2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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20 package jalview.appletgui;
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22 import jalview.schemes.*;
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23 import jalview.datamodel.*;
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24 import jalview.analysis.*;
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25 import jalview.io.*;
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26 import jalview.commands.*;
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28 import java.awt.event.*;
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30 import java.io.InputStreamReader;
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31 import java.io.BufferedReader;
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32 import java.net.URL;
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35 public class AlignFrame extends Frame implements ActionListener,
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36 ItemListener, KeyListener, MouseListener
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38 public AlignmentPanel alignPanel;
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39 public AlignViewport viewport;
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40 int DEFAULT_WIDTH = 700;
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41 int DEFAULT_HEIGHT = 500;
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43 String jalviewServletURL;
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46 public AlignFrame(AlignmentI al,
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47 jalview.bin.JalviewLite applet,
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52 jalviewServletURL = applet.getParameter("APPLICATION_URL");
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56 }catch(Exception ex)
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58 ex.printStackTrace();
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61 viewport = new AlignViewport(al, applet);
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62 alignPanel = new AlignmentPanel(this, viewport);
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64 annotationPanelMenuItem.setState(viewport.showAnnotation);
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66 seqLimits.setState(viewport.showJVSuffix);
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70 String param = applet.getParameter("sortBy");
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73 if (param.equalsIgnoreCase("Id"))
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74 sortIDMenuItem_actionPerformed();
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75 else if (param.equalsIgnoreCase("Pairwise Identity"))
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76 sortPairwiseMenuItem_actionPerformed();
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79 param = applet.getParameter("wrap");
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82 if (param.equalsIgnoreCase("true"))
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84 wrapMenuItem.setState(true);
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85 wrapMenuItem_actionPerformed();
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91 param = applet.getParameter("windowWidth");
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94 int width = Integer.parseInt(param);
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95 DEFAULT_WIDTH = width;
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97 param = applet.getParameter("windowHeight");
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100 int height = Integer.parseInt(param);
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101 DEFAULT_HEIGHT = height;
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104 catch (Exception ex)
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109 //Some JVMS send keyevents to Top frame or lowest panel,
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110 //Havent worked out why yet. So add to both this frame and seqCanvas for now
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111 this.addKeyListener(this);
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112 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
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113 alignPanel.idPanel.idCanvas.addKeyListener(this);
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114 alignPanel.scalePanel.addKeyListener(this);
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115 alignPanel.annotationPanel.addKeyListener(this);
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117 viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
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119 public void propertyChange(java.beans.PropertyChangeEvent evt)
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121 if (evt.getPropertyName().equals("alignment"))
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123 alignmentChanged();
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135 add(alignPanel, BorderLayout.CENTER);
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136 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
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139 alignPanel.validate();
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140 alignPanel.repaint();
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142 public AlignViewport getAlignViewport()
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147 public SeqCanvas getSeqcanvas()
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149 return alignPanel.seqPanel.seqCanvas;
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156 * @param String DOCUMENT ME!
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159 public void parseFeaturesFile(String file, String type)
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161 Hashtable featureLinks = new Hashtable();
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162 boolean featuresFile = false;
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164 featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport.alignment,
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165 alignPanel.seqPanel.seqCanvas.
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166 getFeatureRenderer().featureColours,
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170 catch(Exception ex)
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172 ex.printStackTrace();
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177 if(featureLinks.size()>0)
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178 alignPanel.seqPanel.seqCanvas
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179 .getFeatureRenderer().featureLinks = featureLinks;
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180 viewport.showSequenceFeatures = true;
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181 sequenceFeatures.setState(true);
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182 alignPanel.repaint();
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188 public void keyPressed(KeyEvent evt)
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190 if (viewport.cursorMode
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191 && evt.getKeyCode() >= KeyEvent.VK_0
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192 && evt.getKeyCode() <= KeyEvent.VK_9)
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194 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
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197 switch (evt.getKeyCode())
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199 case 27: // escape key
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200 deselectAllSequenceMenuItem_actionPerformed();
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202 case KeyEvent.VK_X:
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203 if (evt.isControlDown() || evt.isMetaDown())
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205 cut_actionPerformed();
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208 case KeyEvent.VK_C:
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209 if (viewport.cursorMode && !evt.isControlDown())
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211 alignPanel.seqPanel.setCursorColumn();
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213 if (evt.isControlDown() || evt.isMetaDown())
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215 copy_actionPerformed();
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218 case KeyEvent.VK_V:
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219 if (evt.isControlDown() || evt.isMetaDown())
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224 case KeyEvent.VK_A:
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225 if (evt.isControlDown() || evt.isMetaDown())
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227 selectAllSequenceMenuItem_actionPerformed();
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230 case KeyEvent.VK_DOWN:
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231 if(viewport.cursorMode)
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233 alignPanel.seqPanel.moveCursor(0,1);
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236 moveSelectedSequences(false);
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239 case KeyEvent.VK_UP:
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240 if (viewport.cursorMode)
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242 alignPanel.seqPanel.moveCursor(0,-1);
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245 moveSelectedSequences(true);
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248 case KeyEvent.VK_LEFT:
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249 if(viewport.cursorMode)
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251 alignPanel.seqPanel.moveCursor(-1,0);
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255 case KeyEvent.VK_RIGHT:
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256 if (viewport.cursorMode)
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258 alignPanel.seqPanel.moveCursor(1,0);
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261 case KeyEvent.VK_SPACE:
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262 if(viewport.cursorMode)
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264 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
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265 || evt.isShiftDown()
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271 case KeyEvent.VK_DELETE:
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272 case KeyEvent.VK_BACK_SPACE:
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273 if(viewport.cursorMode)
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275 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
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276 || evt.isShiftDown()
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282 cut_actionPerformed();
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283 alignPanel.seqPanel.seqCanvas.repaint();
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287 case KeyEvent.VK_S:
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288 if(viewport.cursorMode)
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290 alignPanel.seqPanel.setCursorRow();
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293 case KeyEvent.VK_P:
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294 if(viewport.cursorMode)
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296 alignPanel.seqPanel.setCursorPosition();
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300 case KeyEvent.VK_ENTER:
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301 case KeyEvent.VK_COMMA:
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302 if(viewport.cursorMode)
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304 alignPanel.seqPanel.setCursorRowAndColumn();
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308 case KeyEvent.VK_Q:
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309 if(viewport.cursorMode)
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311 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
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314 case KeyEvent.VK_M:
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315 if(viewport.cursorMode)
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317 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
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321 case KeyEvent.VK_F2:
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322 viewport.cursorMode = ! viewport.cursorMode;
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323 statusBar.setText("Keyboard editing mode is "+
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324 (viewport.cursorMode ? "on" : "off"));
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325 if(viewport.cursorMode)
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327 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
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328 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
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330 alignPanel.seqPanel.seqCanvas.repaint();
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333 case KeyEvent.VK_F:
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334 if (evt.isControlDown())
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336 findMenuItem_actionPerformed();
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339 case KeyEvent.VK_H:
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341 boolean toggleSeqs = !evt.isControlDown();
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342 boolean toggleCols = !evt.isShiftDown();
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343 boolean hide = false;
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344 SequenceGroup sg = viewport.getSelectionGroup();
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348 if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())
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351 viewport.hideAllSelectedSeqs();
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353 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
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354 viewport.showAllHiddenSeqs();
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359 if (viewport.colSel.getSelected().size() > 0)
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361 viewport.hideSelectedColumns();
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363 viewport.selectionGroup = sg;
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366 viewport.showAllHiddenColumns();
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369 alignPanel.repaint();
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372 case KeyEvent.VK_PAGE_UP:
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373 if (viewport.wrapAlignment)
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374 alignPanel.scrollUp(true);
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376 alignPanel.setScrollValues(viewport.startRes,
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378 - viewport.endSeq + viewport.startSeq);
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380 case KeyEvent.VK_PAGE_DOWN:
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381 if (viewport.wrapAlignment)
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382 alignPanel.scrollUp(false);
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384 alignPanel.setScrollValues(viewport.startRes,
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386 + viewport.endSeq - viewport.startSeq);
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390 public void keyReleased(KeyEvent evt)
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392 public void keyTyped(KeyEvent evt)
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395 public void itemStateChanged(ItemEvent evt)
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397 if(evt.getSource()==colourTextMenuItem)
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398 colourTextMenuItem_actionPerformed();
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399 else if(evt.getSource()==wrapMenuItem)
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400 wrapMenuItem_actionPerformed();
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401 else if(evt.getSource()==scaleAbove)
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402 scaleAbove_actionPerformed();
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403 else if(evt.getSource()==scaleLeft)
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404 scaleLeft_actionPerformed();
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405 else if(evt.getSource()==scaleRight)
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406 scaleRight_actionPerformed();
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407 else if(evt.getSource()==seqLimits)
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408 seqLimits_itemStateChanged();
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409 else if(evt.getSource()==viewBoxesMenuItem)
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410 viewBoxesMenuItem_actionPerformed();
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411 else if(evt.getSource()==viewTextMenuItem)
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412 viewTextMenuItem_actionPerformed();
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413 else if(evt.getSource()==renderGapsMenuItem)
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414 renderGapsMenuItem_actionPerformed();
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415 else if(evt.getSource()==annotationPanelMenuItem)
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416 annotationPanelMenuItem_actionPerformed();
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417 else if(evt.getSource()==sequenceFeatures)
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419 viewport.showSequenceFeatures(sequenceFeatures.getState());
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420 alignPanel.seqPanel.seqCanvas.repaint();
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422 else if(evt.getSource()==conservationMenuItem)
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423 conservationMenuItem_actionPerformed();
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424 else if(evt.getSource()==abovePIDThreshold)
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425 abovePIDThreshold_actionPerformed();
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426 else if(evt.getSource()==applyToAllGroups)
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427 applyToAllGroups_actionPerformed();
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428 else if(evt.getSource()==autoCalculate)
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429 viewport.autocalculateConsensus = autoCalculate.getState();
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431 public void actionPerformed(ActionEvent evt)
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433 Object source = evt.getSource();
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435 if(source==inputText)
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436 inputText_actionPerformed();
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437 else if(source==loadTree)
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438 loadTree_actionPerformed();
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439 else if(source==loadApplication)
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440 launchFullApplication();
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441 else if(source==closeMenuItem)
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442 closeMenuItem_actionPerformed();
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443 else if(source==copy)
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444 copy_actionPerformed();
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445 else if(source==undoMenuItem)
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446 undoMenuItem_actionPerformed();
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447 else if(source==redoMenuItem)
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448 redoMenuItem_actionPerformed();
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449 else if(source==inputText)
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450 inputText_actionPerformed();
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451 else if(source==closeMenuItem)
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452 closeMenuItem_actionPerformed();
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453 else if(source==undoMenuItem)
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454 undoMenuItem_actionPerformed();
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455 else if(source==redoMenuItem)
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456 redoMenuItem_actionPerformed();
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457 else if(source==copy)
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458 copy_actionPerformed();
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459 else if(source==pasteNew)
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460 pasteNew_actionPerformed();
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461 else if(source==pasteThis)
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462 pasteThis_actionPerformed();
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463 else if(source==cut)
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464 cut_actionPerformed();
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465 else if(source==delete)
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466 delete_actionPerformed();
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467 else if(source==deleteGroups)
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468 deleteGroups_actionPerformed();
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469 else if(source==selectAllSequenceMenuItem)
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470 selectAllSequenceMenuItem_actionPerformed();
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471 else if(source==deselectAllSequenceMenuItem)
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472 deselectAllSequenceMenuItem_actionPerformed();
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473 else if(source==invertSequenceMenuItem)
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474 invertSequenceMenuItem_actionPerformed();
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475 else if(source==invertColSel)
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476 { viewport.invertColumnSelection(); alignPanel.repaint(); }
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477 else if(source==remove2LeftMenuItem)
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478 remove2LeftMenuItem_actionPerformed();
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479 else if(source==remove2RightMenuItem)
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480 remove2RightMenuItem_actionPerformed();
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481 else if(source==removeGappedColumnMenuItem)
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482 removeGappedColumnMenuItem_actionPerformed();
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483 else if(source==removeAllGapsMenuItem)
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484 removeAllGapsMenuItem_actionPerformed();
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485 else if(source==findMenuItem)
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486 findMenuItem_actionPerformed();
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487 else if(source==font)
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488 font_actionPerformed();
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489 else if(source==showColumns)
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491 viewport.showAllHiddenColumns(); alignPanel.repaint();
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493 else if(source==showSeqs)
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495 viewport.showAllHiddenSeqs();
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497 else if(source == hideColumns)
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499 viewport.hideSelectedColumns(); alignPanel.repaint();
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501 else if(source == hideSequences && viewport.getSelectionGroup()!=null)
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503 viewport.hideAllSelectedSeqs();
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505 else if(source==featureSettings)
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506 featureSettings_actionPerformed();
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507 else if(source==overviewMenuItem)
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508 overviewMenuItem_actionPerformed();
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509 else if(source==noColourmenuItem)
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510 noColourmenuItem_actionPerformed();
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511 else if(source==clustalColour)
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512 clustalColour_actionPerformed();
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513 else if(source==zappoColour)
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514 zappoColour_actionPerformed();
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515 else if(source==taylorColour)
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516 taylorColour_actionPerformed();
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517 else if(source==hydrophobicityColour)
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518 hydrophobicityColour_actionPerformed();
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519 else if(source==helixColour)
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520 helixColour_actionPerformed();
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521 else if(source==strandColour)
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522 strandColour_actionPerformed();
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523 else if(source==turnColour)
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524 turnColour_actionPerformed();
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525 else if(source==buriedColour)
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526 buriedColour_actionPerformed();
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527 else if(source==nucleotideColour)
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528 nucleotideColour_actionPerformed();
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529 else if(source==modifyPID)
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530 modifyPID_actionPerformed();
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531 else if(source==modifyConservation)
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532 modifyConservation_actionPerformed();
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533 else if(source==userDefinedColour)
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534 userDefinedColour_actionPerformed();
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535 else if(source==PIDColour)
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536 PIDColour_actionPerformed();
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537 else if(source==BLOSUM62Colour)
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538 BLOSUM62Colour_actionPerformed();
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539 else if(source==annotationColour)
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540 new AnnotationColourChooser(viewport, alignPanel);
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541 else if(source==sortPairwiseMenuItem)
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542 sortPairwiseMenuItem_actionPerformed();
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543 else if(source==sortIDMenuItem)
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544 sortIDMenuItem_actionPerformed();
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545 else if(source==sortGroupMenuItem)
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546 sortGroupMenuItem_actionPerformed();
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547 else if(source==removeRedundancyMenuItem)
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548 removeRedundancyMenuItem_actionPerformed();
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549 else if(source==pairwiseAlignmentMenuItem)
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550 pairwiseAlignmentMenuItem_actionPerformed();
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551 else if(source==PCAMenuItem)
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552 PCAMenuItem_actionPerformed();
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553 else if(source==averageDistanceTreeMenuItem)
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554 averageDistanceTreeMenuItem_actionPerformed();
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555 else if(source==neighbourTreeMenuItem)
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556 neighbourTreeMenuItem_actionPerformed();
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557 else if(source==njTreeBlosumMenuItem)
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558 njTreeBlosumMenuItem_actionPerformed();
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559 else if(source==avDistanceTreeBlosumMenuItem)
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560 avTreeBlosumMenuItem_actionPerformed();
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561 else if(source==documentation)
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562 documentation_actionPerformed();
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563 else if(source==about)
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564 about_actionPerformed();
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568 public void inputText_actionPerformed()
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570 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
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571 Frame frame = new Frame();
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573 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
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576 protected void outputText_actionPerformed(ActionEvent e)
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578 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
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579 Frame frame = new Frame();
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581 jalview.bin.JalviewLite.addFrame(frame,
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582 "Alignment output - " + e.getActionCommand(),
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584 cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
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585 viewport.getAlignment().getSequences(),
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586 viewport.showJVSuffix));
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589 void launchFullApplication()
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591 StringBuffer url = new StringBuffer(jalviewServletURL);
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593 url.append("?open="+
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594 appendProtocol( viewport.applet.getParameter("file") ) );
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596 if(viewport.applet.getParameter("features")!=null)
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598 url.append( "&features=" );
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599 url.append( appendProtocol( viewport.applet.getParameter("features") ) );
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602 if(viewport.applet.getParameter("annotations")!=null)
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604 url.append( "&annotations=" );
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605 url.append( appendProtocol( viewport.applet.getParameter("annotations") ) );
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608 if(viewport.applet.getParameter("jnetfile")!=null)
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610 url.append( "&annotations=" );
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611 url.append( appendProtocol( viewport.applet.getParameter("jnetfile") ) );
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614 if(viewport.applet.getParameter("defaultColour")!=null)
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616 url.append("&colour=" +
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617 removeWhiteSpace(viewport.applet.getParameter("defaultColour"))
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621 if(viewport.applet.getParameter("userDefinedColour")!=null)
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623 url.append( "&colour=" +
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624 removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") )
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628 showURL(url.toString(), "FULL_APP");
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632 String removeWhiteSpace(String colour)
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634 StringBuffer sb = new StringBuffer();
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635 for (int i = 0; i < colour.length(); i++)
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637 if (Character.isWhitespace(colour.charAt(i)))
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640 sb.append(colour.charAt(i));
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643 return sb.toString();
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647 String appendProtocol(String url)
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651 }catch(java.net.MalformedURLException ex)
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653 url = viewport.applet.getCodeBase()+url;
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658 public void closeMenuItem_actionPerformed()
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660 PaintRefresher.components.remove(viewport.alignment);
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661 if(PaintRefresher.components.size()==0 && viewport.applet==null)
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667 Stack historyList = new Stack();
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668 Stack redoList = new Stack();
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670 void updateEditMenuBar()
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675 protected void undoMenuItem_actionPerformed()
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679 protected void redoMenuItem_actionPerformed()
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684 // used by undo and redo
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685 void restoreHistoryItem(CommandI command)
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689 public void moveSelectedSequences(boolean up)
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691 SequenceGroup sg = viewport.getSelectionGroup();
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699 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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701 SequenceI seq = viewport.alignment.getSequenceAt(i);
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702 if (!sg.getSequences(false).contains(seq))
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707 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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708 if (sg.getSequences(false).contains(temp))
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713 viewport.alignment.getSequences().setElementAt(temp, i);
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714 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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719 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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721 SequenceI seq = viewport.alignment.getSequenceAt(i);
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722 if (!sg.getSequences(true).contains(seq))
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727 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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728 if (sg.getSequences(true).contains(temp))
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733 viewport.alignment.getSequences().setElementAt(temp, i);
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734 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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738 alignPanel.repaint();
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741 static StringBuffer copiedSequences;
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742 static Vector copiedHiddenColumns;
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743 protected void copy_actionPerformed()
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745 if (viewport.getSelectionGroup() == null)
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750 SequenceGroup sg = viewport.getSelectionGroup();
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751 copiedSequences = new StringBuffer();
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752 Hashtable orderedSeqs = new Hashtable();
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753 for (int i = 0; i < sg.getSize(false); i++)
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755 SequenceI seq = sg.getSequenceAt(i);
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756 int index = viewport.alignment.findIndex(seq);
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757 orderedSeqs.put(index + "", seq);
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760 int index = 0, startRes, endRes;
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763 if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
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765 copiedHiddenColumns = new Vector();
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766 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
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767 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();
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770 int[] region = (int[])
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771 viewport.getColumnSelection().getHiddenColumns().elementAt(i);
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773 copiedHiddenColumns.addElement(new int[]
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774 {region[0] - hiddenOffset,
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775 region[1] - hiddenOffset});
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779 copiedHiddenColumns = null;
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782 for (int i = 0; i < sg.getSize(false); i++)
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784 SequenceI seq = null;
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786 while (seq == null)
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788 if (orderedSeqs.containsKey(index + ""))
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790 seq = (SequenceI) orderedSeqs.get(index + "");
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802 //Returns residue following index if gap
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803 startRes = seq.findPosition(sg.getStartRes());
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806 //Need to find the residue preceeding index if gap
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809 for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
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811 ch = seq.getCharAt(j);
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812 if (!jalview.util.Comparison.isGap( (ch)))
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820 endRes += seq.getStart() -1;
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823 copiedSequences.append(seq.getName() + "\t" +
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826 seq.getSequence(sg.getStartRes(),
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827 sg.getEndRes() + 1) + "\n");
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832 protected void pasteNew_actionPerformed()
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837 protected void pasteThis_actionPerformed()
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839 // addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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840 // HistoryItem.PASTE));
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844 void paste(boolean newAlignment)
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848 if (copiedSequences == null)
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853 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
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854 Vector seqs = new Vector();
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855 while (st.hasMoreElements())
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857 String name = st.nextToken();
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858 int start = Integer.parseInt(st.nextToken());
\r
859 int end = Integer.parseInt(st.nextToken());
\r
860 Sequence sequence = new Sequence(name, st.nextToken(), start, end);
\r
864 viewport.alignment.addSequence(sequence);
\r
868 seqs.addElement(sequence);
\r
874 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
875 for (int i = 0; i < seqs.size(); i++)
\r
877 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
880 String newtitle = new String("Copied sequences");
\r
881 if (getTitle().startsWith("Copied sequences"))
\r
883 newtitle = getTitle();
\r
887 newtitle = newtitle.concat("- from " + getTitle());
\r
889 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
893 if (copiedHiddenColumns != null)
\r
895 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
897 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
898 af.viewport.hideColumns(region[0], region[1]);
\r
903 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
\r
908 viewport.setEndSeq(viewport.alignment.getHeight());
\r
909 viewport.alignment.getWidth();
\r
910 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
914 catch (Exception ex)
\r
915 {} // could be anything being pasted in here
\r
919 protected void cut_actionPerformed()
\r
921 copy_actionPerformed();
\r
922 delete_actionPerformed();
\r
925 protected void delete_actionPerformed()
\r
927 //addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
\r
928 // HistoryItem.HIDE));
\r
929 if (viewport.getSelectionGroup() == null)
\r
935 SequenceGroup sg = viewport.getSelectionGroup();
\r
936 boolean allSequences = false;
\r
937 if(sg.getSize(false)==viewport.alignment.getHeight())
\r
938 allSequences = true;
\r
940 for (int i = 0; i < sg.getSize(false); i++)
\r
942 SequenceI seq = sg.getSequenceAt(i);
\r
943 int index = viewport.getAlignment().findIndex(seq);
\r
944 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
\r
946 // If the cut affects all sequences, remove highlighted columns
\r
949 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
950 sg.getEndRes() + 1);
\r
954 if (seq.getSequence().length() < 1)
\r
956 viewport.getAlignment().deleteSequence(seq);
\r
960 viewport.getAlignment().getSequences().setElementAt(seq, index);
\r
964 viewport.setSelectionGroup(null);
\r
965 viewport.alignment.deleteGroup(sg);
\r
966 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
\r
967 if (viewport.getAlignment().getHeight() < 1)
\r
971 this.setVisible(false);
\r
973 catch (Exception ex)
\r
976 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
980 protected void deleteGroups_actionPerformed()
\r
982 viewport.alignment.deleteAllGroups();
\r
983 viewport.sequenceColours.clear();
\r
984 viewport.setSelectionGroup(null);
\r
986 alignPanel.repaint();
\r
989 public void selectAllSequenceMenuItem_actionPerformed()
\r
991 SequenceGroup sg = new SequenceGroup();
\r
992 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
994 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
996 sg.setEndRes(viewport.alignment.getWidth()-1);
\r
997 viewport.setSelectionGroup(sg);
\r
998 alignPanel.repaint();
\r
999 PaintRefresher.Refresh(null, viewport.alignment);
\r
1002 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1004 if(viewport.cursorMode)
\r
1006 alignPanel.seqPanel.keyboardNo1=null;
\r
1007 alignPanel.seqPanel.keyboardNo2=null;
\r
1009 viewport.setSelectionGroup(null);
\r
1010 viewport.getColumnSelection().clear();
\r
1011 viewport.setSelectionGroup(null);
\r
1012 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1013 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1014 alignPanel.repaint();
\r
1015 PaintRefresher.Refresh(null, viewport.alignment);
\r
1018 public void invertSequenceMenuItem_actionPerformed()
\r
1020 SequenceGroup sg = viewport.getSelectionGroup();
\r
1021 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1023 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1026 PaintRefresher.Refresh(null, viewport.alignment);
\r
1029 public void remove2LeftMenuItem_actionPerformed()
\r
1033 public void remove2RightMenuItem_actionPerformed()
\r
1037 public void removeGappedColumnMenuItem_actionPerformed()
\r
1041 public void removeAllGapsMenuItem_actionPerformed()
\r
1045 public void alignmentChanged()
\r
1047 viewport.alignment.padGaps();
\r
1048 if(viewport.autocalculateConsensus)
\r
1050 viewport.updateConsensus();
\r
1051 viewport.updateConservation();
\r
1054 resetAllColourSchemes();
\r
1055 if(alignPanel.overviewPanel!=null)
\r
1056 alignPanel.overviewPanel.updateOverviewImage();
\r
1058 viewport.alignment.adjustSequenceAnnotations();
\r
1059 alignPanel.repaint();
\r
1062 void resetAllColourSchemes()
\r
1064 ColourSchemeI cs = viewport.globalColourScheme;
\r
1067 if (cs instanceof ClustalxColourScheme)
\r
1069 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
\r
1070 resetClustalX(viewport.alignment.getSequences(),
\r
1071 viewport.alignment.getWidth());
\r
1074 cs.setConsensus(viewport.hconsensus);
\r
1075 if (cs.conservationApplied())
\r
1077 Alignment al = (Alignment) viewport.alignment;
\r
1078 Conservation c = new Conservation("All",
\r
1079 ResidueProperties.propHash, 3,
\r
1080 al.getSequences(), 0,
\r
1081 al.getWidth() - 1);
\r
1083 c.verdict(false, viewport.ConsPercGaps);
\r
1085 cs.setConservation(c);
\r
1089 int s, sSize = viewport.alignment.getGroups().size();
\r
1090 for(s=0; s<sSize; s++)
\r
1092 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
\r
1093 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
\r
1095 ((ClustalxColourScheme)sg.cs).resetClustalX(
\r
1096 sg.getSequences(true), sg.getWidth());
\r
1098 sg.recalcConservation();
\r
1104 public void findMenuItem_actionPerformed()
\r
1106 new Finder(alignPanel);
\r
1109 public void font_actionPerformed()
\r
1111 new FontChooser(alignPanel);
\r
1115 public void seqLimits_itemStateChanged()
\r
1117 viewport.setShowJVSuffix(seqLimits.getState());
\r
1118 alignPanel.fontChanged();
\r
1119 alignPanel.repaint();
\r
1123 protected void colourTextMenuItem_actionPerformed()
\r
1125 viewport.setColourText(colourTextMenuItem.getState());
\r
1126 alignPanel.repaint();
\r
1129 protected void wrapMenuItem_actionPerformed()
\r
1131 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
1132 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
1133 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
1134 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
1135 scaleRight.setEnabled(wrapMenuItem.getState());
\r
1136 alignPanel.repaint();
\r
1140 protected void scaleAbove_actionPerformed()
\r
1142 viewport.setScaleAboveWrapped(scaleAbove.getState());
\r
1143 alignPanel.repaint();
\r
1146 protected void scaleLeft_actionPerformed()
\r
1148 viewport.setScaleLeftWrapped(scaleLeft.getState());
\r
1149 alignPanel.repaint();
\r
1152 protected void scaleRight_actionPerformed()
\r
1154 viewport.setScaleRightWrapped(scaleRight.getState());
\r
1155 alignPanel.repaint();
\r
1158 public void viewBoxesMenuItem_actionPerformed()
\r
1160 viewport.setShowBoxes(viewBoxesMenuItem.getState());
\r
1161 alignPanel.repaint();
\r
1164 public void viewTextMenuItem_actionPerformed()
\r
1166 viewport.setShowText(viewTextMenuItem.getState());
\r
1167 alignPanel.repaint();
\r
1170 protected void renderGapsMenuItem_actionPerformed()
\r
1172 viewport.setRenderGaps(renderGapsMenuItem.getState());
\r
1173 alignPanel.repaint();
\r
1176 public void annotationPanelMenuItem_actionPerformed()
\r
1178 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
\r
1179 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
\r
1182 public void featureSettings_actionPerformed()
\r
1184 new FeatureSettings(viewport, alignPanel);
\r
1187 public void overviewMenuItem_actionPerformed()
\r
1189 if (alignPanel.overviewPanel != null)
\r
1194 Frame frame = new Frame();
\r
1195 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1196 frame.add(overview);
\r
1197 // +50 must allow for applet frame window
\r
1198 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
1199 overview.preferredSize().width,
\r
1200 overview.preferredSize().height + 50);
\r
1203 frame.addWindowListener(new WindowAdapter()
\r
1205 public void windowClosing(WindowEvent e)
\r
1207 alignPanel.setOverviewPanel(null);
\r
1211 alignPanel.setOverviewPanel(overview);
\r
1215 protected void noColourmenuItem_actionPerformed()
\r
1217 changeColour(null);
\r
1220 public void clustalColour_actionPerformed()
\r
1222 abovePIDThreshold.setState(false);
\r
1223 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
\r
1224 viewport.alignment.getWidth()));
\r
1227 public void zappoColour_actionPerformed()
\r
1229 changeColour(new ZappoColourScheme());
\r
1232 public void taylorColour_actionPerformed()
\r
1234 changeColour(new TaylorColourScheme());
\r
1237 public void hydrophobicityColour_actionPerformed()
\r
1239 changeColour(new HydrophobicColourScheme());
\r
1242 public void helixColour_actionPerformed()
\r
1244 changeColour(new HelixColourScheme());
\r
1247 public void strandColour_actionPerformed()
\r
1249 changeColour(new StrandColourScheme());
\r
1252 public void turnColour_actionPerformed()
\r
1254 changeColour(new TurnColourScheme());
\r
1257 public void buriedColour_actionPerformed()
\r
1259 changeColour(new BuriedColourScheme());
\r
1262 public void nucleotideColour_actionPerformed()
\r
1264 changeColour(new NucleotideColourScheme());
\r
1267 protected void applyToAllGroups_actionPerformed()
\r
1269 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
\r
1272 void changeColour(ColourSchemeI cs)
\r
1274 int threshold = 0;
\r
1278 if (viewport.getAbovePIDThreshold())
\r
1280 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
\r
1282 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1284 viewport.setGlobalColourScheme(cs);
\r
1288 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1291 if (viewport.getConservationSelected())
\r
1294 Alignment al = (Alignment) viewport.alignment;
\r
1295 Conservation c = new Conservation("All",
\r
1296 ResidueProperties.propHash, 3,
\r
1297 al.getSequences(), 0,
\r
1298 al.getWidth() - 1);
\r
1301 c.verdict(false, viewport.ConsPercGaps);
\r
1303 cs.setConservation(c);
\r
1305 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1311 cs.setConservation(null);
\r
1314 cs.setConsensus(viewport.hconsensus);
\r
1317 viewport.setGlobalColourScheme(cs);
\r
1319 if (viewport.getColourAppliesToAllGroups())
\r
1321 Vector groups = viewport.alignment.getGroups();
\r
1322 for (int i = 0; i < groups.size(); i++)
\r
1324 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1331 if (cs instanceof ClustalxColourScheme)
\r
1333 sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth());
\r
1339 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1341 catch (Exception ex)
\r
1343 ex.printStackTrace();
\r
1348 if (viewport.getAbovePIDThreshold()
\r
1349 || cs instanceof PIDColourScheme
\r
1350 || cs instanceof Blosum62ColourScheme)
\r
1352 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1353 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth()));
\r
1356 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1358 if (viewport.getConservationSelected())
\r
1360 Conservation c = new Conservation("Group",
\r
1361 ResidueProperties.propHash, 3,
\r
1362 sg.getSequences(true), 0,
\r
1363 viewport.alignment.getWidth() - 1);
\r
1365 c.verdict(false, viewport.ConsPercGaps);
\r
1366 sg.cs.setConservation(c);
\r
1370 sg.cs.setConservation(null);
\r
1371 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1378 if (alignPanel.getOverviewPanel() != null)
\r
1380 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1383 alignPanel.repaint();
\r
1388 protected void modifyPID_actionPerformed()
\r
1390 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1392 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
1394 SliderPanel.showPIDSlider();
\r
1398 protected void modifyConservation_actionPerformed()
\r
1400 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1402 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
1404 SliderPanel.showConservationSlider();
\r
1408 protected void conservationMenuItem_actionPerformed()
\r
1410 viewport.setConservationSelected(conservationMenuItem.getState());
\r
1412 viewport.setAbovePIDThreshold(false);
\r
1413 abovePIDThreshold.setState(false);
\r
1415 changeColour(viewport.getGlobalColourScheme());
\r
1417 modifyConservation_actionPerformed();
\r
1420 public void abovePIDThreshold_actionPerformed()
\r
1422 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
1424 conservationMenuItem.setState(false);
\r
1425 viewport.setConservationSelected(false);
\r
1427 changeColour(viewport.getGlobalColourScheme());
\r
1429 modifyPID_actionPerformed();
\r
1432 public void userDefinedColour_actionPerformed()
\r
1434 new UserDefinedColours(alignPanel, null);
\r
1437 public void PIDColour_actionPerformed()
\r
1439 changeColour(new PIDColourScheme());
\r
1442 public void BLOSUM62Colour_actionPerformed()
\r
1444 changeColour(new Blosum62ColourScheme());
\r
1447 public void sortPairwiseMenuItem_actionPerformed()
\r
1449 // addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1450 // HistoryItem.SORT));
\r
1451 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1452 viewport.getAlignment().getSequenceAt(0));
\r
1453 alignPanel.repaint();
\r
1456 public void sortIDMenuItem_actionPerformed()
\r
1458 // addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1459 // HistoryItem.SORT));
\r
1460 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1461 alignPanel.repaint();
\r
1464 public void sortGroupMenuItem_actionPerformed()
\r
1466 // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1467 // HistoryItem.SORT));
\r
1468 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1469 alignPanel.repaint();
\r
1473 public void removeRedundancyMenuItem_actionPerformed()
\r
1475 new RedundancyPanel(alignPanel);
\r
1478 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
1480 if (viewport.getSelectionGroup()!=null
\r
1481 && viewport.getSelectionGroup().getSize(false) > 1)
\r
1483 Frame frame = new Frame();
\r
1484 frame.add(new PairwiseAlignPanel(alignPanel));
\r
1485 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
1489 public void PCAMenuItem_actionPerformed()
\r
1491 //are the sequences aligned?
\r
1492 if (!viewport.alignment.isAligned())
\r
1494 SequenceI current;
\r
1495 int Width = viewport.getAlignment().getWidth();
\r
1497 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1500 current = viewport.getAlignment().getSequenceAt(i);
\r
1502 if (current.getLength() < Width)
\r
1504 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1507 alignPanel.repaint();
\r
1510 if ( (viewport.getSelectionGroup() != null &&
\r
1511 viewport.getSelectionGroup().getSize(false) < 4 &&
\r
1512 viewport.getSelectionGroup().getSize(false) > 0)
\r
1513 || viewport.getAlignment().getHeight() < 4)
\r
1520 new PCAPanel(viewport);
\r
1522 catch (java.lang.OutOfMemoryError ex)
\r
1528 public void averageDistanceTreeMenuItem_actionPerformed()
\r
1530 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1533 public void neighbourTreeMenuItem_actionPerformed()
\r
1535 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1538 protected void njTreeBlosumMenuItem_actionPerformed()
\r
1540 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1543 protected void avTreeBlosumMenuItem_actionPerformed()
\r
1545 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1548 void NewTreePanel(String type, String pwType, String title)
\r
1550 //are the sequences aligned?
\r
1551 if (!viewport.alignment.isAligned())
\r
1553 SequenceI current;
\r
1554 int Width = viewport.getAlignment().getWidth();
\r
1556 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1559 current = viewport.getAlignment().getSequenceAt(i);
\r
1561 if (current.getLength() < Width)
\r
1563 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1566 alignPanel.repaint();
\r
1570 if ( (viewport.getSelectionGroup() != null &&
\r
1571 viewport.getSelectionGroup().getSize(false) > 1)
\r
1572 || (viewport.getSelectionGroup() == null
\r
1573 && viewport.alignment.getHeight() > 1))
\r
1575 final TreePanel tp = new TreePanel(viewport,
\r
1579 addTreeMenuItem(tp, title);
\r
1581 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
1585 void loadTree_actionPerformed()
\r
1587 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1588 cap.setText("Paste your Newick tree file here.");
\r
1589 cap.treeImport = true;
\r
1590 Frame frame = new Frame();
\r
1592 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
1595 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
1597 TreePanel tp = new TreePanel(viewport,
\r
1601 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
1602 addTreeMenuItem(tp, treeFile);
\r
1605 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1607 final MenuItem item = new MenuItem(title);
\r
1608 sortByTreeMenu.add(item);
\r
1609 item.addActionListener(new java.awt.event.ActionListener()
\r
1611 public void actionPerformed(ActionEvent evt)
\r
1613 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1614 // HistoryItem.SORT));
\r
1615 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1616 alignPanel.repaint();
\r
1620 treePanel.addWindowListener(new WindowAdapter()
\r
1622 public void windowClosing(WindowEvent e)
\r
1624 sortByTreeMenu.remove(item);
\r
1629 protected void documentation_actionPerformed()
\r
1631 showURL("http://www.jalview.org/help.html", "HELP");
\r
1634 protected void about_actionPerformed()
\r
1637 class AboutPanel extends Canvas
\r
1640 public AboutPanel(String version)
\r
1641 { this.version = version; }
\r
1643 public void paint(Graphics g)
\r
1645 g.setColor(Color.white);
\r
1646 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1647 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1648 FontMetrics fm = g.getFontMetrics();
\r
1649 int fh = fm.getHeight();
\r
1651 g.setColor(Color.black);
\r
1652 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
1653 g.drawString("Jalview - Release "+version, 200, y += fh);
\r
1654 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1655 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
1657 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
1660 "For any issues relating to Jalview, email help@jalview.org", x,
\r
1662 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
1663 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
1665 g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh);
\r
1669 String version = "test";
\r
1670 java.net.URL url = getClass().getResource("/.build_properties");
\r
1675 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
1676 url.openStream()));
\r
1678 while ( (line = reader.readLine()) != null)
\r
1680 if (line.indexOf("VERSION") > -1)
\r
1682 version = line.substring(line.indexOf("=") + 1);
\r
1686 catch (Exception ex)
\r
1688 ex.printStackTrace();
\r
1693 Frame frame = new Frame();
\r
1694 frame.add(new AboutPanel(version));
\r
1695 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
\r
1699 public void showURL(String url, String target)
\r
1701 if (viewport.applet == null)
\r
1703 System.out.println("Not running as applet - no browser available.");
\r
1709 System.out.println("Show url: "+url);
\r
1710 viewport.applet.getAppletContext().showDocument(new java.net.URL(url),
\r
1713 catch (Exception ex)
\r
1715 ex.printStackTrace();
\r
1721 //////////////////////////////////////////////////////////////////////////////////
\r
1722 //JBuilder Graphics here
\r
1724 protected MenuBar alignFrameMenuBar = new MenuBar();
\r
1725 protected Menu fileMenu = new Menu("File");
\r
1726 protected MenuItem loadApplication = new MenuItem("View in Full Application");
\r
1727 protected MenuItem loadTree = new MenuItem("Load Associated Tree");
\r
1728 protected MenuItem closeMenuItem = new MenuItem("Close");
\r
1729 protected Menu editMenu = new Menu("Edit");
\r
1730 protected Menu viewMenu = new Menu("View");
\r
1731 protected Menu colourMenu = new Menu("Colour");
\r
1732 protected Menu calculateMenu = new Menu("Calculate");
\r
1733 protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
1734 protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
1735 protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
1736 protected MenuItem remove2LeftMenuItem = new MenuItem();
\r
1737 protected MenuItem remove2RightMenuItem = new MenuItem();
\r
1738 protected MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
1739 protected MenuItem removeAllGapsMenuItem = new MenuItem();
\r
1740 protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
1741 protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
1742 protected MenuItem sortPairwiseMenuItem = new MenuItem();
\r
1743 protected MenuItem sortIDMenuItem = new MenuItem();
\r
1744 protected MenuItem sortGroupMenuItem = new MenuItem();
\r
1745 protected MenuItem removeRedundancyMenuItem = new MenuItem();
\r
1746 protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
1747 protected MenuItem PCAMenuItem = new MenuItem();
\r
1748 protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
1749 protected MenuItem neighbourTreeMenuItem = new MenuItem();
\r
1750 BorderLayout borderLayout1 = new BorderLayout();
\r
1751 public Label statusBar = new Label();
\r
1752 protected Menu outputTextboxMenu = new Menu();
\r
1753 protected MenuItem clustalColour = new MenuItem();
\r
1754 protected MenuItem zappoColour = new MenuItem();
\r
1755 protected MenuItem taylorColour = new MenuItem();
\r
1756 protected MenuItem hydrophobicityColour = new MenuItem();
\r
1757 protected MenuItem helixColour = new MenuItem();
\r
1758 protected MenuItem strandColour = new MenuItem();
\r
1759 protected MenuItem turnColour = new MenuItem();
\r
1760 protected MenuItem buriedColour = new MenuItem();
\r
1761 protected MenuItem userDefinedColour = new MenuItem();
\r
1762 protected MenuItem PIDColour = new MenuItem();
\r
1763 protected MenuItem BLOSUM62Colour = new MenuItem();
\r
1764 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
1765 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
1766 protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
1767 protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
1768 MenuItem overviewMenuItem = new MenuItem();
\r
1769 protected MenuItem undoMenuItem = new MenuItem();
\r
1770 protected MenuItem redoMenuItem = new MenuItem();
\r
1771 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
1772 MenuItem noColourmenuItem = new MenuItem();
\r
1773 protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
1774 protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
1775 MenuItem findMenuItem = new MenuItem();
\r
1776 Menu searchMenu = new Menu();
\r
1777 protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
1778 protected MenuItem nucleotideColour = new MenuItem();
\r
1779 MenuItem deleteGroups = new MenuItem();
\r
1780 MenuItem delete = new MenuItem();
\r
1781 MenuItem copy = new MenuItem();
\r
1782 MenuItem cut = new MenuItem();
\r
1783 Menu pasteMenu = new Menu();
\r
1784 MenuItem pasteNew = new MenuItem();
\r
1785 MenuItem pasteThis = new MenuItem();
\r
1786 protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
1787 protected MenuItem font = new MenuItem();
\r
1788 protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
1789 protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
1790 protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
1791 MenuItem modifyPID = new MenuItem();
\r
1792 MenuItem modifyConservation = new MenuItem();
\r
1793 protected CheckboxMenuItem autoCalculate
\r
1794 = new CheckboxMenuItem("Autocalculate Consensus", true);
\r
1795 protected Menu sortByTreeMenu = new Menu();
\r
1796 Menu sort = new Menu();
\r
1797 Menu calculate = new Menu();
\r
1798 MenuItem inputText = new MenuItem();
\r
1799 Menu helpMenu = new Menu();
\r
1800 MenuItem documentation = new MenuItem();
\r
1801 MenuItem about = new MenuItem();
\r
1802 protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
1803 Panel embeddedMenu;
\r
1804 Label embeddedEdit;
\r
1805 Label embeddedSearch;
\r
1806 Label embeddedView;
\r
1807 Label embeddedColour;
\r
1808 Label embeddedFile;
\r
1809 Label embeddedHelp;
\r
1810 Label embeddedCalculate;
\r
1811 FlowLayout flowLayout1;
\r
1813 private void jbInit() throws Exception {
\r
1815 setMenuBar(alignFrameMenuBar);
\r
1819 // dynamically fill save as menu with available formats
\r
1820 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
1823 item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
1825 item.addActionListener(new java.awt.event.ActionListener()
\r
1827 public void actionPerformed(ActionEvent e)
\r
1829 outputText_actionPerformed(e);
\r
1833 outputTextboxMenu.add(item);
\r
1835 closeMenuItem.addActionListener(this);
\r
1836 loadApplication.addActionListener(this);
\r
1838 loadTree.addActionListener(this);
\r
1839 selectAllSequenceMenuItem.addActionListener(this);
\r
1840 deselectAllSequenceMenuItem.addActionListener(this);
\r
1841 invertSequenceMenuItem.addActionListener(this);
\r
1842 remove2LeftMenuItem.setLabel("Remove Left");
\r
1843 remove2LeftMenuItem.addActionListener(this);
\r
1844 remove2RightMenuItem.setLabel("Remove Right");
\r
1845 remove2RightMenuItem.addActionListener(this);
\r
1846 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
1847 removeGappedColumnMenuItem.addActionListener(this);
\r
1848 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
1849 removeAllGapsMenuItem.addActionListener(this);
\r
1850 viewBoxesMenuItem.setLabel("Boxes");
\r
1851 viewBoxesMenuItem.setState(true);
\r
1852 viewBoxesMenuItem.addItemListener(this);
\r
1853 viewTextMenuItem.setLabel("Text");
\r
1854 viewTextMenuItem.setState(true);
\r
1855 viewTextMenuItem.addItemListener(this);
\r
1856 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
1857 sortPairwiseMenuItem.addActionListener(this);
\r
1858 sortIDMenuItem.setLabel("by ID");
\r
1859 sortIDMenuItem.addActionListener(this);
\r
1860 sortGroupMenuItem.setLabel("by Group");
\r
1861 sortGroupMenuItem.addActionListener(this);
\r
1862 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
1863 removeRedundancyMenuItem.addActionListener(this);
\r
1864 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
1865 pairwiseAlignmentMenuItem.addActionListener(this);
\r
1866 PCAMenuItem.setLabel("Principal Component Analysis");
\r
1867 PCAMenuItem.addActionListener(this);
\r
1868 averageDistanceTreeMenuItem.setLabel(
\r
1869 "Average Distance Using % Identity");
\r
1870 averageDistanceTreeMenuItem.addActionListener(this);
\r
1871 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
1872 neighbourTreeMenuItem.addActionListener(this);
\r
1873 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
1874 statusBar.setBackground(Color.white);
\r
1875 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
1876 statusBar.setText("Status bar");
\r
1877 outputTextboxMenu.setLabel("Output to Textbox");
\r
1878 clustalColour.setLabel("Clustalx");
\r
1880 clustalColour.addActionListener(this);
\r
1881 zappoColour.setLabel("Zappo");
\r
1882 zappoColour.addActionListener(this);
\r
1883 taylorColour.setLabel("Taylor");
\r
1884 taylorColour.addActionListener(this);
\r
1885 hydrophobicityColour.setLabel("Hydrophobicity");
\r
1886 hydrophobicityColour.addActionListener(this);
\r
1887 helixColour.setLabel("Helix Propensity");
\r
1888 helixColour.addActionListener(this);
\r
1889 strandColour.setLabel("Strand Propensity");
\r
1890 strandColour.addActionListener(this);
\r
1891 turnColour.setLabel("Turn Propensity");
\r
1892 turnColour.addActionListener(this);
\r
1893 buriedColour.setLabel("Buried Index");
\r
1894 buriedColour.addActionListener(this);
\r
1895 userDefinedColour.setLabel("User Defined...");
\r
1896 userDefinedColour.addActionListener(this);
\r
1897 PIDColour.setLabel("Percentage Identity");
\r
1898 PIDColour.addActionListener(this);
\r
1899 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
1900 BLOSUM62Colour.addActionListener(this);
\r
1901 avDistanceTreeBlosumMenuItem.setLabel(
\r
1902 "Average Distance Using BLOSUM62");
\r
1903 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
1904 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
1905 njTreeBlosumMenuItem.addActionListener(this);
\r
1906 annotationPanelMenuItem.setLabel("Show Annotations");
\r
1907 annotationPanelMenuItem.addItemListener(this);
\r
1908 colourTextMenuItem.setLabel("Colour Text");
\r
1909 colourTextMenuItem.addItemListener(this);
\r
1910 overviewMenuItem.setLabel("Overview Window");
\r
1911 overviewMenuItem.addActionListener(this);
\r
1912 undoMenuItem.setEnabled(false);
\r
1913 undoMenuItem.setLabel("Undo");
\r
1914 undoMenuItem.addActionListener(this);
\r
1915 redoMenuItem.setEnabled(false);
\r
1916 redoMenuItem.setLabel("Redo");
\r
1917 redoMenuItem.addActionListener(this);
\r
1918 conservationMenuItem.setLabel("by Conservation");
\r
1919 conservationMenuItem.addItemListener(this);
\r
1920 noColourmenuItem.setLabel("None");
\r
1921 noColourmenuItem.addActionListener(this);
\r
1922 wrapMenuItem.setLabel("Wrap");
\r
1923 wrapMenuItem.addItemListener(this);
\r
1924 renderGapsMenuItem.setLabel("Show Gaps");
\r
1925 renderGapsMenuItem.setState(true);
\r
1926 renderGapsMenuItem.addItemListener(this);
\r
1927 findMenuItem.setLabel("Find...");
\r
1928 findMenuItem.addActionListener(this);
\r
1929 searchMenu.setLabel("Search");
\r
1931 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
1932 abovePIDThreshold.addItemListener(this);
\r
1933 nucleotideColour.setLabel("Nucleotide");
\r
1934 nucleotideColour.addActionListener(this);
\r
1935 deleteGroups.setLabel("Undefine Groups");
\r
1936 deleteGroups.addActionListener(this);
\r
1937 copy.setLabel("Copy");
\r
1938 copy.addActionListener(this);
\r
1939 cut.setLabel("Cut");
\r
1940 cut.addActionListener(this);
\r
1941 delete.setLabel("Delete");
\r
1942 delete.addActionListener(this);
\r
1943 pasteMenu.setLabel("Paste");
\r
1944 pasteNew.setLabel("To New Alignment");
\r
1945 pasteNew.addActionListener(this);
\r
1946 pasteThis.setLabel("Add To This Alignment");
\r
1947 pasteThis.addActionListener(this);
\r
1948 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
1949 applyToAllGroups.setState(true);
\r
1950 applyToAllGroups.addItemListener(this);
\r
1951 font.setLabel("Font...");
\r
1952 font.addActionListener(this);
\r
1953 scaleAbove.setLabel("Scale Above");
\r
1954 scaleAbove.setState(true);
\r
1955 scaleAbove.setEnabled(false);
\r
1956 scaleAbove.addItemListener(this);
\r
1957 scaleLeft.setEnabled(false);
\r
1958 scaleLeft.setState(true);
\r
1959 scaleLeft.setLabel("Scale Left");
\r
1960 scaleLeft.addItemListener(this);
\r
1961 scaleRight.setEnabled(false);
\r
1962 scaleRight.setState(true);
\r
1963 scaleRight.setLabel("Scale Right");
\r
1964 scaleRight.addItemListener(this);
\r
1965 modifyPID.setLabel("Modify Identity Threshold...");
\r
1966 modifyPID.addActionListener(this);
\r
1967 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
1968 modifyConservation.addActionListener(this);
\r
1969 sortByTreeMenu.setLabel("By Tree Order");
\r
1970 sort.setLabel("Sort");
\r
1971 calculate.setLabel("Calculate Tree");
\r
1972 autoCalculate.addItemListener(this);
\r
1973 inputText.setLabel("Input from textbox");
\r
1974 inputText.addActionListener(this);
\r
1976 helpMenu.setLabel("Help");
\r
1977 documentation.setLabel("Documentation");
\r
1978 documentation.addActionListener(this);
\r
1980 about.setLabel("About...");
\r
1981 about.addActionListener(this);
\r
1982 seqLimits.setState(true);
\r
1983 seqLimits.setLabel("Show Sequence Limits");
\r
1984 seqLimits.addItemListener(this);
\r
1985 featureSettings.setLabel("Feature Settings...");
\r
1986 featureSettings.addActionListener(this);
\r
1987 sequenceFeatures.setLabel("Sequence Features");
\r
1988 sequenceFeatures.addItemListener(this);
\r
1989 sequenceFeatures.setState(false);
\r
1990 annotationColour.setLabel("by Annotation...");
\r
1991 annotationColour.addActionListener(this);
\r
1992 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
1993 invertColSel.setLabel("Invert Column Selection");
\r
1994 menu1.setLabel("Show");
\r
1995 showColumns.setLabel("All Columns ");
\r
1996 showSeqs.setLabel("All Sequences");
\r
1997 menu2.setLabel("Hide");
\r
1998 hideColumns.setLabel("Selected Columns");
\r
1999 hideSequences.setLabel("Selected Sequences");
\r
2000 invertColSel.addActionListener(this);
\r
2001 showColumns.addActionListener(this);
\r
2002 showSeqs.addActionListener(this);
\r
2003 hideColumns.addActionListener(this);
\r
2004 hideSequences.addActionListener(this);
\r
2007 alignFrameMenuBar.add(fileMenu);
\r
2008 alignFrameMenuBar.add(editMenu);
\r
2009 alignFrameMenuBar.add(searchMenu);
\r
2010 alignFrameMenuBar.add(viewMenu);
\r
2011 alignFrameMenuBar.add(colourMenu);
\r
2012 alignFrameMenuBar.add(calculateMenu);
\r
2013 alignFrameMenuBar.add(helpMenu);
\r
2014 fileMenu.add(inputText);
\r
2015 fileMenu.add(outputTextboxMenu);
\r
2016 if(jalviewServletURL!=null)
\r
2017 fileMenu.add(loadApplication);
\r
2018 fileMenu.addSeparator();
\r
2019 fileMenu.add(loadTree);
\r
2020 fileMenu.add(closeMenuItem);
\r
2021 editMenu.add(undoMenuItem);
\r
2022 editMenu.add(redoMenuItem);
\r
2023 editMenu.add(cut);
\r
2024 editMenu.add(copy);
\r
2025 editMenu.add(pasteMenu);
\r
2026 editMenu.add(delete);
\r
2027 editMenu.addSeparator();
\r
2028 editMenu.add(selectAllSequenceMenuItem);
\r
2029 editMenu.add(deselectAllSequenceMenuItem);
\r
2030 editMenu.add(invertSequenceMenuItem);
\r
2031 editMenu.add(invertColSel);
\r
2032 editMenu.add(deleteGroups);
\r
2033 editMenu.addSeparator();
\r
2034 editMenu.add(remove2LeftMenuItem);
\r
2035 editMenu.add(remove2RightMenuItem);
\r
2036 editMenu.add(removeGappedColumnMenuItem);
\r
2037 editMenu.add(removeAllGapsMenuItem);
\r
2038 editMenu.add(removeRedundancyMenuItem);
\r
2039 searchMenu.add(findMenuItem);
\r
2040 viewMenu.add(font);
\r
2041 viewMenu.addSeparator();
\r
2042 viewMenu.add(menu1);
\r
2043 viewMenu.add(menu2);
\r
2044 viewMenu.addSeparator();
\r
2045 viewMenu.add(wrapMenuItem);
\r
2046 viewMenu.add(scaleAbove);
\r
2047 viewMenu.add(scaleLeft);
\r
2048 viewMenu.add(scaleRight);
\r
2049 viewMenu.addSeparator();
\r
2050 viewMenu.add(seqLimits);
\r
2051 viewMenu.add(viewBoxesMenuItem);
\r
2052 viewMenu.add(viewTextMenuItem);
\r
2053 viewMenu.add(colourTextMenuItem);
\r
2054 viewMenu.add(renderGapsMenuItem);
\r
2055 viewMenu.add(annotationPanelMenuItem);
\r
2056 viewMenu.addSeparator();
\r
2057 viewMenu.add(sequenceFeatures);
\r
2058 viewMenu.add(featureSettings);
\r
2059 viewMenu.addSeparator();
\r
2060 viewMenu.add(overviewMenuItem);
\r
2061 colourMenu.add(applyToAllGroups);
\r
2062 colourMenu.addSeparator();
\r
2063 colourMenu.add(noColourmenuItem);
\r
2064 colourMenu.add(clustalColour);
\r
2065 colourMenu.add(BLOSUM62Colour);
\r
2066 colourMenu.add(PIDColour);
\r
2067 colourMenu.add(zappoColour);
\r
2068 colourMenu.add(taylorColour);
\r
2069 colourMenu.add(hydrophobicityColour);
\r
2070 colourMenu.add(helixColour);
\r
2071 colourMenu.add(strandColour);
\r
2072 colourMenu.add(turnColour);
\r
2073 colourMenu.add(buriedColour);
\r
2074 colourMenu.add(nucleotideColour);
\r
2075 colourMenu.add(userDefinedColour);
\r
2076 colourMenu.addSeparator();
\r
2077 colourMenu.add(conservationMenuItem);
\r
2078 colourMenu.add(modifyConservation);
\r
2079 colourMenu.add(abovePIDThreshold);
\r
2080 colourMenu.add(modifyPID);
\r
2081 colourMenu.add(annotationColour);
\r
2082 calculateMenu.add(sort);
\r
2083 calculateMenu.add(calculate);
\r
2084 calculateMenu.addSeparator();
\r
2085 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
2086 calculateMenu.add(PCAMenuItem);
\r
2087 calculateMenu.add(autoCalculate);
\r
2088 this.add(statusBar, BorderLayout.SOUTH);
\r
2089 pasteMenu.add(pasteNew);
\r
2090 pasteMenu.add(pasteThis);
\r
2091 sort.add(sortIDMenuItem);
\r
2092 sort.add(sortByTreeMenu);
\r
2093 sort.add(sortGroupMenuItem);
\r
2094 sort.add(sortPairwiseMenuItem);
\r
2095 calculate.add(averageDistanceTreeMenuItem);
\r
2096 calculate.add(neighbourTreeMenuItem);
\r
2097 calculate.add(avDistanceTreeBlosumMenuItem);
\r
2098 calculate.add(njTreeBlosumMenuItem);
\r
2099 helpMenu.add(documentation);
\r
2100 helpMenu.add(about);
\r
2101 menu1.add(showColumns);
\r
2102 menu1.add(showSeqs);
\r
2103 menu2.add(hideColumns);
\r
2104 menu2.add(hideSequences);
\r
2107 public void setEmbedded()
\r
2110 embeddedMenu = new Panel();
\r
2111 embeddedEdit = new Label();
\r
2112 embeddedSearch = new Label();
\r
2113 embeddedView = new Label();
\r
2114 embeddedColour = new Label();
\r
2115 embeddedFile = new Label();
\r
2116 embeddedHelp = new Label();
\r
2117 embeddedCalculate = new Label();
\r
2118 flowLayout1 = new FlowLayout();
\r
2119 embeddedMenu.setBackground(Color.lightGray);
\r
2120 embeddedMenu.setLayout(flowLayout1);
\r
2121 embeddedEdit.setText("Edit");
\r
2122 embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2123 embeddedSearch.setText("Search");
\r
2124 embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2125 embeddedView.setText("View");
\r
2126 embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2127 embeddedColour.setText("Colour");
\r
2128 embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2129 embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2130 embeddedFile.setText("File");
\r
2131 embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2132 embeddedHelp.setText("Help");
\r
2133 embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2134 embeddedCalculate.setText("Calculate");
\r
2135 embeddedMenu.add(embeddedFile);
\r
2136 embeddedMenu.add(embeddedEdit);
\r
2137 embeddedMenu.add(embeddedSearch);
\r
2138 embeddedMenu.add(embeddedView);
\r
2139 embeddedMenu.add(embeddedColour);
\r
2140 embeddedMenu.add(embeddedCalculate);
\r
2141 embeddedMenu.add(embeddedHelp);
\r
2142 flowLayout1.setAlignment(FlowLayout.LEFT);
\r
2143 flowLayout1.setHgap(2);
\r
2144 flowLayout1.setVgap(0);
\r
2145 embeddedFile.addMouseListener(this);
\r
2146 embeddedEdit.addMouseListener(this);
\r
2147 embeddedSearch.addMouseListener(this);
\r
2148 embeddedView.addMouseListener(this);
\r
2149 embeddedColour.addMouseListener(this);
\r
2150 embeddedCalculate.addMouseListener(this);
\r
2151 embeddedHelp.addMouseListener(this);
\r
2153 // setVisible(false);
\r
2154 fileMenu.remove(closeMenuItem);
\r
2155 fileMenu.remove(3); // Seperator
\r
2157 viewport.applet.setLayout(new BorderLayout());
\r
2158 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
\r
2159 viewport.applet.add(statusBar, BorderLayout.SOUTH);
\r
2160 // viewport.applet.validate();
\r
2162 alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height
\r
2163 - embeddedMenu.HEIGHT - statusBar.HEIGHT);
\r
2165 viewport.applet.add(alignPanel, BorderLayout.CENTER);
\r
2166 viewport.applet.validate();
\r
2172 PopupMenu filePopup, editPopup, searchPopup,
\r
2173 viewPopup, colourPopup, calculatePopup, helpPopup;
\r
2174 MenuItem featureSettings = new MenuItem();
\r
2175 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
2176 MenuItem annotationColour = new MenuItem();
\r
2177 MenuItem invertColSel = new MenuItem();
\r
2178 Menu menu1 = new Menu();
\r
2179 MenuItem showColumns = new MenuItem();
\r
2180 MenuItem showSeqs = new MenuItem();
\r
2181 Menu menu2 = new Menu();
\r
2182 MenuItem hideColumns = new MenuItem();
\r
2183 MenuItem hideSequences = new MenuItem();
\r
2185 public void mousePressed(MouseEvent evt)
\r
2187 PopupMenu popup = null;
\r
2188 Label source = (Label)evt.getSource();
\r
2189 if(source==embeddedFile)
\r
2191 popup = filePopup = genPopupMenu(filePopup, fileMenu);
\r
2193 else if(source==embeddedEdit)
\r
2195 popup = editPopup = genPopupMenu(editPopup, editMenu);
\r
2197 else if(source==embeddedSearch)
\r
2199 popup = searchPopup = genPopupMenu(searchPopup, searchMenu);
\r
2201 else if(source==embeddedView)
\r
2203 popup = viewPopup = genPopupMenu(viewPopup, viewMenu);
\r
2205 else if(source==embeddedColour)
\r
2207 popup = colourPopup = genPopupMenu(colourPopup, colourMenu);
\r
2209 else if(source==embeddedCalculate)
\r
2211 popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);
\r
2213 else if(source==embeddedHelp)
\r
2215 popup = helpPopup = genPopupMenu(helpPopup, helpMenu);
\r
2218 embeddedMenu.add(popup);
\r
2219 popup.show(embeddedMenu,
\r
2220 source.getBounds().x,
\r
2221 source.getBounds().y + source.getBounds().getSize().height);
\r
2224 PopupMenu genPopupMenu(PopupMenu popup, Menu original)
\r
2230 popup = new PopupMenu();
\r
2231 int m, mSize = original.getItemCount();
\r
2232 for(m=0; m<mSize; m++)
\r
2234 popup.add(original.getItem(m));
\r
2241 public void mouseClicked(MouseEvent evt)
\r
2243 public void mouseReleased(MouseEvent evt)
\r
2245 public void mouseEntered(MouseEvent evt)
\r
2247 public void mouseExited(MouseEvent evt)
\r