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.paintAlignment(true);
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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.paintAlignment(true);
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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 (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0 &&
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198 evt.getKeyCode() <= KeyEvent.VK_NUMPAD9)
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200 && Character.isDigit(evt.getKeyChar()))
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201 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
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204 switch (evt.getKeyCode())
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206 case 27: // escape key
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207 deselectAllSequenceMenuItem_actionPerformed();
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209 case KeyEvent.VK_X:
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210 if (evt.isControlDown() || evt.isMetaDown())
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212 cut_actionPerformed();
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215 case KeyEvent.VK_C:
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216 if (viewport.cursorMode && !evt.isControlDown())
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218 alignPanel.seqPanel.setCursorColumn();
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220 if (evt.isControlDown() || evt.isMetaDown())
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222 copy_actionPerformed();
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225 case KeyEvent.VK_V:
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226 if (evt.isControlDown())
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228 paste(evt.isShiftDown());
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231 case KeyEvent.VK_A:
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232 if (evt.isControlDown() || evt.isMetaDown())
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234 selectAllSequenceMenuItem_actionPerformed();
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237 case KeyEvent.VK_DOWN:
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238 if (viewport.cursorMode)
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240 alignPanel.seqPanel.moveCursor(0, 1);
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244 moveSelectedSequences(false);
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248 case KeyEvent.VK_UP:
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249 if (viewport.cursorMode)
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251 alignPanel.seqPanel.moveCursor(0, -1);
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255 moveSelectedSequences(true);
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259 case KeyEvent.VK_LEFT:
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260 if (evt.isAltDown() || !viewport.cursorMode)
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261 slideSequences(false,
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262 alignPanel.seqPanel.getKeyboardNo1());
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264 alignPanel.seqPanel.moveCursor( -1, 0);
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267 case KeyEvent.VK_RIGHT:
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268 if (evt.isAltDown() || !viewport.cursorMode)
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269 slideSequences(true,
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270 alignPanel.seqPanel.getKeyboardNo1());
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272 alignPanel.seqPanel.moveCursor( 1, 0);
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275 case KeyEvent.VK_SPACE:
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276 if (viewport.cursorMode)
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278 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
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279 || evt.isShiftDown()
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285 case KeyEvent.VK_DELETE:
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286 case KeyEvent.VK_BACK_SPACE:
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287 if (viewport.cursorMode)
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289 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
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290 || evt.isShiftDown()
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291 || evt.isAltDown());
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295 cut_actionPerformed();
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296 alignPanel.seqPanel.seqCanvas.repaint();
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300 case KeyEvent.VK_S:
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301 if (viewport.cursorMode)
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303 alignPanel.seqPanel.setCursorRow();
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306 case KeyEvent.VK_P:
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307 if (viewport.cursorMode)
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309 alignPanel.seqPanel.setCursorPosition();
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313 case KeyEvent.VK_ENTER:
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314 case KeyEvent.VK_COMMA:
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315 if (viewport.cursorMode)
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317 alignPanel.seqPanel.setCursorRowAndColumn();
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321 case KeyEvent.VK_Q:
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322 if (viewport.cursorMode)
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324 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
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327 case KeyEvent.VK_M:
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328 if (viewport.cursorMode)
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330 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
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334 case KeyEvent.VK_F2:
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335 viewport.cursorMode = !viewport.cursorMode;
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336 statusBar.setText("Keyboard editing mode is " +
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337 (viewport.cursorMode ? "on" : "off"));
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338 if (viewport.cursorMode)
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340 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
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341 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
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345 case KeyEvent.VK_F:
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346 if (evt.isControlDown())
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348 findMenuItem_actionPerformed();
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352 case KeyEvent.VK_H:
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354 boolean toggleSeqs = !evt.isControlDown();
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355 boolean toggleCols = !evt.isShiftDown();
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356 boolean hide = false;
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357 SequenceGroup sg = viewport.getSelectionGroup();
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361 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
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364 viewport.hideAllSelectedSeqs();
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366 else if (! (toggleCols && viewport.colSel.getSelected().size() > 0))
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368 viewport.showAllHiddenSeqs();
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374 if (viewport.colSel.getSelected().size() > 0)
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376 viewport.hideSelectedColumns();
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379 viewport.selectionGroup = sg;
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384 viewport.showAllHiddenColumns();
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390 case KeyEvent.VK_PAGE_UP:
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391 if (viewport.wrapAlignment)
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393 alignPanel.scrollUp(true);
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397 alignPanel.setScrollValues(viewport.startRes,
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399 - viewport.endSeq + viewport.startSeq);
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403 case KeyEvent.VK_PAGE_DOWN:
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404 if (viewport.wrapAlignment)
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406 alignPanel.scrollUp(false);
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410 alignPanel.setScrollValues(viewport.startRes,
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412 + viewport.endSeq - viewport.startSeq);
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416 case KeyEvent.VK_Z:
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417 if (evt.isControlDown())
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419 undoMenuItem_actionPerformed();
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423 case KeyEvent.VK_Y:
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424 if (evt.isControlDown())
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426 redoMenuItem_actionPerformed();
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430 case KeyEvent.VK_L:
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431 if (evt.isControlDown())
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433 trimAlignment(true);
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437 case KeyEvent.VK_R:
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438 if (evt.isControlDown())
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440 trimAlignment(false);
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444 case KeyEvent.VK_E:
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445 if (evt.isControlDown())
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447 if (evt.isShiftDown())
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449 this.removeAllGapsMenuItem_actionPerformed();
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453 removeGappedColumnMenuItem_actionPerformed();
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457 case KeyEvent.VK_I:
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458 if (evt.isControlDown())
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460 if (evt.isAltDown())
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462 viewport.invertColumnSelection();
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466 this.invertSequenceMenuItem_actionPerformed();
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471 case KeyEvent.VK_U:
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472 if (evt.isControlDown())
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474 this.deleteGroups_actionPerformed();
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478 case KeyEvent.VK_T:
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479 if (evt.isControlDown())
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486 alignPanel.paintAlignment(true);
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489 public void keyReleased(KeyEvent evt)
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492 public void keyTyped(KeyEvent evt)
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495 public void itemStateChanged(ItemEvent evt)
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497 if (evt.getSource() == colourTextMenuItem)
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499 colourTextMenuItem_actionPerformed();
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501 else if (evt.getSource() == wrapMenuItem)
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503 wrapMenuItem_actionPerformed();
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505 else if (evt.getSource() == scaleAbove)
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507 viewport.setScaleAboveWrapped(scaleAbove.getState());
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509 else if (evt.getSource() == scaleLeft)
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511 viewport.setScaleLeftWrapped(scaleLeft.getState());
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513 else if (evt.getSource() == scaleRight)
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515 viewport.setScaleRightWrapped(scaleRight.getState());
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517 else if (evt.getSource() == seqLimits)
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519 seqLimits_itemStateChanged();
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521 else if (evt.getSource() == viewBoxesMenuItem)
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523 viewport.setShowBoxes(viewBoxesMenuItem.getState());
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525 else if (evt.getSource() == viewTextMenuItem)
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527 viewport.setShowText(viewTextMenuItem.getState());
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529 else if (evt.getSource() == renderGapsMenuItem)
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531 viewport.setRenderGaps(renderGapsMenuItem.getState());
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533 else if (evt.getSource() == annotationPanelMenuItem)
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535 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
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536 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
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538 else if (evt.getSource() == sequenceFeatures)
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540 viewport.showSequenceFeatures(sequenceFeatures.getState());
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541 alignPanel.seqPanel.seqCanvas.repaint();
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543 else if (evt.getSource() == conservationMenuItem)
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545 conservationMenuItem_actionPerformed();
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547 else if (evt.getSource() == abovePIDThreshold)
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549 abovePIDThreshold_actionPerformed();
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551 else if (evt.getSource() == applyToAllGroups)
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553 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
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555 else if (evt.getSource() == autoCalculate)
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557 viewport.autocalculateConsensus = autoCalculate.getState();
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560 alignPanel.paintAlignment(true);
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563 public void actionPerformed(ActionEvent evt)
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565 Object source = evt.getSource();
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567 if (source == inputText)
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569 inputText_actionPerformed();
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571 else if (source == loadTree)
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573 loadTree_actionPerformed();
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575 else if (source == loadApplication)
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577 launchFullApplication();
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579 else if (source == loadAnnotations)
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583 else if (source == outputAnnotations)
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585 outputAnnotations(true);
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587 else if (source == outputFeatures)
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589 outputFeatures(true, "Jalview");
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591 else if (source == closeMenuItem)
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593 closeMenuItem_actionPerformed();
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595 else if (source == copy)
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597 copy_actionPerformed();
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599 else if (source == undoMenuItem)
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601 undoMenuItem_actionPerformed();
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603 else if (source == redoMenuItem)
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605 redoMenuItem_actionPerformed();
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607 else if (source == inputText)
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609 inputText_actionPerformed();
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611 else if (source == closeMenuItem)
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613 closeMenuItem_actionPerformed();
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615 else if (source == undoMenuItem)
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617 undoMenuItem_actionPerformed();
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619 else if (source == redoMenuItem)
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621 redoMenuItem_actionPerformed();
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623 else if (source == copy)
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625 copy_actionPerformed();
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627 else if (source == pasteNew)
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629 pasteNew_actionPerformed();
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631 else if (source == pasteThis)
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633 pasteThis_actionPerformed();
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635 else if (source == cut)
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637 cut_actionPerformed();
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639 else if (source == delete)
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641 delete_actionPerformed();
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643 else if (source == deleteGroups)
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645 deleteGroups_actionPerformed();
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647 else if (source == selectAllSequenceMenuItem)
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649 selectAllSequenceMenuItem_actionPerformed();
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651 else if (source == deselectAllSequenceMenuItem)
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653 deselectAllSequenceMenuItem_actionPerformed();
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655 else if (source == invertSequenceMenuItem)
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657 invertSequenceMenuItem_actionPerformed();
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659 else if (source == invertColSel)
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661 viewport.invertColumnSelection();
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662 alignPanel.paintAlignment(true);
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664 else if (source == remove2LeftMenuItem)
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666 trimAlignment(true);
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668 else if (source == remove2RightMenuItem)
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670 trimAlignment(false);
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672 else if (source == removeGappedColumnMenuItem)
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674 removeGappedColumnMenuItem_actionPerformed();
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676 else if (source == removeAllGapsMenuItem)
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678 removeAllGapsMenuItem_actionPerformed();
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680 else if (source == findMenuItem)
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682 findMenuItem_actionPerformed();
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684 else if (source == font)
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686 new FontChooser(alignPanel);
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688 else if (source == newView)
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692 else if (source == showColumns)
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694 viewport.showAllHiddenColumns();
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695 alignPanel.paintAlignment(true);
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697 else if (source == showSeqs)
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699 viewport.showAllHiddenSeqs();
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701 else if (source == hideColumns)
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703 viewport.hideSelectedColumns();
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704 alignPanel.paintAlignment(true);
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706 else if (source == hideSequences && viewport.getSelectionGroup() != null)
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708 viewport.hideAllSelectedSeqs();
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710 else if (source == featureSettings)
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712 new FeatureSettings(alignPanel);
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714 else if(source== alProperties)
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716 StringBuffer contents = new StringBuffer();
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719 int min=Integer.MAX_VALUE, max=0;
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720 for(int i=0; i<viewport.alignment.getHeight(); i++)
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722 int size = viewport.alignment.getSequenceAt(i).getEnd()
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723 -viewport.alignment.getSequenceAt(i).getStart();
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730 avg = avg/(float)viewport.alignment.getHeight();
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732 contents.append("\nSequences: "+ viewport.alignment.getHeight());
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733 contents.append("\nMinimum Sequence Length: "+min);
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734 contents.append("\nMaximum Sequence Length: "+max);
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735 contents.append("\nAverage Length: "+(int)avg);
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737 if (((Alignment)viewport.alignment).alignmentProperties != null)
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739 Hashtable props = ((Alignment)viewport.alignment).alignmentProperties;
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740 Enumeration en = props.keys();
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741 while(en.hasMoreElements())
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743 String key = en.nextElement().toString();
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744 contents.append("\n"+key+"\t"+props.get(key));
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748 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
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749 cap.setText(contents.toString());
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750 Frame frame = new Frame();
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752 jalview.bin.JalviewLite.addFrame(frame,
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753 "Alignment Properties: "+getTitle()
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756 else if (source == overviewMenuItem)
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758 overviewMenuItem_actionPerformed();
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760 else if (source == noColourmenuItem)
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762 changeColour(null);
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764 else if (source == clustalColour)
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766 abovePIDThreshold.setState(false);
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767 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
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768 viewport.alignment.getWidth()));
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770 else if (source == zappoColour)
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772 changeColour(new ZappoColourScheme());
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774 else if (source == taylorColour)
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776 changeColour(new TaylorColourScheme());
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778 else if (source == hydrophobicityColour)
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780 changeColour(new HydrophobicColourScheme());
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782 else if (source == helixColour)
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784 changeColour(new HelixColourScheme());
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786 else if (source == strandColour)
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788 changeColour(new StrandColourScheme());
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790 else if (source == turnColour)
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792 changeColour(new TurnColourScheme());
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794 else if (source == buriedColour)
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796 changeColour(new BuriedColourScheme());
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798 else if (source == nucleotideColour)
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800 changeColour(new NucleotideColourScheme());
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802 else if (source == modifyPID)
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804 modifyPID_actionPerformed();
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806 else if (source == modifyConservation)
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808 modifyConservation_actionPerformed();
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810 else if (source == userDefinedColour)
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812 new UserDefinedColours(alignPanel, null);
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814 else if (source == PIDColour)
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816 changeColour(new PIDColourScheme());
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818 else if (source == BLOSUM62Colour)
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820 changeColour(new Blosum62ColourScheme());
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822 else if (source == annotationColour)
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824 new AnnotationColourChooser(viewport, alignPanel);
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826 else if (source == sortPairwiseMenuItem)
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828 sortPairwiseMenuItem_actionPerformed();
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830 else if (source == sortIDMenuItem)
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832 sortIDMenuItem_actionPerformed();
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834 else if (source == sortGroupMenuItem)
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836 sortGroupMenuItem_actionPerformed();
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838 else if (source == removeRedundancyMenuItem)
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840 removeRedundancyMenuItem_actionPerformed();
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842 else if (source == pairwiseAlignmentMenuItem)
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844 pairwiseAlignmentMenuItem_actionPerformed();
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846 else if (source == PCAMenuItem)
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848 PCAMenuItem_actionPerformed();
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850 else if (source == averageDistanceTreeMenuItem)
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852 averageDistanceTreeMenuItem_actionPerformed();
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854 else if (source == neighbourTreeMenuItem)
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856 neighbourTreeMenuItem_actionPerformed();
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858 else if (source == njTreeBlosumMenuItem)
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860 njTreeBlosumMenuItem_actionPerformed();
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862 else if (source == avDistanceTreeBlosumMenuItem)
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864 avTreeBlosumMenuItem_actionPerformed();
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866 else if (source == documentation)
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868 documentation_actionPerformed();
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870 else if (source == about)
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872 about_actionPerformed();
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877 public void inputText_actionPerformed()
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879 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
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880 Frame frame = new Frame();
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882 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
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885 protected void outputText_actionPerformed(ActionEvent e)
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887 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
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888 Frame frame = new Frame();
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890 jalview.bin.JalviewLite.addFrame(frame,
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891 "Alignment output - " + e.getActionCommand(),
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893 cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
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894 viewport.getAlignment(),
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895 viewport.showJVSuffix));
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898 public void loadAnnotations()
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900 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
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901 cap.setText("Paste your features / annotations file here.");
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902 cap.setAnnotationImport();
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903 Frame frame = new Frame();
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905 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
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909 public String outputAnnotations(boolean displayTextbox)
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911 String annotation = new AnnotationFile().printAnnotations(
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912 viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,
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913 viewport.alignment.getGroups(),
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914 ((Alignment) viewport.alignment).alignmentProperties);
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916 if (displayTextbox)
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918 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
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919 Frame frame = new Frame();
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921 jalview.bin.JalviewLite.addFrame(frame,
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924 cap.setText(annotation);
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930 public String outputFeatures(boolean displayTextbox, String format)
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933 if (format.equalsIgnoreCase("Jalview"))
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935 features = new FeaturesFile().printJalviewFormat(
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936 viewport.alignment.getSequencesArray(),
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937 viewport.featuresDisplayed);
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941 features = new FeaturesFile().printGFFFormat(
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942 viewport.alignment.getSequencesArray(),
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943 viewport.featuresDisplayed);
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946 if (displayTextbox)
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948 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
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949 Frame frame = new Frame();
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951 jalview.bin.JalviewLite.addFrame(frame,
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955 cap.setText(features);
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961 void launchFullApplication()
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963 StringBuffer url = new StringBuffer(jalviewServletURL);
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965 url.append("?open=" +
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966 appendProtocol(viewport.applet.getParameter("file")));
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968 if (viewport.applet.getParameter("features") != null)
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970 url.append("&features=");
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971 url.append(appendProtocol(viewport.applet.getParameter("features")));
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974 if (viewport.applet.getParameter("annotations") != null)
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976 url.append("&annotations=");
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977 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
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980 if (viewport.applet.getParameter("jnetfile") != null)
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982 url.append("&annotations=");
\r
983 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
\r
986 if (viewport.applet.getParameter("defaultColour") != null)
\r
988 url.append("&colour=" +
\r
989 removeWhiteSpace(viewport.applet.getParameter("defaultColour"))
\r
993 if (viewport.applet.getParameter("userDefinedColour") != null)
\r
995 url.append("&colour=" +
\r
996 removeWhiteSpace(viewport.applet.getParameter(
\r
997 "userDefinedColour"))
\r
1001 showURL(url.toString(), "FULL_APP");
\r
1004 String removeWhiteSpace(String colour)
\r
1006 StringBuffer sb = new StringBuffer();
\r
1007 for (int i = 0; i < colour.length(); i++)
\r
1009 if (Character.isWhitespace(colour.charAt(i)))
\r
1015 sb.append(colour.charAt(i));
\r
1019 return sb.toString();
\r
1022 String appendProtocol(String url)
\r
1028 catch (java.net.MalformedURLException ex)
\r
1030 url = viewport.applet.getCodeBase() + url;
\r
1035 public void closeMenuItem_actionPerformed()
\r
1037 PaintRefresher.RemoveComponent(alignPanel);
\r
1038 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
\r
1039 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
\r
1041 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
\r
1052 void updateEditMenuBar()
\r
1055 if (viewport.historyList.size() > 0)
\r
1057 undoMenuItem.setEnabled(true);
\r
1058 CommandI command = (CommandI) viewport.historyList.peek();
\r
1059 undoMenuItem.setLabel("Undo " + command.getDescription());
\r
1063 undoMenuItem.setEnabled(false);
\r
1064 undoMenuItem.setLabel("Undo");
\r
1067 if (viewport.redoList.size() > 0)
\r
1069 redoMenuItem.setEnabled(true);
\r
1071 CommandI command = (CommandI) viewport.redoList.peek();
\r
1072 redoMenuItem.setLabel("Redo " + command.getDescription());
\r
1076 redoMenuItem.setEnabled(false);
\r
1077 redoMenuItem.setLabel("Redo");
\r
1081 public void addHistoryItem(CommandI command)
\r
1083 if (command.getSize() > 0)
\r
1085 viewport.historyList.push(command);
\r
1086 viewport.redoList.removeAllElements();
\r
1087 updateEditMenuBar();
\r
1088 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
1095 * @param e DOCUMENT ME!
\r
1097 protected void undoMenuItem_actionPerformed()
\r
1099 if (viewport.historyList.size() < 1)
\r
1104 CommandI command = (CommandI) viewport.historyList.pop();
\r
1105 viewport.redoList.push(command);
\r
1106 command.undoCommand();
\r
1108 AlignViewport originalSource = getOriginatingSource(command);
\r
1110 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
1111 updateEditMenuBar();
\r
1112 originalSource.firePropertyChange("alignment", null,
\r
1113 originalSource.alignment.getSequences());
\r
1119 * @param e DOCUMENT ME!
\r
1121 protected void redoMenuItem_actionPerformed()
\r
1123 if (viewport.redoList.size() < 1)
\r
1128 CommandI command = (CommandI) viewport.redoList.pop();
\r
1129 viewport.historyList.push(command);
\r
1130 command.doCommand();
\r
1132 AlignViewport originalSource = getOriginatingSource(command);
\r
1133 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
1135 updateEditMenuBar();
\r
1136 originalSource.firePropertyChange("alignment", null,
\r
1137 originalSource.alignment.getSequences());
\r
1140 AlignViewport getOriginatingSource(CommandI command)
\r
1142 AlignViewport originalSource = null;
\r
1143 //For sequence removal and addition, we need to fire
\r
1144 //the property change event FROM the viewport where the
\r
1145 //original alignment was altered
\r
1146 AlignmentI al = null;
\r
1147 if (command instanceof EditCommand)
\r
1149 EditCommand editCommand = (EditCommand) command;
\r
1150 al = editCommand.getAlignment();
\r
1151 Vector comps = (Vector) PaintRefresher.components
\r
1152 .get(viewport.getSequenceSetId());
\r
1153 for (int i = 0; i < comps.size(); i++)
\r
1155 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
1157 if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)
\r
1159 originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
\r
1166 if (originalSource == null)
\r
1168 //The original view is closed, we must validate
\r
1169 //the current view against the closed view first
\r
1172 PaintRefresher.validateSequences(al, viewport.alignment);
\r
1175 originalSource = viewport;
\r
1178 return originalSource;
\r
1181 public void moveSelectedSequences(boolean up)
\r
1183 SequenceGroup sg = viewport.getSelectionGroup();
\r
1191 for (int i = 1; i < viewport.alignment.getHeight(); i++)
\r
1193 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
1194 if (!sg.getSequences(null).contains(seq))
\r
1199 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
\r
1200 if (sg.getSequences(null).contains(temp))
\r
1205 viewport.alignment.getSequences().setElementAt(temp, i);
\r
1206 viewport.alignment.getSequences().setElementAt(seq, i - 1);
\r
1211 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
\r
1213 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
1214 if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))
\r
1219 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
\r
1220 if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))
\r
1225 viewport.alignment.getSequences().setElementAt(temp, i);
\r
1226 viewport.alignment.getSequences().setElementAt(seq, i + 1);
\r
1230 alignPanel.paintAlignment(true);
\r
1233 synchronized void slideSequences(boolean right, int size)
\r
1235 Vector sg = new Vector();
\r
1236 if(viewport.cursorMode)
\r
1238 sg.addElement(viewport.alignment.getSequenceAt(
\r
1239 alignPanel.seqPanel.seqCanvas.cursorY));
\r
1241 else if(viewport.getSelectionGroup()!=null
\r
1242 && viewport.getSelectionGroup().getSize()!=viewport.alignment.getHeight())
\r
1244 sg = viewport.getSelectionGroup().getSequences(
\r
1245 viewport.hiddenRepSequences);
\r
1253 Vector invertGroup = new Vector();
\r
1255 for (int i = 0; i < viewport.alignment.getHeight(); i++)
\r
1257 if(!sg.contains(viewport.alignment.getSequenceAt(i)))
\r
1258 invertGroup.addElement(viewport.alignment.getSequenceAt(i));
\r
1261 SequenceI[] seqs1 = new SequenceI[sg.size()];
\r
1262 for (int i = 0; i < sg.size(); i++)
\r
1263 seqs1[i] = (SequenceI) sg.elementAt(i);
\r
1265 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
\r
1266 for (int i = 0; i < invertGroup.size(); i++)
\r
1267 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
\r
1269 SlideSequencesCommand ssc;
\r
1271 ssc = new SlideSequencesCommand("Slide Sequences",
\r
1272 seqs2, seqs1, size,
\r
1273 viewport.getGapCharacter()
\r
1276 ssc = new SlideSequencesCommand("Slide Sequences",
\r
1277 seqs1, seqs2, size,
\r
1278 viewport.getGapCharacter()
\r
1281 int groupAdjustment = 0;
\r
1282 if (ssc.getGapsInsertedBegin() && right)
\r
1284 if (viewport.cursorMode)
\r
1285 alignPanel.seqPanel.moveCursor(size, 0);
\r
1287 groupAdjustment = size;
\r
1289 else if (!ssc.getGapsInsertedBegin() && !right)
\r
1291 if (viewport.cursorMode)
\r
1292 alignPanel.seqPanel.moveCursor( -size, 0);
\r
1294 groupAdjustment = -size;
\r
1297 if (groupAdjustment != 0)
\r
1299 viewport.getSelectionGroup().setStartRes(
\r
1300 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
\r
1301 viewport.getSelectionGroup().setEndRes(
\r
1302 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
\r
1306 boolean appendHistoryItem = false;
\r
1307 if(viewport.historyList!=null
\r
1308 && viewport.historyList.size()>0
\r
1309 && viewport.historyList.peek() instanceof SlideSequencesCommand)
\r
1311 appendHistoryItem = ssc.appendSlideCommand(
\r
1312 (SlideSequencesCommand)viewport.historyList.peek())
\r
1316 if(!appendHistoryItem)
\r
1317 addHistoryItem(ssc);
\r
1322 static StringBuffer copiedSequences;
\r
1323 static Vector copiedHiddenColumns;
\r
1324 protected void copy_actionPerformed()
\r
1326 if (viewport.getSelectionGroup() == null)
\r
1331 SequenceGroup sg = viewport.getSelectionGroup();
\r
1332 copiedSequences = new StringBuffer();
\r
1333 Hashtable orderedSeqs = new Hashtable();
\r
1334 for (int i = 0; i < sg.getSize(); i++)
\r
1336 SequenceI seq = sg.getSequenceAt(i);
\r
1337 int index = viewport.alignment.findIndex(seq);
\r
1338 orderedSeqs.put(index + "", seq);
\r
1341 int index = 0, startRes, endRes;
\r
1344 if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
\r
1346 copiedHiddenColumns = new Vector();
\r
1347 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
\r
1348 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();
\r
1351 int[] region = (int[])
\r
1352 viewport.getColumnSelection().getHiddenColumns().elementAt(i);
\r
1354 copiedHiddenColumns.addElement(new int[]
\r
1355 {region[0] - hiddenOffset,
\r
1356 region[1] - hiddenOffset});
\r
1361 copiedHiddenColumns = null;
\r
1364 for (int i = 0; i < sg.getSize(); i++)
\r
1366 SequenceI seq = null;
\r
1368 while (seq == null)
\r
1370 if (orderedSeqs.containsKey(index + ""))
\r
1372 seq = (SequenceI) orderedSeqs.get(index + "");
\r
1384 //Returns residue following index if gap
\r
1385 startRes = seq.findPosition(sg.getStartRes());
\r
1388 //Need to find the residue preceeding index if gap
\r
1391 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
\r
1393 ch = seq.getCharAt(j);
\r
1394 if (!jalview.util.Comparison.isGap( (ch)))
\r
1402 endRes += seq.getStart() - 1;
\r
1405 copiedSequences.append(seq.getName() + "\t" +
\r
1408 seq.getSequenceAsString(sg.getStartRes(),
\r
1409 sg.getEndRes() + 1) + "\n");
\r
1414 protected void pasteNew_actionPerformed()
\r
1419 protected void pasteThis_actionPerformed()
\r
1424 void paste(boolean newAlignment)
\r
1429 if (copiedSequences == null)
\r
1434 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
1435 Vector seqs = new Vector();
\r
1436 while (st.hasMoreElements())
\r
1438 String name = st.nextToken();
\r
1439 int start = Integer.parseInt(st.nextToken());
\r
1440 int end = Integer.parseInt(st.nextToken());
\r
1441 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
\r
1443 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
1444 for (int i = 0; i < seqs.size(); i++)
\r
1446 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
1451 String newtitle = new String("Copied sequences");
\r
1452 if (getTitle().startsWith("Copied sequences"))
\r
1454 newtitle = getTitle();
\r
1458 newtitle = newtitle.concat("- from " + getTitle());
\r
1460 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
1464 if (copiedHiddenColumns != null)
\r
1466 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
1468 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
1469 af.viewport.hideColumns(region[0], region[1]);
\r
1473 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
\r
1478 addSequences(newSeqs);
\r
1482 catch (Exception ex)
\r
1483 {} // could be anything being pasted in here
\r
1487 void addSequences(SequenceI[] seqs)
\r
1489 for (int i = 0; i < seqs.length; i++)
\r
1491 viewport.alignment.addSequence(seqs[i]);
\r
1495 addHistoryItem(new EditCommand(
\r
1497 EditCommand.PASTE,
\r
1500 viewport.alignment.getWidth(),
\r
1501 viewport.alignment)
\r
1504 viewport.setEndSeq(viewport.alignment.getHeight());
\r
1505 viewport.alignment.getWidth();
\r
1506 viewport.firePropertyChange("alignment", null,
\r
1507 viewport.alignment.getSequences());
\r
1511 protected void cut_actionPerformed()
\r
1513 copy_actionPerformed();
\r
1514 delete_actionPerformed();
\r
1517 protected void delete_actionPerformed()
\r
1520 SequenceGroup sg = viewport.getSelectionGroup();
\r
1526 Vector seqs = new Vector();
\r
1528 for (int i = 0; i < sg.getSize(); i++)
\r
1530 seq = sg.getSequenceAt(i);
\r
1531 seqs.addElement(seq);
\r
1534 // If the cut affects all sequences, remove highlighted columns
\r
1535 if (sg.getSize() == viewport.alignment.getHeight())
\r
1537 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
1538 sg.getEndRes() + 1);
\r
1541 SequenceI[] cut = new SequenceI[seqs.size()];
\r
1542 for (int i = 0; i < seqs.size(); i++)
\r
1544 cut[i] = (SequenceI) seqs.elementAt(i);
\r
1548 //ADD HISTORY ITEM
\r
1550 addHistoryItem(new EditCommand("Cut Sequences",
\r
1554 sg.getEndRes() - sg.getStartRes() + 1,
\r
1555 viewport.alignment));
\r
1557 viewport.setSelectionGroup(null);
\r
1558 viewport.alignment.deleteGroup(sg);
\r
1560 viewport.firePropertyChange("alignment", null,
\r
1561 viewport.getAlignment().getSequences());
\r
1563 if (viewport.getAlignment().getHeight() < 1)
\r
1565 this.setVisible(false);
\r
1569 protected void deleteGroups_actionPerformed()
\r
1571 viewport.alignment.deleteAllGroups();
\r
1572 viewport.sequenceColours = null;
\r
1573 viewport.setSelectionGroup(null);
\r
1575 alignPanel.paintAlignment(true);
\r
1578 public void selectAllSequenceMenuItem_actionPerformed()
\r
1580 SequenceGroup sg = new SequenceGroup();
\r
1581 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1583 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
1585 sg.setEndRes(viewport.alignment.getWidth() - 1);
\r
1586 viewport.setSelectionGroup(sg);
\r
1587 alignPanel.paintAlignment(true);
\r
1588 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1591 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1593 if (viewport.cursorMode)
\r
1595 alignPanel.seqPanel.keyboardNo1 = null;
\r
1596 alignPanel.seqPanel.keyboardNo2 = null;
\r
1598 viewport.setSelectionGroup(null);
\r
1599 viewport.getColumnSelection().clear();
\r
1600 viewport.setSelectionGroup(null);
\r
1601 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1602 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1603 alignPanel.paintAlignment(true);
\r
1604 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1607 public void invertSequenceMenuItem_actionPerformed()
\r
1609 SequenceGroup sg = viewport.getSelectionGroup();
\r
1610 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1612 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1615 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1618 void trimAlignment(boolean trimLeft)
\r
1620 ColumnSelection colSel = viewport.getColumnSelection();
\r
1623 if (colSel.size() > 0)
\r
1627 column = colSel.getMin();
\r
1631 column = colSel.getMax();
\r
1635 if (viewport.getSelectionGroup() != null)
\r
1637 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
\r
1638 hiddenRepSequences);
\r
1642 seqs = viewport.alignment.getSequencesArray();
\r
1645 TrimRegionCommand trimRegion;
\r
1648 trimRegion = new TrimRegionCommand("Remove Left",
\r
1649 TrimRegionCommand.TRIM_LEFT,
\r
1652 viewport.alignment,
\r
1654 viewport.selectionGroup);
\r
1655 viewport.setStartRes(0);
\r
1659 trimRegion = new TrimRegionCommand("Remove Right",
\r
1660 TrimRegionCommand.TRIM_RIGHT,
\r
1663 viewport.alignment,
\r
1665 viewport.selectionGroup);
\r
1668 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
\r
1670 addHistoryItem(trimRegion);
\r
1672 Vector groups = viewport.alignment.getGroups();
\r
1674 for (int i = 0; i < groups.size(); i++)
\r
1676 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1678 if ( (trimLeft && !sg.adjustForRemoveLeft(column))
\r
1679 || (!trimLeft && !sg.adjustForRemoveRight(column)))
\r
1681 viewport.alignment.deleteGroup(sg);
\r
1685 viewport.firePropertyChange("alignment", null,
\r
1686 viewport.getAlignment().getSequences());
\r
1690 public void removeGappedColumnMenuItem_actionPerformed()
\r
1692 int start = 0, end = viewport.alignment.getWidth() - 1;
\r
1695 if (viewport.getSelectionGroup() != null)
\r
1697 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
\r
1698 hiddenRepSequences);
\r
1699 start = viewport.getSelectionGroup().getStartRes();
\r
1700 end = viewport.getSelectionGroup().getEndRes();
\r
1704 seqs = viewport.alignment.getSequencesArray();
\r
1707 RemoveGapColCommand removeGapCols =
\r
1708 new RemoveGapColCommand("Remove Gapped Columns",
\r
1711 viewport.alignment);
\r
1713 addHistoryItem(removeGapCols);
\r
1715 statusBar.setText("Removed " + removeGapCols.getSize() + " empty columns.");
\r
1717 //This is to maintain viewport position on first residue
\r
1718 //of first sequence
\r
1719 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1720 int startRes = seq.findPosition(viewport.startRes);
\r
1721 // ShiftList shifts;
\r
1722 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
\r
1723 // edit.alColumnChanges=shifts.getInverse();
\r
1724 // if (viewport.hasHiddenColumns)
\r
1725 // viewport.getColumnSelection().compensateForEdits(shifts);
\r
1726 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
1727 viewport.firePropertyChange("alignment", null,
\r
1728 viewport.getAlignment().getSequences());
\r
1732 public void removeAllGapsMenuItem_actionPerformed()
\r
1734 int start = 0, end = viewport.alignment.getWidth() - 1;
\r
1737 if (viewport.getSelectionGroup() != null)
\r
1739 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
\r
1740 hiddenRepSequences);
\r
1741 start = viewport.getSelectionGroup().getStartRes();
\r
1742 end = viewport.getSelectionGroup().getEndRes();
\r
1746 seqs = viewport.alignment.getSequencesArray();
\r
1749 //This is to maintain viewport position on first residue
\r
1750 //of first sequence
\r
1751 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1752 int startRes = seq.findPosition(viewport.startRes);
\r
1754 addHistoryItem(new RemoveGapsCommand("Remove Gaps",
\r
1757 viewport.alignment));
\r
1759 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
1761 viewport.firePropertyChange("alignment", null,
\r
1762 viewport.getAlignment().getSequences());
\r
1766 public void findMenuItem_actionPerformed()
\r
1768 new Finder(alignPanel);
\r
1771 public void newView()
\r
1774 if (viewport.hasHiddenRows)
\r
1776 newal = new Alignment(viewport.getAlignment().
\r
1777 getHiddenSequences()
\r
1778 .getFullAlignment().
\r
1779 getSequencesArray());
\r
1783 newal = new Alignment(viewport.alignment.getSequencesArray());
\r
1786 if (viewport.alignment.getAlignmentAnnotation() != null)
\r
1788 for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)
\r
1790 if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
\r
1792 newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);
\r
1797 AlignFrame newaf = new AlignFrame(newal,
\r
1802 newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
\r
1803 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
\r
1804 PaintRefresher.Register(newaf.alignPanel,
\r
1805 newaf.alignPanel.av.getSequenceSetId());
\r
1807 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
\r
1808 newaf.alignPanel.av.getSequenceSetId());
\r
1809 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
\r
1810 newaf.alignPanel.av.getSequenceSetId());
\r
1812 Vector comps = (Vector) PaintRefresher.components.get(viewport.
\r
1813 getSequenceSetId());
\r
1814 int viewSize = -1;
\r
1815 for (int i = 0; i < comps.size(); i++)
\r
1817 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
1823 String title = new String(this.getTitle());
\r
1824 if (title.indexOf("(View") > -1)
\r
1826 title = title.substring(0, title.indexOf("(View"));
\r
1829 title += "(View " + viewSize + ")";
\r
1831 newaf.setTitle(title.toString());
\r
1833 newaf.viewport.historyList = viewport.historyList;
\r
1834 newaf.viewport.redoList = viewport.redoList;
\r
1838 public void seqLimits_itemStateChanged()
\r
1840 viewport.setShowJVSuffix(seqLimits.getState());
\r
1841 alignPanel.fontChanged();
\r
1842 alignPanel.paintAlignment(true);
\r
1845 protected void colourTextMenuItem_actionPerformed()
\r
1847 viewport.setColourText(colourTextMenuItem.getState());
\r
1848 alignPanel.paintAlignment(true);
\r
1851 protected void wrapMenuItem_actionPerformed()
\r
1853 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
1854 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
1855 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
1856 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
1857 scaleRight.setEnabled(wrapMenuItem.getState());
\r
1858 alignPanel.paintAlignment(true);
\r
1861 public void overviewMenuItem_actionPerformed()
\r
1863 if (alignPanel.overviewPanel != null)
\r
1868 Frame frame = new Frame();
\r
1869 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1870 frame.add(overview);
\r
1871 // +50 must allow for applet frame window
\r
1872 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
1873 overview.getPreferredSize().width,
\r
1874 overview.getPreferredSize().height + 50);
\r
1877 frame.addWindowListener(new WindowAdapter()
\r
1879 public void windowClosing(WindowEvent e)
\r
1881 alignPanel.setOverviewPanel(null);
\r
1885 alignPanel.setOverviewPanel(overview);
\r
1889 void changeColour(ColourSchemeI cs)
\r
1891 int threshold = 0;
\r
1895 if (viewport.getAbovePIDThreshold())
\r
1897 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
\r
1899 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1901 viewport.setGlobalColourScheme(cs);
\r
1905 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1908 if (viewport.getConservationSelected())
\r
1911 Alignment al = (Alignment) viewport.alignment;
\r
1912 Conservation c = new Conservation("All",
\r
1913 ResidueProperties.propHash, 3,
\r
1914 al.getSequences(), 0,
\r
1915 al.getWidth() - 1);
\r
1918 c.verdict(false, viewport.ConsPercGaps);
\r
1920 cs.setConservation(c);
\r
1922 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1928 cs.setConservation(null);
\r
1931 cs.setConsensus(viewport.hconsensus);
\r
1934 viewport.setGlobalColourScheme(cs);
\r
1936 if (viewport.getColourAppliesToAllGroups())
\r
1938 Vector groups = viewport.alignment.getGroups();
\r
1939 for (int i = 0; i < groups.size(); i++)
\r
1941 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1948 if (cs instanceof ClustalxColourScheme)
\r
1950 sg.cs = new ClustalxColourScheme(
\r
1951 sg.getSequences(viewport.hiddenRepSequences),
\r
1958 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1960 catch (Exception ex)
\r
1962 ex.printStackTrace();
\r
1967 if (viewport.getAbovePIDThreshold()
\r
1968 || cs instanceof PIDColourScheme
\r
1969 || cs instanceof Blosum62ColourScheme)
\r
1971 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1972 sg.cs.setConsensus(AAFrequency.calculate(
\r
1973 sg.getSequences(viewport.hiddenRepSequences), 0, sg.getWidth()));
\r
1977 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1980 if (viewport.getConservationSelected())
\r
1982 Conservation c = new Conservation("Group",
\r
1983 ResidueProperties.propHash, 3,
\r
1984 sg.getSequences(viewport.
\r
1985 hiddenRepSequences), 0,
\r
1986 viewport.alignment.getWidth() - 1);
\r
1988 c.verdict(false, viewport.ConsPercGaps);
\r
1989 sg.cs.setConservation(c);
\r
1993 sg.cs.setConservation(null);
\r
1994 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2000 if (alignPanel.getOverviewPanel() != null)
\r
2002 alignPanel.getOverviewPanel().updateOverviewImage();
\r
2005 jalview.structure.StructureSelectionManager.getStructureSelectionManager()
\r
2006 .sequenceColoursChanged(alignPanel);
\r
2008 alignPanel.paintAlignment(true);
\r
2011 protected void modifyPID_actionPerformed()
\r
2013 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme != null)
\r
2015 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
2017 SliderPanel.showPIDSlider();
\r
2021 protected void modifyConservation_actionPerformed()
\r
2023 if (viewport.getConservationSelected() && viewport.globalColourScheme != null)
\r
2025 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
2027 SliderPanel.showConservationSlider();
\r
2031 protected void conservationMenuItem_actionPerformed()
\r
2033 viewport.setConservationSelected(conservationMenuItem.getState());
\r
2035 viewport.setAbovePIDThreshold(false);
\r
2036 abovePIDThreshold.setState(false);
\r
2038 changeColour(viewport.getGlobalColourScheme());
\r
2040 modifyConservation_actionPerformed();
\r
2043 public void abovePIDThreshold_actionPerformed()
\r
2045 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
2047 conservationMenuItem.setState(false);
\r
2048 viewport.setConservationSelected(false);
\r
2050 changeColour(viewport.getGlobalColourScheme());
\r
2052 modifyPID_actionPerformed();
\r
2055 public void sortPairwiseMenuItem_actionPerformed()
\r
2057 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2058 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
2059 viewport.getAlignment().getSequenceAt(0));
\r
2060 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
\r
2061 viewport.alignment));
\r
2062 alignPanel.paintAlignment(true);
\r
2065 public void sortIDMenuItem_actionPerformed()
\r
2067 // addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
2068 // HistoryItem.SORT));
\r
2069 AlignmentSorter.sortByID(viewport.getAlignment());
\r
2070 alignPanel.paintAlignment(true);
\r
2073 public void sortGroupMenuItem_actionPerformed()
\r
2075 // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
2076 // HistoryItem.SORT));
\r
2077 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
2078 alignPanel.paintAlignment(true);
\r
2082 public void removeRedundancyMenuItem_actionPerformed()
\r
2084 new RedundancyPanel(alignPanel);
\r
2087 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
2089 if (viewport.getSelectionGroup() != null
\r
2090 && viewport.getSelectionGroup().getSize() > 1)
\r
2092 Frame frame = new Frame();
\r
2093 frame.add(new PairwiseAlignPanel(alignPanel));
\r
2094 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
2098 public void PCAMenuItem_actionPerformed()
\r
2100 //are the sequences aligned?
\r
2101 if (!viewport.alignment.isAligned())
\r
2103 SequenceI current;
\r
2104 int Width = viewport.getAlignment().getWidth();
\r
2106 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
2109 current = viewport.getAlignment().getSequenceAt(i);
\r
2111 if (current.getLength() < Width)
\r
2113 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2116 alignPanel.paintAlignment(true);
\r
2119 if ( (viewport.getSelectionGroup() != null &&
\r
2120 viewport.getSelectionGroup().getSize() < 4 &&
\r
2121 viewport.getSelectionGroup().getSize() > 0)
\r
2122 || viewport.getAlignment().getHeight() < 4)
\r
2129 new PCAPanel(viewport);
\r
2131 catch (java.lang.OutOfMemoryError ex)
\r
2137 public void averageDistanceTreeMenuItem_actionPerformed()
\r
2139 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
2142 public void neighbourTreeMenuItem_actionPerformed()
\r
2144 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
2147 protected void njTreeBlosumMenuItem_actionPerformed()
\r
2149 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2152 protected void avTreeBlosumMenuItem_actionPerformed()
\r
2154 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2157 void NewTreePanel(String type, String pwType, String title)
\r
2159 //are the sequences aligned?
\r
2160 if (!viewport.alignment.isAligned())
\r
2162 SequenceI current;
\r
2163 int Width = viewport.getAlignment().getWidth();
\r
2165 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
2168 current = viewport.getAlignment().getSequenceAt(i);
\r
2170 if (current.getLength() < Width)
\r
2172 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2175 alignPanel.paintAlignment(true);
\r
2179 if ( (viewport.getSelectionGroup() != null &&
\r
2180 viewport.getSelectionGroup().getSize() > 1)
\r
2181 || (viewport.getSelectionGroup() == null
\r
2182 && viewport.alignment.getHeight() > 1))
\r
2184 final TreePanel tp = new TreePanel(viewport,
\r
2188 addTreeMenuItem(tp, title);
\r
2190 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
2194 void loadTree_actionPerformed()
\r
2196 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
2197 cap.setText("Paste your Newick tree file here.");
\r
2198 cap.setTreeImport();
\r
2199 Frame frame = new Frame();
\r
2201 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
2204 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
2206 TreePanel tp = new TreePanel(viewport,
\r
2210 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
2211 addTreeMenuItem(tp, treeFile);
\r
2214 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
2216 final MenuItem item = new MenuItem(title);
\r
2217 sortByTreeMenu.add(item);
\r
2218 item.addActionListener(new java.awt.event.ActionListener()
\r
2220 public void actionPerformed(ActionEvent evt)
\r
2222 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2223 // HistoryItem.SORT));
\r
2224 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
2225 alignPanel.paintAlignment(true);
\r
2229 treePanel.addWindowListener(new WindowAdapter()
\r
2231 public void windowClosing(WindowEvent e)
\r
2233 sortByTreeMenu.remove(item);
\r
2238 protected void documentation_actionPerformed()
\r
2240 showURL("http://www.jalview.org/help.html", "HELP");
\r
2243 protected void about_actionPerformed()
\r
2250 public AboutPanel(String version)
\r
2252 this.version = version;
\r
2255 public void paint(Graphics g)
\r
2257 g.setColor(Color.white);
\r
2258 g.fillRect(0, 0, getSize().width, getSize().height);
\r
2259 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2260 FontMetrics fm = g.getFontMetrics();
\r
2261 int fh = fm.getHeight();
\r
2263 g.setColor(Color.black);
\r
2264 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
2265 g.drawString("Jalview - Release " + version, 200, y += fh);
\r
2266 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2267 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
2269 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
2272 "For any issues relating to Jalview, email help@jalview.org", x,
\r
2274 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
2275 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
2277 g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh);
\r
2281 String version = "test";
\r
2282 java.net.URL url = getClass().getResource("/.build_properties");
\r
2287 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
2288 url.openStream()));
\r
2290 while ( (line = reader.readLine()) != null)
\r
2292 if (line.indexOf("VERSION") > -1)
\r
2294 version = line.substring(line.indexOf("=") + 1);
\r
2298 catch (Exception ex)
\r
2300 ex.printStackTrace();
\r
2304 Frame frame = new Frame();
\r
2305 frame.add(new AboutPanel(version));
\r
2306 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
\r
2310 public void showURL(String url, String target)
\r
2312 if (viewport.applet == null)
\r
2314 System.out.println("Not running as applet - no browser available.");
\r
2320 System.out.println("Show url: " + url);
\r
2321 viewport.applet.getAppletContext().showDocument(new java.net.URL(url),
\r
2324 catch (Exception ex)
\r
2326 ex.printStackTrace();
\r
2331 //////////////////////////////////////////////////////////////////////////////////
\r
2332 //JBuilder Graphics here
\r
2334 MenuBar alignFrameMenuBar = new MenuBar();
\r
2335 Menu fileMenu = new Menu("File");
\r
2336 MenuItem loadApplication = new MenuItem("View in Full Application");
\r
2337 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
\r
2338 MenuItem loadAnnotations = new MenuItem(
\r
2339 "Load Features/Annotations ...");
\r
2340 MenuItem outputFeatures = new MenuItem("Export Features ...");
\r
2341 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
\r
2343 MenuItem closeMenuItem = new MenuItem("Close");
\r
2344 Menu editMenu = new Menu("Edit");
\r
2345 Menu viewMenu = new Menu("View");
\r
2346 Menu colourMenu = new Menu("Colour");
\r
2347 Menu calculateMenu = new Menu("Calculate");
\r
2348 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
2349 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
2350 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
2351 MenuItem remove2LeftMenuItem = new MenuItem();
\r
2352 MenuItem remove2RightMenuItem = new MenuItem();
\r
2353 MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
2354 MenuItem removeAllGapsMenuItem = new MenuItem();
\r
2355 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
2356 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
2357 MenuItem sortPairwiseMenuItem = new MenuItem();
\r
2358 MenuItem sortIDMenuItem = new MenuItem();
\r
2359 MenuItem sortGroupMenuItem = new MenuItem();
\r
2360 MenuItem removeRedundancyMenuItem = new MenuItem();
\r
2361 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
2362 MenuItem PCAMenuItem = new MenuItem();
\r
2363 MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
2364 MenuItem neighbourTreeMenuItem = new MenuItem();
\r
2365 BorderLayout borderLayout1 = new BorderLayout();
\r
2366 public Label statusBar = new Label();
\r
2367 Menu outputTextboxMenu = new Menu();
\r
2368 MenuItem clustalColour = new MenuItem();
\r
2369 MenuItem zappoColour = new MenuItem();
\r
2370 MenuItem taylorColour = new MenuItem();
\r
2371 MenuItem hydrophobicityColour = new MenuItem();
\r
2372 MenuItem helixColour = new MenuItem();
\r
2373 MenuItem strandColour = new MenuItem();
\r
2374 MenuItem turnColour = new MenuItem();
\r
2375 MenuItem buriedColour = new MenuItem();
\r
2376 MenuItem userDefinedColour = new MenuItem();
\r
2377 MenuItem PIDColour = new MenuItem();
\r
2378 MenuItem BLOSUM62Colour = new MenuItem();
\r
2379 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
2380 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
2381 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
2382 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
2383 MenuItem alProperties = new MenuItem("Alignment Properties...");
\r
2384 MenuItem overviewMenuItem = new MenuItem();
\r
2385 MenuItem undoMenuItem = new MenuItem();
\r
2386 MenuItem redoMenuItem = new MenuItem();
\r
2387 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
2388 MenuItem noColourmenuItem = new MenuItem();
\r
2389 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
2390 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
2391 MenuItem findMenuItem = new MenuItem();
\r
2392 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
2393 MenuItem nucleotideColour = new MenuItem();
\r
2394 MenuItem deleteGroups = new MenuItem();
\r
2395 MenuItem delete = new MenuItem();
\r
2396 MenuItem copy = new MenuItem();
\r
2397 MenuItem cut = new MenuItem();
\r
2398 Menu pasteMenu = new Menu();
\r
2399 MenuItem pasteNew = new MenuItem();
\r
2400 MenuItem pasteThis = new MenuItem();
\r
2401 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
2402 MenuItem font = new MenuItem();
\r
2403 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
2404 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
2405 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
2406 MenuItem modifyPID = new MenuItem();
\r
2407 MenuItem modifyConservation = new MenuItem();
\r
2408 CheckboxMenuItem autoCalculate
\r
2409 = new CheckboxMenuItem("Autocalculate Consensus", true);
\r
2410 Menu sortByTreeMenu = new Menu();
\r
2411 Menu sort = new Menu();
\r
2412 Menu calculate = new Menu();
\r
2413 MenuItem inputText = new MenuItem();
\r
2414 Menu helpMenu = new Menu();
\r
2415 MenuItem documentation = new MenuItem();
\r
2416 MenuItem about = new MenuItem();
\r
2417 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
2418 Panel embeddedMenu;
\r
2419 Label embeddedEdit;
\r
2420 Label embeddedSelect;
\r
2421 Label embeddedView;
\r
2422 Label embeddedFormat;
\r
2423 Label embeddedColour;
\r
2424 Label embeddedFile;
\r
2425 Label embeddedHelp;
\r
2426 Label embeddedCalculate;
\r
2427 FlowLayout flowLayout1;
\r
2429 private void jbInit()
\r
2433 setMenuBar(alignFrameMenuBar);
\r
2437 // dynamically fill save as menu with available formats
\r
2438 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length;
\r
2442 item = new MenuItem(jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
2444 item.addActionListener(new java.awt.event.ActionListener()
\r
2446 public void actionPerformed(ActionEvent e)
\r
2448 outputText_actionPerformed(e);
\r
2452 outputTextboxMenu.add(item);
\r
2454 closeMenuItem.addActionListener(this);
\r
2455 loadApplication.addActionListener(this);
\r
2457 loadTree.addActionListener(this);
\r
2458 loadAnnotations.addActionListener(this);
\r
2459 outputFeatures.addActionListener(this);
\r
2460 outputAnnotations.addActionListener(this);
\r
2461 selectAllSequenceMenuItem.addActionListener(this);
\r
2462 deselectAllSequenceMenuItem.addActionListener(this);
\r
2463 invertSequenceMenuItem.addActionListener(this);
\r
2464 remove2LeftMenuItem.setLabel("Remove Left");
\r
2465 remove2LeftMenuItem.addActionListener(this);
\r
2466 remove2RightMenuItem.setLabel("Remove Right");
\r
2467 remove2RightMenuItem.addActionListener(this);
\r
2468 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
2469 removeGappedColumnMenuItem.addActionListener(this);
\r
2470 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
2471 removeAllGapsMenuItem.addActionListener(this);
\r
2472 viewBoxesMenuItem.setLabel("Boxes");
\r
2473 viewBoxesMenuItem.setState(true);
\r
2474 viewBoxesMenuItem.addItemListener(this);
\r
2475 viewTextMenuItem.setLabel("Text");
\r
2476 viewTextMenuItem.setState(true);
\r
2477 viewTextMenuItem.addItemListener(this);
\r
2478 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
2479 sortPairwiseMenuItem.addActionListener(this);
\r
2480 sortIDMenuItem.setLabel("by ID");
\r
2481 sortIDMenuItem.addActionListener(this);
\r
2482 sortGroupMenuItem.setLabel("by Group");
\r
2483 sortGroupMenuItem.addActionListener(this);
\r
2484 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
2485 removeRedundancyMenuItem.addActionListener(this);
\r
2486 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
2487 pairwiseAlignmentMenuItem.addActionListener(this);
\r
2488 PCAMenuItem.setLabel("Principal Component Analysis");
\r
2489 PCAMenuItem.addActionListener(this);
\r
2490 averageDistanceTreeMenuItem.setLabel(
\r
2491 "Average Distance Using % Identity");
\r
2492 averageDistanceTreeMenuItem.addActionListener(this);
\r
2493 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
2494 neighbourTreeMenuItem.addActionListener(this);
\r
2495 statusBar.setBackground(Color.white);
\r
2496 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
2497 statusBar.setText("Status bar");
\r
2498 outputTextboxMenu.setLabel("Output to Textbox");
\r
2499 clustalColour.setLabel("Clustalx");
\r
2501 clustalColour.addActionListener(this);
\r
2502 zappoColour.setLabel("Zappo");
\r
2503 zappoColour.addActionListener(this);
\r
2504 taylorColour.setLabel("Taylor");
\r
2505 taylorColour.addActionListener(this);
\r
2506 hydrophobicityColour.setLabel("Hydrophobicity");
\r
2507 hydrophobicityColour.addActionListener(this);
\r
2508 helixColour.setLabel("Helix Propensity");
\r
2509 helixColour.addActionListener(this);
\r
2510 strandColour.setLabel("Strand Propensity");
\r
2511 strandColour.addActionListener(this);
\r
2512 turnColour.setLabel("Turn Propensity");
\r
2513 turnColour.addActionListener(this);
\r
2514 buriedColour.setLabel("Buried Index");
\r
2515 buriedColour.addActionListener(this);
\r
2516 userDefinedColour.setLabel("User Defined...");
\r
2517 userDefinedColour.addActionListener(this);
\r
2518 PIDColour.setLabel("Percentage Identity");
\r
2519 PIDColour.addActionListener(this);
\r
2520 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
2521 BLOSUM62Colour.addActionListener(this);
\r
2522 avDistanceTreeBlosumMenuItem.setLabel(
\r
2523 "Average Distance Using BLOSUM62");
\r
2524 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
2525 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
2526 njTreeBlosumMenuItem.addActionListener(this);
\r
2527 annotationPanelMenuItem.setLabel("Show Annotations");
\r
2528 annotationPanelMenuItem.addItemListener(this);
\r
2529 colourTextMenuItem.setLabel("Colour Text");
\r
2530 colourTextMenuItem.addItemListener(this);
\r
2531 alProperties.addActionListener(this);
\r
2532 overviewMenuItem.setLabel("Overview Window");
\r
2533 overviewMenuItem.addActionListener(this);
\r
2534 undoMenuItem.setEnabled(false);
\r
2535 undoMenuItem.setLabel("Undo");
\r
2536 undoMenuItem.addActionListener(this);
\r
2537 redoMenuItem.setEnabled(false);
\r
2538 redoMenuItem.setLabel("Redo");
\r
2539 redoMenuItem.addActionListener(this);
\r
2540 conservationMenuItem.setLabel("by Conservation");
\r
2541 conservationMenuItem.addItemListener(this);
\r
2542 noColourmenuItem.setLabel("None");
\r
2543 noColourmenuItem.addActionListener(this);
\r
2544 wrapMenuItem.setLabel("Wrap");
\r
2545 wrapMenuItem.addItemListener(this);
\r
2546 renderGapsMenuItem.setLabel("Show Gaps");
\r
2547 renderGapsMenuItem.setState(true);
\r
2548 renderGapsMenuItem.addItemListener(this);
\r
2549 findMenuItem.setLabel("Find...");
\r
2550 findMenuItem.addActionListener(this);
\r
2551 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
2552 abovePIDThreshold.addItemListener(this);
\r
2553 nucleotideColour.setLabel("Nucleotide");
\r
2554 nucleotideColour.addActionListener(this);
\r
2555 deleteGroups.setLabel("Undefine Groups");
\r
2556 deleteGroups.addActionListener(this);
\r
2557 copy.setLabel("Copy");
\r
2558 copy.addActionListener(this);
\r
2559 cut.setLabel("Cut");
\r
2560 cut.addActionListener(this);
\r
2561 delete.setLabel("Delete");
\r
2562 delete.addActionListener(this);
\r
2563 pasteMenu.setLabel("Paste");
\r
2564 pasteNew.setLabel("To New Alignment");
\r
2565 pasteNew.addActionListener(this);
\r
2566 pasteThis.setLabel("Add To This Alignment");
\r
2567 pasteThis.addActionListener(this);
\r
2568 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
2569 applyToAllGroups.setState(true);
\r
2570 applyToAllGroups.addItemListener(this);
\r
2571 font.setLabel("Font...");
\r
2572 font.addActionListener(this);
\r
2573 scaleAbove.setLabel("Scale Above");
\r
2574 scaleAbove.setState(true);
\r
2575 scaleAbove.setEnabled(false);
\r
2576 scaleAbove.addItemListener(this);
\r
2577 scaleLeft.setEnabled(false);
\r
2578 scaleLeft.setState(true);
\r
2579 scaleLeft.setLabel("Scale Left");
\r
2580 scaleLeft.addItemListener(this);
\r
2581 scaleRight.setEnabled(false);
\r
2582 scaleRight.setState(true);
\r
2583 scaleRight.setLabel("Scale Right");
\r
2584 scaleRight.addItemListener(this);
\r
2585 modifyPID.setLabel("Modify Identity Threshold...");
\r
2586 modifyPID.addActionListener(this);
\r
2587 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
2588 modifyConservation.addActionListener(this);
\r
2589 sortByTreeMenu.setLabel("By Tree Order");
\r
2590 sort.setLabel("Sort");
\r
2591 calculate.setLabel("Calculate Tree");
\r
2592 autoCalculate.addItemListener(this);
\r
2593 inputText.setLabel("Input from textbox");
\r
2594 inputText.addActionListener(this);
\r
2596 helpMenu.setLabel("Help");
\r
2597 documentation.setLabel("Documentation");
\r
2598 documentation.addActionListener(this);
\r
2600 about.setLabel("About...");
\r
2601 about.addActionListener(this);
\r
2602 seqLimits.setState(true);
\r
2603 seqLimits.setLabel("Show Sequence Limits");
\r
2604 seqLimits.addItemListener(this);
\r
2605 featureSettings.setLabel("Feature Settings...");
\r
2606 featureSettings.addActionListener(this);
\r
2607 sequenceFeatures.setLabel("Sequence Features");
\r
2608 sequenceFeatures.addItemListener(this);
\r
2609 sequenceFeatures.setState(false);
\r
2610 annotationColour.setLabel("by Annotation...");
\r
2611 annotationColour.addActionListener(this);
\r
2612 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
2613 invertColSel.setLabel("Invert Column Selection");
\r
2614 menu1.setLabel("Show");
\r
2615 showColumns.setLabel("All Columns ");
\r
2616 showSeqs.setLabel("All Sequences");
\r
2617 menu2.setLabel("Hide");
\r
2618 hideColumns.setLabel("Selected Columns");
\r
2619 hideSequences.setLabel("Selected Sequences");
\r
2620 invertColSel.addActionListener(this);
\r
2621 showColumns.addActionListener(this);
\r
2622 showSeqs.addActionListener(this);
\r
2623 hideColumns.addActionListener(this);
\r
2624 hideSequences.addActionListener(this);
\r
2625 formatMenu.setLabel("Format");
\r
2626 selectMenu.setLabel("Select");
\r
2627 newView.setLabel("New View");
\r
2628 newView.addActionListener(this);
\r
2629 alignFrameMenuBar.add(fileMenu);
\r
2630 alignFrameMenuBar.add(editMenu);
\r
2631 alignFrameMenuBar.add(selectMenu);
\r
2632 alignFrameMenuBar.add(viewMenu);
\r
2633 alignFrameMenuBar.add(formatMenu);
\r
2634 alignFrameMenuBar.add(colourMenu);
\r
2635 alignFrameMenuBar.add(calculateMenu);
\r
2636 alignFrameMenuBar.add(helpMenu);
\r
2638 fileMenu.add(inputText);
\r
2639 fileMenu.add(loadTree);
\r
2640 fileMenu.add(loadAnnotations);
\r
2642 fileMenu.addSeparator();
\r
2643 fileMenu.add(outputTextboxMenu);
\r
2644 fileMenu.add(outputFeatures);
\r
2645 fileMenu.add(outputAnnotations);
\r
2647 if (jalviewServletURL != null)
\r
2649 fileMenu.add(loadApplication);
\r
2652 fileMenu.addSeparator();
\r
2653 fileMenu.add(closeMenuItem);
\r
2655 editMenu.add(undoMenuItem);
\r
2656 editMenu.add(redoMenuItem);
\r
2657 editMenu.add(cut);
\r
2658 editMenu.add(copy);
\r
2659 editMenu.add(pasteMenu);
\r
2660 editMenu.add(delete);
\r
2661 editMenu.addSeparator();
\r
2662 editMenu.add(remove2LeftMenuItem);
\r
2663 editMenu.add(remove2RightMenuItem);
\r
2664 editMenu.add(removeGappedColumnMenuItem);
\r
2665 editMenu.add(removeAllGapsMenuItem);
\r
2666 editMenu.add(removeRedundancyMenuItem);
\r
2667 viewMenu.add(newView);
\r
2668 viewMenu.addSeparator();
\r
2669 viewMenu.add(menu1);
\r
2670 viewMenu.add(menu2);
\r
2671 viewMenu.addSeparator();
\r
2672 viewMenu.add(annotationPanelMenuItem);
\r
2673 viewMenu.addSeparator();
\r
2674 viewMenu.add(sequenceFeatures);
\r
2675 viewMenu.add(featureSettings);
\r
2676 viewMenu.addSeparator();
\r
2677 viewMenu.add(alProperties);
\r
2678 viewMenu.addSeparator();
\r
2679 viewMenu.add(overviewMenuItem);
\r
2680 colourMenu.add(applyToAllGroups);
\r
2681 colourMenu.addSeparator();
\r
2682 colourMenu.add(noColourmenuItem);
\r
2683 colourMenu.add(clustalColour);
\r
2684 colourMenu.add(BLOSUM62Colour);
\r
2685 colourMenu.add(PIDColour);
\r
2686 colourMenu.add(zappoColour);
\r
2687 colourMenu.add(taylorColour);
\r
2688 colourMenu.add(hydrophobicityColour);
\r
2689 colourMenu.add(helixColour);
\r
2690 colourMenu.add(strandColour);
\r
2691 colourMenu.add(turnColour);
\r
2692 colourMenu.add(buriedColour);
\r
2693 colourMenu.add(nucleotideColour);
\r
2694 colourMenu.add(userDefinedColour);
\r
2695 colourMenu.addSeparator();
\r
2696 colourMenu.add(conservationMenuItem);
\r
2697 colourMenu.add(modifyConservation);
\r
2698 colourMenu.add(abovePIDThreshold);
\r
2699 colourMenu.add(modifyPID);
\r
2700 colourMenu.add(annotationColour);
\r
2701 calculateMenu.add(sort);
\r
2702 calculateMenu.add(calculate);
\r
2703 calculateMenu.addSeparator();
\r
2704 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
2705 calculateMenu.add(PCAMenuItem);
\r
2706 calculateMenu.add(autoCalculate);
\r
2707 this.add(statusBar, BorderLayout.SOUTH);
\r
2708 pasteMenu.add(pasteNew);
\r
2709 pasteMenu.add(pasteThis);
\r
2710 sort.add(sortIDMenuItem);
\r
2711 sort.add(sortByTreeMenu);
\r
2712 sort.add(sortGroupMenuItem);
\r
2713 sort.add(sortPairwiseMenuItem);
\r
2714 calculate.add(averageDistanceTreeMenuItem);
\r
2715 calculate.add(neighbourTreeMenuItem);
\r
2716 calculate.add(avDistanceTreeBlosumMenuItem);
\r
2717 calculate.add(njTreeBlosumMenuItem);
\r
2718 helpMenu.add(documentation);
\r
2719 helpMenu.add(about);
\r
2720 menu1.add(showColumns);
\r
2721 menu1.add(showSeqs);
\r
2722 menu2.add(hideColumns);
\r
2723 menu2.add(hideSequences);
\r
2724 formatMenu.add(font);
\r
2725 formatMenu.add(seqLimits);
\r
2726 formatMenu.add(wrapMenuItem);
\r
2727 formatMenu.add(scaleAbove);
\r
2728 formatMenu.add(scaleLeft);
\r
2729 formatMenu.add(scaleRight);
\r
2730 formatMenu.add(viewBoxesMenuItem);
\r
2731 formatMenu.add(viewTextMenuItem);
\r
2732 formatMenu.add(colourTextMenuItem);
\r
2733 formatMenu.add(renderGapsMenuItem);
\r
2734 selectMenu.add(findMenuItem);
\r
2735 selectMenu.addSeparator();
\r
2736 selectMenu.add(selectAllSequenceMenuItem);
\r
2737 selectMenu.add(deselectAllSequenceMenuItem);
\r
2738 selectMenu.add(invertSequenceMenuItem);
\r
2739 selectMenu.add(invertColSel);
\r
2740 selectMenu.add(deleteGroups);
\r
2743 public void setEmbedded()
\r
2746 embeddedMenu = new Panel();
\r
2747 embeddedEdit = new Label("Edit");
\r
2748 embeddedSelect = new Label("Select");
\r
2749 embeddedView = new Label("View");
\r
2750 embeddedFormat = new Label("Format");
\r
2751 embeddedColour = new Label("Colour");
\r
2752 embeddedFile = new Label("File");
\r
2753 embeddedHelp = new Label("Help");
\r
2754 embeddedCalculate = new Label("Calculate");
\r
2755 flowLayout1 = new FlowLayout();
\r
2756 embeddedMenu.setBackground(Color.lightGray);
\r
2757 embeddedMenu.setLayout(flowLayout1);
\r
2758 embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2759 embeddedSelect.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2760 embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2761 embeddedFormat.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2762 embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2763 embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2764 embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2765 embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2766 embeddedMenu.add(embeddedFile);
\r
2767 embeddedMenu.add(embeddedEdit);
\r
2768 embeddedMenu.add(embeddedSelect);
\r
2769 embeddedMenu.add(embeddedView);
\r
2770 embeddedMenu.add(embeddedFormat);
\r
2771 embeddedMenu.add(embeddedColour);
\r
2772 embeddedMenu.add(embeddedCalculate);
\r
2773 embeddedMenu.add(embeddedHelp);
\r
2774 flowLayout1.setAlignment(FlowLayout.LEFT);
\r
2775 flowLayout1.setHgap(2);
\r
2776 flowLayout1.setVgap(0);
\r
2777 embeddedFile.addMouseListener(this);
\r
2778 embeddedEdit.addMouseListener(this);
\r
2779 embeddedSelect.addMouseListener(this);
\r
2780 embeddedView.addMouseListener(this);
\r
2781 embeddedFormat.addMouseListener(this);
\r
2782 embeddedColour.addMouseListener(this);
\r
2783 embeddedCalculate.addMouseListener(this);
\r
2784 embeddedHelp.addMouseListener(this);
\r
2786 fileMenu.remove(closeMenuItem);
\r
2787 fileMenu.remove(3); // Seperator
\r
2789 viewport.applet.setLayout(new BorderLayout());
\r
2790 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
\r
2791 viewport.applet.add(statusBar, BorderLayout.SOUTH);
\r
2793 alignPanel.setSize(viewport.applet.getSize().width,
\r
2794 viewport.applet.getSize().height
\r
2795 - embeddedMenu.HEIGHT - statusBar.HEIGHT);
\r
2797 viewport.applet.add(alignPanel, BorderLayout.CENTER);
\r
2798 viewport.applet.validate();
\r
2802 PopupMenu filePopup, editPopup, searchPopup,
\r
2803 viewPopup, formatPopup, colourPopup, calculatePopup, helpPopup;
\r
2804 MenuItem featureSettings = new MenuItem();
\r
2805 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
2806 MenuItem annotationColour = new MenuItem();
\r
2807 MenuItem invertColSel = new MenuItem();
\r
2808 Menu menu1 = new Menu();
\r
2809 MenuItem showColumns = new MenuItem();
\r
2810 MenuItem showSeqs = new MenuItem();
\r
2811 Menu menu2 = new Menu();
\r
2812 MenuItem hideColumns = new MenuItem();
\r
2813 MenuItem hideSequences = new MenuItem();
\r
2814 Menu formatMenu = new Menu();
\r
2815 Menu selectMenu = new Menu();
\r
2816 MenuItem newView = new MenuItem();
\r
2818 public void mousePressed(MouseEvent evt)
\r
2820 PopupMenu popup = null;
\r
2821 Label source = (Label) evt.getSource();
\r
2822 if (source == embeddedFile)
\r
2824 popup = filePopup = genPopupMenu(filePopup, fileMenu);
\r
2826 else if (source == embeddedEdit)
\r
2828 popup = editPopup = genPopupMenu(editPopup, editMenu);
\r
2830 else if (source == embeddedSelect)
\r
2832 popup = searchPopup = genPopupMenu(searchPopup, selectMenu);
\r
2834 else if (source == embeddedView)
\r
2836 popup = viewPopup = genPopupMenu(viewPopup, viewMenu);
\r
2838 else if (source == embeddedFormat)
\r
2840 popup = formatPopup = genPopupMenu(formatPopup, formatMenu);
\r
2842 else if (source == embeddedColour)
\r
2844 popup = colourPopup = genPopupMenu(colourPopup, colourMenu);
\r
2846 else if (source == embeddedCalculate)
\r
2848 popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);
\r
2850 else if (source == embeddedHelp)
\r
2852 popup = helpPopup = genPopupMenu(helpPopup, helpMenu);
\r
2855 embeddedMenu.add(popup);
\r
2856 popup.show(embeddedMenu,
\r
2857 source.getBounds().x,
\r
2858 source.getBounds().y + source.getBounds().getSize().height);
\r
2861 PopupMenu genPopupMenu(PopupMenu popup, Menu original)
\r
2863 if (popup != null)
\r
2867 popup = new PopupMenu();
\r
2868 int m, mSize = original.getItemCount();
\r
2869 for (m = 0; m < mSize; m++)
\r
2871 popup.add(original.getItem(m));
\r
2879 public void mouseClicked(MouseEvent evt)
\r
2882 public void mouseReleased(MouseEvent evt)
\r
2885 public void mouseEntered(MouseEvent evt)
\r
2888 public void mouseExited(MouseEvent evt)
\r