2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2007 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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27 import java.awt.event.*;
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29 import jalview.analysis.*;
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30 import jalview.commands.*;
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31 import jalview.datamodel.*;
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32 import jalview.io.*;
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33 import jalview.schemes.*;
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35 public class AlignFrame
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36 extends Frame implements ActionListener,
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37 ItemListener, KeyListener, MouseListener
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39 public AlignmentPanel alignPanel;
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40 public AlignViewport viewport;
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41 int DEFAULT_WIDTH = 700;
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42 int DEFAULT_HEIGHT = 500;
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44 String jalviewServletURL;
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46 public AlignFrame(AlignmentI al,
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47 jalview.bin.JalviewLite applet,
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54 jalviewServletURL = applet.getParameter("APPLICATION_URL");
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61 catch (Exception ex)
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63 ex.printStackTrace();
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66 viewport = new AlignViewport(al, applet);
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67 alignPanel = new AlignmentPanel(this, viewport);
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69 viewport.updateConservation(alignPanel);
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70 viewport.updateConsensus(alignPanel);
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72 annotationPanelMenuItem.setState(viewport.showAnnotation);
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74 seqLimits.setState(viewport.showJVSuffix);
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78 String param = applet.getParameter("sortBy");
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81 if (param.equalsIgnoreCase("Id"))
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83 sortIDMenuItem_actionPerformed();
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85 else if (param.equalsIgnoreCase("Pairwise Identity"))
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87 sortPairwiseMenuItem_actionPerformed();
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91 param = applet.getParameter("wrap");
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94 if (param.equalsIgnoreCase("true"))
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96 wrapMenuItem.setState(true);
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97 wrapMenuItem_actionPerformed();
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103 param = applet.getParameter("windowWidth");
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106 int width = Integer.parseInt(param);
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107 DEFAULT_WIDTH = width;
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109 param = applet.getParameter("windowHeight");
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112 int height = Integer.parseInt(param);
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113 DEFAULT_HEIGHT = height;
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116 catch (Exception ex)
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121 //Some JVMS send keyevents to Top frame or lowest panel,
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122 //Havent worked out why yet. So add to both this frame and seqCanvas for now
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123 this.addKeyListener(this);
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124 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
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125 alignPanel.idPanel.idCanvas.addKeyListener(this);
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126 alignPanel.scalePanel.addKeyListener(this);
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127 alignPanel.annotationPanel.addKeyListener(this);
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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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143 public AlignViewport getAlignViewport()
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148 public SeqCanvas getSeqcanvas()
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150 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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165 featuresFile = new jalview.io.FeaturesFile(file,
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166 type).parse(viewport.alignment,
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167 alignPanel.seqPanel.seqCanvas.
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168 getFeatureRenderer().featureColours,
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172 catch (Exception ex)
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174 ex.printStackTrace();
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179 if (featureLinks.size() > 0)
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181 alignPanel.seqPanel.seqCanvas
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182 .getFeatureRenderer().featureLinks = featureLinks;
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184 viewport.showSequenceFeatures = true;
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185 sequenceFeatures.setState(true);
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186 alignPanel.repaint();
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191 public void keyPressed(KeyEvent evt)
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193 if (viewport.cursorMode
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194 && evt.getKeyCode() >= KeyEvent.VK_0
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195 && evt.getKeyCode() <= KeyEvent.VK_9)
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197 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
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200 switch (evt.getKeyCode())
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202 case 27: // escape key
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203 deselectAllSequenceMenuItem_actionPerformed();
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205 case KeyEvent.VK_X:
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206 if (evt.isControlDown() || evt.isMetaDown())
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208 cut_actionPerformed();
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211 case KeyEvent.VK_C:
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212 if (viewport.cursorMode && !evt.isControlDown())
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214 alignPanel.seqPanel.setCursorColumn();
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216 if (evt.isControlDown() || evt.isMetaDown())
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218 copy_actionPerformed();
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221 case KeyEvent.VK_V:
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222 if (evt.isControlDown())
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224 paste(evt.isShiftDown());
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227 case KeyEvent.VK_A:
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228 if (evt.isControlDown() || evt.isMetaDown())
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230 selectAllSequenceMenuItem_actionPerformed();
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233 case KeyEvent.VK_DOWN:
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234 if (viewport.cursorMode)
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236 alignPanel.seqPanel.moveCursor(0, 1);
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240 moveSelectedSequences(false);
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244 case KeyEvent.VK_UP:
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245 if (viewport.cursorMode)
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247 alignPanel.seqPanel.moveCursor(0, -1);
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251 moveSelectedSequences(true);
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255 case KeyEvent.VK_LEFT:
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256 if (viewport.cursorMode)
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258 alignPanel.seqPanel.moveCursor( -1, 0);
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262 case KeyEvent.VK_RIGHT:
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263 if (viewport.cursorMode)
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265 alignPanel.seqPanel.moveCursor(1, 0);
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268 case KeyEvent.VK_SPACE:
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269 if (viewport.cursorMode)
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271 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
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272 || evt.isShiftDown()
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278 case KeyEvent.VK_DELETE:
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279 case KeyEvent.VK_BACK_SPACE:
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280 if (viewport.cursorMode)
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282 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
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283 || evt.isShiftDown()
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284 || evt.isAltDown());
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288 cut_actionPerformed();
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289 alignPanel.seqPanel.seqCanvas.repaint();
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293 case KeyEvent.VK_S:
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294 if (viewport.cursorMode)
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296 alignPanel.seqPanel.setCursorRow();
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299 case KeyEvent.VK_P:
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300 if (viewport.cursorMode)
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302 alignPanel.seqPanel.setCursorPosition();
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306 case KeyEvent.VK_ENTER:
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307 case KeyEvent.VK_COMMA:
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308 if (viewport.cursorMode)
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310 alignPanel.seqPanel.setCursorRowAndColumn();
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314 case KeyEvent.VK_Q:
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315 if (viewport.cursorMode)
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317 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
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320 case KeyEvent.VK_M:
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321 if (viewport.cursorMode)
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323 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
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327 case KeyEvent.VK_F2:
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328 viewport.cursorMode = !viewport.cursorMode;
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329 statusBar.setText("Keyboard editing mode is " +
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330 (viewport.cursorMode ? "on" : "off"));
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331 if (viewport.cursorMode)
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333 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
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334 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
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338 case KeyEvent.VK_F:
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339 if (evt.isControlDown())
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341 findMenuItem_actionPerformed();
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345 case KeyEvent.VK_H:
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347 boolean toggleSeqs = !evt.isControlDown();
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348 boolean toggleCols = !evt.isShiftDown();
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349 boolean hide = false;
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350 SequenceGroup sg = viewport.getSelectionGroup();
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354 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
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357 viewport.hideAllSelectedSeqs();
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359 else if (! (toggleCols && viewport.colSel.getSelected().size() > 0))
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361 viewport.showAllHiddenSeqs();
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367 if (viewport.colSel.getSelected().size() > 0)
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369 viewport.hideSelectedColumns();
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372 viewport.selectionGroup = sg;
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377 viewport.showAllHiddenColumns();
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383 case KeyEvent.VK_PAGE_UP:
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384 if (viewport.wrapAlignment)
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386 alignPanel.scrollUp(true);
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390 alignPanel.setScrollValues(viewport.startRes,
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392 - viewport.endSeq + viewport.startSeq);
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396 case KeyEvent.VK_PAGE_DOWN:
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397 if (viewport.wrapAlignment)
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399 alignPanel.scrollUp(false);
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403 alignPanel.setScrollValues(viewport.startRes,
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405 + viewport.endSeq - viewport.startSeq);
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409 case KeyEvent.VK_Z:
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410 if (evt.isControlDown())
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412 undoMenuItem_actionPerformed();
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416 case KeyEvent.VK_Y:
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417 if (evt.isControlDown())
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419 redoMenuItem_actionPerformed();
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423 case KeyEvent.VK_L:
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424 if (evt.isControlDown())
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426 trimAlignment(true);
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430 case KeyEvent.VK_R:
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431 if (evt.isControlDown())
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433 trimAlignment(false);
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437 case KeyEvent.VK_E:
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438 if (evt.isControlDown())
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440 if (evt.isShiftDown())
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442 this.removeAllGapsMenuItem_actionPerformed();
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446 removeGappedColumnMenuItem_actionPerformed();
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450 case KeyEvent.VK_I:
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451 if (evt.isControlDown())
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453 if (evt.isAltDown())
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455 viewport.invertColumnSelection();
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459 this.invertSequenceMenuItem_actionPerformed();
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464 case KeyEvent.VK_U:
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465 if (evt.isControlDown())
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467 this.deleteGroups_actionPerformed();
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471 case KeyEvent.VK_T:
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472 if (evt.isControlDown())
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479 alignPanel.repaint();
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482 public void keyReleased(KeyEvent evt)
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485 public void keyTyped(KeyEvent evt)
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488 public void itemStateChanged(ItemEvent evt)
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490 if (evt.getSource() == colourTextMenuItem)
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492 colourTextMenuItem_actionPerformed();
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494 else if (evt.getSource() == wrapMenuItem)
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496 wrapMenuItem_actionPerformed();
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498 else if (evt.getSource() == scaleAbove)
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500 viewport.setScaleAboveWrapped(scaleAbove.getState());
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502 else if (evt.getSource() == scaleLeft)
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504 viewport.setScaleLeftWrapped(scaleLeft.getState());
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506 else if (evt.getSource() == scaleRight)
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508 viewport.setScaleRightWrapped(scaleRight.getState());
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510 else if (evt.getSource() == seqLimits)
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512 seqLimits_itemStateChanged();
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514 else if (evt.getSource() == viewBoxesMenuItem)
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516 viewport.setShowBoxes(viewBoxesMenuItem.getState());
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518 else if (evt.getSource() == viewTextMenuItem)
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520 viewport.setShowText(viewTextMenuItem.getState());
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522 else if (evt.getSource() == renderGapsMenuItem)
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524 viewport.setRenderGaps(renderGapsMenuItem.getState());
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526 else if (evt.getSource() == annotationPanelMenuItem)
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528 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
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529 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
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531 else if (evt.getSource() == sequenceFeatures)
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533 viewport.showSequenceFeatures(sequenceFeatures.getState());
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534 alignPanel.seqPanel.seqCanvas.repaint();
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536 else if (evt.getSource() == conservationMenuItem)
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538 conservationMenuItem_actionPerformed();
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540 else if (evt.getSource() == abovePIDThreshold)
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542 abovePIDThreshold_actionPerformed();
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544 else if (evt.getSource() == applyToAllGroups)
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546 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
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548 else if (evt.getSource() == autoCalculate)
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550 viewport.autocalculateConsensus = autoCalculate.getState();
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553 alignPanel.repaint();
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556 public void actionPerformed(ActionEvent evt)
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558 Object source = evt.getSource();
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560 if (source == inputText)
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562 inputText_actionPerformed();
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564 else if (source == loadTree)
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566 loadTree_actionPerformed();
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568 else if (source == loadApplication)
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570 launchFullApplication();
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572 else if (source == loadAnnotations)
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576 else if (source == outputAnnotations)
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578 outputAnnotations(true);
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580 else if (source == outputFeatures)
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582 outputFeatures(true, "Jalview");
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584 else if (source == closeMenuItem)
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586 closeMenuItem_actionPerformed();
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588 else if (source == copy)
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590 copy_actionPerformed();
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592 else if (source == undoMenuItem)
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594 undoMenuItem_actionPerformed();
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596 else if (source == redoMenuItem)
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598 redoMenuItem_actionPerformed();
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600 else if (source == inputText)
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602 inputText_actionPerformed();
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604 else if (source == closeMenuItem)
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606 closeMenuItem_actionPerformed();
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608 else if (source == undoMenuItem)
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610 undoMenuItem_actionPerformed();
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612 else if (source == redoMenuItem)
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614 redoMenuItem_actionPerformed();
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616 else if (source == copy)
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618 copy_actionPerformed();
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620 else if (source == pasteNew)
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622 pasteNew_actionPerformed();
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624 else if (source == pasteThis)
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626 pasteThis_actionPerformed();
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628 else if (source == cut)
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630 cut_actionPerformed();
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632 else if (source == delete)
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634 delete_actionPerformed();
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636 else if (source == deleteGroups)
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638 deleteGroups_actionPerformed();
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640 else if (source == selectAllSequenceMenuItem)
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642 selectAllSequenceMenuItem_actionPerformed();
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644 else if (source == deselectAllSequenceMenuItem)
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646 deselectAllSequenceMenuItem_actionPerformed();
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648 else if (source == invertSequenceMenuItem)
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650 invertSequenceMenuItem_actionPerformed();
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652 else if (source == invertColSel)
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654 viewport.invertColumnSelection();
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655 alignPanel.repaint();
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657 else if (source == remove2LeftMenuItem)
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659 trimAlignment(true);
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661 else if (source == remove2RightMenuItem)
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663 trimAlignment(false);
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665 else if (source == removeGappedColumnMenuItem)
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667 removeGappedColumnMenuItem_actionPerformed();
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669 else if (source == removeAllGapsMenuItem)
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671 removeAllGapsMenuItem_actionPerformed();
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673 else if (source == findMenuItem)
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675 findMenuItem_actionPerformed();
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677 else if (source == font)
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679 new FontChooser(alignPanel);
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681 else if (source == newView)
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685 else if (source == showColumns)
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687 viewport.showAllHiddenColumns();
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688 alignPanel.repaint();
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690 else if (source == showSeqs)
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692 viewport.showAllHiddenSeqs();
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694 else if (source == hideColumns)
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696 viewport.hideSelectedColumns();
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697 alignPanel.repaint();
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699 else if (source == hideSequences && viewport.getSelectionGroup() != null)
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701 viewport.hideAllSelectedSeqs();
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703 else if (source == featureSettings)
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705 new FeatureSettings(alignPanel);
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707 else if (source == overviewMenuItem)
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709 overviewMenuItem_actionPerformed();
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711 else if (source == noColourmenuItem)
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713 changeColour(null);
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715 else if (source == clustalColour)
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717 abovePIDThreshold.setState(false);
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718 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
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719 viewport.alignment.getWidth()));
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721 else if (source == zappoColour)
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723 changeColour(new ZappoColourScheme());
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725 else if (source == taylorColour)
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727 changeColour(new TaylorColourScheme());
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729 else if (source == hydrophobicityColour)
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731 changeColour(new HydrophobicColourScheme());
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733 else if (source == helixColour)
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735 changeColour(new HelixColourScheme());
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737 else if (source == strandColour)
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739 changeColour(new StrandColourScheme());
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741 else if (source == turnColour)
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743 changeColour(new TurnColourScheme());
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745 else if (source == buriedColour)
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747 changeColour(new BuriedColourScheme());
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749 else if (source == nucleotideColour)
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751 changeColour(new NucleotideColourScheme());
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753 else if (source == modifyPID)
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755 modifyPID_actionPerformed();
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757 else if (source == modifyConservation)
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759 modifyConservation_actionPerformed();
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761 else if (source == userDefinedColour)
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763 new UserDefinedColours(alignPanel, null);
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765 else if (source == PIDColour)
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767 changeColour(new PIDColourScheme());
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769 else if (source == BLOSUM62Colour)
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771 changeColour(new Blosum62ColourScheme());
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773 else if (source == annotationColour)
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775 new AnnotationColourChooser(viewport, alignPanel);
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777 else if (source == sortPairwiseMenuItem)
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779 sortPairwiseMenuItem_actionPerformed();
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781 else if (source == sortIDMenuItem)
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783 sortIDMenuItem_actionPerformed();
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785 else if (source == sortGroupMenuItem)
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787 sortGroupMenuItem_actionPerformed();
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789 else if (source == removeRedundancyMenuItem)
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791 removeRedundancyMenuItem_actionPerformed();
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793 else if (source == pairwiseAlignmentMenuItem)
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795 pairwiseAlignmentMenuItem_actionPerformed();
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797 else if (source == PCAMenuItem)
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799 PCAMenuItem_actionPerformed();
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801 else if (source == averageDistanceTreeMenuItem)
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803 averageDistanceTreeMenuItem_actionPerformed();
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805 else if (source == neighbourTreeMenuItem)
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807 neighbourTreeMenuItem_actionPerformed();
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809 else if (source == njTreeBlosumMenuItem)
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811 njTreeBlosumMenuItem_actionPerformed();
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813 else if (source == avDistanceTreeBlosumMenuItem)
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815 avTreeBlosumMenuItem_actionPerformed();
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817 else if (source == documentation)
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819 documentation_actionPerformed();
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821 else if (source == about)
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823 about_actionPerformed();
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828 public void inputText_actionPerformed()
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830 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
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831 Frame frame = new Frame();
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833 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
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836 protected void outputText_actionPerformed(ActionEvent e)
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838 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
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839 Frame frame = new Frame();
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841 jalview.bin.JalviewLite.addFrame(frame,
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842 "Alignment output - " + e.getActionCommand(),
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844 cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
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845 viewport.getAlignment(),
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846 viewport.showJVSuffix));
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849 public void loadAnnotations()
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851 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
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852 cap.setText("Paste your features / annotations file here.");
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853 cap.setAnnotationImport();
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854 Frame frame = new Frame();
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856 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
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860 public String outputAnnotations(boolean displayTextbox)
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862 String annotation = new AnnotationFile().printAnnotations(
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863 viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,
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864 viewport.alignment.getGroups());
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866 if (displayTextbox)
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868 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
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869 Frame frame = new Frame();
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871 jalview.bin.JalviewLite.addFrame(frame,
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874 cap.setText(annotation);
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880 public String outputFeatures(boolean displayTextbox, String format)
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883 if (format.equalsIgnoreCase("Jalview"))
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885 features = new FeaturesFile().printJalviewFormat(
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886 viewport.alignment.getSequencesArray(),
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887 viewport.featuresDisplayed);
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891 features = new FeaturesFile().printGFFFormat(
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892 viewport.alignment.getSequencesArray(),
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893 viewport.featuresDisplayed);
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896 if (displayTextbox)
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898 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
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899 Frame frame = new Frame();
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901 jalview.bin.JalviewLite.addFrame(frame,
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905 cap.setText(features);
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911 void launchFullApplication()
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913 StringBuffer url = new StringBuffer(jalviewServletURL);
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915 url.append("?open=" +
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916 appendProtocol(viewport.applet.getParameter("file")));
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918 if (viewport.applet.getParameter("features") != null)
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920 url.append("&features=");
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921 url.append(appendProtocol(viewport.applet.getParameter("features")));
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924 if (viewport.applet.getParameter("annotations") != null)
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926 url.append("&annotations=");
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927 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
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930 if (viewport.applet.getParameter("jnetfile") != null)
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932 url.append("&annotations=");
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933 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
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936 if (viewport.applet.getParameter("defaultColour") != null)
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938 url.append("&colour=" +
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939 removeWhiteSpace(viewport.applet.getParameter("defaultColour"))
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943 if (viewport.applet.getParameter("userDefinedColour") != null)
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945 url.append("&colour=" +
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946 removeWhiteSpace(viewport.applet.getParameter(
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947 "userDefinedColour"))
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951 showURL(url.toString(), "FULL_APP");
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954 String removeWhiteSpace(String colour)
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956 StringBuffer sb = new StringBuffer();
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957 for (int i = 0; i < colour.length(); i++)
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959 if (Character.isWhitespace(colour.charAt(i)))
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965 sb.append(colour.charAt(i));
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969 return sb.toString();
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972 String appendProtocol(String url)
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978 catch (java.net.MalformedURLException ex)
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980 url = viewport.applet.getCodeBase() + url;
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985 public void closeMenuItem_actionPerformed()
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987 PaintRefresher.RemoveComponent(alignPanel);
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988 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
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989 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
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991 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
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1002 void updateEditMenuBar()
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1005 if (viewport.historyList.size() > 0)
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1007 undoMenuItem.setEnabled(true);
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1008 CommandI command = (CommandI) viewport.historyList.peek();
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1009 undoMenuItem.setLabel("Undo " + command.getDescription());
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1013 undoMenuItem.setEnabled(false);
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1014 undoMenuItem.setLabel("Undo");
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1017 if (viewport.redoList.size() > 0)
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1019 redoMenuItem.setEnabled(true);
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1021 CommandI command = (CommandI) viewport.redoList.peek();
\r
1022 redoMenuItem.setLabel("Redo " + command.getDescription());
\r
1026 redoMenuItem.setEnabled(false);
\r
1027 redoMenuItem.setLabel("Redo");
\r
1031 public void addHistoryItem(CommandI command)
\r
1033 if (command.getSize() > 0)
\r
1035 viewport.historyList.push(command);
\r
1036 viewport.redoList.removeAllElements();
\r
1037 updateEditMenuBar();
\r
1038 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
1045 * @param e DOCUMENT ME!
\r
1047 protected void undoMenuItem_actionPerformed()
\r
1049 if (viewport.historyList.size() < 1)
\r
1054 CommandI command = (CommandI) viewport.historyList.pop();
\r
1055 viewport.redoList.push(command);
\r
1056 command.undoCommand();
\r
1058 AlignViewport originalSource = getOriginatingSource(command);
\r
1060 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
1061 updateEditMenuBar();
\r
1062 originalSource.firePropertyChange("alignment", null,
\r
1063 originalSource.alignment.getSequences());
\r
1069 * @param e DOCUMENT ME!
\r
1071 protected void redoMenuItem_actionPerformed()
\r
1073 if (viewport.redoList.size() < 1)
\r
1078 CommandI command = (CommandI) viewport.redoList.pop();
\r
1079 viewport.historyList.push(command);
\r
1080 command.doCommand();
\r
1082 AlignViewport originalSource = getOriginatingSource(command);
\r
1083 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
1085 updateEditMenuBar();
\r
1086 originalSource.firePropertyChange("alignment", null,
\r
1087 originalSource.alignment.getSequences());
\r
1090 AlignViewport getOriginatingSource(CommandI command)
\r
1092 AlignViewport originalSource = null;
\r
1093 //For sequence removal and addition, we need to fire
\r
1094 //the property change event FROM the viewport where the
\r
1095 //original alignment was altered
\r
1096 AlignmentI al = null;
\r
1097 if (command instanceof EditCommand)
\r
1099 EditCommand editCommand = (EditCommand) command;
\r
1100 al = editCommand.getAlignment();
\r
1101 Vector comps = (Vector) PaintRefresher.components
\r
1102 .get(viewport.getSequenceSetId());
\r
1103 for (int i = 0; i < comps.size(); i++)
\r
1105 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
1107 if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)
\r
1109 originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
\r
1116 if (originalSource == null)
\r
1118 //The original view is closed, we must validate
\r
1119 //the current view against the closed view first
\r
1122 PaintRefresher.validateSequences(al, viewport.alignment);
\r
1125 originalSource = viewport;
\r
1128 return originalSource;
\r
1131 public void moveSelectedSequences(boolean up)
\r
1133 SequenceGroup sg = viewport.getSelectionGroup();
\r
1141 for (int i = 1; i < viewport.alignment.getHeight(); i++)
\r
1143 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
1144 if (!sg.getSequences(null).contains(seq))
\r
1149 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
\r
1150 if (sg.getSequences(null).contains(temp))
\r
1155 viewport.alignment.getSequences().setElementAt(temp, i);
\r
1156 viewport.alignment.getSequences().setElementAt(seq, i - 1);
\r
1161 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
\r
1163 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
1164 if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))
\r
1169 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
\r
1170 if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))
\r
1175 viewport.alignment.getSequences().setElementAt(temp, i);
\r
1176 viewport.alignment.getSequences().setElementAt(seq, i + 1);
\r
1180 alignPanel.repaint();
\r
1183 static StringBuffer copiedSequences;
\r
1184 static Vector copiedHiddenColumns;
\r
1185 protected void copy_actionPerformed()
\r
1187 if (viewport.getSelectionGroup() == null)
\r
1192 SequenceGroup sg = viewport.getSelectionGroup();
\r
1193 copiedSequences = new StringBuffer();
\r
1194 Hashtable orderedSeqs = new Hashtable();
\r
1195 for (int i = 0; i < sg.getSize(); i++)
\r
1197 SequenceI seq = sg.getSequenceAt(i);
\r
1198 int index = viewport.alignment.findIndex(seq);
\r
1199 orderedSeqs.put(index + "", seq);
\r
1202 int index = 0, startRes, endRes;
\r
1205 if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
\r
1207 copiedHiddenColumns = new Vector();
\r
1208 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
\r
1209 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();
\r
1212 int[] region = (int[])
\r
1213 viewport.getColumnSelection().getHiddenColumns().elementAt(i);
\r
1215 copiedHiddenColumns.addElement(new int[]
\r
1216 {region[0] - hiddenOffset,
\r
1217 region[1] - hiddenOffset});
\r
1222 copiedHiddenColumns = null;
\r
1225 for (int i = 0; i < sg.getSize(); i++)
\r
1227 SequenceI seq = null;
\r
1229 while (seq == null)
\r
1231 if (orderedSeqs.containsKey(index + ""))
\r
1233 seq = (SequenceI) orderedSeqs.get(index + "");
\r
1245 //Returns residue following index if gap
\r
1246 startRes = seq.findPosition(sg.getStartRes());
\r
1249 //Need to find the residue preceeding index if gap
\r
1252 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
\r
1254 ch = seq.getCharAt(j);
\r
1255 if (!jalview.util.Comparison.isGap( (ch)))
\r
1263 endRes += seq.getStart() - 1;
\r
1266 copiedSequences.append(seq.getName() + "\t" +
\r
1269 seq.getSequenceAsString(sg.getStartRes(),
\r
1270 sg.getEndRes() + 1) + "\n");
\r
1275 protected void pasteNew_actionPerformed()
\r
1280 protected void pasteThis_actionPerformed()
\r
1285 void paste(boolean newAlignment)
\r
1290 if (copiedSequences == null)
\r
1295 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
1296 Vector seqs = new Vector();
\r
1297 while (st.hasMoreElements())
\r
1299 String name = st.nextToken();
\r
1300 int start = Integer.parseInt(st.nextToken());
\r
1301 int end = Integer.parseInt(st.nextToken());
\r
1302 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
\r
1304 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
1305 for (int i = 0; i < seqs.size(); i++)
\r
1307 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
1312 String newtitle = new String("Copied sequences");
\r
1313 if (getTitle().startsWith("Copied sequences"))
\r
1315 newtitle = getTitle();
\r
1319 newtitle = newtitle.concat("- from " + getTitle());
\r
1321 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
1325 if (copiedHiddenColumns != null)
\r
1327 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
1329 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
1330 af.viewport.hideColumns(region[0], region[1]);
\r
1334 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
\r
1339 addSequences(newSeqs);
\r
1343 catch (Exception ex)
\r
1344 {} // could be anything being pasted in here
\r
1348 void addSequences(SequenceI[] seqs)
\r
1350 for (int i = 0; i < seqs.length; i++)
\r
1352 viewport.alignment.addSequence(seqs[i]);
\r
1356 addHistoryItem(new EditCommand(
\r
1358 EditCommand.PASTE,
\r
1361 viewport.alignment.getWidth(),
\r
1362 viewport.alignment)
\r
1365 viewport.setEndSeq(viewport.alignment.getHeight());
\r
1366 viewport.alignment.getWidth();
\r
1367 viewport.firePropertyChange("alignment", null,
\r
1368 viewport.alignment.getSequences());
\r
1372 protected void cut_actionPerformed()
\r
1374 copy_actionPerformed();
\r
1375 delete_actionPerformed();
\r
1378 protected void delete_actionPerformed()
\r
1381 SequenceGroup sg = viewport.getSelectionGroup();
\r
1387 Vector seqs = new Vector();
\r
1389 for (int i = 0; i < sg.getSize(); i++)
\r
1391 seq = sg.getSequenceAt(i);
\r
1392 seqs.addElement(seq);
\r
1395 // If the cut affects all sequences, remove highlighted columns
\r
1396 if (sg.getSize() == viewport.alignment.getHeight())
\r
1398 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
1399 sg.getEndRes() + 1);
\r
1402 SequenceI[] cut = new SequenceI[seqs.size()];
\r
1403 for (int i = 0; i < seqs.size(); i++)
\r
1405 cut[i] = (SequenceI) seqs.elementAt(i);
\r
1409 //ADD HISTORY ITEM
\r
1411 addHistoryItem(new EditCommand("Cut Sequences",
\r
1415 sg.getEndRes() - sg.getStartRes() + 1,
\r
1416 viewport.alignment));
\r
1418 viewport.setSelectionGroup(null);
\r
1419 viewport.alignment.deleteGroup(sg);
\r
1421 viewport.firePropertyChange("alignment", null,
\r
1422 viewport.getAlignment().getSequences());
\r
1424 if (viewport.getAlignment().getHeight() < 1)
\r
1426 this.setVisible(false);
\r
1430 protected void deleteGroups_actionPerformed()
\r
1432 viewport.alignment.deleteAllGroups();
\r
1433 viewport.sequenceColours = null;
\r
1434 viewport.setSelectionGroup(null);
\r
1436 alignPanel.repaint();
\r
1439 public void selectAllSequenceMenuItem_actionPerformed()
\r
1441 SequenceGroup sg = new SequenceGroup();
\r
1442 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1444 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
1446 sg.setEndRes(viewport.alignment.getWidth() - 1);
\r
1447 viewport.setSelectionGroup(sg);
\r
1448 alignPanel.repaint();
\r
1449 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1452 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1454 if (viewport.cursorMode)
\r
1456 alignPanel.seqPanel.keyboardNo1 = null;
\r
1457 alignPanel.seqPanel.keyboardNo2 = null;
\r
1459 viewport.setSelectionGroup(null);
\r
1460 viewport.getColumnSelection().clear();
\r
1461 viewport.setSelectionGroup(null);
\r
1462 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1463 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1464 alignPanel.repaint();
\r
1465 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1468 public void invertSequenceMenuItem_actionPerformed()
\r
1470 SequenceGroup sg = viewport.getSelectionGroup();
\r
1471 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1473 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1476 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1479 void trimAlignment(boolean trimLeft)
\r
1481 ColumnSelection colSel = viewport.getColumnSelection();
\r
1484 if (colSel.size() > 0)
\r
1488 column = colSel.getMin();
\r
1492 column = colSel.getMax();
\r
1496 if (viewport.getSelectionGroup() != null)
\r
1498 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
\r
1499 hiddenRepSequences);
\r
1503 seqs = viewport.alignment.getSequencesArray();
\r
1506 TrimRegionCommand trimRegion;
\r
1509 trimRegion = new TrimRegionCommand("Remove Left",
\r
1510 TrimRegionCommand.TRIM_LEFT,
\r
1513 viewport.alignment,
\r
1515 viewport.selectionGroup);
\r
1516 viewport.setStartRes(0);
\r
1520 trimRegion = new TrimRegionCommand("Remove Right",
\r
1521 TrimRegionCommand.TRIM_RIGHT,
\r
1524 viewport.alignment,
\r
1526 viewport.selectionGroup);
\r
1529 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
\r
1531 addHistoryItem(trimRegion);
\r
1533 Vector groups = viewport.alignment.getGroups();
\r
1535 for (int i = 0; i < groups.size(); i++)
\r
1537 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1539 if ( (trimLeft && !sg.adjustForRemoveLeft(column))
\r
1540 || (!trimLeft && !sg.adjustForRemoveRight(column)))
\r
1542 viewport.alignment.deleteGroup(sg);
\r
1546 viewport.firePropertyChange("alignment", null,
\r
1547 viewport.getAlignment().getSequences());
\r
1551 public void removeGappedColumnMenuItem_actionPerformed()
\r
1553 int start = 0, end = viewport.alignment.getWidth() - 1;
\r
1556 if (viewport.getSelectionGroup() != null)
\r
1558 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
\r
1559 hiddenRepSequences);
\r
1560 start = viewport.getSelectionGroup().getStartRes();
\r
1561 end = viewport.getSelectionGroup().getEndRes();
\r
1565 seqs = viewport.alignment.getSequencesArray();
\r
1568 RemoveGapColCommand removeGapCols =
\r
1569 new RemoveGapColCommand("Remove Gapped Columns",
\r
1572 viewport.alignment);
\r
1574 addHistoryItem(removeGapCols);
\r
1576 statusBar.setText("Removed " + removeGapCols.getSize() + " empty columns.");
\r
1578 //This is to maintain viewport position on first residue
\r
1579 //of first sequence
\r
1580 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1581 int startRes = seq.findPosition(viewport.startRes);
\r
1582 // ShiftList shifts;
\r
1583 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
\r
1584 // edit.alColumnChanges=shifts.getInverse();
\r
1585 // if (viewport.hasHiddenColumns)
\r
1586 // viewport.getColumnSelection().compensateForEdits(shifts);
\r
1587 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
1588 viewport.firePropertyChange("alignment", null,
\r
1589 viewport.getAlignment().getSequences());
\r
1593 public void removeAllGapsMenuItem_actionPerformed()
\r
1595 int start = 0, end = viewport.alignment.getWidth() - 1;
\r
1598 if (viewport.getSelectionGroup() != null)
\r
1600 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
\r
1601 hiddenRepSequences);
\r
1602 start = viewport.getSelectionGroup().getStartRes();
\r
1603 end = viewport.getSelectionGroup().getEndRes();
\r
1607 seqs = viewport.alignment.getSequencesArray();
\r
1610 //This is to maintain viewport position on first residue
\r
1611 //of first sequence
\r
1612 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1613 int startRes = seq.findPosition(viewport.startRes);
\r
1615 addHistoryItem(new RemoveGapsCommand("Remove Gaps",
\r
1618 viewport.alignment));
\r
1620 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
1622 viewport.firePropertyChange("alignment", null,
\r
1623 viewport.getAlignment().getSequences());
\r
1627 public void findMenuItem_actionPerformed()
\r
1629 new Finder(alignPanel);
\r
1632 public void newView()
\r
1635 if (viewport.hasHiddenRows)
\r
1637 newal = new Alignment(viewport.getAlignment().
\r
1638 getHiddenSequences()
\r
1639 .getFullAlignment().
\r
1640 getSequencesArray());
\r
1644 newal = new Alignment(viewport.alignment.getSequencesArray());
\r
1647 if (viewport.alignment.getAlignmentAnnotation() != null)
\r
1649 for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)
\r
1651 if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
\r
1653 newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);
\r
1658 AlignFrame newaf = new AlignFrame(newal,
\r
1663 newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
\r
1664 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
\r
1665 PaintRefresher.Register(newaf.alignPanel,
\r
1666 newaf.alignPanel.av.getSequenceSetId());
\r
1668 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
\r
1669 newaf.alignPanel.av.getSequenceSetId());
\r
1670 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
\r
1671 newaf.alignPanel.av.getSequenceSetId());
\r
1673 Vector comps = (Vector) PaintRefresher.components.get(viewport.
\r
1674 getSequenceSetId());
\r
1675 int viewSize = -1;
\r
1676 for (int i = 0; i < comps.size(); i++)
\r
1678 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
1684 String title = new String(this.getTitle());
\r
1685 if (title.indexOf("(View") > -1)
\r
1687 title = title.substring(0, title.indexOf("(View"));
\r
1690 title += "(View " + viewSize + ")";
\r
1692 newaf.setTitle(title.toString());
\r
1694 newaf.viewport.historyList = viewport.historyList;
\r
1695 newaf.viewport.redoList = viewport.redoList;
\r
1699 public void seqLimits_itemStateChanged()
\r
1701 viewport.setShowJVSuffix(seqLimits.getState());
\r
1702 alignPanel.fontChanged();
\r
1703 alignPanel.repaint();
\r
1706 protected void colourTextMenuItem_actionPerformed()
\r
1708 viewport.setColourText(colourTextMenuItem.getState());
\r
1709 alignPanel.repaint();
\r
1712 protected void wrapMenuItem_actionPerformed()
\r
1714 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
1715 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
1716 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
1717 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
1718 scaleRight.setEnabled(wrapMenuItem.getState());
\r
1719 alignPanel.repaint();
\r
1722 public void overviewMenuItem_actionPerformed()
\r
1724 if (alignPanel.overviewPanel != null)
\r
1729 Frame frame = new Frame();
\r
1730 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1731 frame.add(overview);
\r
1732 // +50 must allow for applet frame window
\r
1733 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
1734 overview.getPreferredSize().width,
\r
1735 overview.getPreferredSize().height + 50);
\r
1738 frame.addWindowListener(new WindowAdapter()
\r
1740 public void windowClosing(WindowEvent e)
\r
1742 alignPanel.setOverviewPanel(null);
\r
1746 alignPanel.setOverviewPanel(overview);
\r
1750 void changeColour(ColourSchemeI cs)
\r
1752 int threshold = 0;
\r
1756 if (viewport.getAbovePIDThreshold())
\r
1758 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
\r
1760 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1762 viewport.setGlobalColourScheme(cs);
\r
1766 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1769 if (viewport.getConservationSelected())
\r
1772 Alignment al = (Alignment) viewport.alignment;
\r
1773 Conservation c = new Conservation("All",
\r
1774 ResidueProperties.propHash, 3,
\r
1775 al.getSequences(), 0,
\r
1776 al.getWidth() - 1);
\r
1779 c.verdict(false, viewport.ConsPercGaps);
\r
1781 cs.setConservation(c);
\r
1783 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1789 cs.setConservation(null);
\r
1792 cs.setConsensus(viewport.hconsensus);
\r
1795 viewport.setGlobalColourScheme(cs);
\r
1797 if (viewport.getColourAppliesToAllGroups())
\r
1799 Vector groups = viewport.alignment.getGroups();
\r
1800 for (int i = 0; i < groups.size(); i++)
\r
1802 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1809 if (cs instanceof ClustalxColourScheme)
\r
1811 sg.cs = new ClustalxColourScheme(
\r
1812 sg.getSequences(viewport.hiddenRepSequences),
\r
1819 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1821 catch (Exception ex)
\r
1823 ex.printStackTrace();
\r
1828 if (viewport.getAbovePIDThreshold()
\r
1829 || cs instanceof PIDColourScheme
\r
1830 || cs instanceof Blosum62ColourScheme)
\r
1832 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1833 sg.cs.setConsensus(AAFrequency.calculate(
\r
1834 sg.getSequences(viewport.hiddenRepSequences), 0, sg.getWidth()));
\r
1838 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1841 if (viewport.getConservationSelected())
\r
1843 Conservation c = new Conservation("Group",
\r
1844 ResidueProperties.propHash, 3,
\r
1845 sg.getSequences(viewport.
\r
1846 hiddenRepSequences), 0,
\r
1847 viewport.alignment.getWidth() - 1);
\r
1849 c.verdict(false, viewport.ConsPercGaps);
\r
1850 sg.cs.setConservation(c);
\r
1854 sg.cs.setConservation(null);
\r
1855 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1861 if (alignPanel.getOverviewPanel() != null)
\r
1863 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1866 alignPanel.repaint();
\r
1869 protected void modifyPID_actionPerformed()
\r
1871 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme != null)
\r
1873 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
1875 SliderPanel.showPIDSlider();
\r
1879 protected void modifyConservation_actionPerformed()
\r
1881 if (viewport.getConservationSelected() && viewport.globalColourScheme != null)
\r
1883 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
1885 SliderPanel.showConservationSlider();
\r
1889 protected void conservationMenuItem_actionPerformed()
\r
1891 viewport.setConservationSelected(conservationMenuItem.getState());
\r
1893 viewport.setAbovePIDThreshold(false);
\r
1894 abovePIDThreshold.setState(false);
\r
1896 changeColour(viewport.getGlobalColourScheme());
\r
1898 modifyConservation_actionPerformed();
\r
1901 public void abovePIDThreshold_actionPerformed()
\r
1903 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
1905 conservationMenuItem.setState(false);
\r
1906 viewport.setConservationSelected(false);
\r
1908 changeColour(viewport.getGlobalColourScheme());
\r
1910 modifyPID_actionPerformed();
\r
1913 public void sortPairwiseMenuItem_actionPerformed()
\r
1915 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
1916 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1917 viewport.getAlignment().getSequenceAt(0));
\r
1918 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
\r
1919 viewport.alignment));
\r
1920 alignPanel.repaint();
\r
1923 public void sortIDMenuItem_actionPerformed()
\r
1925 // addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1926 // HistoryItem.SORT));
\r
1927 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1928 alignPanel.repaint();
\r
1931 public void sortGroupMenuItem_actionPerformed()
\r
1933 // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1934 // HistoryItem.SORT));
\r
1935 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1936 alignPanel.repaint();
\r
1940 public void removeRedundancyMenuItem_actionPerformed()
\r
1942 new RedundancyPanel(alignPanel);
\r
1945 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
1947 if (viewport.getSelectionGroup() != null
\r
1948 && viewport.getSelectionGroup().getSize() > 1)
\r
1950 Frame frame = new Frame();
\r
1951 frame.add(new PairwiseAlignPanel(alignPanel));
\r
1952 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
1956 public void PCAMenuItem_actionPerformed()
\r
1958 //are the sequences aligned?
\r
1959 if (!viewport.alignment.isAligned())
\r
1961 SequenceI current;
\r
1962 int Width = viewport.getAlignment().getWidth();
\r
1964 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1967 current = viewport.getAlignment().getSequenceAt(i);
\r
1969 if (current.getLength() < Width)
\r
1971 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1974 alignPanel.repaint();
\r
1977 if ( (viewport.getSelectionGroup() != null &&
\r
1978 viewport.getSelectionGroup().getSize() < 4 &&
\r
1979 viewport.getSelectionGroup().getSize() > 0)
\r
1980 || viewport.getAlignment().getHeight() < 4)
\r
1987 new PCAPanel(viewport);
\r
1989 catch (java.lang.OutOfMemoryError ex)
\r
1995 public void averageDistanceTreeMenuItem_actionPerformed()
\r
1997 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
2000 public void neighbourTreeMenuItem_actionPerformed()
\r
2002 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
2005 protected void njTreeBlosumMenuItem_actionPerformed()
\r
2007 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2010 protected void avTreeBlosumMenuItem_actionPerformed()
\r
2012 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2015 void NewTreePanel(String type, String pwType, String title)
\r
2017 //are the sequences aligned?
\r
2018 if (!viewport.alignment.isAligned())
\r
2020 SequenceI current;
\r
2021 int Width = viewport.getAlignment().getWidth();
\r
2023 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
2026 current = viewport.getAlignment().getSequenceAt(i);
\r
2028 if (current.getLength() < Width)
\r
2030 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2033 alignPanel.repaint();
\r
2037 if ( (viewport.getSelectionGroup() != null &&
\r
2038 viewport.getSelectionGroup().getSize() > 1)
\r
2039 || (viewport.getSelectionGroup() == null
\r
2040 && viewport.alignment.getHeight() > 1))
\r
2042 final TreePanel tp = new TreePanel(viewport,
\r
2046 addTreeMenuItem(tp, title);
\r
2048 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
2052 void loadTree_actionPerformed()
\r
2054 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
2055 cap.setText("Paste your Newick tree file here.");
\r
2056 cap.setTreeImport();
\r
2057 Frame frame = new Frame();
\r
2059 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
2062 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
2064 TreePanel tp = new TreePanel(viewport,
\r
2068 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
2069 addTreeMenuItem(tp, treeFile);
\r
2072 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
2074 final MenuItem item = new MenuItem(title);
\r
2075 sortByTreeMenu.add(item);
\r
2076 item.addActionListener(new java.awt.event.ActionListener()
\r
2078 public void actionPerformed(ActionEvent evt)
\r
2080 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2081 // HistoryItem.SORT));
\r
2082 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
2083 alignPanel.repaint();
\r
2087 treePanel.addWindowListener(new WindowAdapter()
\r
2089 public void windowClosing(WindowEvent e)
\r
2091 sortByTreeMenu.remove(item);
\r
2096 protected void documentation_actionPerformed()
\r
2098 showURL("http://www.jalview.org/help.html", "HELP");
\r
2101 protected void about_actionPerformed()
\r
2108 public AboutPanel(String version)
\r
2110 this.version = version;
\r
2113 public void paint(Graphics g)
\r
2115 g.setColor(Color.white);
\r
2116 g.fillRect(0, 0, getSize().width, getSize().height);
\r
2117 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2118 FontMetrics fm = g.getFontMetrics();
\r
2119 int fh = fm.getHeight();
\r
2121 g.setColor(Color.black);
\r
2122 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
2123 g.drawString("Jalview - Release " + version, 200, y += fh);
\r
2124 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2125 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
2127 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
2130 "For any issues relating to Jalview, email help@jalview.org", x,
\r
2132 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
2133 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
2135 g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh);
\r
2139 String version = "test";
\r
2140 java.net.URL url = getClass().getResource("/.build_properties");
\r
2145 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
2146 url.openStream()));
\r
2148 while ( (line = reader.readLine()) != null)
\r
2150 if (line.indexOf("VERSION") > -1)
\r
2152 version = line.substring(line.indexOf("=") + 1);
\r
2156 catch (Exception ex)
\r
2158 ex.printStackTrace();
\r
2162 Frame frame = new Frame();
\r
2163 frame.add(new AboutPanel(version));
\r
2164 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
\r
2168 public void showURL(String url, String target)
\r
2170 if (viewport.applet == null)
\r
2172 System.out.println("Not running as applet - no browser available.");
\r
2178 System.out.println("Show url: " + url);
\r
2179 viewport.applet.getAppletContext().showDocument(new java.net.URL(url),
\r
2182 catch (Exception ex)
\r
2184 ex.printStackTrace();
\r
2189 //////////////////////////////////////////////////////////////////////////////////
\r
2190 //JBuilder Graphics here
\r
2192 protected MenuBar alignFrameMenuBar = new MenuBar();
\r
2193 protected Menu fileMenu = new Menu("File");
\r
2194 protected MenuItem loadApplication = new MenuItem("View in Full Application");
\r
2195 protected MenuItem loadTree = new MenuItem("Load Associated Tree ...");
\r
2196 protected MenuItem loadAnnotations = new MenuItem(
\r
2197 "Load Features/Annotations ...");
\r
2198 protected MenuItem outputFeatures = new MenuItem("Export Features ...");
\r
2199 protected MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
\r
2201 protected MenuItem closeMenuItem = new MenuItem("Close");
\r
2202 protected Menu editMenu = new Menu("Edit");
\r
2203 protected Menu viewMenu = new Menu("View");
\r
2204 protected Menu colourMenu = new Menu("Colour");
\r
2205 protected Menu calculateMenu = new Menu("Calculate");
\r
2206 protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
2207 protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
2208 protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
2209 protected MenuItem remove2LeftMenuItem = new MenuItem();
\r
2210 protected MenuItem remove2RightMenuItem = new MenuItem();
\r
2211 protected MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
2212 protected MenuItem removeAllGapsMenuItem = new MenuItem();
\r
2213 protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
2214 protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
2215 protected MenuItem sortPairwiseMenuItem = new MenuItem();
\r
2216 protected MenuItem sortIDMenuItem = new MenuItem();
\r
2217 protected MenuItem sortGroupMenuItem = new MenuItem();
\r
2218 protected MenuItem removeRedundancyMenuItem = new MenuItem();
\r
2219 protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
2220 protected MenuItem PCAMenuItem = new MenuItem();
\r
2221 protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
2222 protected MenuItem neighbourTreeMenuItem = new MenuItem();
\r
2223 BorderLayout borderLayout1 = new BorderLayout();
\r
2224 public Label statusBar = new Label();
\r
2225 protected Menu outputTextboxMenu = new Menu();
\r
2226 protected MenuItem clustalColour = new MenuItem();
\r
2227 protected MenuItem zappoColour = new MenuItem();
\r
2228 protected MenuItem taylorColour = new MenuItem();
\r
2229 protected MenuItem hydrophobicityColour = new MenuItem();
\r
2230 protected MenuItem helixColour = new MenuItem();
\r
2231 protected MenuItem strandColour = new MenuItem();
\r
2232 protected MenuItem turnColour = new MenuItem();
\r
2233 protected MenuItem buriedColour = new MenuItem();
\r
2234 protected MenuItem userDefinedColour = new MenuItem();
\r
2235 protected MenuItem PIDColour = new MenuItem();
\r
2236 protected MenuItem BLOSUM62Colour = new MenuItem();
\r
2237 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
2238 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
2239 protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
2240 protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
2241 MenuItem overviewMenuItem = new MenuItem();
\r
2242 protected MenuItem undoMenuItem = new MenuItem();
\r
2243 protected MenuItem redoMenuItem = new MenuItem();
\r
2244 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
2245 MenuItem noColourmenuItem = new MenuItem();
\r
2246 protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
2247 protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
2248 MenuItem findMenuItem = new MenuItem();
\r
2249 protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
2250 protected MenuItem nucleotideColour = new MenuItem();
\r
2251 MenuItem deleteGroups = new MenuItem();
\r
2252 MenuItem delete = new MenuItem();
\r
2253 MenuItem copy = new MenuItem();
\r
2254 MenuItem cut = new MenuItem();
\r
2255 Menu pasteMenu = new Menu();
\r
2256 MenuItem pasteNew = new MenuItem();
\r
2257 MenuItem pasteThis = new MenuItem();
\r
2258 protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
2259 protected MenuItem font = new MenuItem();
\r
2260 protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
2261 protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
2262 protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
2263 MenuItem modifyPID = new MenuItem();
\r
2264 MenuItem modifyConservation = new MenuItem();
\r
2265 protected CheckboxMenuItem autoCalculate
\r
2266 = new CheckboxMenuItem("Autocalculate Consensus", true);
\r
2267 protected Menu sortByTreeMenu = new Menu();
\r
2268 Menu sort = new Menu();
\r
2269 Menu calculate = new Menu();
\r
2270 MenuItem inputText = new MenuItem();
\r
2271 Menu helpMenu = new Menu();
\r
2272 MenuItem documentation = new MenuItem();
\r
2273 MenuItem about = new MenuItem();
\r
2274 protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
2275 Panel embeddedMenu;
\r
2276 Label embeddedEdit;
\r
2277 Label embeddedSelect;
\r
2278 Label embeddedView;
\r
2279 Label embeddedFormat;
\r
2280 Label embeddedColour;
\r
2281 Label embeddedFile;
\r
2282 Label embeddedHelp;
\r
2283 Label embeddedCalculate;
\r
2284 FlowLayout flowLayout1;
\r
2286 private void jbInit()
\r
2290 setMenuBar(alignFrameMenuBar);
\r
2294 // dynamically fill save as menu with available formats
\r
2295 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length;
\r
2299 item = new MenuItem(jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
2301 item.addActionListener(new java.awt.event.ActionListener()
\r
2303 public void actionPerformed(ActionEvent e)
\r
2305 outputText_actionPerformed(e);
\r
2309 outputTextboxMenu.add(item);
\r
2311 closeMenuItem.addActionListener(this);
\r
2312 loadApplication.addActionListener(this);
\r
2314 loadTree.addActionListener(this);
\r
2315 loadAnnotations.addActionListener(this);
\r
2316 outputFeatures.addActionListener(this);
\r
2317 outputAnnotations.addActionListener(this);
\r
2318 selectAllSequenceMenuItem.addActionListener(this);
\r
2319 deselectAllSequenceMenuItem.addActionListener(this);
\r
2320 invertSequenceMenuItem.addActionListener(this);
\r
2321 remove2LeftMenuItem.setLabel("Remove Left");
\r
2322 remove2LeftMenuItem.addActionListener(this);
\r
2323 remove2RightMenuItem.setLabel("Remove Right");
\r
2324 remove2RightMenuItem.addActionListener(this);
\r
2325 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
2326 removeGappedColumnMenuItem.addActionListener(this);
\r
2327 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
2328 removeAllGapsMenuItem.addActionListener(this);
\r
2329 viewBoxesMenuItem.setLabel("Boxes");
\r
2330 viewBoxesMenuItem.setState(true);
\r
2331 viewBoxesMenuItem.addItemListener(this);
\r
2332 viewTextMenuItem.setLabel("Text");
\r
2333 viewTextMenuItem.setState(true);
\r
2334 viewTextMenuItem.addItemListener(this);
\r
2335 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
2336 sortPairwiseMenuItem.addActionListener(this);
\r
2337 sortIDMenuItem.setLabel("by ID");
\r
2338 sortIDMenuItem.addActionListener(this);
\r
2339 sortGroupMenuItem.setLabel("by Group");
\r
2340 sortGroupMenuItem.addActionListener(this);
\r
2341 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
2342 removeRedundancyMenuItem.addActionListener(this);
\r
2343 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
2344 pairwiseAlignmentMenuItem.addActionListener(this);
\r
2345 PCAMenuItem.setLabel("Principal Component Analysis");
\r
2346 PCAMenuItem.addActionListener(this);
\r
2347 averageDistanceTreeMenuItem.setLabel(
\r
2348 "Average Distance Using % Identity");
\r
2349 averageDistanceTreeMenuItem.addActionListener(this);
\r
2350 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
2351 neighbourTreeMenuItem.addActionListener(this);
\r
2352 statusBar.setBackground(Color.white);
\r
2353 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
2354 statusBar.setText("Status bar");
\r
2355 outputTextboxMenu.setLabel("Output to Textbox");
\r
2356 clustalColour.setLabel("Clustalx");
\r
2358 clustalColour.addActionListener(this);
\r
2359 zappoColour.setLabel("Zappo");
\r
2360 zappoColour.addActionListener(this);
\r
2361 taylorColour.setLabel("Taylor");
\r
2362 taylorColour.addActionListener(this);
\r
2363 hydrophobicityColour.setLabel("Hydrophobicity");
\r
2364 hydrophobicityColour.addActionListener(this);
\r
2365 helixColour.setLabel("Helix Propensity");
\r
2366 helixColour.addActionListener(this);
\r
2367 strandColour.setLabel("Strand Propensity");
\r
2368 strandColour.addActionListener(this);
\r
2369 turnColour.setLabel("Turn Propensity");
\r
2370 turnColour.addActionListener(this);
\r
2371 buriedColour.setLabel("Buried Index");
\r
2372 buriedColour.addActionListener(this);
\r
2373 userDefinedColour.setLabel("User Defined...");
\r
2374 userDefinedColour.addActionListener(this);
\r
2375 PIDColour.setLabel("Percentage Identity");
\r
2376 PIDColour.addActionListener(this);
\r
2377 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
2378 BLOSUM62Colour.addActionListener(this);
\r
2379 avDistanceTreeBlosumMenuItem.setLabel(
\r
2380 "Average Distance Using BLOSUM62");
\r
2381 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
2382 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
2383 njTreeBlosumMenuItem.addActionListener(this);
\r
2384 annotationPanelMenuItem.setLabel("Show Annotations");
\r
2385 annotationPanelMenuItem.addItemListener(this);
\r
2386 colourTextMenuItem.setLabel("Colour Text");
\r
2387 colourTextMenuItem.addItemListener(this);
\r
2388 overviewMenuItem.setLabel("Overview Window");
\r
2389 overviewMenuItem.addActionListener(this);
\r
2390 undoMenuItem.setEnabled(false);
\r
2391 undoMenuItem.setLabel("Undo");
\r
2392 undoMenuItem.addActionListener(this);
\r
2393 redoMenuItem.setEnabled(false);
\r
2394 redoMenuItem.setLabel("Redo");
\r
2395 redoMenuItem.addActionListener(this);
\r
2396 conservationMenuItem.setLabel("by Conservation");
\r
2397 conservationMenuItem.addItemListener(this);
\r
2398 noColourmenuItem.setLabel("None");
\r
2399 noColourmenuItem.addActionListener(this);
\r
2400 wrapMenuItem.setLabel("Wrap");
\r
2401 wrapMenuItem.addItemListener(this);
\r
2402 renderGapsMenuItem.setLabel("Show Gaps");
\r
2403 renderGapsMenuItem.setState(true);
\r
2404 renderGapsMenuItem.addItemListener(this);
\r
2405 findMenuItem.setLabel("Find...");
\r
2406 findMenuItem.addActionListener(this);
\r
2407 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
2408 abovePIDThreshold.addItemListener(this);
\r
2409 nucleotideColour.setLabel("Nucleotide");
\r
2410 nucleotideColour.addActionListener(this);
\r
2411 deleteGroups.setLabel("Undefine Groups");
\r
2412 deleteGroups.addActionListener(this);
\r
2413 copy.setLabel("Copy");
\r
2414 copy.addActionListener(this);
\r
2415 cut.setLabel("Cut");
\r
2416 cut.addActionListener(this);
\r
2417 delete.setLabel("Delete");
\r
2418 delete.addActionListener(this);
\r
2419 pasteMenu.setLabel("Paste");
\r
2420 pasteNew.setLabel("To New Alignment");
\r
2421 pasteNew.addActionListener(this);
\r
2422 pasteThis.setLabel("Add To This Alignment");
\r
2423 pasteThis.addActionListener(this);
\r
2424 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
2425 applyToAllGroups.setState(true);
\r
2426 applyToAllGroups.addItemListener(this);
\r
2427 font.setLabel("Font...");
\r
2428 font.addActionListener(this);
\r
2429 scaleAbove.setLabel("Scale Above");
\r
2430 scaleAbove.setState(true);
\r
2431 scaleAbove.setEnabled(false);
\r
2432 scaleAbove.addItemListener(this);
\r
2433 scaleLeft.setEnabled(false);
\r
2434 scaleLeft.setState(true);
\r
2435 scaleLeft.setLabel("Scale Left");
\r
2436 scaleLeft.addItemListener(this);
\r
2437 scaleRight.setEnabled(false);
\r
2438 scaleRight.setState(true);
\r
2439 scaleRight.setLabel("Scale Right");
\r
2440 scaleRight.addItemListener(this);
\r
2441 modifyPID.setLabel("Modify Identity Threshold...");
\r
2442 modifyPID.addActionListener(this);
\r
2443 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
2444 modifyConservation.addActionListener(this);
\r
2445 sortByTreeMenu.setLabel("By Tree Order");
\r
2446 sort.setLabel("Sort");
\r
2447 calculate.setLabel("Calculate Tree");
\r
2448 autoCalculate.addItemListener(this);
\r
2449 inputText.setLabel("Input from textbox");
\r
2450 inputText.addActionListener(this);
\r
2452 helpMenu.setLabel("Help");
\r
2453 documentation.setLabel("Documentation");
\r
2454 documentation.addActionListener(this);
\r
2456 about.setLabel("About...");
\r
2457 about.addActionListener(this);
\r
2458 seqLimits.setState(true);
\r
2459 seqLimits.setLabel("Show Sequence Limits");
\r
2460 seqLimits.addItemListener(this);
\r
2461 featureSettings.setLabel("Feature Settings...");
\r
2462 featureSettings.addActionListener(this);
\r
2463 sequenceFeatures.setLabel("Sequence Features");
\r
2464 sequenceFeatures.addItemListener(this);
\r
2465 sequenceFeatures.setState(false);
\r
2466 annotationColour.setLabel("by Annotation...");
\r
2467 annotationColour.addActionListener(this);
\r
2468 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
2469 invertColSel.setLabel("Invert Column Selection");
\r
2470 menu1.setLabel("Show");
\r
2471 showColumns.setLabel("All Columns ");
\r
2472 showSeqs.setLabel("All Sequences");
\r
2473 menu2.setLabel("Hide");
\r
2474 hideColumns.setLabel("Selected Columns");
\r
2475 hideSequences.setLabel("Selected Sequences");
\r
2476 invertColSel.addActionListener(this);
\r
2477 showColumns.addActionListener(this);
\r
2478 showSeqs.addActionListener(this);
\r
2479 hideColumns.addActionListener(this);
\r
2480 hideSequences.addActionListener(this);
\r
2481 formatMenu.setLabel("Format");
\r
2482 selectMenu.setLabel("Select");
\r
2483 newView.setLabel("New View");
\r
2484 newView.addActionListener(this);
\r
2485 alignFrameMenuBar.add(fileMenu);
\r
2486 alignFrameMenuBar.add(editMenu);
\r
2487 alignFrameMenuBar.add(selectMenu);
\r
2488 alignFrameMenuBar.add(viewMenu);
\r
2489 alignFrameMenuBar.add(formatMenu);
\r
2490 alignFrameMenuBar.add(colourMenu);
\r
2491 alignFrameMenuBar.add(calculateMenu);
\r
2492 alignFrameMenuBar.add(helpMenu);
\r
2494 fileMenu.add(inputText);
\r
2495 fileMenu.add(loadTree);
\r
2496 fileMenu.add(loadAnnotations);
\r
2498 fileMenu.addSeparator();
\r
2499 fileMenu.add(outputTextboxMenu);
\r
2500 fileMenu.add(outputFeatures);
\r
2501 fileMenu.add(outputAnnotations);
\r
2503 if (jalviewServletURL != null)
\r
2505 fileMenu.add(loadApplication);
\r
2508 fileMenu.addSeparator();
\r
2509 fileMenu.add(closeMenuItem);
\r
2511 editMenu.add(undoMenuItem);
\r
2512 editMenu.add(redoMenuItem);
\r
2513 editMenu.add(cut);
\r
2514 editMenu.add(copy);
\r
2515 editMenu.add(pasteMenu);
\r
2516 editMenu.add(delete);
\r
2517 editMenu.addSeparator();
\r
2518 editMenu.add(remove2LeftMenuItem);
\r
2519 editMenu.add(remove2RightMenuItem);
\r
2520 editMenu.add(removeGappedColumnMenuItem);
\r
2521 editMenu.add(removeAllGapsMenuItem);
\r
2522 editMenu.add(removeRedundancyMenuItem);
\r
2523 viewMenu.add(newView);
\r
2524 viewMenu.addSeparator();
\r
2525 viewMenu.add(menu1);
\r
2526 viewMenu.add(menu2);
\r
2527 viewMenu.addSeparator();
\r
2528 viewMenu.add(annotationPanelMenuItem);
\r
2529 viewMenu.addSeparator();
\r
2530 viewMenu.add(sequenceFeatures);
\r
2531 viewMenu.add(featureSettings);
\r
2532 viewMenu.addSeparator();
\r
2533 viewMenu.add(overviewMenuItem);
\r
2534 colourMenu.add(applyToAllGroups);
\r
2535 colourMenu.addSeparator();
\r
2536 colourMenu.add(noColourmenuItem);
\r
2537 colourMenu.add(clustalColour);
\r
2538 colourMenu.add(BLOSUM62Colour);
\r
2539 colourMenu.add(PIDColour);
\r
2540 colourMenu.add(zappoColour);
\r
2541 colourMenu.add(taylorColour);
\r
2542 colourMenu.add(hydrophobicityColour);
\r
2543 colourMenu.add(helixColour);
\r
2544 colourMenu.add(strandColour);
\r
2545 colourMenu.add(turnColour);
\r
2546 colourMenu.add(buriedColour);
\r
2547 colourMenu.add(nucleotideColour);
\r
2548 colourMenu.add(userDefinedColour);
\r
2549 colourMenu.addSeparator();
\r
2550 colourMenu.add(conservationMenuItem);
\r
2551 colourMenu.add(modifyConservation);
\r
2552 colourMenu.add(abovePIDThreshold);
\r
2553 colourMenu.add(modifyPID);
\r
2554 colourMenu.add(annotationColour);
\r
2555 calculateMenu.add(sort);
\r
2556 calculateMenu.add(calculate);
\r
2557 calculateMenu.addSeparator();
\r
2558 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
2559 calculateMenu.add(PCAMenuItem);
\r
2560 calculateMenu.add(autoCalculate);
\r
2561 this.add(statusBar, BorderLayout.SOUTH);
\r
2562 pasteMenu.add(pasteNew);
\r
2563 pasteMenu.add(pasteThis);
\r
2564 sort.add(sortIDMenuItem);
\r
2565 sort.add(sortByTreeMenu);
\r
2566 sort.add(sortGroupMenuItem);
\r
2567 sort.add(sortPairwiseMenuItem);
\r
2568 calculate.add(averageDistanceTreeMenuItem);
\r
2569 calculate.add(neighbourTreeMenuItem);
\r
2570 calculate.add(avDistanceTreeBlosumMenuItem);
\r
2571 calculate.add(njTreeBlosumMenuItem);
\r
2572 helpMenu.add(documentation);
\r
2573 helpMenu.add(about);
\r
2574 menu1.add(showColumns);
\r
2575 menu1.add(showSeqs);
\r
2576 menu2.add(hideColumns);
\r
2577 menu2.add(hideSequences);
\r
2578 formatMenu.add(font);
\r
2579 formatMenu.add(seqLimits);
\r
2580 formatMenu.add(wrapMenuItem);
\r
2581 formatMenu.add(scaleAbove);
\r
2582 formatMenu.add(scaleLeft);
\r
2583 formatMenu.add(scaleRight);
\r
2584 formatMenu.add(viewBoxesMenuItem);
\r
2585 formatMenu.add(viewTextMenuItem);
\r
2586 formatMenu.add(colourTextMenuItem);
\r
2587 formatMenu.add(renderGapsMenuItem);
\r
2588 selectMenu.add(findMenuItem);
\r
2589 selectMenu.addSeparator();
\r
2590 selectMenu.add(selectAllSequenceMenuItem);
\r
2591 selectMenu.add(deselectAllSequenceMenuItem);
\r
2592 selectMenu.add(invertSequenceMenuItem);
\r
2593 selectMenu.add(invertColSel);
\r
2594 selectMenu.add(deleteGroups);
\r
2597 public void setEmbedded()
\r
2600 embeddedMenu = new Panel();
\r
2601 embeddedEdit = new Label("Edit");
\r
2602 embeddedSelect = new Label("Select");
\r
2603 embeddedView = new Label("View");
\r
2604 embeddedFormat = new Label("Format");
\r
2605 embeddedColour = new Label("Colour");
\r
2606 embeddedFile = new Label("File");
\r
2607 embeddedHelp = new Label("Help");
\r
2608 embeddedCalculate = new Label("Calculate");
\r
2609 flowLayout1 = new FlowLayout();
\r
2610 embeddedMenu.setBackground(Color.lightGray);
\r
2611 embeddedMenu.setLayout(flowLayout1);
\r
2612 embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2613 embeddedSelect.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2614 embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2615 embeddedFormat.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2616 embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2617 embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2618 embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2619 embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2620 embeddedMenu.add(embeddedFile);
\r
2621 embeddedMenu.add(embeddedEdit);
\r
2622 embeddedMenu.add(embeddedSelect);
\r
2623 embeddedMenu.add(embeddedView);
\r
2624 embeddedMenu.add(embeddedFormat);
\r
2625 embeddedMenu.add(embeddedColour);
\r
2626 embeddedMenu.add(embeddedCalculate);
\r
2627 embeddedMenu.add(embeddedHelp);
\r
2628 flowLayout1.setAlignment(FlowLayout.LEFT);
\r
2629 flowLayout1.setHgap(2);
\r
2630 flowLayout1.setVgap(0);
\r
2631 embeddedFile.addMouseListener(this);
\r
2632 embeddedEdit.addMouseListener(this);
\r
2633 embeddedSelect.addMouseListener(this);
\r
2634 embeddedView.addMouseListener(this);
\r
2635 embeddedFormat.addMouseListener(this);
\r
2636 embeddedColour.addMouseListener(this);
\r
2637 embeddedCalculate.addMouseListener(this);
\r
2638 embeddedHelp.addMouseListener(this);
\r
2640 fileMenu.remove(closeMenuItem);
\r
2641 fileMenu.remove(3); // Seperator
\r
2643 viewport.applet.setLayout(new BorderLayout());
\r
2644 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
\r
2645 viewport.applet.add(statusBar, BorderLayout.SOUTH);
\r
2647 alignPanel.setSize(viewport.applet.getSize().width,
\r
2648 viewport.applet.getSize().height
\r
2649 - embeddedMenu.HEIGHT - statusBar.HEIGHT);
\r
2651 viewport.applet.add(alignPanel, BorderLayout.CENTER);
\r
2652 viewport.applet.validate();
\r
2656 PopupMenu filePopup, editPopup, searchPopup,
\r
2657 viewPopup, formatPopup, colourPopup, calculatePopup, helpPopup;
\r
2658 MenuItem featureSettings = new MenuItem();
\r
2659 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
2660 MenuItem annotationColour = new MenuItem();
\r
2661 MenuItem invertColSel = new MenuItem();
\r
2662 Menu menu1 = new Menu();
\r
2663 MenuItem showColumns = new MenuItem();
\r
2664 MenuItem showSeqs = new MenuItem();
\r
2665 Menu menu2 = new Menu();
\r
2666 MenuItem hideColumns = new MenuItem();
\r
2667 MenuItem hideSequences = new MenuItem();
\r
2668 Menu formatMenu = new Menu();
\r
2669 Menu selectMenu = new Menu();
\r
2670 MenuItem newView = new MenuItem();
\r
2672 public void mousePressed(MouseEvent evt)
\r
2674 PopupMenu popup = null;
\r
2675 Label source = (Label) evt.getSource();
\r
2676 if (source == embeddedFile)
\r
2678 popup = filePopup = genPopupMenu(filePopup, fileMenu);
\r
2680 else if (source == embeddedEdit)
\r
2682 popup = editPopup = genPopupMenu(editPopup, editMenu);
\r
2684 else if (source == embeddedSelect)
\r
2686 popup = searchPopup = genPopupMenu(searchPopup, selectMenu);
\r
2688 else if (source == embeddedView)
\r
2690 popup = viewPopup = genPopupMenu(viewPopup, viewMenu);
\r
2692 else if (source == embeddedFormat)
\r
2694 popup = formatPopup = genPopupMenu(formatPopup, formatMenu);
\r
2696 else if (source == embeddedColour)
\r
2698 popup = colourPopup = genPopupMenu(colourPopup, colourMenu);
\r
2700 else if (source == embeddedCalculate)
\r
2702 popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);
\r
2704 else if (source == embeddedHelp)
\r
2706 popup = helpPopup = genPopupMenu(helpPopup, helpMenu);
\r
2709 embeddedMenu.add(popup);
\r
2710 popup.show(embeddedMenu,
\r
2711 source.getBounds().x,
\r
2712 source.getBounds().y + source.getBounds().getSize().height);
\r
2715 PopupMenu genPopupMenu(PopupMenu popup, Menu original)
\r
2717 if (popup != null)
\r
2721 popup = new PopupMenu();
\r
2722 int m, mSize = original.getItemCount();
\r
2723 for (m = 0; m < mSize; m++)
\r
2725 popup.add(original.getItem(m));
\r
2733 public void mouseClicked(MouseEvent evt)
\r
2736 public void mouseReleased(MouseEvent evt)
\r
2739 public void mouseEntered(MouseEvent evt)
\r
2742 public void mouseExited(MouseEvent evt)
\r