 fileMenu.add(outputTextboxMenu);
\r
2151 if(jalviewServletURL!=null)
\r
2152 fileMenu.add(loadApplication);
\r
2153 fileMenu.addSeparator();
\r
2154 fileMenu.add(loadTree);
\r
2155 fileMenu.add(closeMenuItem);
\r
2156 editMenu.add(undoMenuItem);
\r
2157 editMenu.add(redoMenuItem);
\r
2158 editMenu.add(cut);
\r
2159 editMenu.add(copy);
\r
2160 editMenu.add(pasteMenu);
\r
2161 editMenu.add(delete);
\r
2162 editMenu.addSeparator();
\r
2163 editMenu.add(selectAllSequenceMenuItem);
\r
2164 editMenu.add(deselectAllSequenceMenuItem);
\r
2165 editMenu.add(invertSequenceMenuItem);
\r
2166 editMenu.add(invertColSel);
\r
2167 editMenu.add(deleteGroups);
\r
2168 editMenu.addSeparator();
\r
2169 editMenu.add(remove2LeftMenuItem);
\r
2170 editMenu.add(remove2RightMenuItem);
\r
2171 editMenu.add(removeGappedColumnMenuItem);
\r
2172 editMenu.add(removeAllGapsMenuItem);
\r
2173 editMenu.add(removeRedundancyMenuItem);
\r
2174 searchMenu.add(findMenuItem);
\r
2175 viewMenu.add(font);
\r
2176 viewMenu.addSeparator();
\r
2177 viewMenu.add(menu1);
\r
2178 viewMenu.add(menu2);
\r
2179 viewMenu.addSeparator();
\r
2180 viewMenu.add(wrapMenuItem);
\r
2181 viewMenu.add(scaleAbove);
\r
2182 viewMenu.add(scaleLeft);
\r
2183 viewMenu.add(scaleRight);
\r
2184 viewMenu.addSeparator();
\r
2185 viewMenu.add(seqLimits);
\r
2186 viewMenu.add(viewBoxesMenuItem);
\r
2187 viewMenu.add(viewTextMenuItem);
\r
2188 viewMenu.add(colourTextMenuItem);
\r
2189 viewMenu.add(renderGapsMenuItem);
\r
2190 viewMenu.add(annotationPanelMenuItem);
\r
2191 viewMenu.addSeparator();
\r
2192 viewMenu.add(sequenceFeatures);
\r
2193 viewMenu.add(featureSettings);
\r
2194 viewMenu.addSeparator();
\r
2195 viewMenu.add(overviewMenuItem);
\r
2196 colourMenu.add(applyToAllGroups);
\r
2197 colourMenu.addSeparator();
\r
2198 colourMenu.add(noColourmenuItem);
\r
2199 colourMenu.add(clustalColour);
\r
2200 colourMenu.add(BLOSUM62Colour);
\r
2201 colourMenu.add(PIDColour);
\r
2202 colourMenu.add(zappoColour);
\r
2203 colourMenu.add(taylorColour);
\r
2204 colourMenu.add(hydrophobicityColour);
\r
2205 colourMenu.add(helixColour);
\r
2206 colourMenu.add(strandColour);
\r
2207 colourMenu.add(turnColour);
\r
2208 colourMenu.add(buriedColour);
\r
2209 colourMenu.add(nucleotideColour);
\r
2210 colourMenu.add(userDefinedColour);
\r
2211 colourMenu.addSeparator();
\r
2212 colourMenu.add(conservationMenuItem);
\r
2213 colourMenu.add(modifyConservation);
\r
2214 colourMenu.add(abovePIDThreshold);
\r
2215 colourMenu.add(modifyPID);
\r
2216 colourMenu.add(annotationColour);
\r
2217 calculateMenu.add(sort);
\r
2218 calculateMenu.add(calculate);
\r
2219 calculateMenu.addSeparator();
\r
2220 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
2221 calculateMenu.add(PCAMenuItem);
\r
2222 calculateMenu.add(autoCalculate);
\r
2223 this.add(statusBar, BorderLayout.SOUTH);
\r
2224 pasteMenu.add(pasteNew);
\r
2225 pasteMenu.add(pasteThis);
\r
2226 sort.add(sortIDMenuItem);
\r
2227 sort.add(sortByTreeMenu);
\r
2228 sort.add(sortGroupMenuItem);
\r
2229 sort.add(sortPairwiseMenuItem);
\r
2230 calculate.add(averageDistanceTreeMenuItem);
\r
2231 calculate.add(neighbourTreeMenuItem);
\r
2232 calculate.add(avDistanceTreeBlosumMenuItem);
\r
2233 calculate.add(njTreeBlosumMenuItem);
\r
2234 helpMenu.add(documentation);
\r
2235 helpMenu.add(about);
\r
2236 menu1.add(showColumns);
\r
2237 menu1.add(showSeqs);
\r
2238 menu2.add(hideColumns);
\r
2239 menu2.add(hideSequences);
\r
2242 public void setEmbedded()
\r
2245 embeddedMenu = new Panel();
\r
2246 embeddedEdit = new Label();
\r
2247 embeddedSearch = new Label();
\r
2248 embeddedView = new Label();
\r
2249 embeddedColour = new Label();
\r
2250 embeddedFile = new Label();
\r
2251 embeddedHelp = new Label();
\r
2252 embeddedCalculate = new Label();
\r
2253 flowLayout1 = new FlowLayout();
\r
2254 embeddedMenu.setBackground(Color.lightGray);
\r
2255 embeddedMenu.setLayout(flowLayout1);
\r
2256 embeddedEdit.setText("Edit");
\r
2257 embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2258 embeddedSearch.setText("Search");
\r
2259 embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2260 embeddedView.setText("View");
\r
2261 embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2262 embeddedColour.setText("Colour");
\r
2263 embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2264 embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2265 embeddedFile.setText("File");
\r
2266 embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2267 embeddedHelp.setText("Help");
\r
2268 embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2269 embeddedCalculate.setText("Calculate");
\r
2270 embeddedMenu.add(embeddedFile);
\r
2271 embeddedMenu.add(embeddedEdit);
\r
2272 embeddedMenu.add(embeddedSearch);
\r
2273 embeddedMenu.add(embeddedView);
\r
2274 embeddedMenu.add(embeddedColour);
\r
2275 embeddedMenu.add(embeddedCalculate);
\r
2276 embeddedMenu.add(embeddedHelp);
\r
2277 flowLayout1.setAlignment(FlowLayout.LEFT);
\r
2278 flowLayout1.setHgap(2);
\r
2279 flowLayout1.setVgap(0);
\r
2280 embeddedFile.addMouseListener(this);
\r
2281 embeddedEdit.addMouseListener(this);
\r
2282 embeddedSearch.addMouseListener(this);
\r
2283 embeddedView.addMouseListener(this);
\r
2284 embeddedColour.addMouseListener(this);
\r
2285 embeddedCalculate.addMouseListener(this);
\r
2286 embeddedHelp.addMouseListener(this);
\r
2288 // setVisible(false);
\r
2289 fileMenu.remove(closeMenuItem);
\r
2290 fileMenu.remove(3); // Seperator
\r
2292 viewport.applet.setLayout(new BorderLayout());
\r
2293 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
\r
2294 viewport.applet.add(statusBar, BorderLayout.SOUTH);
\r
2295 // viewport.applet.validate();
\r
2297 alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height
\r
2298 - embeddedMenu.HEIGHT - statusBar.HEIGHT);
\r
2300 viewport.applet.add(alignPanel, BorderLayout.CENTER);
\r
2301 viewport.applet.validate();
\r
2307 PopupMenu filePopup, editPopup, searchPopup,
\r
2308 viewPopup, colourPopup, calculatePopup, helpPopup;
\r
2309 MenuItem featureSettings = new MenuItem();
\r
2310 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
2311 MenuItem annotationColour = new MenuItem();
\r
2312 MenuItem invertColSel = new MenuItem();
\r
2313 Menu menu1 = new Menu();
\r
2314 MenuItem showColumns = new MenuItem();
\r
2315 MenuItem showSeqs = new MenuItem();
\r
2316 Menu menu2 = new Menu();
\r
2317 MenuItem hideColumns = new MenuItem();
\r
2318 MenuItem hideSequences = new MenuItem();
\r
2320 public void mousePressed(MouseEvent evt)
\r
2322 PopupMenu popup = null;
\r
2323 Label source = (Label)evt.getSource();
\r
2324 if(source==embeddedFile)
\r
2326 popup = filePopup = genPopupMenu(filePopup, fileMenu);
\r
2328 else if(source==embeddedEdit)
\r
2330 popup = editPopup = genPopupMenu(editPopup, editMenu);
\r
2332 else if(source==embeddedSearch)
\r
2334 popup = searchPopup = genPopupMenu(searchPopup, searchMenu);
\r
2336 else if(source==embeddedView)
\r
2338 popup = viewPopup = genPopupMenu(viewPopup, viewMenu);
\r
2340 else if(source==embeddedColour)
\r
2342 popup = colourPopup = genPopupMenu(colourPopup, colourMenu);
\r
2344 else if(source==embeddedCalculate)
\r
2346 popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);
\r
2348 else if(source==embeddedHelp)
\r
2350 popup = helpPopup = genPopupMenu(helpPopup, helpMenu);
\r
2353 embeddedMenu.add(popup);
\r
2354 popup.show(embeddedMenu,
\r
2355 source.getBounds().x,
\r
2356 source.getBounds().y + source.getBounds().getSize().height);
\r
2359 PopupMenu genPopupMenu(PopupMenu popup, Menu original)
\r
2365 popup = new PopupMenu();
\r
2366 int m, mSize = original.getItemCount();
\r
2367 for(m=0; m<mSize; m++)
\r
2369 popup.add(original.getItem(m));
\r
2376 public void mouseClicked(MouseEvent evt)
\r
2378 public void mouseReleased(MouseEvent evt)
\r
2380 public void mouseEntered(MouseEvent evt)
\r
2382 public void mouseExited(MouseEvent evt)
\r