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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264 || evt.isShiftDown()
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270 case KeyEvent.VK_DELETE:
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271 case KeyEvent.VK_BACK_SPACE:
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272 if(viewport.cursorMode)
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274 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
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275 || evt.isShiftDown()
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281 cut_actionPerformed();
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282 alignPanel.seqPanel.seqCanvas.repaint();
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286 case KeyEvent.VK_S:
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287 if(viewport.cursorMode)
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289 alignPanel.seqPanel.setCursorRow();
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292 case KeyEvent.VK_P:
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293 if(viewport.cursorMode)
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295 alignPanel.seqPanel.setCursorPosition();
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299 case KeyEvent.VK_ENTER:
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300 case KeyEvent.VK_COMMA:
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301 if(viewport.cursorMode)
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303 alignPanel.seqPanel.setCursorRowAndColumn();
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307 case KeyEvent.VK_Q:
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308 if(viewport.cursorMode)
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310 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
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313 case KeyEvent.VK_M:
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314 if(viewport.cursorMode)
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316 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
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320 case KeyEvent.VK_F2:
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321 viewport.cursorMode = ! viewport.cursorMode;
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322 statusBar.setText("Keyboard editing mode is "+
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323 (viewport.cursorMode ? "on" : "off"));
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324 if(viewport.cursorMode)
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326 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
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327 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
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329 alignPanel.seqPanel.seqCanvas.repaint();
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332 case KeyEvent.VK_F:
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333 if (evt.isControlDown())
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335 findMenuItem_actionPerformed();
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338 case KeyEvent.VK_H:
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340 boolean toggleSeqs = !evt.isControlDown();
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341 boolean toggleCols = !evt.isShiftDown();
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342 boolean hide = false;
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343 SequenceGroup sg = viewport.getSelectionGroup();
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347 if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())
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350 viewport.hideAllSelectedSeqs();
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352 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
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353 viewport.showAllHiddenSeqs();
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358 if (viewport.colSel.getSelected().size() > 0)
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360 viewport.hideSelectedColumns();
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362 viewport.selectionGroup = sg;
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365 viewport.showAllHiddenColumns();
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368 alignPanel.repaint();
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374 public void keyReleased(KeyEvent evt)
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376 public void keyTyped(KeyEvent evt)
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379 public void itemStateChanged(ItemEvent evt)
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381 if(evt.getSource()==colourTextMenuItem)
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382 colourTextMenuItem_actionPerformed();
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383 else if(evt.getSource()==wrapMenuItem)
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384 wrapMenuItem_actionPerformed();
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385 else if(evt.getSource()==scaleAbove)
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386 scaleAbove_actionPerformed();
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387 else if(evt.getSource()==scaleLeft)
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388 scaleLeft_actionPerformed();
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389 else if(evt.getSource()==scaleRight)
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390 scaleRight_actionPerformed();
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391 else if(evt.getSource()==seqLimits)
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392 seqLimits_itemStateChanged();
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393 else if(evt.getSource()==viewBoxesMenuItem)
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394 viewBoxesMenuItem_actionPerformed();
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395 else if(evt.getSource()==viewTextMenuItem)
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396 viewTextMenuItem_actionPerformed();
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397 else if(evt.getSource()==renderGapsMenuItem)
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398 renderGapsMenuItem_actionPerformed();
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399 else if(evt.getSource()==annotationPanelMenuItem)
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400 annotationPanelMenuItem_actionPerformed();
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401 else if(evt.getSource()==sequenceFeatures)
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403 viewport.showSequenceFeatures(sequenceFeatures.getState());
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404 alignPanel.seqPanel.seqCanvas.repaint();
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406 else if(evt.getSource()==conservationMenuItem)
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407 conservationMenuItem_actionPerformed();
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408 else if(evt.getSource()==abovePIDThreshold)
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409 abovePIDThreshold_actionPerformed();
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410 else if(evt.getSource()==applyToAllGroups)
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411 applyToAllGroups_actionPerformed();
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412 else if(evt.getSource()==autoCalculate)
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413 viewport.autocalculateConsensus = autoCalculate.getState();
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415 public void actionPerformed(ActionEvent evt)
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417 Object source = evt.getSource();
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419 if(source==inputText)
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420 inputText_actionPerformed();
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421 else if(source==loadTree)
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422 loadTree_actionPerformed();
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423 else if(source==loadApplication)
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424 launchFullApplication();
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425 else if(source==closeMenuItem)
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426 closeMenuItem_actionPerformed();
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427 else if(source==copy)
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428 copy_actionPerformed();
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429 else if(source==undoMenuItem)
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430 undoMenuItem_actionPerformed();
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431 else if(source==redoMenuItem)
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432 redoMenuItem_actionPerformed();
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433 else if(source==inputText)
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434 inputText_actionPerformed();
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435 else if(source==closeMenuItem)
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436 closeMenuItem_actionPerformed();
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437 else if(source==undoMenuItem)
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438 undoMenuItem_actionPerformed();
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439 else if(source==redoMenuItem)
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440 redoMenuItem_actionPerformed();
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441 else if(source==copy)
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442 copy_actionPerformed();
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443 else if(source==pasteNew)
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444 pasteNew_actionPerformed();
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445 else if(source==pasteThis)
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446 pasteThis_actionPerformed();
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447 else if(source==cut)
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448 cut_actionPerformed();
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449 else if(source==delete)
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450 delete_actionPerformed();
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451 else if(source==deleteGroups)
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452 deleteGroups_actionPerformed();
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453 else if(source==selectAllSequenceMenuItem)
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454 selectAllSequenceMenuItem_actionPerformed();
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455 else if(source==deselectAllSequenceMenuItem)
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456 deselectAllSequenceMenuItem_actionPerformed();
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457 else if(source==invertSequenceMenuItem)
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458 invertSequenceMenuItem_actionPerformed();
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459 else if(source==invertColSel)
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460 { viewport.invertColumnSelection(); alignPanel.repaint(); }
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461 else if(source==remove2LeftMenuItem)
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462 remove2LeftMenuItem_actionPerformed();
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463 else if(source==remove2RightMenuItem)
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464 remove2RightMenuItem_actionPerformed();
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465 else if(source==removeGappedColumnMenuItem)
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466 removeGappedColumnMenuItem_actionPerformed();
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467 else if(source==removeAllGapsMenuItem)
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468 removeAllGapsMenuItem_actionPerformed();
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469 else if(source==findMenuItem)
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470 findMenuItem_actionPerformed();
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471 else if(source==font)
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472 font_actionPerformed();
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473 else if(source==showColumns)
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475 viewport.showAllHiddenColumns(); alignPanel.repaint();
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477 else if(source==showSeqs)
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479 viewport.showAllHiddenSeqs();
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481 else if(source == hideColumns)
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483 viewport.hideSelectedColumns(); alignPanel.repaint();
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485 else if(source == hideSequences && viewport.getSelectionGroup()!=null)
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487 viewport.hideAllSelectedSeqs();
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489 else if(source==featureSettings)
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490 featureSettings_actionPerformed();
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491 else if(source==overviewMenuItem)
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492 overviewMenuItem_actionPerformed();
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493 else if(source==noColourmenuItem)
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494 noColourmenuItem_actionPerformed();
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495 else if(source==clustalColour)
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496 clustalColour_actionPerformed();
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497 else if(source==zappoColour)
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498 zappoColour_actionPerformed();
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499 else if(source==taylorColour)
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500 taylorColour_actionPerformed();
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501 else if(source==hydrophobicityColour)
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502 hydrophobicityColour_actionPerformed();
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503 else if(source==helixColour)
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504 helixColour_actionPerformed();
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505 else if(source==strandColour)
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506 strandColour_actionPerformed();
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507 else if(source==turnColour)
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508 turnColour_actionPerformed();
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509 else if(source==buriedColour)
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510 buriedColour_actionPerformed();
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511 else if(source==nucleotideColour)
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512 nucleotideColour_actionPerformed();
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513 else if(source==modifyPID)
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514 modifyPID_actionPerformed();
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515 else if(source==modifyConservation)
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516 modifyConservation_actionPerformed();
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517 else if(source==userDefinedColour)
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518 userDefinedColour_actionPerformed();
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519 else if(source==PIDColour)
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520 PIDColour_actionPerformed();
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521 else if(source==BLOSUM62Colour)
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522 BLOSUM62Colour_actionPerformed();
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523 else if(source==annotationColour)
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524 new AnnotationColourChooser(viewport, alignPanel);
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525 else if(source==sortPairwiseMenuItem)
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526 sortPairwiseMenuItem_actionPerformed();
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527 else if(source==sortIDMenuItem)
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528 sortIDMenuItem_actionPerformed();
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529 else if(source==sortGroupMenuItem)
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530 sortGroupMenuItem_actionPerformed();
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531 else if(source==removeRedundancyMenuItem)
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532 removeRedundancyMenuItem_actionPerformed();
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533 else if(source==pairwiseAlignmentMenuItem)
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534 pairwiseAlignmentMenuItem_actionPerformed();
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535 else if(source==PCAMenuItem)
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536 PCAMenuItem_actionPerformed();
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537 else if(source==averageDistanceTreeMenuItem)
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538 averageDistanceTreeMenuItem_actionPerformed();
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539 else if(source==neighbourTreeMenuItem)
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540 neighbourTreeMenuItem_actionPerformed();
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541 else if(source==njTreeBlosumMenuItem)
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542 njTreeBlosumMenuItem_actionPerformed();
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543 else if(source==avDistanceTreeBlosumMenuItem)
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544 avTreeBlosumMenuItem_actionPerformed();
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545 else if(source==documentation)
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546 documentation_actionPerformed();
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547 else if(source==about)
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548 about_actionPerformed();
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552 public void inputText_actionPerformed()
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554 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
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555 Frame frame = new Frame();
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557 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
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560 protected void outputText_actionPerformed(ActionEvent e)
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562 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
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563 Frame frame = new Frame();
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565 jalview.bin.JalviewLite.addFrame(frame,
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566 "Alignment output - " + e.getActionCommand(),
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568 cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
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569 viewport.getAlignment().getSequences(),
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570 viewport.showJVSuffix));
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573 void launchFullApplication()
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575 StringBuffer url = new StringBuffer(jalviewServletURL);
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577 url.append("?open="+
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578 appendProtocol( viewport.applet.getParameter("file") ) );
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580 if(viewport.applet.getParameter("features")!=null)
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582 url.append( "&features=" );
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583 url.append( appendProtocol( viewport.applet.getParameter("features") ) );
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586 if(viewport.applet.getParameter("annotations")!=null)
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588 url.append( "&annotations=" );
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589 url.append( appendProtocol( viewport.applet.getParameter("annotations") ) );
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592 if(viewport.applet.getParameter("jnetfile")!=null)
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594 url.append( "&annotations=" );
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595 url.append( appendProtocol( viewport.applet.getParameter("jnetfile") ) );
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598 if(viewport.applet.getParameter("defaultColour")!=null)
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600 url.append("&colour=" +
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601 removeWhiteSpace(viewport.applet.getParameter("defaultColour"))
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605 if(viewport.applet.getParameter("userDefinedColour")!=null)
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607 url.append( "&colour=" +
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608 removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") )
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612 showURL(url.toString(), "FULL_APP");
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616 String removeWhiteSpace(String colour)
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618 StringBuffer sb = new StringBuffer();
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619 for (int i = 0; i < colour.length(); i++)
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621 if (Character.isWhitespace(colour.charAt(i)))
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624 sb.append(colour.charAt(i));
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627 return sb.toString();
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631 String appendProtocol(String url)
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635 }catch(java.net.MalformedURLException ex)
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637 url = viewport.applet.getCodeBase()+url;
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642 public void closeMenuItem_actionPerformed()
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644 PaintRefresher.components.remove(viewport.alignment);
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645 if(PaintRefresher.components.size()==0 && viewport.applet==null)
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651 Stack historyList = new Stack();
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652 Stack redoList = new Stack();
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654 void updateEditMenuBar()
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656 if (historyList.size() > 0)
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658 undoMenuItem.setEnabled(true);
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659 HistoryItem hi = (HistoryItem) historyList.peek();
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660 undoMenuItem.setLabel("Undo " + hi.getDescription());
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664 undoMenuItem.setEnabled(false);
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665 undoMenuItem.setLabel("Undo");
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668 if (redoList.size() > 0)
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670 redoMenuItem.setEnabled(true);
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671 HistoryItem hi = (HistoryItem) redoList.peek();
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672 redoMenuItem.setLabel("Redo " + hi.getDescription());
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676 redoMenuItem.setEnabled(false);
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677 redoMenuItem.setLabel("Redo");
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681 public void addHistoryItem(HistoryItem hi)
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683 historyList.push(hi);
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684 redoList.removeAllElements();
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685 updateEditMenuBar();
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688 protected void undoMenuItem_actionPerformed()
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690 HistoryItem nh,hi = (HistoryItem) historyList.pop();
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691 redoList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment,
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692 HistoryItem.HIDE));
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693 if (hi.alColumnChanges!=null)
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694 nh.alColumnChanges=hi.alColumnChanges.getInverse();
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695 restoreHistoryItem(hi);
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696 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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699 protected void redoMenuItem_actionPerformed()
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701 HistoryItem nh,hi = (HistoryItem) redoList.pop();
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702 historyList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment,
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703 HistoryItem.HIDE));
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704 if (hi.alColumnChanges!=null)
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705 nh.alColumnChanges=hi.alColumnChanges.getInverse();
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706 restoreHistoryItem(hi);
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707 updateEditMenuBar();
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708 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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711 // used by undo and redo
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712 void restoreHistoryItem(HistoryItem hi)
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714 hi.restore(viewport.getColumnSelection());
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715 updateEditMenuBar();
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717 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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720 public void moveSelectedSequences(boolean up)
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722 SequenceGroup sg = viewport.getSelectionGroup();
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730 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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732 SequenceI seq = viewport.alignment.getSequenceAt(i);
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733 if (!sg.getSequences(false).contains(seq))
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738 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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739 if (sg.getSequences(false).contains(temp))
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744 viewport.alignment.getSequences().setElementAt(temp, i);
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745 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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750 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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752 SequenceI seq = viewport.alignment.getSequenceAt(i);
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753 if (!sg.getSequences(true).contains(seq))
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758 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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759 if (sg.getSequences(true).contains(temp))
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764 viewport.alignment.getSequences().setElementAt(temp, i);
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765 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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769 alignPanel.repaint();
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772 static StringBuffer copiedSequences;
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773 static Vector copiedHiddenColumns;
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774 protected void copy_actionPerformed()
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776 if (viewport.getSelectionGroup() == null)
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781 SequenceGroup sg = viewport.getSelectionGroup();
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782 copiedSequences = new StringBuffer();
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783 Hashtable orderedSeqs = new Hashtable();
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784 for (int i = 0; i < sg.getSize(false); i++)
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786 SequenceI seq = sg.getSequenceAt(i);
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787 int index = viewport.alignment.findIndex(seq);
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788 orderedSeqs.put(index + "", seq);
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791 int index = 0, startRes, endRes;
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794 if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
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796 copiedHiddenColumns = new Vector();
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797 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
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798 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();
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801 int[] region = (int[])
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802 viewport.getColumnSelection().getHiddenColumns().elementAt(i);
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804 copiedHiddenColumns.addElement(new int[]
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805 {region[0] - hiddenOffset,
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806 region[1] - hiddenOffset});
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810 copiedHiddenColumns = null;
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813 for (int i = 0; i < sg.getSize(false); i++)
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815 SequenceI seq = null;
\r
817 while (seq == null)
\r
819 if (orderedSeqs.containsKey(index + ""))
\r
821 seq = (SequenceI) orderedSeqs.get(index + "");
\r
833 //Returns residue following index if gap
\r
834 startRes = seq.findPosition(sg.getStartRes());
\r
837 //Need to find the residue preceeding index if gap
\r
840 for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
\r
842 ch = seq.getCharAt(j);
\r
843 if (!jalview.util.Comparison.isGap( (ch)))
\r
851 endRes += seq.getStart() -1;
\r
854 copiedSequences.append(seq.getName() + "\t" +
\r
857 seq.getSequence(sg.getStartRes(),
\r
858 sg.getEndRes() + 1) + "\n");
\r
863 protected void pasteNew_actionPerformed()
\r
868 protected void pasteThis_actionPerformed()
\r
870 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
\r
871 HistoryItem.PASTE));
\r
875 void paste(boolean newAlignment)
\r
879 if (copiedSequences == null)
\r
884 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
885 Vector seqs = new Vector();
\r
886 while (st.hasMoreElements())
\r
888 String name = st.nextToken();
\r
889 int start = Integer.parseInt(st.nextToken());
\r
890 int end = Integer.parseInt(st.nextToken());
\r
891 Sequence sequence = new Sequence(name, st.nextToken(), start, end);
\r
895 viewport.alignment.addSequence(sequence);
\r
899 seqs.addElement(sequence);
\r
905 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
906 for (int i = 0; i < seqs.size(); i++)
\r
908 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
911 String newtitle = new String("Copied sequences");
\r
912 if (getTitle().startsWith("Copied sequences"))
\r
914 newtitle = getTitle();
\r
918 newtitle = newtitle.concat("- from " + getTitle());
\r
920 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
924 if (copiedHiddenColumns != null)
\r
926 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
928 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
929 af.viewport.hideColumns(region[0], region[1]);
\r
934 jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
\r
935 NEW_WINDOW_HEIGHT);
\r
939 viewport.setEndSeq(viewport.alignment.getHeight());
\r
940 viewport.alignment.getWidth();
\r
941 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
945 catch (Exception ex)
\r
946 {} // could be anything being pasted in here
\r
950 protected void cut_actionPerformed()
\r
952 copy_actionPerformed();
\r
953 delete_actionPerformed();
\r
956 protected void delete_actionPerformed()
\r
958 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
\r
959 HistoryItem.HIDE));
\r
960 if (viewport.getSelectionGroup() == null)
\r
966 SequenceGroup sg = viewport.getSelectionGroup();
\r
967 boolean allSequences = false;
\r
968 if(sg.getSize(false)==viewport.alignment.getHeight())
\r
969 allSequences = true;
\r
971 for (int i = 0; i < sg.getSize(false); i++)
\r
973 SequenceI seq = sg.getSequenceAt(i);
\r
974 int index = viewport.getAlignment().findIndex(seq);
\r
975 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
\r
977 // If the cut affects all sequences, remove highlighted columns
\r
980 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
981 sg.getEndRes() + 1);
\r
985 if (seq.getSequence().length() < 1)
\r
987 viewport.getAlignment().deleteSequence(seq);
\r
991 viewport.getAlignment().getSequences().setElementAt(seq, index);
\r
995 viewport.setSelectionGroup(null);
\r
996 viewport.alignment.deleteGroup(sg);
\r
997 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
\r
998 if (viewport.getAlignment().getHeight() < 1)
\r
1002 this.setVisible(false);
\r
1004 catch (Exception ex)
\r
1007 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1011 protected void deleteGroups_actionPerformed()
\r
1013 viewport.alignment.deleteAllGroups();
\r
1014 viewport.setSelectionGroup(null);
\r
1016 alignPanel.repaint();
\r
1019 public void selectAllSequenceMenuItem_actionPerformed()
\r
1021 SequenceGroup sg = new SequenceGroup();
\r
1022 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1024 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
1026 sg.setEndRes(viewport.alignment.getWidth()-1);
\r
1027 viewport.setSelectionGroup(sg);
\r
1028 alignPanel.repaint();
\r
1029 PaintRefresher.Refresh(null, viewport.alignment);
\r
1032 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1034 if(viewport.cursorMode)
\r
1036 alignPanel.seqPanel.keyboardNo1=null;
\r
1037 alignPanel.seqPanel.keyboardNo2=null;
\r
1039 viewport.setSelectionGroup(null);
\r
1040 viewport.getColumnSelection().clear();
\r
1041 viewport.setSelectionGroup(null);
\r
1042 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1043 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1044 alignPanel.repaint();
\r
1045 PaintRefresher.Refresh(null, viewport.alignment);
\r
1048 public void invertSequenceMenuItem_actionPerformed()
\r
1050 SequenceGroup sg = viewport.getSelectionGroup();
\r
1051 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1053 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1056 PaintRefresher.Refresh(null, viewport.alignment);
\r
1059 public void remove2LeftMenuItem_actionPerformed()
\r
1061 ColumnSelection colSel = viewport.getColumnSelection();
\r
1062 if (colSel.size() > 0)
\r
1065 addHistoryItem(edit=new HistoryItem("Remove Left", viewport.alignment,
\r
1066 HistoryItem.HIDE));
\r
1067 int min = colSel.getMin();
\r
1068 viewport.getAlignment().trimLeft(min);
\r
1069 colSel.compensateForEdit(0, min);
\r
1070 edit.addShift(0, min);
\r
1071 if (viewport.getSelectionGroup() != null)
\r
1073 viewport.getSelectionGroup().adjustForRemoveLeft(min);
\r
1076 Vector groups = viewport.alignment.getGroups();
\r
1077 for (int i = 0; i < groups.size(); i++)
\r
1079 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1080 if (!sg.adjustForRemoveLeft(min))
\r
1082 viewport.alignment.deleteGroup(sg);
\r
1085 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1089 public void remove2RightMenuItem_actionPerformed()
\r
1091 ColumnSelection colSel = viewport.getColumnSelection();
\r
1092 if (colSel.size() > 0)
\r
1094 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
\r
1095 HistoryItem.HIDE));
\r
1096 int max = colSel.getMax();
\r
1097 viewport.getAlignment().trimRight(max);
\r
1099 if (viewport.getSelectionGroup() != null)
\r
1101 viewport.getSelectionGroup().adjustForRemoveRight(max);
\r
1104 Vector groups = viewport.alignment.getGroups();
\r
1105 for (int i = 0; i < groups.size(); i++)
\r
1107 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1108 if (!sg.adjustForRemoveRight(max))
\r
1110 viewport.alignment.deleteGroup(sg);
\r
1113 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1118 public void removeGappedColumnMenuItem_actionPerformed()
\r
1121 addHistoryItem(edit=new HistoryItem("Remove Gapped Columns",
\r
1122 viewport.alignment,
\r
1123 HistoryItem.HIDE));
\r
1125 //This is to maintain viewport position on first residue
\r
1126 //of first sequence
\r
1127 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1128 int startRes = seq.findPosition(viewport.startRes);
\r
1130 viewport.getAlignment().removeGaps();
\r
1132 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1134 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1137 public void removeAllGapsMenuItem_actionPerformed()
\r
1139 // TODO: hidden regions should not be touched by removeAllGaps - a minimal number of gaps will remain in alignment segments containing uneven length subsequences
\r
1140 // TODO: columnSelection.compensateforedits should be called (and passed to history item)
\r
1141 HistoryItem editgaps;
\r
1142 addHistoryItem(editgaps=new HistoryItem("Remove Gaps", viewport.alignment,
\r
1143 HistoryItem.HIDE));
\r
1145 //This is to maintain viewport position on first residue
\r
1146 //of first sequence
\r
1147 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1148 int startRes = seq.findPosition(viewport.startRes);
\r
1150 SequenceI current;
\r
1153 int start=0, end = viewport.alignment.getWidth();
\r
1155 if (viewport.getSelectionGroup() != null
\r
1156 && viewport.getSelectionGroup().getSequences(false) != null
\r
1157 && viewport.getSelectionGroup().getSize(false)>0)
\r
1159 seqs = viewport.getSelectionGroup().getSequences(true);
\r
1160 start = viewport.getSelectionGroup().getStartRes();
\r
1161 end = viewport.getSelectionGroup().getEndRes()+1;
\r
1164 seqs = viewport.alignment.getSequences();
\r
1166 /* Commented out regions below are partial implementation of todo above.
\r
1167 * divide start,end into visible chunks, and for each:
\r
1168 int diff=end-start+1;
\r
1170 int dr[] = new int[seqs.size()];
\r
1172 for (int i = 0; i < seqs.size(); i++)
\r
1174 current = (SequenceI) seqs.elementAt(i);
\r
1176 current.removeGaps(start, end);
\r
1177 /*if (d<diff) // can only shift
\r
1183 /* // after the end of each chunk -
\r
1185 // record shift for history.
\r
1186 editgaps.addShift(start, diff);
\r
1187 if (viewport.hasHiddenColumns && diffmax>diff) {
\r
1189 StringBuffer gaps=new StringBuffer(diffmax);
\r
1190 for (int i=0,j=diffmax-diff; i<j; i++)
\r
1191 gaps.append(viewport.getGapCharacter());
\r
1192 for (int i=0, j=seqs.size(); i<j; i++) {
\r
1193 current = (SequenceI) seqs.elementAt(i);
\r
1194 if (dr[i]-diff>0) {
\r
1195 String sq = current.getSequence();
\r
1196 current.setSequence(sq.substring(0, hcend-dr[i])+gaps.substring(0, dr[i]-diff)+sq.substring());
\r
1202 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1203 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1206 public void alignmentChanged()
\r
1208 viewport.alignment.padGaps();
\r
1209 if(viewport.autocalculateConsensus)
\r
1211 viewport.updateConsensus();
\r
1212 viewport.updateConservation();
\r
1215 resetAllColourSchemes();
\r
1216 if(alignPanel.overviewPanel!=null)
\r
1217 alignPanel.overviewPanel.updateOverviewImage();
\r
1219 viewport.alignment.adjustSequenceAnnotations();
\r
1220 alignPanel.repaint();
\r
1223 void resetAllColourSchemes()
\r
1225 ColourSchemeI cs = viewport.globalColourScheme;
\r
1228 if (cs instanceof ClustalxColourScheme)
\r
1230 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
\r
1231 resetClustalX(viewport.alignment.getSequences(),
\r
1232 viewport.alignment.getWidth());
\r
1235 cs.setConsensus(viewport.vconsensus);
\r
1236 if (cs.conservationApplied())
\r
1238 Alignment al = (Alignment) viewport.alignment;
\r
1239 Conservation c = new Conservation("All",
\r
1240 ResidueProperties.propHash, 3,
\r
1241 al.getSequences(), 0,
\r
1242 al.getWidth() - 1);
\r
1244 c.verdict(false, viewport.ConsPercGaps);
\r
1246 cs.setConservation(c);
\r
1250 int s, sSize = viewport.alignment.getGroups().size();
\r
1251 for(s=0; s<sSize; s++)
\r
1253 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
\r
1254 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
\r
1256 ((ClustalxColourScheme)sg.cs).resetClustalX(
\r
1257 sg.getSequences(true), sg.getWidth());
\r
1259 sg.recalcConservation();
\r
1265 public void findMenuItem_actionPerformed()
\r
1267 new Finder(alignPanel);
\r
1270 public void font_actionPerformed()
\r
1272 new FontChooser(alignPanel);
\r
1276 public void seqLimits_itemStateChanged()
\r
1278 viewport.setShowJVSuffix(seqLimits.getState());
\r
1279 alignPanel.fontChanged();
\r
1280 alignPanel.repaint();
\r
1284 protected void colourTextMenuItem_actionPerformed()
\r
1286 viewport.setColourText(colourTextMenuItem.getState());
\r
1287 alignPanel.repaint();
\r
1290 protected void wrapMenuItem_actionPerformed()
\r
1292 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
1293 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
1294 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
1295 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
1296 scaleRight.setEnabled(wrapMenuItem.getState());
\r
1297 alignPanel.repaint();
\r
1301 protected void scaleAbove_actionPerformed()
\r
1303 viewport.setScaleAboveWrapped(scaleAbove.getState());
\r
1304 alignPanel.repaint();
\r
1307 protected void scaleLeft_actionPerformed()
\r
1309 viewport.setScaleLeftWrapped(scaleLeft.getState());
\r
1310 alignPanel.repaint();
\r
1313 protected void scaleRight_actionPerformed()
\r
1315 viewport.setScaleRightWrapped(scaleRight.getState());
\r
1316 alignPanel.repaint();
\r
1319 public void viewBoxesMenuItem_actionPerformed()
\r
1321 viewport.setShowBoxes(viewBoxesMenuItem.getState());
\r
1322 alignPanel.repaint();
\r
1325 public void viewTextMenuItem_actionPerformed()
\r
1327 viewport.setShowText(viewTextMenuItem.getState());
\r
1328 alignPanel.repaint();
\r
1331 protected void renderGapsMenuItem_actionPerformed()
\r
1333 viewport.setRenderGaps(renderGapsMenuItem.getState());
\r
1334 alignPanel.repaint();
\r
1337 public void annotationPanelMenuItem_actionPerformed()
\r
1339 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
\r
1340 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
\r
1343 public void featureSettings_actionPerformed()
\r
1345 new FeatureSettings(viewport, alignPanel);
\r
1348 public void overviewMenuItem_actionPerformed()
\r
1350 if (alignPanel.overviewPanel != null)
\r
1355 Frame frame = new Frame();
\r
1356 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1357 frame.add(overview);
\r
1358 // +50 must allow for applet frame window
\r
1359 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
1360 overview.preferredSize().width,
\r
1361 overview.preferredSize().height + 50);
\r
1364 frame.addWindowListener(new WindowAdapter()
\r
1366 public void windowClosing(WindowEvent e)
\r
1368 alignPanel.setOverviewPanel(null);
\r
1372 alignPanel.setOverviewPanel(overview);
\r
1376 protected void noColourmenuItem_actionPerformed()
\r
1378 changeColour(null);
\r
1381 public void clustalColour_actionPerformed()
\r
1383 abovePIDThreshold.setState(false);
\r
1384 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
\r
1385 viewport.alignment.getWidth()));
\r
1388 public void zappoColour_actionPerformed()
\r
1390 changeColour(new ZappoColourScheme());
\r
1393 public void taylorColour_actionPerformed()
\r
1395 changeColour(new TaylorColourScheme());
\r
1398 public void hydrophobicityColour_actionPerformed()
\r
1400 changeColour(new HydrophobicColourScheme());
\r
1403 public void helixColour_actionPerformed()
\r
1405 changeColour(new HelixColourScheme());
\r
1408 public void strandColour_actionPerformed()
\r
1410 changeColour(new StrandColourScheme());
\r
1413 public void turnColour_actionPerformed()
\r
1415 changeColour(new TurnColourScheme());
\r
1418 public void buriedColour_actionPerformed()
\r
1420 changeColour(new BuriedColourScheme());
\r
1423 public void nucleotideColour_actionPerformed()
\r
1425 changeColour(new NucleotideColourScheme());
\r
1428 protected void applyToAllGroups_actionPerformed()
\r
1430 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
\r
1433 void changeColour(ColourSchemeI cs)
\r
1435 int threshold = 0;
\r
1439 if (viewport.getAbovePIDThreshold())
\r
1441 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
\r
1443 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1445 viewport.setGlobalColourScheme(cs);
\r
1449 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1452 if (viewport.getConservationSelected())
\r
1455 Alignment al = (Alignment) viewport.alignment;
\r
1456 Conservation c = new Conservation("All",
\r
1457 ResidueProperties.propHash, 3,
\r
1458 al.getSequences(), 0,
\r
1459 al.getWidth() - 1);
\r
1462 c.verdict(false, viewport.ConsPercGaps);
\r
1464 cs.setConservation(c);
\r
1466 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1472 cs.setConservation(null);
\r
1475 cs.setConsensus(viewport.vconsensus);
\r
1478 viewport.setGlobalColourScheme(cs);
\r
1480 if (viewport.getColourAppliesToAllGroups())
\r
1482 Vector groups = viewport.alignment.getGroups();
\r
1483 for (int i = 0; i < groups.size(); i++)
\r
1485 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1492 if (cs instanceof ClustalxColourScheme)
\r
1494 sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth());
\r
1500 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1502 catch (Exception ex)
\r
1504 ex.printStackTrace();
\r
1509 if (viewport.getAbovePIDThreshold()
\r
1510 || cs instanceof PIDColourScheme
\r
1511 || cs instanceof Blosum62ColourScheme)
\r
1513 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1514 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth()));
\r
1517 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1519 if (viewport.getConservationSelected())
\r
1521 Conservation c = new Conservation("Group",
\r
1522 ResidueProperties.propHash, 3,
\r
1523 sg.getSequences(true), 0,
\r
1524 viewport.alignment.getWidth() - 1);
\r
1526 c.verdict(false, viewport.ConsPercGaps);
\r
1527 sg.cs.setConservation(c);
\r
1531 sg.cs.setConservation(null);
\r
1532 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1539 if (alignPanel.getOverviewPanel() != null)
\r
1541 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1544 alignPanel.repaint();
\r
1549 protected void modifyPID_actionPerformed()
\r
1551 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1553 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
1555 SliderPanel.showPIDSlider();
\r
1559 protected void modifyConservation_actionPerformed()
\r
1561 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1563 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
1565 SliderPanel.showConservationSlider();
\r
1569 protected void conservationMenuItem_actionPerformed()
\r
1571 viewport.setConservationSelected(conservationMenuItem.getState());
\r
1573 viewport.setAbovePIDThreshold(false);
\r
1574 abovePIDThreshold.setState(false);
\r
1576 changeColour(viewport.getGlobalColourScheme());
\r
1578 modifyConservation_actionPerformed();
\r
1581 public void abovePIDThreshold_actionPerformed()
\r
1583 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
1585 conservationMenuItem.setState(false);
\r
1586 viewport.setConservationSelected(false);
\r
1588 changeColour(viewport.getGlobalColourScheme());
\r
1590 modifyPID_actionPerformed();
\r
1593 public void userDefinedColour_actionPerformed()
\r
1595 new UserDefinedColours(alignPanel, null);
\r
1598 public void PIDColour_actionPerformed()
\r
1600 changeColour(new PIDColourScheme());
\r
1603 public void BLOSUM62Colour_actionPerformed()
\r
1605 changeColour(new Blosum62ColourScheme());
\r
1608 public void sortPairwiseMenuItem_actionPerformed()
\r
1610 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1611 HistoryItem.SORT));
\r
1612 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1613 viewport.getAlignment().getSequenceAt(0));
\r
1614 alignPanel.repaint();
\r
1617 public void sortIDMenuItem_actionPerformed()
\r
1619 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1620 HistoryItem.SORT));
\r
1621 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1622 alignPanel.repaint();
\r
1625 public void sortGroupMenuItem_actionPerformed()
\r
1627 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1628 HistoryItem.SORT));
\r
1629 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1630 alignPanel.repaint();
\r
1634 public void removeRedundancyMenuItem_actionPerformed()
\r
1636 new RedundancyPanel(alignPanel);
\r
1639 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
1641 if (viewport.getSelectionGroup()!=null
\r
1642 && viewport.getSelectionGroup().getSize(false) > 1)
\r
1644 Frame frame = new Frame();
\r
1645 frame.add(new PairwiseAlignPanel(alignPanel));
\r
1646 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
1650 public void PCAMenuItem_actionPerformed()
\r
1652 //are the sequences aligned?
\r
1653 if (!viewport.alignment.isAligned())
\r
1655 SequenceI current;
\r
1656 int Width = viewport.getAlignment().getWidth();
\r
1658 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1661 current = viewport.getAlignment().getSequenceAt(i);
\r
1663 if (current.getLength() < Width)
\r
1665 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1668 alignPanel.repaint();
\r
1671 if ( (viewport.getSelectionGroup() != null &&
\r
1672 viewport.getSelectionGroup().getSize(false) < 4 &&
\r
1673 viewport.getSelectionGroup().getSize(false) > 0)
\r
1674 || viewport.getAlignment().getHeight() < 4)
\r
1681 new PCAPanel(viewport);
\r
1683 catch (java.lang.OutOfMemoryError ex)
\r
1689 public void averageDistanceTreeMenuItem_actionPerformed()
\r
1691 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1694 public void neighbourTreeMenuItem_actionPerformed()
\r
1696 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1699 protected void njTreeBlosumMenuItem_actionPerformed()
\r
1701 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1704 protected void avTreeBlosumMenuItem_actionPerformed()
\r
1706 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1709 void NewTreePanel(String type, String pwType, String title)
\r
1711 //are the sequences aligned?
\r
1712 if (!viewport.alignment.isAligned())
\r
1714 SequenceI current;
\r
1715 int Width = viewport.getAlignment().getWidth();
\r
1717 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1720 current = viewport.getAlignment().getSequenceAt(i);
\r
1722 if (current.getLength() < Width)
\r
1724 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1727 alignPanel.repaint();
\r
1731 if ( (viewport.getSelectionGroup() != null &&
\r
1732 viewport.getSelectionGroup().getSize(false) > 1)
\r
1733 || (viewport.getSelectionGroup() == null
\r
1734 && viewport.alignment.getHeight() > 1))
\r
1736 final TreePanel tp = new TreePanel(viewport,
\r
1740 addTreeMenuItem(tp, title);
\r
1742 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
1746 void loadTree_actionPerformed()
\r
1748 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1749 cap.setText("Paste your Newick tree file here.");
\r
1750 cap.treeImport = true;
\r
1751 Frame frame = new Frame();
\r
1753 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
1756 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
1758 TreePanel tp = new TreePanel(viewport,
\r
1762 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
1763 addTreeMenuItem(tp, treeFile);
\r
1766 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1768 final MenuItem item = new MenuItem(title);
\r
1769 sortByTreeMenu.add(item);
\r
1770 item.addActionListener(new java.awt.event.ActionListener()
\r
1772 public void actionPerformed(ActionEvent evt)
\r
1774 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1775 HistoryItem.SORT));
\r
1776 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1777 alignPanel.repaint();
\r
1781 treePanel.addWindowListener(new WindowAdapter()
\r
1783 public void windowClosing(WindowEvent e)
\r
1785 sortByTreeMenu.remove(item);
\r
1790 protected void documentation_actionPerformed()
\r
1792 showURL("http://www.jalview.org/help.html", "HELP");
\r
1795 protected void about_actionPerformed()
\r
1798 class AboutPanel extends Canvas
\r
1801 public AboutPanel(String version)
\r
1802 { this.version = version; }
\r
1804 public void paint(Graphics g)
\r
1806 g.setColor(Color.white);
\r
1807 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1808 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1809 FontMetrics fm = g.getFontMetrics();
\r
1810 int fh = fm.getHeight();
\r
1812 g.setColor(Color.black);
\r
1813 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
1814 g.drawString("Jalview - Release "+version, 200, y += fh);
\r
1815 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1816 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
1818 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
1821 "For any issues relating to Jalview, email help@jalview.org", x,
\r
1823 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
1824 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
1826 g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh);
\r
1830 String version = "test";
\r
1831 java.net.URL url = getClass().getResource("/.build_properties");
\r
1836 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
1837 url.openStream()));
\r
1839 while ( (line = reader.readLine()) != null)
\r
1841 if (line.indexOf("VERSION") > -1)
\r
1843 version = line.substring(line.indexOf("=") + 1);
\r
1847 catch (Exception ex)
\r
1849 ex.printStackTrace();
\r
1854 Frame frame = new Frame();
\r
1855 frame.add(new AboutPanel(version));
\r
1856 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
\r
1860 public void showURL(String url, String target)
\r
1862 if (viewport.applet == null)
\r
1864 System.out.println("Not running as applet - no browser available.");
\r
1870 System.out.println("Show url: "+url);
\r
1871 viewport.applet.getAppletContext().showDocument(new java.net.URL(url),
\r
1874 catch (Exception ex)
\r
1876 ex.printStackTrace();
\r
1882 //////////////////////////////////////////////////////////////////////////////////
\r
1883 //JBuilder Graphics here
\r
1885 protected MenuBar alignFrameMenuBar = new MenuBar();
\r
1886 protected Menu fileMenu = new Menu("File");
\r
1887 protected MenuItem loadApplication = new MenuItem("View in Full Application");
\r
1888 protected MenuItem loadTree = new MenuItem("Load Associated Tree");
\r
1889 protected MenuItem closeMenuItem = new MenuItem("Close");
\r
1890 protected Menu editMenu = new Menu("Edit");
\r
1891 protected Menu viewMenu = new Menu("View");
\r
1892 protected Menu colourMenu = new Menu("Colour");
\r
1893 protected Menu calculateMenu = new Menu("Calculate");
\r
1894 protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
1895 protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
1896 protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
1897 protected MenuItem remove2LeftMenuItem = new MenuItem();
\r
1898 protected MenuItem remove2RightMenuItem = new MenuItem();
\r
1899 protected MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
1900 protected MenuItem removeAllGapsMenuItem = new MenuItem();
\r
1901 protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
1902 protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
1903 protected MenuItem sortPairwiseMenuItem = new MenuItem();
\r
1904 protected MenuItem sortIDMenuItem = new MenuItem();
\r
1905 protected MenuItem sortGroupMenuItem = new MenuItem();
\r
1906 protected MenuItem removeRedundancyMenuItem = new MenuItem();
\r
1907 protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
1908 protected MenuItem PCAMenuItem = new MenuItem();
\r
1909 protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
1910 protected MenuItem neighbourTreeMenuItem = new MenuItem();
\r
1911 BorderLayout borderLayout1 = new BorderLayout();
\r
1912 public Label statusBar = new Label();
\r
1913 protected Menu outputTextboxMenu = new Menu();
\r
1914 protected MenuItem clustalColour = new MenuItem();
\r
1915 protected MenuItem zappoColour = new MenuItem();
\r
1916 protected MenuItem taylorColour = new MenuItem();
\r
1917 protected MenuItem hydrophobicityColour = new MenuItem();
\r
1918 protected MenuItem helixColour = new MenuItem();
\r
1919 protected MenuItem strandColour = new MenuItem();
\r
1920 protected MenuItem turnColour = new MenuItem();
\r
1921 protected MenuItem buriedColour = new MenuItem();
\r
1922 protected MenuItem userDefinedColour = new MenuItem();
\r
1923 protected MenuItem PIDColour = new MenuItem();
\r
1924 protected MenuItem BLOSUM62Colour = new MenuItem();
\r
1925 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
1926 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
1927 protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
1928 protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
1929 MenuItem overviewMenuItem = new MenuItem();
\r
1930 protected MenuItem undoMenuItem = new MenuItem();
\r
1931 protected MenuItem redoMenuItem = new MenuItem();
\r
1932 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
1933 MenuItem noColourmenuItem = new MenuItem();
\r
1934 protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
1935 protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
1936 MenuItem findMenuItem = new MenuItem();
\r
1937 Menu searchMenu = new Menu();
\r
1938 protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
1939 protected MenuItem nucleotideColour = new MenuItem();
\r
1940 MenuItem deleteGroups = new MenuItem();
\r
1941 MenuItem delete = new MenuItem();
\r
1942 MenuItem copy = new MenuItem();
\r
1943 MenuItem cut = new MenuItem();
\r
1944 Menu pasteMenu = new Menu();
\r
1945 MenuItem pasteNew = new MenuItem();
\r
1946 MenuItem pasteThis = new MenuItem();
\r
1947 protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
1948 protected MenuItem font = new MenuItem();
\r
1949 protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
1950 protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
1951 protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
1952 MenuItem modifyPID = new MenuItem();
\r
1953 MenuItem modifyConservation = new MenuItem();
\r
1954 protected CheckboxMenuItem autoCalculate
\r
1955 = new CheckboxMenuItem("Autocalculate Consensus", true);
\r
1956 protected Menu sortByTreeMenu = new Menu();
\r
1957 Menu sort = new Menu();
\r
1958 Menu calculate = new Menu();
\r
1959 MenuItem inputText = new MenuItem();
\r
1960 Menu helpMenu = new Menu();
\r
1961 MenuItem documentation = new MenuItem();
\r
1962 MenuItem about = new MenuItem();
\r
1963 protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
1964 Panel embeddedMenu;
\r
1965 Label embeddedEdit;
\r
1966 Label embeddedSearch;
\r
1967 Label embeddedView;
\r
1968 Label embeddedColour;
\r
1969 Label embeddedFile;
\r
1970 Label embeddedHelp;
\r
1971 Label embeddedCalculate;
\r
1972 FlowLayout flowLayout1;
\r
1974 private void jbInit() throws Exception {
\r
1976 setMenuBar(alignFrameMenuBar);
\r
1980 // dynamically fill save as menu with available formats
\r
1981 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
1984 item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
1986 item.addActionListener(new java.awt.event.ActionListener()
\r
1988 public void actionPerformed(ActionEvent e)
\r
1990 outputText_actionPerformed(e);
\r
1994 outputTextboxMenu.add(item);
\r
1996 closeMenuItem.addActionListener(this);
\r
1997 loadApplication.addActionListener(this);
\r
1999 loadTree.addActionListener(this);
\r
2000 selectAllSequenceMenuItem.addActionListener(this);
\r
2001 deselectAllSequenceMenuItem.addActionListener(this);
\r
2002 invertSequenceMenuItem.addActionListener(this);
\r
2003 remove2LeftMenuItem.setLabel("Remove Left");
\r
2004 remove2LeftMenuItem.addActionListener(this);
\r
2005 remove2RightMenuItem.setLabel("Remove Right");
\r
2006 remove2RightMenuItem.addActionListener(this);
\r
2007 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
2008 removeGappedColumnMenuItem.addActionListener(this);
\r
2009 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
2010 removeAllGapsMenuItem.addActionListener(this);
\r
2011 viewBoxesMenuItem.setLabel("Boxes");
\r
2012 viewBoxesMenuItem.setState(true);
\r
2013 viewBoxesMenuItem.addItemListener(this);
\r
2014 viewTextMenuItem.setLabel("Text");
\r
2015 viewTextMenuItem.setState(true);
\r
2016 viewTextMenuItem.addItemListener(this);
\r
2017 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
2018 sortPairwiseMenuItem.addActionListener(this);
\r
2019 sortIDMenuItem.setLabel("by ID");
\r
2020 sortIDMenuItem.addActionListener(this);
\r
2021 sortGroupMenuItem.setLabel("by Group");
\r
2022 sortGroupMenuItem.addActionListener(this);
\r
2023 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
2024 removeRedundancyMenuItem.addActionListener(this);
\r
2025 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
2026 pairwiseAlignmentMenuItem.addActionListener(this);
\r
2027 PCAMenuItem.setLabel("Principal Component Analysis");
\r
2028 PCAMenuItem.addActionListener(this);
\r
2029 averageDistanceTreeMenuItem.setLabel(
\r
2030 "Average Distance Using % Identity");
\r
2031 averageDistanceTreeMenuItem.addActionListener(this);
\r
2032 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
2033 neighbourTreeMenuItem.addActionListener(this);
\r
2034 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
2035 statusBar.setBackground(Color.white);
\r
2036 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
2037 statusBar.setText("Status bar");
\r
2038 outputTextboxMenu.setLabel("Output to Textbox");
\r
2039 clustalColour.setLabel("Clustalx");
\r
2041 clustalColour.addActionListener(this);
\r
2042 zappoColour.setLabel("Zappo");
\r
2043 zappoColour.addActionListener(this);
\r
2044 taylorColour.setLabel("Taylor");
\r
2045 taylorColour.addActionListener(this);
\r
2046 hydrophobicityColour.setLabel("Hydrophobicity");
\r
2047 hydrophobicityColour.addActionListener(this);
\r
2048 helixColour.setLabel("Helix Propensity");
\r
2049 helixColour.addActionListener(this);
\r
2050 strandColour.setLabel("Strand Propensity");
\r
2051 strandColour.addActionListener(this);
\r
2052 turnColour.setLabel("Turn Propensity");
\r
2053 turnColour.addActionListener(this);
\r
2054 buriedColour.setLabel("Buried Index");
\r
2055 buriedColour.addActionListener(this);
\r
2056 userDefinedColour.setLabel("User Defined...");
\r
2057 userDefinedColour.addActionListener(this);
\r
2058 PIDColour.setLabel("Percentage Identity");
\r
2059 PIDColour.addActionListener(this);
\r
2060 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
2061 BLOSUM62Colour.addActionListener(this);
\r
2062 avDistanceTreeBlosumMenuItem.setLabel(
\r
2063 "Average Distance Using BLOSUM62");
\r
2064 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
2065 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
2066 njTreeBlosumMenuItem.addActionListener(this);
\r
2067 annotationPanelMenuItem.setLabel("Show Annotations");
\r
2068 annotationPanelMenuItem.addItemListener(this);
\r
2069 colourTextMenuItem.setLabel("Colour Text");
\r
2070 colourTextMenuItem.addItemListener(this);
\r
2071 overviewMenuItem.setLabel("Overview Window");
\r
2072 overviewMenuItem.addActionListener(this);
\r
2073 undoMenuItem.setEnabled(false);
\r
2074 undoMenuItem.setLabel("Undo");
\r
2075 undoMenuItem.addActionListener(this);
\r
2076 redoMenuItem.setEnabled(false);
\r
2077 redoMenuItem.setLabel("Redo");
\r
2078 redoMenuItem.addActionListener(this);
\r
2079 conservationMenuItem.setLabel("by Conservation");
\r
2080 conservationMenuItem.addItemListener(this);
\r
2081 noColourmenuItem.setLabel("None");
\r
2082 noColourmenuItem.addActionListener(this);
\r
2083 wrapMenuItem.setLabel("Wrap");
\r
2084 wrapMenuItem.addItemListener(this);
\r
2085 renderGapsMenuItem.setLabel("Show Gaps");
\r
2086 renderGapsMenuItem.setState(true);
\r
2087 renderGapsMenuItem.addItemListener(this);
\r
2088 findMenuItem.setLabel("Find...");
\r
2089 findMenuItem.addActionListener(this);
\r
2090 searchMenu.setLabel("Search");
\r
2092 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
2093 abovePIDThreshold.addItemListener(this);
\r
2094 nucleotideColour.setLabel("Nucleotide");
\r
2095 nucleotideColour.addActionListener(this);
\r
2096 deleteGroups.setLabel("Undefine Groups");
\r
2097 deleteGroups.addActionListener(this);
\r
2098 copy.setLabel("Copy");
\r
2099 copy.addActionListener(this);
\r
2100 cut.setLabel("Cut");
\r
2101 cut.addActionListener(this);
\r
2102 delete.setLabel("Delete");
\r
2103 delete.addActionListener(this);
\r
2104 pasteMenu.setLabel("Paste");
\r
2105 pasteNew.setLabel("To New Alignment");
\r
2106 pasteNew.addActionListener(this);
\r
2107 pasteThis.setLabel("Add To This Alignment");
\r
2108 pasteThis.addActionListener(this);
\r
2109 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
2110 applyToAllGroups.setState(true);
\r
2111 applyToAllGroups.addItemListener(this);
\r
2112 font.setLabel("Font...");
\r
2113 font.addActionListener(this);
\r
2114 scaleAbove.setLabel("Scale Above");
\r
2115 scaleAbove.setState(true);
\r
2116 scaleAbove.setEnabled(false);
\r
2117 scaleAbove.addItemListener(this);
\r
2118 scaleLeft.setEnabled(false);
\r
2119 scaleLeft.setState(true);
\r
2120 scaleLeft.setLabel("Scale Left");
\r
2121 scaleLeft.addItemListener(this);
\r
2122 scaleRight.setEnabled(false);
\r
2123 scaleRight.setState(true);
\r
2124 scaleRight.setLabel("Scale Right");
\r
2125 scaleRight.addItemListener(this);
\r
2126 modifyPID.setLabel("Modify Identity Threshold...");
\r
2127 modifyPID.addActionListener(this);
\r
2128 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
2129 modifyConservation.addActionListener(this);
\r
2130 sortByTreeMenu.setLabel("By Tree Order");
\r
2131 sort.setLabel("Sort");
\r
2132 calculate.setLabel("Calculate Tree");
\r
2133 autoCalculate.addItemListener(this);
\r
2134 inputText.setLabel("Input from textbox");
\r
2135 inputText.addActionListener(this);
\r
2137 helpMenu.setLabel("Help");
\r
2138 documentation.setLabel("Documentation");
\r
2139 documentation.addActionListener(this);
\r
2141 about.setLabel("About...");
\r
2142 about.addActionListener(this);
\r
2143 seqLimits.setState(true);
\r
2144 seqLimits.setLabel("Show Sequence Limits");
\r
2145 seqLimits.addItemListener(this);
\r
2146 featureSettings.setLabel("Feature Settings...");
\r
2147 featureSettings.addActionListener(this);
\r
2148 sequenceFeatures.setLabel("Sequence Features");
\r
2149 sequenceFeatures.addItemListener(this);
\r
2150 sequenceFeatures.setState(false);
\r
2151 annotationColour.setLabel("by Annotation...");
\r
2152 annotationColour.addActionListener(this);
\r
2153 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
2154 invertColSel.setLabel("Invert Column Selection");
\r
2155 menu1.setLabel("Show");
\r
2156 showColumns.setLabel("All Columns ");
\r
2157 showSeqs.setLabel("All Sequences");
\r
2158 menu2.setLabel("Hide");
\r
2159 hideColumns.setLabel("Selected Columns");
\r
2160 hideSequences.setLabel("Selected Sequences");
\r
2161 invertColSel.addActionListener(this);
\r
2162 showColumns.addActionListener(this);
\r
2163 showSeqs.addActionListener(this);
\r
2164 hideColumns.addActionListener(this);
\r
2165 hideSequences.addActionListener(this);
\r
2168 alignFrameMenuBar.add(fileMenu);
\r
2169 alignFrameMenuBar.add(editMenu);
\r
2170 alignFrameMenuBar.add(searchMenu);
\r
2171 alignFrameMenuBar.add(viewMenu);
\r
2172 alignFrameMenuBar.add(colourMenu);
\r
2173 alignFrameMenuBar.add(calculateMenu);
\r
2174 alignFrameMenuBar.add(helpMenu);
\r
2175 fileMenu.add(inputText);
\r
2176 fileMenu.add(outputTextboxMenu);
\r
2177 if(jalviewServletURL!=null)
\r
2178 fileMenu.add(loadApplication);
\r
2179 fileMenu.addSeparator();
\r
2180 fileMenu.add(loadTree);
\r
2181 fileMenu.add(closeMenuItem);
\r
2182 editMenu.add(undoMenuItem);
\r
2183 editMenu.add(redoMenuItem);
\r
2184 editMenu.add(cut);
\r
2185 editMenu.add(copy);
\r
2186 editMenu.add(pasteMenu);
\r
2187 editMenu.add(delete);
\r
2188 editMenu.addSeparator();
\r
2189 editMenu.add(selectAllSequenceMenuItem);
\r
2190 editMenu.add(deselectAllSequenceMenuItem);
\r
2191 editMenu.add(invertSequenceMenuItem);
\r
2192 editMenu.add(invertColSel);
\r
2193 editMenu.add(deleteGroups);
\r
2194 editMenu.addSeparator();
\r
2195 editMenu.add(remove2LeftMenuItem);
\r
2196 editMenu.add(remove2RightMenuItem);
\r
2197 editMenu.add(removeGappedColumnMenuItem);
\r
2198 editMenu.add(removeAllGapsMenuItem);
\r
2199 editMenu.add(removeRedundancyMenuItem);
\r
2200 searchMenu.add(findMenuItem);
\r
2201 viewMenu.add(font);
\r
2202 viewMenu.addSeparator();
\r
2203 viewMenu.add(menu1);
\r
2204 viewMenu.add(menu2);
\r
2205 viewMenu.addSeparator();
\r
2206 viewMenu.add(wrapMenuItem);
\r
2207 viewMenu.add(scaleAbove);
\r
2208 viewMenu.add(scaleLeft);
\r
2209 viewMenu.add(scaleRight);
\r
2210 viewMenu.addSeparator();
\r
2211 viewMenu.add(seqLimits);
\r
2212 viewMenu.add(viewBoxesMenuItem);
\r
2213 viewMenu.add(viewTextMenuItem);
\r
2214 viewMenu.add(colourTextMenuItem);
\r
2215 viewMenu.add(renderGapsMenuItem);
\r
2216 viewMenu.add(annotationPanelMenuItem);
\r
2217 viewMenu.addSeparator();
\r
2218 viewMenu.add(sequenceFeatures);
\r
2219 viewMenu.add(featureSettings);
\r
2220 viewMenu.addSeparator();
\r
2221 viewMenu.add(overviewMenuItem);
\r
2222 colourMenu.add(applyToAllGroups);
\r
2223 colourMenu.addSeparator();
\r
2224 colourMenu.add(noColourmenuItem);
\r
2225 colourMenu.add(clustalColour);
\r
2226 colourMenu.add(BLOSUM62Colour);
\r
2227 colourMenu.add(PIDColour);
\r
2228 colourMenu.add(zappoColour);
\r
2229 colourMenu.add(taylorColour);
\r
2230 colourMenu.add(hydrophobicityColour);
\r
2231 colourMenu.add(helixColour);
\r
2232 colourMenu.add(strandColour);
\r
2233 colourMenu.add(turnColour);
\r
2234 colourMenu.add(buriedColour);
\r
2235 colourMenu.add(nucleotideColour);
\r
2236 colourMenu.add(userDefinedColour);
\r
2237 colourMenu.addSeparator();
\r
2238 colourMenu.add(conservationMenuItem);
\r
2239 colourMenu.add(modifyConservation);
\r
2240 colourMenu.add(abovePIDThreshold);
\r
2241 colourMenu.add(modifyPID);
\r
2242 colourMenu.add(annotationColour);
\r
2243 calculateMenu.add(sort);
\r
2244 calculateMenu.add(calculate);
\r
2245 calculateMenu.addSeparator();
\r
2246 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
2247 calculateMenu.add(PCAMenuItem);
\r
2248 calculateMenu.add(autoCalculate);
\r
2249 this.add(statusBar, BorderLayout.SOUTH);
\r
2250 pasteMenu.add(pasteNew);
\r
2251 pasteMenu.add(pasteThis);
\r
2252 sort.add(sortIDMenuItem);
\r
2253 sort.add(sortByTreeMenu);
\r
2254 sort.add(sortGroupMenuItem);
\r
2255 sort.add(sortPairwiseMenuItem);
\r
2256 calculate.add(averageDistanceTreeMenuItem);
\r
2257 calculate.add(neighbourTreeMenuItem);
\r
2258 calculate.add(avDistanceTreeBlosumMenuItem);
\r
2259 calculate.add(njTreeBlosumMenuItem);
\r
2260 helpMenu.add(documentation);
\r
2261 helpMenu.add(about);
\r
2262 menu1.add(showColumns);
\r
2263 menu1.add(showSeqs);
\r
2264 menu2.add(hideColumns);
\r
2265 menu2.add(hideSequences);
\r
2268 public void setEmbedded()
\r
2271 embeddedMenu = new Panel();
\r
2272 embeddedEdit = new Label();
\r
2273 embeddedSearch = new Label();
\r
2274 embeddedView = new Label();
\r
2275 embeddedColour = new Label();
\r
2276 embeddedFile = new Label();
\r
2277 embeddedHelp = new Label();
\r
2278 embeddedCalculate = new Label();
\r
2279 flowLayout1 = new FlowLayout();
\r
2280 embeddedMenu.setBackground(Color.lightGray);
\r
2281 embeddedMenu.setLayout(flowLayout1);
\r
2282 embeddedEdit.setText("Edit");
\r
2283 embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2284 embeddedSearch.setText("Search");
\r
2285 embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2286 embeddedView.setText("View");
\r
2287 embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2288 embeddedColour.setText("Colour");
\r
2289 embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2290 embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2291 embeddedFile.setText("File");
\r
2292 embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2293 embeddedHelp.setText("Help");
\r
2294 embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2295 embeddedCalculate.setText("Calculate");
\r
2296 embeddedMenu.add(embeddedFile);
\r
2297 embeddedMenu.add(embeddedEdit);
\r
2298 embeddedMenu.add(embeddedSearch);
\r
2299 embeddedMenu.add(embeddedView);
\r
2300 embeddedMenu.add(embeddedColour);
\r
2301 embeddedMenu.add(embeddedCalculate);
\r
2302 embeddedMenu.add(embeddedHelp);
\r
2303 flowLayout1.setAlignment(FlowLayout.LEFT);
\r
2304 flowLayout1.setHgap(2);
\r
2305 flowLayout1.setVgap(0);
\r
2306 embeddedFile.addMouseListener(this);
\r
2307 embeddedEdit.addMouseListener(this);
\r
2308 embeddedSearch.addMouseListener(this);
\r
2309 embeddedView.addMouseListener(this);
\r
2310 embeddedColour.addMouseListener(this);
\r
2311 embeddedCalculate.addMouseListener(this);
\r
2312 embeddedHelp.addMouseListener(this);
\r
2314 // setVisible(false);
\r
2315 fileMenu.remove(closeMenuItem);
\r
2316 fileMenu.remove(3); // Seperator
\r
2318 viewport.applet.setLayout(new BorderLayout());
\r
2319 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
\r
2320 viewport.applet.add(statusBar, BorderLayout.SOUTH);
\r
2321 // viewport.applet.validate();
\r
2323 alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height
\r
2324 - embeddedMenu.HEIGHT - statusBar.HEIGHT);
\r
2326 viewport.applet.add(alignPanel, BorderLayout.CENTER);
\r
2327 viewport.applet.validate();
\r
2333 PopupMenu filePopup, editPopup, searchPopup,
\r
2334 viewPopup, colourPopup, calculatePopup, helpPopup;
\r
2335 MenuItem featureSettings = new MenuItem();
\r
2336 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
2337 MenuItem annotationColour = new MenuItem();
\r
2338 MenuItem invertColSel = new MenuItem();
\r
2339 Menu menu1 = new Menu();
\r
2340 MenuItem showColumns = new MenuItem();
\r
2341 MenuItem showSeqs = new MenuItem();
\r
2342 Menu menu2 = new Menu();
\r
2343 MenuItem hideColumns = new MenuItem();
\r
2344 MenuItem hideSequences = new MenuItem();
\r
2346 public void mousePressed(MouseEvent evt)
\r
2348 PopupMenu popup = null;
\r
2349 Label source = (Label)evt.getSource();
\r
2350 if(source==embeddedFile)
\r
2352 popup = filePopup = genPopupMenu(filePopup, fileMenu);
\r
2354 else if(source==embeddedEdit)
\r
2356 popup = editPopup = genPopupMenu(editPopup, editMenu);
\r
2358 else if(source==embeddedSearch)
\r
2360 popup = searchPopup = genPopupMenu(searchPopup, searchMenu);
\r
2362 else if(source==embeddedView)
\r
2364 popup = viewPopup = genPopupMenu(viewPopup, viewMenu);
\r
2366 else if(source==embeddedColour)
\r
2368 popup = colourPopup = genPopupMenu(colourPopup, colourMenu);
\r
2370 else if(source==embeddedCalculate)
\r
2372 popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);
\r
2374 else if(source==embeddedHelp)
\r
2376 popup = helpPopup = genPopupMenu(helpPopup, helpMenu);
\r
2379 embeddedMenu.add(popup);
\r
2380 popup.show(embeddedMenu,
\r
2381 source.getBounds().x,
\r
2382 source.getBounds().y + source.getBounds().getSize().height);
\r
2385 PopupMenu genPopupMenu(PopupMenu popup, Menu original)
\r
2391 popup = new PopupMenu();
\r
2392 int m, mSize = original.getItemCount();
\r
2393 for(m=0; m<mSize; m++)
\r
2395 popup.add(original.getItem(m));
\r
2402 public void mouseClicked(MouseEvent evt)
\r
2404 public void mouseReleased(MouseEvent evt)
\r
2406 public void mouseEntered(MouseEvent evt)
\r
2408 public void mouseExited(MouseEvent evt)
\r