2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
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3 * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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5 * This file is part of Jalview.
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7 * Jalview is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License
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9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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11 * Jalview is distributed in the hope that it will be useful, but
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12 * WITHOUT ANY WARRANTY; without even the implied warranty
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13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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14 * PURPOSE. See the GNU General Public License for more details.
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16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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18 package jalview.appletgui;
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24 import java.awt.event.*;
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26 import jalview.analysis.*;
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27 import jalview.api.SequenceStructureBinding;
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28 import jalview.bin.JalviewLite;
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29 import jalview.commands.*;
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30 import jalview.datamodel.*;
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31 import jalview.io.*;
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32 import jalview.schemes.*;
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33 import jalview.structure.StructureSelectionManager;
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35 public class AlignFrame extends EmbmenuFrame implements ActionListener,
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36 ItemListener, KeyListener
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38 public AlignmentPanel alignPanel;
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40 public AlignViewport viewport;
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42 int DEFAULT_WIDTH = 700;
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44 int DEFAULT_HEIGHT = 500;
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46 String jalviewServletURL;
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48 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
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49 String title, boolean embedded)
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54 jalviewServletURL = applet.getParameter("APPLICATION_URL");
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60 } catch (Exception ex)
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62 ex.printStackTrace();
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65 viewport = new AlignViewport(al, applet);
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66 alignPanel = new AlignmentPanel(this, viewport);
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68 viewport.updateConservation(alignPanel);
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69 viewport.updateConsensus(alignPanel);
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71 annotationPanelMenuItem.setState(viewport.showAnnotation);
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72 displayNonconservedMenuItem.setState(viewport.getShowunconserved());
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73 followMouseOverFlag.setState(viewport.getFollowHighlight());
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74 showGroupConsensus.setState(viewport.showGroupConsensus);
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75 showGroupConservation.setState(viewport.showGroupConservation);
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76 showConsensusHistogram.setState(viewport.showConsensusHistogram);
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77 showSequenceLogo.setState(viewport.showSequenceLogo);
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79 seqLimits.setState(viewport.showJVSuffix);
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83 String param = applet.getParameter("sortBy");
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86 if (param.equalsIgnoreCase("Id"))
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88 sortIDMenuItem_actionPerformed();
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90 else if (param.equalsIgnoreCase("Pairwise Identity"))
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92 sortPairwiseMenuItem_actionPerformed();
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94 else if (param.equalsIgnoreCase("Length"))
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96 sortLengthMenuItem_actionPerformed();
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100 param = applet.getParameter("wrap");
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103 if (param.equalsIgnoreCase("true"))
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105 wrapMenuItem.setState(true);
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106 wrapMenuItem_actionPerformed();
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109 param = applet.getParameter("centrecolumnlabels");
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112 centreColumnLabelFlag.setState(true);
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113 centreColumnLabelFlag_stateChanged();
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117 param = applet.getParameter("windowWidth");
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120 int width = Integer.parseInt(param);
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121 DEFAULT_WIDTH = width;
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123 param = applet.getParameter("windowHeight");
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126 int height = Integer.parseInt(param);
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127 DEFAULT_HEIGHT = height;
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129 } catch (Exception ex)
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135 // Some JVMS send keyevents to Top frame or lowest panel,
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136 // Havent worked out why yet. So add to both this frame and seqCanvas for
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138 this.addKeyListener(this);
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139 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
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140 alignPanel.idPanel.idCanvas.addKeyListener(this);
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141 alignPanel.scalePanel.addKeyListener(this);
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142 alignPanel.annotationPanel.addKeyListener(this);
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143 alignPanel.annotationPanelHolder.addKeyListener(this);
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144 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
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145 alignPanel.alabels.addKeyListener(this);
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146 createAlignFrameWindow(embedded, title);
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149 alignPanel.adjustAnnotationHeight();
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150 alignPanel.paintAlignment(true);
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153 public AlignViewport getAlignViewport()
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158 public SeqCanvas getSeqcanvas()
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160 return alignPanel.seqPanel.seqCanvas;
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170 public void parseFeaturesFile(String file, String type)
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172 Hashtable featureLinks = new Hashtable();
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173 boolean featuresFile = false;
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176 featuresFile = new jalview.io.FeaturesFile(file, type)
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177 .parse(viewport.alignment,
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178 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
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179 featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));
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180 } catch (Exception ex)
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182 ex.printStackTrace();
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187 if (featureLinks.size() > 0)
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189 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
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191 viewport.showSequenceFeatures = true;
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192 sequenceFeatures.setState(true);
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193 if (viewport.featureSettings != null)
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195 viewport.featureSettings.refreshTable();
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197 alignPanel.paintAlignment(true);
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202 public void keyPressed(KeyEvent evt)
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204 if (viewport.cursorMode
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205 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
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206 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
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207 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
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208 && Character.isDigit(evt.getKeyChar()))
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209 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
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211 switch (evt.getKeyCode())
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213 case 27: // escape key
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214 deselectAllSequenceMenuItem_actionPerformed();
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216 alignPanel.alabels.cancelDrag();
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218 case KeyEvent.VK_X:
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219 if (evt.isControlDown() || evt.isMetaDown())
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221 cut_actionPerformed();
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224 case KeyEvent.VK_C:
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225 if (viewport.cursorMode && !evt.isControlDown())
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227 alignPanel.seqPanel.setCursorColumn();
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229 if (evt.isControlDown() || evt.isMetaDown())
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231 copy_actionPerformed();
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234 case KeyEvent.VK_V:
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235 if (evt.isControlDown())
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237 paste(evt.isShiftDown());
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240 case KeyEvent.VK_A:
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241 if (evt.isControlDown() || evt.isMetaDown())
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243 selectAllSequenceMenuItem_actionPerformed();
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246 case KeyEvent.VK_DOWN:
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247 if (viewport.cursorMode)
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249 alignPanel.seqPanel.moveCursor(0, 1);
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253 moveSelectedSequences(false);
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257 case KeyEvent.VK_UP:
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258 if (viewport.cursorMode)
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260 alignPanel.seqPanel.moveCursor(0, -1);
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264 moveSelectedSequences(true);
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268 case KeyEvent.VK_LEFT:
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269 if (evt.isAltDown() || !viewport.cursorMode)
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270 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
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272 alignPanel.seqPanel.moveCursor(-1, 0);
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275 case KeyEvent.VK_RIGHT:
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276 if (evt.isAltDown() || !viewport.cursorMode)
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277 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
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279 alignPanel.seqPanel.moveCursor(1, 0);
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282 case KeyEvent.VK_SPACE:
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283 if (viewport.cursorMode)
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285 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
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286 || evt.isShiftDown() || evt.isAltDown());
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290 case KeyEvent.VK_DELETE:
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291 case KeyEvent.VK_BACK_SPACE:
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292 if (viewport.cursorMode)
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294 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
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295 || evt.isShiftDown() || evt.isAltDown());
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299 cut_actionPerformed();
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300 alignPanel.seqPanel.seqCanvas.repaint();
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304 case KeyEvent.VK_S:
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305 if (viewport.cursorMode)
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307 alignPanel.seqPanel.setCursorRow();
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310 case KeyEvent.VK_P:
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311 if (viewport.cursorMode)
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313 alignPanel.seqPanel.setCursorPosition();
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317 case KeyEvent.VK_ENTER:
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318 case KeyEvent.VK_COMMA:
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319 if (viewport.cursorMode)
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321 alignPanel.seqPanel.setCursorRowAndColumn();
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325 case KeyEvent.VK_Q:
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326 if (viewport.cursorMode)
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328 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
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331 case KeyEvent.VK_M:
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332 if (viewport.cursorMode)
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334 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
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338 case KeyEvent.VK_F2:
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339 viewport.cursorMode = !viewport.cursorMode;
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340 statusBar.setText("Keyboard editing mode is "
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341 + (viewport.cursorMode ? "on" : "off"));
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342 if (viewport.cursorMode)
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344 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
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345 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
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349 case KeyEvent.VK_F:
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350 if (evt.isControlDown())
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352 findMenuItem_actionPerformed();
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356 case KeyEvent.VK_H:
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358 boolean toggleSeqs = !evt.isControlDown();
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359 boolean toggleCols = !evt.isShiftDown();
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360 toggleHiddenRegions(toggleSeqs, toggleCols);
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364 case KeyEvent.VK_PAGE_UP:
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365 if (viewport.wrapAlignment)
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367 alignPanel.scrollUp(true);
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371 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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372 - viewport.endSeq + viewport.startSeq);
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376 case KeyEvent.VK_PAGE_DOWN:
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377 if (viewport.wrapAlignment)
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379 alignPanel.scrollUp(false);
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383 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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384 + viewport.endSeq - viewport.startSeq);
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388 case KeyEvent.VK_Z:
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389 if (evt.isControlDown())
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391 undoMenuItem_actionPerformed();
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395 case KeyEvent.VK_Y:
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396 if (evt.isControlDown())
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398 redoMenuItem_actionPerformed();
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402 case KeyEvent.VK_L:
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403 if (evt.isControlDown())
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405 trimAlignment(true);
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409 case KeyEvent.VK_R:
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410 if (evt.isControlDown())
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412 trimAlignment(false);
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416 case KeyEvent.VK_E:
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417 if (evt.isControlDown())
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419 if (evt.isShiftDown())
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421 this.removeAllGapsMenuItem_actionPerformed();
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425 removeGappedColumnMenuItem_actionPerformed();
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429 case KeyEvent.VK_I:
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430 if (evt.isControlDown())
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432 if (evt.isAltDown())
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434 invertColSel_actionPerformed();
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438 invertSequenceMenuItem_actionPerformed();
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443 case KeyEvent.VK_U:
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444 if (evt.isControlDown())
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446 this.deleteGroups_actionPerformed();
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450 case KeyEvent.VK_T:
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451 if (evt.isControlDown())
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458 alignPanel.paintAlignment(true);
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462 * called by key handler and the hide all/show all menu items
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464 * @param toggleSeqs
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465 * @param toggleCols
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467 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
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469 boolean hide = false;
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470 SequenceGroup sg = viewport.getSelectionGroup();
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471 if (!toggleSeqs && !toggleCols)
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473 // Hide everything by the current selection - this is a hack - we do the
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474 // invert and then hide
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475 // first check that there will be visible columns after the invert.
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476 if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
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477 .getSelected().size() > 0)
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478 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
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481 // now invert the sequence set, if required - empty selection implies
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482 // that no hiding is required.
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485 invertSequenceMenuItem_actionPerformed();
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486 sg = viewport.getSelectionGroup();
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490 viewport.expandColSelection(sg, true);
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491 // finally invert the column selection and get the new sequence
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492 // selection and indicate it should be hidden.
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493 invertColSel_actionPerformed();
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500 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
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503 viewport.hideAllSelectedSeqs();
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505 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
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507 viewport.showAllHiddenSeqs();
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513 if (viewport.colSel.getSelected().size() > 0)
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515 viewport.hideSelectedColumns();
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518 viewport.selectionGroup = sg;
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523 viewport.showAllHiddenColumns();
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528 public void keyReleased(KeyEvent evt)
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532 public void keyTyped(KeyEvent evt)
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536 public void itemStateChanged(ItemEvent evt)
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538 if (evt.getSource() == displayNonconservedMenuItem)
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540 displayNonconservedMenuItem_actionPerformed();
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542 else if (evt.getSource() == colourTextMenuItem)
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544 colourTextMenuItem_actionPerformed();
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546 else if (evt.getSource() == wrapMenuItem)
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548 wrapMenuItem_actionPerformed();
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550 else if (evt.getSource() == scaleAbove)
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552 viewport.setScaleAboveWrapped(scaleAbove.getState());
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554 else if (evt.getSource() == scaleLeft)
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556 viewport.setScaleLeftWrapped(scaleLeft.getState());
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558 else if (evt.getSource() == scaleRight)
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560 viewport.setScaleRightWrapped(scaleRight.getState());
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562 else if (evt.getSource() == seqLimits)
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564 seqLimits_itemStateChanged();
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566 else if (evt.getSource() == viewBoxesMenuItem)
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568 viewport.setShowBoxes(viewBoxesMenuItem.getState());
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570 else if (evt.getSource() == viewTextMenuItem)
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572 viewport.setShowText(viewTextMenuItem.getState());
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574 else if (evt.getSource() == renderGapsMenuItem)
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576 viewport.setRenderGaps(renderGapsMenuItem.getState());
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578 else if (evt.getSource() == annotationPanelMenuItem)
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580 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
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581 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
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583 else if (evt.getSource() == sequenceFeatures)
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585 viewport.showSequenceFeatures(sequenceFeatures.getState());
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586 alignPanel.seqPanel.seqCanvas.repaint();
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588 else if (evt.getSource() == conservationMenuItem)
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590 conservationMenuItem_actionPerformed();
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592 else if (evt.getSource() == abovePIDThreshold)
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594 abovePIDThreshold_actionPerformed();
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596 else if (evt.getSource() == applyToAllGroups)
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598 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
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600 else if (evt.getSource() == autoCalculate)
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602 viewport.autocalculateConsensus = autoCalculate.getState();
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604 else if (evt.getSource() == sortByTree)
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606 viewport.sortByTree = sortByTree.getState();
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608 else if (evt.getSource() == this.centreColumnLabelFlag)
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610 centreColumnLabelFlag_stateChanged();
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612 else if (evt.getSource() == this.followMouseOverFlag)
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614 mouseOverFlag_stateChanged();
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616 else if (evt.getSource() == showGroupConsensus)
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618 showGroupConsensus_actionPerformed();
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620 else if (evt.getSource() == showGroupConservation)
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622 showGroupConservation_actionPerformed();
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624 else if (evt.getSource() == showSequenceLogo)
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626 showSequenceLogo_actionPerformed();
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628 else if (evt.getSource() == showConsensusHistogram)
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630 showConsensusHistogram_actionPerformed();
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632 else if (evt.getSource() == applyAutoAnnotationSettings)
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634 applyAutoAnnotationSettings_actionPerformed();
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636 alignPanel.paintAlignment(true);
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639 private void mouseOverFlag_stateChanged()
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641 viewport.followHighlight = followMouseOverFlag.getState();
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642 // TODO: could kick the scrollTo mechanism to reset view for current
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646 private void centreColumnLabelFlag_stateChanged()
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648 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
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649 this.alignPanel.annotationPanel.repaint();
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652 public void actionPerformed(ActionEvent evt)
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654 Object source = evt.getSource();
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656 if (source == inputText)
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658 inputText_actionPerformed();
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660 else if (source == loadTree)
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662 loadTree_actionPerformed();
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664 else if (source == loadApplication)
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666 launchFullApplication();
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668 else if (source == loadAnnotations)
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672 else if (source == outputAnnotations)
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674 outputAnnotations(true);
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676 else if (source == outputFeatures)
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678 outputFeatures(true, "Jalview");
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680 else if (source == closeMenuItem)
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682 closeMenuItem_actionPerformed();
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684 else if (source == copy)
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686 copy_actionPerformed();
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688 else if (source == undoMenuItem)
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690 undoMenuItem_actionPerformed();
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692 else if (source == redoMenuItem)
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694 redoMenuItem_actionPerformed();
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696 else if (source == inputText)
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698 inputText_actionPerformed();
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700 else if (source == closeMenuItem)
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702 closeMenuItem_actionPerformed();
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704 else if (source == undoMenuItem)
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706 undoMenuItem_actionPerformed();
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708 else if (source == redoMenuItem)
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710 redoMenuItem_actionPerformed();
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712 else if (source == copy)
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714 copy_actionPerformed();
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716 else if (source == pasteNew)
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718 pasteNew_actionPerformed();
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720 else if (source == pasteThis)
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722 pasteThis_actionPerformed();
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724 else if (source == cut)
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726 cut_actionPerformed();
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728 else if (source == delete)
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730 delete_actionPerformed();
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732 else if (source == grpsFromSelection)
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734 makeGrpsFromSelection_actionPerformed();
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736 else if (source == deleteGroups)
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738 deleteGroups_actionPerformed();
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740 else if (source == selectAllSequenceMenuItem)
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742 selectAllSequenceMenuItem_actionPerformed();
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744 else if (source == deselectAllSequenceMenuItem)
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746 deselectAllSequenceMenuItem_actionPerformed();
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748 else if (source == invertSequenceMenuItem)
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750 invertSequenceMenuItem_actionPerformed();
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752 else if (source == invertColSel)
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754 viewport.invertColumnSelection();
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755 alignPanel.paintAlignment(true);
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757 else if (source == remove2LeftMenuItem)
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759 trimAlignment(true);
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761 else if (source == remove2RightMenuItem)
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763 trimAlignment(false);
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765 else if (source == removeGappedColumnMenuItem)
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767 removeGappedColumnMenuItem_actionPerformed();
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769 else if (source == removeAllGapsMenuItem)
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771 removeAllGapsMenuItem_actionPerformed();
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773 else if (source == findMenuItem)
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775 findMenuItem_actionPerformed();
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777 else if (source == font)
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779 new FontChooser(alignPanel);
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781 else if (source == newView)
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785 else if (source == showColumns)
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787 viewport.showAllHiddenColumns();
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788 alignPanel.paintAlignment(true);
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790 else if (source == showSeqs)
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792 viewport.showAllHiddenSeqs();
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793 alignPanel.paintAlignment(true);
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795 else if (source == hideColumns)
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797 viewport.hideSelectedColumns();
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798 alignPanel.paintAlignment(true);
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800 else if (source == hideSequences
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801 && viewport.getSelectionGroup() != null)
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803 viewport.hideAllSelectedSeqs();
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804 alignPanel.paintAlignment(true);
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806 else if (source == hideAllButSelection)
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808 toggleHiddenRegions(false, false);
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809 alignPanel.paintAlignment(true);
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811 else if (source == hideAllSelection)
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813 SequenceGroup sg = viewport.getSelectionGroup();
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814 viewport.expandColSelection(sg, false);
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815 viewport.hideAllSelectedSeqs();
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816 viewport.hideSelectedColumns();
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817 alignPanel.paintAlignment(true);
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819 else if (source == showAllHidden)
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821 viewport.showAllHiddenColumns();
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822 viewport.showAllHiddenSeqs();
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823 alignPanel.paintAlignment(true);
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825 else if (source == showGroupConsensus)
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827 showGroupConsensus_actionPerformed();
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829 else if (source == showGroupConservation)
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831 showGroupConservation_actionPerformed();
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833 else if (source == showSequenceLogo)
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835 showSequenceLogo_actionPerformed();
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837 else if (source == showConsensusHistogram)
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839 showConsensusHistogram_actionPerformed();
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841 else if (source == applyAutoAnnotationSettings)
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843 applyAutoAnnotationSettings_actionPerformed();
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845 else if (source == featureSettings)
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847 new FeatureSettings(alignPanel);
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849 else if (source == alProperties)
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851 StringBuffer contents = new jalview.io.AlignmentProperties(
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852 viewport.alignment).formatAsString();
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853 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
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854 cap.setText(contents.toString());
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855 Frame frame = new Frame();
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857 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
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858 + getTitle(), 400, 250);
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860 else if (source == overviewMenuItem)
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862 overviewMenuItem_actionPerformed();
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864 else if (source == noColourmenuItem)
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866 changeColour(null);
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868 else if (source == clustalColour)
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870 abovePIDThreshold.setState(false);
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871 changeColour(new ClustalxColourScheme(
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872 viewport.alignment.getSequences(),
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873 viewport.alignment.getWidth()));
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875 else if (source == zappoColour)
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877 changeColour(new ZappoColourScheme());
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879 else if (source == taylorColour)
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881 changeColour(new TaylorColourScheme());
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883 else if (source == hydrophobicityColour)
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885 changeColour(new HydrophobicColourScheme());
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887 else if (source == helixColour)
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889 changeColour(new HelixColourScheme());
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891 else if (source == strandColour)
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893 changeColour(new StrandColourScheme());
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895 else if (source == turnColour)
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897 changeColour(new TurnColourScheme());
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899 else if (source == buriedColour)
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901 changeColour(new BuriedColourScheme());
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903 else if (source == nucleotideColour)
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905 changeColour(new NucleotideColourScheme());
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907 else if (source == modifyPID)
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909 modifyPID_actionPerformed();
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911 else if (source == modifyConservation)
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913 modifyConservation_actionPerformed();
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915 else if (source == userDefinedColour)
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917 new UserDefinedColours(alignPanel, null);
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919 else if (source == PIDColour)
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921 changeColour(new PIDColourScheme());
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923 else if (source == BLOSUM62Colour)
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925 changeColour(new Blosum62ColourScheme());
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927 else if (source == annotationColour)
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929 new AnnotationColourChooser(viewport, alignPanel);
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931 else if (source == sortPairwiseMenuItem)
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933 sortPairwiseMenuItem_actionPerformed();
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935 else if (source == sortIDMenuItem)
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937 sortIDMenuItem_actionPerformed();
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939 else if (source == sortLengthMenuItem)
\r
941 sortLengthMenuItem_actionPerformed();
\r
943 else if (source == sortGroupMenuItem)
\r
945 sortGroupMenuItem_actionPerformed();
\r
947 else if (source == removeRedundancyMenuItem)
\r
949 removeRedundancyMenuItem_actionPerformed();
\r
951 else if (source == pairwiseAlignmentMenuItem)
\r
953 pairwiseAlignmentMenuItem_actionPerformed();
\r
955 else if (source == PCAMenuItem)
\r
957 PCAMenuItem_actionPerformed();
\r
959 else if (source == averageDistanceTreeMenuItem)
\r
961 averageDistanceTreeMenuItem_actionPerformed();
\r
963 else if (source == neighbourTreeMenuItem)
\r
965 neighbourTreeMenuItem_actionPerformed();
\r
967 else if (source == njTreeBlosumMenuItem)
\r
969 njTreeBlosumMenuItem_actionPerformed();
\r
971 else if (source == avDistanceTreeBlosumMenuItem)
\r
973 avTreeBlosumMenuItem_actionPerformed();
\r
975 else if (source == documentation)
\r
977 documentation_actionPerformed();
\r
979 else if (source == about)
\r
981 about_actionPerformed();
\r
986 public void inputText_actionPerformed()
\r
988 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
989 Frame frame = new Frame();
\r
991 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
\r
994 protected void outputText_actionPerformed(ActionEvent e)
\r
996 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
997 Frame frame = new Frame();
\r
999 jalview.bin.JalviewLite.addFrame(frame,
\r
1000 "Alignment output - " + e.getActionCommand(), 600, 500);
\r
1001 cap.setText(new AppletFormatAdapter().formatSequences(
\r
1002 e.getActionCommand(), viewport.getAlignment(),
\r
1003 viewport.showJVSuffix));
\r
1006 public void loadAnnotations()
\r
1008 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1009 cap.setText("Paste your features / annotations file here.");
\r
1010 cap.setAnnotationImport();
\r
1011 Frame frame = new Frame();
\r
1013 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
\r
1017 public String outputAnnotations(boolean displayTextbox)
\r
1019 String annotation = new AnnotationFile().printAnnotations(
\r
1020 viewport.showAnnotation ? viewport.alignment
\r
1021 .getAlignmentAnnotation() : null, viewport.alignment
\r
1023 ((Alignment) viewport.alignment).alignmentProperties);
\r
1025 if (displayTextbox)
\r
1027 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
1028 Frame frame = new Frame();
\r
1030 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
\r
1031 cap.setText(annotation);
\r
1034 return annotation;
\r
1037 private Hashtable getDisplayedFeatureCols()
\r
1039 if (alignPanel.getFeatureRenderer() != null && viewport.featuresDisplayed!=null)
\r
1041 FeatureRenderer fr = alignPanel.getFeatureRenderer();
\r
1042 Hashtable fcols = new Hashtable();
\r
1043 Enumeration en = viewport.featuresDisplayed.keys();
\r
1044 while (en.hasMoreElements())
\r
1046 Object col = en.nextElement();
\r
1047 fcols.put(col, fr.featureColours.get(col));
\r
1054 public String outputFeatures(boolean displayTextbox, String format)
\r
1057 if (format.equalsIgnoreCase("Jalview"))
\r
1059 features = new FeaturesFile().printJalviewFormat(
\r
1060 viewport.alignment.getSequencesArray(),
\r
1061 getDisplayedFeatureCols());
\r
1065 features = new FeaturesFile().printGFFFormat(
\r
1066 viewport.alignment.getSequencesArray(),
\r
1067 getDisplayedFeatureCols());
\r
1070 if (displayTextbox)
\r
1072 boolean frimport=false;
\r
1073 if (features==null || features.equals("No Features Visible"))
\r
1075 features = "# No features visible - paste some and import them here.";
\r
1079 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
\r
1082 cap.setAnnotationImport();
\r
1084 Frame frame = new Frame();
\r
1086 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
\r
1087 cap.setText(features);
\r
1089 if (features==null)
\r
1096 void launchFullApplication()
\r
1098 StringBuffer url = new StringBuffer(jalviewServletURL);
\r
1100 url.append("?open="
\r
1101 + appendProtocol(viewport.applet.getParameter("file")));
\r
1103 if (viewport.applet.getParameter("features") != null)
\r
1105 url.append("&features=");
\r
1106 url.append(appendProtocol(viewport.applet.getParameter("features")));
\r
1109 if (viewport.applet.getParameter("annotations") != null)
\r
1111 url.append("&annotations=");
\r
1112 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
\r
1115 if (viewport.applet.getParameter("jnetfile") != null)
\r
1117 url.append("&annotations=");
\r
1118 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
\r
1121 if (viewport.applet.getParameter("defaultColour") != null)
\r
1123 url.append("&colour="
\r
1124 + removeWhiteSpace(viewport.applet
\r
1125 .getParameter("defaultColour")));
\r
1128 if (viewport.applet.getParameter("userDefinedColour") != null)
\r
1130 url.append("&colour="
\r
1131 + removeWhiteSpace(viewport.applet
\r
1132 .getParameter("userDefinedColour")));
\r
1134 if (viewport.applet.getParameter("tree") != null)
\r
1136 url.append("&tree="
\r
1137 + appendProtocol(viewport.applet.getParameter("tree")));
\r
1139 if (viewport.applet.getParameter("treeFile") != null)
\r
1141 url.append("&tree="
\r
1142 + appendProtocol(viewport.applet.getParameter("treeFile")));
\r
1145 showURL(url.toString(), "FULL_APP");
\r
1148 String removeWhiteSpace(String colour)
\r
1150 StringBuffer sb = new StringBuffer();
\r
1151 for (int i = 0; i < colour.length(); i++)
\r
1153 if (Character.isWhitespace(colour.charAt(i)))
\r
1159 sb.append(colour.charAt(i));
\r
1163 return sb.toString();
\r
1166 String appendProtocol(String url)
\r
1171 url = URLEncoder.encode(url);
\r
1174 * When we finally deprecate 1.1 compatibility, we can start to use
\r
1175 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
\r
1176 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
\r
1177 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
\r
1178 * ex.printStackTrace(); }
\r
1180 catch (java.net.MalformedURLException ex)
\r
1182 url = viewport.applet.getCodeBase() + url;
\r
1187 public void closeMenuItem_actionPerformed()
\r
1189 PaintRefresher.RemoveComponent(alignPanel);
\r
1190 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
\r
1191 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
\r
1193 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
\r
1199 alignPanel = null;
\r
1206 void updateEditMenuBar()
\r
1209 if (viewport.historyList.size() > 0)
\r
1211 undoMenuItem.setEnabled(true);
\r
1212 CommandI command = (CommandI) viewport.historyList.peek();
\r
1213 undoMenuItem.setLabel("Undo " + command.getDescription());
\r
1217 undoMenuItem.setEnabled(false);
\r
1218 undoMenuItem.setLabel("Undo");
\r
1221 if (viewport.redoList.size() > 0)
\r
1223 redoMenuItem.setEnabled(true);
\r
1225 CommandI command = (CommandI) viewport.redoList.peek();
\r
1226 redoMenuItem.setLabel("Redo " + command.getDescription());
\r
1230 redoMenuItem.setEnabled(false);
\r
1231 redoMenuItem.setLabel("Redo");
\r
1235 public void addHistoryItem(CommandI command)
\r
1237 if (command.getSize() > 0)
\r
1239 viewport.historyList.push(command);
\r
1240 viewport.redoList.removeAllElements();
\r
1241 updateEditMenuBar();
\r
1242 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
1252 protected void undoMenuItem_actionPerformed()
\r
1254 if (viewport.historyList.size() < 1)
\r
1259 CommandI command = (CommandI) viewport.historyList.pop();
\r
1260 viewport.redoList.push(command);
\r
1261 command.undoCommand(null);
\r
1263 AlignViewport originalSource = getOriginatingSource(command);
\r
1265 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
1266 updateEditMenuBar();
\r
1267 originalSource.firePropertyChange("alignment", null,
\r
1268 originalSource.alignment.getSequences());
\r
1277 protected void redoMenuItem_actionPerformed()
\r
1279 if (viewport.redoList.size() < 1)
\r
1284 CommandI command = (CommandI) viewport.redoList.pop();
\r
1285 viewport.historyList.push(command);
\r
1286 command.doCommand(null);
\r
1288 AlignViewport originalSource = getOriginatingSource(command);
\r
1289 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
1291 updateEditMenuBar();
\r
1292 originalSource.firePropertyChange("alignment", null,
\r
1293 originalSource.alignment.getSequences());
\r
1296 AlignViewport getOriginatingSource(CommandI command)
\r
1298 AlignViewport originalSource = null;
\r
1299 // For sequence removal and addition, we need to fire
\r
1300 // the property change event FROM the viewport where the
\r
1301 // original alignment was altered
\r
1302 AlignmentI al = null;
\r
1303 if (command instanceof EditCommand)
\r
1305 EditCommand editCommand = (EditCommand) command;
\r
1306 al = editCommand.getAlignment();
\r
1307 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
1308 .getSequenceSetId());
\r
1309 for (int i = 0; i < comps.size(); i++)
\r
1311 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
1313 if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
\r
1315 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
\r
1322 if (originalSource == null)
\r
1324 // The original view is closed, we must validate
\r
1325 // the current view against the closed view first
\r
1328 PaintRefresher.validateSequences(al, viewport.alignment);
\r
1331 originalSource = viewport;
\r
1334 return originalSource;
\r
1337 public void moveSelectedSequences(boolean up)
\r
1339 SequenceGroup sg = viewport.getSelectionGroup();
\r
1347 for (int i = 1; i < viewport.alignment.getHeight(); i++)
\r
1349 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
1350 if (!sg.getSequences(null).contains(seq))
\r
1355 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
\r
1356 if (sg.getSequences(null).contains(temp))
\r
1361 viewport.alignment.getSequences().setElementAt(temp, i);
\r
1362 viewport.alignment.getSequences().setElementAt(seq, i - 1);
\r
1367 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
\r
1369 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
1370 if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))
\r
1375 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
\r
1376 if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))
\r
1381 viewport.alignment.getSequences().setElementAt(temp, i);
\r
1382 viewport.alignment.getSequences().setElementAt(seq, i + 1);
\r
1386 alignPanel.paintAlignment(true);
\r
1389 synchronized void slideSequences(boolean right, int size)
\r
1391 Vector sg = new Vector();
\r
1392 if (viewport.cursorMode)
\r
1394 sg.addElement(viewport.alignment
\r
1395 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
\r
1397 else if (viewport.getSelectionGroup() != null
\r
1398 && viewport.getSelectionGroup().getSize() != viewport.alignment
\r
1401 sg = viewport.getSelectionGroup().getSequences(
\r
1402 viewport.hiddenRepSequences);
\r
1405 if (sg.size() < 1)
\r
1410 Vector invertGroup = new Vector();
\r
1412 for (int i = 0; i < viewport.alignment.getHeight(); i++)
\r
1414 if (!sg.contains(viewport.alignment.getSequenceAt(i)))
\r
1415 invertGroup.addElement(viewport.alignment.getSequenceAt(i));
\r
1418 SequenceI[] seqs1 = new SequenceI[sg.size()];
\r
1419 for (int i = 0; i < sg.size(); i++)
\r
1420 seqs1[i] = (SequenceI) sg.elementAt(i);
\r
1422 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
\r
1423 for (int i = 0; i < invertGroup.size(); i++)
\r
1424 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
\r
1426 SlideSequencesCommand ssc;
\r
1428 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
\r
1429 size, viewport.getGapCharacter());
\r
1431 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
\r
1432 size, viewport.getGapCharacter());
\r
1434 int groupAdjustment = 0;
\r
1435 if (ssc.getGapsInsertedBegin() && right)
\r
1437 if (viewport.cursorMode)
\r
1438 alignPanel.seqPanel.moveCursor(size, 0);
\r
1440 groupAdjustment = size;
\r
1442 else if (!ssc.getGapsInsertedBegin() && !right)
\r
1444 if (viewport.cursorMode)
\r
1445 alignPanel.seqPanel.moveCursor(-size, 0);
\r
1447 groupAdjustment = -size;
\r
1450 if (groupAdjustment != 0)
\r
1452 viewport.getSelectionGroup().setStartRes(
\r
1453 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
\r
1454 viewport.getSelectionGroup().setEndRes(
\r
1455 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
\r
1458 boolean appendHistoryItem = false;
\r
1459 if (viewport.historyList != null && viewport.historyList.size() > 0
\r
1460 && viewport.historyList.peek() instanceof SlideSequencesCommand)
\r
1462 appendHistoryItem = ssc
\r
1463 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
\r
1467 if (!appendHistoryItem)
\r
1468 addHistoryItem(ssc);
\r
1473 static StringBuffer copiedSequences;
\r
1475 static Vector copiedHiddenColumns;
\r
1477 protected void copy_actionPerformed()
\r
1479 if (viewport.getSelectionGroup() == null)
\r
1484 SequenceGroup sg = viewport.getSelectionGroup();
\r
1485 copiedSequences = new StringBuffer();
\r
1486 Hashtable orderedSeqs = new Hashtable();
\r
1487 for (int i = 0; i < sg.getSize(); i++)
\r
1489 SequenceI seq = sg.getSequenceAt(i);
\r
1490 int index = viewport.alignment.findIndex(seq);
\r
1491 orderedSeqs.put(index + "", seq);
\r
1494 int index = 0, startRes, endRes;
\r
1497 if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
\r
1499 copiedHiddenColumns = new Vector();
\r
1500 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
\r
1501 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
\r
1504 int[] region = (int[]) viewport.getColumnSelection()
\r
1505 .getHiddenColumns().elementAt(i);
\r
1507 copiedHiddenColumns.addElement(new int[]
\r
1508 { region[0] - hiddenOffset, region[1] - hiddenOffset });
\r
1513 copiedHiddenColumns = null;
\r
1516 for (int i = 0; i < sg.getSize(); i++)
\r
1518 SequenceI seq = null;
\r
1520 while (seq == null)
\r
1522 if (orderedSeqs.containsKey(index + ""))
\r
1524 seq = (SequenceI) orderedSeqs.get(index + "");
\r
1536 // Returns residue following index if gap
\r
1537 startRes = seq.findPosition(sg.getStartRes());
\r
1540 // Need to find the residue preceeding index if gap
\r
1543 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
\r
1545 ch = seq.getCharAt(j);
\r
1546 if (!jalview.util.Comparison.isGap((ch)))
\r
1554 endRes += seq.getStart() - 1;
\r
1557 copiedSequences.append(seq.getName()
\r
1563 + seq.getSequenceAsString(sg.getStartRes(),
\r
1564 sg.getEndRes() + 1) + "\n");
\r
1569 protected void pasteNew_actionPerformed()
\r
1574 protected void pasteThis_actionPerformed()
\r
1579 void paste(boolean newAlignment)
\r
1584 if (copiedSequences == null)
\r
1589 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
1590 Vector seqs = new Vector();
\r
1591 while (st.hasMoreElements())
\r
1593 String name = st.nextToken();
\r
1594 int start = Integer.parseInt(st.nextToken());
\r
1595 int end = Integer.parseInt(st.nextToken());
\r
1596 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
\r
1598 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
1599 for (int i = 0; i < seqs.size(); i++)
\r
1601 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
1606 String newtitle = new String("Copied sequences");
\r
1607 if (getTitle().startsWith("Copied sequences"))
\r
1609 newtitle = getTitle();
\r
1613 newtitle = newtitle.concat("- from " + getTitle());
\r
1615 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
1616 viewport.applet, newtitle, false);
\r
1617 if (copiedHiddenColumns != null)
\r
1619 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
1621 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
1622 af.viewport.hideColumns(region[0], region[1]);
\r
1626 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
\r
1631 addSequences(newSeqs);
\r
1634 } catch (Exception ex)
\r
1636 } // could be anything being pasted in here
\r
1640 void addSequences(SequenceI[] seqs)
\r
1642 for (int i = 0; i < seqs.length; i++)
\r
1644 viewport.alignment.addSequence(seqs[i]);
\r
1648 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
\r
1649 seqs, 0, viewport.alignment.getWidth(), viewport.alignment));
\r
1651 viewport.setEndSeq(viewport.alignment.getHeight());
\r
1652 viewport.alignment.getWidth();
\r
1653 viewport.firePropertyChange("alignment", null,
\r
1654 viewport.alignment.getSequences());
\r
1658 protected void cut_actionPerformed()
\r
1660 copy_actionPerformed();
\r
1661 delete_actionPerformed();
\r
1664 protected void delete_actionPerformed()
\r
1667 SequenceGroup sg = viewport.getSelectionGroup();
\r
1673 Vector seqs = new Vector();
\r
1675 for (int i = 0; i < sg.getSize(); i++)
\r
1677 seq = sg.getSequenceAt(i);
\r
1678 seqs.addElement(seq);
\r
1681 // If the cut affects all sequences, remove highlighted columns
\r
1682 if (sg.getSize() == viewport.alignment.getHeight())
\r
1684 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
1685 sg.getEndRes() + 1);
\r
1688 SequenceI[] cut = new SequenceI[seqs.size()];
\r
1689 for (int i = 0; i < seqs.size(); i++)
\r
1691 cut[i] = (SequenceI) seqs.elementAt(i);
\r
1695 * //ADD HISTORY ITEM
\r
1697 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
\r
1698 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
\r
1699 viewport.alignment));
\r
1701 viewport.setSelectionGroup(null);
\r
1702 viewport.alignment.deleteGroup(sg);
\r
1704 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1707 if (viewport.getAlignment().getHeight() < 1)
\r
1709 this.setVisible(false);
\r
1711 viewport.sendSelection();
\r
1715 * group consensus toggled
\r
1718 protected void showGroupConsensus_actionPerformed()
\r
1720 viewport.setShowGroupConsensus(showGroupConsensus.getState());
\r
1721 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1726 * group conservation toggled.
\r
1728 protected void showGroupConservation_actionPerformed()
\r
1730 viewport.setShowGroupConservation(showGroupConservation.getState());
\r
1731 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1738 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
\r
1739 * .event.ActionEvent)
\r
1741 protected void showConsensusHistogram_actionPerformed()
\r
1743 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
\r
1744 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1750 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
\r
1751 * .event.ActionEvent)
\r
1753 protected void showSequenceLogo_actionPerformed()
\r
1755 viewport.setShowSequenceLogo(showSequenceLogo.getState());
\r
1756 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1759 protected void applyAutoAnnotationSettings_actionPerformed()
\r
1761 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1764 protected void makeGrpsFromSelection_actionPerformed()
\r
1766 if (viewport.getSelectionGroup() != null)
\r
1768 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
\r
1769 viewport.getSequenceSelection(),
\r
1770 viewport.getAlignmentView(true).getSequenceStrings(
\r
1771 viewport.getGapCharacter()),
\r
1772 viewport.alignment.getGroups());
\r
1773 viewport.alignment.deleteAllGroups();
\r
1774 viewport.sequenceColours = null;
\r
1775 viewport.setSelectionGroup(null);
\r
1776 // set view properties for each group
\r
1777 for (int g = 0; g < gps.length; g++)
\r
1779 // gps[g].setShowunconserved(viewport.getShowUnconserved());
\r
1780 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
\r
1781 viewport.alignment.addGroup(gps[g]);
\r
1782 Color col = new Color((int) (Math.random() * 255),
\r
1783 (int) (Math.random() * 255), (int) (Math.random() * 255));
\r
1784 col = col.brighter();
\r
1785 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
\r
1786 .hasMoreElements(); viewport.setSequenceColour(
\r
1787 (SequenceI) sq.nextElement(), col))
\r
1790 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
\r
1791 alignPanel.updateAnnotation();
\r
1792 alignPanel.paintAlignment(true);
\r
1796 protected void deleteGroups_actionPerformed()
\r
1798 viewport.alignment.deleteAllGroups();
\r
1799 viewport.sequenceColours = null;
\r
1800 viewport.setSelectionGroup(null);
\r
1802 alignPanel.paintAlignment(true);
\r
1805 public void selectAllSequenceMenuItem_actionPerformed()
\r
1807 SequenceGroup sg = new SequenceGroup();
\r
1808 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1810 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
1812 sg.setEndRes(viewport.alignment.getWidth() - 1);
\r
1813 viewport.setSelectionGroup(sg);
\r
1814 alignPanel.paintAlignment(true);
\r
1815 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1816 viewport.sendSelection();
\r
1819 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1821 if (viewport.cursorMode)
\r
1823 alignPanel.seqPanel.keyboardNo1 = null;
\r
1824 alignPanel.seqPanel.keyboardNo2 = null;
\r
1826 viewport.setSelectionGroup(null);
\r
1827 viewport.getColumnSelection().clear();
\r
1828 viewport.setSelectionGroup(null);
\r
1829 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1830 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1831 alignPanel.paintAlignment(true);
\r
1832 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1833 viewport.sendSelection();
\r
1836 public void invertSequenceMenuItem_actionPerformed()
\r
1838 SequenceGroup sg = viewport.getSelectionGroup();
\r
1839 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1841 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1844 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1845 viewport.sendSelection();
\r
1848 public void invertColSel_actionPerformed()
\r
1850 viewport.invertColumnSelection();
\r
1851 alignPanel.paintAlignment(true);
\r
1852 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1853 viewport.sendSelection();
\r
1856 void trimAlignment(boolean trimLeft)
\r
1858 ColumnSelection colSel = viewport.getColumnSelection();
\r
1861 if (colSel.size() > 0)
\r
1865 column = colSel.getMin();
\r
1869 column = colSel.getMax();
\r
1873 if (viewport.getSelectionGroup() != null)
\r
1875 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
1876 viewport.hiddenRepSequences);
\r
1880 seqs = viewport.alignment.getSequencesArray();
\r
1883 TrimRegionCommand trimRegion;
\r
1886 trimRegion = new TrimRegionCommand("Remove Left",
\r
1887 TrimRegionCommand.TRIM_LEFT, seqs, column,
\r
1888 viewport.alignment, viewport.colSel,
\r
1889 viewport.selectionGroup);
\r
1890 viewport.setStartRes(0);
\r
1894 trimRegion = new TrimRegionCommand("Remove Right",
\r
1895 TrimRegionCommand.TRIM_RIGHT, seqs, column,
\r
1896 viewport.alignment, viewport.colSel,
\r
1897 viewport.selectionGroup);
\r
1900 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
\r
1902 addHistoryItem(trimRegion);
\r
1904 Vector groups = viewport.alignment.getGroups();
\r
1906 for (int i = 0; i < groups.size(); i++)
\r
1908 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1910 if ((trimLeft && !sg.adjustForRemoveLeft(column))
\r
1911 || (!trimLeft && !sg.adjustForRemoveRight(column)))
\r
1913 viewport.alignment.deleteGroup(sg);
\r
1917 viewport.firePropertyChange("alignment", null, viewport
\r
1918 .getAlignment().getSequences());
\r
1922 public void removeGappedColumnMenuItem_actionPerformed()
\r
1924 int start = 0, end = viewport.alignment.getWidth() - 1;
\r
1927 if (viewport.getSelectionGroup() != null)
\r
1929 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
1930 viewport.hiddenRepSequences);
\r
1931 start = viewport.getSelectionGroup().getStartRes();
\r
1932 end = viewport.getSelectionGroup().getEndRes();
\r
1936 seqs = viewport.alignment.getSequencesArray();
\r
1939 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
\r
1940 "Remove Gapped Columns", seqs, start, end, viewport.alignment);
\r
1942 addHistoryItem(removeGapCols);
\r
1944 statusBar.setText("Removed " + removeGapCols.getSize()
\r
1945 + " empty columns.");
\r
1947 // This is to maintain viewport position on first residue
\r
1948 // of first sequence
\r
1949 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1950 int startRes = seq.findPosition(viewport.startRes);
\r
1951 // ShiftList shifts;
\r
1952 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
\r
1953 // edit.alColumnChanges=shifts.getInverse();
\r
1954 // if (viewport.hasHiddenColumns)
\r
1955 // viewport.getColumnSelection().compensateForEdits(shifts);
\r
1956 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
1957 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1962 public void removeAllGapsMenuItem_actionPerformed()
\r
1964 int start = 0, end = viewport.alignment.getWidth() - 1;
\r
1967 if (viewport.getSelectionGroup() != null)
\r
1969 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
1970 viewport.hiddenRepSequences);
\r
1971 start = viewport.getSelectionGroup().getStartRes();
\r
1972 end = viewport.getSelectionGroup().getEndRes();
\r
1976 seqs = viewport.alignment.getSequencesArray();
\r
1979 // This is to maintain viewport position on first residue
\r
1980 // of first sequence
\r
1981 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1982 int startRes = seq.findPosition(viewport.startRes);
\r
1984 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
\r
1985 viewport.alignment));
\r
1987 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
1989 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1994 public void findMenuItem_actionPerformed()
\r
1996 new Finder(alignPanel);
\r
2000 * create a new view derived from the current view
\r
2002 * @param viewtitle
\r
2003 * @return frame for the new view
\r
2005 public AlignFrame newView(String viewtitle)
\r
2008 if (viewport.hasHiddenRows)
\r
2010 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
\r
2011 .getFullAlignment().getSequencesArray());
\r
2015 newal = new Alignment(viewport.alignment.getSequencesArray());
\r
2018 if (viewport.alignment.getAlignmentAnnotation() != null)
\r
2020 for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)
\r
2022 if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
\r
2024 newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);
\r
2029 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
\r
2031 newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
\r
2032 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
\r
2033 PaintRefresher.Register(newaf.alignPanel,
\r
2034 newaf.alignPanel.av.getSequenceSetId());
\r
2036 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
\r
2037 newaf.alignPanel.av.getSequenceSetId());
\r
2038 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
\r
2039 newaf.alignPanel.av.getSequenceSetId());
\r
2041 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
2042 .getSequenceSetId());
\r
2043 int viewSize = -1;
\r
2044 for (int i = 0; i < comps.size(); i++)
\r
2046 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
2052 String title = new String(this.getTitle());
\r
2053 if (viewtitle != null)
\r
2055 title = viewtitle + " ( " + title + ")";
\r
2059 if (title.indexOf("(View") > -1)
\r
2061 title = title.substring(0, title.indexOf("(View"));
\r
2063 title += "(View " + viewSize + ")";
\r
2066 newaf.setTitle(title.toString());
\r
2068 newaf.viewport.historyList = viewport.historyList;
\r
2069 newaf.viewport.redoList = viewport.redoList;
\r
2075 * @return list of feature groups on the view
\r
2077 public String[] getFeatureGroups()
\r
2079 FeatureRenderer fr = null;
\r
2080 if (alignPanel != null
\r
2081 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2083 return fr.getGroups();
\r
2089 * get sequence feature groups that are hidden or shown
\r
2095 public String[] getFeatureGroupsOfState(boolean visible)
\r
2097 FeatureRenderer fr = null;
\r
2098 if (alignPanel != null
\r
2099 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2101 return fr.getGroups(visible);
\r
2107 * Change the display state for the given feature groups
\r
2110 * list of group strings
\r
2112 * visible or invisible
\r
2114 public void setFeatureGroupState(String[] groups, boolean state)
\r
2116 FeatureRenderer fr = null;
\r
2117 this.sequenceFeatures.setState(true);
\r
2118 viewport.showSequenceFeatures(true);
\r
2119 if (alignPanel != null
\r
2120 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2122 fr.setGroupState(groups, state);
\r
2123 alignPanel.seqPanel.seqCanvas.repaint();
\r
2124 if (alignPanel.overviewPanel != null)
\r
2126 alignPanel.overviewPanel.updateOverviewImage();
\r
2131 public void seqLimits_itemStateChanged()
\r
2133 viewport.setShowJVSuffix(seqLimits.getState());
\r
2134 alignPanel.fontChanged();
\r
2135 alignPanel.paintAlignment(true);
\r
2138 protected void colourTextMenuItem_actionPerformed()
\r
2140 viewport.setColourText(colourTextMenuItem.getState());
\r
2141 alignPanel.paintAlignment(true);
\r
2144 protected void displayNonconservedMenuItem_actionPerformed()
\r
2146 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
\r
2147 alignPanel.paintAlignment(true);
\r
2150 protected void wrapMenuItem_actionPerformed()
\r
2152 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
2153 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
2154 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
2155 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
2156 scaleRight.setEnabled(wrapMenuItem.getState());
\r
2157 alignPanel.paintAlignment(true);
\r
2160 public void overviewMenuItem_actionPerformed()
\r
2162 if (alignPanel.overviewPanel != null)
\r
2167 Frame frame = new Frame();
\r
2168 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
2169 frame.add(overview);
\r
2170 // +50 must allow for applet frame window
\r
2171 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
2172 overview.getPreferredSize().width,
\r
2173 overview.getPreferredSize().height + 50);
\r
2176 frame.addWindowListener(new WindowAdapter()
\r
2178 public void windowClosing(WindowEvent e)
\r
2180 alignPanel.setOverviewPanel(null);
\r
2184 alignPanel.setOverviewPanel(overview);
\r
2188 void changeColour(ColourSchemeI cs)
\r
2190 int threshold = 0;
\r
2194 if (viewport.getAbovePIDThreshold())
\r
2196 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
2199 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2201 viewport.setGlobalColourScheme(cs);
\r
2205 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2208 if (viewport.getConservationSelected())
\r
2211 Alignment al = (Alignment) viewport.alignment;
\r
2212 Conservation c = new Conservation("All",
\r
2213 ResidueProperties.propHash, 3, al.getSequences(), 0,
\r
2214 al.getWidth() - 1);
\r
2217 c.verdict(false, viewport.ConsPercGaps);
\r
2219 cs.setConservation(c);
\r
2221 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
\r
2222 cs, "Background"));
\r
2227 cs.setConservation(null);
\r
2230 cs.setConsensus(viewport.hconsensus);
\r
2233 viewport.setGlobalColourScheme(cs);
\r
2235 if (viewport.getColourAppliesToAllGroups())
\r
2237 Vector groups = viewport.alignment.getGroups();
\r
2238 for (int i = 0; i < groups.size(); i++)
\r
2240 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
2247 if (cs instanceof ClustalxColourScheme)
\r
2249 sg.cs = new ClustalxColourScheme(
\r
2250 sg.getSequences(viewport.hiddenRepSequences),
\r
2257 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
2258 } catch (Exception ex)
\r
2260 ex.printStackTrace();
\r
2265 if (viewport.getAbovePIDThreshold()
\r
2266 || cs instanceof PIDColourScheme
\r
2267 || cs instanceof Blosum62ColourScheme)
\r
2269 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2270 sg.cs.setConsensus(AAFrequency.calculate(
\r
2271 sg.getSequences(viewport.hiddenRepSequences), 0,
\r
2276 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2279 if (viewport.getConservationSelected())
\r
2281 Conservation c = new Conservation("Group",
\r
2282 ResidueProperties.propHash, 3,
\r
2283 sg.getSequences(viewport.hiddenRepSequences), 0,
\r
2284 viewport.alignment.getWidth() - 1);
\r
2286 c.verdict(false, viewport.ConsPercGaps);
\r
2287 sg.cs.setConservation(c);
\r
2291 sg.cs.setConservation(null);
\r
2292 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2298 if (alignPanel.getOverviewPanel() != null)
\r
2300 alignPanel.getOverviewPanel().updateOverviewImage();
\r
2303 jalview.structure.StructureSelectionManager
\r
2304 .getStructureSelectionManager(viewport.applet).sequenceColoursChanged(
\r
2307 alignPanel.paintAlignment(true);
\r
2310 protected void modifyPID_actionPerformed()
\r
2312 if (viewport.getAbovePIDThreshold()
\r
2313 && viewport.globalColourScheme != null)
\r
2315 SliderPanel.setPIDSliderSource(alignPanel,
\r
2316 viewport.getGlobalColourScheme(), "Background");
\r
2317 SliderPanel.showPIDSlider();
\r
2321 protected void modifyConservation_actionPerformed()
\r
2323 if (viewport.getConservationSelected()
\r
2324 && viewport.globalColourScheme != null)
\r
2326 SliderPanel.setConservationSlider(alignPanel,
\r
2327 viewport.globalColourScheme, "Background");
\r
2328 SliderPanel.showConservationSlider();
\r
2332 protected void conservationMenuItem_actionPerformed()
\r
2334 viewport.setConservationSelected(conservationMenuItem.getState());
\r
2336 viewport.setAbovePIDThreshold(false);
\r
2337 abovePIDThreshold.setState(false);
\r
2339 changeColour(viewport.getGlobalColourScheme());
\r
2341 modifyConservation_actionPerformed();
\r
2344 public void abovePIDThreshold_actionPerformed()
\r
2346 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
2348 conservationMenuItem.setState(false);
\r
2349 viewport.setConservationSelected(false);
\r
2351 changeColour(viewport.getGlobalColourScheme());
\r
2353 modifyPID_actionPerformed();
\r
2356 public void sortPairwiseMenuItem_actionPerformed()
\r
2358 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2359 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
\r
2360 .getAlignment().getSequenceAt(0), null);
\r
2362 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
\r
2363 viewport.alignment));
\r
2364 alignPanel.paintAlignment(true);
\r
2367 public void sortIDMenuItem_actionPerformed()
\r
2369 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2370 AlignmentSorter.sortByID(viewport.getAlignment());
\r
2371 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
\r
2372 alignPanel.paintAlignment(true);
\r
2375 public void sortLengthMenuItem_actionPerformed()
\r
2377 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2378 AlignmentSorter.sortByLength(viewport.getAlignment());
\r
2379 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
\r
2380 viewport.alignment));
\r
2381 alignPanel.paintAlignment(true);
\r
2384 public void sortGroupMenuItem_actionPerformed()
\r
2386 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2387 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
2388 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
\r
2389 viewport.alignment));
\r
2390 alignPanel.paintAlignment(true);
\r
2394 public void removeRedundancyMenuItem_actionPerformed()
\r
2396 new RedundancyPanel(alignPanel);
\r
2399 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
2401 if (viewport.getSelectionGroup() != null
\r
2402 && viewport.getSelectionGroup().getSize() > 1)
\r
2404 Frame frame = new Frame();
\r
2405 frame.add(new PairwiseAlignPanel(alignPanel));
\r
2406 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
\r
2411 public void PCAMenuItem_actionPerformed()
\r
2413 // are the sequences aligned?
\r
2414 if (!viewport.alignment.isAligned(false))
\r
2416 SequenceI current;
\r
2417 int Width = viewport.getAlignment().getWidth();
\r
2419 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2421 current = viewport.getAlignment().getSequenceAt(i);
\r
2423 if (current.getLength() < Width)
\r
2425 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2428 alignPanel.paintAlignment(true);
\r
2431 if ((viewport.getSelectionGroup() != null
\r
2432 && viewport.getSelectionGroup().getSize() < 4 && viewport
\r
2433 .getSelectionGroup().getSize() > 0)
\r
2434 || viewport.getAlignment().getHeight() < 4)
\r
2441 new PCAPanel(viewport);
\r
2442 } catch (java.lang.OutOfMemoryError ex)
\r
2448 public void averageDistanceTreeMenuItem_actionPerformed()
\r
2450 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
2453 public void neighbourTreeMenuItem_actionPerformed()
\r
2455 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
2458 protected void njTreeBlosumMenuItem_actionPerformed()
\r
2460 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2463 protected void avTreeBlosumMenuItem_actionPerformed()
\r
2465 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2468 void NewTreePanel(String type, String pwType, String title)
\r
2470 // are the sequences aligned?
\r
2471 if (!viewport.alignment.isAligned(false))
\r
2473 SequenceI current;
\r
2474 int Width = viewport.getAlignment().getWidth();
\r
2476 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2478 current = viewport.getAlignment().getSequenceAt(i);
\r
2480 if (current.getLength() < Width)
\r
2482 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2485 alignPanel.paintAlignment(true);
\r
2489 if ((viewport.getSelectionGroup() != null && viewport
\r
2490 .getSelectionGroup().getSize() > 1)
\r
2491 || (viewport.getSelectionGroup() == null && viewport.alignment
\r
2492 .getHeight() > 1))
\r
2494 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
\r
2496 addTreeMenuItem(tp, title);
\r
2498 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
2502 void loadTree_actionPerformed()
\r
2504 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
2505 cap.setText("Paste your Newick tree file here.");
\r
2506 cap.setTreeImport();
\r
2507 Frame frame = new Frame();
\r
2509 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
2512 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
2514 TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
\r
2515 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
2516 addTreeMenuItem(tp, treeFile);
\r
2520 * sort the alignment using the given treePanel
\r
2522 * @param treePanel
\r
2523 * tree used to sort view
\r
2525 * string used for undo event name
\r
2527 public void sortByTree(TreePanel treePanel, String title)
\r
2529 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2531 .sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
2532 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2533 // HistoryItem.SORT));
\r
2534 addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
\r
2535 viewport.alignment));
\r
2536 alignPanel.paintAlignment(true);
\r
2540 * Do any automatic reordering of the alignment and add the necessary bits to
\r
2541 * the menu structure for the new tree
\r
2543 * @param treePanel
\r
2546 protected void addTreeMenuItem(final TreePanel treePanel,
\r
2547 final String title)
\r
2549 final MenuItem item = new MenuItem(title);
\r
2550 sortByTreeMenu.add(item);
\r
2551 item.addActionListener(new java.awt.event.ActionListener()
\r
2553 public void actionPerformed(ActionEvent evt)
\r
2555 sortByTree(treePanel, title); // treePanel.getTitle());
\r
2559 treePanel.addWindowListener(new WindowAdapter()
\r
2561 public void windowOpened(WindowEvent e)
\r
2563 if (viewport.sortByTree)
\r
2565 sortByTree(treePanel, title);
\r
2567 super.windowOpened(e);
\r
2570 public void windowClosing(WindowEvent e)
\r
2572 sortByTreeMenu.remove(item);
\r
2576 public boolean sortBy(AlignmentOrder alorder, String undoname)
\r
2578 SequenceI[] oldOrder = viewport.getAlignment()
\r
2579 .getSequencesArray();
\r
2580 if (viewport.applet.debug)
\r
2582 System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");
\r
2584 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
\r
2585 if (undoname!=null)
\r
2587 addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.alignment));
\r
2589 alignPanel.paintAlignment(true);
\r
2593 protected void documentation_actionPerformed()
\r
2595 alignPanel.av.applet.openJalviewHelpUrl();
\r
2598 protected void about_actionPerformed()
\r
2601 class AboutPanel extends Canvas
\r
2607 public AboutPanel(String version, String builddate)
\r
2609 this.version = version;
\r
2610 this.builddate = builddate;
\r
2613 public void paint(Graphics g)
\r
2615 g.setColor(Color.white);
\r
2616 g.fillRect(0, 0, getSize().width, getSize().height);
\r
2617 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2618 FontMetrics fm = g.getFontMetrics();
\r
2619 int fh = fm.getHeight();
\r
2621 g.setColor(Color.black);
\r
2622 // TODO: update this text for each release or centrally store it for
\r
2623 // lite and application
\r
2624 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
2625 g.drawString("JalviewLite - Release " + version, x, y += fh);
\r
2626 g.setFont(new Font("Helvetica", Font.BOLD, 12));
\r
2627 g.drawString("Build date: " + builddate, x, y += fh);
\r
2628 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2630 "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",
\r
2631 x, y += fh * 1.5);
\r
2632 g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
\r
2634 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
\r
2637 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
\r
2639 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
\r
2641 "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
\r
2644 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
\r
2646 g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
\r
2651 Frame frame = new Frame();
\r
2652 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
\r
2653 .getBuildDate()));
\r
2654 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
\r
2658 public void showURL(String url, String target)
\r
2660 if (viewport.applet == null)
\r
2662 System.out.println("Not running as applet - no browser available.");
\r
2666 viewport.applet.showURL(url, target);
\r
2670 // ////////////////////////////////////////////////////////////////////////////////
\r
2671 // JBuilder Graphics here
\r
2673 MenuBar alignFrameMenuBar = new MenuBar();
\r
2675 Menu fileMenu = new Menu("File");
\r
2677 MenuItem loadApplication = new MenuItem("View in Full Application");
\r
2679 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
\r
2681 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
\r
2683 MenuItem outputFeatures = new MenuItem("Export Features ...");
\r
2685 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
\r
2687 MenuItem closeMenuItem = new MenuItem("Close");
\r
2689 Menu editMenu = new Menu("Edit");
\r
2691 Menu viewMenu = new Menu("View");
\r
2693 Menu colourMenu = new Menu("Colour");
\r
2695 Menu calculateMenu = new Menu("Calculate");
\r
2697 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
2699 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
2701 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
2703 MenuItem remove2LeftMenuItem = new MenuItem();
\r
2705 MenuItem remove2RightMenuItem = new MenuItem();
\r
2707 MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
2709 MenuItem removeAllGapsMenuItem = new MenuItem();
\r
2711 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
2713 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
2715 MenuItem sortPairwiseMenuItem = new MenuItem();
\r
2717 MenuItem sortIDMenuItem = new MenuItem();
\r
2719 MenuItem sortLengthMenuItem = new MenuItem();
\r
2721 MenuItem sortGroupMenuItem = new MenuItem();
\r
2723 MenuItem removeRedundancyMenuItem = new MenuItem();
\r
2725 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
2727 MenuItem PCAMenuItem = new MenuItem();
\r
2729 MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
2731 MenuItem neighbourTreeMenuItem = new MenuItem();
\r
2733 BorderLayout borderLayout1 = new BorderLayout();
\r
2735 public Label statusBar = new Label();
\r
2737 Menu outputTextboxMenu = new Menu();
\r
2739 MenuItem clustalColour = new MenuItem();
\r
2741 MenuItem zappoColour = new MenuItem();
\r
2743 MenuItem taylorColour = new MenuItem();
\r
2745 MenuItem hydrophobicityColour = new MenuItem();
\r
2747 MenuItem helixColour = new MenuItem();
\r
2749 MenuItem strandColour = new MenuItem();
\r
2751 MenuItem turnColour = new MenuItem();
\r
2753 MenuItem buriedColour = new MenuItem();
\r
2755 MenuItem userDefinedColour = new MenuItem();
\r
2757 MenuItem PIDColour = new MenuItem();
\r
2759 MenuItem BLOSUM62Colour = new MenuItem();
\r
2761 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
2763 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
2765 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
2767 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
2769 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
\r
2771 MenuItem alProperties = new MenuItem("Alignment Properties...");
\r
2773 MenuItem overviewMenuItem = new MenuItem();
\r
2775 MenuItem undoMenuItem = new MenuItem();
\r
2777 MenuItem redoMenuItem = new MenuItem();
\r
2779 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
2781 MenuItem noColourmenuItem = new MenuItem();
\r
2783 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
2785 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
2787 MenuItem findMenuItem = new MenuItem();
\r
2789 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
2791 MenuItem nucleotideColour = new MenuItem();
\r
2793 MenuItem deleteGroups = new MenuItem();
\r
2795 MenuItem grpsFromSelection = new MenuItem();
\r
2797 MenuItem delete = new MenuItem();
\r
2799 MenuItem copy = new MenuItem();
\r
2801 MenuItem cut = new MenuItem();
\r
2803 Menu pasteMenu = new Menu();
\r
2805 MenuItem pasteNew = new MenuItem();
\r
2807 MenuItem pasteThis = new MenuItem();
\r
2809 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
2811 MenuItem font = new MenuItem();
\r
2813 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
2815 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
2817 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
2819 MenuItem modifyPID = new MenuItem();
\r
2821 MenuItem modifyConservation = new MenuItem();
\r
2823 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
\r
2824 "Autocalculate Consensus", true);
\r
2826 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
\r
2827 "Sort Alignment With New Tree", true);
\r
2829 Menu sortByTreeMenu = new Menu();
\r
2831 Menu sort = new Menu();
\r
2833 Menu calculate = new Menu();
\r
2835 MenuItem inputText = new MenuItem();
\r
2837 Menu helpMenu = new Menu();
\r
2839 MenuItem documentation = new MenuItem();
\r
2841 MenuItem about = new MenuItem();
\r
2843 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
2845 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
\r
2847 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
\r
2848 Menu autoAnnMenu=new Menu();
\r
2849 CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();
\r
2850 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
\r
2851 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
\r
2852 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
\r
2853 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
\r
2855 private void jbInit() throws Exception
\r
2858 setMenuBar(alignFrameMenuBar);
\r
2862 // dynamically fill save as menu with available formats
\r
2863 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
2866 item = new MenuItem(
\r
2867 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
2869 item.addActionListener(new java.awt.event.ActionListener()
\r
2871 public void actionPerformed(ActionEvent e)
\r
2873 outputText_actionPerformed(e);
\r
2877 outputTextboxMenu.add(item);
\r
2879 closeMenuItem.addActionListener(this);
\r
2880 loadApplication.addActionListener(this);
\r
2882 loadTree.addActionListener(this);
\r
2883 loadAnnotations.addActionListener(this);
\r
2884 outputFeatures.addActionListener(this);
\r
2885 outputAnnotations.addActionListener(this);
\r
2886 selectAllSequenceMenuItem.addActionListener(this);
\r
2887 deselectAllSequenceMenuItem.addActionListener(this);
\r
2888 invertSequenceMenuItem.addActionListener(this);
\r
2889 remove2LeftMenuItem.setLabel("Remove Left");
\r
2890 remove2LeftMenuItem.addActionListener(this);
\r
2891 remove2RightMenuItem.setLabel("Remove Right");
\r
2892 remove2RightMenuItem.addActionListener(this);
\r
2893 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
2894 removeGappedColumnMenuItem.addActionListener(this);
\r
2895 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
2896 removeAllGapsMenuItem.addActionListener(this);
\r
2897 viewBoxesMenuItem.setLabel("Boxes");
\r
2898 viewBoxesMenuItem.setState(true);
\r
2899 viewBoxesMenuItem.addItemListener(this);
\r
2900 viewTextMenuItem.setLabel("Text");
\r
2901 viewTextMenuItem.setState(true);
\r
2902 viewTextMenuItem.addItemListener(this);
\r
2903 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
2904 sortPairwiseMenuItem.addActionListener(this);
\r
2905 sortIDMenuItem.setLabel("by ID");
\r
2906 sortIDMenuItem.addActionListener(this);
\r
2907 sortLengthMenuItem.setLabel("by Length");
\r
2908 sortLengthMenuItem.addActionListener(this);
\r
2909 sortGroupMenuItem.setLabel("by Group");
\r
2910 sortGroupMenuItem.addActionListener(this);
\r
2911 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
2912 removeRedundancyMenuItem.addActionListener(this);
\r
2913 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
2914 pairwiseAlignmentMenuItem.addActionListener(this);
\r
2915 PCAMenuItem.setLabel("Principal Component Analysis");
\r
2916 PCAMenuItem.addActionListener(this);
\r
2917 averageDistanceTreeMenuItem
\r
2918 .setLabel("Average Distance Using % Identity");
\r
2919 averageDistanceTreeMenuItem.addActionListener(this);
\r
2920 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
2921 neighbourTreeMenuItem.addActionListener(this);
\r
2922 statusBar.setBackground(Color.white);
\r
2923 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
2924 statusBar.setText("Status bar");
\r
2925 outputTextboxMenu.setLabel("Output to Textbox");
\r
2926 clustalColour.setLabel("Clustalx");
\r
2928 clustalColour.addActionListener(this);
\r
2929 zappoColour.setLabel("Zappo");
\r
2930 zappoColour.addActionListener(this);
\r
2931 taylorColour.setLabel("Taylor");
\r
2932 taylorColour.addActionListener(this);
\r
2933 hydrophobicityColour.setLabel("Hydrophobicity");
\r
2934 hydrophobicityColour.addActionListener(this);
\r
2935 helixColour.setLabel("Helix Propensity");
\r
2936 helixColour.addActionListener(this);
\r
2937 strandColour.setLabel("Strand Propensity");
\r
2938 strandColour.addActionListener(this);
\r
2939 turnColour.setLabel("Turn Propensity");
\r
2940 turnColour.addActionListener(this);
\r
2941 buriedColour.setLabel("Buried Index");
\r
2942 buriedColour.addActionListener(this);
\r
2943 userDefinedColour.setLabel("User Defined...");
\r
2944 userDefinedColour.addActionListener(this);
\r
2945 PIDColour.setLabel("Percentage Identity");
\r
2946 PIDColour.addActionListener(this);
\r
2947 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
2948 BLOSUM62Colour.addActionListener(this);
\r
2949 avDistanceTreeBlosumMenuItem
\r
2950 .setLabel("Average Distance Using BLOSUM62");
\r
2951 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
2952 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
2953 njTreeBlosumMenuItem.addActionListener(this);
\r
2954 annotationPanelMenuItem.setLabel("Show Annotations");
\r
2955 annotationPanelMenuItem.addItemListener(this);
\r
2956 colourTextMenuItem.setLabel("Colour Text");
\r
2957 colourTextMenuItem.addItemListener(this);
\r
2958 displayNonconservedMenuItem.setLabel("Show nonconserved");
\r
2959 displayNonconservedMenuItem.addItemListener(this);
\r
2960 alProperties.addActionListener(this);
\r
2961 overviewMenuItem.setLabel("Overview Window");
\r
2962 overviewMenuItem.addActionListener(this);
\r
2963 undoMenuItem.setEnabled(false);
\r
2964 undoMenuItem.setLabel("Undo");
\r
2965 undoMenuItem.addActionListener(this);
\r
2966 redoMenuItem.setEnabled(false);
\r
2967 redoMenuItem.setLabel("Redo");
\r
2968 redoMenuItem.addActionListener(this);
\r
2969 conservationMenuItem.setLabel("by Conservation");
\r
2970 conservationMenuItem.addItemListener(this);
\r
2971 noColourmenuItem.setLabel("None");
\r
2972 noColourmenuItem.addActionListener(this);
\r
2973 wrapMenuItem.setLabel("Wrap");
\r
2974 wrapMenuItem.addItemListener(this);
\r
2975 renderGapsMenuItem.setLabel("Show Gaps");
\r
2976 renderGapsMenuItem.setState(true);
\r
2977 renderGapsMenuItem.addItemListener(this);
\r
2978 findMenuItem.setLabel("Find...");
\r
2979 findMenuItem.addActionListener(this);
\r
2980 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
2981 abovePIDThreshold.addItemListener(this);
\r
2982 nucleotideColour.setLabel("Nucleotide");
\r
2983 nucleotideColour.addActionListener(this);
\r
2984 deleteGroups.setLabel("Undefine Groups");
\r
2985 deleteGroups.addActionListener(this);
\r
2986 grpsFromSelection.setLabel("Make Groups for selection");
\r
2987 grpsFromSelection.addActionListener(this);
\r
2988 copy.setLabel("Copy");
\r
2989 copy.addActionListener(this);
\r
2990 cut.setLabel("Cut");
\r
2991 cut.addActionListener(this);
\r
2992 delete.setLabel("Delete");
\r
2993 delete.addActionListener(this);
\r
2994 pasteMenu.setLabel("Paste");
\r
2995 pasteNew.setLabel("To New Alignment");
\r
2996 pasteNew.addActionListener(this);
\r
2997 pasteThis.setLabel("Add To This Alignment");
\r
2998 pasteThis.addActionListener(this);
\r
2999 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
3000 applyToAllGroups.setState(true);
\r
3001 applyToAllGroups.addItemListener(this);
\r
3002 font.setLabel("Font...");
\r
3003 font.addActionListener(this);
\r
3004 scaleAbove.setLabel("Scale Above");
\r
3005 scaleAbove.setState(true);
\r
3006 scaleAbove.setEnabled(false);
\r
3007 scaleAbove.addItemListener(this);
\r
3008 scaleLeft.setEnabled(false);
\r
3009 scaleLeft.setState(true);
\r
3010 scaleLeft.setLabel("Scale Left");
\r
3011 scaleLeft.addItemListener(this);
\r
3012 scaleRight.setEnabled(false);
\r
3013 scaleRight.setState(true);
\r
3014 scaleRight.setLabel("Scale Right");
\r
3015 scaleRight.addItemListener(this);
\r
3016 modifyPID.setLabel("Modify Identity Threshold...");
\r
3017 modifyPID.addActionListener(this);
\r
3018 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
3019 modifyConservation.addActionListener(this);
\r
3020 sortByTreeMenu.setLabel("By Tree Order");
\r
3021 sort.setLabel("Sort");
\r
3022 calculate.setLabel("Calculate Tree");
\r
3023 autoCalculate.addItemListener(this);
\r
3024 sortByTree.addItemListener(this);
\r
3025 inputText.setLabel("Input from textbox");
\r
3026 inputText.addActionListener(this);
\r
3027 centreColumnLabelFlag.setLabel("Centre column labels");
\r
3028 centreColumnLabelFlag.addItemListener(this);
\r
3029 followMouseOverFlag.setLabel("Automatic Scrolling");
\r
3030 followMouseOverFlag.addItemListener(this);
\r
3031 helpMenu.setLabel("Help");
\r
3032 documentation.setLabel("Documentation");
\r
3033 documentation.addActionListener(this);
\r
3035 about.setLabel("About...");
\r
3036 about.addActionListener(this);
\r
3037 seqLimits.setState(true);
\r
3038 seqLimits.setLabel("Show Sequence Limits");
\r
3039 seqLimits.addItemListener(this);
\r
3040 featureSettings.setLabel("Feature Settings...");
\r
3041 featureSettings.addActionListener(this);
\r
3042 sequenceFeatures.setLabel("Sequence Features");
\r
3043 sequenceFeatures.addItemListener(this);
\r
3044 sequenceFeatures.setState(false);
\r
3045 annotationColour.setLabel("by Annotation...");
\r
3046 annotationColour.addActionListener(this);
\r
3047 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
3048 invertColSel.setLabel("Invert Column Selection");
\r
3049 menu1.setLabel("Show");
\r
3050 showColumns.setLabel("All Columns ");
\r
3051 showSeqs.setLabel("All Sequences");
\r
3052 menu2.setLabel("Hide");
\r
3053 hideColumns.setLabel("Selected Columns");
\r
3054 hideSequences.setLabel("Selected Sequences");
\r
3055 hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
\r
3056 hideAllSelection.setLabel("Selected Region");
\r
3057 showAllHidden.setLabel("All Sequences and Columns");
\r
3058 showGroupConsensus.setLabel("Group Consensus");
\r
3059 showGroupConservation.setLabel("Group Conservation");
\r
3060 showConsensusHistogram.setLabel("Show Consensus Histogram");
\r
3061 showSequenceLogo.setLabel("Show Consensus Logo");
\r
3062 applyAutoAnnotationSettings.setLabel("Apply to all groups");
\r
3063 applyAutoAnnotationSettings.setState(true);
\r
3064 autoAnnMenu.setLabel("Autocalculated Annotation");
\r
3066 invertColSel.addActionListener(this);
\r
3067 showColumns.addActionListener(this);
\r
3068 showSeqs.addActionListener(this);
\r
3069 hideColumns.addActionListener(this);
\r
3070 hideSequences.addActionListener(this);
\r
3071 hideAllButSelection.addActionListener(this);
\r
3072 hideAllSelection.addActionListener(this);
\r
3073 showAllHidden.addActionListener(this);
\r
3074 showGroupConsensus.addItemListener(this);
\r
3075 showGroupConservation.addItemListener(this);
\r
3076 showConsensusHistogram.addItemListener(this);
\r
3077 showSequenceLogo.addItemListener(this);
\r
3078 applyAutoAnnotationSettings.addItemListener(this);
\r
3079 formatMenu.setLabel("Format");
\r
3080 selectMenu.setLabel("Select");
\r
3081 newView.setLabel("New View");
\r
3082 newView.addActionListener(this);
\r
3083 alignFrameMenuBar.add(fileMenu);
\r
3084 alignFrameMenuBar.add(editMenu);
\r
3085 alignFrameMenuBar.add(selectMenu);
\r
3086 alignFrameMenuBar.add(viewMenu);
\r
3087 alignFrameMenuBar.add(formatMenu);
\r
3088 alignFrameMenuBar.add(colourMenu);
\r
3089 alignFrameMenuBar.add(calculateMenu);
\r
3090 alignFrameMenuBar.add(helpMenu);
\r
3092 fileMenu.add(inputText);
\r
3093 fileMenu.add(loadTree);
\r
3094 fileMenu.add(loadAnnotations);
\r
3096 fileMenu.addSeparator();
\r
3097 fileMenu.add(outputTextboxMenu);
\r
3098 fileMenu.add(outputFeatures);
\r
3099 fileMenu.add(outputAnnotations);
\r
3101 if (jalviewServletURL != null)
\r
3103 fileMenu.add(loadApplication);
\r
3106 fileMenu.addSeparator();
\r
3107 fileMenu.add(closeMenuItem);
\r
3109 editMenu.add(undoMenuItem);
\r
3110 editMenu.add(redoMenuItem);
\r
3111 editMenu.add(cut);
\r
3112 editMenu.add(copy);
\r
3113 editMenu.add(pasteMenu);
\r
3114 editMenu.add(delete);
\r
3115 editMenu.addSeparator();
\r
3116 editMenu.add(remove2LeftMenuItem);
\r
3117 editMenu.add(remove2RightMenuItem);
\r
3118 editMenu.add(removeGappedColumnMenuItem);
\r
3119 editMenu.add(removeAllGapsMenuItem);
\r
3120 editMenu.add(removeRedundancyMenuItem);
\r
3121 viewMenu.add(newView);
\r
3122 viewMenu.addSeparator();
\r
3123 viewMenu.add(menu1);
\r
3124 viewMenu.add(menu2);
\r
3125 viewMenu.addSeparator();
\r
3126 viewMenu.add(followMouseOverFlag);
\r
3127 viewMenu.add(annotationPanelMenuItem);
\r
3128 autoAnnMenu.add(applyAutoAnnotationSettings);
\r
3129 autoAnnMenu.add(showConsensusHistogram);
\r
3130 autoAnnMenu.add(showSequenceLogo);
\r
3131 autoAnnMenu.addSeparator();
\r
3132 autoAnnMenu.add(showGroupConservation);
\r
3133 autoAnnMenu.add(showGroupConsensus);
\r
3134 viewMenu.add(autoAnnMenu);
\r
3135 viewMenu.addSeparator();
\r
3136 viewMenu.add(sequenceFeatures);
\r
3137 viewMenu.add(featureSettings);
\r
3138 viewMenu.addSeparator();
\r
3139 viewMenu.add(alProperties);
\r
3140 viewMenu.addSeparator();
\r
3141 viewMenu.add(overviewMenuItem);
\r
3142 colourMenu.add(applyToAllGroups);
\r
3143 colourMenu.addSeparator();
\r
3144 colourMenu.add(noColourmenuItem);
\r
3145 colourMenu.add(clustalColour);
\r
3146 colourMenu.add(BLOSUM62Colour);
\r
3147 colourMenu.add(PIDColour);
\r
3148 colourMenu.add(zappoColour);
\r
3149 colourMenu.add(taylorColour);
\r
3150 colourMenu.add(hydrophobicityColour);
\r
3151 colourMenu.add(helixColour);
\r
3152 colourMenu.add(strandColour);
\r
3153 colourMenu.add(turnColour);
\r
3154 colourMenu.add(buriedColour);
\r
3155 colourMenu.add(nucleotideColour);
\r
3156 colourMenu.add(userDefinedColour);
\r
3157 colourMenu.addSeparator();
\r
3158 colourMenu.add(conservationMenuItem);
\r
3159 colourMenu.add(modifyConservation);
\r
3160 colourMenu.add(abovePIDThreshold);
\r
3161 colourMenu.add(modifyPID);
\r
3162 colourMenu.add(annotationColour);
\r
3163 calculateMenu.add(sort);
\r
3164 calculateMenu.add(calculate);
\r
3165 calculateMenu.addSeparator();
\r
3166 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
3167 calculateMenu.add(PCAMenuItem);
\r
3168 calculateMenu.add(autoCalculate);
\r
3169 calculateMenu.add(sortByTree);
\r
3170 this.add(statusBar, BorderLayout.SOUTH);
\r
3171 pasteMenu.add(pasteNew);
\r
3172 pasteMenu.add(pasteThis);
\r
3173 sort.add(sortIDMenuItem);
\r
3174 sort.add(sortLengthMenuItem);
\r
3175 sort.add(sortByTreeMenu);
\r
3176 sort.add(sortGroupMenuItem);
\r
3177 sort.add(sortPairwiseMenuItem);
\r
3178 calculate.add(averageDistanceTreeMenuItem);
\r
3179 calculate.add(neighbourTreeMenuItem);
\r
3180 calculate.add(avDistanceTreeBlosumMenuItem);
\r
3181 calculate.add(njTreeBlosumMenuItem);
\r
3182 helpMenu.add(documentation);
\r
3183 helpMenu.add(about);
\r
3184 menu1.add(showColumns);
\r
3185 menu1.add(showSeqs);
\r
3186 menu1.add(showAllHidden);
\r
3187 menu2.add(hideColumns);
\r
3188 menu2.add(hideSequences);
\r
3189 menu2.add(hideAllSelection);
\r
3190 menu2.add(hideAllButSelection);
\r
3191 formatMenu.add(font);
\r
3192 formatMenu.add(seqLimits);
\r
3193 formatMenu.add(wrapMenuItem);
\r
3194 formatMenu.add(scaleAbove);
\r
3195 formatMenu.add(scaleLeft);
\r
3196 formatMenu.add(scaleRight);
\r
3197 formatMenu.add(viewBoxesMenuItem);
\r
3198 formatMenu.add(viewTextMenuItem);
\r
3199 formatMenu.add(colourTextMenuItem);
\r
3200 formatMenu.add(displayNonconservedMenuItem);
\r
3201 formatMenu.add(renderGapsMenuItem);
\r
3202 formatMenu.add(centreColumnLabelFlag);
\r
3203 selectMenu.add(findMenuItem);
\r
3204 selectMenu.addSeparator();
\r
3205 selectMenu.add(selectAllSequenceMenuItem);
\r
3206 selectMenu.add(deselectAllSequenceMenuItem);
\r
3207 selectMenu.add(invertSequenceMenuItem);
\r
3208 selectMenu.add(invertColSel);
\r
3209 selectMenu.add(grpsFromSelection);
\r
3210 selectMenu.add(deleteGroups);
\r
3214 MenuItem featureSettings = new MenuItem();
\r
3216 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
3218 MenuItem annotationColour = new MenuItem();
\r
3220 MenuItem invertColSel = new MenuItem();
\r
3222 Menu menu1 = new Menu();
\r
3224 MenuItem showColumns = new MenuItem();
\r
3226 MenuItem showSeqs = new MenuItem();
\r
3228 Menu menu2 = new Menu();
\r
3230 MenuItem hideColumns = new MenuItem();
\r
3232 MenuItem hideSequences = new MenuItem();
\r
3234 MenuItem hideAllButSelection = new MenuItem();
\r
3236 MenuItem hideAllSelection = new MenuItem();
\r
3238 MenuItem showAllHidden = new MenuItem();
\r
3240 Menu formatMenu = new Menu();
\r
3242 Menu selectMenu = new Menu();
\r
3244 MenuItem newView = new MenuItem();
\r
3247 * Attach the alignFrame panels after embedding menus, if necessary. This used
\r
3248 * to be called setEmbedded, but is now creates the dropdown menus in a
\r
3249 * platform independent manner to avoid OSX/Mac menu appendage daftness.
\r
3251 * @param reallyEmbedded
\r
3252 * true to attach the view to the applet area on the page rather than
\r
3255 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
\r
3257 if (reallyEmbedded)
\r
3260 // Explicly build the embedded menu panel for the on-page applet
\r
3262 // view cannot be closed if its actually on the page
\r
3263 fileMenu.remove(closeMenuItem);
\r
3264 fileMenu.remove(3); // Remove Seperator
\r
3265 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
\r
3266 Font.PLAIN, 10, false); // use our own fonts.
\r
3267 // and actually add the components to the applet area
\r
3268 viewport.applet.setLayout(new BorderLayout());
\r
3269 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
\r
3270 viewport.applet.add(statusBar, BorderLayout.SOUTH);
\r
3271 alignPanel.setSize(viewport.applet.getSize().width,
\r
3272 viewport.applet.getSize().height - embeddedMenu.HEIGHT
\r
3273 - statusBar.HEIGHT);
\r
3274 viewport.applet.add(alignPanel, BorderLayout.CENTER);
\r
3275 final AlignFrame me = this;
\r
3276 viewport.applet.addFocusListener(new FocusListener()
\r
3280 public void focusLost(FocusEvent e)
\r
3282 if (me.viewport.applet.currentAlignFrame==me) {
\r
3283 me.viewport.applet.currentAlignFrame = null;
\r
3287 public void focusGained(FocusEvent e)
\r
3289 me.viewport.applet.currentAlignFrame = me;
\r
3292 viewport.applet.validate();
\r
3297 // test and embed menu bar if necessary.
\r
3299 if (embedMenuIfNeeded(alignPanel))
\r
3301 // adjust for status bar height too
\r
3302 alignPanel.setSize(getSize().width, getSize().height
\r
3303 - statusBar.HEIGHT);
\r
3305 add(statusBar, BorderLayout.SOUTH);
\r
3306 add(alignPanel, BorderLayout.CENTER);
\r
3307 // and register with the applet so it can pass external API calls to us
\r
3308 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
\r
3314 * create a new binding between structures in an existing jmol viewer instance
\r
3315 * and an alignpanel with sequences that have existing PDBFile entries. Note,
\r
3316 * this does not open a new Jmol window, or modify the display of the
\r
3317 * structures in the original jmol window. Note This method doesn't work
\r
3318 * without an additional javascript library to exchange messages between the
\r
3319 * distinct applets. See http://issues.jalview.org/browse/JAL-621
\r
3322 * JmolViewer instance
\r
3323 * @param sequenceIds
\r
3324 * - sequence Ids to search for associations
\r
3326 public SequenceStructureBinding addStructureViewInstance(
\r
3327 Object jmolviewer, String[] sequenceIds)
\r
3329 org.jmol.api.JmolViewer viewer = null;
\r
3332 viewer = (org.jmol.api.JmolViewer) jmolviewer;
\r
3333 } catch (ClassCastException ex)
\r
3335 System.err.println("Unsupported viewer object :"
\r
3336 + jmolviewer.getClass());
\r
3338 if (viewer == null)
\r
3340 System.err.println("Can't use this object as a structure viewer:"
\r
3341 + jmolviewer.getClass());
\r
3344 SequenceI[] seqs = null;
\r
3345 if (sequenceIds == null || sequenceIds.length == 0)
\r
3347 seqs = viewport.getAlignment().getSequencesArray();
\r
3351 Vector sqi = new Vector();
\r
3352 AlignmentI al = viewport.getAlignment();
\r
3353 for (int sid = 0; sid < sequenceIds.length; sid++)
\r
3355 SequenceI sq = al.findName(sequenceIds[sid]);
\r
3358 sqi.addElement(sq);
\r
3361 if (sqi.size() > 0)
\r
3363 seqs = new SequenceI[sqi.size()];
\r
3364 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
\r
3366 seqs[sid] = (SequenceI) sqi.elementAt(sid);
\r
3374 ExtJmol jmv = null;
\r
3375 // TODO: search for a jmv that involves viewer
\r
3377 { // create a new viewer/jalview binding.
\r
3378 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs});
\r
3384 * bind a pdb file to a sequence in the current view
\r
3386 * @param sequenceId
\r
3387 * - sequenceId within the dataset.
\r
3388 * @param pdbEntryString
\r
3389 * - the short name for the PDB file
\r
3391 * - pdb file - either a URL or a valid PDB file.
\r
3392 * @return true if binding was as success TODO: consider making an exception
\r
3393 * structure for indicating when PDB parsing or sequenceId location
\r
3396 public boolean addPdbFile(String sequenceId, String pdbEntryString,
\r
3399 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
\r
3400 boolean needtoadd = false;
\r
3401 if (toaddpdb != null)
\r
3403 Vector pdbe = toaddpdb.getPDBId();
\r
3404 PDBEntry pdbentry = null;
\r
3405 if (pdbe != null && pdbe.size() > 0)
\r
3407 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
\r
3409 pdbentry = (PDBEntry) pdbe.elementAt(pe);
\r
3410 if (!pdbentry.getId().equals(pdbEntryString)
\r
3411 && !pdbentry.getFile().equals(pdbFile))
\r
3421 if (pdbentry == null)
\r
3423 pdbentry = new PDBEntry();
\r
3424 pdbentry.setId(pdbEntryString);
\r
3425 pdbentry.setFile(pdbFile);
\r
3426 needtoadd = true; // add this new entry to sequence.
\r
3428 // resolve data source
\r
3429 // TODO: this code should be a refactored to an io package
\r
3430 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
\r
3431 if (protocol == null)
\r
3437 // make a note of the access mode and add
\r
3438 if (pdbentry.getProperty() == null)
\r
3440 pdbentry.setProperty(new Hashtable());
\r
3442 pdbentry.getProperty().put("protocol", protocol);
\r
3443 toaddpdb.addPDBId(pdbentry);
\r
3449 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
\r
3453 Vector sequences = new Vector();
\r
3454 for (int i = 0; i < seqs.length; i++)
\r
3456 if (seqs[i] != null)
\r
3458 sequences.addElement(new Object[]
\r
3459 { seqs[i], (chains != null) ? chains[i] : null });
\r
3462 seqs = new SequenceI[sequences.size()];
\r
3463 chains = new String[sequences.size()];
\r
3464 for (int i = 0, isize = sequences.size(); i < isize; i++)
\r
3466 Object[] oj = (Object[]) sequences.elementAt(i);
\r
3468 seqs[i] = (SequenceI) oj[0];
\r
3469 chains[i] = (String) oj[1];
\r
3472 return new Object[]
\r
3477 public void newStructureView(JalviewLite applet, PDBEntry pdb,
\r
3478 SequenceI[] seqs, String[] chains, String protocol)
\r
3480 // Scrub any null sequences from the array
\r
3481 Object[] sqch = cleanSeqChainArrays(seqs, chains);
\r
3482 seqs = (SequenceI[]) sqch[0];
\r
3483 chains = (String[]) sqch[1];
\r
3484 if (seqs == null || seqs.length == 0)
\r
3487 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
\r
3489 if (protocol == null || protocol.trim().length() == 0
\r
3490 || protocol.equals("null"))
\r
3492 protocol = (String) pdb.getProperty().get("protocol");
\r
3493 if (protocol == null)
\r
3495 System.err.println("Couldn't work out protocol to open structure: "
\r
3500 if (applet.useXtrnalSviewer)
\r
3502 // register the association(s) and quit, don't create any windows.
\r
3503 if (StructureSelectionManager.getStructureSelectionManager(applet).setMapping(seqs, chains, pdb.getFile(), protocol)==null) {
\r
3504 System.err.println("Failed to map "+pdb.getFile()+" ("+protocol+") to any sequences");
\r
3508 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
\r
3510 // can only do alignments with Jmol
\r
3511 // find the last jmol window assigned to this alignment
\r
3512 jalview.appletgui.AppletJmol ajm = null, tajm;
\r
3513 Vector jmols = applet
\r
3514 .getAppletWindow(jalview.appletgui.AppletJmol.class);
\r
3515 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
\r
3517 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
\r
3518 if (tajm.ap.alignFrame == this)
\r
3527 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
\r
3528 // try and add the pdb structure
\r
3533 // otherwise, create a new window
\r
3534 if (applet.jmolAvailable)
\r
3536 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
\r
3538 applet.lastFrameX += 40;
\r
3539 applet.lastFrameY += 40;
\r
3543 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
\r
3548 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
\r
3549 SequenceI[][] seqs, String[][] chains, String[] protocols)
\r
3551 // TODO Auto-generated method stub
\r
3552 System.err.println("Aligned Structure View: Not yet implemented.");
\r
3556 * modify the current selection, providing the user has not made a selection already.
\r
3557 * @param sel - sequences from this alignment
\r
3558 * @param csel - columns to be selected on the alignment
\r
3560 public void select(SequenceGroup sel, ColumnSelection csel)
\r
3562 alignPanel.seqPanel.selection(sel, csel, null);
\r
3565 public void scrollTo(int row, int column)
\r
3567 alignPanel.seqPanel.scrollTo(row, column);
\r
3569 public void scrollToRow(int row)
\r
3571 alignPanel.seqPanel.scrollToRow(row);
\r
3573 public void scrollToColumn(int column)
\r
3575 alignPanel.seqPanel.scrollToColumn(column);
\r
3578 * @return the alignments unique ID.
\r
3580 public String getSequenceSetId() {
\r
3581 return viewport.getSequenceSetId();
\r