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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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 boolean toggleSeqs = !evt.isControlDown();
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335 boolean toggleCols = !evt.isShiftDown();
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336 boolean hide = false;
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337 SequenceGroup sg = viewport.getSelectionGroup();
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341 if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())
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344 viewport.hideAllSelectedSeqs();
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346 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
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347 viewport.showAllHiddenSeqs();
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352 if (viewport.colSel.getSelected().size() > 0)
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354 viewport.hideSelectedColumns();
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356 viewport.selectionGroup = sg;
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359 viewport.showAllHiddenColumns();
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362 alignPanel.repaint();
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368 public void keyReleased(KeyEvent evt)
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370 public void keyTyped(KeyEvent evt)
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373 public void itemStateChanged(ItemEvent evt)
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375 if(evt.getSource()==colourTextMenuItem)
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376 colourTextMenuItem_actionPerformed();
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377 else if(evt.getSource()==wrapMenuItem)
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378 wrapMenuItem_actionPerformed();
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379 else if(evt.getSource()==scaleAbove)
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380 scaleAbove_actionPerformed();
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381 else if(evt.getSource()==scaleLeft)
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382 scaleLeft_actionPerformed();
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383 else if(evt.getSource()==scaleRight)
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384 scaleRight_actionPerformed();
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385 else if(evt.getSource()==seqLimits)
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386 seqLimits_itemStateChanged();
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387 else if(evt.getSource()==viewBoxesMenuItem)
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388 viewBoxesMenuItem_actionPerformed();
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389 else if(evt.getSource()==viewTextMenuItem)
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390 viewTextMenuItem_actionPerformed();
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391 else if(evt.getSource()==renderGapsMenuItem)
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392 renderGapsMenuItem_actionPerformed();
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393 else if(evt.getSource()==annotationPanelMenuItem)
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394 annotationPanelMenuItem_actionPerformed();
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395 else if(evt.getSource()==sequenceFeatures)
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397 viewport.showSequenceFeatures(sequenceFeatures.getState());
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398 alignPanel.seqPanel.seqCanvas.repaint();
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400 else if(evt.getSource()==conservationMenuItem)
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401 conservationMenuItem_actionPerformed();
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402 else if(evt.getSource()==abovePIDThreshold)
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403 abovePIDThreshold_actionPerformed();
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404 else if(evt.getSource()==applyToAllGroups)
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405 applyToAllGroups_actionPerformed();
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406 else if(evt.getSource()==autoCalculate)
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407 viewport.autocalculateConsensus = autoCalculate.getState();
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409 public void actionPerformed(ActionEvent evt)
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411 Object source = evt.getSource();
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413 if(source==inputText)
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414 inputText_actionPerformed();
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415 else if(source==loadTree)
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416 loadTree_actionPerformed();
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417 else if(source==loadApplication)
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418 launchFullApplication();
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419 else if(source==closeMenuItem)
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420 closeMenuItem_actionPerformed();
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421 else if(source==copy)
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422 copy_actionPerformed();
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423 else if(source==undoMenuItem)
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424 undoMenuItem_actionPerformed();
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425 else if(source==redoMenuItem)
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426 redoMenuItem_actionPerformed();
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427 else if(source==inputText)
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428 inputText_actionPerformed();
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429 else if(source==closeMenuItem)
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430 closeMenuItem_actionPerformed();
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431 else if(source==undoMenuItem)
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432 undoMenuItem_actionPerformed();
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433 else if(source==redoMenuItem)
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434 redoMenuItem_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==pasteNew)
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438 pasteNew_actionPerformed();
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439 else if(source==pasteThis)
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440 pasteThis_actionPerformed();
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441 else if(source==cut)
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442 cut_actionPerformed();
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443 else if(source==delete)
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444 delete_actionPerformed();
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445 else if(source==deleteGroups)
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446 deleteGroups_actionPerformed();
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447 else if(source==selectAllSequenceMenuItem)
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448 selectAllSequenceMenuItem_actionPerformed();
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449 else if(source==deselectAllSequenceMenuItem)
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450 deselectAllSequenceMenuItem_actionPerformed();
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451 else if(source==invertSequenceMenuItem)
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452 invertSequenceMenuItem_actionPerformed();
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453 else if(source==invertColSel)
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454 { viewport.invertColumnSelection(); alignPanel.repaint(); }
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455 else if(source==remove2LeftMenuItem)
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456 remove2LeftMenuItem_actionPerformed();
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457 else if(source==remove2RightMenuItem)
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458 remove2RightMenuItem_actionPerformed();
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459 else if(source==removeGappedColumnMenuItem)
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460 removeGappedColumnMenuItem_actionPerformed();
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461 else if(source==removeAllGapsMenuItem)
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462 removeAllGapsMenuItem_actionPerformed();
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463 else if(source==findMenuItem)
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464 findMenuItem_actionPerformed();
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465 else if(source==font)
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466 font_actionPerformed();
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467 else if(source==showColumns)
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469 viewport.showAllHiddenColumns(); alignPanel.repaint();
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471 else if(source==showSeqs)
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473 viewport.showAllHiddenSeqs();
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475 else if(source == hideColumns)
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477 viewport.hideSelectedColumns(); alignPanel.repaint();
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479 else if(source == hideSequences && viewport.getSelectionGroup()!=null)
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481 viewport.hideAllSelectedSeqs();
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483 else if(source==featureSettings)
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484 featureSettings_actionPerformed();
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485 else if(source==overviewMenuItem)
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486 overviewMenuItem_actionPerformed();
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487 else if(source==noColourmenuItem)
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488 noColourmenuItem_actionPerformed();
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489 else if(source==clustalColour)
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490 clustalColour_actionPerformed();
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491 else if(source==zappoColour)
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492 zappoColour_actionPerformed();
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493 else if(source==taylorColour)
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494 taylorColour_actionPerformed();
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495 else if(source==hydrophobicityColour)
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496 hydrophobicityColour_actionPerformed();
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497 else if(source==helixColour)
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498 helixColour_actionPerformed();
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499 else if(source==strandColour)
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500 strandColour_actionPerformed();
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501 else if(source==turnColour)
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502 turnColour_actionPerformed();
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503 else if(source==buriedColour)
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504 buriedColour_actionPerformed();
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505 else if(source==nucleotideColour)
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506 nucleotideColour_actionPerformed();
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507 else if(source==modifyPID)
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508 modifyPID_actionPerformed();
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509 else if(source==modifyConservation)
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510 modifyConservation_actionPerformed();
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511 else if(source==userDefinedColour)
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512 userDefinedColour_actionPerformed();
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513 else if(source==PIDColour)
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514 PIDColour_actionPerformed();
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515 else if(source==BLOSUM62Colour)
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516 BLOSUM62Colour_actionPerformed();
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517 else if(source==annotationColour)
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518 new AnnotationColourChooser(viewport, alignPanel);
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519 else if(source==sortPairwiseMenuItem)
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520 sortPairwiseMenuItem_actionPerformed();
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521 else if(source==sortIDMenuItem)
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522 sortIDMenuItem_actionPerformed();
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523 else if(source==sortGroupMenuItem)
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524 sortGroupMenuItem_actionPerformed();
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525 else if(source==removeRedundancyMenuItem)
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526 removeRedundancyMenuItem_actionPerformed();
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527 else if(source==pairwiseAlignmentMenuItem)
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528 pairwiseAlignmentMenuItem_actionPerformed();
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529 else if(source==PCAMenuItem)
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530 PCAMenuItem_actionPerformed();
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531 else if(source==averageDistanceTreeMenuItem)
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532 averageDistanceTreeMenuItem_actionPerformed();
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533 else if(source==neighbourTreeMenuItem)
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534 neighbourTreeMenuItem_actionPerformed();
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535 else if(source==njTreeBlosumMenuItem)
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536 njTreeBlosumMenuItem_actionPerformed();
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537 else if(source==avDistanceTreeBlosumMenuItem)
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538 avTreeBlosumMenuItem_actionPerformed();
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539 else if(source==documentation)
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540 documentation_actionPerformed();
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541 else if(source==about)
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542 about_actionPerformed();
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546 public void inputText_actionPerformed()
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548 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
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549 Frame frame = new Frame();
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551 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
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554 protected void outputText_actionPerformed(ActionEvent e)
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556 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
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557 Frame frame = new Frame();
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559 jalview.bin.JalviewLite.addFrame(frame,
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560 "Alignment output - " + e.getActionCommand(),
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562 cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
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563 viewport.getAlignment().getSequences(),
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564 viewport.showJVSuffix));
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567 void launchFullApplication()
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569 StringBuffer url = new StringBuffer(jalviewServletURL);
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571 url.append("?open="+
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572 appendProtocol( viewport.applet.getParameter("file") ) );
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574 if(viewport.applet.getParameter("features")!=null)
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576 url.append( "&features=" );
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577 url.append( appendProtocol( viewport.applet.getParameter("features") ) );
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580 if(viewport.applet.getParameter("annotations")!=null)
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582 url.append( "&annotations=" );
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583 url.append( appendProtocol( viewport.applet.getParameter("annotations") ) );
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586 if(viewport.applet.getParameter("jnetfile")!=null)
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588 url.append( "&annotations=" );
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589 url.append( appendProtocol( viewport.applet.getParameter("jnetfile") ) );
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592 if(viewport.applet.getParameter("defaultColour")!=null)
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594 url.append("&colour=" +
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595 removeWhiteSpace(viewport.applet.getParameter("defaultColour"))
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599 if(viewport.applet.getParameter("userDefinedColour")!=null)
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601 url.append( "&colour=" +
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602 removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") )
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606 showURL(url.toString(), "FULL_APP");
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610 String removeWhiteSpace(String colour)
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612 StringBuffer sb = new StringBuffer();
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613 for (int i = 0; i < colour.length(); i++)
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615 if (Character.isWhitespace(colour.charAt(i)))
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618 sb.append(colour.charAt(i));
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621 return sb.toString();
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625 String appendProtocol(String url)
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629 }catch(java.net.MalformedURLException ex)
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631 url = viewport.applet.getCodeBase()+url;
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636 public void closeMenuItem_actionPerformed()
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638 PaintRefresher.components.remove(viewport.alignment);
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639 if(PaintRefresher.components.size()==0 && viewport.applet==null)
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645 Stack historyList = new Stack();
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646 Stack redoList = new Stack();
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648 void updateEditMenuBar()
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650 if (historyList.size() > 0)
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652 undoMenuItem.setEnabled(true);
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653 HistoryItem hi = (HistoryItem) historyList.peek();
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654 undoMenuItem.setLabel("Undo " + hi.getDescription());
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658 undoMenuItem.setEnabled(false);
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659 undoMenuItem.setLabel("Undo");
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662 if (redoList.size() > 0)
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664 redoMenuItem.setEnabled(true);
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665 HistoryItem hi = (HistoryItem) redoList.peek();
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666 redoMenuItem.setLabel("Redo " + hi.getDescription());
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670 redoMenuItem.setEnabled(false);
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671 redoMenuItem.setLabel("Redo");
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675 public void addHistoryItem(HistoryItem hi)
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677 historyList.push(hi);
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678 redoList.removeAllElements();
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679 updateEditMenuBar();
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682 protected void undoMenuItem_actionPerformed()
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684 HistoryItem nh,hi = (HistoryItem) historyList.pop();
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685 redoList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment,
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686 HistoryItem.HIDE));
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687 if (hi.alColumnChanges!=null)
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688 nh.alColumnChanges=hi.alColumnChanges.getInverse();
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689 restoreHistoryItem(hi);
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690 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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693 protected void redoMenuItem_actionPerformed()
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695 HistoryItem nh,hi = (HistoryItem) redoList.pop();
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696 historyList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment,
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697 HistoryItem.HIDE));
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698 if (hi.alColumnChanges!=null)
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699 nh.alColumnChanges=hi.alColumnChanges.getInverse();
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700 restoreHistoryItem(hi);
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701 updateEditMenuBar();
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702 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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705 // used by undo and redo
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706 void restoreHistoryItem(HistoryItem hi)
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708 hi.restore(viewport.getColumnSelection());
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709 updateEditMenuBar();
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711 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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714 public void moveSelectedSequences(boolean up)
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716 SequenceGroup sg = viewport.getSelectionGroup();
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724 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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726 SequenceI seq = viewport.alignment.getSequenceAt(i);
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727 if (!sg.getSequences(false).contains(seq))
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732 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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733 if (sg.getSequences(false).contains(temp))
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738 viewport.alignment.getSequences().setElementAt(temp, i);
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739 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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744 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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746 SequenceI seq = viewport.alignment.getSequenceAt(i);
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747 if (!sg.getSequences(true).contains(seq))
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752 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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753 if (sg.getSequences(true).contains(temp))
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758 viewport.alignment.getSequences().setElementAt(temp, i);
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759 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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763 alignPanel.repaint();
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766 static StringBuffer copiedSequences;
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767 static Vector copiedHiddenColumns;
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768 protected void copy_actionPerformed()
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770 if (viewport.getSelectionGroup() == null)
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775 SequenceGroup sg = viewport.getSelectionGroup();
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776 copiedSequences = new StringBuffer();
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777 Hashtable orderedSeqs = new Hashtable();
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778 for (int i = 0; i < sg.getSize(false); i++)
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780 SequenceI seq = sg.getSequenceAt(i);
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781 int index = viewport.alignment.findIndex(seq);
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782 orderedSeqs.put(index + "", seq);
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785 int index = 0, startRes, endRes;
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788 if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
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790 copiedHiddenColumns = new Vector();
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791 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
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792 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();
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795 int[] region = (int[])
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796 viewport.getColumnSelection().getHiddenColumns().elementAt(i);
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798 copiedHiddenColumns.addElement(new int[]
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799 {region[0] - hiddenOffset,
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800 region[1] - hiddenOffset});
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804 copiedHiddenColumns = null;
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807 for (int i = 0; i < sg.getSize(false); i++)
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809 SequenceI seq = null;
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811 while (seq == null)
\r
813 if (orderedSeqs.containsKey(index + ""))
\r
815 seq = (SequenceI) orderedSeqs.get(index + "");
\r
827 //Returns residue following index if gap
\r
828 startRes = seq.findPosition(sg.getStartRes());
\r
831 //Need to find the residue preceeding index if gap
\r
834 for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
\r
836 ch = seq.getCharAt(j);
\r
837 if (!jalview.util.Comparison.isGap( (ch)))
\r
845 endRes += seq.getStart() -1;
\r
848 copiedSequences.append(seq.getName() + "\t" +
\r
851 seq.getSequence(sg.getStartRes(),
\r
852 sg.getEndRes() + 1) + "\n");
\r
857 protected void pasteNew_actionPerformed()
\r
862 protected void pasteThis_actionPerformed()
\r
864 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
\r
865 HistoryItem.PASTE));
\r
869 void paste(boolean newAlignment)
\r
873 if (copiedSequences == null)
\r
878 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
879 Vector seqs = new Vector();
\r
880 while (st.hasMoreElements())
\r
882 String name = st.nextToken();
\r
883 int start = Integer.parseInt(st.nextToken());
\r
884 int end = Integer.parseInt(st.nextToken());
\r
885 Sequence sequence = new Sequence(name, st.nextToken(), start, end);
\r
889 viewport.alignment.addSequence(sequence);
\r
893 seqs.addElement(sequence);
\r
899 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
900 for (int i = 0; i < seqs.size(); i++)
\r
902 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
905 String newtitle = new String("Copied sequences");
\r
906 if (getTitle().startsWith("Copied sequences"))
\r
908 newtitle = getTitle();
\r
912 newtitle = newtitle.concat("- from " + getTitle());
\r
914 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
918 if (copiedHiddenColumns != null)
\r
920 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
922 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
923 af.viewport.hideColumns(region[0], region[1]);
\r
928 jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
\r
929 NEW_WINDOW_HEIGHT);
\r
933 viewport.setEndSeq(viewport.alignment.getHeight());
\r
934 viewport.alignment.getWidth();
\r
935 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
939 catch (Exception ex)
\r
940 {} // could be anything being pasted in here
\r
944 protected void cut_actionPerformed()
\r
946 copy_actionPerformed();
\r
947 delete_actionPerformed();
\r
950 protected void delete_actionPerformed()
\r
952 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
\r
953 HistoryItem.HIDE));
\r
954 if (viewport.getSelectionGroup() == null)
\r
960 SequenceGroup sg = viewport.getSelectionGroup();
\r
961 boolean allSequences = false;
\r
962 if(sg.getSize(false)==viewport.alignment.getHeight())
\r
963 allSequences = true;
\r
965 for (int i = 0; i < sg.getSize(false); i++)
\r
967 SequenceI seq = sg.getSequenceAt(i);
\r
968 int index = viewport.getAlignment().findIndex(seq);
\r
969 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
\r
971 // If the cut affects all sequences, remove highlighted columns
\r
974 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
975 sg.getEndRes() + 1);
\r
979 if (seq.getSequence().length() < 1)
\r
981 viewport.getAlignment().deleteSequence(seq);
\r
985 viewport.getAlignment().getSequences().setElementAt(seq, index);
\r
989 viewport.setSelectionGroup(null);
\r
990 viewport.alignment.deleteGroup(sg);
\r
991 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
\r
992 if (viewport.getAlignment().getHeight() < 1)
\r
996 this.setVisible(false);
\r
998 catch (Exception ex)
\r
1001 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1005 protected void deleteGroups_actionPerformed()
\r
1007 viewport.alignment.deleteAllGroups();
\r
1008 viewport.setSelectionGroup(null);
\r
1010 alignPanel.repaint();
\r
1013 public void selectAllSequenceMenuItem_actionPerformed()
\r
1015 SequenceGroup sg = new SequenceGroup();
\r
1016 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1018 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
1020 sg.setEndRes(viewport.alignment.getWidth()-1);
\r
1021 viewport.setSelectionGroup(sg);
\r
1022 alignPanel.repaint();
\r
1023 PaintRefresher.Refresh(null, viewport.alignment);
\r
1026 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1028 if(viewport.cursorMode)
\r
1030 alignPanel.seqPanel.keyboardNo1=null;
\r
1031 alignPanel.seqPanel.keyboardNo2=null;
\r
1033 viewport.setSelectionGroup(null);
\r
1034 viewport.getColumnSelection().clear();
\r
1035 viewport.setSelectionGroup(null);
\r
1036 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1037 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1038 alignPanel.repaint();
\r
1039 PaintRefresher.Refresh(null, viewport.alignment);
\r
1042 public void invertSequenceMenuItem_actionPerformed()
\r
1044 SequenceGroup sg = viewport.getSelectionGroup();
\r
1045 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1047 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1050 PaintRefresher.Refresh(null, viewport.alignment);
\r
1053 public void remove2LeftMenuItem_actionPerformed()
\r
1055 ColumnSelection colSel = viewport.getColumnSelection();
\r
1056 if (colSel.size() > 0)
\r
1059 addHistoryItem(edit=new HistoryItem("Remove Left", viewport.alignment,
\r
1060 HistoryItem.HIDE));
\r
1061 int min = colSel.getMin();
\r
1062 viewport.getAlignment().trimLeft(min);
\r
1063 colSel.compensateForEdit(0, min);
\r
1064 edit.addShift(0, min);
\r
1065 if (viewport.getSelectionGroup() != null)
\r
1067 viewport.getSelectionGroup().adjustForRemoveLeft(min);
\r
1070 Vector groups = viewport.alignment.getGroups();
\r
1071 for (int i = 0; i < groups.size(); i++)
\r
1073 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1074 if (!sg.adjustForRemoveLeft(min))
\r
1076 viewport.alignment.deleteGroup(sg);
\r
1079 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1083 public void remove2RightMenuItem_actionPerformed()
\r
1085 ColumnSelection colSel = viewport.getColumnSelection();
\r
1086 if (colSel.size() > 0)
\r
1088 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
\r
1089 HistoryItem.HIDE));
\r
1090 int max = colSel.getMax();
\r
1091 viewport.getAlignment().trimRight(max);
\r
1093 if (viewport.getSelectionGroup() != null)
\r
1095 viewport.getSelectionGroup().adjustForRemoveRight(max);
\r
1098 Vector groups = viewport.alignment.getGroups();
\r
1099 for (int i = 0; i < groups.size(); i++)
\r
1101 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1102 if (!sg.adjustForRemoveRight(max))
\r
1104 viewport.alignment.deleteGroup(sg);
\r
1107 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1112 public void removeGappedColumnMenuItem_actionPerformed()
\r
1115 addHistoryItem(edit=new HistoryItem("Remove Gapped Columns",
\r
1116 viewport.alignment,
\r
1117 HistoryItem.HIDE));
\r
1119 //This is to maintain viewport position on first residue
\r
1120 //of first sequence
\r
1121 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1122 int startRes = seq.findPosition(viewport.startRes);
\r
1124 viewport.getAlignment().removeGaps();
\r
1126 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1128 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1131 public void removeAllGapsMenuItem_actionPerformed()
\r
1133 // TODO: hidden regions should not be touched by removeAllGaps - a minimal number of gaps will remain in alignment segments containing uneven length subsequences
\r
1134 // TODO: columnSelection.compensateforedits should be called (and passed to history item)
\r
1135 HistoryItem editgaps;
\r
1136 addHistoryItem(editgaps=new HistoryItem("Remove Gaps", viewport.alignment,
\r
1137 HistoryItem.HIDE));
\r
1139 //This is to maintain viewport position on first residue
\r
1140 //of first sequence
\r
1141 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1142 int startRes = seq.findPosition(viewport.startRes);
\r
1144 SequenceI current;
\r
1147 int start=0, end = viewport.alignment.getWidth();
\r
1149 if (viewport.getSelectionGroup() != null
\r
1150 && viewport.getSelectionGroup().getSequences(false) != null
\r
1151 && viewport.getSelectionGroup().getSize(false)>0)
\r
1153 seqs = viewport.getSelectionGroup().getSequences(true);
\r
1154 start = viewport.getSelectionGroup().getStartRes();
\r
1155 end = viewport.getSelectionGroup().getEndRes()+1;
\r
1158 seqs = viewport.alignment.getSequences();
\r
1160 /* Commented out regions below are partial implementation of todo above.
\r
1161 * divide start,end into visible chunks, and for each:
\r
1162 int diff=end-start+1;
\r
1164 int dr[] = new int[seqs.size()];
\r
1166 for (int i = 0; i < seqs.size(); i++)
\r
1168 current = (SequenceI) seqs.elementAt(i);
\r
1170 current.removeGaps(start, end);
\r
1171 /*if (d<diff) // can only shift
\r
1177 /* // after the end of each chunk -
\r
1179 // record shift for history.
\r
1180 editgaps.addShift(start, diff);
\r
1181 if (viewport.hasHiddenColumns && diffmax>diff) {
\r
1183 StringBuffer gaps=new StringBuffer(diffmax);
\r
1184 for (int i=0,j=diffmax-diff; i<j; i++)
\r
1185 gaps.append(viewport.getGapCharacter());
\r
1186 for (int i=0, j=seqs.size(); i<j; i++) {
\r
1187 current = (SequenceI) seqs.elementAt(i);
\r
1188 if (dr[i]-diff>0) {
\r
1189 String sq = current.getSequence();
\r
1190 current.setSequence(sq.substring(0, hcend-dr[i])+gaps.substring(0, dr[i]-diff)+sq.substring());
\r
1196 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1197 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1200 public void alignmentChanged()
\r
1202 viewport.alignment.padGaps();
\r
1203 if(viewport.autocalculateConsensus)
\r
1205 viewport.updateConsensus();
\r
1206 viewport.updateConservation();
\r
1209 resetAllColourSchemes();
\r
1210 if(alignPanel.overviewPanel!=null)
\r
1211 alignPanel.overviewPanel.updateOverviewImage();
\r
1213 viewport.alignment.adjustSequenceAnnotations();
\r
1214 alignPanel.repaint();
\r
1217 void resetAllColourSchemes()
\r
1219 ColourSchemeI cs = viewport.globalColourScheme;
\r
1222 if (cs instanceof ClustalxColourScheme)
\r
1224 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
\r
1225 resetClustalX(viewport.alignment.getSequences(),
\r
1226 viewport.alignment.getWidth());
\r
1229 cs.setConsensus(viewport.vconsensus);
\r
1230 if (cs.conservationApplied())
\r
1232 Alignment al = (Alignment) viewport.alignment;
\r
1233 Conservation c = new Conservation("All",
\r
1234 ResidueProperties.propHash, 3,
\r
1235 al.getSequences(), 0,
\r
1236 al.getWidth() - 1);
\r
1238 c.verdict(false, viewport.ConsPercGaps);
\r
1240 cs.setConservation(c);
\r
1244 int s, sSize = viewport.alignment.getGroups().size();
\r
1245 for(s=0; s<sSize; s++)
\r
1247 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
\r
1248 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
\r
1250 ((ClustalxColourScheme)sg.cs).resetClustalX(
\r
1251 sg.getSequences(true), sg.getWidth());
\r
1253 sg.recalcConservation();
\r
1259 public void findMenuItem_actionPerformed()
\r
1261 new Finder(alignPanel);
\r
1264 public void font_actionPerformed()
\r
1266 new FontChooser(alignPanel);
\r
1270 public void seqLimits_itemStateChanged()
\r
1272 viewport.setShowJVSuffix(seqLimits.getState());
\r
1273 alignPanel.fontChanged();
\r
1274 alignPanel.repaint();
\r
1278 protected void colourTextMenuItem_actionPerformed()
\r
1280 viewport.setColourText(colourTextMenuItem.getState());
\r
1281 alignPanel.repaint();
\r
1284 protected void wrapMenuItem_actionPerformed()
\r
1286 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
1287 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
1288 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
1289 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
1290 scaleRight.setEnabled(wrapMenuItem.getState());
\r
1291 alignPanel.repaint();
\r
1295 protected void scaleAbove_actionPerformed()
\r
1297 viewport.setScaleAboveWrapped(scaleAbove.getState());
\r
1298 alignPanel.repaint();
\r
1301 protected void scaleLeft_actionPerformed()
\r
1303 viewport.setScaleLeftWrapped(scaleLeft.getState());
\r
1304 alignPanel.repaint();
\r
1307 protected void scaleRight_actionPerformed()
\r
1309 viewport.setScaleRightWrapped(scaleRight.getState());
\r
1310 alignPanel.repaint();
\r
1313 public void viewBoxesMenuItem_actionPerformed()
\r
1315 viewport.setShowBoxes(viewBoxesMenuItem.getState());
\r
1316 alignPanel.repaint();
\r
1319 public void viewTextMenuItem_actionPerformed()
\r
1321 viewport.setShowText(viewTextMenuItem.getState());
\r
1322 alignPanel.repaint();
\r
1325 protected void renderGapsMenuItem_actionPerformed()
\r
1327 viewport.setRenderGaps(renderGapsMenuItem.getState());
\r
1328 alignPanel.repaint();
\r
1331 public void annotationPanelMenuItem_actionPerformed()
\r
1333 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
\r
1334 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
\r
1337 public void featureSettings_actionPerformed()
\r
1339 new FeatureSettings(viewport, alignPanel);
\r
1342 public void overviewMenuItem_actionPerformed()
\r
1344 if (alignPanel.overviewPanel != null)
\r
1349 Frame frame = new Frame();
\r
1350 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1351 frame.add(overview);
\r
1352 // +50 must allow for applet frame window
\r
1353 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
1354 overview.preferredSize().width,
\r
1355 overview.preferredSize().height + 50);
\r
1358 frame.addWindowListener(new WindowAdapter()
\r
1360 public void windowClosing(WindowEvent e)
\r
1362 alignPanel.setOverviewPanel(null);
\r
1366 alignPanel.setOverviewPanel(overview);
\r
1370 protected void noColourmenuItem_actionPerformed()
\r
1372 changeColour(null);
\r
1375 public void clustalColour_actionPerformed()
\r
1377 abovePIDThreshold.setState(false);
\r
1378 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
\r
1379 viewport.alignment.getWidth()));
\r
1382 public void zappoColour_actionPerformed()
\r
1384 changeColour(new ZappoColourScheme());
\r
1387 public void taylorColour_actionPerformed()
\r
1389 changeColour(new TaylorColourScheme());
\r
1392 public void hydrophobicityColour_actionPerformed()
\r
1394 changeColour(new HydrophobicColourScheme());
\r
1397 public void helixColour_actionPerformed()
\r
1399 changeColour(new HelixColourScheme());
\r
1402 public void strandColour_actionPerformed()
\r
1404 changeColour(new StrandColourScheme());
\r
1407 public void turnColour_actionPerformed()
\r
1409 changeColour(new TurnColourScheme());
\r
1412 public void buriedColour_actionPerformed()
\r
1414 changeColour(new BuriedColourScheme());
\r
1417 public void nucleotideColour_actionPerformed()
\r
1419 changeColour(new NucleotideColourScheme());
\r
1422 protected void applyToAllGroups_actionPerformed()
\r
1424 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
\r
1427 void changeColour(ColourSchemeI cs)
\r
1429 int threshold = 0;
\r
1433 if (viewport.getAbovePIDThreshold())
\r
1435 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
\r
1437 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1439 viewport.setGlobalColourScheme(cs);
\r
1443 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1446 if (viewport.getConservationSelected())
\r
1449 Alignment al = (Alignment) viewport.alignment;
\r
1450 Conservation c = new Conservation("All",
\r
1451 ResidueProperties.propHash, 3,
\r
1452 al.getSequences(), 0,
\r
1453 al.getWidth() - 1);
\r
1456 c.verdict(false, viewport.ConsPercGaps);
\r
1458 cs.setConservation(c);
\r
1460 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1466 cs.setConservation(null);
\r
1469 cs.setConsensus(viewport.vconsensus);
\r
1472 viewport.setGlobalColourScheme(cs);
\r
1474 if (viewport.getColourAppliesToAllGroups())
\r
1476 Vector groups = viewport.alignment.getGroups();
\r
1477 for (int i = 0; i < groups.size(); i++)
\r
1479 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1486 if (cs instanceof ClustalxColourScheme)
\r
1488 sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth());
\r
1494 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1496 catch (Exception ex)
\r
1498 ex.printStackTrace();
\r
1503 if (viewport.getAbovePIDThreshold()
\r
1504 || cs instanceof PIDColourScheme
\r
1505 || cs instanceof Blosum62ColourScheme)
\r
1507 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1508 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth()));
\r
1511 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1513 if (viewport.getConservationSelected())
\r
1515 Conservation c = new Conservation("Group",
\r
1516 ResidueProperties.propHash, 3,
\r
1517 sg.getSequences(true), 0,
\r
1518 viewport.alignment.getWidth() - 1);
\r
1520 c.verdict(false, viewport.ConsPercGaps);
\r
1521 sg.cs.setConservation(c);
\r
1525 sg.cs.setConservation(null);
\r
1526 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1533 if (alignPanel.getOverviewPanel() != null)
\r
1535 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1538 alignPanel.repaint();
\r
1543 protected void modifyPID_actionPerformed()
\r
1545 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1547 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
1549 SliderPanel.showPIDSlider();
\r
1553 protected void modifyConservation_actionPerformed()
\r
1555 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1557 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
1559 SliderPanel.showConservationSlider();
\r
1563 protected void conservationMenuItem_actionPerformed()
\r
1565 viewport.setConservationSelected(conservationMenuItem.getState());
\r
1567 viewport.setAbovePIDThreshold(false);
\r
1568 abovePIDThreshold.setState(false);
\r
1570 changeColour(viewport.getGlobalColourScheme());
\r
1572 modifyConservation_actionPerformed();
\r
1575 public void abovePIDThreshold_actionPerformed()
\r
1577 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
1579 conservationMenuItem.setState(false);
\r
1580 viewport.setConservationSelected(false);
\r
1582 changeColour(viewport.getGlobalColourScheme());
\r
1584 modifyPID_actionPerformed();
\r
1587 public void userDefinedColour_actionPerformed()
\r
1589 new UserDefinedColours(alignPanel, null);
\r
1592 public void PIDColour_actionPerformed()
\r
1594 changeColour(new PIDColourScheme());
\r
1597 public void BLOSUM62Colour_actionPerformed()
\r
1599 changeColour(new Blosum62ColourScheme());
\r
1602 public void sortPairwiseMenuItem_actionPerformed()
\r
1604 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1605 HistoryItem.SORT));
\r
1606 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1607 viewport.getAlignment().getSequenceAt(0));
\r
1608 alignPanel.repaint();
\r
1611 public void sortIDMenuItem_actionPerformed()
\r
1613 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1614 HistoryItem.SORT));
\r
1615 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1616 alignPanel.repaint();
\r
1619 public void sortGroupMenuItem_actionPerformed()
\r
1621 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1622 HistoryItem.SORT));
\r
1623 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1624 alignPanel.repaint();
\r
1628 public void removeRedundancyMenuItem_actionPerformed()
\r
1630 new RedundancyPanel(alignPanel);
\r
1633 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
1635 if (viewport.getSelectionGroup()!=null
\r
1636 && viewport.getSelectionGroup().getSize(false) > 1)
\r
1638 Frame frame = new Frame();
\r
1639 frame.add(new PairwiseAlignPanel(alignPanel));
\r
1640 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
1644 public void PCAMenuItem_actionPerformed()
\r
1646 //are the sequences aligned?
\r
1647 if (!viewport.alignment.isAligned())
\r
1649 SequenceI current;
\r
1650 int Width = viewport.getAlignment().getWidth();
\r
1652 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1655 current = viewport.getAlignment().getSequenceAt(i);
\r
1657 if (current.getLength() < Width)
\r
1659 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1662 alignPanel.repaint();
\r
1665 if ( (viewport.getSelectionGroup() != null &&
\r
1666 viewport.getSelectionGroup().getSize(false) < 4 &&
\r
1667 viewport.getSelectionGroup().getSize(false) > 0)
\r
1668 || viewport.getAlignment().getHeight() < 4)
\r
1675 new PCAPanel(viewport);
\r
1677 catch (java.lang.OutOfMemoryError ex)
\r
1683 public void averageDistanceTreeMenuItem_actionPerformed()
\r
1685 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1688 public void neighbourTreeMenuItem_actionPerformed()
\r
1690 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1693 protected void njTreeBlosumMenuItem_actionPerformed()
\r
1695 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1698 protected void avTreeBlosumMenuItem_actionPerformed()
\r
1700 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1703 void NewTreePanel(String type, String pwType, String title)
\r
1705 //are the sequences aligned?
\r
1706 if (!viewport.alignment.isAligned())
\r
1708 SequenceI current;
\r
1709 int Width = viewport.getAlignment().getWidth();
\r
1711 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1714 current = viewport.getAlignment().getSequenceAt(i);
\r
1716 if (current.getLength() < Width)
\r
1718 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1721 alignPanel.repaint();
\r
1725 if ( (viewport.getSelectionGroup() != null &&
\r
1726 viewport.getSelectionGroup().getSize(false) > 1)
\r
1727 || (viewport.getSelectionGroup() == null
\r
1728 && viewport.alignment.getHeight() > 1))
\r
1730 final TreePanel tp = new TreePanel(viewport,
\r
1734 addTreeMenuItem(tp, title);
\r
1736 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
1740 void loadTree_actionPerformed()
\r
1742 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1743 cap.setText("Paste your Newick tree file here.");
\r
1744 cap.treeImport = true;
\r
1745 Frame frame = new Frame();
\r
1747 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
1750 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
1752 TreePanel tp = new TreePanel(viewport,
\r
1756 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
1757 addTreeMenuItem(tp, treeFile);
\r
1760 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1762 final MenuItem item = new MenuItem(title);
\r
1763 sortByTreeMenu.add(item);
\r
1764 item.addActionListener(new java.awt.event.ActionListener()
\r
1766 public void actionPerformed(ActionEvent evt)
\r
1768 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1769 HistoryItem.SORT));
\r
1770 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1771 alignPanel.repaint();
\r
1775 treePanel.addWindowListener(new WindowAdapter()
\r
1777 public void windowClosing(WindowEvent e)
\r
1779 sortByTreeMenu.remove(item);
\r
1784 protected void documentation_actionPerformed()
\r
1786 showURL("http://www.jalview.org/help.html", "HELP");
\r
1789 protected void about_actionPerformed()
\r
1792 class AboutPanel extends Canvas
\r
1795 public AboutPanel(String version)
\r
1796 { this.version = version; }
\r
1798 public void paint(Graphics g)
\r
1800 g.setColor(Color.white);
\r
1801 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1802 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1803 FontMetrics fm = g.getFontMetrics();
\r
1804 int fh = fm.getHeight();
\r
1806 g.setColor(Color.black);
\r
1807 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
1808 g.drawString("Jalview - Release "+version, 200, y += fh);
\r
1809 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1810 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
1812 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
1815 "For any issues relating to Jalview, email help@jalview.org", x,
\r
1817 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
1818 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
1820 g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh);
\r
1824 String version = "test";
\r
1825 java.net.URL url = getClass().getResource("/.build_properties");
\r
1830 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
1831 url.openStream()));
\r
1833 while ( (line = reader.readLine()) != null)
\r
1835 if (line.indexOf("VERSION") > -1)
\r
1837 version = line.substring(line.indexOf("=") + 1);
\r
1841 catch (Exception ex)
\r
1843 ex.printStackTrace();
\r
1848 Frame frame = new Frame();
\r
1849 frame.add(new AboutPanel(version));
\r
1850 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
\r
1854 public void showURL(String url, String target)
\r
1856 if (viewport.applet == null)
\r
1858 System.out.println("Not running as applet - no browser available.");
\r
1864 System.out.println("Show url: "+url);
\r
1865 viewport.applet.getAppletContext().showDocument(new java.net.URL(url),
\r
1868 catch (Exception ex)
\r
1870 ex.printStackTrace();
\r
1876 //////////////////////////////////////////////////////////////////////////////////
\r
1877 //JBuilder Graphics here
\r
1879 protected MenuBar alignFrameMenuBar = new MenuBar();
\r
1880 protected Menu fileMenu = new Menu("File");
\r
1881 protected MenuItem loadApplication = new MenuItem("View in Full Application");
\r
1882 protected MenuItem loadTree = new MenuItem("Load Associated Tree");
\r
1883 protected MenuItem closeMenuItem = new MenuItem("Close");
\r
1884 protected Menu editMenu = new Menu("Edit");
\r
1885 protected Menu viewMenu = new Menu("View");
\r
1886 protected Menu colourMenu = new Menu("Colour");
\r
1887 protected Menu calculateMenu = new Menu("Calculate");
\r
1888 protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
1889 protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
1890 protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
1891 protected MenuItem remove2LeftMenuItem = new MenuItem();
\r
1892 protected MenuItem remove2RightMenuItem = new MenuItem();
\r
1893 protected MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
1894 protected MenuItem removeAllGapsMenuItem = new MenuItem();
\r
1895 protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
1896 protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
1897 protected MenuItem sortPairwiseMenuItem = new MenuItem();
\r
1898 protected MenuItem sortIDMenuItem = new MenuItem();
\r
1899 protected MenuItem sortGroupMenuItem = new MenuItem();
\r
1900 protected MenuItem removeRedundancyMenuItem = new MenuItem();
\r
1901 protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
1902 protected MenuItem PCAMenuItem = new MenuItem();
\r
1903 protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
1904 protected MenuItem neighbourTreeMenuItem = new MenuItem();
\r
1905 BorderLayout borderLayout1 = new BorderLayout();
\r
1906 public Label statusBar = new Label();
\r
1907 protected Menu outputTextboxMenu = new Menu();
\r
1908 protected MenuItem clustalColour = new MenuItem();
\r
1909 protected MenuItem zappoColour = new MenuItem();
\r
1910 protected MenuItem taylorColour = new MenuItem();
\r
1911 protected MenuItem hydrophobicityColour = new MenuItem();
\r
1912 protected MenuItem helixColour = new MenuItem();
\r
1913 protected MenuItem strandColour = new MenuItem();
\r
1914 protected MenuItem turnColour = new MenuItem();
\r
1915 protected MenuItem buriedColour = new MenuItem();
\r
1916 protected MenuItem userDefinedColour = new MenuItem();
\r
1917 protected MenuItem PIDColour = new MenuItem();
\r
1918 protected MenuItem BLOSUM62Colour = new MenuItem();
\r
1919 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
1920 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
1921 protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
1922 protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
1923 MenuItem overviewMenuItem = new MenuItem();
\r
1924 protected MenuItem undoMenuItem = new MenuItem();
\r
1925 protected MenuItem redoMenuItem = new MenuItem();
\r
1926 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
1927 MenuItem noColourmenuItem = new MenuItem();
\r
1928 protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
1929 protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
1930 MenuItem findMenuItem = new MenuItem();
\r
1931 Menu searchMenu = new Menu();
\r
1932 protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
1933 protected MenuItem nucleotideColour = new MenuItem();
\r
1934 MenuItem deleteGroups = new MenuItem();
\r
1935 MenuItem delete = new MenuItem();
\r
1936 MenuItem copy = new MenuItem();
\r
1937 MenuItem cut = new MenuItem();
\r
1938 Menu pasteMenu = new Menu();
\r
1939 MenuItem pasteNew = new MenuItem();
\r
1940 MenuItem pasteThis = new MenuItem();
\r
1941 protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
1942 protected MenuItem font = new MenuItem();
\r
1943 protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
1944 protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
1945 protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
1946 MenuItem modifyPID = new MenuItem();
\r
1947 MenuItem modifyConservation = new MenuItem();
\r
1948 protected CheckboxMenuItem autoCalculate
\r
1949 = new CheckboxMenuItem("Autocalculate Consensus", true);
\r
1950 protected Menu sortByTreeMenu = new Menu();
\r
1951 Menu sort = new Menu();
\r
1952 Menu calculate = new Menu();
\r
1953 MenuItem inputText = new MenuItem();
\r
1954 Menu helpMenu = new Menu();
\r
1955 MenuItem documentation = new MenuItem();
\r
1956 MenuItem about = new MenuItem();
\r
1957 protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
1958 Panel embeddedMenu;
\r
1959 Label embeddedEdit;
\r
1960 Label embeddedSearch;
\r
1961 Label embeddedView;
\r
1962 Label embeddedColour;
\r
1963 Label embeddedFile;
\r
1964 Label embeddedHelp;
\r
1965 Label embeddedCalculate;
\r
1966 FlowLayout flowLayout1;
\r
1968 private void jbInit() throws Exception {
\r
1970 setMenuBar(alignFrameMenuBar);
\r
1974 // dynamically fill save as menu with available formats
\r
1975 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
1978 item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
1980 item.addActionListener(new java.awt.event.ActionListener()
\r
1982 public void actionPerformed(ActionEvent e)
\r
1984 outputText_actionPerformed(e);
\r
1988 outputTextboxMenu.add(item);
\r
1990 closeMenuItem.addActionListener(this);
\r
1991 loadApplication.addActionListener(this);
\r
1993 loadTree.addActionListener(this);
\r
1994 selectAllSequenceMenuItem.addActionListener(this);
\r
1995 deselectAllSequenceMenuItem.addActionListener(this);
\r
1996 invertSequenceMenuItem.addActionListener(this);
\r
1997 remove2LeftMenuItem.setLabel("Remove Left");
\r
1998 remove2LeftMenuItem.addActionListener(this);
\r
1999 remove2RightMenuItem.setLabel("Remove Right");
\r
2000 remove2RightMenuItem.addActionListener(this);
\r
2001 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
2002 removeGappedColumnMenuItem.addActionListener(this);
\r
2003 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
2004 removeAllGapsMenuItem.addActionListener(this);
\r
2005 viewBoxesMenuItem.setLabel("Boxes");
\r
2006 viewBoxesMenuItem.setState(true);
\r
2007 viewBoxesMenuItem.addItemListener(this);
\r
2008 viewTextMenuItem.setLabel("Text");
\r
2009 viewTextMenuItem.setState(true);
\r
2010 viewTextMenuItem.addItemListener(this);
\r
2011 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
2012 sortPairwiseMenuItem.addActionListener(this);
\r
2013 sortIDMenuItem.setLabel("by ID");
\r
2014 sortIDMenuItem.addActionListener(this);
\r
2015 sortGroupMenuItem.setLabel("by Group");
\r
2016 sortGroupMenuItem.addActionListener(this);
\r
2017 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
2018 removeRedundancyMenuItem.addActionListener(this);
\r
2019 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
2020 pairwiseAlignmentMenuItem.addActionListener(this);
\r
2021 PCAMenuItem.setLabel("Principal Component Analysis");
\r
2022 PCAMenuItem.addActionListener(this);
\r
2023 averageDistanceTreeMenuItem.setLabel(
\r
2024 "Average Distance Using % Identity");
\r
2025 averageDistanceTreeMenuItem.addActionListener(this);
\r
2026 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
2027 neighbourTreeMenuItem.addActionListener(this);
\r
2028 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
2029 statusBar.setBackground(Color.white);
\r
2030 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
2031 statusBar.setText("Status bar");
\r
2032 outputTextboxMenu.setLabel("Output to Textbox");
\r
2033 clustalColour.setLabel("Clustalx");
\r
2035 clustalColour.addActionListener(this);
\r
2036 zappoColour.setLabel("Zappo");
\r
2037 zappoColour.addActionListener(this);
\r
2038 taylorColour.setLabel("Taylor");
\r
2039 taylorColour.addActionListener(this);
\r
2040 hydrophobicityColour.setLabel("Hydrophobicity");
\r
2041 hydrophobicityColour.addActionListener(this);
\r
2042 helixColour.setLabel("Helix Propensity");
\r
2043 helixColour.addActionListener(this);
\r
2044 strandColour.setLabel("Strand Propensity");
\r
2045 strandColour.addActionListener(this);
\r
2046 turnColour.setLabel("Turn Propensity");
\r
2047 turnColour.addActionListener(this);
\r
2048 buriedColour.setLabel("Buried Index");
\r
2049 buriedColour.addActionListener(this);
\r
2050 userDefinedColour.setLabel("User Defined...");
\r
2051 userDefinedColour.addActionListener(this);
\r
2052 PIDColour.setLabel("Percentage Identity");
\r
2053 PIDColour.addActionListener(this);
\r
2054 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
2055 BLOSUM62Colour.addActionListener(this);
\r
2056 avDistanceTreeBlosumMenuItem.setLabel(
\r
2057 "Average Distance Using BLOSUM62");
\r
2058 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
2059 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
2060 njTreeBlosumMenuItem.addActionListener(this);
\r
2061 annotationPanelMenuItem.setLabel("Show Annotations");
\r
2062 annotationPanelMenuItem.addItemListener(this);
\r
2063 colourTextMenuItem.setLabel("Colour Text");
\r
2064 colourTextMenuItem.addItemListener(this);
\r
2065 overviewMenuItem.setLabel("Overview Window");
\r
2066 overviewMenuItem.addActionListener(this);
\r
2067 undoMenuItem.setEnabled(false);
\r
2068 undoMenuItem.setLabel("Undo");
\r
2069 undoMenuItem.addActionListener(this);
\r
2070 redoMenuItem.setEnabled(false);
\r
2071 redoMenuItem.setLabel("Redo");
\r
2072 redoMenuItem.addActionListener(this);
\r
2073 conservationMenuItem.setLabel("by Conservation");
\r
2074 conservationMenuItem.addItemListener(this);
\r
2075 noColourmenuItem.setLabel("None");
\r
2076 noColourmenuItem.addActionListener(this);
\r
2077 wrapMenuItem.setLabel("Wrap");
\r
2078 wrapMenuItem.addItemListener(this);
\r
2079 renderGapsMenuItem.setLabel("Show Gaps");
\r
2080 renderGapsMenuItem.setState(true);
\r
2081 renderGapsMenuItem.addItemListener(this);
\r
2082 findMenuItem.setLabel("Find...");
\r
2083 findMenuItem.addActionListener(this);
\r
2084 searchMenu.setLabel("Search");
\r
2086 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
2087 abovePIDThreshold.addItemListener(this);
\r
2088 nucleotideColour.setLabel("Nucleotide");
\r
2089 nucleotideColour.addActionListener(this);
\r
2090 deleteGroups.setLabel("Undefine Groups");
\r
2091 deleteGroups.addActionListener(this);
\r
2092 copy.setLabel("Copy");
\r
2093 copy.addActionListener(this);
\r
2094 cut.setLabel("Cut");
\r
2095 cut.addActionListener(this);
\r
2096 delete.setLabel("Delete");
\r
2097 delete.addActionListener(this);
\r
2098 pasteMenu.setLabel("Paste");
\r
2099 pasteNew.setLabel("To New Alignment");
\r
2100 pasteNew.addActionListener(this);
\r
2101 pasteThis.setLabel("Add To This Alignment");
\r
2102 pasteThis.addActionListener(this);
\r
2103 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
2104 applyToAllGroups.setState(true);
\r
2105 applyToAllGroups.addItemListener(this);
\r
2106 font.setLabel("Font...");
\r
2107 font.addActionListener(this);
\r
2108 scaleAbove.setLabel("Scale Above");
\r
2109 scaleAbove.setState(true);
\r
2110 scaleAbove.setEnabled(false);
\r
2111 scaleAbove.addItemListener(this);
\r
2112 scaleLeft.setEnabled(false);
\r
2113 scaleLeft.setState(true);
\r
2114 scaleLeft.setLabel("Scale Left");
\r
2115 scaleLeft.addItemListener(this);
\r
2116 scaleRight.setEnabled(false);
\r
2117 scaleRight.setState(true);
\r
2118 scaleRight.setLabel("Scale Right");
\r
2119 scaleRight.addItemListener(this);
\r
2120 modifyPID.setLabel("Modify Identity Threshold...");
\r
2121 modifyPID.addActionListener(this);
\r
2122 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
2123 modifyConservation.addActionListener(this);
\r
2124 sortByTreeMenu.setLabel("By Tree Order");
\r
2125 sort.setLabel("Sort");
\r
2126 calculate.setLabel("Calculate Tree");
\r
2127 autoCalculate.addItemListener(this);
\r
2128 inputText.setLabel("Input from textbox");
\r
2129 inputText.addActionListener(this);
\r
2131 helpMenu.setLabel("Help");
\r
2132 documentation.setLabel("Documentation");
\r
2133 documentation.addActionListener(this);
\r
2135 about.setLabel("About...");
\r
2136 about.addActionListener(this);
\r
2137 seqLimits.setState(true);
\r
2138 seqLimits.setLabel("Show Sequence Limits");
\r
2139 seqLimits.addItemListener(this);
\r
2140 featureSettings.setLabel("Feature Settings...");
\r
2141 featureSettings.addActionListener(this);
\r
2142 sequenceFeatures.setLabel("Sequence Features");
\r
2143 sequenceFeatures.addItemListener(this);
\r
2144 sequenceFeatures.setState(false);
\r
2145 annotationColour.setLabel("by Annotation...");
\r
2146 annotationColour.addActionListener(this);
\r
2147 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
2148 invertColSel.setLabel("Invert Column Selection");
\r
2149 menu1.setLabel("Show");
\r
2150 showColumns.setLabel("All Columns ");
\r
2151 showSeqs.setLabel("All Sequences");
\r
2152 menu2.setLabel("Hide");
\r
2153 hideColumns.setLabel("Selected Columns");
\r
2154 hideSequences.setLabel("Selected Sequences");
\r
2155 invertColSel.addActionListener(this);
\r
2156 showColumns.addActionListener(this);
\r
2157 showSeqs.addActionListener(this);
\r
2158 hideColumns.addActionListener(this);
\r
2159 hideSequences.addActionListener(this);
\r
2162 alignFrameMenuBar.add(fileMenu);
\r
2163 alignFrameMenuBar.add(editMenu);
\r
2164 alignFrameMenuBar.add(searchMenu);
\r
2165 alignFrameMenuBar.add(viewMenu);
\r
2166 alignFrameMenuBar.add(colourMenu);
\r
2167 alignFrameMenuBar.add(calculateMenu);
\r
2168 alignFrameMenuBar.add(helpMenu);
\r
2169 fileMenu.add(inputText);
\r
2170 fileMenu.add(outputTextboxMenu);
\r
2171 if(jalviewServletURL!=null)
\r
2172 fileMenu.add(loadApplication);
\r
2173 fileMenu.addSeparator();
\r
2174 fileMenu.add(loadTree);
\r
2175 fileMenu.add(closeMenuItem);
\r
2176 editMenu.add(undoMenuItem);
\r
2177 editMenu.add(redoMenuItem);
\r
2178 editMenu.add(cut);
\r
2179 editMenu.add(copy);
\r
2180 editMenu.add(pasteMenu);
\r
2181 editMenu.add(delete);
\r
2182 editMenu.addSeparator();
\r
2183 editMenu.add(selectAllSequenceMenuItem);
\r
2184 editMenu.add(deselectAllSequenceMenuItem);
\r
2185 editMenu.add(invertSequenceMenuItem);
\r
2186 editMenu.add(invertColSel);
\r
2187 editMenu.add(deleteGroups);
\r
2188 editMenu.addSeparator();
\r
2189 editMenu.add(remove2LeftMenuItem);
\r
2190 editMenu.add(remove2RightMenuItem);
\r
2191 editMenu.add(removeGappedColumnMenuItem);
\r
2192 editMenu.add(removeAllGapsMenuItem);
\r
2193 editMenu.add(removeRedundancyMenuItem);
\r
2194 searchMenu.add(findMenuItem);
\r
2195 viewMenu.add(font);
\r
2196 viewMenu.addSeparator();
\r
2197 viewMenu.add(menu1);
\r
2198 viewMenu.add(menu2);
\r
2199 viewMenu.addSeparator();
\r
2200 viewMenu.add(wrapMenuItem);
\r
2201 viewMenu.add(scaleAbove);
\r
2202 viewMenu.add(scaleLeft);
\r
2203 viewMenu.add(scaleRight);
\r
2204 viewMenu.addSeparator();
\r
2205 viewMenu.add(seqLimits);
\r
2206 viewMenu.add(viewBoxesMenuItem);
\r
2207 viewMenu.add(viewTextMenuItem);
\r
2208 viewMenu.add(colourTextMenuItem);
\r
2209 viewMenu.add(renderGapsMenuItem);
\r
2210 viewMenu.add(annotationPanelMenuItem);
\r
2211 viewMenu.addSeparator();
\r
2212 viewMenu.add(sequenceFeatures);
\r
2213 viewMenu.add(featureSettings);
\r
2214 viewMenu.addSeparator();
\r
2215 viewMenu.add(overviewMenuItem);
\r
2216 colourMenu.add(applyToAllGroups);
\r
2217 colourMenu.addSeparator();
\r
2218 colourMenu.add(noColourmenuItem);
\r
2219 colourMenu.add(clustalColour);
\r
2220 colourMenu.add(BLOSUM62Colour);
\r
2221 colourMenu.add(PIDColour);
\r
2222 colourMenu.add(zappoColour);
\r
2223 colourMenu.add(taylorColour);
\r
2224 colourMenu.add(hydrophobicityColour);
\r
2225 colourMenu.add(helixColour);
\r
2226 colourMenu.add(strandColour);
\r
2227 colourMenu.add(turnColour);
\r
2228 colourMenu.add(buriedColour);
\r
2229 colourMenu.add(nucleotideColour);
\r
2230 colourMenu.add(userDefinedColour);
\r
2231 colourMenu.addSeparator();
\r
2232 colourMenu.add(conservationMenuItem);
\r
2233 colourMenu.add(modifyConservation);
\r
2234 colourMenu.add(abovePIDThreshold);
\r
2235 colourMenu.add(modifyPID);
\r
2236 colourMenu.add(annotationColour);
\r
2237 calculateMenu.add(sort);
\r
2238 calculateMenu.add(calculate);
\r
2239 calculateMenu.addSeparator();
\r
2240 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
2241 calculateMenu.add(PCAMenuItem);
\r
2242 calculateMenu.add(autoCalculate);
\r
2243 this.add(statusBar, BorderLayout.SOUTH);
\r
2244 pasteMenu.add(pasteNew);
\r
2245 pasteMenu.add(pasteThis);
\r
2246 sort.add(sortIDMenuItem);
\r
2247 sort.add(sortByTreeMenu);
\r
2248 sort.add(sortGroupMenuItem);
\r
2249 sort.add(sortPairwiseMenuItem);
\r
2250 calculate.add(averageDistanceTreeMenuItem);
\r
2251 calculate.add(neighbourTreeMenuItem);
\r
2252 calculate.add(avDistanceTreeBlosumMenuItem);
\r
2253 calculate.add(njTreeBlosumMenuItem);
\r
2254 helpMenu.add(documentation);
\r
2255 helpMenu.add(about);
\r
2256 menu1.add(showColumns);
\r
2257 menu1.add(showSeqs);
\r
2258 menu2.add(hideColumns);
\r
2259 menu2.add(hideSequences);
\r
2262 public void setEmbedded()
\r
2265 embeddedMenu = new Panel();
\r
2266 embeddedEdit = new Label();
\r
2267 embeddedSearch = new Label();
\r
2268 embeddedView = new Label();
\r
2269 embeddedColour = new Label();
\r
2270 embeddedFile = new Label();
\r
2271 embeddedHelp = new Label();
\r
2272 embeddedCalculate = new Label();
\r
2273 flowLayout1 = new FlowLayout();
\r
2274 embeddedMenu.setBackground(Color.lightGray);
\r
2275 embeddedMenu.setLayout(flowLayout1);
\r
2276 embeddedEdit.setText("Edit");
\r
2277 embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2278 embeddedSearch.setText("Search");
\r
2279 embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2280 embeddedView.setText("View");
\r
2281 embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2282 embeddedColour.setText("Colour");
\r
2283 embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2284 embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2285 embeddedFile.setText("File");
\r
2286 embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2287 embeddedHelp.setText("Help");
\r
2288 embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2289 embeddedCalculate.setText("Calculate");
\r
2290 embeddedMenu.add(embeddedFile);
\r
2291 embeddedMenu.add(embeddedEdit);
\r
2292 embeddedMenu.add(embeddedSearch);
\r
2293 embeddedMenu.add(embeddedView);
\r
2294 embeddedMenu.add(embeddedColour);
\r
2295 embeddedMenu.add(embeddedCalculate);
\r
2296 embeddedMenu.add(embeddedHelp);
\r
2297 flowLayout1.setAlignment(FlowLayout.LEFT);
\r
2298 flowLayout1.setHgap(2);
\r
2299 flowLayout1.setVgap(0);
\r
2300 embeddedFile.addMouseListener(this);
\r
2301 embeddedEdit.addMouseListener(this);
\r
2302 embeddedSearch.addMouseListener(this);
\r
2303 embeddedView.addMouseListener(this);
\r
2304 embeddedColour.addMouseListener(this);
\r
2305 embeddedCalculate.addMouseListener(this);
\r
2306 embeddedHelp.addMouseListener(this);
\r
2308 // setVisible(false);
\r
2309 fileMenu.remove(closeMenuItem);
\r
2310 fileMenu.remove(3); // Seperator
\r
2312 viewport.applet.setLayout(new BorderLayout());
\r
2313 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
\r
2314 viewport.applet.add(statusBar, BorderLayout.SOUTH);
\r
2315 // viewport.applet.validate();
\r
2317 alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height
\r
2318 - embeddedMenu.HEIGHT - statusBar.HEIGHT);
\r
2320 viewport.applet.add(alignPanel, BorderLayout.CENTER);
\r
2321 viewport.applet.validate();
\r
2327 PopupMenu filePopup, editPopup, searchPopup,
\r
2328 viewPopup, colourPopup, calculatePopup, helpPopup;
\r
2329 MenuItem featureSettings = new MenuItem();
\r
2330 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
2331 MenuItem annotationColour = new MenuItem();
\r
2332 MenuItem invertColSel = new MenuItem();
\r
2333 Menu menu1 = new Menu();
\r
2334 MenuItem showColumns = new MenuItem();
\r
2335 MenuItem showSeqs = new MenuItem();
\r
2336 Menu menu2 = new Menu();
\r
2337 MenuItem hideColumns = new MenuItem();
\r
2338 MenuItem hideSequences = new MenuItem();
\r
2340 public void mousePressed(MouseEvent evt)
\r
2342 PopupMenu popup = null;
\r
2343 Label source = (Label)evt.getSource();
\r
2344 if(source==embeddedFile)
\r
2346 popup = filePopup = genPopupMenu(filePopup, fileMenu);
\r
2348 else if(source==embeddedEdit)
\r
2350 popup = editPopup = genPopupMenu(editPopup, editMenu);
\r
2352 else if(source==embeddedSearch)
\r
2354 popup = searchPopup = genPopupMenu(searchPopup, searchMenu);
\r
2356 else if(source==embeddedView)
\r
2358 popup = viewPopup = genPopupMenu(viewPopup, viewMenu);
\r
2360 else if(source==embeddedColour)
\r
2362 popup = colourPopup = genPopupMenu(colourPopup, colourMenu);
\r
2364 else if(source==embeddedCalculate)
\r
2366 popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);
\r
2368 else if(source==embeddedHelp)
\r
2370 popup = helpPopup = genPopupMenu(helpPopup, helpMenu);
\r
2373 embeddedMenu.add(popup);
\r
2374 popup.show(embeddedMenu,
\r
2375 source.getBounds().x,
\r
2376 source.getBounds().y + source.getBounds().getSize().height);
\r
2379 PopupMenu genPopupMenu(PopupMenu popup, Menu original)
\r
2385 popup = new PopupMenu();
\r
2386 int m, mSize = original.getItemCount();
\r
2387 for(m=0; m<mSize; m++)
\r
2389 popup.add(original.getItem(m));
\r
2396 public void mouseClicked(MouseEvent evt)
\r
2398 public void mouseReleased(MouseEvent evt)
\r
2400 public void mouseEntered(MouseEvent evt)
\r
2402 public void mouseExited(MouseEvent evt)
\r