2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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20 package jalview.appletgui;
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22 import jalview.schemes.*;
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23 import jalview.datamodel.*;
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24 import jalview.analysis.*;
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25 import jalview.io.*;
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26 import jalview.commands.*;
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28 import java.awt.event.*;
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30 import java.io.InputStreamReader;
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31 import java.io.BufferedReader;
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32 import java.net.URL;
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35 public class AlignFrame extends Frame implements ActionListener,
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36 ItemListener, KeyListener, MouseListener
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38 public AlignmentPanel alignPanel;
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39 public AlignViewport viewport;
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40 int DEFAULT_WIDTH = 700;
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41 int DEFAULT_HEIGHT = 500;
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43 String jalviewServletURL;
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46 public AlignFrame(AlignmentI al,
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47 jalview.bin.JalviewLite applet,
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53 jalviewServletURL = applet.getParameter("APPLICATION_URL");
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57 }catch(Exception ex)
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59 ex.printStackTrace();
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62 viewport = new AlignViewport(al, applet);
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63 alignPanel = new AlignmentPanel(this, viewport);
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65 viewport.updateConservation(alignPanel);
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66 viewport.updateConsensus(alignPanel);
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68 annotationPanelMenuItem.setState(viewport.showAnnotation);
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70 seqLimits.setState(viewport.showJVSuffix);
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74 String param = applet.getParameter("sortBy");
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77 if (param.equalsIgnoreCase("Id"))
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78 sortIDMenuItem_actionPerformed();
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79 else if (param.equalsIgnoreCase("Pairwise Identity"))
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80 sortPairwiseMenuItem_actionPerformed();
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83 param = applet.getParameter("wrap");
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86 if (param.equalsIgnoreCase("true"))
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88 wrapMenuItem.setState(true);
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89 wrapMenuItem_actionPerformed();
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95 param = applet.getParameter("windowWidth");
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98 int width = Integer.parseInt(param);
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99 DEFAULT_WIDTH = width;
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101 param = applet.getParameter("windowHeight");
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104 int height = Integer.parseInt(param);
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105 DEFAULT_HEIGHT = height;
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108 catch (Exception ex)
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113 //Some JVMS send keyevents to Top frame or lowest panel,
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114 //Havent worked out why yet. So add to both this frame and seqCanvas for now
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115 this.addKeyListener(this);
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116 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
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117 alignPanel.idPanel.idCanvas.addKeyListener(this);
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118 alignPanel.scalePanel.addKeyListener(this);
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119 alignPanel.annotationPanel.addKeyListener(this);
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128 add(alignPanel, BorderLayout.CENTER);
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129 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
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132 alignPanel.validate();
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133 alignPanel.repaint();
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135 public AlignViewport getAlignViewport()
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140 public SeqCanvas getSeqcanvas()
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142 return alignPanel.seqPanel.seqCanvas;
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149 * @param String DOCUMENT ME!
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152 public void parseFeaturesFile(String file, String type)
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154 Hashtable featureLinks = new Hashtable();
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155 boolean featuresFile = false;
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157 featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport.alignment,
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158 alignPanel.seqPanel.seqCanvas.
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159 getFeatureRenderer().featureColours,
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163 catch(Exception ex)
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165 ex.printStackTrace();
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170 if(featureLinks.size()>0)
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171 alignPanel.seqPanel.seqCanvas
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172 .getFeatureRenderer().featureLinks = featureLinks;
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173 viewport.showSequenceFeatures = true;
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174 sequenceFeatures.setState(true);
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175 alignPanel.repaint();
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181 public void keyPressed(KeyEvent evt)
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183 if (viewport.cursorMode
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184 && evt.getKeyCode() >= KeyEvent.VK_0
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185 && evt.getKeyCode() <= KeyEvent.VK_9)
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187 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
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190 switch (evt.getKeyCode())
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192 case 27: // escape key
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193 deselectAllSequenceMenuItem_actionPerformed();
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195 case KeyEvent.VK_X:
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196 if (evt.isControlDown() || evt.isMetaDown())
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198 cut_actionPerformed();
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201 case KeyEvent.VK_C:
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202 if (viewport.cursorMode && !evt.isControlDown())
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204 alignPanel.seqPanel.setCursorColumn();
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206 if (evt.isControlDown() || evt.isMetaDown())
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208 copy_actionPerformed();
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211 case KeyEvent.VK_V:
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212 if (evt.isControlDown())
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214 paste(evt.isShiftDown());
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217 case KeyEvent.VK_A:
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218 if (evt.isControlDown() || evt.isMetaDown())
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220 selectAllSequenceMenuItem_actionPerformed();
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223 case KeyEvent.VK_DOWN:
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224 if(viewport.cursorMode)
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226 alignPanel.seqPanel.moveCursor(0,1);
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229 moveSelectedSequences(false);
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232 case KeyEvent.VK_UP:
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233 if (viewport.cursorMode)
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235 alignPanel.seqPanel.moveCursor(0,-1);
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238 moveSelectedSequences(true);
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241 case KeyEvent.VK_LEFT:
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242 if(viewport.cursorMode)
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244 alignPanel.seqPanel.moveCursor(-1,0);
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248 case KeyEvent.VK_RIGHT:
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249 if (viewport.cursorMode)
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251 alignPanel.seqPanel.moveCursor(1,0);
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254 case KeyEvent.VK_SPACE:
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255 if(viewport.cursorMode)
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257 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
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258 || evt.isShiftDown()
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264 case KeyEvent.VK_DELETE:
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265 case KeyEvent.VK_BACK_SPACE:
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266 if(viewport.cursorMode)
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268 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
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269 || evt.isShiftDown()
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270 || evt.isAltDown());
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274 cut_actionPerformed();
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275 alignPanel.seqPanel.seqCanvas.repaint();
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279 case KeyEvent.VK_S:
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280 if(viewport.cursorMode)
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282 alignPanel.seqPanel.setCursorRow();
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285 case KeyEvent.VK_P:
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286 if(viewport.cursorMode)
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288 alignPanel.seqPanel.setCursorPosition();
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292 case KeyEvent.VK_ENTER:
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293 case KeyEvent.VK_COMMA:
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294 if(viewport.cursorMode)
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296 alignPanel.seqPanel.setCursorRowAndColumn();
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300 case KeyEvent.VK_Q:
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301 if(viewport.cursorMode)
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303 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
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306 case KeyEvent.VK_M:
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307 if(viewport.cursorMode)
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309 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
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313 case KeyEvent.VK_F2:
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314 viewport.cursorMode = ! viewport.cursorMode;
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315 statusBar.setText("Keyboard editing mode is "+
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316 (viewport.cursorMode ? "on" : "off"));
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317 if(viewport.cursorMode)
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319 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
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320 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
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324 case KeyEvent.VK_F:
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325 if (evt.isControlDown())
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327 findMenuItem_actionPerformed();
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331 case KeyEvent.VK_H:
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333 boolean toggleSeqs = !evt.isControlDown();
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334 boolean toggleCols = !evt.isShiftDown();
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335 boolean hide = false;
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336 SequenceGroup sg = viewport.getSelectionGroup();
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340 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
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343 viewport.hideAllSelectedSeqs();
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345 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
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346 viewport.showAllHiddenSeqs();
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351 if (viewport.colSel.getSelected().size() > 0)
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353 viewport.hideSelectedColumns();
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355 viewport.selectionGroup = sg;
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358 viewport.showAllHiddenColumns();
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363 case KeyEvent.VK_PAGE_UP:
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364 if (viewport.wrapAlignment)
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365 alignPanel.scrollUp(true);
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367 alignPanel.setScrollValues(viewport.startRes,
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369 - viewport.endSeq + viewport.startSeq);
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372 case KeyEvent.VK_PAGE_DOWN:
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373 if (viewport.wrapAlignment)
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374 alignPanel.scrollUp(false);
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376 alignPanel.setScrollValues(viewport.startRes,
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378 + viewport.endSeq - viewport.startSeq);
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381 case KeyEvent.VK_Z:
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382 if (evt.isControlDown())
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384 undoMenuItem_actionPerformed();
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388 case KeyEvent.VK_Y:
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389 if (evt.isControlDown())
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391 redoMenuItem_actionPerformed();
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395 case KeyEvent.VK_L:
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396 if (evt.isControlDown())
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398 trimAlignment(true);
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402 case KeyEvent.VK_R:
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403 if (evt.isControlDown())
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405 trimAlignment(false);
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409 case KeyEvent.VK_E:
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410 if (evt.isControlDown())
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412 if (evt.isShiftDown())
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413 this.removeAllGapsMenuItem_actionPerformed();
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415 removeGappedColumnMenuItem_actionPerformed();
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418 case KeyEvent.VK_I:
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419 if (evt.isControlDown())
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421 if (evt.isAltDown())
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422 viewport.invertColumnSelection();
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424 this.invertSequenceMenuItem_actionPerformed();
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428 case KeyEvent.VK_U:
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429 if (evt.isControlDown())
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431 this.deleteGroups_actionPerformed();
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435 case KeyEvent.VK_T:
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436 if (evt.isControlDown())
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444 alignPanel.repaint();
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446 public void keyReleased(KeyEvent evt)
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448 public void keyTyped(KeyEvent evt)
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451 public void itemStateChanged(ItemEvent evt)
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453 if(evt.getSource()==colourTextMenuItem)
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454 colourTextMenuItem_actionPerformed();
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455 else if(evt.getSource()==wrapMenuItem)
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456 wrapMenuItem_actionPerformed();
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457 else if(evt.getSource()==scaleAbove)
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458 viewport.setScaleAboveWrapped(scaleAbove.getState());
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459 else if(evt.getSource()==scaleLeft)
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460 viewport.setScaleLeftWrapped(scaleLeft.getState());
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461 else if(evt.getSource()==scaleRight)
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462 viewport.setScaleRightWrapped(scaleRight.getState());
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463 else if(evt.getSource()==seqLimits)
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464 seqLimits_itemStateChanged();
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465 else if(evt.getSource()==viewBoxesMenuItem)
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466 viewport.setShowBoxes(viewBoxesMenuItem.getState());
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467 else if(evt.getSource()==viewTextMenuItem)
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468 viewport.setShowText(viewTextMenuItem.getState());
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469 else if(evt.getSource()==renderGapsMenuItem)
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470 viewport.setRenderGaps(renderGapsMenuItem.getState());
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471 else if(evt.getSource()==annotationPanelMenuItem)
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473 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
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474 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
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476 else if(evt.getSource()==sequenceFeatures)
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478 viewport.showSequenceFeatures(sequenceFeatures.getState());
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479 alignPanel.seqPanel.seqCanvas.repaint();
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481 else if(evt.getSource()==conservationMenuItem)
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482 conservationMenuItem_actionPerformed();
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483 else if(evt.getSource()==abovePIDThreshold)
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484 abovePIDThreshold_actionPerformed();
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485 else if(evt.getSource()==applyToAllGroups)
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486 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
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487 else if(evt.getSource()==autoCalculate)
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488 viewport.autocalculateConsensus = autoCalculate.getState();
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490 alignPanel.repaint();
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492 public void actionPerformed(ActionEvent evt)
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494 Object source = evt.getSource();
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496 if(source==inputText)
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497 inputText_actionPerformed();
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498 else if(source==loadTree)
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499 loadTree_actionPerformed();
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500 else if(source==loadApplication)
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501 launchFullApplication();
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502 else if (source == loadAnnotations)
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504 else if (source == outputAnnotations)
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505 outputAnnotations();
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506 else if(source == outputFeatures)
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508 else if(source==closeMenuItem)
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509 closeMenuItem_actionPerformed();
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510 else if(source==copy)
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511 copy_actionPerformed();
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512 else if(source==undoMenuItem)
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513 undoMenuItem_actionPerformed();
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514 else if(source==redoMenuItem)
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515 redoMenuItem_actionPerformed();
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516 else if(source==inputText)
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517 inputText_actionPerformed();
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518 else if(source==closeMenuItem)
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519 closeMenuItem_actionPerformed();
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520 else if(source==undoMenuItem)
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521 undoMenuItem_actionPerformed();
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522 else if(source==redoMenuItem)
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523 redoMenuItem_actionPerformed();
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524 else if(source==copy)
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525 copy_actionPerformed();
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526 else if(source==pasteNew)
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527 pasteNew_actionPerformed();
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528 else if(source==pasteThis)
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529 pasteThis_actionPerformed();
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530 else if(source==cut)
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531 cut_actionPerformed();
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532 else if(source==delete)
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533 delete_actionPerformed();
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534 else if(source==deleteGroups)
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535 deleteGroups_actionPerformed();
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536 else if(source==selectAllSequenceMenuItem)
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537 selectAllSequenceMenuItem_actionPerformed();
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538 else if(source==deselectAllSequenceMenuItem)
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539 deselectAllSequenceMenuItem_actionPerformed();
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540 else if(source==invertSequenceMenuItem)
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541 invertSequenceMenuItem_actionPerformed();
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542 else if(source==invertColSel)
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543 { viewport.invertColumnSelection(); alignPanel.repaint(); }
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544 else if(source==remove2LeftMenuItem)
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545 trimAlignment(true);
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546 else if(source==remove2RightMenuItem)
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547 trimAlignment(false);
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548 else if(source==removeGappedColumnMenuItem)
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549 removeGappedColumnMenuItem_actionPerformed();
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550 else if(source==removeAllGapsMenuItem)
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551 removeAllGapsMenuItem_actionPerformed();
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552 else if(source==findMenuItem)
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553 findMenuItem_actionPerformed();
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554 else if(source==font)
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555 new FontChooser(alignPanel);
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556 else if (source == newView)
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558 else if(source==showColumns)
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560 viewport.showAllHiddenColumns(); alignPanel.repaint();
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562 else if(source==showSeqs)
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564 viewport.showAllHiddenSeqs();
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566 else if(source == hideColumns)
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568 viewport.hideSelectedColumns(); alignPanel.repaint();
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570 else if(source == hideSequences && viewport.getSelectionGroup()!=null)
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572 viewport.hideAllSelectedSeqs();
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574 else if(source==featureSettings)
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575 new FeatureSettings(alignPanel);
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576 else if(source==overviewMenuItem)
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577 overviewMenuItem_actionPerformed();
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578 else if(source==noColourmenuItem)
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579 changeColour(null);
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580 else if(source==clustalColour)
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582 abovePIDThreshold.setState(false);
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583 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
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584 viewport.alignment.getWidth()));
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586 else if(source==zappoColour)
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587 changeColour(new ZappoColourScheme());
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588 else if(source==taylorColour)
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589 changeColour(new TaylorColourScheme());
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590 else if(source==hydrophobicityColour)
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591 changeColour(new HydrophobicColourScheme());
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592 else if(source==helixColour)
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593 changeColour(new HelixColourScheme());
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594 else if(source==strandColour)
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595 changeColour(new StrandColourScheme());
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596 else if(source==turnColour)
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597 changeColour(new TurnColourScheme());
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598 else if(source==buriedColour)
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599 changeColour(new BuriedColourScheme());
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600 else if(source==nucleotideColour)
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601 changeColour(new NucleotideColourScheme());
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602 else if(source==modifyPID)
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603 modifyPID_actionPerformed();
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604 else if(source==modifyConservation)
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605 modifyConservation_actionPerformed();
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606 else if(source==userDefinedColour)
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607 new UserDefinedColours(alignPanel, null);
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608 else if(source==PIDColour)
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609 changeColour(new PIDColourScheme());
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610 else if(source==BLOSUM62Colour)
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611 changeColour(new Blosum62ColourScheme());
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612 else if(source==annotationColour)
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613 new AnnotationColourChooser(viewport, alignPanel);
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614 else if(source==sortPairwiseMenuItem)
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615 sortPairwiseMenuItem_actionPerformed();
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616 else if(source==sortIDMenuItem)
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617 sortIDMenuItem_actionPerformed();
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618 else if(source==sortGroupMenuItem)
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619 sortGroupMenuItem_actionPerformed();
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620 else if(source==removeRedundancyMenuItem)
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621 removeRedundancyMenuItem_actionPerformed();
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622 else if(source==pairwiseAlignmentMenuItem)
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623 pairwiseAlignmentMenuItem_actionPerformed();
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624 else if(source==PCAMenuItem)
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625 PCAMenuItem_actionPerformed();
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626 else if(source==averageDistanceTreeMenuItem)
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627 averageDistanceTreeMenuItem_actionPerformed();
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628 else if(source==neighbourTreeMenuItem)
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629 neighbourTreeMenuItem_actionPerformed();
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630 else if(source==njTreeBlosumMenuItem)
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631 njTreeBlosumMenuItem_actionPerformed();
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632 else if(source==avDistanceTreeBlosumMenuItem)
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633 avTreeBlosumMenuItem_actionPerformed();
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634 else if(source==documentation)
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635 documentation_actionPerformed();
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636 else if(source==about)
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637 about_actionPerformed();
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641 public void inputText_actionPerformed()
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643 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
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644 Frame frame = new Frame();
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646 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
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649 protected void outputText_actionPerformed(ActionEvent e)
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651 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
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652 Frame frame = new Frame();
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654 jalview.bin.JalviewLite.addFrame(frame,
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655 "Alignment output - " + e.getActionCommand(),
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657 cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
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658 viewport.getAlignment().getSequences(),
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659 viewport.showJVSuffix));
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662 public void loadAnnotations()
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664 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
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665 cap.setText("Paste your features / annotations file here.");
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666 cap.setAnnotationImport();
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667 Frame frame = new Frame();
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669 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
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673 public void outputAnnotations()
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675 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
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676 Frame frame = new Frame();
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678 jalview.bin.JalviewLite.addFrame(frame,
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681 cap.setText( new AnnotationFile().printAnnotations(
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682 viewport.alignment.getAlignmentAnnotation() ) );
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685 public void outputFeatures()
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687 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
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688 Frame frame = new Frame();
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690 jalview.bin.JalviewLite.addFrame(frame,
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694 cap.setText(new FeaturesFile().printJalviewFormat(
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695 viewport.alignment.getSequencesArray(),
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696 viewport.featuresDisplayed));
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699 void launchFullApplication()
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701 StringBuffer url = new StringBuffer(jalviewServletURL);
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703 url.append("?open="+
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704 appendProtocol( viewport.applet.getParameter("file") ) );
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706 if(viewport.applet.getParameter("features")!=null)
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708 url.append( "&features=" );
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709 url.append( appendProtocol( viewport.applet.getParameter("features") ) );
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712 if(viewport.applet.getParameter("annotations")!=null)
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714 url.append( "&annotations=" );
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715 url.append( appendProtocol( viewport.applet.getParameter("annotations") ) );
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718 if(viewport.applet.getParameter("jnetfile")!=null)
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720 url.append( "&annotations=" );
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721 url.append( appendProtocol( viewport.applet.getParameter("jnetfile") ) );
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724 if(viewport.applet.getParameter("defaultColour")!=null)
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726 url.append("&colour=" +
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727 removeWhiteSpace(viewport.applet.getParameter("defaultColour"))
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731 if(viewport.applet.getParameter("userDefinedColour")!=null)
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733 url.append( "&colour=" +
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734 removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") )
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738 showURL(url.toString(), "FULL_APP");
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742 String removeWhiteSpace(String colour)
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744 StringBuffer sb = new StringBuffer();
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745 for (int i = 0; i < colour.length(); i++)
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747 if (Character.isWhitespace(colour.charAt(i)))
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750 sb.append(colour.charAt(i));
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753 return sb.toString();
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757 String appendProtocol(String url)
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761 }catch(java.net.MalformedURLException ex)
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763 url = viewport.applet.getCodeBase()+url;
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768 public void closeMenuItem_actionPerformed()
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770 PaintRefresher.RemoveComponent(alignPanel);
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771 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
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772 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
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774 if(PaintRefresher.components.size()==0 && viewport.applet==null)
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784 void updateEditMenuBar()
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787 if (viewport.historyList.size() > 0)
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789 undoMenuItem.setEnabled(true);
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790 CommandI command = (CommandI) viewport.historyList.peek();
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791 undoMenuItem.setLabel("Undo " + command.getDescription());
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795 undoMenuItem.setEnabled(false);
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796 undoMenuItem.setLabel("Undo");
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799 if (viewport.redoList.size() > 0)
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801 redoMenuItem.setEnabled(true);
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803 CommandI command = (CommandI) viewport.redoList.peek();
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804 redoMenuItem.setLabel("Redo " + command.getDescription());
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808 redoMenuItem.setEnabled(false);
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809 redoMenuItem.setLabel("Redo");
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813 public void addHistoryItem(CommandI command)
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815 if(command.getSize()>0)
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817 viewport.historyList.push(command);
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818 viewport.redoList.removeAllElements();
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819 updateEditMenuBar();
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820 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
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827 * @param e DOCUMENT ME!
\r
829 protected void undoMenuItem_actionPerformed()
\r
831 if(viewport.historyList.size()<1)
\r
834 CommandI command = (CommandI)viewport.historyList.pop();
\r
835 viewport.redoList.push(command);
\r
836 command.undoCommand();
\r
838 AlignViewport originalSource = getOriginatingSource(command);
\r
840 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
841 updateEditMenuBar();
\r
842 originalSource.firePropertyChange("alignment", null,originalSource.alignment.getSequences());
\r
848 * @param e DOCUMENT ME!
\r
850 protected void redoMenuItem_actionPerformed()
\r
852 if(viewport.redoList.size()<1)
\r
855 CommandI command = (CommandI) viewport.redoList.pop();
\r
856 viewport.historyList.push(command);
\r
857 command.doCommand();
\r
859 AlignViewport originalSource = getOriginatingSource(command);
\r
860 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
\r
862 updateEditMenuBar();
\r
863 originalSource.firePropertyChange("alignment", null, originalSource.alignment.getSequences());
\r
866 AlignViewport getOriginatingSource(CommandI command)
\r
868 AlignViewport originalSource = null;
\r
869 //For sequence removal and addition, we need to fire
\r
870 //the property change event FROM the viewport where the
\r
871 //original alignment was altered
\r
872 AlignmentI al = null;
\r
873 if (command instanceof EditCommand)
\r
875 EditCommand editCommand = (EditCommand) command;
\r
876 al = editCommand.getAlignment();
\r
877 Vector comps = (Vector) PaintRefresher.components
\r
878 .get(viewport.getSequenceSetId());
\r
879 for (int i = 0; i < comps.size(); i++)
\r
881 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
883 if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)
\r
885 originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
\r
892 if (originalSource == null)
\r
894 //The original view is closed, we must validate
\r
895 //the current view against the closed view first
\r
897 PaintRefresher.validateSequences(al, viewport.alignment);
\r
899 originalSource = viewport;
\r
903 return originalSource;
\r
906 public void moveSelectedSequences(boolean up)
\r
908 SequenceGroup sg = viewport.getSelectionGroup();
\r
916 for (int i = 1; i < viewport.alignment.getHeight(); i++)
\r
918 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
919 if (!sg.getSequences(null).contains(seq))
\r
924 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
\r
925 if (sg.getSequences(null).contains(temp))
\r
930 viewport.alignment.getSequences().setElementAt(temp, i);
\r
931 viewport.alignment.getSequences().setElementAt(seq, i - 1);
\r
936 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
\r
938 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
939 if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))
\r
944 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
\r
945 if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))
\r
950 viewport.alignment.getSequences().setElementAt(temp, i);
\r
951 viewport.alignment.getSequences().setElementAt(seq, i + 1);
\r
955 alignPanel.repaint();
\r
958 static StringBuffer copiedSequences;
\r
959 static Vector copiedHiddenColumns;
\r
960 protected void copy_actionPerformed()
\r
962 if (viewport.getSelectionGroup() == null)
\r
967 SequenceGroup sg = viewport.getSelectionGroup();
\r
968 copiedSequences = new StringBuffer();
\r
969 Hashtable orderedSeqs = new Hashtable();
\r
970 for (int i = 0; i < sg.getSize(); i++)
\r
972 SequenceI seq = sg.getSequenceAt(i);
\r
973 int index = viewport.alignment.findIndex(seq);
\r
974 orderedSeqs.put(index + "", seq);
\r
977 int index = 0, startRes, endRes;
\r
980 if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
\r
982 copiedHiddenColumns = new Vector();
\r
983 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
\r
984 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();
\r
987 int[] region = (int[])
\r
988 viewport.getColumnSelection().getHiddenColumns().elementAt(i);
\r
990 copiedHiddenColumns.addElement(new int[]
\r
991 {region[0] - hiddenOffset,
\r
992 region[1] - hiddenOffset});
\r
996 copiedHiddenColumns = null;
\r
999 for (int i = 0; i < sg.getSize(); i++)
\r
1001 SequenceI seq = null;
\r
1003 while (seq == null)
\r
1005 if (orderedSeqs.containsKey(index + ""))
\r
1007 seq = (SequenceI) orderedSeqs.get(index + "");
\r
1019 //Returns residue following index if gap
\r
1020 startRes = seq.findPosition(sg.getStartRes());
\r
1023 //Need to find the residue preceeding index if gap
\r
1026 for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
\r
1028 ch = seq.getCharAt(j);
\r
1029 if (!jalview.util.Comparison.isGap( (ch)))
\r
1037 endRes += seq.getStart() -1;
\r
1040 copiedSequences.append(seq.getName() + "\t" +
\r
1043 seq.getSequenceAsString(sg.getStartRes(),
\r
1044 sg.getEndRes() + 1) + "\n");
\r
1049 protected void pasteNew_actionPerformed()
\r
1054 protected void pasteThis_actionPerformed()
\r
1059 void paste(boolean newAlignment)
\r
1064 if (copiedSequences == null)
\r
1069 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
1070 Vector seqs = new Vector();
\r
1071 while (st.hasMoreElements())
\r
1073 String name = st.nextToken();
\r
1074 int start = Integer.parseInt(st.nextToken());
\r
1075 int end = Integer.parseInt(st.nextToken());
\r
1076 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
\r
1078 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
1079 for (int i = 0; i < seqs.size(); i++)
\r
1081 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
1086 String newtitle = new String("Copied sequences");
\r
1087 if (getTitle().startsWith("Copied sequences"))
\r
1089 newtitle = getTitle();
\r
1093 newtitle = newtitle.concat("- from " + getTitle());
\r
1095 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
1099 if (copiedHiddenColumns != null)
\r
1101 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
1103 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
1104 af.viewport.hideColumns(region[0], region[1]);
\r
1109 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
\r
1114 addSequences(newSeqs);
\r
1118 catch (Exception ex)
\r
1119 {} // could be anything being pasted in here
\r
1123 void addSequences(SequenceI[] seqs)
\r
1125 for (int i = 0; i < seqs.length; i++)
\r
1127 viewport.alignment.addSequence(seqs[i]);
\r
1131 addHistoryItem(new EditCommand(
\r
1133 EditCommand.PASTE,
\r
1136 viewport.alignment.getWidth(),
\r
1137 viewport.alignment)
\r
1140 viewport.setEndSeq(viewport.alignment.getHeight());
\r
1141 viewport.alignment.getWidth();
\r
1142 viewport.firePropertyChange("alignment", null,
\r
1143 viewport.alignment.getSequences());
\r
1147 protected void cut_actionPerformed()
\r
1149 copy_actionPerformed();
\r
1150 delete_actionPerformed();
\r
1153 protected void delete_actionPerformed()
\r
1156 SequenceGroup sg = viewport.getSelectionGroup();
\r
1162 Vector seqs = new Vector();
\r
1164 for (int i = 0; i < sg.getSize(); i++)
\r
1166 seq = sg.getSequenceAt(i);
\r
1167 seqs.addElement(seq);
\r
1171 // If the cut affects all sequences, remove highlighted columns
\r
1172 if (sg.getSize() == viewport.alignment.getHeight())
\r
1174 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
1175 sg.getEndRes() + 1);
\r
1179 SequenceI [] cut = new SequenceI[seqs.size()];
\r
1180 for(int i=0; i<seqs.size(); i++)
\r
1181 cut[i] = (SequenceI)seqs.elementAt(i);
\r
1185 //ADD HISTORY ITEM
\r
1187 addHistoryItem(new EditCommand("Cut Sequences",
\r
1191 sg.getEndRes()-sg.getStartRes()+1,
\r
1192 viewport.alignment));
\r
1195 viewport.setSelectionGroup(null);
\r
1196 viewport.alignment.deleteGroup(sg);
\r
1198 viewport.firePropertyChange("alignment", null,
\r
1199 viewport.getAlignment().getSequences());
\r
1201 if (viewport.getAlignment().getHeight() < 1)
\r
1203 this.setVisible(false);
\r
1207 protected void deleteGroups_actionPerformed()
\r
1209 viewport.alignment.deleteAllGroups();
\r
1210 viewport.sequenceColours=null;
\r
1211 viewport.setSelectionGroup(null);
\r
1213 alignPanel.repaint();
\r
1216 public void selectAllSequenceMenuItem_actionPerformed()
\r
1218 SequenceGroup sg = new SequenceGroup();
\r
1219 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1221 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
1223 sg.setEndRes(viewport.alignment.getWidth()-1);
\r
1224 viewport.setSelectionGroup(sg);
\r
1225 alignPanel.repaint();
\r
1226 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1229 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1231 if(viewport.cursorMode)
\r
1233 alignPanel.seqPanel.keyboardNo1=null;
\r
1234 alignPanel.seqPanel.keyboardNo2=null;
\r
1236 viewport.setSelectionGroup(null);
\r
1237 viewport.getColumnSelection().clear();
\r
1238 viewport.setSelectionGroup(null);
\r
1239 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1240 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1241 alignPanel.repaint();
\r
1242 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1245 public void invertSequenceMenuItem_actionPerformed()
\r
1247 SequenceGroup sg = viewport.getSelectionGroup();
\r
1248 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1250 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1253 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1256 void trimAlignment(boolean trimLeft)
\r
1258 ColumnSelection colSel = viewport.getColumnSelection();
\r
1261 if (colSel.size() > 0)
\r
1264 column = colSel.getMin();
\r
1266 column = colSel.getMax();
\r
1268 SequenceI [] seqs;
\r
1269 if(viewport.getSelectionGroup()!=null)
\r
1270 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);
\r
1272 seqs = viewport.alignment.getSequencesArray();
\r
1275 TrimRegionCommand trimRegion;
\r
1278 trimRegion = new TrimRegionCommand("Remove Left",
\r
1279 TrimRegionCommand.TRIM_LEFT,
\r
1282 viewport.alignment,
\r
1284 viewport.selectionGroup);
\r
1285 viewport.setStartRes(0);
\r
1289 trimRegion = new TrimRegionCommand("Remove Right",
\r
1290 TrimRegionCommand.TRIM_RIGHT,
\r
1293 viewport.alignment,
\r
1295 viewport.selectionGroup);
\r
1298 statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
\r
1301 addHistoryItem(trimRegion);
\r
1303 Vector groups = viewport.alignment.getGroups();
\r
1305 for (int i = 0; i < groups.size(); i++)
\r
1307 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1309 if ( (trimLeft && !sg.adjustForRemoveLeft(column))
\r
1310 || (!trimLeft && !sg.adjustForRemoveRight(column)))
\r
1312 viewport.alignment.deleteGroup(sg);
\r
1316 viewport.firePropertyChange("alignment", null,
\r
1317 viewport.getAlignment().getSequences());
\r
1322 public void removeGappedColumnMenuItem_actionPerformed()
\r
1324 int start = 0, end = viewport.alignment.getWidth()-1;
\r
1327 if (viewport.getSelectionGroup() != null)
\r
1329 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);
\r
1330 start = viewport.getSelectionGroup().getStartRes();
\r
1331 end = viewport.getSelectionGroup().getEndRes();
\r
1334 seqs = viewport.alignment.getSequencesArray();
\r
1337 RemoveGapColCommand removeGapCols =
\r
1338 new RemoveGapColCommand("Remove Gapped Columns",
\r
1341 viewport.getGapCharacter());
\r
1343 addHistoryItem(removeGapCols);
\r
1345 statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");
\r
1347 //This is to maintain viewport position on first residue
\r
1348 //of first sequence
\r
1349 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1350 int startRes = seq.findPosition(viewport.startRes);
\r
1351 // ShiftList shifts;
\r
1352 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
\r
1353 // edit.alColumnChanges=shifts.getInverse();
\r
1354 // if (viewport.hasHiddenColumns)
\r
1355 // viewport.getColumnSelection().compensateForEdits(shifts);
\r
1356 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1357 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1361 public void removeAllGapsMenuItem_actionPerformed()
\r
1363 int start = 0, end = viewport.alignment.getWidth()-1;
\r
1366 if (viewport.getSelectionGroup() != null)
\r
1368 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);
\r
1369 start = viewport.getSelectionGroup().getStartRes();
\r
1370 end = viewport.getSelectionGroup().getEndRes();
\r
1373 seqs = viewport.alignment.getSequencesArray();
\r
1375 //This is to maintain viewport position on first residue
\r
1376 //of first sequence
\r
1377 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1378 int startRes = seq.findPosition(viewport.startRes);
\r
1380 addHistoryItem(new RemoveGapsCommand("Remove Gaps",
\r
1383 viewport.getGapCharacter()));
\r
1385 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1387 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1391 public void findMenuItem_actionPerformed()
\r
1393 new Finder(alignPanel);
\r
1396 public void newView()
\r
1399 if (viewport.hasHiddenRows)
\r
1400 newal = new Alignment(viewport.getAlignment().
\r
1401 getHiddenSequences()
\r
1402 .getFullAlignment().
\r
1403 getSequencesArray());
\r
1405 newal = new Alignment(viewport.alignment.getSequencesArray());
\r
1407 AlignFrame newaf = new AlignFrame(newal,
\r
1412 newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
\r
1413 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
\r
1414 PaintRefresher.Register(newaf.alignPanel,
\r
1415 newaf.alignPanel.av.getSequenceSetId());
\r
1417 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
\r
1418 newaf.alignPanel.av.getSequenceSetId());
\r
1419 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
\r
1420 newaf.alignPanel.av.getSequenceSetId());
\r
1422 Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());
\r
1423 int viewSize = -1;
\r
1424 for (int i = 0; i < comps.size(); i++)
\r
1426 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
1430 String title = new String(this.getTitle());
\r
1431 if (title.indexOf("(View") > -1)
\r
1432 title = title.substring(0, title.indexOf("(View"));
\r
1434 title+= "(View "+viewSize+")";
\r
1436 newaf.setTitle(title.toString());
\r
1439 newaf.viewport.historyList = viewport.historyList;
\r
1440 newaf.viewport.redoList = viewport.redoList;
\r
1445 public void seqLimits_itemStateChanged()
\r
1447 viewport.setShowJVSuffix(seqLimits.getState());
\r
1448 alignPanel.fontChanged();
\r
1449 alignPanel.repaint();
\r
1453 protected void colourTextMenuItem_actionPerformed()
\r
1455 viewport.setColourText(colourTextMenuItem.getState());
\r
1456 alignPanel.repaint();
\r
1459 protected void wrapMenuItem_actionPerformed()
\r
1461 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
1462 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
1463 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
1464 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
1465 scaleRight.setEnabled(wrapMenuItem.getState());
\r
1466 alignPanel.repaint();
\r
1470 public void overviewMenuItem_actionPerformed()
\r
1472 if (alignPanel.overviewPanel != null)
\r
1477 Frame frame = new Frame();
\r
1478 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1479 frame.add(overview);
\r
1480 // +50 must allow for applet frame window
\r
1481 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
1482 overview.preferredSize().width,
\r
1483 overview.preferredSize().height + 50);
\r
1486 frame.addWindowListener(new WindowAdapter()
\r
1488 public void windowClosing(WindowEvent e)
\r
1490 alignPanel.setOverviewPanel(null);
\r
1494 alignPanel.setOverviewPanel(overview);
\r
1499 void changeColour(ColourSchemeI cs)
\r
1501 int threshold = 0;
\r
1505 if (viewport.getAbovePIDThreshold())
\r
1507 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
\r
1509 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1511 viewport.setGlobalColourScheme(cs);
\r
1515 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1518 if (viewport.getConservationSelected())
\r
1521 Alignment al = (Alignment) viewport.alignment;
\r
1522 Conservation c = new Conservation("All",
\r
1523 ResidueProperties.propHash, 3,
\r
1524 al.getSequences(), 0,
\r
1525 al.getWidth() - 1);
\r
1528 c.verdict(false, viewport.ConsPercGaps);
\r
1530 cs.setConservation(c);
\r
1532 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1538 cs.setConservation(null);
\r
1541 cs.setConsensus(viewport.hconsensus);
\r
1544 viewport.setGlobalColourScheme(cs);
\r
1546 if (viewport.getColourAppliesToAllGroups())
\r
1548 Vector groups = viewport.alignment.getGroups();
\r
1549 for (int i = 0; i < groups.size(); i++)
\r
1551 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1558 if (cs instanceof ClustalxColourScheme)
\r
1560 sg.cs = new ClustalxColourScheme(
\r
1561 sg.getSequences(viewport.hiddenRepSequences),
\r
1568 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1570 catch (Exception ex)
\r
1572 ex.printStackTrace();
\r
1577 if (viewport.getAbovePIDThreshold()
\r
1578 || cs instanceof PIDColourScheme
\r
1579 || cs instanceof Blosum62ColourScheme)
\r
1581 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1582 sg.cs.setConsensus(AAFrequency.calculate(
\r
1583 sg.getSequences(viewport.hiddenRepSequences), 0, sg.getWidth()));
\r
1586 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1588 if (viewport.getConservationSelected())
\r
1590 Conservation c = new Conservation("Group",
\r
1591 ResidueProperties.propHash, 3,
\r
1592 sg.getSequences(viewport.hiddenRepSequences), 0,
\r
1593 viewport.alignment.getWidth() - 1);
\r
1595 c.verdict(false, viewport.ConsPercGaps);
\r
1596 sg.cs.setConservation(c);
\r
1600 sg.cs.setConservation(null);
\r
1601 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1608 if (alignPanel.getOverviewPanel() != null)
\r
1610 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1613 alignPanel.repaint();
\r
1618 protected void modifyPID_actionPerformed()
\r
1620 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1622 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
1624 SliderPanel.showPIDSlider();
\r
1628 protected void modifyConservation_actionPerformed()
\r
1630 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1632 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
1634 SliderPanel.showConservationSlider();
\r
1638 protected void conservationMenuItem_actionPerformed()
\r
1640 viewport.setConservationSelected(conservationMenuItem.getState());
\r
1642 viewport.setAbovePIDThreshold(false);
\r
1643 abovePIDThreshold.setState(false);
\r
1645 changeColour(viewport.getGlobalColourScheme());
\r
1647 modifyConservation_actionPerformed();
\r
1650 public void abovePIDThreshold_actionPerformed()
\r
1652 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
1654 conservationMenuItem.setState(false);
\r
1655 viewport.setConservationSelected(false);
\r
1657 changeColour(viewport.getGlobalColourScheme());
\r
1659 modifyPID_actionPerformed();
\r
1664 public void sortPairwiseMenuItem_actionPerformed()
\r
1666 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
\r
1667 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1668 viewport.getAlignment().getSequenceAt(0));
\r
1669 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment));
\r
1670 alignPanel.repaint();
\r
1673 public void sortIDMenuItem_actionPerformed()
\r
1675 // addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1676 // HistoryItem.SORT));
\r
1677 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1678 alignPanel.repaint();
\r
1681 public void sortGroupMenuItem_actionPerformed()
\r
1683 // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1684 // HistoryItem.SORT));
\r
1685 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1686 alignPanel.repaint();
\r
1690 public void removeRedundancyMenuItem_actionPerformed()
\r
1692 new RedundancyPanel(alignPanel);
\r
1695 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
1697 if (viewport.getSelectionGroup()!=null
\r
1698 && viewport.getSelectionGroup().getSize() > 1)
\r
1700 Frame frame = new Frame();
\r
1701 frame.add(new PairwiseAlignPanel(alignPanel));
\r
1702 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
1706 public void PCAMenuItem_actionPerformed()
\r
1708 //are the sequences aligned?
\r
1709 if (!viewport.alignment.isAligned())
\r
1711 SequenceI current;
\r
1712 int Width = viewport.getAlignment().getWidth();
\r
1714 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1717 current = viewport.getAlignment().getSequenceAt(i);
\r
1719 if (current.getLength() < Width)
\r
1721 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1724 alignPanel.repaint();
\r
1727 if ( (viewport.getSelectionGroup() != null &&
\r
1728 viewport.getSelectionGroup().getSize() < 4 &&
\r
1729 viewport.getSelectionGroup().getSize() > 0)
\r
1730 || viewport.getAlignment().getHeight() < 4)
\r
1737 new PCAPanel(viewport);
\r
1739 catch (java.lang.OutOfMemoryError ex)
\r
1745 public void averageDistanceTreeMenuItem_actionPerformed()
\r
1747 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1750 public void neighbourTreeMenuItem_actionPerformed()
\r
1752 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1755 protected void njTreeBlosumMenuItem_actionPerformed()
\r
1757 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1760 protected void avTreeBlosumMenuItem_actionPerformed()
\r
1762 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
1765 void NewTreePanel(String type, String pwType, String title)
\r
1767 //are the sequences aligned?
\r
1768 if (!viewport.alignment.isAligned())
\r
1770 SequenceI current;
\r
1771 int Width = viewport.getAlignment().getWidth();
\r
1773 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1776 current = viewport.getAlignment().getSequenceAt(i);
\r
1778 if (current.getLength() < Width)
\r
1780 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1783 alignPanel.repaint();
\r
1787 if ( (viewport.getSelectionGroup() != null &&
\r
1788 viewport.getSelectionGroup().getSize() > 1)
\r
1789 || (viewport.getSelectionGroup() == null
\r
1790 && viewport.alignment.getHeight() > 1))
\r
1792 final TreePanel tp = new TreePanel(viewport,
\r
1796 addTreeMenuItem(tp, title);
\r
1798 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
1802 void loadTree_actionPerformed()
\r
1804 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1805 cap.setText("Paste your Newick tree file here.");
\r
1806 cap.setTreeImport();
\r
1807 Frame frame = new Frame();
\r
1809 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
1812 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
1814 TreePanel tp = new TreePanel(viewport,
\r
1818 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
1819 addTreeMenuItem(tp, treeFile);
\r
1822 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1824 final MenuItem item = new MenuItem(title);
\r
1825 sortByTreeMenu.add(item);
\r
1826 item.addActionListener(new java.awt.event.ActionListener()
\r
1828 public void actionPerformed(ActionEvent evt)
\r
1830 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1831 // HistoryItem.SORT));
\r
1832 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1833 alignPanel.repaint();
\r
1837 treePanel.addWindowListener(new WindowAdapter()
\r
1839 public void windowClosing(WindowEvent e)
\r
1841 sortByTreeMenu.remove(item);
\r
1846 protected void documentation_actionPerformed()
\r
1848 showURL("http://www.jalview.org/help.html", "HELP");
\r
1851 protected void about_actionPerformed()
\r
1854 class AboutPanel extends Canvas
\r
1857 public AboutPanel(String version)
\r
1858 { this.version = version; }
\r
1860 public void paint(Graphics g)
\r
1862 g.setColor(Color.white);
\r
1863 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1864 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1865 FontMetrics fm = g.getFontMetrics();
\r
1866 int fh = fm.getHeight();
\r
1868 g.setColor(Color.black);
\r
1869 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
1870 g.drawString("Jalview - Release "+version, 200, y += fh);
\r
1871 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1872 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
1874 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
1877 "For any issues relating to Jalview, email help@jalview.org", x,
\r
1879 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
1880 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
1882 g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh);
\r
1886 String version = "test";
\r
1887 java.net.URL url = getClass().getResource("/.build_properties");
\r
1892 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
1893 url.openStream()));
\r
1895 while ( (line = reader.readLine()) != null)
\r
1897 if (line.indexOf("VERSION") > -1)
\r
1899 version = line.substring(line.indexOf("=") + 1);
\r
1903 catch (Exception ex)
\r
1905 ex.printStackTrace();
\r
1910 Frame frame = new Frame();
\r
1911 frame.add(new AboutPanel(version));
\r
1912 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
\r
1916 public void showURL(String url, String target)
\r
1918 if (viewport.applet == null)
\r
1920 System.out.println("Not running as applet - no browser available.");
\r
1926 System.out.println("Show url: "+url);
\r
1927 viewport.applet.getAppletContext().showDocument(new java.net.URL(url),
\r
1930 catch (Exception ex)
\r
1932 ex.printStackTrace();
\r
1938 //////////////////////////////////////////////////////////////////////////////////
\r
1939 //JBuilder Graphics here
\r
1941 protected MenuBar alignFrameMenuBar = new MenuBar();
\r
1942 protected Menu fileMenu = new Menu("File");
\r
1943 protected MenuItem loadApplication = new MenuItem("View in Full Application");
\r
1944 protected MenuItem loadTree = new MenuItem("Load Associated Tree ...");
\r
1945 protected MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
\r
1946 protected MenuItem outputFeatures = new MenuItem("Export Features ...");
\r
1947 protected MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
\r
1949 protected MenuItem closeMenuItem = new MenuItem("Close");
\r
1950 protected Menu editMenu = new Menu("Edit");
\r
1951 protected Menu viewMenu = new Menu("View");
\r
1952 protected Menu colourMenu = new Menu("Colour");
\r
1953 protected Menu calculateMenu = new Menu("Calculate");
\r
1954 protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
1955 protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
1956 protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
1957 protected MenuItem remove2LeftMenuItem = new MenuItem();
\r
1958 protected MenuItem remove2RightMenuItem = new MenuItem();
\r
1959 protected MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
1960 protected MenuItem removeAllGapsMenuItem = new MenuItem();
\r
1961 protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
1962 protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
1963 protected MenuItem sortPairwiseMenuItem = new MenuItem();
\r
1964 protected MenuItem sortIDMenuItem = new MenuItem();
\r
1965 protected MenuItem sortGroupMenuItem = new MenuItem();
\r
1966 protected MenuItem removeRedundancyMenuItem = new MenuItem();
\r
1967 protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
1968 protected MenuItem PCAMenuItem = new MenuItem();
\r
1969 protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
1970 protected MenuItem neighbourTreeMenuItem = new MenuItem();
\r
1971 BorderLayout borderLayout1 = new BorderLayout();
\r
1972 public Label statusBar = new Label();
\r
1973 protected Menu outputTextboxMenu = new Menu();
\r
1974 protected MenuItem clustalColour = new MenuItem();
\r
1975 protected MenuItem zappoColour = new MenuItem();
\r
1976 protected MenuItem taylorColour = new MenuItem();
\r
1977 protected MenuItem hydrophobicityColour = new MenuItem();
\r
1978 protected MenuItem helixColour = new MenuItem();
\r
1979 protected MenuItem strandColour = new MenuItem();
\r
1980 protected MenuItem turnColour = new MenuItem();
\r
1981 protected MenuItem buriedColour = new MenuItem();
\r
1982 protected MenuItem userDefinedColour = new MenuItem();
\r
1983 protected MenuItem PIDColour = new MenuItem();
\r
1984 protected MenuItem BLOSUM62Colour = new MenuItem();
\r
1985 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
1986 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
1987 protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
1988 protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
1989 MenuItem overviewMenuItem = new MenuItem();
\r
1990 protected MenuItem undoMenuItem = new MenuItem();
\r
1991 protected MenuItem redoMenuItem = new MenuItem();
\r
1992 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
1993 MenuItem noColourmenuItem = new MenuItem();
\r
1994 protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
1995 protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
1996 MenuItem findMenuItem = new MenuItem();
\r
1997 protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
1998 protected MenuItem nucleotideColour = new MenuItem();
\r
1999 MenuItem deleteGroups = new MenuItem();
\r
2000 MenuItem delete = new MenuItem();
\r
2001 MenuItem copy = new MenuItem();
\r
2002 MenuItem cut = new MenuItem();
\r
2003 Menu pasteMenu = new Menu();
\r
2004 MenuItem pasteNew = new MenuItem();
\r
2005 MenuItem pasteThis = new MenuItem();
\r
2006 protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
2007 protected MenuItem font = new MenuItem();
\r
2008 protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
2009 protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
2010 protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
2011 MenuItem modifyPID = new MenuItem();
\r
2012 MenuItem modifyConservation = new MenuItem();
\r
2013 protected CheckboxMenuItem autoCalculate
\r
2014 = new CheckboxMenuItem("Autocalculate Consensus", true);
\r
2015 protected Menu sortByTreeMenu = new Menu();
\r
2016 Menu sort = new Menu();
\r
2017 Menu calculate = new Menu();
\r
2018 MenuItem inputText = new MenuItem();
\r
2019 Menu helpMenu = new Menu();
\r
2020 MenuItem documentation = new MenuItem();
\r
2021 MenuItem about = new MenuItem();
\r
2022 protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
2023 Panel embeddedMenu;
\r
2024 Label embeddedEdit;
\r
2025 Label embeddedSelect;
\r
2026 Label embeddedView;
\r
2027 Label embeddedFormat;
\r
2028 Label embeddedColour;
\r
2029 Label embeddedFile;
\r
2030 Label embeddedHelp;
\r
2031 Label embeddedCalculate;
\r
2032 FlowLayout flowLayout1;
\r
2034 private void jbInit() throws Exception {
\r
2036 setMenuBar(alignFrameMenuBar);
\r
2040 // dynamically fill save as menu with available formats
\r
2041 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
2044 item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
2046 item.addActionListener(new java.awt.event.ActionListener()
\r
2048 public void actionPerformed(ActionEvent e)
\r
2050 outputText_actionPerformed(e);
\r
2054 outputTextboxMenu.add(item);
\r
2056 closeMenuItem.addActionListener(this);
\r
2057 loadApplication.addActionListener(this);
\r
2059 loadTree.addActionListener(this);
\r
2060 loadAnnotations.addActionListener(this);
\r
2061 outputFeatures.addActionListener(this);
\r
2062 outputAnnotations.addActionListener(this);
\r
2063 selectAllSequenceMenuItem.addActionListener(this);
\r
2064 deselectAllSequenceMenuItem.addActionListener(this);
\r
2065 invertSequenceMenuItem.addActionListener(this);
\r
2066 remove2LeftMenuItem.setLabel("Remove Left");
\r
2067 remove2LeftMenuItem.addActionListener(this);
\r
2068 remove2RightMenuItem.setLabel("Remove Right");
\r
2069 remove2RightMenuItem.addActionListener(this);
\r
2070 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
2071 removeGappedColumnMenuItem.addActionListener(this);
\r
2072 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
2073 removeAllGapsMenuItem.addActionListener(this);
\r
2074 viewBoxesMenuItem.setLabel("Boxes");
\r
2075 viewBoxesMenuItem.setState(true);
\r
2076 viewBoxesMenuItem.addItemListener(this);
\r
2077 viewTextMenuItem.setLabel("Text");
\r
2078 viewTextMenuItem.setState(true);
\r
2079 viewTextMenuItem.addItemListener(this);
\r
2080 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
2081 sortPairwiseMenuItem.addActionListener(this);
\r
2082 sortIDMenuItem.setLabel("by ID");
\r
2083 sortIDMenuItem.addActionListener(this);
\r
2084 sortGroupMenuItem.setLabel("by Group");
\r
2085 sortGroupMenuItem.addActionListener(this);
\r
2086 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
2087 removeRedundancyMenuItem.addActionListener(this);
\r
2088 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
2089 pairwiseAlignmentMenuItem.addActionListener(this);
\r
2090 PCAMenuItem.setLabel("Principal Component Analysis");
\r
2091 PCAMenuItem.addActionListener(this);
\r
2092 averageDistanceTreeMenuItem.setLabel(
\r
2093 "Average Distance Using % Identity");
\r
2094 averageDistanceTreeMenuItem.addActionListener(this);
\r
2095 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
2096 neighbourTreeMenuItem.addActionListener(this);
\r
2097 statusBar.setBackground(Color.white);
\r
2098 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
2099 statusBar.setText("Status bar");
\r
2100 outputTextboxMenu.setLabel("Output to Textbox");
\r
2101 clustalColour.setLabel("Clustalx");
\r
2103 clustalColour.addActionListener(this);
\r
2104 zappoColour.setLabel("Zappo");
\r
2105 zappoColour.addActionListener(this);
\r
2106 taylorColour.setLabel("Taylor");
\r
2107 taylorColour.addActionListener(this);
\r
2108 hydrophobicityColour.setLabel("Hydrophobicity");
\r
2109 hydrophobicityColour.addActionListener(this);
\r
2110 helixColour.setLabel("Helix Propensity");
\r
2111 helixColour.addActionListener(this);
\r
2112 strandColour.setLabel("Strand Propensity");
\r
2113 strandColour.addActionListener(this);
\r
2114 turnColour.setLabel("Turn Propensity");
\r
2115 turnColour.addActionListener(this);
\r
2116 buriedColour.setLabel("Buried Index");
\r
2117 buriedColour.addActionListener(this);
\r
2118 userDefinedColour.setLabel("User Defined...");
\r
2119 userDefinedColour.addActionListener(this);
\r
2120 PIDColour.setLabel("Percentage Identity");
\r
2121 PIDColour.addActionListener(this);
\r
2122 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
2123 BLOSUM62Colour.addActionListener(this);
\r
2124 avDistanceTreeBlosumMenuItem.setLabel(
\r
2125 "Average Distance Using BLOSUM62");
\r
2126 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
2127 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
2128 njTreeBlosumMenuItem.addActionListener(this);
\r
2129 annotationPanelMenuItem.setLabel("Show Annotations");
\r
2130 annotationPanelMenuItem.addItemListener(this);
\r
2131 colourTextMenuItem.setLabel("Colour Text");
\r
2132 colourTextMenuItem.addItemListener(this);
\r
2133 overviewMenuItem.setLabel("Overview Window");
\r
2134 overviewMenuItem.addActionListener(this);
\r
2135 undoMenuItem.setEnabled(false);
\r
2136 undoMenuItem.setLabel("Undo");
\r
2137 undoMenuItem.addActionListener(this);
\r
2138 redoMenuItem.setEnabled(false);
\r
2139 redoMenuItem.setLabel("Redo");
\r
2140 redoMenuItem.addActionListener(this);
\r
2141 conservationMenuItem.setLabel("by Conservation");
\r
2142 conservationMenuItem.addItemListener(this);
\r
2143 noColourmenuItem.setLabel("None");
\r
2144 noColourmenuItem.addActionListener(this);
\r
2145 wrapMenuItem.setLabel("Wrap");
\r
2146 wrapMenuItem.addItemListener(this);
\r
2147 renderGapsMenuItem.setLabel("Show Gaps");
\r
2148 renderGapsMenuItem.setState(true);
\r
2149 renderGapsMenuItem.addItemListener(this);
\r
2150 findMenuItem.setLabel("Find...");
\r
2151 findMenuItem.addActionListener(this);
\r
2152 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
2153 abovePIDThreshold.addItemListener(this);
\r
2154 nucleotideColour.setLabel("Nucleotide");
\r
2155 nucleotideColour.addActionListener(this);
\r
2156 deleteGroups.setLabel("Undefine Groups");
\r
2157 deleteGroups.addActionListener(this);
\r
2158 copy.setLabel("Copy");
\r
2159 copy.addActionListener(this);
\r
2160 cut.setLabel("Cut");
\r
2161 cut.addActionListener(this);
\r
2162 delete.setLabel("Delete");
\r
2163 delete.addActionListener(this);
\r
2164 pasteMenu.setLabel("Paste");
\r
2165 pasteNew.setLabel("To New Alignment");
\r
2166 pasteNew.addActionListener(this);
\r
2167 pasteThis.setLabel("Add To This Alignment");
\r
2168 pasteThis.addActionListener(this);
\r
2169 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
2170 applyToAllGroups.setState(true);
\r
2171 applyToAllGroups.addItemListener(this);
\r
2172 font.setLabel("Font...");
\r
2173 font.addActionListener(this);
\r
2174 scaleAbove.setLabel("Scale Above");
\r
2175 scaleAbove.setState(true);
\r
2176 scaleAbove.setEnabled(false);
\r
2177 scaleAbove.addItemListener(this);
\r
2178 scaleLeft.setEnabled(false);
\r
2179 scaleLeft.setState(true);
\r
2180 scaleLeft.setLabel("Scale Left");
\r
2181 scaleLeft.addItemListener(this);
\r
2182 scaleRight.setEnabled(false);
\r
2183 scaleRight.setState(true);
\r
2184 scaleRight.setLabel("Scale Right");
\r
2185 scaleRight.addItemListener(this);
\r
2186 modifyPID.setLabel("Modify Identity Threshold...");
\r
2187 modifyPID.addActionListener(this);
\r
2188 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
2189 modifyConservation.addActionListener(this);
\r
2190 sortByTreeMenu.setLabel("By Tree Order");
\r
2191 sort.setLabel("Sort");
\r
2192 calculate.setLabel("Calculate Tree");
\r
2193 autoCalculate.addItemListener(this);
\r
2194 inputText.setLabel("Input from textbox");
\r
2195 inputText.addActionListener(this);
\r
2197 helpMenu.setLabel("Help");
\r
2198 documentation.setLabel("Documentation");
\r
2199 documentation.addActionListener(this);
\r
2201 about.setLabel("About...");
\r
2202 about.addActionListener(this);
\r
2203 seqLimits.setState(true);
\r
2204 seqLimits.setLabel("Show Sequence Limits");
\r
2205 seqLimits.addItemListener(this);
\r
2206 featureSettings.setLabel("Feature Settings...");
\r
2207 featureSettings.addActionListener(this);
\r
2208 sequenceFeatures.setLabel("Sequence Features");
\r
2209 sequenceFeatures.addItemListener(this);
\r
2210 sequenceFeatures.setState(false);
\r
2211 annotationColour.setLabel("by Annotation...");
\r
2212 annotationColour.addActionListener(this);
\r
2213 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
2214 invertColSel.setLabel("Invert Column Selection");
\r
2215 menu1.setLabel("Show");
\r
2216 showColumns.setLabel("All Columns ");
\r
2217 showSeqs.setLabel("All Sequences");
\r
2218 menu2.setLabel("Hide");
\r
2219 hideColumns.setLabel("Selected Columns");
\r
2220 hideSequences.setLabel("Selected Sequences");
\r
2221 invertColSel.addActionListener(this);
\r
2222 showColumns.addActionListener(this);
\r
2223 showSeqs.addActionListener(this);
\r
2224 hideColumns.addActionListener(this);
\r
2225 hideSequences.addActionListener(this);
\r
2226 formatMenu.setLabel("Format");
\r
2227 selectMenu.setLabel("Select");
\r
2228 newView.setLabel("New View");
\r
2229 newView.addActionListener(this);
\r
2230 alignFrameMenuBar.add(fileMenu);
\r
2231 alignFrameMenuBar.add(editMenu);
\r
2232 alignFrameMenuBar.add(selectMenu);
\r
2233 alignFrameMenuBar.add(viewMenu);
\r
2234 alignFrameMenuBar.add(formatMenu);
\r
2235 alignFrameMenuBar.add(colourMenu);
\r
2236 alignFrameMenuBar.add(calculateMenu);
\r
2237 alignFrameMenuBar.add(helpMenu);
\r
2239 fileMenu.add(inputText);
\r
2240 fileMenu.add(loadTree);
\r
2241 fileMenu.add(loadAnnotations);
\r
2243 fileMenu.addSeparator();
\r
2244 fileMenu.add(outputTextboxMenu);
\r
2245 fileMenu.add(outputFeatures);
\r
2246 fileMenu.add(outputAnnotations);
\r
2248 if(jalviewServletURL!=null)
\r
2249 fileMenu.add(loadApplication);
\r
2251 fileMenu.addSeparator();
\r
2252 fileMenu.add(closeMenuItem);
\r
2254 editMenu.add(undoMenuItem);
\r
2255 editMenu.add(redoMenuItem);
\r
2256 editMenu.add(cut);
\r
2257 editMenu.add(copy);
\r
2258 editMenu.add(pasteMenu);
\r
2259 editMenu.add(delete);
\r
2260 editMenu.addSeparator();
\r
2261 editMenu.add(remove2LeftMenuItem);
\r
2262 editMenu.add(remove2RightMenuItem);
\r
2263 editMenu.add(removeGappedColumnMenuItem);
\r
2264 editMenu.add(removeAllGapsMenuItem);
\r
2265 editMenu.add(removeRedundancyMenuItem);
\r
2266 viewMenu.add(newView);
\r
2267 viewMenu.addSeparator();
\r
2268 viewMenu.add(menu1);
\r
2269 viewMenu.add(menu2);
\r
2270 viewMenu.addSeparator();
\r
2271 viewMenu.add(annotationPanelMenuItem);
\r
2272 viewMenu.addSeparator();
\r
2273 viewMenu.add(sequenceFeatures);
\r
2274 viewMenu.add(featureSettings);
\r
2275 viewMenu.addSeparator();
\r
2276 viewMenu.add(overviewMenuItem);
\r
2277 colourMenu.add(applyToAllGroups);
\r
2278 colourMenu.addSeparator();
\r
2279 colourMenu.add(noColourmenuItem);
\r
2280 colourMenu.add(clustalColour);
\r
2281 colourMenu.add(BLOSUM62Colour);
\r
2282 colourMenu.add(PIDColour);
\r
2283 colourMenu.add(zappoColour);
\r
2284 colourMenu.add(taylorColour);
\r
2285 colourMenu.add(hydrophobicityColour);
\r
2286 colourMenu.add(helixColour);
\r
2287 colourMenu.add(strandColour);
\r
2288 colourMenu.add(turnColour);
\r
2289 colourMenu.add(buriedColour);
\r
2290 colourMenu.add(nucleotideColour);
\r
2291 colourMenu.add(userDefinedColour);
\r
2292 colourMenu.addSeparator();
\r
2293 colourMenu.add(conservationMenuItem);
\r
2294 colourMenu.add(modifyConservation);
\r
2295 colourMenu.add(abovePIDThreshold);
\r
2296 colourMenu.add(modifyPID);
\r
2297 colourMenu.add(annotationColour);
\r
2298 calculateMenu.add(sort);
\r
2299 calculateMenu.add(calculate);
\r
2300 calculateMenu.addSeparator();
\r
2301 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
2302 calculateMenu.add(PCAMenuItem);
\r
2303 calculateMenu.add(autoCalculate);
\r
2304 this.add(statusBar, BorderLayout.SOUTH);
\r
2305 pasteMenu.add(pasteNew);
\r
2306 pasteMenu.add(pasteThis);
\r
2307 sort.add(sortIDMenuItem);
\r
2308 sort.add(sortByTreeMenu);
\r
2309 sort.add(sortGroupMenuItem);
\r
2310 sort.add(sortPairwiseMenuItem);
\r
2311 calculate.add(averageDistanceTreeMenuItem);
\r
2312 calculate.add(neighbourTreeMenuItem);
\r
2313 calculate.add(avDistanceTreeBlosumMenuItem);
\r
2314 calculate.add(njTreeBlosumMenuItem);
\r
2315 helpMenu.add(documentation);
\r
2316 helpMenu.add(about);
\r
2317 menu1.add(showColumns);
\r
2318 menu1.add(showSeqs);
\r
2319 menu2.add(hideColumns);
\r
2320 menu2.add(hideSequences);
\r
2321 formatMenu.add(font);
\r
2322 formatMenu.add(seqLimits);
\r
2323 formatMenu.add(wrapMenuItem);
\r
2324 formatMenu.add(scaleAbove);
\r
2325 formatMenu.add(scaleLeft);
\r
2326 formatMenu.add(scaleRight);
\r
2327 formatMenu.add(viewBoxesMenuItem);
\r
2328 formatMenu.add(viewTextMenuItem);
\r
2329 formatMenu.add(colourTextMenuItem);
\r
2330 formatMenu.add(renderGapsMenuItem);
\r
2331 selectMenu.add(findMenuItem);
\r
2332 selectMenu.addSeparator();
\r
2333 selectMenu.add(selectAllSequenceMenuItem);
\r
2334 selectMenu.add(deselectAllSequenceMenuItem);
\r
2335 selectMenu.add(invertSequenceMenuItem);
\r
2336 selectMenu.add(invertColSel);
\r
2337 selectMenu.add(deleteGroups);
\r
2340 public void setEmbedded()
\r
2343 embeddedMenu = new Panel();
\r
2344 embeddedEdit = new Label("Edit");
\r
2345 embeddedSelect = new Label("Select");
\r
2346 embeddedView = new Label("View");
\r
2347 embeddedFormat = new Label("Format");
\r
2348 embeddedColour = new Label("Colour");
\r
2349 embeddedFile = new Label("File");
\r
2350 embeddedHelp = new Label("Help");
\r
2351 embeddedCalculate = new Label("Calculate");
\r
2352 flowLayout1 = new FlowLayout();
\r
2353 embeddedMenu.setBackground(Color.lightGray);
\r
2354 embeddedMenu.setLayout(flowLayout1);
\r
2355 embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2356 embeddedSelect.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2357 embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2358 embeddedFormat.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2359 embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2360 embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2361 embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2362 embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2363 embeddedMenu.add(embeddedFile);
\r
2364 embeddedMenu.add(embeddedEdit);
\r
2365 embeddedMenu.add(embeddedSelect);
\r
2366 embeddedMenu.add(embeddedView);
\r
2367 embeddedMenu.add(embeddedFormat);
\r
2368 embeddedMenu.add(embeddedColour);
\r
2369 embeddedMenu.add(embeddedCalculate);
\r
2370 embeddedMenu.add(embeddedHelp);
\r
2371 flowLayout1.setAlignment(FlowLayout.LEFT);
\r
2372 flowLayout1.setHgap(2);
\r
2373 flowLayout1.setVgap(0);
\r
2374 embeddedFile.addMouseListener(this);
\r
2375 embeddedEdit.addMouseListener(this);
\r
2376 embeddedSelect.addMouseListener(this);
\r
2377 embeddedView.addMouseListener(this);
\r
2378 embeddedFormat.addMouseListener(this);
\r
2379 embeddedColour.addMouseListener(this);
\r
2380 embeddedCalculate.addMouseListener(this);
\r
2381 embeddedHelp.addMouseListener(this);
\r
2383 fileMenu.remove(closeMenuItem);
\r
2384 fileMenu.remove(3); // Seperator
\r
2386 viewport.applet.setLayout(new BorderLayout());
\r
2387 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
\r
2388 viewport.applet.add(statusBar, BorderLayout.SOUTH);
\r
2390 alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height
\r
2391 - embeddedMenu.HEIGHT - statusBar.HEIGHT);
\r
2393 viewport.applet.add(alignPanel, BorderLayout.CENTER);
\r
2394 viewport.applet.validate();
\r
2400 PopupMenu filePopup, editPopup, searchPopup,
\r
2401 viewPopup, formatPopup, colourPopup, calculatePopup, helpPopup;
\r
2402 MenuItem featureSettings = new MenuItem();
\r
2403 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
2404 MenuItem annotationColour = new MenuItem();
\r
2405 MenuItem invertColSel = new MenuItem();
\r
2406 Menu menu1 = new Menu();
\r
2407 MenuItem showColumns = new MenuItem();
\r
2408 MenuItem showSeqs = new MenuItem();
\r
2409 Menu menu2 = new Menu();
\r
2410 MenuItem hideColumns = new MenuItem();
\r
2411 MenuItem hideSequences = new MenuItem();
\r
2412 Menu formatMenu = new Menu();
\r
2413 Menu selectMenu = new Menu();
\r
2414 MenuItem newView = new MenuItem();
\r
2416 public void mousePressed(MouseEvent evt)
\r
2418 PopupMenu popup = null;
\r
2419 Label source = (Label)evt.getSource();
\r
2420 if(source==embeddedFile)
\r
2422 popup = filePopup = genPopupMenu(filePopup, fileMenu);
\r
2424 else if(source==embeddedEdit)
\r
2426 popup = editPopup = genPopupMenu(editPopup, editMenu);
\r
2428 else if(source==embeddedSelect)
\r
2430 popup = searchPopup = genPopupMenu(searchPopup, selectMenu);
\r
2432 else if(source==embeddedView)
\r
2434 popup = viewPopup = genPopupMenu(viewPopup, viewMenu);
\r
2436 else if (source ==embeddedFormat)
\r
2438 popup = formatPopup = genPopupMenu(formatPopup, formatMenu);
\r
2440 else if(source==embeddedColour)
\r
2442 popup = colourPopup = genPopupMenu(colourPopup, colourMenu);
\r
2444 else if(source==embeddedCalculate)
\r
2446 popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);
\r
2448 else if(source==embeddedHelp)
\r
2450 popup = helpPopup = genPopupMenu(helpPopup, helpMenu);
\r
2453 embeddedMenu.add(popup);
\r
2454 popup.show(embeddedMenu,
\r
2455 source.getBounds().x,
\r
2456 source.getBounds().y + source.getBounds().getSize().height);
\r
2459 PopupMenu genPopupMenu(PopupMenu popup, Menu original)
\r
2465 popup = new PopupMenu();
\r
2466 int m, mSize = original.getItemCount();
\r
2467 for(m=0; m<mSize; m++)
\r
2469 popup.add(original.getItem(m));
\r
2476 public void mouseClicked(MouseEvent evt)
\r
2478 public void mouseReleased(MouseEvent evt)
\r
2480 public void mouseEntered(MouseEvent evt)
\r
2482 public void mouseExited(MouseEvent evt)
\r