2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
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3 * Copyright (C) 2010 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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147 alignPanel.validate();
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148 alignPanel.paintAlignment(true);
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151 public AlignViewport getAlignViewport()
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156 public SeqCanvas getSeqcanvas()
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158 return alignPanel.seqPanel.seqCanvas;
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168 public void parseFeaturesFile(String file, String type)
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170 Hashtable featureLinks = new Hashtable();
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171 boolean featuresFile = false;
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174 featuresFile = new jalview.io.FeaturesFile(file, type)
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175 .parse(viewport.alignment,
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176 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
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177 featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));
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178 } catch (Exception ex)
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180 ex.printStackTrace();
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185 if (featureLinks.size() > 0)
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187 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
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189 viewport.showSequenceFeatures = true;
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190 sequenceFeatures.setState(true);
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191 if (viewport.featureSettings != null)
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193 viewport.featureSettings.refreshTable();
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195 alignPanel.paintAlignment(true);
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200 public void keyPressed(KeyEvent evt)
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202 if (viewport.cursorMode
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203 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
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204 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
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205 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
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206 && Character.isDigit(evt.getKeyChar()))
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207 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
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209 switch (evt.getKeyCode())
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211 case 27: // escape key
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212 deselectAllSequenceMenuItem_actionPerformed();
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214 alignPanel.alabels.cancelDrag();
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216 case KeyEvent.VK_X:
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217 if (evt.isControlDown() || evt.isMetaDown())
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219 cut_actionPerformed();
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222 case KeyEvent.VK_C:
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223 if (viewport.cursorMode && !evt.isControlDown())
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225 alignPanel.seqPanel.setCursorColumn();
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227 if (evt.isControlDown() || evt.isMetaDown())
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229 copy_actionPerformed();
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232 case KeyEvent.VK_V:
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233 if (evt.isControlDown())
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235 paste(evt.isShiftDown());
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238 case KeyEvent.VK_A:
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239 if (evt.isControlDown() || evt.isMetaDown())
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241 selectAllSequenceMenuItem_actionPerformed();
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244 case KeyEvent.VK_DOWN:
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245 if (viewport.cursorMode)
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247 alignPanel.seqPanel.moveCursor(0, 1);
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251 moveSelectedSequences(false);
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255 case KeyEvent.VK_UP:
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256 if (viewport.cursorMode)
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258 alignPanel.seqPanel.moveCursor(0, -1);
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262 moveSelectedSequences(true);
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266 case KeyEvent.VK_LEFT:
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267 if (evt.isAltDown() || !viewport.cursorMode)
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268 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
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270 alignPanel.seqPanel.moveCursor(-1, 0);
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273 case KeyEvent.VK_RIGHT:
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274 if (evt.isAltDown() || !viewport.cursorMode)
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275 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
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277 alignPanel.seqPanel.moveCursor(1, 0);
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280 case KeyEvent.VK_SPACE:
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281 if (viewport.cursorMode)
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283 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
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284 || evt.isShiftDown() || evt.isAltDown());
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288 case KeyEvent.VK_DELETE:
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289 case KeyEvent.VK_BACK_SPACE:
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290 if (viewport.cursorMode)
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292 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
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293 || evt.isShiftDown() || evt.isAltDown());
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297 cut_actionPerformed();
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298 alignPanel.seqPanel.seqCanvas.repaint();
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302 case KeyEvent.VK_S:
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303 if (viewport.cursorMode)
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305 alignPanel.seqPanel.setCursorRow();
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308 case KeyEvent.VK_P:
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309 if (viewport.cursorMode)
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311 alignPanel.seqPanel.setCursorPosition();
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315 case KeyEvent.VK_ENTER:
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316 case KeyEvent.VK_COMMA:
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317 if (viewport.cursorMode)
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319 alignPanel.seqPanel.setCursorRowAndColumn();
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323 case KeyEvent.VK_Q:
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324 if (viewport.cursorMode)
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326 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
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329 case KeyEvent.VK_M:
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330 if (viewport.cursorMode)
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332 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
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336 case KeyEvent.VK_F2:
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337 viewport.cursorMode = !viewport.cursorMode;
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338 statusBar.setText("Keyboard editing mode is "
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339 + (viewport.cursorMode ? "on" : "off"));
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340 if (viewport.cursorMode)
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342 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
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343 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
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347 case KeyEvent.VK_F:
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348 if (evt.isControlDown())
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350 findMenuItem_actionPerformed();
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354 case KeyEvent.VK_H:
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356 boolean toggleSeqs = !evt.isControlDown();
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357 boolean toggleCols = !evt.isShiftDown();
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358 toggleHiddenRegions(toggleSeqs, toggleCols);
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362 case KeyEvent.VK_PAGE_UP:
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363 if (viewport.wrapAlignment)
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365 alignPanel.scrollUp(true);
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369 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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370 - viewport.endSeq + viewport.startSeq);
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374 case KeyEvent.VK_PAGE_DOWN:
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375 if (viewport.wrapAlignment)
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377 alignPanel.scrollUp(false);
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381 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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382 + viewport.endSeq - viewport.startSeq);
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386 case KeyEvent.VK_Z:
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387 if (evt.isControlDown())
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389 undoMenuItem_actionPerformed();
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393 case KeyEvent.VK_Y:
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394 if (evt.isControlDown())
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396 redoMenuItem_actionPerformed();
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400 case KeyEvent.VK_L:
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401 if (evt.isControlDown())
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403 trimAlignment(true);
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407 case KeyEvent.VK_R:
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408 if (evt.isControlDown())
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410 trimAlignment(false);
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414 case KeyEvent.VK_E:
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415 if (evt.isControlDown())
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417 if (evt.isShiftDown())
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419 this.removeAllGapsMenuItem_actionPerformed();
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423 removeGappedColumnMenuItem_actionPerformed();
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427 case KeyEvent.VK_I:
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428 if (evt.isControlDown())
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430 if (evt.isAltDown())
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432 invertColSel_actionPerformed();
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436 invertSequenceMenuItem_actionPerformed();
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441 case KeyEvent.VK_U:
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442 if (evt.isControlDown())
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444 this.deleteGroups_actionPerformed();
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448 case KeyEvent.VK_T:
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449 if (evt.isControlDown())
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456 alignPanel.paintAlignment(true);
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460 * called by key handler and the hide all/show all menu items
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462 * @param toggleSeqs
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463 * @param toggleCols
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465 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
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467 boolean hide = false;
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468 SequenceGroup sg = viewport.getSelectionGroup();
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469 if (!toggleSeqs && !toggleCols)
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471 // Hide everything by the current selection - this is a hack - we do the
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472 // invert and then hide
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473 // first check that there will be visible columns after the invert.
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474 if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
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475 .getSelected().size() > 0)
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476 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
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479 // now invert the sequence set, if required - empty selection implies
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480 // that no hiding is required.
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483 invertSequenceMenuItem_actionPerformed();
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484 sg = viewport.getSelectionGroup();
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488 viewport.expandColSelection(sg, true);
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489 // finally invert the column selection and get the new sequence
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490 // selection and indicate it should be hidden.
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491 invertColSel_actionPerformed();
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498 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
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501 viewport.hideAllSelectedSeqs();
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503 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
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505 viewport.showAllHiddenSeqs();
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511 if (viewport.colSel.getSelected().size() > 0)
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513 viewport.hideSelectedColumns();
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516 viewport.selectionGroup = sg;
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521 viewport.showAllHiddenColumns();
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526 public void keyReleased(KeyEvent evt)
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530 public void keyTyped(KeyEvent evt)
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534 public void itemStateChanged(ItemEvent evt)
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536 if (evt.getSource() == displayNonconservedMenuItem)
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538 displayNonconservedMenuItem_actionPerformed();
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540 else if (evt.getSource() == colourTextMenuItem)
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542 colourTextMenuItem_actionPerformed();
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544 else if (evt.getSource() == wrapMenuItem)
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546 wrapMenuItem_actionPerformed();
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548 else if (evt.getSource() == scaleAbove)
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550 viewport.setScaleAboveWrapped(scaleAbove.getState());
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552 else if (evt.getSource() == scaleLeft)
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554 viewport.setScaleLeftWrapped(scaleLeft.getState());
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556 else if (evt.getSource() == scaleRight)
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558 viewport.setScaleRightWrapped(scaleRight.getState());
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560 else if (evt.getSource() == seqLimits)
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562 seqLimits_itemStateChanged();
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564 else if (evt.getSource() == viewBoxesMenuItem)
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566 viewport.setShowBoxes(viewBoxesMenuItem.getState());
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568 else if (evt.getSource() == viewTextMenuItem)
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570 viewport.setShowText(viewTextMenuItem.getState());
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572 else if (evt.getSource() == renderGapsMenuItem)
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574 viewport.setRenderGaps(renderGapsMenuItem.getState());
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576 else if (evt.getSource() == annotationPanelMenuItem)
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578 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
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579 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
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581 else if (evt.getSource() == sequenceFeatures)
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583 viewport.showSequenceFeatures(sequenceFeatures.getState());
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584 alignPanel.seqPanel.seqCanvas.repaint();
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586 else if (evt.getSource() == conservationMenuItem)
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588 conservationMenuItem_actionPerformed();
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590 else if (evt.getSource() == abovePIDThreshold)
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592 abovePIDThreshold_actionPerformed();
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594 else if (evt.getSource() == applyToAllGroups)
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596 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
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598 else if (evt.getSource() == autoCalculate)
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600 viewport.autocalculateConsensus = autoCalculate.getState();
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602 else if (evt.getSource() == this.centreColumnLabelFlag)
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604 centreColumnLabelFlag_stateChanged();
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606 else if (evt.getSource() == this.followMouseOverFlag)
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608 mouseOverFlag_stateChanged();
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610 else if (evt.getSource() == showGroupConsensus)
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612 showGroupConsensus_actionPerformed();
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614 else if (evt.getSource() == showGroupConservation)
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616 showGroupConservation_actionPerformed();
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618 else if (evt.getSource() == showSequenceLogo)
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620 showSequenceLogo_actionPerformed();
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622 else if (evt.getSource() == showConsensusHistogram)
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624 showConsensusHistogram_actionPerformed();
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626 else if (evt.getSource() == applyAutoAnnotationSettings)
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628 applyAutoAnnotationSettings_actionPerformed();
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630 alignPanel.paintAlignment(true);
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633 private void mouseOverFlag_stateChanged()
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635 viewport.followHighlight = followMouseOverFlag.getState();
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636 // TODO: could kick the scrollTo mechanism to reset view for current
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640 private void centreColumnLabelFlag_stateChanged()
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642 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
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643 this.alignPanel.annotationPanel.repaint();
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646 public void actionPerformed(ActionEvent evt)
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648 Object source = evt.getSource();
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650 if (source == inputText)
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652 inputText_actionPerformed();
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654 else if (source == loadTree)
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656 loadTree_actionPerformed();
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658 else if (source == loadApplication)
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660 launchFullApplication();
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662 else if (source == loadAnnotations)
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666 else if (source == outputAnnotations)
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668 outputAnnotations(true);
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670 else if (source == outputFeatures)
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672 outputFeatures(true, "Jalview");
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674 else if (source == closeMenuItem)
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676 closeMenuItem_actionPerformed();
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678 else if (source == copy)
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680 copy_actionPerformed();
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682 else if (source == undoMenuItem)
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684 undoMenuItem_actionPerformed();
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686 else if (source == redoMenuItem)
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688 redoMenuItem_actionPerformed();
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690 else if (source == inputText)
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692 inputText_actionPerformed();
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694 else if (source == closeMenuItem)
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696 closeMenuItem_actionPerformed();
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698 else if (source == undoMenuItem)
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700 undoMenuItem_actionPerformed();
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702 else if (source == redoMenuItem)
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704 redoMenuItem_actionPerformed();
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706 else if (source == copy)
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708 copy_actionPerformed();
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710 else if (source == pasteNew)
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712 pasteNew_actionPerformed();
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714 else if (source == pasteThis)
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716 pasteThis_actionPerformed();
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718 else if (source == cut)
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720 cut_actionPerformed();
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722 else if (source == delete)
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724 delete_actionPerformed();
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726 else if (source == grpsFromSelection)
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728 makeGrpsFromSelection_actionPerformed();
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730 else if (source == deleteGroups)
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732 deleteGroups_actionPerformed();
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734 else if (source == selectAllSequenceMenuItem)
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736 selectAllSequenceMenuItem_actionPerformed();
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738 else if (source == deselectAllSequenceMenuItem)
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740 deselectAllSequenceMenuItem_actionPerformed();
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742 else if (source == invertSequenceMenuItem)
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744 invertSequenceMenuItem_actionPerformed();
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746 else if (source == invertColSel)
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748 viewport.invertColumnSelection();
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749 alignPanel.paintAlignment(true);
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751 else if (source == remove2LeftMenuItem)
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753 trimAlignment(true);
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755 else if (source == remove2RightMenuItem)
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757 trimAlignment(false);
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759 else if (source == removeGappedColumnMenuItem)
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761 removeGappedColumnMenuItem_actionPerformed();
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763 else if (source == removeAllGapsMenuItem)
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765 removeAllGapsMenuItem_actionPerformed();
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767 else if (source == findMenuItem)
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769 findMenuItem_actionPerformed();
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771 else if (source == font)
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773 new FontChooser(alignPanel);
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775 else if (source == newView)
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779 else if (source == showColumns)
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781 viewport.showAllHiddenColumns();
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782 alignPanel.paintAlignment(true);
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784 else if (source == showSeqs)
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786 viewport.showAllHiddenSeqs();
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787 alignPanel.paintAlignment(true);
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789 else if (source == hideColumns)
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791 viewport.hideSelectedColumns();
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792 alignPanel.paintAlignment(true);
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794 else if (source == hideSequences
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795 && viewport.getSelectionGroup() != null)
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797 viewport.hideAllSelectedSeqs();
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798 alignPanel.paintAlignment(true);
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800 else if (source == hideAllButSelection)
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802 toggleHiddenRegions(false, false);
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803 alignPanel.paintAlignment(true);
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805 else if (source == hideAllSelection)
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807 SequenceGroup sg = viewport.getSelectionGroup();
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808 viewport.expandColSelection(sg, false);
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809 viewport.hideAllSelectedSeqs();
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810 viewport.hideSelectedColumns();
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811 alignPanel.paintAlignment(true);
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813 else if (source == showAllHidden)
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815 viewport.showAllHiddenColumns();
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816 viewport.showAllHiddenSeqs();
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817 alignPanel.paintAlignment(true);
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819 else if (source == showGroupConsensus)
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821 showGroupConsensus_actionPerformed();
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823 else if (source == showGroupConservation)
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825 showGroupConservation_actionPerformed();
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827 else if (source == showSequenceLogo)
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829 showSequenceLogo_actionPerformed();
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831 else if (source == showConsensusHistogram)
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833 showConsensusHistogram_actionPerformed();
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835 else if (source == applyAutoAnnotationSettings)
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837 applyAutoAnnotationSettings_actionPerformed();
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839 else if (source == featureSettings)
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841 new FeatureSettings(alignPanel);
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843 else if (source == alProperties)
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845 StringBuffer contents = new jalview.io.AlignmentProperties(
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846 viewport.alignment).formatAsString();
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847 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
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848 cap.setText(contents.toString());
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849 Frame frame = new Frame();
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851 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
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852 + getTitle(), 400, 250);
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854 else if (source == overviewMenuItem)
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856 overviewMenuItem_actionPerformed();
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858 else if (source == noColourmenuItem)
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860 changeColour(null);
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862 else if (source == clustalColour)
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864 abovePIDThreshold.setState(false);
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865 changeColour(new ClustalxColourScheme(
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866 viewport.alignment.getSequences(),
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867 viewport.alignment.getWidth()));
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869 else if (source == zappoColour)
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871 changeColour(new ZappoColourScheme());
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873 else if (source == taylorColour)
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875 changeColour(new TaylorColourScheme());
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877 else if (source == hydrophobicityColour)
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879 changeColour(new HydrophobicColourScheme());
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881 else if (source == helixColour)
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883 changeColour(new HelixColourScheme());
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885 else if (source == strandColour)
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887 changeColour(new StrandColourScheme());
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889 else if (source == turnColour)
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891 changeColour(new TurnColourScheme());
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893 else if (source == buriedColour)
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895 changeColour(new BuriedColourScheme());
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897 else if (source == nucleotideColour)
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899 changeColour(new NucleotideColourScheme());
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901 else if (source == modifyPID)
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903 modifyPID_actionPerformed();
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905 else if (source == modifyConservation)
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907 modifyConservation_actionPerformed();
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909 else if (source == userDefinedColour)
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911 new UserDefinedColours(alignPanel, null);
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913 else if (source == PIDColour)
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915 changeColour(new PIDColourScheme());
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917 else if (source == BLOSUM62Colour)
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919 changeColour(new Blosum62ColourScheme());
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921 else if (source == annotationColour)
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923 new AnnotationColourChooser(viewport, alignPanel);
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925 else if (source == sortPairwiseMenuItem)
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927 sortPairwiseMenuItem_actionPerformed();
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929 else if (source == sortIDMenuItem)
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931 sortIDMenuItem_actionPerformed();
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933 else if (source == sortLengthMenuItem)
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935 sortLengthMenuItem_actionPerformed();
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937 else if (source == sortGroupMenuItem)
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939 sortGroupMenuItem_actionPerformed();
\r
941 else if (source == removeRedundancyMenuItem)
\r
943 removeRedundancyMenuItem_actionPerformed();
\r
945 else if (source == pairwiseAlignmentMenuItem)
\r
947 pairwiseAlignmentMenuItem_actionPerformed();
\r
949 else if (source == PCAMenuItem)
\r
951 PCAMenuItem_actionPerformed();
\r
953 else if (source == averageDistanceTreeMenuItem)
\r
955 averageDistanceTreeMenuItem_actionPerformed();
\r
957 else if (source == neighbourTreeMenuItem)
\r
959 neighbourTreeMenuItem_actionPerformed();
\r
961 else if (source == njTreeBlosumMenuItem)
\r
963 njTreeBlosumMenuItem_actionPerformed();
\r
965 else if (source == avDistanceTreeBlosumMenuItem)
\r
967 avTreeBlosumMenuItem_actionPerformed();
\r
969 else if (source == documentation)
\r
971 documentation_actionPerformed();
\r
973 else if (source == about)
\r
975 about_actionPerformed();
\r
980 public void inputText_actionPerformed()
\r
982 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
983 Frame frame = new Frame();
\r
985 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
\r
988 protected void outputText_actionPerformed(ActionEvent e)
\r
990 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
991 Frame frame = new Frame();
\r
993 jalview.bin.JalviewLite.addFrame(frame,
\r
994 "Alignment output - " + e.getActionCommand(), 600, 500);
\r
995 cap.setText(new AppletFormatAdapter().formatSequences(
\r
996 e.getActionCommand(), viewport.getAlignment(),
\r
997 viewport.showJVSuffix));
\r
1000 public void loadAnnotations()
\r
1002 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1003 cap.setText("Paste your features / annotations file here.");
\r
1004 cap.setAnnotationImport();
\r
1005 Frame frame = new Frame();
\r
1007 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
\r
1011 public String outputAnnotations(boolean displayTextbox)
\r
1013 String annotation = new AnnotationFile().printAnnotations(
\r
1014 viewport.showAnnotation ? viewport.alignment
\r
1015 .getAlignmentAnnotation() : null, viewport.alignment
\r
1017 ((Alignment) viewport.alignment).alignmentProperties);
\r
1019 if (displayTextbox)
\r
1021 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
1022 Frame frame = new Frame();
\r
1024 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
\r
1025 cap.setText(annotation);
\r
1028 return annotation;
\r
1031 private Hashtable getDisplayedFeatureCols()
\r
1033 if (alignPanel.getFeatureRenderer() != null)
\r
1035 FeatureRenderer fr = alignPanel.getFeatureRenderer();
\r
1036 Hashtable fcols = new Hashtable();
\r
1037 Enumeration en = viewport.featuresDisplayed.keys();
\r
1038 while (en.hasMoreElements())
\r
1040 Object col = en.nextElement();
\r
1041 fcols.put(col, fr.featureColours.get(col));
\r
1048 public String outputFeatures(boolean displayTextbox, String format)
\r
1051 if (format.equalsIgnoreCase("Jalview"))
\r
1053 features = new FeaturesFile().printJalviewFormat(
\r
1054 viewport.alignment.getSequencesArray(),
\r
1055 getDisplayedFeatureCols());
\r
1059 features = new FeaturesFile().printGFFFormat(
\r
1060 viewport.alignment.getSequencesArray(),
\r
1061 getDisplayedFeatureCols());
\r
1064 if (displayTextbox)
\r
1066 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
1067 Frame frame = new Frame();
\r
1069 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
\r
1071 cap.setText(features);
\r
1077 void launchFullApplication()
\r
1079 StringBuffer url = new StringBuffer(jalviewServletURL);
\r
1081 url.append("?open="
\r
1082 + appendProtocol(viewport.applet.getParameter("file")));
\r
1084 if (viewport.applet.getParameter("features") != null)
\r
1086 url.append("&features=");
\r
1087 url.append(appendProtocol(viewport.applet.getParameter("features")));
\r
1090 if (viewport.applet.getParameter("annotations") != null)
\r
1092 url.append("&annotations=");
\r
1093 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
\r
1096 if (viewport.applet.getParameter("jnetfile") != null)
\r
1098 url.append("&annotations=");
\r
1099 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
\r
1102 if (viewport.applet.getParameter("defaultColour") != null)
\r
1104 url.append("&colour="
\r
1105 + removeWhiteSpace(viewport.applet
\r
1106 .getParameter("defaultColour")));
\r
1109 if (viewport.applet.getParameter("userDefinedColour") != null)
\r
1111 url.append("&colour="
\r
1112 + removeWhiteSpace(viewport.applet
\r
1113 .getParameter("userDefinedColour")));
\r
1115 if (viewport.applet.getParameter("tree") != null)
\r
1117 url.append("&tree="
\r
1118 + appendProtocol(viewport.applet.getParameter("tree")));
\r
1120 if (viewport.applet.getParameter("treeFile") != null)
\r
1122 url.append("&tree="
\r
1123 + appendProtocol(viewport.applet.getParameter("treeFile")));
\r
1126 showURL(url.toString(), "FULL_APP");
\r
1129 String removeWhiteSpace(String colour)
\r
1131 StringBuffer sb = new StringBuffer();
\r
1132 for (int i = 0; i < colour.length(); i++)
\r
1134 if (Character.isWhitespace(colour.charAt(i)))
\r
1140 sb.append(colour.charAt(i));
\r
1144 return sb.toString();
\r
1147 String appendProtocol(String url)
\r
1152 url = URLEncoder.encode(url);
\r
1155 * When we finally deprecate 1.1 compatibility, we can start to use
\r
1156 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
\r
1157 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
\r
1158 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
\r
1159 * ex.printStackTrace(); }
\r
1161 catch (java.net.MalformedURLException ex)
\r
1163 url = viewport.applet.getCodeBase() + url;
\r
1168 public void closeMenuItem_actionPerformed()
\r
1170 PaintRefresher.RemoveComponent(alignPanel);
\r
1171 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
\r
1172 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
\r
1174 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
\r
1185 void updateEditMenuBar()
\r
1188 if (viewport.historyList.size() > 0)
\r
1190 undoMenuItem.setEnabled(true);
\r
1191 CommandI command = (CommandI) viewport.historyList.peek();
\r
1192 undoMenuItem.setLabel("Undo " + command.getDescription());
\r
1196 undoMenuItem.setEnabled(false);
\r
1197 undoMenuItem.setLabel("Undo");
\r
1200 if (viewport.redoList.size() > 0)
\r
1202 redoMenuItem.setEnabled(true);
\r
1204 CommandI command = (CommandI) viewport.redoList.peek();
\r
1205 redoMenuItem.setLabel("Redo " + command.getDescription());
\r
1209 redoMenuItem.setEnabled(false);
\r
1210 redoMenuItem.setLabel("Redo");
\r
1214 public void addHistoryItem(CommandI command)
\r
1216 if (command.getSize() > 0)
\r
1218 viewport.historyList.push(command);
\r
1219 viewport.redoList.removeAllElements();
\r
1220 updateEditMenuBar();
\r
1221 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
1231 protected void undoMenuItem_actionPerformed()
\r
1233 if (viewport.historyList.size() < 1)
\r
1238 CommandI command = (CommandI) viewport.historyList.pop();
\r
1239 viewport.redoList.push(command);
\r
1240 command.undoCommand(null);
\r
1242 AlignViewport originalSource = getOriginatingSource(command);
\r
1244 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
1245 updateEditMenuBar();
\r
1246 originalSource.firePropertyChange("alignment", null,
\r
1247 originalSource.alignment.getSequences());
\r
1256 protected void redoMenuItem_actionPerformed()
\r
1258 if (viewport.redoList.size() < 1)
\r
1263 CommandI command = (CommandI) viewport.redoList.pop();
\r
1264 viewport.historyList.push(command);
\r
1265 command.doCommand(null);
\r
1267 AlignViewport originalSource = getOriginatingSource(command);
\r
1268 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
1270 updateEditMenuBar();
\r
1271 originalSource.firePropertyChange("alignment", null,
\r
1272 originalSource.alignment.getSequences());
\r
1275 AlignViewport getOriginatingSource(CommandI command)
\r
1277 AlignViewport originalSource = null;
\r
1278 // For sequence removal and addition, we need to fire
\r
1279 // the property change event FROM the viewport where the
\r
1280 // original alignment was altered
\r
1281 AlignmentI al = null;
\r
1282 if (command instanceof EditCommand)
\r
1284 EditCommand editCommand = (EditCommand) command;
\r
1285 al = editCommand.getAlignment();
\r
1286 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
1287 .getSequenceSetId());
\r
1288 for (int i = 0; i < comps.size(); i++)
\r
1290 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
1292 if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
\r
1294 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
\r
1301 if (originalSource == null)
\r
1303 // The original view is closed, we must validate
\r
1304 // the current view against the closed view first
\r
1307 PaintRefresher.validateSequences(al, viewport.alignment);
\r
1310 originalSource = viewport;
\r
1313 return originalSource;
\r
1316 public void moveSelectedSequences(boolean up)
\r
1318 SequenceGroup sg = viewport.getSelectionGroup();
\r
1326 for (int i = 1; i < viewport.alignment.getHeight(); i++)
\r
1328 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
1329 if (!sg.getSequences(null).contains(seq))
\r
1334 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
\r
1335 if (sg.getSequences(null).contains(temp))
\r
1340 viewport.alignment.getSequences().setElementAt(temp, i);
\r
1341 viewport.alignment.getSequences().setElementAt(seq, i - 1);
\r
1346 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
\r
1348 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
1349 if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))
\r
1354 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
\r
1355 if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))
\r
1360 viewport.alignment.getSequences().setElementAt(temp, i);
\r
1361 viewport.alignment.getSequences().setElementAt(seq, i + 1);
\r
1365 alignPanel.paintAlignment(true);
\r
1368 synchronized void slideSequences(boolean right, int size)
\r
1370 Vector sg = new Vector();
\r
1371 if (viewport.cursorMode)
\r
1373 sg.addElement(viewport.alignment
\r
1374 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
\r
1376 else if (viewport.getSelectionGroup() != null
\r
1377 && viewport.getSelectionGroup().getSize() != viewport.alignment
\r
1380 sg = viewport.getSelectionGroup().getSequences(
\r
1381 viewport.hiddenRepSequences);
\r
1384 if (sg.size() < 1)
\r
1389 Vector invertGroup = new Vector();
\r
1391 for (int i = 0; i < viewport.alignment.getHeight(); i++)
\r
1393 if (!sg.contains(viewport.alignment.getSequenceAt(i)))
\r
1394 invertGroup.addElement(viewport.alignment.getSequenceAt(i));
\r
1397 SequenceI[] seqs1 = new SequenceI[sg.size()];
\r
1398 for (int i = 0; i < sg.size(); i++)
\r
1399 seqs1[i] = (SequenceI) sg.elementAt(i);
\r
1401 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
\r
1402 for (int i = 0; i < invertGroup.size(); i++)
\r
1403 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
\r
1405 SlideSequencesCommand ssc;
\r
1407 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
\r
1408 size, viewport.getGapCharacter());
\r
1410 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
\r
1411 size, viewport.getGapCharacter());
\r
1413 int groupAdjustment = 0;
\r
1414 if (ssc.getGapsInsertedBegin() && right)
\r
1416 if (viewport.cursorMode)
\r
1417 alignPanel.seqPanel.moveCursor(size, 0);
\r
1419 groupAdjustment = size;
\r
1421 else if (!ssc.getGapsInsertedBegin() && !right)
\r
1423 if (viewport.cursorMode)
\r
1424 alignPanel.seqPanel.moveCursor(-size, 0);
\r
1426 groupAdjustment = -size;
\r
1429 if (groupAdjustment != 0)
\r
1431 viewport.getSelectionGroup().setStartRes(
\r
1432 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
\r
1433 viewport.getSelectionGroup().setEndRes(
\r
1434 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
\r
1437 boolean appendHistoryItem = false;
\r
1438 if (viewport.historyList != null && viewport.historyList.size() > 0
\r
1439 && viewport.historyList.peek() instanceof SlideSequencesCommand)
\r
1441 appendHistoryItem = ssc
\r
1442 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
\r
1446 if (!appendHistoryItem)
\r
1447 addHistoryItem(ssc);
\r
1452 static StringBuffer copiedSequences;
\r
1454 static Vector copiedHiddenColumns;
\r
1456 protected void copy_actionPerformed()
\r
1458 if (viewport.getSelectionGroup() == null)
\r
1463 SequenceGroup sg = viewport.getSelectionGroup();
\r
1464 copiedSequences = new StringBuffer();
\r
1465 Hashtable orderedSeqs = new Hashtable();
\r
1466 for (int i = 0; i < sg.getSize(); i++)
\r
1468 SequenceI seq = sg.getSequenceAt(i);
\r
1469 int index = viewport.alignment.findIndex(seq);
\r
1470 orderedSeqs.put(index + "", seq);
\r
1473 int index = 0, startRes, endRes;
\r
1476 if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
\r
1478 copiedHiddenColumns = new Vector();
\r
1479 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
\r
1480 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
\r
1483 int[] region = (int[]) viewport.getColumnSelection()
\r
1484 .getHiddenColumns().elementAt(i);
\r
1486 copiedHiddenColumns.addElement(new int[]
\r
1487 { region[0] - hiddenOffset, region[1] - hiddenOffset });
\r
1492 copiedHiddenColumns = null;
\r
1495 for (int i = 0; i < sg.getSize(); i++)
\r
1497 SequenceI seq = null;
\r
1499 while (seq == null)
\r
1501 if (orderedSeqs.containsKey(index + ""))
\r
1503 seq = (SequenceI) orderedSeqs.get(index + "");
\r
1515 // Returns residue following index if gap
\r
1516 startRes = seq.findPosition(sg.getStartRes());
\r
1519 // Need to find the residue preceeding index if gap
\r
1522 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
\r
1524 ch = seq.getCharAt(j);
\r
1525 if (!jalview.util.Comparison.isGap((ch)))
\r
1533 endRes += seq.getStart() - 1;
\r
1536 copiedSequences.append(seq.getName()
\r
1542 + seq.getSequenceAsString(sg.getStartRes(),
\r
1543 sg.getEndRes() + 1) + "\n");
\r
1548 protected void pasteNew_actionPerformed()
\r
1553 protected void pasteThis_actionPerformed()
\r
1558 void paste(boolean newAlignment)
\r
1563 if (copiedSequences == null)
\r
1568 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
1569 Vector seqs = new Vector();
\r
1570 while (st.hasMoreElements())
\r
1572 String name = st.nextToken();
\r
1573 int start = Integer.parseInt(st.nextToken());
\r
1574 int end = Integer.parseInt(st.nextToken());
\r
1575 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
\r
1577 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
1578 for (int i = 0; i < seqs.size(); i++)
\r
1580 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
1585 String newtitle = new String("Copied sequences");
\r
1586 if (getTitle().startsWith("Copied sequences"))
\r
1588 newtitle = getTitle();
\r
1592 newtitle = newtitle.concat("- from " + getTitle());
\r
1594 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
1595 viewport.applet, newtitle, false);
\r
1596 if (copiedHiddenColumns != null)
\r
1598 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
1600 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
1601 af.viewport.hideColumns(region[0], region[1]);
\r
1605 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
\r
1610 addSequences(newSeqs);
\r
1613 } catch (Exception ex)
\r
1615 } // could be anything being pasted in here
\r
1619 void addSequences(SequenceI[] seqs)
\r
1621 for (int i = 0; i < seqs.length; i++)
\r
1623 viewport.alignment.addSequence(seqs[i]);
\r
1627 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
\r
1628 seqs, 0, viewport.alignment.getWidth(), viewport.alignment));
\r
1630 viewport.setEndSeq(viewport.alignment.getHeight());
\r
1631 viewport.alignment.getWidth();
\r
1632 viewport.firePropertyChange("alignment", null,
\r
1633 viewport.alignment.getSequences());
\r
1637 protected void cut_actionPerformed()
\r
1639 copy_actionPerformed();
\r
1640 delete_actionPerformed();
\r
1643 protected void delete_actionPerformed()
\r
1646 SequenceGroup sg = viewport.getSelectionGroup();
\r
1652 Vector seqs = new Vector();
\r
1654 for (int i = 0; i < sg.getSize(); i++)
\r
1656 seq = sg.getSequenceAt(i);
\r
1657 seqs.addElement(seq);
\r
1660 // If the cut affects all sequences, remove highlighted columns
\r
1661 if (sg.getSize() == viewport.alignment.getHeight())
\r
1663 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
1664 sg.getEndRes() + 1);
\r
1667 SequenceI[] cut = new SequenceI[seqs.size()];
\r
1668 for (int i = 0; i < seqs.size(); i++)
\r
1670 cut[i] = (SequenceI) seqs.elementAt(i);
\r
1674 * //ADD HISTORY ITEM
\r
1676 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
\r
1677 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
\r
1678 viewport.alignment));
\r
1680 viewport.setSelectionGroup(null);
\r
1681 viewport.alignment.deleteGroup(sg);
\r
1683 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1686 if (viewport.getAlignment().getHeight() < 1)
\r
1688 this.setVisible(false);
\r
1690 viewport.sendSelection();
\r
1694 * group consensus toggled
\r
1697 protected void showGroupConsensus_actionPerformed()
\r
1699 viewport.setShowGroupConsensus(showGroupConsensus.getState());
\r
1700 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1705 * group conservation toggled.
\r
1707 protected void showGroupConservation_actionPerformed()
\r
1709 viewport.setShowGroupConservation(showGroupConservation.getState());
\r
1710 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1717 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
\r
1718 * .event.ActionEvent)
\r
1720 protected void showConsensusHistogram_actionPerformed()
\r
1722 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
\r
1723 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1729 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
\r
1730 * .event.ActionEvent)
\r
1732 protected void showSequenceLogo_actionPerformed()
\r
1734 viewport.setShowSequenceLogo(showSequenceLogo.getState());
\r
1735 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1738 protected void applyAutoAnnotationSettings_actionPerformed()
\r
1740 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1743 protected void makeGrpsFromSelection_actionPerformed()
\r
1745 if (viewport.getSelectionGroup() != null)
\r
1747 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
\r
1748 viewport.getSequenceSelection(),
\r
1749 viewport.getAlignmentView(true).getSequenceStrings(
\r
1750 viewport.getGapCharacter()),
\r
1751 viewport.alignment.getGroups());
\r
1752 viewport.alignment.deleteAllGroups();
\r
1753 viewport.sequenceColours = null;
\r
1754 viewport.setSelectionGroup(null);
\r
1755 // set view properties for each group
\r
1756 for (int g = 0; g < gps.length; g++)
\r
1758 // gps[g].setShowunconserved(viewport.getShowUnconserved());
\r
1759 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
\r
1760 viewport.alignment.addGroup(gps[g]);
\r
1761 Color col = new Color((int) (Math.random() * 255),
\r
1762 (int) (Math.random() * 255), (int) (Math.random() * 255));
\r
1763 col = col.brighter();
\r
1764 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
\r
1765 .hasMoreElements(); viewport.setSequenceColour(
\r
1766 (SequenceI) sq.nextElement(), col))
\r
1769 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
\r
1770 alignPanel.updateAnnotation();
\r
1771 alignPanel.paintAlignment(true);
\r
1775 protected void deleteGroups_actionPerformed()
\r
1777 viewport.alignment.deleteAllGroups();
\r
1778 viewport.sequenceColours = null;
\r
1779 viewport.setSelectionGroup(null);
\r
1781 alignPanel.paintAlignment(true);
\r
1784 public void selectAllSequenceMenuItem_actionPerformed()
\r
1786 SequenceGroup sg = new SequenceGroup();
\r
1787 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1789 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
1791 sg.setEndRes(viewport.alignment.getWidth() - 1);
\r
1792 viewport.setSelectionGroup(sg);
\r
1793 alignPanel.paintAlignment(true);
\r
1794 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1795 viewport.sendSelection();
\r
1798 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1800 if (viewport.cursorMode)
\r
1802 alignPanel.seqPanel.keyboardNo1 = null;
\r
1803 alignPanel.seqPanel.keyboardNo2 = null;
\r
1805 viewport.setSelectionGroup(null);
\r
1806 viewport.getColumnSelection().clear();
\r
1807 viewport.setSelectionGroup(null);
\r
1808 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1809 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1810 alignPanel.paintAlignment(true);
\r
1811 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1812 viewport.sendSelection();
\r
1815 public void invertSequenceMenuItem_actionPerformed()
\r
1817 SequenceGroup sg = viewport.getSelectionGroup();
\r
1818 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1820 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1823 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1824 viewport.sendSelection();
\r
1827 public void invertColSel_actionPerformed()
\r
1829 viewport.invertColumnSelection();
\r
1830 alignPanel.paintAlignment(true);
\r
1831 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1832 viewport.sendSelection();
\r
1835 void trimAlignment(boolean trimLeft)
\r
1837 ColumnSelection colSel = viewport.getColumnSelection();
\r
1840 if (colSel.size() > 0)
\r
1844 column = colSel.getMin();
\r
1848 column = colSel.getMax();
\r
1852 if (viewport.getSelectionGroup() != null)
\r
1854 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
1855 viewport.hiddenRepSequences);
\r
1859 seqs = viewport.alignment.getSequencesArray();
\r
1862 TrimRegionCommand trimRegion;
\r
1865 trimRegion = new TrimRegionCommand("Remove Left",
\r
1866 TrimRegionCommand.TRIM_LEFT, seqs, column,
\r
1867 viewport.alignment, viewport.colSel,
\r
1868 viewport.selectionGroup);
\r
1869 viewport.setStartRes(0);
\r
1873 trimRegion = new TrimRegionCommand("Remove Right",
\r
1874 TrimRegionCommand.TRIM_RIGHT, seqs, column,
\r
1875 viewport.alignment, viewport.colSel,
\r
1876 viewport.selectionGroup);
\r
1879 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
\r
1881 addHistoryItem(trimRegion);
\r
1883 Vector groups = viewport.alignment.getGroups();
\r
1885 for (int i = 0; i < groups.size(); i++)
\r
1887 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1889 if ((trimLeft && !sg.adjustForRemoveLeft(column))
\r
1890 || (!trimLeft && !sg.adjustForRemoveRight(column)))
\r
1892 viewport.alignment.deleteGroup(sg);
\r
1896 viewport.firePropertyChange("alignment", null, viewport
\r
1897 .getAlignment().getSequences());
\r
1901 public void removeGappedColumnMenuItem_actionPerformed()
\r
1903 int start = 0, end = viewport.alignment.getWidth() - 1;
\r
1906 if (viewport.getSelectionGroup() != null)
\r
1908 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
1909 viewport.hiddenRepSequences);
\r
1910 start = viewport.getSelectionGroup().getStartRes();
\r
1911 end = viewport.getSelectionGroup().getEndRes();
\r
1915 seqs = viewport.alignment.getSequencesArray();
\r
1918 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
\r
1919 "Remove Gapped Columns", seqs, start, end, viewport.alignment);
\r
1921 addHistoryItem(removeGapCols);
\r
1923 statusBar.setText("Removed " + removeGapCols.getSize()
\r
1924 + " empty columns.");
\r
1926 // This is to maintain viewport position on first residue
\r
1927 // of first sequence
\r
1928 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1929 int startRes = seq.findPosition(viewport.startRes);
\r
1930 // ShiftList shifts;
\r
1931 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
\r
1932 // edit.alColumnChanges=shifts.getInverse();
\r
1933 // if (viewport.hasHiddenColumns)
\r
1934 // viewport.getColumnSelection().compensateForEdits(shifts);
\r
1935 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
1936 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1941 public void removeAllGapsMenuItem_actionPerformed()
\r
1943 int start = 0, end = viewport.alignment.getWidth() - 1;
\r
1946 if (viewport.getSelectionGroup() != null)
\r
1948 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
1949 viewport.hiddenRepSequences);
\r
1950 start = viewport.getSelectionGroup().getStartRes();
\r
1951 end = viewport.getSelectionGroup().getEndRes();
\r
1955 seqs = viewport.alignment.getSequencesArray();
\r
1958 // This is to maintain viewport position on first residue
\r
1959 // of first sequence
\r
1960 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1961 int startRes = seq.findPosition(viewport.startRes);
\r
1963 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
\r
1964 viewport.alignment));
\r
1966 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
1968 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1973 public void findMenuItem_actionPerformed()
\r
1975 new Finder(alignPanel);
\r
1979 * create a new view derived from the current view
\r
1981 * @param viewtitle
\r
1982 * @return frame for the new view
\r
1984 public AlignFrame newView(String viewtitle)
\r
1987 if (viewport.hasHiddenRows)
\r
1989 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
\r
1990 .getFullAlignment().getSequencesArray());
\r
1994 newal = new Alignment(viewport.alignment.getSequencesArray());
\r
1997 if (viewport.alignment.getAlignmentAnnotation() != null)
\r
1999 for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)
\r
2001 if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
\r
2003 newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);
\r
2008 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
\r
2010 newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
\r
2011 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
\r
2012 PaintRefresher.Register(newaf.alignPanel,
\r
2013 newaf.alignPanel.av.getSequenceSetId());
\r
2015 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
\r
2016 newaf.alignPanel.av.getSequenceSetId());
\r
2017 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
\r
2018 newaf.alignPanel.av.getSequenceSetId());
\r
2020 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
2021 .getSequenceSetId());
\r
2022 int viewSize = -1;
\r
2023 for (int i = 0; i < comps.size(); i++)
\r
2025 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
2031 String title = new String(this.getTitle());
\r
2032 if (viewtitle != null)
\r
2034 title = viewtitle + " ( " + title + ")";
\r
2038 if (title.indexOf("(View") > -1)
\r
2040 title = title.substring(0, title.indexOf("(View"));
\r
2042 title += "(View " + viewSize + ")";
\r
2045 newaf.setTitle(title.toString());
\r
2047 newaf.viewport.historyList = viewport.historyList;
\r
2048 newaf.viewport.redoList = viewport.redoList;
\r
2054 * @return list of feature groups on the view
\r
2056 public String[] getFeatureGroups()
\r
2058 FeatureRenderer fr = null;
\r
2059 if (alignPanel != null
\r
2060 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2062 return fr.getGroups();
\r
2068 * get sequence feature groups that are hidden or shown
\r
2074 public String[] getFeatureGroupsOfState(boolean visible)
\r
2076 FeatureRenderer fr = null;
\r
2077 if (alignPanel != null
\r
2078 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2080 return fr.getGroups(visible);
\r
2086 * Change the display state for the given feature groups
\r
2089 * list of group strings
\r
2091 * visible or invisible
\r
2093 public void setFeatureGroupState(String[] groups, boolean state)
\r
2095 FeatureRenderer fr = null;
\r
2096 this.sequenceFeatures.setState(true);
\r
2097 viewport.showSequenceFeatures(true);
\r
2098 if (alignPanel != null
\r
2099 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2101 fr.setGroupState(groups, state);
\r
2102 alignPanel.seqPanel.seqCanvas.repaint();
\r
2103 if (alignPanel.overviewPanel != null)
\r
2105 alignPanel.overviewPanel.updateOverviewImage();
\r
2110 public void seqLimits_itemStateChanged()
\r
2112 viewport.setShowJVSuffix(seqLimits.getState());
\r
2113 alignPanel.fontChanged();
\r
2114 alignPanel.paintAlignment(true);
\r
2117 protected void colourTextMenuItem_actionPerformed()
\r
2119 viewport.setColourText(colourTextMenuItem.getState());
\r
2120 alignPanel.paintAlignment(true);
\r
2123 protected void displayNonconservedMenuItem_actionPerformed()
\r
2125 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
\r
2126 alignPanel.paintAlignment(true);
\r
2129 protected void wrapMenuItem_actionPerformed()
\r
2131 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
2132 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
2133 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
2134 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
2135 scaleRight.setEnabled(wrapMenuItem.getState());
\r
2136 alignPanel.paintAlignment(true);
\r
2139 public void overviewMenuItem_actionPerformed()
\r
2141 if (alignPanel.overviewPanel != null)
\r
2146 Frame frame = new Frame();
\r
2147 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
2148 frame.add(overview);
\r
2149 // +50 must allow for applet frame window
\r
2150 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
2151 overview.getPreferredSize().width,
\r
2152 overview.getPreferredSize().height + 50);
\r
2155 frame.addWindowListener(new WindowAdapter()
\r
2157 public void windowClosing(WindowEvent e)
\r
2159 alignPanel.setOverviewPanel(null);
\r
2163 alignPanel.setOverviewPanel(overview);
\r
2167 void changeColour(ColourSchemeI cs)
\r
2169 int threshold = 0;
\r
2173 if (viewport.getAbovePIDThreshold())
\r
2175 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
2178 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2180 viewport.setGlobalColourScheme(cs);
\r
2184 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2187 if (viewport.getConservationSelected())
\r
2190 Alignment al = (Alignment) viewport.alignment;
\r
2191 Conservation c = new Conservation("All",
\r
2192 ResidueProperties.propHash, 3, al.getSequences(), 0,
\r
2193 al.getWidth() - 1);
\r
2196 c.verdict(false, viewport.ConsPercGaps);
\r
2198 cs.setConservation(c);
\r
2200 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
\r
2201 cs, "Background"));
\r
2206 cs.setConservation(null);
\r
2209 cs.setConsensus(viewport.hconsensus);
\r
2212 viewport.setGlobalColourScheme(cs);
\r
2214 if (viewport.getColourAppliesToAllGroups())
\r
2216 Vector groups = viewport.alignment.getGroups();
\r
2217 for (int i = 0; i < groups.size(); i++)
\r
2219 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
2226 if (cs instanceof ClustalxColourScheme)
\r
2228 sg.cs = new ClustalxColourScheme(
\r
2229 sg.getSequences(viewport.hiddenRepSequences),
\r
2236 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
2237 } catch (Exception ex)
\r
2239 ex.printStackTrace();
\r
2244 if (viewport.getAbovePIDThreshold()
\r
2245 || cs instanceof PIDColourScheme
\r
2246 || cs instanceof Blosum62ColourScheme)
\r
2248 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2249 sg.cs.setConsensus(AAFrequency.calculate(
\r
2250 sg.getSequences(viewport.hiddenRepSequences), 0,
\r
2255 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2258 if (viewport.getConservationSelected())
\r
2260 Conservation c = new Conservation("Group",
\r
2261 ResidueProperties.propHash, 3,
\r
2262 sg.getSequences(viewport.hiddenRepSequences), 0,
\r
2263 viewport.alignment.getWidth() - 1);
\r
2265 c.verdict(false, viewport.ConsPercGaps);
\r
2266 sg.cs.setConservation(c);
\r
2270 sg.cs.setConservation(null);
\r
2271 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2277 if (alignPanel.getOverviewPanel() != null)
\r
2279 alignPanel.getOverviewPanel().updateOverviewImage();
\r
2282 jalview.structure.StructureSelectionManager
\r
2283 .getStructureSelectionManager().sequenceColoursChanged(
\r
2286 alignPanel.paintAlignment(true);
\r
2289 protected void modifyPID_actionPerformed()
\r
2291 if (viewport.getAbovePIDThreshold()
\r
2292 && viewport.globalColourScheme != null)
\r
2294 SliderPanel.setPIDSliderSource(alignPanel,
\r
2295 viewport.getGlobalColourScheme(), "Background");
\r
2296 SliderPanel.showPIDSlider();
\r
2300 protected void modifyConservation_actionPerformed()
\r
2302 if (viewport.getConservationSelected()
\r
2303 && viewport.globalColourScheme != null)
\r
2305 SliderPanel.setConservationSlider(alignPanel,
\r
2306 viewport.globalColourScheme, "Background");
\r
2307 SliderPanel.showConservationSlider();
\r
2311 protected void conservationMenuItem_actionPerformed()
\r
2313 viewport.setConservationSelected(conservationMenuItem.getState());
\r
2315 viewport.setAbovePIDThreshold(false);
\r
2316 abovePIDThreshold.setState(false);
\r
2318 changeColour(viewport.getGlobalColourScheme());
\r
2320 modifyConservation_actionPerformed();
\r
2323 public void abovePIDThreshold_actionPerformed()
\r
2325 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
2327 conservationMenuItem.setState(false);
\r
2328 viewport.setConservationSelected(false);
\r
2330 changeColour(viewport.getGlobalColourScheme());
\r
2332 modifyPID_actionPerformed();
\r
2335 public void sortPairwiseMenuItem_actionPerformed()
\r
2337 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2338 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
\r
2339 .getAlignment().getSequenceAt(0), null);
\r
2341 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
\r
2342 viewport.alignment));
\r
2343 alignPanel.paintAlignment(true);
\r
2346 public void sortIDMenuItem_actionPerformed()
\r
2348 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2349 AlignmentSorter.sortByID(viewport.getAlignment());
\r
2350 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
\r
2351 alignPanel.paintAlignment(true);
\r
2354 public void sortLengthMenuItem_actionPerformed()
\r
2356 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2357 AlignmentSorter.sortByLength(viewport.getAlignment());
\r
2358 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
\r
2359 viewport.alignment));
\r
2360 alignPanel.paintAlignment(true);
\r
2363 public void sortGroupMenuItem_actionPerformed()
\r
2365 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2366 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
2367 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
\r
2368 viewport.alignment));
\r
2369 alignPanel.paintAlignment(true);
\r
2373 public void removeRedundancyMenuItem_actionPerformed()
\r
2375 new RedundancyPanel(alignPanel);
\r
2378 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
2380 if (viewport.getSelectionGroup() != null
\r
2381 && viewport.getSelectionGroup().getSize() > 1)
\r
2383 Frame frame = new Frame();
\r
2384 frame.add(new PairwiseAlignPanel(alignPanel));
\r
2385 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
\r
2390 public void PCAMenuItem_actionPerformed()
\r
2392 // are the sequences aligned?
\r
2393 if (!viewport.alignment.isAligned(false))
\r
2395 SequenceI current;
\r
2396 int Width = viewport.getAlignment().getWidth();
\r
2398 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2400 current = viewport.getAlignment().getSequenceAt(i);
\r
2402 if (current.getLength() < Width)
\r
2404 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2407 alignPanel.paintAlignment(true);
\r
2410 if ((viewport.getSelectionGroup() != null
\r
2411 && viewport.getSelectionGroup().getSize() < 4 && viewport
\r
2412 .getSelectionGroup().getSize() > 0)
\r
2413 || viewport.getAlignment().getHeight() < 4)
\r
2420 new PCAPanel(viewport);
\r
2421 } catch (java.lang.OutOfMemoryError ex)
\r
2427 public void averageDistanceTreeMenuItem_actionPerformed()
\r
2429 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
2432 public void neighbourTreeMenuItem_actionPerformed()
\r
2434 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
2437 protected void njTreeBlosumMenuItem_actionPerformed()
\r
2439 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2442 protected void avTreeBlosumMenuItem_actionPerformed()
\r
2444 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2447 void NewTreePanel(String type, String pwType, String title)
\r
2449 // are the sequences aligned?
\r
2450 if (!viewport.alignment.isAligned(false))
\r
2452 SequenceI current;
\r
2453 int Width = viewport.getAlignment().getWidth();
\r
2455 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2457 current = viewport.getAlignment().getSequenceAt(i);
\r
2459 if (current.getLength() < Width)
\r
2461 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2464 alignPanel.paintAlignment(true);
\r
2468 if ((viewport.getSelectionGroup() != null && viewport
\r
2469 .getSelectionGroup().getSize() > 1)
\r
2470 || (viewport.getSelectionGroup() == null && viewport.alignment
\r
2471 .getHeight() > 1))
\r
2473 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
\r
2475 addTreeMenuItem(tp, title);
\r
2477 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
2481 void loadTree_actionPerformed()
\r
2483 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
2484 cap.setText("Paste your Newick tree file here.");
\r
2485 cap.setTreeImport();
\r
2486 Frame frame = new Frame();
\r
2488 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
2491 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
2493 TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
\r
2494 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
2495 addTreeMenuItem(tp, treeFile);
\r
2499 * sort the alignment using the given treePanel
\r
2501 * @param treePanel
\r
2502 * tree used to sort view
\r
2504 * string used for undo event name
\r
2506 public void sortByTree(TreePanel treePanel, String title)
\r
2508 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2510 .sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
2511 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2512 // HistoryItem.SORT));
\r
2513 addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
\r
2514 viewport.alignment));
\r
2515 alignPanel.paintAlignment(true);
\r
2519 * Do any automatic reordering of the alignment and add the necessary bits to
\r
2520 * the menu structure for the new tree
\r
2522 * @param treePanel
\r
2525 protected void addTreeMenuItem(final TreePanel treePanel,
\r
2526 final String title)
\r
2528 final MenuItem item = new MenuItem(title);
\r
2529 sortByTreeMenu.add(item);
\r
2530 item.addActionListener(new java.awt.event.ActionListener()
\r
2532 public void actionPerformed(ActionEvent evt)
\r
2534 sortByTree(treePanel, title); // treePanel.getTitle());
\r
2538 treePanel.addWindowListener(new WindowAdapter()
\r
2540 public void windowOpened(WindowEvent e)
\r
2542 if (viewport.sortByTree)
\r
2544 sortByTree(treePanel, title);
\r
2546 super.windowOpened(e);
\r
2549 public void windowClosing(WindowEvent e)
\r
2551 sortByTreeMenu.remove(item);
\r
2555 public boolean sortBy(AlignmentOrder alorder, String undoname)
\r
2557 SequenceI[] oldOrder = viewport.getAlignment()
\r
2558 .getSequencesArray();
\r
2559 if (viewport.applet.debug)
\r
2561 System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");
\r
2563 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
\r
2564 if (undoname!=null)
\r
2566 addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.alignment));
\r
2568 alignPanel.paintAlignment(true);
\r
2571 protected void documentation_actionPerformed()
\r
2573 showURL("http://www.jalview.org/help.html", "HELP");
\r
2576 protected void about_actionPerformed()
\r
2579 class AboutPanel extends Canvas
\r
2585 public AboutPanel(String version, String builddate)
\r
2587 this.version = version;
\r
2588 this.builddate = builddate;
\r
2591 public void paint(Graphics g)
\r
2593 g.setColor(Color.white);
\r
2594 g.fillRect(0, 0, getSize().width, getSize().height);
\r
2595 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2596 FontMetrics fm = g.getFontMetrics();
\r
2597 int fh = fm.getHeight();
\r
2599 g.setColor(Color.black);
\r
2600 // TODO: update this text for each release or centrally store it for
\r
2601 // lite and application
\r
2602 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
2603 g.drawString("JalviewLite - Release " + version, x, y += fh);
\r
2604 g.setFont(new Font("Helvetica", Font.BOLD, 12));
\r
2605 g.drawString("Build date: " + builddate, x, y += fh);
\r
2606 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2608 "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",
\r
2609 x, y += fh * 1.5);
\r
2610 g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
\r
2612 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
\r
2615 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
\r
2617 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
\r
2619 "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
\r
2622 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
\r
2624 g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
\r
2629 Frame frame = new Frame();
\r
2630 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
\r
2631 .getBuildDate()));
\r
2632 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
\r
2636 public void showURL(String url, String target)
\r
2638 if (viewport.applet == null)
\r
2640 System.out.println("Not running as applet - no browser available.");
\r
2646 if (url.indexOf(":") == -1)
\r
2648 // TODO: verify (Bas Vroling bug) prepend codebase or server URL to
\r
2650 // Should really use docbase, not codebase.
\r
2651 if (url.indexOf("/") == 0)
\r
2653 String codebase = viewport.applet.getCodeBase().toString();
\r
2654 url = codebase.substring(0, codebase.length()
\r
2655 - viewport.applet.getCodeBase().getFile().length())
\r
2660 url = viewport.applet.getCodeBase() + url;
\r
2662 System.out.println("Show url (prepended codebase): " + url);
\r
2666 System.out.println("Show url: " + url);
\r
2668 if (url.indexOf("javascript:") == 0)
\r
2670 // no target for the javascript context
\r
2671 viewport.applet.getAppletContext().showDocument(
\r
2672 new java.net.URL(url));
\r
2676 viewport.applet.getAppletContext().showDocument(
\r
2677 new java.net.URL(url), target);
\r
2679 } catch (Exception ex)
\r
2681 ex.printStackTrace();
\r
2686 // ////////////////////////////////////////////////////////////////////////////////
\r
2687 // JBuilder Graphics here
\r
2689 MenuBar alignFrameMenuBar = new MenuBar();
\r
2691 Menu fileMenu = new Menu("File");
\r
2693 MenuItem loadApplication = new MenuItem("View in Full Application");
\r
2695 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
\r
2697 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
\r
2699 MenuItem outputFeatures = new MenuItem("Export Features ...");
\r
2701 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
\r
2703 MenuItem closeMenuItem = new MenuItem("Close");
\r
2705 Menu editMenu = new Menu("Edit");
\r
2707 Menu viewMenu = new Menu("View");
\r
2709 Menu colourMenu = new Menu("Colour");
\r
2711 Menu calculateMenu = new Menu("Calculate");
\r
2713 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
2715 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
2717 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
2719 MenuItem remove2LeftMenuItem = new MenuItem();
\r
2721 MenuItem remove2RightMenuItem = new MenuItem();
\r
2723 MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
2725 MenuItem removeAllGapsMenuItem = new MenuItem();
\r
2727 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
2729 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
2731 MenuItem sortPairwiseMenuItem = new MenuItem();
\r
2733 MenuItem sortIDMenuItem = new MenuItem();
\r
2735 MenuItem sortLengthMenuItem = new MenuItem();
\r
2737 MenuItem sortGroupMenuItem = new MenuItem();
\r
2739 MenuItem removeRedundancyMenuItem = new MenuItem();
\r
2741 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
2743 MenuItem PCAMenuItem = new MenuItem();
\r
2745 MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
2747 MenuItem neighbourTreeMenuItem = new MenuItem();
\r
2749 BorderLayout borderLayout1 = new BorderLayout();
\r
2751 public Label statusBar = new Label();
\r
2753 Menu outputTextboxMenu = new Menu();
\r
2755 MenuItem clustalColour = new MenuItem();
\r
2757 MenuItem zappoColour = new MenuItem();
\r
2759 MenuItem taylorColour = new MenuItem();
\r
2761 MenuItem hydrophobicityColour = new MenuItem();
\r
2763 MenuItem helixColour = new MenuItem();
\r
2765 MenuItem strandColour = new MenuItem();
\r
2767 MenuItem turnColour = new MenuItem();
\r
2769 MenuItem buriedColour = new MenuItem();
\r
2771 MenuItem userDefinedColour = new MenuItem();
\r
2773 MenuItem PIDColour = new MenuItem();
\r
2775 MenuItem BLOSUM62Colour = new MenuItem();
\r
2777 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
2779 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
2781 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
2783 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
2785 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
\r
2787 MenuItem alProperties = new MenuItem("Alignment Properties...");
\r
2789 MenuItem overviewMenuItem = new MenuItem();
\r
2791 MenuItem undoMenuItem = new MenuItem();
\r
2793 MenuItem redoMenuItem = new MenuItem();
\r
2795 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
2797 MenuItem noColourmenuItem = new MenuItem();
\r
2799 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
2801 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
2803 MenuItem findMenuItem = new MenuItem();
\r
2805 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
2807 MenuItem nucleotideColour = new MenuItem();
\r
2809 MenuItem deleteGroups = new MenuItem();
\r
2811 MenuItem grpsFromSelection = new MenuItem();
\r
2813 MenuItem delete = new MenuItem();
\r
2815 MenuItem copy = new MenuItem();
\r
2817 MenuItem cut = new MenuItem();
\r
2819 Menu pasteMenu = new Menu();
\r
2821 MenuItem pasteNew = new MenuItem();
\r
2823 MenuItem pasteThis = new MenuItem();
\r
2825 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
2827 MenuItem font = new MenuItem();
\r
2829 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
2831 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
2833 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
2835 MenuItem modifyPID = new MenuItem();
\r
2837 MenuItem modifyConservation = new MenuItem();
\r
2839 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
\r
2840 "Autocalculate Consensus", true);
\r
2842 Menu sortByTreeMenu = new Menu();
\r
2844 Menu sort = new Menu();
\r
2846 Menu calculate = new Menu();
\r
2848 MenuItem inputText = new MenuItem();
\r
2850 Menu helpMenu = new Menu();
\r
2852 MenuItem documentation = new MenuItem();
\r
2854 MenuItem about = new MenuItem();
\r
2856 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
2858 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
\r
2860 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
\r
2861 Menu autoAnnMenu=new Menu();
\r
2862 CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();
\r
2863 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
\r
2864 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
\r
2865 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
\r
2866 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
\r
2868 private void jbInit() throws Exception
\r
2871 setMenuBar(alignFrameMenuBar);
\r
2875 // dynamically fill save as menu with available formats
\r
2876 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
2879 item = new MenuItem(
\r
2880 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
2882 item.addActionListener(new java.awt.event.ActionListener()
\r
2884 public void actionPerformed(ActionEvent e)
\r
2886 outputText_actionPerformed(e);
\r
2890 outputTextboxMenu.add(item);
\r
2892 closeMenuItem.addActionListener(this);
\r
2893 loadApplication.addActionListener(this);
\r
2895 loadTree.addActionListener(this);
\r
2896 loadAnnotations.addActionListener(this);
\r
2897 outputFeatures.addActionListener(this);
\r
2898 outputAnnotations.addActionListener(this);
\r
2899 selectAllSequenceMenuItem.addActionListener(this);
\r
2900 deselectAllSequenceMenuItem.addActionListener(this);
\r
2901 invertSequenceMenuItem.addActionListener(this);
\r
2902 remove2LeftMenuItem.setLabel("Remove Left");
\r
2903 remove2LeftMenuItem.addActionListener(this);
\r
2904 remove2RightMenuItem.setLabel("Remove Right");
\r
2905 remove2RightMenuItem.addActionListener(this);
\r
2906 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
2907 removeGappedColumnMenuItem.addActionListener(this);
\r
2908 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
2909 removeAllGapsMenuItem.addActionListener(this);
\r
2910 viewBoxesMenuItem.setLabel("Boxes");
\r
2911 viewBoxesMenuItem.setState(true);
\r
2912 viewBoxesMenuItem.addItemListener(this);
\r
2913 viewTextMenuItem.setLabel("Text");
\r
2914 viewTextMenuItem.setState(true);
\r
2915 viewTextMenuItem.addItemListener(this);
\r
2916 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
2917 sortPairwiseMenuItem.addActionListener(this);
\r
2918 sortIDMenuItem.setLabel("by ID");
\r
2919 sortIDMenuItem.addActionListener(this);
\r
2920 sortLengthMenuItem.setLabel("by Length");
\r
2921 sortLengthMenuItem.addActionListener(this);
\r
2922 sortGroupMenuItem.setLabel("by Group");
\r
2923 sortGroupMenuItem.addActionListener(this);
\r
2924 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
2925 removeRedundancyMenuItem.addActionListener(this);
\r
2926 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
2927 pairwiseAlignmentMenuItem.addActionListener(this);
\r
2928 PCAMenuItem.setLabel("Principal Component Analysis");
\r
2929 PCAMenuItem.addActionListener(this);
\r
2930 averageDistanceTreeMenuItem
\r
2931 .setLabel("Average Distance Using % Identity");
\r
2932 averageDistanceTreeMenuItem.addActionListener(this);
\r
2933 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
2934 neighbourTreeMenuItem.addActionListener(this);
\r
2935 statusBar.setBackground(Color.white);
\r
2936 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
2937 statusBar.setText("Status bar");
\r
2938 outputTextboxMenu.setLabel("Output to Textbox");
\r
2939 clustalColour.setLabel("Clustalx");
\r
2941 clustalColour.addActionListener(this);
\r
2942 zappoColour.setLabel("Zappo");
\r
2943 zappoColour.addActionListener(this);
\r
2944 taylorColour.setLabel("Taylor");
\r
2945 taylorColour.addActionListener(this);
\r
2946 hydrophobicityColour.setLabel("Hydrophobicity");
\r
2947 hydrophobicityColour.addActionListener(this);
\r
2948 helixColour.setLabel("Helix Propensity");
\r
2949 helixColour.addActionListener(this);
\r
2950 strandColour.setLabel("Strand Propensity");
\r
2951 strandColour.addActionListener(this);
\r
2952 turnColour.setLabel("Turn Propensity");
\r
2953 turnColour.addActionListener(this);
\r
2954 buriedColour.setLabel("Buried Index");
\r
2955 buriedColour.addActionListener(this);
\r
2956 userDefinedColour.setLabel("User Defined...");
\r
2957 userDefinedColour.addActionListener(this);
\r
2958 PIDColour.setLabel("Percentage Identity");
\r
2959 PIDColour.addActionListener(this);
\r
2960 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
2961 BLOSUM62Colour.addActionListener(this);
\r
2962 avDistanceTreeBlosumMenuItem
\r
2963 .setLabel("Average Distance Using BLOSUM62");
\r
2964 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
2965 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
2966 njTreeBlosumMenuItem.addActionListener(this);
\r
2967 annotationPanelMenuItem.setLabel("Show Annotations");
\r
2968 annotationPanelMenuItem.addItemListener(this);
\r
2969 colourTextMenuItem.setLabel("Colour Text");
\r
2970 colourTextMenuItem.addItemListener(this);
\r
2971 displayNonconservedMenuItem.setLabel("Show nonconserved");
\r
2972 displayNonconservedMenuItem.addItemListener(this);
\r
2973 alProperties.addActionListener(this);
\r
2974 overviewMenuItem.setLabel("Overview Window");
\r
2975 overviewMenuItem.addActionListener(this);
\r
2976 undoMenuItem.setEnabled(false);
\r
2977 undoMenuItem.setLabel("Undo");
\r
2978 undoMenuItem.addActionListener(this);
\r
2979 redoMenuItem.setEnabled(false);
\r
2980 redoMenuItem.setLabel("Redo");
\r
2981 redoMenuItem.addActionListener(this);
\r
2982 conservationMenuItem.setLabel("by Conservation");
\r
2983 conservationMenuItem.addItemListener(this);
\r
2984 noColourmenuItem.setLabel("None");
\r
2985 noColourmenuItem.addActionListener(this);
\r
2986 wrapMenuItem.setLabel("Wrap");
\r
2987 wrapMenuItem.addItemListener(this);
\r
2988 renderGapsMenuItem.setLabel("Show Gaps");
\r
2989 renderGapsMenuItem.setState(true);
\r
2990 renderGapsMenuItem.addItemListener(this);
\r
2991 findMenuItem.setLabel("Find...");
\r
2992 findMenuItem.addActionListener(this);
\r
2993 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
2994 abovePIDThreshold.addItemListener(this);
\r
2995 nucleotideColour.setLabel("Nucleotide");
\r
2996 nucleotideColour.addActionListener(this);
\r
2997 deleteGroups.setLabel("Undefine Groups");
\r
2998 deleteGroups.addActionListener(this);
\r
2999 grpsFromSelection.setLabel("Make Groups for selection");
\r
3000 grpsFromSelection.addActionListener(this);
\r
3001 copy.setLabel("Copy");
\r
3002 copy.addActionListener(this);
\r
3003 cut.setLabel("Cut");
\r
3004 cut.addActionListener(this);
\r
3005 delete.setLabel("Delete");
\r
3006 delete.addActionListener(this);
\r
3007 pasteMenu.setLabel("Paste");
\r
3008 pasteNew.setLabel("To New Alignment");
\r
3009 pasteNew.addActionListener(this);
\r
3010 pasteThis.setLabel("Add To This Alignment");
\r
3011 pasteThis.addActionListener(this);
\r
3012 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
3013 applyToAllGroups.setState(true);
\r
3014 applyToAllGroups.addItemListener(this);
\r
3015 font.setLabel("Font...");
\r
3016 font.addActionListener(this);
\r
3017 scaleAbove.setLabel("Scale Above");
\r
3018 scaleAbove.setState(true);
\r
3019 scaleAbove.setEnabled(false);
\r
3020 scaleAbove.addItemListener(this);
\r
3021 scaleLeft.setEnabled(false);
\r
3022 scaleLeft.setState(true);
\r
3023 scaleLeft.setLabel("Scale Left");
\r
3024 scaleLeft.addItemListener(this);
\r
3025 scaleRight.setEnabled(false);
\r
3026 scaleRight.setState(true);
\r
3027 scaleRight.setLabel("Scale Right");
\r
3028 scaleRight.addItemListener(this);
\r
3029 modifyPID.setLabel("Modify Identity Threshold...");
\r
3030 modifyPID.addActionListener(this);
\r
3031 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
3032 modifyConservation.addActionListener(this);
\r
3033 sortByTreeMenu.setLabel("By Tree Order");
\r
3034 sort.setLabel("Sort");
\r
3035 calculate.setLabel("Calculate Tree");
\r
3036 autoCalculate.addItemListener(this);
\r
3037 inputText.setLabel("Input from textbox");
\r
3038 inputText.addActionListener(this);
\r
3039 centreColumnLabelFlag.setLabel("Centre column labels");
\r
3040 centreColumnLabelFlag.addItemListener(this);
\r
3041 followMouseOverFlag.setLabel("Automatic Scrolling");
\r
3042 followMouseOverFlag.addItemListener(this);
\r
3043 helpMenu.setLabel("Help");
\r
3044 documentation.setLabel("Documentation");
\r
3045 documentation.addActionListener(this);
\r
3047 about.setLabel("About...");
\r
3048 about.addActionListener(this);
\r
3049 seqLimits.setState(true);
\r
3050 seqLimits.setLabel("Show Sequence Limits");
\r
3051 seqLimits.addItemListener(this);
\r
3052 featureSettings.setLabel("Feature Settings...");
\r
3053 featureSettings.addActionListener(this);
\r
3054 sequenceFeatures.setLabel("Sequence Features");
\r
3055 sequenceFeatures.addItemListener(this);
\r
3056 sequenceFeatures.setState(false);
\r
3057 annotationColour.setLabel("by Annotation...");
\r
3058 annotationColour.addActionListener(this);
\r
3059 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
3060 invertColSel.setLabel("Invert Column Selection");
\r
3061 menu1.setLabel("Show");
\r
3062 showColumns.setLabel("All Columns ");
\r
3063 showSeqs.setLabel("All Sequences");
\r
3064 menu2.setLabel("Hide");
\r
3065 hideColumns.setLabel("Selected Columns");
\r
3066 hideSequences.setLabel("Selected Sequences");
\r
3067 hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
\r
3068 hideAllSelection.setLabel("Selected Region");
\r
3069 showAllHidden.setLabel("All Sequences and Columns");
\r
3070 showGroupConsensus.setLabel("Group Consensus");
\r
3071 showGroupConservation.setLabel("Group Conservation");
\r
3072 showConsensusHistogram.setLabel("Show Consensus Histogram");
\r
3073 showSequenceLogo.setLabel("Show Consensus Logo");
\r
3074 applyAutoAnnotationSettings.setLabel("Apply to all groups");
\r
3075 applyAutoAnnotationSettings.setState(true);
\r
3076 autoAnnMenu.setLabel("Autocalculated Annotation");
\r
3078 invertColSel.addActionListener(this);
\r
3079 showColumns.addActionListener(this);
\r
3080 showSeqs.addActionListener(this);
\r
3081 hideColumns.addActionListener(this);
\r
3082 hideSequences.addActionListener(this);
\r
3083 hideAllButSelection.addActionListener(this);
\r
3084 hideAllSelection.addActionListener(this);
\r
3085 showAllHidden.addActionListener(this);
\r
3086 showGroupConsensus.addItemListener(this);
\r
3087 showGroupConservation.addItemListener(this);
\r
3088 showConsensusHistogram.addItemListener(this);
\r
3089 showSequenceLogo.addItemListener(this);
\r
3090 applyAutoAnnotationSettings.addItemListener(this);
\r
3091 formatMenu.setLabel("Format");
\r
3092 selectMenu.setLabel("Select");
\r
3093 newView.setLabel("New View");
\r
3094 newView.addActionListener(this);
\r
3095 alignFrameMenuBar.add(fileMenu);
\r
3096 alignFrameMenuBar.add(editMenu);
\r
3097 alignFrameMenuBar.add(selectMenu);
\r
3098 alignFrameMenuBar.add(viewMenu);
\r
3099 alignFrameMenuBar.add(formatMenu);
\r
3100 alignFrameMenuBar.add(colourMenu);
\r
3101 alignFrameMenuBar.add(calculateMenu);
\r
3102 alignFrameMenuBar.add(helpMenu);
\r
3104 fileMenu.add(inputText);
\r
3105 fileMenu.add(loadTree);
\r
3106 fileMenu.add(loadAnnotations);
\r
3108 fileMenu.addSeparator();
\r
3109 fileMenu.add(outputTextboxMenu);
\r
3110 fileMenu.add(outputFeatures);
\r
3111 fileMenu.add(outputAnnotations);
\r
3113 if (jalviewServletURL != null)
\r
3115 fileMenu.add(loadApplication);
\r
3118 fileMenu.addSeparator();
\r
3119 fileMenu.add(closeMenuItem);
\r
3121 editMenu.add(undoMenuItem);
\r
3122 editMenu.add(redoMenuItem);
\r
3123 editMenu.add(cut);
\r
3124 editMenu.add(copy);
\r
3125 editMenu.add(pasteMenu);
\r
3126 editMenu.add(delete);
\r
3127 editMenu.addSeparator();
\r
3128 editMenu.add(remove2LeftMenuItem);
\r
3129 editMenu.add(remove2RightMenuItem);
\r
3130 editMenu.add(removeGappedColumnMenuItem);
\r
3131 editMenu.add(removeAllGapsMenuItem);
\r
3132 editMenu.add(removeRedundancyMenuItem);
\r
3133 viewMenu.add(newView);
\r
3134 viewMenu.addSeparator();
\r
3135 viewMenu.add(menu1);
\r
3136 viewMenu.add(menu2);
\r
3137 viewMenu.addSeparator();
\r
3138 viewMenu.add(followMouseOverFlag);
\r
3139 viewMenu.add(annotationPanelMenuItem);
\r
3140 autoAnnMenu.add(applyAutoAnnotationSettings);
\r
3141 autoAnnMenu.add(showConsensusHistogram);
\r
3142 autoAnnMenu.add(showSequenceLogo);
\r
3143 autoAnnMenu.addSeparator();
\r
3144 autoAnnMenu.add(showGroupConservation);
\r
3145 autoAnnMenu.add(showGroupConsensus);
\r
3146 viewMenu.add(autoAnnMenu);
\r
3147 viewMenu.addSeparator();
\r
3148 viewMenu.add(sequenceFeatures);
\r
3149 viewMenu.add(featureSettings);
\r
3150 viewMenu.addSeparator();
\r
3151 viewMenu.add(alProperties);
\r
3152 viewMenu.addSeparator();
\r
3153 viewMenu.add(overviewMenuItem);
\r
3154 colourMenu.add(applyToAllGroups);
\r
3155 colourMenu.addSeparator();
\r
3156 colourMenu.add(noColourmenuItem);
\r
3157 colourMenu.add(clustalColour);
\r
3158 colourMenu.add(BLOSUM62Colour);
\r
3159 colourMenu.add(PIDColour);
\r
3160 colourMenu.add(zappoColour);
\r
3161 colourMenu.add(taylorColour);
\r
3162 colourMenu.add(hydrophobicityColour);
\r
3163 colourMenu.add(helixColour);
\r
3164 colourMenu.add(strandColour);
\r
3165 colourMenu.add(turnColour);
\r
3166 colourMenu.add(buriedColour);
\r
3167 colourMenu.add(nucleotideColour);
\r
3168 colourMenu.add(userDefinedColour);
\r
3169 colourMenu.addSeparator();
\r
3170 colourMenu.add(conservationMenuItem);
\r
3171 colourMenu.add(modifyConservation);
\r
3172 colourMenu.add(abovePIDThreshold);
\r
3173 colourMenu.add(modifyPID);
\r
3174 colourMenu.add(annotationColour);
\r
3175 calculateMenu.add(sort);
\r
3176 calculateMenu.add(calculate);
\r
3177 calculateMenu.addSeparator();
\r
3178 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
3179 calculateMenu.add(PCAMenuItem);
\r
3180 calculateMenu.add(autoCalculate);
\r
3181 this.add(statusBar, BorderLayout.SOUTH);
\r
3182 pasteMenu.add(pasteNew);
\r
3183 pasteMenu.add(pasteThis);
\r
3184 sort.add(sortIDMenuItem);
\r
3185 sort.add(sortLengthMenuItem);
\r
3186 sort.add(sortByTreeMenu);
\r
3187 sort.add(sortGroupMenuItem);
\r
3188 sort.add(sortPairwiseMenuItem);
\r
3189 calculate.add(averageDistanceTreeMenuItem);
\r
3190 calculate.add(neighbourTreeMenuItem);
\r
3191 calculate.add(avDistanceTreeBlosumMenuItem);
\r
3192 calculate.add(njTreeBlosumMenuItem);
\r
3193 helpMenu.add(documentation);
\r
3194 helpMenu.add(about);
\r
3195 menu1.add(showColumns);
\r
3196 menu1.add(showSeqs);
\r
3197 menu1.add(showAllHidden);
\r
3198 menu2.add(hideColumns);
\r
3199 menu2.add(hideSequences);
\r
3200 menu2.add(hideAllSelection);
\r
3201 menu2.add(hideAllButSelection);
\r
3202 formatMenu.add(font);
\r
3203 formatMenu.add(seqLimits);
\r
3204 formatMenu.add(wrapMenuItem);
\r
3205 formatMenu.add(scaleAbove);
\r
3206 formatMenu.add(scaleLeft);
\r
3207 formatMenu.add(scaleRight);
\r
3208 formatMenu.add(viewBoxesMenuItem);
\r
3209 formatMenu.add(viewTextMenuItem);
\r
3210 formatMenu.add(colourTextMenuItem);
\r
3211 formatMenu.add(displayNonconservedMenuItem);
\r
3212 formatMenu.add(renderGapsMenuItem);
\r
3213 formatMenu.add(centreColumnLabelFlag);
\r
3214 selectMenu.add(findMenuItem);
\r
3215 selectMenu.addSeparator();
\r
3216 selectMenu.add(selectAllSequenceMenuItem);
\r
3217 selectMenu.add(deselectAllSequenceMenuItem);
\r
3218 selectMenu.add(invertSequenceMenuItem);
\r
3219 selectMenu.add(invertColSel);
\r
3220 selectMenu.add(grpsFromSelection);
\r
3221 selectMenu.add(deleteGroups);
\r
3225 MenuItem featureSettings = new MenuItem();
\r
3227 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
3229 MenuItem annotationColour = new MenuItem();
\r
3231 MenuItem invertColSel = new MenuItem();
\r
3233 Menu menu1 = new Menu();
\r
3235 MenuItem showColumns = new MenuItem();
\r
3237 MenuItem showSeqs = new MenuItem();
\r
3239 Menu menu2 = new Menu();
\r
3241 MenuItem hideColumns = new MenuItem();
\r
3243 MenuItem hideSequences = new MenuItem();
\r
3245 MenuItem hideAllButSelection = new MenuItem();
\r
3247 MenuItem hideAllSelection = new MenuItem();
\r
3249 MenuItem showAllHidden = new MenuItem();
\r
3251 Menu formatMenu = new Menu();
\r
3253 Menu selectMenu = new Menu();
\r
3255 MenuItem newView = new MenuItem();
\r
3258 * Attach the alignFrame panels after embedding menus, if necessary. This used
\r
3259 * to be called setEmbedded, but is now creates the dropdown menus in a
\r
3260 * platform independent manner to avoid OSX/Mac menu appendage daftness.
\r
3262 * @param reallyEmbedded
\r
3263 * true to attach the view to the applet area on the page rather than
\r
3266 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
\r
3268 if (reallyEmbedded)
\r
3271 // Explicly build the embedded menu panel for the on-page applet
\r
3273 // view cannot be closed if its actually on the page
\r
3274 fileMenu.remove(closeMenuItem);
\r
3275 fileMenu.remove(3); // Remove Seperator
\r
3276 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
\r
3277 Font.PLAIN, 10, false); // use our own fonts.
\r
3278 // and actually add the components to the applet area
\r
3279 viewport.applet.setLayout(new BorderLayout());
\r
3280 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
\r
3281 viewport.applet.add(statusBar, BorderLayout.SOUTH);
\r
3282 alignPanel.setSize(viewport.applet.getSize().width,
\r
3283 viewport.applet.getSize().height - embeddedMenu.HEIGHT
\r
3284 - statusBar.HEIGHT);
\r
3285 viewport.applet.add(alignPanel, BorderLayout.CENTER);
\r
3286 final AlignFrame me = this;
\r
3287 viewport.applet.addFocusListener(new FocusListener()
\r
3291 public void focusLost(FocusEvent e)
\r
3293 if (me.viewport.applet.currentAlignFrame==me) {
\r
3294 me.viewport.applet.currentAlignFrame = null;
\r
3298 public void focusGained(FocusEvent e)
\r
3300 me.viewport.applet.currentAlignFrame = me;
\r
3303 viewport.applet.validate();
\r
3308 // test and embed menu bar if necessary.
\r
3310 if (embedMenuIfNeeded(alignPanel))
\r
3312 // adjust for status bar height too
\r
3313 alignPanel.setSize(getSize().width, getSize().height
\r
3314 - statusBar.HEIGHT);
\r
3316 add(statusBar, BorderLayout.SOUTH);
\r
3317 add(alignPanel, BorderLayout.CENTER);
\r
3318 // and register with the applet so it can pass external API calls to us
\r
3319 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
\r
3325 * create a new binding between structures in an existing jmol viewer instance
\r
3326 * and an alignpanel with sequences that have existing PDBFile entries. Note,
\r
3327 * this does not open a new Jmol window, or modify the display of the
\r
3328 * structures in the original jmol window. Note This method doesn't work
\r
3329 * without an additional javascript library to exchange messages between the
\r
3330 * distinct applets. See http://issues.jalview.org/browse/JAL-621
\r
3333 * JmolViewer instance
\r
3334 * @param sequenceIds
\r
3335 * - sequence Ids to search for associations
\r
3337 public SequenceStructureBinding addStructureViewInstance(
\r
3338 Object jmolviewer, String[] sequenceIds)
\r
3340 org.jmol.api.JmolViewer viewer = null;
\r
3343 viewer = (org.jmol.api.JmolViewer) jmolviewer;
\r
3344 } catch (ClassCastException ex)
\r
3346 System.err.println("Unsupported viewer object :"
\r
3347 + jmolviewer.getClass());
\r
3349 if (viewer == null)
\r
3351 System.err.println("Can't use this object as a structure viewer:"
\r
3352 + jmolviewer.getClass());
\r
3355 SequenceI[] seqs = null;
\r
3356 if (sequenceIds == null || sequenceIds.length == 0)
\r
3358 seqs = viewport.getAlignment().getSequencesArray();
\r
3362 Vector sqi = new Vector();
\r
3363 AlignmentI al = viewport.getAlignment();
\r
3364 for (int sid = 0; sid < sequenceIds.length; sid++)
\r
3366 SequenceI sq = al.findName(sequenceIds[sid]);
\r
3369 sqi.addElement(sq);
\r
3372 if (sqi.size() > 0)
\r
3374 seqs = new SequenceI[sqi.size()];
\r
3375 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
\r
3377 seqs[sid] = (SequenceI) sqi.elementAt(sid);
\r
3385 ExtJmol jmv = null;
\r
3386 // TODO: search for a jmv that involves viewer
\r
3388 { // create a new viewer/jalview binding.
\r
3389 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs});
\r
3395 * bind a pdb file to a sequence in the current view
\r
3397 * @param sequenceId
\r
3398 * - sequenceId within the dataset.
\r
3399 * @param pdbEntryString
\r
3400 * - the short name for the PDB file
\r
3402 * - pdb file - either a URL or a valid PDB file.
\r
3403 * @return true if binding was as success TODO: consider making an exception
\r
3404 * structure for indicating when PDB parsing or sequenceId location
\r
3407 public boolean addPdbFile(String sequenceId, String pdbEntryString,
\r
3410 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
\r
3411 boolean needtoadd = false;
\r
3412 if (toaddpdb != null)
\r
3414 Vector pdbe = toaddpdb.getPDBId();
\r
3415 PDBEntry pdbentry = null;
\r
3416 if (pdbe != null && pdbe.size() > 0)
\r
3418 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
\r
3420 pdbentry = (PDBEntry) pdbe.elementAt(pe);
\r
3421 if (!pdbentry.getId().equals(pdbEntryString)
\r
3422 && !pdbentry.getFile().equals(pdbFile))
\r
3432 if (pdbentry == null)
\r
3434 pdbentry = new PDBEntry();
\r
3435 pdbentry.setId(pdbEntryString);
\r
3436 pdbentry.setFile(pdbFile);
\r
3437 needtoadd = true; // add this new entry to sequence.
\r
3439 // resolve data source
\r
3440 // TODO: this code should be a refactored to an io package
\r
3441 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
\r
3442 if (protocol == null)
\r
3448 // make a note of the access mode and add
\r
3449 if (pdbentry.getProperty() == null)
\r
3451 pdbentry.setProperty(new Hashtable());
\r
3453 pdbentry.getProperty().put("protocol", protocol);
\r
3454 toaddpdb.addPDBId(pdbentry);
\r
3460 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
\r
3464 Vector sequences = new Vector();
\r
3465 for (int i = 0; i < seqs.length; i++)
\r
3467 if (seqs[i] != null)
\r
3469 sequences.addElement(new Object[]
\r
3470 { seqs[i], (chains != null) ? chains[i] : null });
\r
3473 seqs = new SequenceI[sequences.size()];
\r
3474 chains = new String[sequences.size()];
\r
3475 for (int i = 0, isize = sequences.size(); i < isize; i++)
\r
3477 Object[] oj = (Object[]) sequences.elementAt(i);
\r
3479 seqs[i] = (SequenceI) oj[0];
\r
3480 chains[i] = (String) oj[1];
\r
3483 return new Object[]
\r
3488 public void newStructureView(JalviewLite applet, PDBEntry pdb,
\r
3489 SequenceI[] seqs, String[] chains, String protocol)
\r
3491 // Scrub any null sequences from the array
\r
3492 Object[] sqch = cleanSeqChainArrays(seqs, chains);
\r
3493 seqs = (SequenceI[]) sqch[0];
\r
3494 chains = (String[]) sqch[1];
\r
3495 if (seqs == null || seqs.length == 0)
\r
3498 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
\r
3500 if (protocol == null || protocol.trim().length() == 0
\r
3501 || protocol.equals("null"))
\r
3503 protocol = (String) pdb.getProperty().get("protocol");
\r
3504 if (protocol == null)
\r
3506 System.err.println("Couldn't work out protocol to open structure: "
\r
3511 if (applet.useXtrnalSviewer)
\r
3513 // register the association(s) and quit, don't create any windows.
\r
3514 if (StructureSelectionManager.getStructureSelectionManager().setMapping(seqs, chains, pdb.getFile(), protocol)==null) {
\r
3515 System.err.println("Failed to map "+pdb.getFile()+" ("+protocol+") to any sequences");
\r
3519 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
\r
3521 // can only do alignments with Jmol
\r
3522 // find the last jmol window assigned to this alignment
\r
3523 jalview.appletgui.AppletJmol ajm = null, tajm;
\r
3524 Vector jmols = applet
\r
3525 .getAppletWindow(jalview.appletgui.AppletJmol.class);
\r
3526 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
\r
3528 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
\r
3529 if (tajm.ap.alignFrame == this)
\r
3538 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
\r
3539 // try and add the pdb structure
\r
3544 // otherwise, create a new window
\r
3545 if (applet.jmolAvailable)
\r
3547 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
\r
3549 applet.lastFrameX += 40;
\r
3550 applet.lastFrameY += 40;
\r
3554 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
\r
3559 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
\r
3560 SequenceI[][] seqs, String[][] chains, String[] protocols)
\r
3562 // TODO Auto-generated method stub
\r
3563 System.err.println("Aligned Structure View: Not yet implemented.");
\r
3567 * modify the current selection, providing the user has not made a selection already.
\r
3568 * @param sel - sequences from this alignment
\r
3569 * @param csel - columns to be selected on the alignment
\r
3571 public void select(SequenceGroup sel, ColumnSelection csel)
\r
3573 alignPanel.seqPanel.selection(sel, csel, null);
\r