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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149 alignPanel.adjustAnnotationHeight();
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150 alignPanel.paintAlignment(true);
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153 public AlignViewport getAlignViewport()
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158 public SeqCanvas getSeqcanvas()
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160 return alignPanel.seqPanel.seqCanvas;
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170 public void parseFeaturesFile(String file, String type)
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172 Hashtable featureLinks = new Hashtable();
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173 boolean featuresFile = false;
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176 featuresFile = new jalview.io.FeaturesFile(file, type)
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177 .parse(viewport.alignment,
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178 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
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179 featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));
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180 } catch (Exception ex)
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182 ex.printStackTrace();
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187 if (featureLinks.size() > 0)
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189 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
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191 viewport.showSequenceFeatures = true;
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192 sequenceFeatures.setState(true);
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193 if (viewport.featureSettings != null)
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195 viewport.featureSettings.refreshTable();
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197 alignPanel.paintAlignment(true);
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202 public void keyPressed(KeyEvent evt)
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204 if (viewport.cursorMode
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205 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
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206 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
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207 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
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208 && Character.isDigit(evt.getKeyChar()))
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209 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
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211 switch (evt.getKeyCode())
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213 case 27: // escape key
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214 deselectAllSequenceMenuItem_actionPerformed();
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216 alignPanel.alabels.cancelDrag();
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218 case KeyEvent.VK_X:
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219 if (evt.isControlDown() || evt.isMetaDown())
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221 cut_actionPerformed();
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224 case KeyEvent.VK_C:
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225 if (viewport.cursorMode && !evt.isControlDown())
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227 alignPanel.seqPanel.setCursorColumn();
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229 if (evt.isControlDown() || evt.isMetaDown())
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231 copy_actionPerformed();
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234 case KeyEvent.VK_V:
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235 if (evt.isControlDown())
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237 paste(evt.isShiftDown());
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240 case KeyEvent.VK_A:
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241 if (evt.isControlDown() || evt.isMetaDown())
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243 selectAllSequenceMenuItem_actionPerformed();
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246 case KeyEvent.VK_DOWN:
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247 if (viewport.cursorMode)
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249 alignPanel.seqPanel.moveCursor(0, 1);
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253 moveSelectedSequences(false);
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257 case KeyEvent.VK_UP:
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258 if (viewport.cursorMode)
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260 alignPanel.seqPanel.moveCursor(0, -1);
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264 moveSelectedSequences(true);
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268 case KeyEvent.VK_LEFT:
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269 if (evt.isAltDown() || !viewport.cursorMode)
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270 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
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272 alignPanel.seqPanel.moveCursor(-1, 0);
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275 case KeyEvent.VK_RIGHT:
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276 if (evt.isAltDown() || !viewport.cursorMode)
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277 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
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279 alignPanel.seqPanel.moveCursor(1, 0);
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282 case KeyEvent.VK_SPACE:
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283 if (viewport.cursorMode)
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285 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
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286 || evt.isShiftDown() || evt.isAltDown());
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290 case KeyEvent.VK_DELETE:
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291 case KeyEvent.VK_BACK_SPACE:
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292 if (viewport.cursorMode)
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294 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
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295 || evt.isShiftDown() || evt.isAltDown());
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299 cut_actionPerformed();
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300 alignPanel.seqPanel.seqCanvas.repaint();
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304 case KeyEvent.VK_S:
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305 if (viewport.cursorMode)
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307 alignPanel.seqPanel.setCursorRow();
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310 case KeyEvent.VK_P:
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311 if (viewport.cursorMode)
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313 alignPanel.seqPanel.setCursorPosition();
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317 case KeyEvent.VK_ENTER:
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318 case KeyEvent.VK_COMMA:
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319 if (viewport.cursorMode)
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321 alignPanel.seqPanel.setCursorRowAndColumn();
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325 case KeyEvent.VK_Q:
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326 if (viewport.cursorMode)
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328 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
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331 case KeyEvent.VK_M:
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332 if (viewport.cursorMode)
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334 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
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338 case KeyEvent.VK_F2:
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339 viewport.cursorMode = !viewport.cursorMode;
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340 statusBar.setText("Keyboard editing mode is "
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341 + (viewport.cursorMode ? "on" : "off"));
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342 if (viewport.cursorMode)
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344 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
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345 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
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349 case KeyEvent.VK_F:
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350 if (evt.isControlDown())
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352 findMenuItem_actionPerformed();
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356 case KeyEvent.VK_H:
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358 boolean toggleSeqs = !evt.isControlDown();
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359 boolean toggleCols = !evt.isShiftDown();
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360 toggleHiddenRegions(toggleSeqs, toggleCols);
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364 case KeyEvent.VK_PAGE_UP:
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365 if (viewport.wrapAlignment)
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367 alignPanel.scrollUp(true);
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371 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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372 - viewport.endSeq + viewport.startSeq);
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376 case KeyEvent.VK_PAGE_DOWN:
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377 if (viewport.wrapAlignment)
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379 alignPanel.scrollUp(false);
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383 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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384 + viewport.endSeq - viewport.startSeq);
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388 case KeyEvent.VK_Z:
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389 if (evt.isControlDown())
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391 undoMenuItem_actionPerformed();
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395 case KeyEvent.VK_Y:
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396 if (evt.isControlDown())
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398 redoMenuItem_actionPerformed();
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402 case KeyEvent.VK_L:
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403 if (evt.isControlDown())
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405 trimAlignment(true);
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409 case KeyEvent.VK_R:
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410 if (evt.isControlDown())
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412 trimAlignment(false);
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416 case KeyEvent.VK_E:
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417 if (evt.isControlDown())
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419 if (evt.isShiftDown())
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421 this.removeAllGapsMenuItem_actionPerformed();
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425 removeGappedColumnMenuItem_actionPerformed();
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429 case KeyEvent.VK_I:
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430 if (evt.isControlDown())
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432 if (evt.isAltDown())
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434 invertColSel_actionPerformed();
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438 invertSequenceMenuItem_actionPerformed();
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443 case KeyEvent.VK_U:
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444 if (evt.isControlDown())
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446 this.deleteGroups_actionPerformed();
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450 case KeyEvent.VK_T:
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451 if (evt.isControlDown())
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458 alignPanel.paintAlignment(true);
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462 * called by key handler and the hide all/show all menu items
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464 * @param toggleSeqs
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465 * @param toggleCols
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467 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
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469 boolean hide = false;
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470 SequenceGroup sg = viewport.getSelectionGroup();
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471 if (!toggleSeqs && !toggleCols)
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473 // Hide everything by the current selection - this is a hack - we do the
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474 // invert and then hide
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475 // first check that there will be visible columns after the invert.
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476 if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
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477 .getSelected().size() > 0)
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478 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
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481 // now invert the sequence set, if required - empty selection implies
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482 // that no hiding is required.
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485 invertSequenceMenuItem_actionPerformed();
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486 sg = viewport.getSelectionGroup();
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490 viewport.expandColSelection(sg, true);
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491 // finally invert the column selection and get the new sequence
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492 // selection and indicate it should be hidden.
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493 invertColSel_actionPerformed();
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500 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
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503 viewport.hideAllSelectedSeqs();
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505 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
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507 viewport.showAllHiddenSeqs();
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513 if (viewport.colSel.getSelected().size() > 0)
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515 viewport.hideSelectedColumns();
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518 viewport.selectionGroup = sg;
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523 viewport.showAllHiddenColumns();
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528 public void keyReleased(KeyEvent evt)
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532 public void keyTyped(KeyEvent evt)
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536 public void itemStateChanged(ItemEvent evt)
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538 if (evt.getSource() == displayNonconservedMenuItem)
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540 displayNonconservedMenuItem_actionPerformed();
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542 else if (evt.getSource() == colourTextMenuItem)
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544 colourTextMenuItem_actionPerformed();
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546 else if (evt.getSource() == wrapMenuItem)
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548 wrapMenuItem_actionPerformed();
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550 else if (evt.getSource() == scaleAbove)
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552 viewport.setScaleAboveWrapped(scaleAbove.getState());
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554 else if (evt.getSource() == scaleLeft)
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556 viewport.setScaleLeftWrapped(scaleLeft.getState());
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558 else if (evt.getSource() == scaleRight)
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560 viewport.setScaleRightWrapped(scaleRight.getState());
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562 else if (evt.getSource() == seqLimits)
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564 seqLimits_itemStateChanged();
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566 else if (evt.getSource() == viewBoxesMenuItem)
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568 viewport.setShowBoxes(viewBoxesMenuItem.getState());
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570 else if (evt.getSource() == viewTextMenuItem)
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572 viewport.setShowText(viewTextMenuItem.getState());
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574 else if (evt.getSource() == renderGapsMenuItem)
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576 viewport.setRenderGaps(renderGapsMenuItem.getState());
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578 else if (evt.getSource() == annotationPanelMenuItem)
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580 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
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581 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
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583 else if (evt.getSource() == sequenceFeatures)
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585 viewport.showSequenceFeatures(sequenceFeatures.getState());
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586 alignPanel.seqPanel.seqCanvas.repaint();
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588 else if (evt.getSource() == conservationMenuItem)
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590 conservationMenuItem_actionPerformed();
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592 else if (evt.getSource() == abovePIDThreshold)
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594 abovePIDThreshold_actionPerformed();
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596 else if (evt.getSource() == applyToAllGroups)
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598 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
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600 else if (evt.getSource() == autoCalculate)
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602 viewport.autocalculateConsensus = autoCalculate.getState();
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604 else if (evt.getSource() == this.centreColumnLabelFlag)
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606 centreColumnLabelFlag_stateChanged();
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608 else if (evt.getSource() == this.followMouseOverFlag)
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610 mouseOverFlag_stateChanged();
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612 else if (evt.getSource() == showGroupConsensus)
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614 showGroupConsensus_actionPerformed();
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616 else if (evt.getSource() == showGroupConservation)
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618 showGroupConservation_actionPerformed();
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620 else if (evt.getSource() == showSequenceLogo)
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622 showSequenceLogo_actionPerformed();
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624 else if (evt.getSource() == showConsensusHistogram)
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626 showConsensusHistogram_actionPerformed();
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628 else if (evt.getSource() == applyAutoAnnotationSettings)
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630 applyAutoAnnotationSettings_actionPerformed();
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632 alignPanel.paintAlignment(true);
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635 private void mouseOverFlag_stateChanged()
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637 viewport.followHighlight = followMouseOverFlag.getState();
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638 // TODO: could kick the scrollTo mechanism to reset view for current
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642 private void centreColumnLabelFlag_stateChanged()
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644 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
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645 this.alignPanel.annotationPanel.repaint();
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648 public void actionPerformed(ActionEvent evt)
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650 Object source = evt.getSource();
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652 if (source == inputText)
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654 inputText_actionPerformed();
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656 else if (source == loadTree)
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658 loadTree_actionPerformed();
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660 else if (source == loadApplication)
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662 launchFullApplication();
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664 else if (source == loadAnnotations)
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668 else if (source == outputAnnotations)
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670 outputAnnotations(true);
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672 else if (source == outputFeatures)
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674 outputFeatures(true, "Jalview");
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676 else if (source == closeMenuItem)
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678 closeMenuItem_actionPerformed();
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680 else if (source == copy)
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682 copy_actionPerformed();
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684 else if (source == undoMenuItem)
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686 undoMenuItem_actionPerformed();
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688 else if (source == redoMenuItem)
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690 redoMenuItem_actionPerformed();
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692 else if (source == inputText)
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694 inputText_actionPerformed();
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696 else if (source == closeMenuItem)
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698 closeMenuItem_actionPerformed();
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700 else if (source == undoMenuItem)
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702 undoMenuItem_actionPerformed();
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704 else if (source == redoMenuItem)
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706 redoMenuItem_actionPerformed();
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708 else if (source == copy)
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710 copy_actionPerformed();
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712 else if (source == pasteNew)
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714 pasteNew_actionPerformed();
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716 else if (source == pasteThis)
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718 pasteThis_actionPerformed();
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720 else if (source == cut)
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722 cut_actionPerformed();
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724 else if (source == delete)
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726 delete_actionPerformed();
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728 else if (source == grpsFromSelection)
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730 makeGrpsFromSelection_actionPerformed();
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732 else if (source == deleteGroups)
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734 deleteGroups_actionPerformed();
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736 else if (source == selectAllSequenceMenuItem)
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738 selectAllSequenceMenuItem_actionPerformed();
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740 else if (source == deselectAllSequenceMenuItem)
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742 deselectAllSequenceMenuItem_actionPerformed();
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744 else if (source == invertSequenceMenuItem)
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746 invertSequenceMenuItem_actionPerformed();
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748 else if (source == invertColSel)
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750 viewport.invertColumnSelection();
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751 alignPanel.paintAlignment(true);
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753 else if (source == remove2LeftMenuItem)
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755 trimAlignment(true);
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757 else if (source == remove2RightMenuItem)
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759 trimAlignment(false);
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761 else if (source == removeGappedColumnMenuItem)
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763 removeGappedColumnMenuItem_actionPerformed();
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765 else if (source == removeAllGapsMenuItem)
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767 removeAllGapsMenuItem_actionPerformed();
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769 else if (source == findMenuItem)
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771 findMenuItem_actionPerformed();
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773 else if (source == font)
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775 new FontChooser(alignPanel);
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777 else if (source == newView)
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781 else if (source == showColumns)
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783 viewport.showAllHiddenColumns();
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784 alignPanel.paintAlignment(true);
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786 else if (source == showSeqs)
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788 viewport.showAllHiddenSeqs();
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789 alignPanel.paintAlignment(true);
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791 else if (source == hideColumns)
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793 viewport.hideSelectedColumns();
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794 alignPanel.paintAlignment(true);
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796 else if (source == hideSequences
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797 && viewport.getSelectionGroup() != null)
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799 viewport.hideAllSelectedSeqs();
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800 alignPanel.paintAlignment(true);
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802 else if (source == hideAllButSelection)
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804 toggleHiddenRegions(false, false);
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805 alignPanel.paintAlignment(true);
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807 else if (source == hideAllSelection)
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809 SequenceGroup sg = viewport.getSelectionGroup();
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810 viewport.expandColSelection(sg, false);
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811 viewport.hideAllSelectedSeqs();
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812 viewport.hideSelectedColumns();
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813 alignPanel.paintAlignment(true);
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815 else if (source == showAllHidden)
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817 viewport.showAllHiddenColumns();
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818 viewport.showAllHiddenSeqs();
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819 alignPanel.paintAlignment(true);
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821 else if (source == showGroupConsensus)
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823 showGroupConsensus_actionPerformed();
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825 else if (source == showGroupConservation)
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827 showGroupConservation_actionPerformed();
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829 else if (source == showSequenceLogo)
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831 showSequenceLogo_actionPerformed();
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833 else if (source == showConsensusHistogram)
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835 showConsensusHistogram_actionPerformed();
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837 else if (source == applyAutoAnnotationSettings)
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839 applyAutoAnnotationSettings_actionPerformed();
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841 else if (source == featureSettings)
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843 new FeatureSettings(alignPanel);
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845 else if (source == alProperties)
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847 StringBuffer contents = new jalview.io.AlignmentProperties(
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848 viewport.alignment).formatAsString();
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849 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
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850 cap.setText(contents.toString());
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851 Frame frame = new Frame();
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853 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
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854 + getTitle(), 400, 250);
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856 else if (source == overviewMenuItem)
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858 overviewMenuItem_actionPerformed();
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860 else if (source == noColourmenuItem)
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862 changeColour(null);
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864 else if (source == clustalColour)
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866 abovePIDThreshold.setState(false);
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867 changeColour(new ClustalxColourScheme(
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868 viewport.alignment.getSequences(),
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869 viewport.alignment.getWidth()));
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871 else if (source == zappoColour)
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873 changeColour(new ZappoColourScheme());
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875 else if (source == taylorColour)
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877 changeColour(new TaylorColourScheme());
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879 else if (source == hydrophobicityColour)
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881 changeColour(new HydrophobicColourScheme());
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883 else if (source == helixColour)
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885 changeColour(new HelixColourScheme());
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887 else if (source == strandColour)
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889 changeColour(new StrandColourScheme());
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891 else if (source == turnColour)
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893 changeColour(new TurnColourScheme());
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895 else if (source == buriedColour)
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897 changeColour(new BuriedColourScheme());
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899 else if (source == nucleotideColour)
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901 changeColour(new NucleotideColourScheme());
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903 else if (source == modifyPID)
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905 modifyPID_actionPerformed();
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907 else if (source == modifyConservation)
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909 modifyConservation_actionPerformed();
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911 else if (source == userDefinedColour)
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913 new UserDefinedColours(alignPanel, null);
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915 else if (source == PIDColour)
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917 changeColour(new PIDColourScheme());
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919 else if (source == BLOSUM62Colour)
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921 changeColour(new Blosum62ColourScheme());
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923 else if (source == annotationColour)
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925 new AnnotationColourChooser(viewport, alignPanel);
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927 else if (source == sortPairwiseMenuItem)
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929 sortPairwiseMenuItem_actionPerformed();
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931 else if (source == sortIDMenuItem)
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933 sortIDMenuItem_actionPerformed();
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935 else if (source == sortLengthMenuItem)
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937 sortLengthMenuItem_actionPerformed();
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939 else if (source == sortGroupMenuItem)
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941 sortGroupMenuItem_actionPerformed();
\r
943 else if (source == removeRedundancyMenuItem)
\r
945 removeRedundancyMenuItem_actionPerformed();
\r
947 else if (source == pairwiseAlignmentMenuItem)
\r
949 pairwiseAlignmentMenuItem_actionPerformed();
\r
951 else if (source == PCAMenuItem)
\r
953 PCAMenuItem_actionPerformed();
\r
955 else if (source == averageDistanceTreeMenuItem)
\r
957 averageDistanceTreeMenuItem_actionPerformed();
\r
959 else if (source == neighbourTreeMenuItem)
\r
961 neighbourTreeMenuItem_actionPerformed();
\r
963 else if (source == njTreeBlosumMenuItem)
\r
965 njTreeBlosumMenuItem_actionPerformed();
\r
967 else if (source == avDistanceTreeBlosumMenuItem)
\r
969 avTreeBlosumMenuItem_actionPerformed();
\r
971 else if (source == documentation)
\r
973 documentation_actionPerformed();
\r
975 else if (source == about)
\r
977 about_actionPerformed();
\r
982 public void inputText_actionPerformed()
\r
984 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
985 Frame frame = new Frame();
\r
987 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
\r
990 protected void outputText_actionPerformed(ActionEvent e)
\r
992 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
993 Frame frame = new Frame();
\r
995 jalview.bin.JalviewLite.addFrame(frame,
\r
996 "Alignment output - " + e.getActionCommand(), 600, 500);
\r
997 cap.setText(new AppletFormatAdapter().formatSequences(
\r
998 e.getActionCommand(), viewport.getAlignment(),
\r
999 viewport.showJVSuffix));
\r
1002 public void loadAnnotations()
\r
1004 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1005 cap.setText("Paste your features / annotations file here.");
\r
1006 cap.setAnnotationImport();
\r
1007 Frame frame = new Frame();
\r
1009 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
\r
1013 public String outputAnnotations(boolean displayTextbox)
\r
1015 String annotation = new AnnotationFile().printAnnotations(
\r
1016 viewport.showAnnotation ? viewport.alignment
\r
1017 .getAlignmentAnnotation() : null, viewport.alignment
\r
1019 ((Alignment) viewport.alignment).alignmentProperties);
\r
1021 if (displayTextbox)
\r
1023 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
1024 Frame frame = new Frame();
\r
1026 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
\r
1027 cap.setText(annotation);
\r
1030 return annotation;
\r
1033 private Hashtable getDisplayedFeatureCols()
\r
1035 if (alignPanel.getFeatureRenderer() != null && viewport.featuresDisplayed!=null)
\r
1037 FeatureRenderer fr = alignPanel.getFeatureRenderer();
\r
1038 Hashtable fcols = new Hashtable();
\r
1039 Enumeration en = viewport.featuresDisplayed.keys();
\r
1040 while (en.hasMoreElements())
\r
1042 Object col = en.nextElement();
\r
1043 fcols.put(col, fr.featureColours.get(col));
\r
1050 public String outputFeatures(boolean displayTextbox, String format)
\r
1053 if (format.equalsIgnoreCase("Jalview"))
\r
1055 features = new FeaturesFile().printJalviewFormat(
\r
1056 viewport.alignment.getSequencesArray(),
\r
1057 getDisplayedFeatureCols());
\r
1061 features = new FeaturesFile().printGFFFormat(
\r
1062 viewport.alignment.getSequencesArray(),
\r
1063 getDisplayedFeatureCols());
\r
1066 if (displayTextbox)
\r
1068 boolean frimport=false;
\r
1069 if (features==null || features.equals("No Features Visible"))
\r
1071 features = "# No features visible - paste some and import them here.";
\r
1075 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
\r
1078 cap.setAnnotationImport();
\r
1080 Frame frame = new Frame();
\r
1082 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
\r
1083 cap.setText(features);
\r
1085 if (features==null)
\r
1092 void launchFullApplication()
\r
1094 StringBuffer url = new StringBuffer(jalviewServletURL);
\r
1096 url.append("?open="
\r
1097 + appendProtocol(viewport.applet.getParameter("file")));
\r
1099 if (viewport.applet.getParameter("features") != null)
\r
1101 url.append("&features=");
\r
1102 url.append(appendProtocol(viewport.applet.getParameter("features")));
\r
1105 if (viewport.applet.getParameter("annotations") != null)
\r
1107 url.append("&annotations=");
\r
1108 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
\r
1111 if (viewport.applet.getParameter("jnetfile") != null)
\r
1113 url.append("&annotations=");
\r
1114 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
\r
1117 if (viewport.applet.getParameter("defaultColour") != null)
\r
1119 url.append("&colour="
\r
1120 + removeWhiteSpace(viewport.applet
\r
1121 .getParameter("defaultColour")));
\r
1124 if (viewport.applet.getParameter("userDefinedColour") != null)
\r
1126 url.append("&colour="
\r
1127 + removeWhiteSpace(viewport.applet
\r
1128 .getParameter("userDefinedColour")));
\r
1130 if (viewport.applet.getParameter("tree") != null)
\r
1132 url.append("&tree="
\r
1133 + appendProtocol(viewport.applet.getParameter("tree")));
\r
1135 if (viewport.applet.getParameter("treeFile") != null)
\r
1137 url.append("&tree="
\r
1138 + appendProtocol(viewport.applet.getParameter("treeFile")));
\r
1141 showURL(url.toString(), "FULL_APP");
\r
1144 String removeWhiteSpace(String colour)
\r
1146 StringBuffer sb = new StringBuffer();
\r
1147 for (int i = 0; i < colour.length(); i++)
\r
1149 if (Character.isWhitespace(colour.charAt(i)))
\r
1155 sb.append(colour.charAt(i));
\r
1159 return sb.toString();
\r
1162 String appendProtocol(String url)
\r
1167 url = URLEncoder.encode(url);
\r
1170 * When we finally deprecate 1.1 compatibility, we can start to use
\r
1171 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
\r
1172 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
\r
1173 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
\r
1174 * ex.printStackTrace(); }
\r
1176 catch (java.net.MalformedURLException ex)
\r
1178 url = viewport.applet.getCodeBase() + url;
\r
1183 public void closeMenuItem_actionPerformed()
\r
1185 PaintRefresher.RemoveComponent(alignPanel);
\r
1186 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
\r
1187 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
\r
1189 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
\r
1195 alignPanel = null;
\r
1202 void updateEditMenuBar()
\r
1205 if (viewport.historyList.size() > 0)
\r
1207 undoMenuItem.setEnabled(true);
\r
1208 CommandI command = (CommandI) viewport.historyList.peek();
\r
1209 undoMenuItem.setLabel("Undo " + command.getDescription());
\r
1213 undoMenuItem.setEnabled(false);
\r
1214 undoMenuItem.setLabel("Undo");
\r
1217 if (viewport.redoList.size() > 0)
\r
1219 redoMenuItem.setEnabled(true);
\r
1221 CommandI command = (CommandI) viewport.redoList.peek();
\r
1222 redoMenuItem.setLabel("Redo " + command.getDescription());
\r
1226 redoMenuItem.setEnabled(false);
\r
1227 redoMenuItem.setLabel("Redo");
\r
1231 public void addHistoryItem(CommandI command)
\r
1233 if (command.getSize() > 0)
\r
1235 viewport.historyList.push(command);
\r
1236 viewport.redoList.removeAllElements();
\r
1237 updateEditMenuBar();
\r
1238 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
1248 protected void undoMenuItem_actionPerformed()
\r
1250 if (viewport.historyList.size() < 1)
\r
1255 CommandI command = (CommandI) viewport.historyList.pop();
\r
1256 viewport.redoList.push(command);
\r
1257 command.undoCommand(null);
\r
1259 AlignViewport originalSource = getOriginatingSource(command);
\r
1261 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
1262 updateEditMenuBar();
\r
1263 originalSource.firePropertyChange("alignment", null,
\r
1264 originalSource.alignment.getSequences());
\r
1273 protected void redoMenuItem_actionPerformed()
\r
1275 if (viewport.redoList.size() < 1)
\r
1280 CommandI command = (CommandI) viewport.redoList.pop();
\r
1281 viewport.historyList.push(command);
\r
1282 command.doCommand(null);
\r
1284 AlignViewport originalSource = getOriginatingSource(command);
\r
1285 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
1287 updateEditMenuBar();
\r
1288 originalSource.firePropertyChange("alignment", null,
\r
1289 originalSource.alignment.getSequences());
\r
1292 AlignViewport getOriginatingSource(CommandI command)
\r
1294 AlignViewport originalSource = null;
\r
1295 // For sequence removal and addition, we need to fire
\r
1296 // the property change event FROM the viewport where the
\r
1297 // original alignment was altered
\r
1298 AlignmentI al = null;
\r
1299 if (command instanceof EditCommand)
\r
1301 EditCommand editCommand = (EditCommand) command;
\r
1302 al = editCommand.getAlignment();
\r
1303 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
1304 .getSequenceSetId());
\r
1305 for (int i = 0; i < comps.size(); i++)
\r
1307 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
1309 if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
\r
1311 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
\r
1318 if (originalSource == null)
\r
1320 // The original view is closed, we must validate
\r
1321 // the current view against the closed view first
\r
1324 PaintRefresher.validateSequences(al, viewport.alignment);
\r
1327 originalSource = viewport;
\r
1330 return originalSource;
\r
1333 public void moveSelectedSequences(boolean up)
\r
1335 SequenceGroup sg = viewport.getSelectionGroup();
\r
1343 for (int i = 1; i < viewport.alignment.getHeight(); i++)
\r
1345 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
1346 if (!sg.getSequences(null).contains(seq))
\r
1351 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
\r
1352 if (sg.getSequences(null).contains(temp))
\r
1357 viewport.alignment.getSequences().setElementAt(temp, i);
\r
1358 viewport.alignment.getSequences().setElementAt(seq, i - 1);
\r
1363 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
\r
1365 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
1366 if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))
\r
1371 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
\r
1372 if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))
\r
1377 viewport.alignment.getSequences().setElementAt(temp, i);
\r
1378 viewport.alignment.getSequences().setElementAt(seq, i + 1);
\r
1382 alignPanel.paintAlignment(true);
\r
1385 synchronized void slideSequences(boolean right, int size)
\r
1387 Vector sg = new Vector();
\r
1388 if (viewport.cursorMode)
\r
1390 sg.addElement(viewport.alignment
\r
1391 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
\r
1393 else if (viewport.getSelectionGroup() != null
\r
1394 && viewport.getSelectionGroup().getSize() != viewport.alignment
\r
1397 sg = viewport.getSelectionGroup().getSequences(
\r
1398 viewport.hiddenRepSequences);
\r
1401 if (sg.size() < 1)
\r
1406 Vector invertGroup = new Vector();
\r
1408 for (int i = 0; i < viewport.alignment.getHeight(); i++)
\r
1410 if (!sg.contains(viewport.alignment.getSequenceAt(i)))
\r
1411 invertGroup.addElement(viewport.alignment.getSequenceAt(i));
\r
1414 SequenceI[] seqs1 = new SequenceI[sg.size()];
\r
1415 for (int i = 0; i < sg.size(); i++)
\r
1416 seqs1[i] = (SequenceI) sg.elementAt(i);
\r
1418 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
\r
1419 for (int i = 0; i < invertGroup.size(); i++)
\r
1420 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
\r
1422 SlideSequencesCommand ssc;
\r
1424 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
\r
1425 size, viewport.getGapCharacter());
\r
1427 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
\r
1428 size, viewport.getGapCharacter());
\r
1430 int groupAdjustment = 0;
\r
1431 if (ssc.getGapsInsertedBegin() && right)
\r
1433 if (viewport.cursorMode)
\r
1434 alignPanel.seqPanel.moveCursor(size, 0);
\r
1436 groupAdjustment = size;
\r
1438 else if (!ssc.getGapsInsertedBegin() && !right)
\r
1440 if (viewport.cursorMode)
\r
1441 alignPanel.seqPanel.moveCursor(-size, 0);
\r
1443 groupAdjustment = -size;
\r
1446 if (groupAdjustment != 0)
\r
1448 viewport.getSelectionGroup().setStartRes(
\r
1449 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
\r
1450 viewport.getSelectionGroup().setEndRes(
\r
1451 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
\r
1454 boolean appendHistoryItem = false;
\r
1455 if (viewport.historyList != null && viewport.historyList.size() > 0
\r
1456 && viewport.historyList.peek() instanceof SlideSequencesCommand)
\r
1458 appendHistoryItem = ssc
\r
1459 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
\r
1463 if (!appendHistoryItem)
\r
1464 addHistoryItem(ssc);
\r
1469 static StringBuffer copiedSequences;
\r
1471 static Vector copiedHiddenColumns;
\r
1473 protected void copy_actionPerformed()
\r
1475 if (viewport.getSelectionGroup() == null)
\r
1480 SequenceGroup sg = viewport.getSelectionGroup();
\r
1481 copiedSequences = new StringBuffer();
\r
1482 Hashtable orderedSeqs = new Hashtable();
\r
1483 for (int i = 0; i < sg.getSize(); i++)
\r
1485 SequenceI seq = sg.getSequenceAt(i);
\r
1486 int index = viewport.alignment.findIndex(seq);
\r
1487 orderedSeqs.put(index + "", seq);
\r
1490 int index = 0, startRes, endRes;
\r
1493 if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
\r
1495 copiedHiddenColumns = new Vector();
\r
1496 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
\r
1497 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
\r
1500 int[] region = (int[]) viewport.getColumnSelection()
\r
1501 .getHiddenColumns().elementAt(i);
\r
1503 copiedHiddenColumns.addElement(new int[]
\r
1504 { region[0] - hiddenOffset, region[1] - hiddenOffset });
\r
1509 copiedHiddenColumns = null;
\r
1512 for (int i = 0; i < sg.getSize(); i++)
\r
1514 SequenceI seq = null;
\r
1516 while (seq == null)
\r
1518 if (orderedSeqs.containsKey(index + ""))
\r
1520 seq = (SequenceI) orderedSeqs.get(index + "");
\r
1532 // Returns residue following index if gap
\r
1533 startRes = seq.findPosition(sg.getStartRes());
\r
1536 // Need to find the residue preceeding index if gap
\r
1539 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
\r
1541 ch = seq.getCharAt(j);
\r
1542 if (!jalview.util.Comparison.isGap((ch)))
\r
1550 endRes += seq.getStart() - 1;
\r
1553 copiedSequences.append(seq.getName()
\r
1559 + seq.getSequenceAsString(sg.getStartRes(),
\r
1560 sg.getEndRes() + 1) + "\n");
\r
1565 protected void pasteNew_actionPerformed()
\r
1570 protected void pasteThis_actionPerformed()
\r
1575 void paste(boolean newAlignment)
\r
1580 if (copiedSequences == null)
\r
1585 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
1586 Vector seqs = new Vector();
\r
1587 while (st.hasMoreElements())
\r
1589 String name = st.nextToken();
\r
1590 int start = Integer.parseInt(st.nextToken());
\r
1591 int end = Integer.parseInt(st.nextToken());
\r
1592 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
\r
1594 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
1595 for (int i = 0; i < seqs.size(); i++)
\r
1597 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
1602 String newtitle = new String("Copied sequences");
\r
1603 if (getTitle().startsWith("Copied sequences"))
\r
1605 newtitle = getTitle();
\r
1609 newtitle = newtitle.concat("- from " + getTitle());
\r
1611 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
1612 viewport.applet, newtitle, false);
\r
1613 if (copiedHiddenColumns != null)
\r
1615 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
1617 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
1618 af.viewport.hideColumns(region[0], region[1]);
\r
1622 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
\r
1627 addSequences(newSeqs);
\r
1630 } catch (Exception ex)
\r
1632 } // could be anything being pasted in here
\r
1636 void addSequences(SequenceI[] seqs)
\r
1638 for (int i = 0; i < seqs.length; i++)
\r
1640 viewport.alignment.addSequence(seqs[i]);
\r
1644 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
\r
1645 seqs, 0, viewport.alignment.getWidth(), viewport.alignment));
\r
1647 viewport.setEndSeq(viewport.alignment.getHeight());
\r
1648 viewport.alignment.getWidth();
\r
1649 viewport.firePropertyChange("alignment", null,
\r
1650 viewport.alignment.getSequences());
\r
1654 protected void cut_actionPerformed()
\r
1656 copy_actionPerformed();
\r
1657 delete_actionPerformed();
\r
1660 protected void delete_actionPerformed()
\r
1663 SequenceGroup sg = viewport.getSelectionGroup();
\r
1669 Vector seqs = new Vector();
\r
1671 for (int i = 0; i < sg.getSize(); i++)
\r
1673 seq = sg.getSequenceAt(i);
\r
1674 seqs.addElement(seq);
\r
1677 // If the cut affects all sequences, remove highlighted columns
\r
1678 if (sg.getSize() == viewport.alignment.getHeight())
\r
1680 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
1681 sg.getEndRes() + 1);
\r
1684 SequenceI[] cut = new SequenceI[seqs.size()];
\r
1685 for (int i = 0; i < seqs.size(); i++)
\r
1687 cut[i] = (SequenceI) seqs.elementAt(i);
\r
1691 * //ADD HISTORY ITEM
\r
1693 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
\r
1694 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
\r
1695 viewport.alignment));
\r
1697 viewport.setSelectionGroup(null);
\r
1698 viewport.alignment.deleteGroup(sg);
\r
1700 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1703 if (viewport.getAlignment().getHeight() < 1)
\r
1705 this.setVisible(false);
\r
1707 viewport.sendSelection();
\r
1711 * group consensus toggled
\r
1714 protected void showGroupConsensus_actionPerformed()
\r
1716 viewport.setShowGroupConsensus(showGroupConsensus.getState());
\r
1717 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1722 * group conservation toggled.
\r
1724 protected void showGroupConservation_actionPerformed()
\r
1726 viewport.setShowGroupConservation(showGroupConservation.getState());
\r
1727 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1734 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
\r
1735 * .event.ActionEvent)
\r
1737 protected void showConsensusHistogram_actionPerformed()
\r
1739 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
\r
1740 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1746 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
\r
1747 * .event.ActionEvent)
\r
1749 protected void showSequenceLogo_actionPerformed()
\r
1751 viewport.setShowSequenceLogo(showSequenceLogo.getState());
\r
1752 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1755 protected void applyAutoAnnotationSettings_actionPerformed()
\r
1757 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1760 protected void makeGrpsFromSelection_actionPerformed()
\r
1762 if (viewport.getSelectionGroup() != null)
\r
1764 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
\r
1765 viewport.getSequenceSelection(),
\r
1766 viewport.getAlignmentView(true).getSequenceStrings(
\r
1767 viewport.getGapCharacter()),
\r
1768 viewport.alignment.getGroups());
\r
1769 viewport.alignment.deleteAllGroups();
\r
1770 viewport.sequenceColours = null;
\r
1771 viewport.setSelectionGroup(null);
\r
1772 // set view properties for each group
\r
1773 for (int g = 0; g < gps.length; g++)
\r
1775 // gps[g].setShowunconserved(viewport.getShowUnconserved());
\r
1776 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
\r
1777 viewport.alignment.addGroup(gps[g]);
\r
1778 Color col = new Color((int) (Math.random() * 255),
\r
1779 (int) (Math.random() * 255), (int) (Math.random() * 255));
\r
1780 col = col.brighter();
\r
1781 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
\r
1782 .hasMoreElements(); viewport.setSequenceColour(
\r
1783 (SequenceI) sq.nextElement(), col))
\r
1786 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
\r
1787 alignPanel.updateAnnotation();
\r
1788 alignPanel.paintAlignment(true);
\r
1792 protected void deleteGroups_actionPerformed()
\r
1794 viewport.alignment.deleteAllGroups();
\r
1795 viewport.sequenceColours = null;
\r
1796 viewport.setSelectionGroup(null);
\r
1798 alignPanel.paintAlignment(true);
\r
1801 public void selectAllSequenceMenuItem_actionPerformed()
\r
1803 SequenceGroup sg = new SequenceGroup();
\r
1804 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1806 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
1808 sg.setEndRes(viewport.alignment.getWidth() - 1);
\r
1809 viewport.setSelectionGroup(sg);
\r
1810 alignPanel.paintAlignment(true);
\r
1811 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1812 viewport.sendSelection();
\r
1815 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1817 if (viewport.cursorMode)
\r
1819 alignPanel.seqPanel.keyboardNo1 = null;
\r
1820 alignPanel.seqPanel.keyboardNo2 = null;
\r
1822 viewport.setSelectionGroup(null);
\r
1823 viewport.getColumnSelection().clear();
\r
1824 viewport.setSelectionGroup(null);
\r
1825 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1826 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1827 alignPanel.paintAlignment(true);
\r
1828 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1829 viewport.sendSelection();
\r
1832 public void invertSequenceMenuItem_actionPerformed()
\r
1834 SequenceGroup sg = viewport.getSelectionGroup();
\r
1835 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1837 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1840 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1841 viewport.sendSelection();
\r
1844 public void invertColSel_actionPerformed()
\r
1846 viewport.invertColumnSelection();
\r
1847 alignPanel.paintAlignment(true);
\r
1848 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1849 viewport.sendSelection();
\r
1852 void trimAlignment(boolean trimLeft)
\r
1854 ColumnSelection colSel = viewport.getColumnSelection();
\r
1857 if (colSel.size() > 0)
\r
1861 column = colSel.getMin();
\r
1865 column = colSel.getMax();
\r
1869 if (viewport.getSelectionGroup() != null)
\r
1871 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
1872 viewport.hiddenRepSequences);
\r
1876 seqs = viewport.alignment.getSequencesArray();
\r
1879 TrimRegionCommand trimRegion;
\r
1882 trimRegion = new TrimRegionCommand("Remove Left",
\r
1883 TrimRegionCommand.TRIM_LEFT, seqs, column,
\r
1884 viewport.alignment, viewport.colSel,
\r
1885 viewport.selectionGroup);
\r
1886 viewport.setStartRes(0);
\r
1890 trimRegion = new TrimRegionCommand("Remove Right",
\r
1891 TrimRegionCommand.TRIM_RIGHT, seqs, column,
\r
1892 viewport.alignment, viewport.colSel,
\r
1893 viewport.selectionGroup);
\r
1896 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
\r
1898 addHistoryItem(trimRegion);
\r
1900 Vector groups = viewport.alignment.getGroups();
\r
1902 for (int i = 0; i < groups.size(); i++)
\r
1904 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1906 if ((trimLeft && !sg.adjustForRemoveLeft(column))
\r
1907 || (!trimLeft && !sg.adjustForRemoveRight(column)))
\r
1909 viewport.alignment.deleteGroup(sg);
\r
1913 viewport.firePropertyChange("alignment", null, viewport
\r
1914 .getAlignment().getSequences());
\r
1918 public void removeGappedColumnMenuItem_actionPerformed()
\r
1920 int start = 0, end = viewport.alignment.getWidth() - 1;
\r
1923 if (viewport.getSelectionGroup() != null)
\r
1925 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
1926 viewport.hiddenRepSequences);
\r
1927 start = viewport.getSelectionGroup().getStartRes();
\r
1928 end = viewport.getSelectionGroup().getEndRes();
\r
1932 seqs = viewport.alignment.getSequencesArray();
\r
1935 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
\r
1936 "Remove Gapped Columns", seqs, start, end, viewport.alignment);
\r
1938 addHistoryItem(removeGapCols);
\r
1940 statusBar.setText("Removed " + removeGapCols.getSize()
\r
1941 + " empty columns.");
\r
1943 // This is to maintain viewport position on first residue
\r
1944 // of first sequence
\r
1945 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1946 int startRes = seq.findPosition(viewport.startRes);
\r
1947 // ShiftList shifts;
\r
1948 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
\r
1949 // edit.alColumnChanges=shifts.getInverse();
\r
1950 // if (viewport.hasHiddenColumns)
\r
1951 // viewport.getColumnSelection().compensateForEdits(shifts);
\r
1952 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
1953 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1958 public void removeAllGapsMenuItem_actionPerformed()
\r
1960 int start = 0, end = viewport.alignment.getWidth() - 1;
\r
1963 if (viewport.getSelectionGroup() != null)
\r
1965 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
1966 viewport.hiddenRepSequences);
\r
1967 start = viewport.getSelectionGroup().getStartRes();
\r
1968 end = viewport.getSelectionGroup().getEndRes();
\r
1972 seqs = viewport.alignment.getSequencesArray();
\r
1975 // This is to maintain viewport position on first residue
\r
1976 // of first sequence
\r
1977 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1978 int startRes = seq.findPosition(viewport.startRes);
\r
1980 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
\r
1981 viewport.alignment));
\r
1983 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
1985 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1990 public void findMenuItem_actionPerformed()
\r
1992 new Finder(alignPanel);
\r
1996 * create a new view derived from the current view
\r
1998 * @param viewtitle
\r
1999 * @return frame for the new view
\r
2001 public AlignFrame newView(String viewtitle)
\r
2004 if (viewport.hasHiddenRows)
\r
2006 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
\r
2007 .getFullAlignment().getSequencesArray());
\r
2011 newal = new Alignment(viewport.alignment.getSequencesArray());
\r
2014 if (viewport.alignment.getAlignmentAnnotation() != null)
\r
2016 for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)
\r
2018 if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
\r
2020 newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);
\r
2025 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
\r
2027 newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
\r
2028 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
\r
2029 PaintRefresher.Register(newaf.alignPanel,
\r
2030 newaf.alignPanel.av.getSequenceSetId());
\r
2032 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
\r
2033 newaf.alignPanel.av.getSequenceSetId());
\r
2034 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
\r
2035 newaf.alignPanel.av.getSequenceSetId());
\r
2037 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
2038 .getSequenceSetId());
\r
2039 int viewSize = -1;
\r
2040 for (int i = 0; i < comps.size(); i++)
\r
2042 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
2048 String title = new String(this.getTitle());
\r
2049 if (viewtitle != null)
\r
2051 title = viewtitle + " ( " + title + ")";
\r
2055 if (title.indexOf("(View") > -1)
\r
2057 title = title.substring(0, title.indexOf("(View"));
\r
2059 title += "(View " + viewSize + ")";
\r
2062 newaf.setTitle(title.toString());
\r
2064 newaf.viewport.historyList = viewport.historyList;
\r
2065 newaf.viewport.redoList = viewport.redoList;
\r
2071 * @return list of feature groups on the view
\r
2073 public String[] getFeatureGroups()
\r
2075 FeatureRenderer fr = null;
\r
2076 if (alignPanel != null
\r
2077 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2079 return fr.getGroups();
\r
2085 * get sequence feature groups that are hidden or shown
\r
2091 public String[] getFeatureGroupsOfState(boolean visible)
\r
2093 FeatureRenderer fr = null;
\r
2094 if (alignPanel != null
\r
2095 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2097 return fr.getGroups(visible);
\r
2103 * Change the display state for the given feature groups
\r
2106 * list of group strings
\r
2108 * visible or invisible
\r
2110 public void setFeatureGroupState(String[] groups, boolean state)
\r
2112 FeatureRenderer fr = null;
\r
2113 this.sequenceFeatures.setState(true);
\r
2114 viewport.showSequenceFeatures(true);
\r
2115 if (alignPanel != null
\r
2116 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2118 fr.setGroupState(groups, state);
\r
2119 alignPanel.seqPanel.seqCanvas.repaint();
\r
2120 if (alignPanel.overviewPanel != null)
\r
2122 alignPanel.overviewPanel.updateOverviewImage();
\r
2127 public void seqLimits_itemStateChanged()
\r
2129 viewport.setShowJVSuffix(seqLimits.getState());
\r
2130 alignPanel.fontChanged();
\r
2131 alignPanel.paintAlignment(true);
\r
2134 protected void colourTextMenuItem_actionPerformed()
\r
2136 viewport.setColourText(colourTextMenuItem.getState());
\r
2137 alignPanel.paintAlignment(true);
\r
2140 protected void displayNonconservedMenuItem_actionPerformed()
\r
2142 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
\r
2143 alignPanel.paintAlignment(true);
\r
2146 protected void wrapMenuItem_actionPerformed()
\r
2148 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
2149 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
2150 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
2151 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
2152 scaleRight.setEnabled(wrapMenuItem.getState());
\r
2153 alignPanel.paintAlignment(true);
\r
2156 public void overviewMenuItem_actionPerformed()
\r
2158 if (alignPanel.overviewPanel != null)
\r
2163 Frame frame = new Frame();
\r
2164 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
2165 frame.add(overview);
\r
2166 // +50 must allow for applet frame window
\r
2167 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
2168 overview.getPreferredSize().width,
\r
2169 overview.getPreferredSize().height + 50);
\r
2172 frame.addWindowListener(new WindowAdapter()
\r
2174 public void windowClosing(WindowEvent e)
\r
2176 alignPanel.setOverviewPanel(null);
\r
2180 alignPanel.setOverviewPanel(overview);
\r
2184 void changeColour(ColourSchemeI cs)
\r
2186 int threshold = 0;
\r
2190 if (viewport.getAbovePIDThreshold())
\r
2192 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
2195 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2197 viewport.setGlobalColourScheme(cs);
\r
2201 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2204 if (viewport.getConservationSelected())
\r
2207 Alignment al = (Alignment) viewport.alignment;
\r
2208 Conservation c = new Conservation("All",
\r
2209 ResidueProperties.propHash, 3, al.getSequences(), 0,
\r
2210 al.getWidth() - 1);
\r
2213 c.verdict(false, viewport.ConsPercGaps);
\r
2215 cs.setConservation(c);
\r
2217 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
\r
2218 cs, "Background"));
\r
2223 cs.setConservation(null);
\r
2226 cs.setConsensus(viewport.hconsensus);
\r
2229 viewport.setGlobalColourScheme(cs);
\r
2231 if (viewport.getColourAppliesToAllGroups())
\r
2233 Vector groups = viewport.alignment.getGroups();
\r
2234 for (int i = 0; i < groups.size(); i++)
\r
2236 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
2243 if (cs instanceof ClustalxColourScheme)
\r
2245 sg.cs = new ClustalxColourScheme(
\r
2246 sg.getSequences(viewport.hiddenRepSequences),
\r
2253 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
2254 } catch (Exception ex)
\r
2256 ex.printStackTrace();
\r
2261 if (viewport.getAbovePIDThreshold()
\r
2262 || cs instanceof PIDColourScheme
\r
2263 || cs instanceof Blosum62ColourScheme)
\r
2265 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2266 sg.cs.setConsensus(AAFrequency.calculate(
\r
2267 sg.getSequences(viewport.hiddenRepSequences), 0,
\r
2272 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2275 if (viewport.getConservationSelected())
\r
2277 Conservation c = new Conservation("Group",
\r
2278 ResidueProperties.propHash, 3,
\r
2279 sg.getSequences(viewport.hiddenRepSequences), 0,
\r
2280 viewport.alignment.getWidth() - 1);
\r
2282 c.verdict(false, viewport.ConsPercGaps);
\r
2283 sg.cs.setConservation(c);
\r
2287 sg.cs.setConservation(null);
\r
2288 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2294 if (alignPanel.getOverviewPanel() != null)
\r
2296 alignPanel.getOverviewPanel().updateOverviewImage();
\r
2299 jalview.structure.StructureSelectionManager
\r
2300 .getStructureSelectionManager(viewport.applet).sequenceColoursChanged(
\r
2303 alignPanel.paintAlignment(true);
\r
2306 protected void modifyPID_actionPerformed()
\r
2308 if (viewport.getAbovePIDThreshold()
\r
2309 && viewport.globalColourScheme != null)
\r
2311 SliderPanel.setPIDSliderSource(alignPanel,
\r
2312 viewport.getGlobalColourScheme(), "Background");
\r
2313 SliderPanel.showPIDSlider();
\r
2317 protected void modifyConservation_actionPerformed()
\r
2319 if (viewport.getConservationSelected()
\r
2320 && viewport.globalColourScheme != null)
\r
2322 SliderPanel.setConservationSlider(alignPanel,
\r
2323 viewport.globalColourScheme, "Background");
\r
2324 SliderPanel.showConservationSlider();
\r
2328 protected void conservationMenuItem_actionPerformed()
\r
2330 viewport.setConservationSelected(conservationMenuItem.getState());
\r
2332 viewport.setAbovePIDThreshold(false);
\r
2333 abovePIDThreshold.setState(false);
\r
2335 changeColour(viewport.getGlobalColourScheme());
\r
2337 modifyConservation_actionPerformed();
\r
2340 public void abovePIDThreshold_actionPerformed()
\r
2342 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
2344 conservationMenuItem.setState(false);
\r
2345 viewport.setConservationSelected(false);
\r
2347 changeColour(viewport.getGlobalColourScheme());
\r
2349 modifyPID_actionPerformed();
\r
2352 public void sortPairwiseMenuItem_actionPerformed()
\r
2354 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2355 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
\r
2356 .getAlignment().getSequenceAt(0), null);
\r
2358 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
\r
2359 viewport.alignment));
\r
2360 alignPanel.paintAlignment(true);
\r
2363 public void sortIDMenuItem_actionPerformed()
\r
2365 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2366 AlignmentSorter.sortByID(viewport.getAlignment());
\r
2367 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
\r
2368 alignPanel.paintAlignment(true);
\r
2371 public void sortLengthMenuItem_actionPerformed()
\r
2373 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2374 AlignmentSorter.sortByLength(viewport.getAlignment());
\r
2375 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
\r
2376 viewport.alignment));
\r
2377 alignPanel.paintAlignment(true);
\r
2380 public void sortGroupMenuItem_actionPerformed()
\r
2382 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2383 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
2384 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
\r
2385 viewport.alignment));
\r
2386 alignPanel.paintAlignment(true);
\r
2390 public void removeRedundancyMenuItem_actionPerformed()
\r
2392 new RedundancyPanel(alignPanel);
\r
2395 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
2397 if (viewport.getSelectionGroup() != null
\r
2398 && viewport.getSelectionGroup().getSize() > 1)
\r
2400 Frame frame = new Frame();
\r
2401 frame.add(new PairwiseAlignPanel(alignPanel));
\r
2402 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
\r
2407 public void PCAMenuItem_actionPerformed()
\r
2409 // are the sequences aligned?
\r
2410 if (!viewport.alignment.isAligned(false))
\r
2412 SequenceI current;
\r
2413 int Width = viewport.getAlignment().getWidth();
\r
2415 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2417 current = viewport.getAlignment().getSequenceAt(i);
\r
2419 if (current.getLength() < Width)
\r
2421 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2424 alignPanel.paintAlignment(true);
\r
2427 if ((viewport.getSelectionGroup() != null
\r
2428 && viewport.getSelectionGroup().getSize() < 4 && viewport
\r
2429 .getSelectionGroup().getSize() > 0)
\r
2430 || viewport.getAlignment().getHeight() < 4)
\r
2437 new PCAPanel(viewport);
\r
2438 } catch (java.lang.OutOfMemoryError ex)
\r
2444 public void averageDistanceTreeMenuItem_actionPerformed()
\r
2446 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
2449 public void neighbourTreeMenuItem_actionPerformed()
\r
2451 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
2454 protected void njTreeBlosumMenuItem_actionPerformed()
\r
2456 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2459 protected void avTreeBlosumMenuItem_actionPerformed()
\r
2461 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2464 void NewTreePanel(String type, String pwType, String title)
\r
2466 // are the sequences aligned?
\r
2467 if (!viewport.alignment.isAligned(false))
\r
2469 SequenceI current;
\r
2470 int Width = viewport.getAlignment().getWidth();
\r
2472 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2474 current = viewport.getAlignment().getSequenceAt(i);
\r
2476 if (current.getLength() < Width)
\r
2478 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2481 alignPanel.paintAlignment(true);
\r
2485 if ((viewport.getSelectionGroup() != null && viewport
\r
2486 .getSelectionGroup().getSize() > 1)
\r
2487 || (viewport.getSelectionGroup() == null && viewport.alignment
\r
2488 .getHeight() > 1))
\r
2490 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
\r
2492 addTreeMenuItem(tp, title);
\r
2494 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
2498 void loadTree_actionPerformed()
\r
2500 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
2501 cap.setText("Paste your Newick tree file here.");
\r
2502 cap.setTreeImport();
\r
2503 Frame frame = new Frame();
\r
2505 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
2508 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
2510 TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
\r
2511 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
2512 addTreeMenuItem(tp, treeFile);
\r
2516 * sort the alignment using the given treePanel
\r
2518 * @param treePanel
\r
2519 * tree used to sort view
\r
2521 * string used for undo event name
\r
2523 public void sortByTree(TreePanel treePanel, String title)
\r
2525 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2527 .sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
2528 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2529 // HistoryItem.SORT));
\r
2530 addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
\r
2531 viewport.alignment));
\r
2532 alignPanel.paintAlignment(true);
\r
2536 * Do any automatic reordering of the alignment and add the necessary bits to
\r
2537 * the menu structure for the new tree
\r
2539 * @param treePanel
\r
2542 protected void addTreeMenuItem(final TreePanel treePanel,
\r
2543 final String title)
\r
2545 final MenuItem item = new MenuItem(title);
\r
2546 sortByTreeMenu.add(item);
\r
2547 item.addActionListener(new java.awt.event.ActionListener()
\r
2549 public void actionPerformed(ActionEvent evt)
\r
2551 sortByTree(treePanel, title); // treePanel.getTitle());
\r
2555 treePanel.addWindowListener(new WindowAdapter()
\r
2557 public void windowOpened(WindowEvent e)
\r
2559 if (viewport.sortByTree)
\r
2561 sortByTree(treePanel, title);
\r
2563 super.windowOpened(e);
\r
2566 public void windowClosing(WindowEvent e)
\r
2568 sortByTreeMenu.remove(item);
\r
2572 public boolean sortBy(AlignmentOrder alorder, String undoname)
\r
2574 SequenceI[] oldOrder = viewport.getAlignment()
\r
2575 .getSequencesArray();
\r
2576 if (viewport.applet.debug)
\r
2578 System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");
\r
2580 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
\r
2581 if (undoname!=null)
\r
2583 addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.alignment));
\r
2585 alignPanel.paintAlignment(true);
\r
2588 protected void documentation_actionPerformed()
\r
2590 alignPanel.av.applet.openJalviewHelpUrl();
\r
2593 protected void about_actionPerformed()
\r
2596 class AboutPanel extends Canvas
\r
2602 public AboutPanel(String version, String builddate)
\r
2604 this.version = version;
\r
2605 this.builddate = builddate;
\r
2608 public void paint(Graphics g)
\r
2610 g.setColor(Color.white);
\r
2611 g.fillRect(0, 0, getSize().width, getSize().height);
\r
2612 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2613 FontMetrics fm = g.getFontMetrics();
\r
2614 int fh = fm.getHeight();
\r
2616 g.setColor(Color.black);
\r
2617 // TODO: update this text for each release or centrally store it for
\r
2618 // lite and application
\r
2619 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
2620 g.drawString("JalviewLite - Release " + version, x, y += fh);
\r
2621 g.setFont(new Font("Helvetica", Font.BOLD, 12));
\r
2622 g.drawString("Build date: " + builddate, x, y += fh);
\r
2623 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2625 "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",
\r
2626 x, y += fh * 1.5);
\r
2627 g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
\r
2629 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
\r
2632 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
\r
2634 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
\r
2636 "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
\r
2639 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
\r
2641 g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
\r
2646 Frame frame = new Frame();
\r
2647 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
\r
2648 .getBuildDate()));
\r
2649 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
\r
2653 public void showURL(String url, String target)
\r
2655 if (viewport.applet == null)
\r
2657 System.out.println("Not running as applet - no browser available.");
\r
2661 viewport.applet.showURL(url, target);
\r
2665 // ////////////////////////////////////////////////////////////////////////////////
\r
2666 // JBuilder Graphics here
\r
2668 MenuBar alignFrameMenuBar = new MenuBar();
\r
2670 Menu fileMenu = new Menu("File");
\r
2672 MenuItem loadApplication = new MenuItem("View in Full Application");
\r
2674 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
\r
2676 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
\r
2678 MenuItem outputFeatures = new MenuItem("Export Features ...");
\r
2680 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
\r
2682 MenuItem closeMenuItem = new MenuItem("Close");
\r
2684 Menu editMenu = new Menu("Edit");
\r
2686 Menu viewMenu = new Menu("View");
\r
2688 Menu colourMenu = new Menu("Colour");
\r
2690 Menu calculateMenu = new Menu("Calculate");
\r
2692 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
2694 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
2696 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
2698 MenuItem remove2LeftMenuItem = new MenuItem();
\r
2700 MenuItem remove2RightMenuItem = new MenuItem();
\r
2702 MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
2704 MenuItem removeAllGapsMenuItem = new MenuItem();
\r
2706 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
2708 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
2710 MenuItem sortPairwiseMenuItem = new MenuItem();
\r
2712 MenuItem sortIDMenuItem = new MenuItem();
\r
2714 MenuItem sortLengthMenuItem = new MenuItem();
\r
2716 MenuItem sortGroupMenuItem = new MenuItem();
\r
2718 MenuItem removeRedundancyMenuItem = new MenuItem();
\r
2720 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
2722 MenuItem PCAMenuItem = new MenuItem();
\r
2724 MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
2726 MenuItem neighbourTreeMenuItem = new MenuItem();
\r
2728 BorderLayout borderLayout1 = new BorderLayout();
\r
2730 public Label statusBar = new Label();
\r
2732 Menu outputTextboxMenu = new Menu();
\r
2734 MenuItem clustalColour = new MenuItem();
\r
2736 MenuItem zappoColour = new MenuItem();
\r
2738 MenuItem taylorColour = new MenuItem();
\r
2740 MenuItem hydrophobicityColour = new MenuItem();
\r
2742 MenuItem helixColour = new MenuItem();
\r
2744 MenuItem strandColour = new MenuItem();
\r
2746 MenuItem turnColour = new MenuItem();
\r
2748 MenuItem buriedColour = new MenuItem();
\r
2750 MenuItem userDefinedColour = new MenuItem();
\r
2752 MenuItem PIDColour = new MenuItem();
\r
2754 MenuItem BLOSUM62Colour = new MenuItem();
\r
2756 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
2758 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
2760 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
2762 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
2764 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
\r
2766 MenuItem alProperties = new MenuItem("Alignment Properties...");
\r
2768 MenuItem overviewMenuItem = new MenuItem();
\r
2770 MenuItem undoMenuItem = new MenuItem();
\r
2772 MenuItem redoMenuItem = new MenuItem();
\r
2774 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
2776 MenuItem noColourmenuItem = new MenuItem();
\r
2778 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
2780 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
2782 MenuItem findMenuItem = new MenuItem();
\r
2784 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
2786 MenuItem nucleotideColour = new MenuItem();
\r
2788 MenuItem deleteGroups = new MenuItem();
\r
2790 MenuItem grpsFromSelection = new MenuItem();
\r
2792 MenuItem delete = new MenuItem();
\r
2794 MenuItem copy = new MenuItem();
\r
2796 MenuItem cut = new MenuItem();
\r
2798 Menu pasteMenu = new Menu();
\r
2800 MenuItem pasteNew = new MenuItem();
\r
2802 MenuItem pasteThis = new MenuItem();
\r
2804 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
2806 MenuItem font = new MenuItem();
\r
2808 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
2810 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
2812 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
2814 MenuItem modifyPID = new MenuItem();
\r
2816 MenuItem modifyConservation = new MenuItem();
\r
2818 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
\r
2819 "Autocalculate Consensus", true);
\r
2821 Menu sortByTreeMenu = new Menu();
\r
2823 Menu sort = new Menu();
\r
2825 Menu calculate = new Menu();
\r
2827 MenuItem inputText = new MenuItem();
\r
2829 Menu helpMenu = new Menu();
\r
2831 MenuItem documentation = new MenuItem();
\r
2833 MenuItem about = new MenuItem();
\r
2835 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
2837 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
\r
2839 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
\r
2840 Menu autoAnnMenu=new Menu();
\r
2841 CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();
\r
2842 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
\r
2843 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
\r
2844 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
\r
2845 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
\r
2847 private void jbInit() throws Exception
\r
2850 setMenuBar(alignFrameMenuBar);
\r
2854 // dynamically fill save as menu with available formats
\r
2855 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
2858 item = new MenuItem(
\r
2859 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
2861 item.addActionListener(new java.awt.event.ActionListener()
\r
2863 public void actionPerformed(ActionEvent e)
\r
2865 outputText_actionPerformed(e);
\r
2869 outputTextboxMenu.add(item);
\r
2871 closeMenuItem.addActionListener(this);
\r
2872 loadApplication.addActionListener(this);
\r
2874 loadTree.addActionListener(this);
\r
2875 loadAnnotations.addActionListener(this);
\r
2876 outputFeatures.addActionListener(this);
\r
2877 outputAnnotations.addActionListener(this);
\r
2878 selectAllSequenceMenuItem.addActionListener(this);
\r
2879 deselectAllSequenceMenuItem.addActionListener(this);
\r
2880 invertSequenceMenuItem.addActionListener(this);
\r
2881 remove2LeftMenuItem.setLabel("Remove Left");
\r
2882 remove2LeftMenuItem.addActionListener(this);
\r
2883 remove2RightMenuItem.setLabel("Remove Right");
\r
2884 remove2RightMenuItem.addActionListener(this);
\r
2885 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
2886 removeGappedColumnMenuItem.addActionListener(this);
\r
2887 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
2888 removeAllGapsMenuItem.addActionListener(this);
\r
2889 viewBoxesMenuItem.setLabel("Boxes");
\r
2890 viewBoxesMenuItem.setState(true);
\r
2891 viewBoxesMenuItem.addItemListener(this);
\r
2892 viewTextMenuItem.setLabel("Text");
\r
2893 viewTextMenuItem.setState(true);
\r
2894 viewTextMenuItem.addItemListener(this);
\r
2895 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
2896 sortPairwiseMenuItem.addActionListener(this);
\r
2897 sortIDMenuItem.setLabel("by ID");
\r
2898 sortIDMenuItem.addActionListener(this);
\r
2899 sortLengthMenuItem.setLabel("by Length");
\r
2900 sortLengthMenuItem.addActionListener(this);
\r
2901 sortGroupMenuItem.setLabel("by Group");
\r
2902 sortGroupMenuItem.addActionListener(this);
\r
2903 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
2904 removeRedundancyMenuItem.addActionListener(this);
\r
2905 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
2906 pairwiseAlignmentMenuItem.addActionListener(this);
\r
2907 PCAMenuItem.setLabel("Principal Component Analysis");
\r
2908 PCAMenuItem.addActionListener(this);
\r
2909 averageDistanceTreeMenuItem
\r
2910 .setLabel("Average Distance Using % Identity");
\r
2911 averageDistanceTreeMenuItem.addActionListener(this);
\r
2912 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
2913 neighbourTreeMenuItem.addActionListener(this);
\r
2914 statusBar.setBackground(Color.white);
\r
2915 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
2916 statusBar.setText("Status bar");
\r
2917 outputTextboxMenu.setLabel("Output to Textbox");
\r
2918 clustalColour.setLabel("Clustalx");
\r
2920 clustalColour.addActionListener(this);
\r
2921 zappoColour.setLabel("Zappo");
\r
2922 zappoColour.addActionListener(this);
\r
2923 taylorColour.setLabel("Taylor");
\r
2924 taylorColour.addActionListener(this);
\r
2925 hydrophobicityColour.setLabel("Hydrophobicity");
\r
2926 hydrophobicityColour.addActionListener(this);
\r
2927 helixColour.setLabel("Helix Propensity");
\r
2928 helixColour.addActionListener(this);
\r
2929 strandColour.setLabel("Strand Propensity");
\r
2930 strandColour.addActionListener(this);
\r
2931 turnColour.setLabel("Turn Propensity");
\r
2932 turnColour.addActionListener(this);
\r
2933 buriedColour.setLabel("Buried Index");
\r
2934 buriedColour.addActionListener(this);
\r
2935 userDefinedColour.setLabel("User Defined...");
\r
2936 userDefinedColour.addActionListener(this);
\r
2937 PIDColour.setLabel("Percentage Identity");
\r
2938 PIDColour.addActionListener(this);
\r
2939 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
2940 BLOSUM62Colour.addActionListener(this);
\r
2941 avDistanceTreeBlosumMenuItem
\r
2942 .setLabel("Average Distance Using BLOSUM62");
\r
2943 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
2944 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
2945 njTreeBlosumMenuItem.addActionListener(this);
\r
2946 annotationPanelMenuItem.setLabel("Show Annotations");
\r
2947 annotationPanelMenuItem.addItemListener(this);
\r
2948 colourTextMenuItem.setLabel("Colour Text");
\r
2949 colourTextMenuItem.addItemListener(this);
\r
2950 displayNonconservedMenuItem.setLabel("Show nonconserved");
\r
2951 displayNonconservedMenuItem.addItemListener(this);
\r
2952 alProperties.addActionListener(this);
\r
2953 overviewMenuItem.setLabel("Overview Window");
\r
2954 overviewMenuItem.addActionListener(this);
\r
2955 undoMenuItem.setEnabled(false);
\r
2956 undoMenuItem.setLabel("Undo");
\r
2957 undoMenuItem.addActionListener(this);
\r
2958 redoMenuItem.setEnabled(false);
\r
2959 redoMenuItem.setLabel("Redo");
\r
2960 redoMenuItem.addActionListener(this);
\r
2961 conservationMenuItem.setLabel("by Conservation");
\r
2962 conservationMenuItem.addItemListener(this);
\r
2963 noColourmenuItem.setLabel("None");
\r
2964 noColourmenuItem.addActionListener(this);
\r
2965 wrapMenuItem.setLabel("Wrap");
\r
2966 wrapMenuItem.addItemListener(this);
\r
2967 renderGapsMenuItem.setLabel("Show Gaps");
\r
2968 renderGapsMenuItem.setState(true);
\r
2969 renderGapsMenuItem.addItemListener(this);
\r
2970 findMenuItem.setLabel("Find...");
\r
2971 findMenuItem.addActionListener(this);
\r
2972 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
2973 abovePIDThreshold.addItemListener(this);
\r
2974 nucleotideColour.setLabel("Nucleotide");
\r
2975 nucleotideColour.addActionListener(this);
\r
2976 deleteGroups.setLabel("Undefine Groups");
\r
2977 deleteGroups.addActionListener(this);
\r
2978 grpsFromSelection.setLabel("Make Groups for selection");
\r
2979 grpsFromSelection.addActionListener(this);
\r
2980 copy.setLabel("Copy");
\r
2981 copy.addActionListener(this);
\r
2982 cut.setLabel("Cut");
\r
2983 cut.addActionListener(this);
\r
2984 delete.setLabel("Delete");
\r
2985 delete.addActionListener(this);
\r
2986 pasteMenu.setLabel("Paste");
\r
2987 pasteNew.setLabel("To New Alignment");
\r
2988 pasteNew.addActionListener(this);
\r
2989 pasteThis.setLabel("Add To This Alignment");
\r
2990 pasteThis.addActionListener(this);
\r
2991 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
2992 applyToAllGroups.setState(true);
\r
2993 applyToAllGroups.addItemListener(this);
\r
2994 font.setLabel("Font...");
\r
2995 font.addActionListener(this);
\r
2996 scaleAbove.setLabel("Scale Above");
\r
2997 scaleAbove.setState(true);
\r
2998 scaleAbove.setEnabled(false);
\r
2999 scaleAbove.addItemListener(this);
\r
3000 scaleLeft.setEnabled(false);
\r
3001 scaleLeft.setState(true);
\r
3002 scaleLeft.setLabel("Scale Left");
\r
3003 scaleLeft.addItemListener(this);
\r
3004 scaleRight.setEnabled(false);
\r
3005 scaleRight.setState(true);
\r
3006 scaleRight.setLabel("Scale Right");
\r
3007 scaleRight.addItemListener(this);
\r
3008 modifyPID.setLabel("Modify Identity Threshold...");
\r
3009 modifyPID.addActionListener(this);
\r
3010 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
3011 modifyConservation.addActionListener(this);
\r
3012 sortByTreeMenu.setLabel("By Tree Order");
\r
3013 sort.setLabel("Sort");
\r
3014 calculate.setLabel("Calculate Tree");
\r
3015 autoCalculate.addItemListener(this);
\r
3016 inputText.setLabel("Input from textbox");
\r
3017 inputText.addActionListener(this);
\r
3018 centreColumnLabelFlag.setLabel("Centre column labels");
\r
3019 centreColumnLabelFlag.addItemListener(this);
\r
3020 followMouseOverFlag.setLabel("Automatic Scrolling");
\r
3021 followMouseOverFlag.addItemListener(this);
\r
3022 helpMenu.setLabel("Help");
\r
3023 documentation.setLabel("Documentation");
\r
3024 documentation.addActionListener(this);
\r
3026 about.setLabel("About...");
\r
3027 about.addActionListener(this);
\r
3028 seqLimits.setState(true);
\r
3029 seqLimits.setLabel("Show Sequence Limits");
\r
3030 seqLimits.addItemListener(this);
\r
3031 featureSettings.setLabel("Feature Settings...");
\r
3032 featureSettings.addActionListener(this);
\r
3033 sequenceFeatures.setLabel("Sequence Features");
\r
3034 sequenceFeatures.addItemListener(this);
\r
3035 sequenceFeatures.setState(false);
\r
3036 annotationColour.setLabel("by Annotation...");
\r
3037 annotationColour.addActionListener(this);
\r
3038 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
3039 invertColSel.setLabel("Invert Column Selection");
\r
3040 menu1.setLabel("Show");
\r
3041 showColumns.setLabel("All Columns ");
\r
3042 showSeqs.setLabel("All Sequences");
\r
3043 menu2.setLabel("Hide");
\r
3044 hideColumns.setLabel("Selected Columns");
\r
3045 hideSequences.setLabel("Selected Sequences");
\r
3046 hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
\r
3047 hideAllSelection.setLabel("Selected Region");
\r
3048 showAllHidden.setLabel("All Sequences and Columns");
\r
3049 showGroupConsensus.setLabel("Group Consensus");
\r
3050 showGroupConservation.setLabel("Group Conservation");
\r
3051 showConsensusHistogram.setLabel("Show Consensus Histogram");
\r
3052 showSequenceLogo.setLabel("Show Consensus Logo");
\r
3053 applyAutoAnnotationSettings.setLabel("Apply to all groups");
\r
3054 applyAutoAnnotationSettings.setState(true);
\r
3055 autoAnnMenu.setLabel("Autocalculated Annotation");
\r
3057 invertColSel.addActionListener(this);
\r
3058 showColumns.addActionListener(this);
\r
3059 showSeqs.addActionListener(this);
\r
3060 hideColumns.addActionListener(this);
\r
3061 hideSequences.addActionListener(this);
\r
3062 hideAllButSelection.addActionListener(this);
\r
3063 hideAllSelection.addActionListener(this);
\r
3064 showAllHidden.addActionListener(this);
\r
3065 showGroupConsensus.addItemListener(this);
\r
3066 showGroupConservation.addItemListener(this);
\r
3067 showConsensusHistogram.addItemListener(this);
\r
3068 showSequenceLogo.addItemListener(this);
\r
3069 applyAutoAnnotationSettings.addItemListener(this);
\r
3070 formatMenu.setLabel("Format");
\r
3071 selectMenu.setLabel("Select");
\r
3072 newView.setLabel("New View");
\r
3073 newView.addActionListener(this);
\r
3074 alignFrameMenuBar.add(fileMenu);
\r
3075 alignFrameMenuBar.add(editMenu);
\r
3076 alignFrameMenuBar.add(selectMenu);
\r
3077 alignFrameMenuBar.add(viewMenu);
\r
3078 alignFrameMenuBar.add(formatMenu);
\r
3079 alignFrameMenuBar.add(colourMenu);
\r
3080 alignFrameMenuBar.add(calculateMenu);
\r
3081 alignFrameMenuBar.add(helpMenu);
\r
3083 fileMenu.add(inputText);
\r
3084 fileMenu.add(loadTree);
\r
3085 fileMenu.add(loadAnnotations);
\r
3087 fileMenu.addSeparator();
\r
3088 fileMenu.add(outputTextboxMenu);
\r
3089 fileMenu.add(outputFeatures);
\r
3090 fileMenu.add(outputAnnotations);
\r
3092 if (jalviewServletURL != null)
\r
3094 fileMenu.add(loadApplication);
\r
3097 fileMenu.addSeparator();
\r
3098 fileMenu.add(closeMenuItem);
\r
3100 editMenu.add(undoMenuItem);
\r
3101 editMenu.add(redoMenuItem);
\r
3102 editMenu.add(cut);
\r
3103 editMenu.add(copy);
\r
3104 editMenu.add(pasteMenu);
\r
3105 editMenu.add(delete);
\r
3106 editMenu.addSeparator();
\r
3107 editMenu.add(remove2LeftMenuItem);
\r
3108 editMenu.add(remove2RightMenuItem);
\r
3109 editMenu.add(removeGappedColumnMenuItem);
\r
3110 editMenu.add(removeAllGapsMenuItem);
\r
3111 editMenu.add(removeRedundancyMenuItem);
\r
3112 viewMenu.add(newView);
\r
3113 viewMenu.addSeparator();
\r
3114 viewMenu.add(menu1);
\r
3115 viewMenu.add(menu2);
\r
3116 viewMenu.addSeparator();
\r
3117 viewMenu.add(followMouseOverFlag);
\r
3118 viewMenu.add(annotationPanelMenuItem);
\r
3119 autoAnnMenu.add(applyAutoAnnotationSettings);
\r
3120 autoAnnMenu.add(showConsensusHistogram);
\r
3121 autoAnnMenu.add(showSequenceLogo);
\r
3122 autoAnnMenu.addSeparator();
\r
3123 autoAnnMenu.add(showGroupConservation);
\r
3124 autoAnnMenu.add(showGroupConsensus);
\r
3125 viewMenu.add(autoAnnMenu);
\r
3126 viewMenu.addSeparator();
\r
3127 viewMenu.add(sequenceFeatures);
\r
3128 viewMenu.add(featureSettings);
\r
3129 viewMenu.addSeparator();
\r
3130 viewMenu.add(alProperties);
\r
3131 viewMenu.addSeparator();
\r
3132 viewMenu.add(overviewMenuItem);
\r
3133 colourMenu.add(applyToAllGroups);
\r
3134 colourMenu.addSeparator();
\r
3135 colourMenu.add(noColourmenuItem);
\r
3136 colourMenu.add(clustalColour);
\r
3137 colourMenu.add(BLOSUM62Colour);
\r
3138 colourMenu.add(PIDColour);
\r
3139 colourMenu.add(zappoColour);
\r
3140 colourMenu.add(taylorColour);
\r
3141 colourMenu.add(hydrophobicityColour);
\r
3142 colourMenu.add(helixColour);
\r
3143 colourMenu.add(strandColour);
\r
3144 colourMenu.add(turnColour);
\r
3145 colourMenu.add(buriedColour);
\r
3146 colourMenu.add(nucleotideColour);
\r
3147 colourMenu.add(userDefinedColour);
\r
3148 colourMenu.addSeparator();
\r
3149 colourMenu.add(conservationMenuItem);
\r
3150 colourMenu.add(modifyConservation);
\r
3151 colourMenu.add(abovePIDThreshold);
\r
3152 colourMenu.add(modifyPID);
\r
3153 colourMenu.add(annotationColour);
\r
3154 calculateMenu.add(sort);
\r
3155 calculateMenu.add(calculate);
\r
3156 calculateMenu.addSeparator();
\r
3157 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
3158 calculateMenu.add(PCAMenuItem);
\r
3159 calculateMenu.add(autoCalculate);
\r
3160 this.add(statusBar, BorderLayout.SOUTH);
\r
3161 pasteMenu.add(pasteNew);
\r
3162 pasteMenu.add(pasteThis);
\r
3163 sort.add(sortIDMenuItem);
\r
3164 sort.add(sortLengthMenuItem);
\r
3165 sort.add(sortByTreeMenu);
\r
3166 sort.add(sortGroupMenuItem);
\r
3167 sort.add(sortPairwiseMenuItem);
\r
3168 calculate.add(averageDistanceTreeMenuItem);
\r
3169 calculate.add(neighbourTreeMenuItem);
\r
3170 calculate.add(avDistanceTreeBlosumMenuItem);
\r
3171 calculate.add(njTreeBlosumMenuItem);
\r
3172 helpMenu.add(documentation);
\r
3173 helpMenu.add(about);
\r
3174 menu1.add(showColumns);
\r
3175 menu1.add(showSeqs);
\r
3176 menu1.add(showAllHidden);
\r
3177 menu2.add(hideColumns);
\r
3178 menu2.add(hideSequences);
\r
3179 menu2.add(hideAllSelection);
\r
3180 menu2.add(hideAllButSelection);
\r
3181 formatMenu.add(font);
\r
3182 formatMenu.add(seqLimits);
\r
3183 formatMenu.add(wrapMenuItem);
\r
3184 formatMenu.add(scaleAbove);
\r
3185 formatMenu.add(scaleLeft);
\r
3186 formatMenu.add(scaleRight);
\r
3187 formatMenu.add(viewBoxesMenuItem);
\r
3188 formatMenu.add(viewTextMenuItem);
\r
3189 formatMenu.add(colourTextMenuItem);
\r
3190 formatMenu.add(displayNonconservedMenuItem);
\r
3191 formatMenu.add(renderGapsMenuItem);
\r
3192 formatMenu.add(centreColumnLabelFlag);
\r
3193 selectMenu.add(findMenuItem);
\r
3194 selectMenu.addSeparator();
\r
3195 selectMenu.add(selectAllSequenceMenuItem);
\r
3196 selectMenu.add(deselectAllSequenceMenuItem);
\r
3197 selectMenu.add(invertSequenceMenuItem);
\r
3198 selectMenu.add(invertColSel);
\r
3199 selectMenu.add(grpsFromSelection);
\r
3200 selectMenu.add(deleteGroups);
\r
3204 MenuItem featureSettings = new MenuItem();
\r
3206 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
3208 MenuItem annotationColour = new MenuItem();
\r
3210 MenuItem invertColSel = new MenuItem();
\r
3212 Menu menu1 = new Menu();
\r
3214 MenuItem showColumns = new MenuItem();
\r
3216 MenuItem showSeqs = new MenuItem();
\r
3218 Menu menu2 = new Menu();
\r
3220 MenuItem hideColumns = new MenuItem();
\r
3222 MenuItem hideSequences = new MenuItem();
\r
3224 MenuItem hideAllButSelection = new MenuItem();
\r
3226 MenuItem hideAllSelection = new MenuItem();
\r
3228 MenuItem showAllHidden = new MenuItem();
\r
3230 Menu formatMenu = new Menu();
\r
3232 Menu selectMenu = new Menu();
\r
3234 MenuItem newView = new MenuItem();
\r
3237 * Attach the alignFrame panels after embedding menus, if necessary. This used
\r
3238 * to be called setEmbedded, but is now creates the dropdown menus in a
\r
3239 * platform independent manner to avoid OSX/Mac menu appendage daftness.
\r
3241 * @param reallyEmbedded
\r
3242 * true to attach the view to the applet area on the page rather than
\r
3245 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
\r
3247 if (reallyEmbedded)
\r
3250 // Explicly build the embedded menu panel for the on-page applet
\r
3252 // view cannot be closed if its actually on the page
\r
3253 fileMenu.remove(closeMenuItem);
\r
3254 fileMenu.remove(3); // Remove Seperator
\r
3255 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
\r
3256 Font.PLAIN, 10, false); // use our own fonts.
\r
3257 // and actually add the components to the applet area
\r
3258 viewport.applet.setLayout(new BorderLayout());
\r
3259 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
\r
3260 viewport.applet.add(statusBar, BorderLayout.SOUTH);
\r
3261 alignPanel.setSize(viewport.applet.getSize().width,
\r
3262 viewport.applet.getSize().height - embeddedMenu.HEIGHT
\r
3263 - statusBar.HEIGHT);
\r
3264 viewport.applet.add(alignPanel, BorderLayout.CENTER);
\r
3265 final AlignFrame me = this;
\r
3266 viewport.applet.addFocusListener(new FocusListener()
\r
3270 public void focusLost(FocusEvent e)
\r
3272 if (me.viewport.applet.currentAlignFrame==me) {
\r
3273 me.viewport.applet.currentAlignFrame = null;
\r
3277 public void focusGained(FocusEvent e)
\r
3279 me.viewport.applet.currentAlignFrame = me;
\r
3282 viewport.applet.validate();
\r
3287 // test and embed menu bar if necessary.
\r
3289 if (embedMenuIfNeeded(alignPanel))
\r
3291 // adjust for status bar height too
\r
3292 alignPanel.setSize(getSize().width, getSize().height
\r
3293 - statusBar.HEIGHT);
\r
3295 add(statusBar, BorderLayout.SOUTH);
\r
3296 add(alignPanel, BorderLayout.CENTER);
\r
3297 // and register with the applet so it can pass external API calls to us
\r
3298 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
\r
3304 * create a new binding between structures in an existing jmol viewer instance
\r
3305 * and an alignpanel with sequences that have existing PDBFile entries. Note,
\r
3306 * this does not open a new Jmol window, or modify the display of the
\r
3307 * structures in the original jmol window. Note This method doesn't work
\r
3308 * without an additional javascript library to exchange messages between the
\r
3309 * distinct applets. See http://issues.jalview.org/browse/JAL-621
\r
3312 * JmolViewer instance
\r
3313 * @param sequenceIds
\r
3314 * - sequence Ids to search for associations
\r
3316 public SequenceStructureBinding addStructureViewInstance(
\r
3317 Object jmolviewer, String[] sequenceIds)
\r
3319 org.jmol.api.JmolViewer viewer = null;
\r
3322 viewer = (org.jmol.api.JmolViewer) jmolviewer;
\r
3323 } catch (ClassCastException ex)
\r
3325 System.err.println("Unsupported viewer object :"
\r
3326 + jmolviewer.getClass());
\r
3328 if (viewer == null)
\r
3330 System.err.println("Can't use this object as a structure viewer:"
\r
3331 + jmolviewer.getClass());
\r
3334 SequenceI[] seqs = null;
\r
3335 if (sequenceIds == null || sequenceIds.length == 0)
\r
3337 seqs = viewport.getAlignment().getSequencesArray();
\r
3341 Vector sqi = new Vector();
\r
3342 AlignmentI al = viewport.getAlignment();
\r
3343 for (int sid = 0; sid < sequenceIds.length; sid++)
\r
3345 SequenceI sq = al.findName(sequenceIds[sid]);
\r
3348 sqi.addElement(sq);
\r
3351 if (sqi.size() > 0)
\r
3353 seqs = new SequenceI[sqi.size()];
\r
3354 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
\r
3356 seqs[sid] = (SequenceI) sqi.elementAt(sid);
\r
3364 ExtJmol jmv = null;
\r
3365 // TODO: search for a jmv that involves viewer
\r
3367 { // create a new viewer/jalview binding.
\r
3368 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs});
\r
3374 * bind a pdb file to a sequence in the current view
\r
3376 * @param sequenceId
\r
3377 * - sequenceId within the dataset.
\r
3378 * @param pdbEntryString
\r
3379 * - the short name for the PDB file
\r
3381 * - pdb file - either a URL or a valid PDB file.
\r
3382 * @return true if binding was as success TODO: consider making an exception
\r
3383 * structure for indicating when PDB parsing or sequenceId location
\r
3386 public boolean addPdbFile(String sequenceId, String pdbEntryString,
\r
3389 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
\r
3390 boolean needtoadd = false;
\r
3391 if (toaddpdb != null)
\r
3393 Vector pdbe = toaddpdb.getPDBId();
\r
3394 PDBEntry pdbentry = null;
\r
3395 if (pdbe != null && pdbe.size() > 0)
\r
3397 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
\r
3399 pdbentry = (PDBEntry) pdbe.elementAt(pe);
\r
3400 if (!pdbentry.getId().equals(pdbEntryString)
\r
3401 && !pdbentry.getFile().equals(pdbFile))
\r
3411 if (pdbentry == null)
\r
3413 pdbentry = new PDBEntry();
\r
3414 pdbentry.setId(pdbEntryString);
\r
3415 pdbentry.setFile(pdbFile);
\r
3416 needtoadd = true; // add this new entry to sequence.
\r
3418 // resolve data source
\r
3419 // TODO: this code should be a refactored to an io package
\r
3420 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
\r
3421 if (protocol == null)
\r
3427 // make a note of the access mode and add
\r
3428 if (pdbentry.getProperty() == null)
\r
3430 pdbentry.setProperty(new Hashtable());
\r
3432 pdbentry.getProperty().put("protocol", protocol);
\r
3433 toaddpdb.addPDBId(pdbentry);
\r
3439 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
\r
3443 Vector sequences = new Vector();
\r
3444 for (int i = 0; i < seqs.length; i++)
\r
3446 if (seqs[i] != null)
\r
3448 sequences.addElement(new Object[]
\r
3449 { seqs[i], (chains != null) ? chains[i] : null });
\r
3452 seqs = new SequenceI[sequences.size()];
\r
3453 chains = new String[sequences.size()];
\r
3454 for (int i = 0, isize = sequences.size(); i < isize; i++)
\r
3456 Object[] oj = (Object[]) sequences.elementAt(i);
\r
3458 seqs[i] = (SequenceI) oj[0];
\r
3459 chains[i] = (String) oj[1];
\r
3462 return new Object[]
\r
3467 public void newStructureView(JalviewLite applet, PDBEntry pdb,
\r
3468 SequenceI[] seqs, String[] chains, String protocol)
\r
3470 // Scrub any null sequences from the array
\r
3471 Object[] sqch = cleanSeqChainArrays(seqs, chains);
\r
3472 seqs = (SequenceI[]) sqch[0];
\r
3473 chains = (String[]) sqch[1];
\r
3474 if (seqs == null || seqs.length == 0)
\r
3477 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
\r
3479 if (protocol == null || protocol.trim().length() == 0
\r
3480 || protocol.equals("null"))
\r
3482 protocol = (String) pdb.getProperty().get("protocol");
\r
3483 if (protocol == null)
\r
3485 System.err.println("Couldn't work out protocol to open structure: "
\r
3490 if (applet.useXtrnalSviewer)
\r
3492 // register the association(s) and quit, don't create any windows.
\r
3493 if (StructureSelectionManager.getStructureSelectionManager(applet).setMapping(seqs, chains, pdb.getFile(), protocol)==null) {
\r
3494 System.err.println("Failed to map "+pdb.getFile()+" ("+protocol+") to any sequences");
\r
3498 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
\r
3500 // can only do alignments with Jmol
\r
3501 // find the last jmol window assigned to this alignment
\r
3502 jalview.appletgui.AppletJmol ajm = null, tajm;
\r
3503 Vector jmols = applet
\r
3504 .getAppletWindow(jalview.appletgui.AppletJmol.class);
\r
3505 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
\r
3507 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
\r
3508 if (tajm.ap.alignFrame == this)
\r
3517 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
\r
3518 // try and add the pdb structure
\r
3523 // otherwise, create a new window
\r
3524 if (applet.jmolAvailable)
\r
3526 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
\r
3528 applet.lastFrameX += 40;
\r
3529 applet.lastFrameY += 40;
\r
3533 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
\r
3538 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
\r
3539 SequenceI[][] seqs, String[][] chains, String[] protocols)
\r
3541 // TODO Auto-generated method stub
\r
3542 System.err.println("Aligned Structure View: Not yet implemented.");
\r
3546 * modify the current selection, providing the user has not made a selection already.
\r
3547 * @param sel - sequences from this alignment
\r
3548 * @param csel - columns to be selected on the alignment
\r
3550 public void select(SequenceGroup sel, ColumnSelection csel)
\r
3552 alignPanel.seqPanel.selection(sel, csel, null);
\r
3555 public void scrollTo(int row, int column)
\r
3557 alignPanel.seqPanel.scrollTo(row, column);
\r
3559 public void scrollToRow(int row)
\r
3561 alignPanel.seqPanel.scrollToRow(row);
\r
3563 public void scrollToColumn(int column)
\r
3565 alignPanel.seqPanel.scrollToColumn(column);
\r
3568 * @return the alignments unique ID.
\r
3570 public String getSequenceSetId() {
\r
3571 return viewport.getSequenceSetId();
\r