2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
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3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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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164 * Load a features file onto the alignment
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166 * @param file file URL, content, or other resolvable path
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167 * @param type is protocol for accessing data referred to by file
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170 public void parseFeaturesFile(String file, String type)
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172 parseFeaturesFile(file, type, true);
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176 * Load a features file onto the alignment
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178 * @param file file URL, content, or other resolvable path
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179 * @param type is protocol for accessing data referred to by file
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180 * @param autoenabledisplay when true, display features flag will be automatically enabled if features are loaded
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182 public void parseFeaturesFile(String file, String type, boolean autoenabledisplay)
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184 Hashtable featureLinks = new Hashtable();
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185 boolean featuresFile = false;
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188 featuresFile = new jalview.io.FeaturesFile(file, type)
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189 .parse(viewport.alignment,
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190 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
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191 featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));
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192 } catch (Exception ex)
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194 ex.printStackTrace();
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199 if (featureLinks.size() > 0)
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201 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
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203 if (autoenabledisplay)
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205 viewport.showSequenceFeatures = true;
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206 sequenceFeatures.setState(true);
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208 if (viewport.featureSettings != null)
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210 viewport.featureSettings.refreshTable();
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212 alignPanel.paintAlignment(true);
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217 public void keyPressed(KeyEvent evt)
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219 if (viewport.cursorMode
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220 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
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221 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
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222 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
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223 && Character.isDigit(evt.getKeyChar()))
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224 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
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226 switch (evt.getKeyCode())
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228 case 27: // escape key
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229 deselectAllSequenceMenuItem_actionPerformed();
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231 alignPanel.alabels.cancelDrag();
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233 case KeyEvent.VK_X:
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234 if (evt.isControlDown() || evt.isMetaDown())
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236 cut_actionPerformed();
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239 case KeyEvent.VK_C:
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240 if (viewport.cursorMode && !evt.isControlDown())
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242 alignPanel.seqPanel.setCursorColumn();
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244 if (evt.isControlDown() || evt.isMetaDown())
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246 copy_actionPerformed();
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249 case KeyEvent.VK_V:
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250 if (evt.isControlDown())
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252 paste(evt.isShiftDown());
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255 case KeyEvent.VK_A:
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256 if (evt.isControlDown() || evt.isMetaDown())
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258 selectAllSequenceMenuItem_actionPerformed();
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261 case KeyEvent.VK_DOWN:
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262 if (viewport.cursorMode)
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264 alignPanel.seqPanel.moveCursor(0, 1);
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268 moveSelectedSequences(false);
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272 case KeyEvent.VK_UP:
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273 if (viewport.cursorMode)
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275 alignPanel.seqPanel.moveCursor(0, -1);
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279 moveSelectedSequences(true);
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283 case KeyEvent.VK_LEFT:
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284 if (evt.isAltDown() || !viewport.cursorMode)
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285 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
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287 alignPanel.seqPanel.moveCursor(-1, 0);
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290 case KeyEvent.VK_RIGHT:
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291 if (evt.isAltDown() || !viewport.cursorMode)
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292 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
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294 alignPanel.seqPanel.moveCursor(1, 0);
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297 case KeyEvent.VK_SPACE:
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298 if (viewport.cursorMode)
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300 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
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301 || evt.isShiftDown() || evt.isAltDown());
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305 case KeyEvent.VK_DELETE:
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306 case KeyEvent.VK_BACK_SPACE:
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307 if (viewport.cursorMode)
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309 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
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310 || evt.isShiftDown() || evt.isAltDown());
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314 cut_actionPerformed();
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315 alignPanel.seqPanel.seqCanvas.repaint();
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319 case KeyEvent.VK_S:
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320 if (viewport.cursorMode)
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322 alignPanel.seqPanel.setCursorRow();
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325 case KeyEvent.VK_P:
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326 if (viewport.cursorMode)
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328 alignPanel.seqPanel.setCursorPosition();
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332 case KeyEvent.VK_ENTER:
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333 case KeyEvent.VK_COMMA:
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334 if (viewport.cursorMode)
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336 alignPanel.seqPanel.setCursorRowAndColumn();
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340 case KeyEvent.VK_Q:
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341 if (viewport.cursorMode)
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343 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
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346 case KeyEvent.VK_M:
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347 if (viewport.cursorMode)
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349 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
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353 case KeyEvent.VK_F2:
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354 viewport.cursorMode = !viewport.cursorMode;
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355 statusBar.setText("Keyboard editing mode is "
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356 + (viewport.cursorMode ? "on" : "off"));
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357 if (viewport.cursorMode)
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359 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
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360 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
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364 case KeyEvent.VK_F:
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365 if (evt.isControlDown())
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367 findMenuItem_actionPerformed();
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371 case KeyEvent.VK_H:
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373 boolean toggleSeqs = !evt.isControlDown();
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374 boolean toggleCols = !evt.isShiftDown();
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375 toggleHiddenRegions(toggleSeqs, toggleCols);
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379 case KeyEvent.VK_PAGE_UP:
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380 if (viewport.wrapAlignment)
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382 alignPanel.scrollUp(true);
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386 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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387 - viewport.endSeq + viewport.startSeq);
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391 case KeyEvent.VK_PAGE_DOWN:
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392 if (viewport.wrapAlignment)
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394 alignPanel.scrollUp(false);
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398 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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399 + viewport.endSeq - viewport.startSeq);
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403 case KeyEvent.VK_Z:
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404 if (evt.isControlDown())
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406 undoMenuItem_actionPerformed();
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410 case KeyEvent.VK_Y:
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411 if (evt.isControlDown())
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413 redoMenuItem_actionPerformed();
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417 case KeyEvent.VK_L:
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418 if (evt.isControlDown())
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420 trimAlignment(true);
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424 case KeyEvent.VK_R:
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425 if (evt.isControlDown())
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427 trimAlignment(false);
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431 case KeyEvent.VK_E:
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432 if (evt.isControlDown())
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434 if (evt.isShiftDown())
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436 this.removeAllGapsMenuItem_actionPerformed();
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440 removeGappedColumnMenuItem_actionPerformed();
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444 case KeyEvent.VK_I:
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445 if (evt.isControlDown())
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447 if (evt.isAltDown())
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449 invertColSel_actionPerformed();
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453 invertSequenceMenuItem_actionPerformed();
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458 case KeyEvent.VK_U:
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459 if (evt.isControlDown())
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461 this.deleteGroups_actionPerformed();
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465 case KeyEvent.VK_T:
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466 if (evt.isControlDown())
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473 alignPanel.paintAlignment(true);
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477 * called by key handler and the hide all/show all menu items
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479 * @param toggleSeqs
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480 * @param toggleCols
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482 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
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484 boolean hide = false;
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485 SequenceGroup sg = viewport.getSelectionGroup();
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486 if (!toggleSeqs && !toggleCols)
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488 // Hide everything by the current selection - this is a hack - we do the
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489 // invert and then hide
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490 // first check that there will be visible columns after the invert.
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491 if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
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492 .getSelected().size() > 0)
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493 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
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496 // now invert the sequence set, if required - empty selection implies
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497 // that no hiding is required.
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500 invertSequenceMenuItem_actionPerformed();
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501 sg = viewport.getSelectionGroup();
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505 viewport.expandColSelection(sg, true);
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506 // finally invert the column selection and get the new sequence
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507 // selection and indicate it should be hidden.
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508 invertColSel_actionPerformed();
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515 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
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518 viewport.hideAllSelectedSeqs();
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520 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
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522 viewport.showAllHiddenSeqs();
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528 if (viewport.colSel.getSelected().size() > 0)
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530 viewport.hideSelectedColumns();
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533 viewport.selectionGroup = sg;
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538 viewport.showAllHiddenColumns();
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543 public void keyReleased(KeyEvent evt)
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547 public void keyTyped(KeyEvent evt)
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551 public void itemStateChanged(ItemEvent evt)
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553 if (evt.getSource() == displayNonconservedMenuItem)
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555 displayNonconservedMenuItem_actionPerformed();
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557 else if (evt.getSource() == colourTextMenuItem)
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559 colourTextMenuItem_actionPerformed();
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561 else if (evt.getSource() == wrapMenuItem)
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563 wrapMenuItem_actionPerformed();
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565 else if (evt.getSource() == scaleAbove)
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567 viewport.setScaleAboveWrapped(scaleAbove.getState());
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569 else if (evt.getSource() == scaleLeft)
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571 viewport.setScaleLeftWrapped(scaleLeft.getState());
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573 else if (evt.getSource() == scaleRight)
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575 viewport.setScaleRightWrapped(scaleRight.getState());
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577 else if (evt.getSource() == seqLimits)
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579 seqLimits_itemStateChanged();
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581 else if (evt.getSource() == viewBoxesMenuItem)
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583 viewport.setShowBoxes(viewBoxesMenuItem.getState());
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585 else if (evt.getSource() == viewTextMenuItem)
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587 viewport.setShowText(viewTextMenuItem.getState());
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589 else if (evt.getSource() == renderGapsMenuItem)
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591 viewport.setRenderGaps(renderGapsMenuItem.getState());
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593 else if (evt.getSource() == annotationPanelMenuItem)
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595 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
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596 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
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598 else if (evt.getSource() == sequenceFeatures)
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600 viewport.showSequenceFeatures(sequenceFeatures.getState());
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601 alignPanel.seqPanel.seqCanvas.repaint();
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603 else if (evt.getSource() == conservationMenuItem)
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605 conservationMenuItem_actionPerformed();
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607 else if (evt.getSource() == abovePIDThreshold)
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609 abovePIDThreshold_actionPerformed();
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611 else if (evt.getSource() == applyToAllGroups)
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613 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
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615 else if (evt.getSource() == autoCalculate)
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617 viewport.autocalculateConsensus = autoCalculate.getState();
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619 else if (evt.getSource() == sortByTree)
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621 viewport.sortByTree = sortByTree.getState();
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623 else if (evt.getSource() == this.centreColumnLabelFlag)
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625 centreColumnLabelFlag_stateChanged();
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627 else if (evt.getSource() == this.followMouseOverFlag)
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629 mouseOverFlag_stateChanged();
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631 else if (evt.getSource() == showGroupConsensus)
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633 showGroupConsensus_actionPerformed();
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635 else if (evt.getSource() == showGroupConservation)
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637 showGroupConservation_actionPerformed();
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639 else if (evt.getSource() == showSequenceLogo)
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641 showSequenceLogo_actionPerformed();
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643 else if (evt.getSource() == showConsensusHistogram)
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645 showConsensusHistogram_actionPerformed();
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647 else if (evt.getSource() == applyAutoAnnotationSettings)
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649 applyAutoAnnotationSettings_actionPerformed();
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651 alignPanel.paintAlignment(true);
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654 private void mouseOverFlag_stateChanged()
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656 viewport.followHighlight = followMouseOverFlag.getState();
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657 // TODO: could kick the scrollTo mechanism to reset view for current
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661 private void centreColumnLabelFlag_stateChanged()
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663 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
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664 this.alignPanel.annotationPanel.repaint();
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667 public void actionPerformed(ActionEvent evt)
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669 Object source = evt.getSource();
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671 if (source == inputText)
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673 inputText_actionPerformed();
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675 else if (source == loadTree)
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677 loadTree_actionPerformed();
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679 else if (source == loadApplication)
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681 launchFullApplication();
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683 else if (source == loadAnnotations)
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687 else if (source == outputAnnotations)
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689 outputAnnotations(true);
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691 else if (source == outputFeatures)
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693 outputFeatures(true, "Jalview");
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695 else if (source == closeMenuItem)
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697 closeMenuItem_actionPerformed();
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699 else if (source == copy)
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701 copy_actionPerformed();
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703 else if (source == undoMenuItem)
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705 undoMenuItem_actionPerformed();
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707 else if (source == redoMenuItem)
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709 redoMenuItem_actionPerformed();
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711 else if (source == inputText)
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713 inputText_actionPerformed();
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715 else if (source == closeMenuItem)
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717 closeMenuItem_actionPerformed();
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719 else if (source == undoMenuItem)
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721 undoMenuItem_actionPerformed();
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723 else if (source == redoMenuItem)
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725 redoMenuItem_actionPerformed();
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727 else if (source == copy)
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729 copy_actionPerformed();
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731 else if (source == pasteNew)
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733 pasteNew_actionPerformed();
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735 else if (source == pasteThis)
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737 pasteThis_actionPerformed();
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739 else if (source == cut)
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741 cut_actionPerformed();
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743 else if (source == delete)
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745 delete_actionPerformed();
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747 else if (source == grpsFromSelection)
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749 makeGrpsFromSelection_actionPerformed();
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751 else if (source == deleteGroups)
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753 deleteGroups_actionPerformed();
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755 else if (source == selectAllSequenceMenuItem)
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757 selectAllSequenceMenuItem_actionPerformed();
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759 else if (source == deselectAllSequenceMenuItem)
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761 deselectAllSequenceMenuItem_actionPerformed();
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763 else if (source == invertSequenceMenuItem)
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765 invertSequenceMenuItem_actionPerformed();
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767 else if (source == invertColSel)
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769 viewport.invertColumnSelection();
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770 alignPanel.paintAlignment(true);
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772 else if (source == remove2LeftMenuItem)
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774 trimAlignment(true);
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776 else if (source == remove2RightMenuItem)
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778 trimAlignment(false);
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780 else if (source == removeGappedColumnMenuItem)
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782 removeGappedColumnMenuItem_actionPerformed();
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784 else if (source == removeAllGapsMenuItem)
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786 removeAllGapsMenuItem_actionPerformed();
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788 else if (source == findMenuItem)
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790 findMenuItem_actionPerformed();
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792 else if (source == font)
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794 new FontChooser(alignPanel);
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796 else if (source == newView)
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800 else if (source == showColumns)
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802 viewport.showAllHiddenColumns();
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803 alignPanel.paintAlignment(true);
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805 else if (source == showSeqs)
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807 viewport.showAllHiddenSeqs();
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808 alignPanel.paintAlignment(true);
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810 else if (source == hideColumns)
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812 viewport.hideSelectedColumns();
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813 alignPanel.paintAlignment(true);
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815 else if (source == hideSequences
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816 && viewport.getSelectionGroup() != null)
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818 viewport.hideAllSelectedSeqs();
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819 alignPanel.paintAlignment(true);
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821 else if (source == hideAllButSelection)
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823 toggleHiddenRegions(false, false);
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824 alignPanel.paintAlignment(true);
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826 else if (source == hideAllSelection)
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828 SequenceGroup sg = viewport.getSelectionGroup();
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829 viewport.expandColSelection(sg, false);
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830 viewport.hideAllSelectedSeqs();
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831 viewport.hideSelectedColumns();
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832 alignPanel.paintAlignment(true);
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834 else if (source == showAllHidden)
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836 viewport.showAllHiddenColumns();
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837 viewport.showAllHiddenSeqs();
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838 alignPanel.paintAlignment(true);
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840 else if (source == showGroupConsensus)
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842 showGroupConsensus_actionPerformed();
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844 else if (source == showGroupConservation)
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846 showGroupConservation_actionPerformed();
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848 else if (source == showSequenceLogo)
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850 showSequenceLogo_actionPerformed();
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852 else if (source == showConsensusHistogram)
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854 showConsensusHistogram_actionPerformed();
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856 else if (source == applyAutoAnnotationSettings)
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858 applyAutoAnnotationSettings_actionPerformed();
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860 else if (source == featureSettings)
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862 new FeatureSettings(alignPanel);
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864 else if (source == alProperties)
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866 StringBuffer contents = new jalview.io.AlignmentProperties(
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867 viewport.alignment).formatAsString();
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868 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
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869 cap.setText(contents.toString());
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870 Frame frame = new Frame();
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872 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
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873 + getTitle(), 400, 250);
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875 else if (source == overviewMenuItem)
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877 overviewMenuItem_actionPerformed();
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879 else if (source == noColourmenuItem)
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881 changeColour(null);
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883 else if (source == clustalColour)
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885 abovePIDThreshold.setState(false);
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886 changeColour(new ClustalxColourScheme(
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887 viewport.alignment.getSequences(),
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888 viewport.alignment.getWidth()));
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890 else if (source == zappoColour)
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892 changeColour(new ZappoColourScheme());
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894 else if (source == taylorColour)
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896 changeColour(new TaylorColourScheme());
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898 else if (source == hydrophobicityColour)
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900 changeColour(new HydrophobicColourScheme());
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902 else if (source == helixColour)
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904 changeColour(new HelixColourScheme());
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906 else if (source == strandColour)
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908 changeColour(new StrandColourScheme());
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910 else if (source == turnColour)
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912 changeColour(new TurnColourScheme());
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914 else if (source == buriedColour)
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916 changeColour(new BuriedColourScheme());
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918 else if (source == nucleotideColour)
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920 changeColour(new NucleotideColourScheme());
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922 else if (source == modifyPID)
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924 modifyPID_actionPerformed();
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926 else if (source == modifyConservation)
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928 modifyConservation_actionPerformed();
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930 else if (source == userDefinedColour)
\r
932 new UserDefinedColours(alignPanel, null);
\r
934 else if (source == PIDColour)
\r
936 changeColour(new PIDColourScheme());
\r
938 else if (source == BLOSUM62Colour)
\r
940 changeColour(new Blosum62ColourScheme());
\r
942 else if (source == annotationColour)
\r
944 new AnnotationColourChooser(viewport, alignPanel);
\r
946 else if (source == sortPairwiseMenuItem)
\r
948 sortPairwiseMenuItem_actionPerformed();
\r
950 else if (source == sortIDMenuItem)
\r
952 sortIDMenuItem_actionPerformed();
\r
954 else if (source == sortLengthMenuItem)
\r
956 sortLengthMenuItem_actionPerformed();
\r
958 else if (source == sortGroupMenuItem)
\r
960 sortGroupMenuItem_actionPerformed();
\r
962 else if (source == removeRedundancyMenuItem)
\r
964 removeRedundancyMenuItem_actionPerformed();
\r
966 else if (source == pairwiseAlignmentMenuItem)
\r
968 pairwiseAlignmentMenuItem_actionPerformed();
\r
970 else if (source == PCAMenuItem)
\r
972 PCAMenuItem_actionPerformed();
\r
974 else if (source == averageDistanceTreeMenuItem)
\r
976 averageDistanceTreeMenuItem_actionPerformed();
\r
978 else if (source == neighbourTreeMenuItem)
\r
980 neighbourTreeMenuItem_actionPerformed();
\r
982 else if (source == njTreeBlosumMenuItem)
\r
984 njTreeBlosumMenuItem_actionPerformed();
\r
986 else if (source == avDistanceTreeBlosumMenuItem)
\r
988 avTreeBlosumMenuItem_actionPerformed();
\r
990 else if (source == documentation)
\r
992 documentation_actionPerformed();
\r
994 else if (source == about)
\r
996 about_actionPerformed();
\r
1001 public void inputText_actionPerformed()
\r
1003 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1004 Frame frame = new Frame();
\r
1006 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
\r
1009 protected void outputText_actionPerformed(ActionEvent e)
\r
1011 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1012 Frame frame = new Frame();
\r
1014 jalview.bin.JalviewLite.addFrame(frame,
\r
1015 "Alignment output - " + e.getActionCommand(), 600, 500);
\r
1016 cap.setText(new AppletFormatAdapter().formatSequences(
\r
1017 e.getActionCommand(), viewport.getAlignment(),
\r
1018 viewport.showJVSuffix));
\r
1021 public void loadAnnotations()
\r
1023 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1024 cap.setText("Paste your features / annotations file here.");
\r
1025 cap.setAnnotationImport();
\r
1026 Frame frame = new Frame();
\r
1028 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
\r
1032 public String outputAnnotations(boolean displayTextbox)
\r
1034 String annotation = new AnnotationFile().printAnnotations(
\r
1035 viewport.showAnnotation ? viewport.alignment
\r
1036 .getAlignmentAnnotation() : null, viewport.alignment
\r
1038 ((Alignment) viewport.alignment).alignmentProperties);
\r
1040 if (displayTextbox)
\r
1042 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
1043 Frame frame = new Frame();
\r
1045 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
\r
1046 cap.setText(annotation);
\r
1049 return annotation;
\r
1052 private Hashtable getDisplayedFeatureCols()
\r
1054 if (alignPanel.getFeatureRenderer() != null && viewport.featuresDisplayed!=null)
\r
1056 FeatureRenderer fr = alignPanel.getFeatureRenderer();
\r
1057 Hashtable fcols = new Hashtable();
\r
1058 Enumeration en = viewport.featuresDisplayed.keys();
\r
1059 while (en.hasMoreElements())
\r
1061 Object col = en.nextElement();
\r
1062 fcols.put(col, fr.featureColours.get(col));
\r
1069 public String outputFeatures(boolean displayTextbox, String format)
\r
1072 if (format.equalsIgnoreCase("Jalview"))
\r
1074 features = new FeaturesFile().printJalviewFormat(
\r
1075 viewport.alignment.getSequencesArray(),
\r
1076 getDisplayedFeatureCols());
\r
1080 features = new FeaturesFile().printGFFFormat(
\r
1081 viewport.alignment.getSequencesArray(),
\r
1082 getDisplayedFeatureCols());
\r
1085 if (displayTextbox)
\r
1087 boolean frimport=false;
\r
1088 if (features==null || features.equals("No Features Visible"))
\r
1090 features = "# No features visible - paste some and import them here.";
\r
1094 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
\r
1097 cap.setAnnotationImport();
\r
1099 Frame frame = new Frame();
\r
1101 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
\r
1102 cap.setText(features);
\r
1104 if (features==null)
\r
1111 void launchFullApplication()
\r
1113 StringBuffer url = new StringBuffer(jalviewServletURL);
\r
1115 url.append("?open="
\r
1116 + appendProtocol(viewport.applet.getParameter("file")));
\r
1118 if (viewport.applet.getParameter("features") != null)
\r
1120 url.append("&features=");
\r
1121 url.append(appendProtocol(viewport.applet.getParameter("features")));
\r
1124 if (viewport.applet.getParameter("annotations") != null)
\r
1126 url.append("&annotations=");
\r
1127 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
\r
1130 if (viewport.applet.getParameter("jnetfile") != null)
\r
1132 url.append("&annotations=");
\r
1133 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
\r
1136 if (viewport.applet.getParameter("defaultColour") != null)
\r
1138 url.append("&colour="
\r
1139 + removeWhiteSpace(viewport.applet
\r
1140 .getParameter("defaultColour")));
\r
1143 if (viewport.applet.getParameter("userDefinedColour") != null)
\r
1145 url.append("&colour="
\r
1146 + removeWhiteSpace(viewport.applet
\r
1147 .getParameter("userDefinedColour")));
\r
1149 if (viewport.applet.getParameter("tree") != null)
\r
1151 url.append("&tree="
\r
1152 + appendProtocol(viewport.applet.getParameter("tree")));
\r
1154 if (viewport.applet.getParameter("treeFile") != null)
\r
1156 url.append("&tree="
\r
1157 + appendProtocol(viewport.applet.getParameter("treeFile")));
\r
1160 showURL(url.toString(), "FULL_APP");
\r
1163 String removeWhiteSpace(String colour)
\r
1165 StringBuffer sb = new StringBuffer();
\r
1166 for (int i = 0; i < colour.length(); i++)
\r
1168 if (Character.isWhitespace(colour.charAt(i)))
\r
1174 sb.append(colour.charAt(i));
\r
1178 return sb.toString();
\r
1181 String appendProtocol(String url)
\r
1186 url = URLEncoder.encode(url);
\r
1189 * When we finally deprecate 1.1 compatibility, we can start to use
\r
1190 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
\r
1191 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
\r
1192 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
\r
1193 * ex.printStackTrace(); }
\r
1195 catch (java.net.MalformedURLException ex)
\r
1197 url = viewport.applet.getCodeBase() + url;
\r
1202 public void closeMenuItem_actionPerformed()
\r
1204 PaintRefresher.RemoveComponent(alignPanel);
\r
1205 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
\r
1206 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
\r
1208 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
\r
1214 alignPanel = null;
\r
1221 void updateEditMenuBar()
\r
1224 if (viewport.historyList.size() > 0)
\r
1226 undoMenuItem.setEnabled(true);
\r
1227 CommandI command = (CommandI) viewport.historyList.peek();
\r
1228 undoMenuItem.setLabel("Undo " + command.getDescription());
\r
1232 undoMenuItem.setEnabled(false);
\r
1233 undoMenuItem.setLabel("Undo");
\r
1236 if (viewport.redoList.size() > 0)
\r
1238 redoMenuItem.setEnabled(true);
\r
1240 CommandI command = (CommandI) viewport.redoList.peek();
\r
1241 redoMenuItem.setLabel("Redo " + command.getDescription());
\r
1245 redoMenuItem.setEnabled(false);
\r
1246 redoMenuItem.setLabel("Redo");
\r
1250 public void addHistoryItem(CommandI command)
\r
1252 if (command.getSize() > 0)
\r
1254 viewport.historyList.push(command);
\r
1255 viewport.redoList.removeAllElements();
\r
1256 updateEditMenuBar();
\r
1257 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
1267 protected void undoMenuItem_actionPerformed()
\r
1269 if (viewport.historyList.size() < 1)
\r
1274 CommandI command = (CommandI) viewport.historyList.pop();
\r
1275 viewport.redoList.push(command);
\r
1276 command.undoCommand(null);
\r
1278 AlignViewport originalSource = getOriginatingSource(command);
\r
1280 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
1281 updateEditMenuBar();
\r
1282 originalSource.firePropertyChange("alignment", null,
\r
1283 originalSource.alignment.getSequences());
\r
1292 protected void redoMenuItem_actionPerformed()
\r
1294 if (viewport.redoList.size() < 1)
\r
1299 CommandI command = (CommandI) viewport.redoList.pop();
\r
1300 viewport.historyList.push(command);
\r
1301 command.doCommand(null);
\r
1303 AlignViewport originalSource = getOriginatingSource(command);
\r
1304 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
1306 updateEditMenuBar();
\r
1307 originalSource.firePropertyChange("alignment", null,
\r
1308 originalSource.alignment.getSequences());
\r
1311 AlignViewport getOriginatingSource(CommandI command)
\r
1313 AlignViewport originalSource = null;
\r
1314 // For sequence removal and addition, we need to fire
\r
1315 // the property change event FROM the viewport where the
\r
1316 // original alignment was altered
\r
1317 AlignmentI al = null;
\r
1318 if (command instanceof EditCommand)
\r
1320 EditCommand editCommand = (EditCommand) command;
\r
1321 al = editCommand.getAlignment();
\r
1322 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
1323 .getSequenceSetId());
\r
1324 for (int i = 0; i < comps.size(); i++)
\r
1326 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
1328 if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
\r
1330 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
\r
1337 if (originalSource == null)
\r
1339 // The original view is closed, we must validate
\r
1340 // the current view against the closed view first
\r
1343 PaintRefresher.validateSequences(al, viewport.alignment);
\r
1346 originalSource = viewport;
\r
1349 return originalSource;
\r
1352 public void moveSelectedSequences(boolean up)
\r
1354 SequenceGroup sg = viewport.getSelectionGroup();
\r
1362 for (int i = 1; i < viewport.alignment.getHeight(); i++)
\r
1364 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
1365 if (!sg.getSequences(null).contains(seq))
\r
1370 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
\r
1371 if (sg.getSequences(null).contains(temp))
\r
1376 viewport.alignment.getSequences().setElementAt(temp, i);
\r
1377 viewport.alignment.getSequences().setElementAt(seq, i - 1);
\r
1382 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
\r
1384 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
1385 if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))
\r
1390 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
\r
1391 if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))
\r
1396 viewport.alignment.getSequences().setElementAt(temp, i);
\r
1397 viewport.alignment.getSequences().setElementAt(seq, i + 1);
\r
1401 alignPanel.paintAlignment(true);
\r
1404 synchronized void slideSequences(boolean right, int size)
\r
1406 Vector sg = new Vector();
\r
1407 if (viewport.cursorMode)
\r
1409 sg.addElement(viewport.alignment
\r
1410 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
\r
1412 else if (viewport.getSelectionGroup() != null
\r
1413 && viewport.getSelectionGroup().getSize() != viewport.alignment
\r
1416 sg = viewport.getSelectionGroup().getSequences(
\r
1417 viewport.hiddenRepSequences);
\r
1420 if (sg.size() < 1)
\r
1425 Vector invertGroup = new Vector();
\r
1427 for (int i = 0; i < viewport.alignment.getHeight(); i++)
\r
1429 if (!sg.contains(viewport.alignment.getSequenceAt(i)))
\r
1430 invertGroup.addElement(viewport.alignment.getSequenceAt(i));
\r
1433 SequenceI[] seqs1 = new SequenceI[sg.size()];
\r
1434 for (int i = 0; i < sg.size(); i++)
\r
1435 seqs1[i] = (SequenceI) sg.elementAt(i);
\r
1437 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
\r
1438 for (int i = 0; i < invertGroup.size(); i++)
\r
1439 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
\r
1441 SlideSequencesCommand ssc;
\r
1443 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
\r
1444 size, viewport.getGapCharacter());
\r
1446 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
\r
1447 size, viewport.getGapCharacter());
\r
1449 int groupAdjustment = 0;
\r
1450 if (ssc.getGapsInsertedBegin() && right)
\r
1452 if (viewport.cursorMode)
\r
1453 alignPanel.seqPanel.moveCursor(size, 0);
\r
1455 groupAdjustment = size;
\r
1457 else if (!ssc.getGapsInsertedBegin() && !right)
\r
1459 if (viewport.cursorMode)
\r
1460 alignPanel.seqPanel.moveCursor(-size, 0);
\r
1462 groupAdjustment = -size;
\r
1465 if (groupAdjustment != 0)
\r
1467 viewport.getSelectionGroup().setStartRes(
\r
1468 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
\r
1469 viewport.getSelectionGroup().setEndRes(
\r
1470 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
\r
1473 boolean appendHistoryItem = false;
\r
1474 if (viewport.historyList != null && viewport.historyList.size() > 0
\r
1475 && viewport.historyList.peek() instanceof SlideSequencesCommand)
\r
1477 appendHistoryItem = ssc
\r
1478 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
\r
1482 if (!appendHistoryItem)
\r
1483 addHistoryItem(ssc);
\r
1488 static StringBuffer copiedSequences;
\r
1490 static Vector copiedHiddenColumns;
\r
1492 protected void copy_actionPerformed()
\r
1494 if (viewport.getSelectionGroup() == null)
\r
1499 SequenceGroup sg = viewport.getSelectionGroup();
\r
1500 copiedSequences = new StringBuffer();
\r
1501 Hashtable orderedSeqs = new Hashtable();
\r
1502 for (int i = 0; i < sg.getSize(); i++)
\r
1504 SequenceI seq = sg.getSequenceAt(i);
\r
1505 int index = viewport.alignment.findIndex(seq);
\r
1506 orderedSeqs.put(index + "", seq);
\r
1509 int index = 0, startRes, endRes;
\r
1512 if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
\r
1514 copiedHiddenColumns = new Vector();
\r
1515 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
\r
1516 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
\r
1519 int[] region = (int[]) viewport.getColumnSelection()
\r
1520 .getHiddenColumns().elementAt(i);
\r
1522 copiedHiddenColumns.addElement(new int[]
\r
1523 { region[0] - hiddenOffset, region[1] - hiddenOffset });
\r
1528 copiedHiddenColumns = null;
\r
1531 for (int i = 0; i < sg.getSize(); i++)
\r
1533 SequenceI seq = null;
\r
1535 while (seq == null)
\r
1537 if (orderedSeqs.containsKey(index + ""))
\r
1539 seq = (SequenceI) orderedSeqs.get(index + "");
\r
1551 // Returns residue following index if gap
\r
1552 startRes = seq.findPosition(sg.getStartRes());
\r
1555 // Need to find the residue preceeding index if gap
\r
1558 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
\r
1560 ch = seq.getCharAt(j);
\r
1561 if (!jalview.util.Comparison.isGap((ch)))
\r
1569 endRes += seq.getStart() - 1;
\r
1572 copiedSequences.append(seq.getName()
\r
1578 + seq.getSequenceAsString(sg.getStartRes(),
\r
1579 sg.getEndRes() + 1) + "\n");
\r
1584 protected void pasteNew_actionPerformed()
\r
1589 protected void pasteThis_actionPerformed()
\r
1594 void paste(boolean newAlignment)
\r
1599 if (copiedSequences == null)
\r
1604 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
1605 Vector seqs = new Vector();
\r
1606 while (st.hasMoreElements())
\r
1608 String name = st.nextToken();
\r
1609 int start = Integer.parseInt(st.nextToken());
\r
1610 int end = Integer.parseInt(st.nextToken());
\r
1611 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
\r
1613 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
1614 for (int i = 0; i < seqs.size(); i++)
\r
1616 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
1621 String newtitle = new String("Copied sequences");
\r
1622 if (getTitle().startsWith("Copied sequences"))
\r
1624 newtitle = getTitle();
\r
1628 newtitle = newtitle.concat("- from " + getTitle());
\r
1630 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
1631 viewport.applet, newtitle, false);
\r
1632 if (copiedHiddenColumns != null)
\r
1634 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
1636 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
1637 af.viewport.hideColumns(region[0], region[1]);
\r
1641 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
\r
1646 addSequences(newSeqs);
\r
1649 } catch (Exception ex)
\r
1651 } // could be anything being pasted in here
\r
1655 void addSequences(SequenceI[] seqs)
\r
1657 for (int i = 0; i < seqs.length; i++)
\r
1659 viewport.alignment.addSequence(seqs[i]);
\r
1663 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
\r
1664 seqs, 0, viewport.alignment.getWidth(), viewport.alignment));
\r
1666 viewport.setEndSeq(viewport.alignment.getHeight());
\r
1667 viewport.alignment.getWidth();
\r
1668 viewport.firePropertyChange("alignment", null,
\r
1669 viewport.alignment.getSequences());
\r
1673 protected void cut_actionPerformed()
\r
1675 copy_actionPerformed();
\r
1676 delete_actionPerformed();
\r
1679 protected void delete_actionPerformed()
\r
1682 SequenceGroup sg = viewport.getSelectionGroup();
\r
1688 Vector seqs = new Vector();
\r
1690 for (int i = 0; i < sg.getSize(); i++)
\r
1692 seq = sg.getSequenceAt(i);
\r
1693 seqs.addElement(seq);
\r
1696 // If the cut affects all sequences, remove highlighted columns
\r
1697 if (sg.getSize() == viewport.alignment.getHeight())
\r
1699 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
1700 sg.getEndRes() + 1);
\r
1703 SequenceI[] cut = new SequenceI[seqs.size()];
\r
1704 for (int i = 0; i < seqs.size(); i++)
\r
1706 cut[i] = (SequenceI) seqs.elementAt(i);
\r
1710 * //ADD HISTORY ITEM
\r
1712 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
\r
1713 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
\r
1714 viewport.alignment));
\r
1716 viewport.setSelectionGroup(null);
\r
1717 viewport.alignment.deleteGroup(sg);
\r
1719 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1722 if (viewport.getAlignment().getHeight() < 1)
\r
1724 this.setVisible(false);
\r
1726 viewport.sendSelection();
\r
1730 * group consensus toggled
\r
1733 protected void showGroupConsensus_actionPerformed()
\r
1735 viewport.setShowGroupConsensus(showGroupConsensus.getState());
\r
1736 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1741 * group conservation toggled.
\r
1743 protected void showGroupConservation_actionPerformed()
\r
1745 viewport.setShowGroupConservation(showGroupConservation.getState());
\r
1746 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1753 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
\r
1754 * .event.ActionEvent)
\r
1756 protected void showConsensusHistogram_actionPerformed()
\r
1758 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
\r
1759 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1765 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
\r
1766 * .event.ActionEvent)
\r
1768 protected void showSequenceLogo_actionPerformed()
\r
1770 viewport.setShowSequenceLogo(showSequenceLogo.getState());
\r
1771 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1774 protected void applyAutoAnnotationSettings_actionPerformed()
\r
1776 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1779 protected void makeGrpsFromSelection_actionPerformed()
\r
1781 if (viewport.getSelectionGroup() != null)
\r
1783 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
\r
1784 viewport.getSequenceSelection(),
\r
1785 viewport.getAlignmentView(true).getSequenceStrings(
\r
1786 viewport.getGapCharacter()),
\r
1787 viewport.alignment.getGroups());
\r
1788 viewport.alignment.deleteAllGroups();
\r
1789 viewport.sequenceColours = null;
\r
1790 viewport.setSelectionGroup(null);
\r
1791 // set view properties for each group
\r
1792 for (int g = 0; g < gps.length; g++)
\r
1794 // gps[g].setShowunconserved(viewport.getShowUnconserved());
\r
1795 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
\r
1796 viewport.alignment.addGroup(gps[g]);
\r
1797 Color col = new Color((int) (Math.random() * 255),
\r
1798 (int) (Math.random() * 255), (int) (Math.random() * 255));
\r
1799 col = col.brighter();
\r
1800 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
\r
1801 .hasMoreElements(); viewport.setSequenceColour(
\r
1802 (SequenceI) sq.nextElement(), col))
\r
1805 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
\r
1806 alignPanel.updateAnnotation();
\r
1807 alignPanel.paintAlignment(true);
\r
1811 protected void deleteGroups_actionPerformed()
\r
1813 viewport.alignment.deleteAllGroups();
\r
1814 viewport.sequenceColours = null;
\r
1815 viewport.setSelectionGroup(null);
\r
1817 alignPanel.paintAlignment(true);
\r
1820 public void selectAllSequenceMenuItem_actionPerformed()
\r
1822 SequenceGroup sg = new SequenceGroup();
\r
1823 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1825 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
1827 sg.setEndRes(viewport.alignment.getWidth() - 1);
\r
1828 viewport.setSelectionGroup(sg);
\r
1829 alignPanel.paintAlignment(true);
\r
1830 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1831 viewport.sendSelection();
\r
1834 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1836 if (viewport.cursorMode)
\r
1838 alignPanel.seqPanel.keyboardNo1 = null;
\r
1839 alignPanel.seqPanel.keyboardNo2 = null;
\r
1841 viewport.setSelectionGroup(null);
\r
1842 viewport.getColumnSelection().clear();
\r
1843 viewport.setSelectionGroup(null);
\r
1844 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1845 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1846 alignPanel.paintAlignment(true);
\r
1847 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1848 viewport.sendSelection();
\r
1851 public void invertSequenceMenuItem_actionPerformed()
\r
1853 SequenceGroup sg = viewport.getSelectionGroup();
\r
1854 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1856 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1859 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1860 viewport.sendSelection();
\r
1863 public void invertColSel_actionPerformed()
\r
1865 viewport.invertColumnSelection();
\r
1866 alignPanel.paintAlignment(true);
\r
1867 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1868 viewport.sendSelection();
\r
1871 void trimAlignment(boolean trimLeft)
\r
1873 ColumnSelection colSel = viewport.getColumnSelection();
\r
1876 if (colSel.size() > 0)
\r
1880 column = colSel.getMin();
\r
1884 column = colSel.getMax();
\r
1888 if (viewport.getSelectionGroup() != null)
\r
1890 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
1891 viewport.hiddenRepSequences);
\r
1895 seqs = viewport.alignment.getSequencesArray();
\r
1898 TrimRegionCommand trimRegion;
\r
1901 trimRegion = new TrimRegionCommand("Remove Left",
\r
1902 TrimRegionCommand.TRIM_LEFT, seqs, column,
\r
1903 viewport.alignment, viewport.colSel,
\r
1904 viewport.selectionGroup);
\r
1905 viewport.setStartRes(0);
\r
1909 trimRegion = new TrimRegionCommand("Remove Right",
\r
1910 TrimRegionCommand.TRIM_RIGHT, seqs, column,
\r
1911 viewport.alignment, viewport.colSel,
\r
1912 viewport.selectionGroup);
\r
1915 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
\r
1917 addHistoryItem(trimRegion);
\r
1919 Vector groups = viewport.alignment.getGroups();
\r
1921 for (int i = 0; i < groups.size(); i++)
\r
1923 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1925 if ((trimLeft && !sg.adjustForRemoveLeft(column))
\r
1926 || (!trimLeft && !sg.adjustForRemoveRight(column)))
\r
1928 viewport.alignment.deleteGroup(sg);
\r
1932 viewport.firePropertyChange("alignment", null, viewport
\r
1933 .getAlignment().getSequences());
\r
1937 public void removeGappedColumnMenuItem_actionPerformed()
\r
1939 int start = 0, end = viewport.alignment.getWidth() - 1;
\r
1942 if (viewport.getSelectionGroup() != null)
\r
1944 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
1945 viewport.hiddenRepSequences);
\r
1946 start = viewport.getSelectionGroup().getStartRes();
\r
1947 end = viewport.getSelectionGroup().getEndRes();
\r
1951 seqs = viewport.alignment.getSequencesArray();
\r
1954 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
\r
1955 "Remove Gapped Columns", seqs, start, end, viewport.alignment);
\r
1957 addHistoryItem(removeGapCols);
\r
1959 statusBar.setText("Removed " + removeGapCols.getSize()
\r
1960 + " empty columns.");
\r
1962 // This is to maintain viewport position on first residue
\r
1963 // of first sequence
\r
1964 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1965 int startRes = seq.findPosition(viewport.startRes);
\r
1966 // ShiftList shifts;
\r
1967 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
\r
1968 // edit.alColumnChanges=shifts.getInverse();
\r
1969 // if (viewport.hasHiddenColumns)
\r
1970 // viewport.getColumnSelection().compensateForEdits(shifts);
\r
1971 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
1972 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1977 public void removeAllGapsMenuItem_actionPerformed()
\r
1979 int start = 0, end = viewport.alignment.getWidth() - 1;
\r
1982 if (viewport.getSelectionGroup() != null)
\r
1984 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
1985 viewport.hiddenRepSequences);
\r
1986 start = viewport.getSelectionGroup().getStartRes();
\r
1987 end = viewport.getSelectionGroup().getEndRes();
\r
1991 seqs = viewport.alignment.getSequencesArray();
\r
1994 // This is to maintain viewport position on first residue
\r
1995 // of first sequence
\r
1996 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1997 int startRes = seq.findPosition(viewport.startRes);
\r
1999 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
\r
2000 viewport.alignment));
\r
2002 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
2004 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
2009 public void findMenuItem_actionPerformed()
\r
2011 new Finder(alignPanel);
\r
2015 * create a new view derived from the current view
\r
2017 * @param viewtitle
\r
2018 * @return frame for the new view
\r
2020 public AlignFrame newView(String viewtitle)
\r
2023 if (viewport.hasHiddenRows)
\r
2025 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
\r
2026 .getFullAlignment().getSequencesArray());
\r
2030 newal = new Alignment(viewport.alignment.getSequencesArray());
\r
2033 if (viewport.alignment.getAlignmentAnnotation() != null)
\r
2035 for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)
\r
2037 if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
\r
2039 newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);
\r
2044 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
\r
2046 newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
\r
2047 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
\r
2048 PaintRefresher.Register(newaf.alignPanel,
\r
2049 newaf.alignPanel.av.getSequenceSetId());
\r
2051 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
\r
2052 newaf.alignPanel.av.getSequenceSetId());
\r
2053 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
\r
2054 newaf.alignPanel.av.getSequenceSetId());
\r
2056 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
2057 .getSequenceSetId());
\r
2058 int viewSize = -1;
\r
2059 for (int i = 0; i < comps.size(); i++)
\r
2061 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
2067 String title = new String(this.getTitle());
\r
2068 if (viewtitle != null)
\r
2070 title = viewtitle + " ( " + title + ")";
\r
2074 if (title.indexOf("(View") > -1)
\r
2076 title = title.substring(0, title.indexOf("(View"));
\r
2078 title += "(View " + viewSize + ")";
\r
2081 newaf.setTitle(title.toString());
\r
2083 newaf.viewport.historyList = viewport.historyList;
\r
2084 newaf.viewport.redoList = viewport.redoList;
\r
2090 * @return list of feature groups on the view
\r
2092 public String[] getFeatureGroups()
\r
2094 FeatureRenderer fr = null;
\r
2095 if (alignPanel != null
\r
2096 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2098 return fr.getGroups();
\r
2104 * get sequence feature groups that are hidden or shown
\r
2110 public String[] getFeatureGroupsOfState(boolean visible)
\r
2112 FeatureRenderer fr = null;
\r
2113 if (alignPanel != null
\r
2114 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2116 return fr.getGroups(visible);
\r
2122 * Change the display state for the given feature groups
\r
2125 * list of group strings
\r
2127 * visible or invisible
\r
2129 public void setFeatureGroupState(String[] groups, boolean state)
\r
2131 FeatureRenderer fr = null;
\r
2132 this.sequenceFeatures.setState(true);
\r
2133 viewport.showSequenceFeatures(true);
\r
2134 if (alignPanel != null
\r
2135 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2137 fr.setGroupState(groups, state);
\r
2138 alignPanel.seqPanel.seqCanvas.repaint();
\r
2139 if (alignPanel.overviewPanel != null)
\r
2141 alignPanel.overviewPanel.updateOverviewImage();
\r
2146 public void seqLimits_itemStateChanged()
\r
2148 viewport.setShowJVSuffix(seqLimits.getState());
\r
2149 alignPanel.fontChanged();
\r
2150 alignPanel.paintAlignment(true);
\r
2153 protected void colourTextMenuItem_actionPerformed()
\r
2155 viewport.setColourText(colourTextMenuItem.getState());
\r
2156 alignPanel.paintAlignment(true);
\r
2159 protected void displayNonconservedMenuItem_actionPerformed()
\r
2161 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
\r
2162 alignPanel.paintAlignment(true);
\r
2165 protected void wrapMenuItem_actionPerformed()
\r
2167 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
2168 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
2169 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
2170 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
2171 scaleRight.setEnabled(wrapMenuItem.getState());
\r
2172 alignPanel.paintAlignment(true);
\r
2175 public void overviewMenuItem_actionPerformed()
\r
2177 if (alignPanel.overviewPanel != null)
\r
2182 Frame frame = new Frame();
\r
2183 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
2184 frame.add(overview);
\r
2185 // +50 must allow for applet frame window
\r
2186 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
2187 overview.getPreferredSize().width,
\r
2188 overview.getPreferredSize().height + 50);
\r
2191 frame.addWindowListener(new WindowAdapter()
\r
2193 public void windowClosing(WindowEvent e)
\r
2195 alignPanel.setOverviewPanel(null);
\r
2199 alignPanel.setOverviewPanel(overview);
\r
2203 void changeColour(ColourSchemeI cs)
\r
2205 int threshold = 0;
\r
2209 if (viewport.getAbovePIDThreshold())
\r
2211 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
2214 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2216 viewport.setGlobalColourScheme(cs);
\r
2220 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2223 if (viewport.getConservationSelected())
\r
2226 Alignment al = (Alignment) viewport.alignment;
\r
2227 Conservation c = new Conservation("All",
\r
2228 ResidueProperties.propHash, 3, al.getSequences(), 0,
\r
2229 al.getWidth() - 1);
\r
2232 c.verdict(false, viewport.ConsPercGaps);
\r
2234 cs.setConservation(c);
\r
2236 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
\r
2237 cs, "Background"));
\r
2242 cs.setConservation(null);
\r
2245 cs.setConsensus(viewport.hconsensus);
\r
2248 viewport.setGlobalColourScheme(cs);
\r
2250 if (viewport.getColourAppliesToAllGroups())
\r
2252 Vector groups = viewport.alignment.getGroups();
\r
2253 for (int i = 0; i < groups.size(); i++)
\r
2255 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
2262 if (cs instanceof ClustalxColourScheme)
\r
2264 sg.cs = new ClustalxColourScheme(
\r
2265 sg.getSequences(viewport.hiddenRepSequences),
\r
2272 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
2273 } catch (Exception ex)
\r
2275 ex.printStackTrace();
\r
2280 if (viewport.getAbovePIDThreshold()
\r
2281 || cs instanceof PIDColourScheme
\r
2282 || cs instanceof Blosum62ColourScheme)
\r
2284 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2285 sg.cs.setConsensus(AAFrequency.calculate(
\r
2286 sg.getSequences(viewport.hiddenRepSequences), 0,
\r
2291 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2294 if (viewport.getConservationSelected())
\r
2296 Conservation c = new Conservation("Group",
\r
2297 ResidueProperties.propHash, 3,
\r
2298 sg.getSequences(viewport.hiddenRepSequences), 0,
\r
2299 viewport.alignment.getWidth() - 1);
\r
2301 c.verdict(false, viewport.ConsPercGaps);
\r
2302 sg.cs.setConservation(c);
\r
2306 sg.cs.setConservation(null);
\r
2307 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2313 if (alignPanel.getOverviewPanel() != null)
\r
2315 alignPanel.getOverviewPanel().updateOverviewImage();
\r
2318 jalview.structure.StructureSelectionManager
\r
2319 .getStructureSelectionManager(viewport.applet).sequenceColoursChanged(
\r
2322 alignPanel.paintAlignment(true);
\r
2325 protected void modifyPID_actionPerformed()
\r
2327 if (viewport.getAbovePIDThreshold()
\r
2328 && viewport.globalColourScheme != null)
\r
2330 SliderPanel.setPIDSliderSource(alignPanel,
\r
2331 viewport.getGlobalColourScheme(), "Background");
\r
2332 SliderPanel.showPIDSlider();
\r
2336 protected void modifyConservation_actionPerformed()
\r
2338 if (viewport.getConservationSelected()
\r
2339 && viewport.globalColourScheme != null)
\r
2341 SliderPanel.setConservationSlider(alignPanel,
\r
2342 viewport.globalColourScheme, "Background");
\r
2343 SliderPanel.showConservationSlider();
\r
2347 protected void conservationMenuItem_actionPerformed()
\r
2349 viewport.setConservationSelected(conservationMenuItem.getState());
\r
2351 viewport.setAbovePIDThreshold(false);
\r
2352 abovePIDThreshold.setState(false);
\r
2354 changeColour(viewport.getGlobalColourScheme());
\r
2356 modifyConservation_actionPerformed();
\r
2359 public void abovePIDThreshold_actionPerformed()
\r
2361 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
2363 conservationMenuItem.setState(false);
\r
2364 viewport.setConservationSelected(false);
\r
2366 changeColour(viewport.getGlobalColourScheme());
\r
2368 modifyPID_actionPerformed();
\r
2371 public void sortPairwiseMenuItem_actionPerformed()
\r
2373 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2374 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
\r
2375 .getAlignment().getSequenceAt(0), null);
\r
2377 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
\r
2378 viewport.alignment));
\r
2379 alignPanel.paintAlignment(true);
\r
2382 public void sortIDMenuItem_actionPerformed()
\r
2384 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2385 AlignmentSorter.sortByID(viewport.getAlignment());
\r
2386 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
\r
2387 alignPanel.paintAlignment(true);
\r
2390 public void sortLengthMenuItem_actionPerformed()
\r
2392 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2393 AlignmentSorter.sortByLength(viewport.getAlignment());
\r
2394 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
\r
2395 viewport.alignment));
\r
2396 alignPanel.paintAlignment(true);
\r
2399 public void sortGroupMenuItem_actionPerformed()
\r
2401 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2402 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
2403 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
\r
2404 viewport.alignment));
\r
2405 alignPanel.paintAlignment(true);
\r
2409 public void removeRedundancyMenuItem_actionPerformed()
\r
2411 new RedundancyPanel(alignPanel);
\r
2414 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
2416 if (viewport.getSelectionGroup() != null
\r
2417 && viewport.getSelectionGroup().getSize() > 1)
\r
2419 Frame frame = new Frame();
\r
2420 frame.add(new PairwiseAlignPanel(alignPanel));
\r
2421 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
\r
2426 public void PCAMenuItem_actionPerformed()
\r
2428 // are the sequences aligned?
\r
2429 if (!viewport.alignment.isAligned(false))
\r
2431 SequenceI current;
\r
2432 int Width = viewport.getAlignment().getWidth();
\r
2434 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2436 current = viewport.getAlignment().getSequenceAt(i);
\r
2438 if (current.getLength() < Width)
\r
2440 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2443 alignPanel.paintAlignment(true);
\r
2446 if ((viewport.getSelectionGroup() != null
\r
2447 && viewport.getSelectionGroup().getSize() < 4 && viewport
\r
2448 .getSelectionGroup().getSize() > 0)
\r
2449 || viewport.getAlignment().getHeight() < 4)
\r
2456 new PCAPanel(viewport);
\r
2457 } catch (java.lang.OutOfMemoryError ex)
\r
2463 public void averageDistanceTreeMenuItem_actionPerformed()
\r
2465 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
2468 public void neighbourTreeMenuItem_actionPerformed()
\r
2470 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
2473 protected void njTreeBlosumMenuItem_actionPerformed()
\r
2475 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2478 protected void avTreeBlosumMenuItem_actionPerformed()
\r
2480 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2483 void NewTreePanel(String type, String pwType, String title)
\r
2485 // are the sequences aligned?
\r
2486 if (!viewport.alignment.isAligned(false))
\r
2488 SequenceI current;
\r
2489 int Width = viewport.getAlignment().getWidth();
\r
2491 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2493 current = viewport.getAlignment().getSequenceAt(i);
\r
2495 if (current.getLength() < Width)
\r
2497 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2500 alignPanel.paintAlignment(true);
\r
2504 if ((viewport.getSelectionGroup() != null && viewport
\r
2505 .getSelectionGroup().getSize() > 1)
\r
2506 || (viewport.getSelectionGroup() == null && viewport.alignment
\r
2507 .getHeight() > 1))
\r
2509 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
\r
2511 addTreeMenuItem(tp, title);
\r
2513 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
2517 void loadTree_actionPerformed()
\r
2519 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
2520 cap.setText("Paste your Newick tree file here.");
\r
2521 cap.setTreeImport();
\r
2522 Frame frame = new Frame();
\r
2524 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
2527 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
2529 TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
\r
2530 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
2531 addTreeMenuItem(tp, treeFile);
\r
2535 * sort the alignment using the given treePanel
\r
2537 * @param treePanel
\r
2538 * tree used to sort view
\r
2540 * string used for undo event name
\r
2542 public void sortByTree(TreePanel treePanel, String title)
\r
2544 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2546 .sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
2547 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2548 // HistoryItem.SORT));
\r
2549 addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
\r
2550 viewport.alignment));
\r
2551 alignPanel.paintAlignment(true);
\r
2555 * Do any automatic reordering of the alignment and add the necessary bits to
\r
2556 * the menu structure for the new tree
\r
2558 * @param treePanel
\r
2561 protected void addTreeMenuItem(final TreePanel treePanel,
\r
2562 final String title)
\r
2564 final MenuItem item = new MenuItem(title);
\r
2565 sortByTreeMenu.add(item);
\r
2566 item.addActionListener(new java.awt.event.ActionListener()
\r
2568 public void actionPerformed(ActionEvent evt)
\r
2570 sortByTree(treePanel, title); // treePanel.getTitle());
\r
2574 treePanel.addWindowListener(new WindowAdapter()
\r
2576 public void windowOpened(WindowEvent e)
\r
2578 if (viewport.sortByTree)
\r
2580 sortByTree(treePanel, title);
\r
2582 super.windowOpened(e);
\r
2585 public void windowClosing(WindowEvent e)
\r
2587 sortByTreeMenu.remove(item);
\r
2591 public boolean sortBy(AlignmentOrder alorder, String undoname)
\r
2593 SequenceI[] oldOrder = viewport.getAlignment()
\r
2594 .getSequencesArray();
\r
2595 if (viewport.applet.debug)
\r
2597 System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");
\r
2599 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
\r
2600 if (undoname!=null)
\r
2602 addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.alignment));
\r
2604 alignPanel.paintAlignment(true);
\r
2608 protected void documentation_actionPerformed()
\r
2610 alignPanel.av.applet.openJalviewHelpUrl();
\r
2613 protected void about_actionPerformed()
\r
2616 class AboutPanel extends Canvas
\r
2622 public AboutPanel(String version, String builddate)
\r
2624 this.version = version;
\r
2625 this.builddate = builddate;
\r
2628 public void paint(Graphics g)
\r
2630 g.setColor(Color.white);
\r
2631 g.fillRect(0, 0, getSize().width, getSize().height);
\r
2632 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2633 FontMetrics fm = g.getFontMetrics();
\r
2634 int fh = fm.getHeight();
\r
2636 g.setColor(Color.black);
\r
2637 // TODO: update this text for each release or centrally store it for
\r
2638 // lite and application
\r
2639 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
2640 g.drawString("JalviewLite - Release " + version, x, y += fh);
\r
2641 g.setFont(new Font("Helvetica", Font.BOLD, 12));
\r
2642 g.drawString("Build date: " + builddate, x, y += fh);
\r
2643 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2645 "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",
\r
2646 x, y += fh * 1.5);
\r
2647 g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
\r
2649 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
\r
2652 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
\r
2654 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
\r
2656 "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
\r
2659 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
\r
2661 g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
\r
2666 Frame frame = new Frame();
\r
2667 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
\r
2668 .getBuildDate()));
\r
2669 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
\r
2673 public void showURL(String url, String target)
\r
2675 if (viewport.applet == null)
\r
2677 System.out.println("Not running as applet - no browser available.");
\r
2681 viewport.applet.showURL(url, target);
\r
2685 // ////////////////////////////////////////////////////////////////////////////////
\r
2686 // JBuilder Graphics here
\r
2688 MenuBar alignFrameMenuBar = new MenuBar();
\r
2690 Menu fileMenu = new Menu("File");
\r
2692 MenuItem loadApplication = new MenuItem("View in Full Application");
\r
2694 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
\r
2696 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
\r
2698 MenuItem outputFeatures = new MenuItem("Export Features ...");
\r
2700 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
\r
2702 MenuItem closeMenuItem = new MenuItem("Close");
\r
2704 Menu editMenu = new Menu("Edit");
\r
2706 Menu viewMenu = new Menu("View");
\r
2708 Menu colourMenu = new Menu("Colour");
\r
2710 Menu calculateMenu = new Menu("Calculate");
\r
2712 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
2714 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
2716 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
2718 MenuItem remove2LeftMenuItem = new MenuItem();
\r
2720 MenuItem remove2RightMenuItem = new MenuItem();
\r
2722 MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
2724 MenuItem removeAllGapsMenuItem = new MenuItem();
\r
2726 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
2728 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
2730 MenuItem sortPairwiseMenuItem = new MenuItem();
\r
2732 MenuItem sortIDMenuItem = new MenuItem();
\r
2734 MenuItem sortLengthMenuItem = new MenuItem();
\r
2736 MenuItem sortGroupMenuItem = new MenuItem();
\r
2738 MenuItem removeRedundancyMenuItem = new MenuItem();
\r
2740 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
2742 MenuItem PCAMenuItem = new MenuItem();
\r
2744 MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
2746 MenuItem neighbourTreeMenuItem = new MenuItem();
\r
2748 BorderLayout borderLayout1 = new BorderLayout();
\r
2750 public Label statusBar = new Label();
\r
2752 Menu outputTextboxMenu = new Menu();
\r
2754 MenuItem clustalColour = new MenuItem();
\r
2756 MenuItem zappoColour = new MenuItem();
\r
2758 MenuItem taylorColour = new MenuItem();
\r
2760 MenuItem hydrophobicityColour = new MenuItem();
\r
2762 MenuItem helixColour = new MenuItem();
\r
2764 MenuItem strandColour = new MenuItem();
\r
2766 MenuItem turnColour = new MenuItem();
\r
2768 MenuItem buriedColour = new MenuItem();
\r
2770 MenuItem userDefinedColour = new MenuItem();
\r
2772 MenuItem PIDColour = new MenuItem();
\r
2774 MenuItem BLOSUM62Colour = new MenuItem();
\r
2776 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
2778 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
2780 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
2782 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
2784 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
\r
2786 MenuItem alProperties = new MenuItem("Alignment Properties...");
\r
2788 MenuItem overviewMenuItem = new MenuItem();
\r
2790 MenuItem undoMenuItem = new MenuItem();
\r
2792 MenuItem redoMenuItem = new MenuItem();
\r
2794 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
2796 MenuItem noColourmenuItem = new MenuItem();
\r
2798 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
2800 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
2802 MenuItem findMenuItem = new MenuItem();
\r
2804 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
2806 MenuItem nucleotideColour = new MenuItem();
\r
2808 MenuItem deleteGroups = new MenuItem();
\r
2810 MenuItem grpsFromSelection = new MenuItem();
\r
2812 MenuItem delete = new MenuItem();
\r
2814 MenuItem copy = new MenuItem();
\r
2816 MenuItem cut = new MenuItem();
\r
2818 Menu pasteMenu = new Menu();
\r
2820 MenuItem pasteNew = new MenuItem();
\r
2822 MenuItem pasteThis = new MenuItem();
\r
2824 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
2826 MenuItem font = new MenuItem();
\r
2828 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
2830 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
2832 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
2834 MenuItem modifyPID = new MenuItem();
\r
2836 MenuItem modifyConservation = new MenuItem();
\r
2838 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
\r
2839 "Autocalculate Consensus", true);
\r
2841 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
\r
2842 "Sort Alignment With New Tree", true);
\r
2844 Menu sortByTreeMenu = new Menu();
\r
2846 Menu sort = new Menu();
\r
2848 Menu calculate = new Menu();
\r
2850 MenuItem inputText = new MenuItem();
\r
2852 Menu helpMenu = new Menu();
\r
2854 MenuItem documentation = new MenuItem();
\r
2856 MenuItem about = new MenuItem();
\r
2858 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
2860 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
\r
2862 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
\r
2863 Menu autoAnnMenu=new Menu();
\r
2864 CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();
\r
2865 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
\r
2866 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
\r
2867 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
\r
2868 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
\r
2870 private void jbInit() throws Exception
\r
2873 setMenuBar(alignFrameMenuBar);
\r
2877 // dynamically fill save as menu with available formats
\r
2878 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
2881 item = new MenuItem(
\r
2882 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
2884 item.addActionListener(new java.awt.event.ActionListener()
\r
2886 public void actionPerformed(ActionEvent e)
\r
2888 outputText_actionPerformed(e);
\r
2892 outputTextboxMenu.add(item);
\r
2894 closeMenuItem.addActionListener(this);
\r
2895 loadApplication.addActionListener(this);
\r
2897 loadTree.addActionListener(this);
\r
2898 loadAnnotations.addActionListener(this);
\r
2899 outputFeatures.addActionListener(this);
\r
2900 outputAnnotations.addActionListener(this);
\r
2901 selectAllSequenceMenuItem.addActionListener(this);
\r
2902 deselectAllSequenceMenuItem.addActionListener(this);
\r
2903 invertSequenceMenuItem.addActionListener(this);
\r
2904 remove2LeftMenuItem.setLabel("Remove Left");
\r
2905 remove2LeftMenuItem.addActionListener(this);
\r
2906 remove2RightMenuItem.setLabel("Remove Right");
\r
2907 remove2RightMenuItem.addActionListener(this);
\r
2908 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
2909 removeGappedColumnMenuItem.addActionListener(this);
\r
2910 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
2911 removeAllGapsMenuItem.addActionListener(this);
\r
2912 viewBoxesMenuItem.setLabel("Boxes");
\r
2913 viewBoxesMenuItem.setState(true);
\r
2914 viewBoxesMenuItem.addItemListener(this);
\r
2915 viewTextMenuItem.setLabel("Text");
\r
2916 viewTextMenuItem.setState(true);
\r
2917 viewTextMenuItem.addItemListener(this);
\r
2918 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
2919 sortPairwiseMenuItem.addActionListener(this);
\r
2920 sortIDMenuItem.setLabel("by ID");
\r
2921 sortIDMenuItem.addActionListener(this);
\r
2922 sortLengthMenuItem.setLabel("by Length");
\r
2923 sortLengthMenuItem.addActionListener(this);
\r
2924 sortGroupMenuItem.setLabel("by Group");
\r
2925 sortGroupMenuItem.addActionListener(this);
\r
2926 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
2927 removeRedundancyMenuItem.addActionListener(this);
\r
2928 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
2929 pairwiseAlignmentMenuItem.addActionListener(this);
\r
2930 PCAMenuItem.setLabel("Principal Component Analysis");
\r
2931 PCAMenuItem.addActionListener(this);
\r
2932 averageDistanceTreeMenuItem
\r
2933 .setLabel("Average Distance Using % Identity");
\r
2934 averageDistanceTreeMenuItem.addActionListener(this);
\r
2935 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
2936 neighbourTreeMenuItem.addActionListener(this);
\r
2937 statusBar.setBackground(Color.white);
\r
2938 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
2939 statusBar.setText("Status bar");
\r
2940 outputTextboxMenu.setLabel("Output to Textbox");
\r
2941 clustalColour.setLabel("Clustalx");
\r
2943 clustalColour.addActionListener(this);
\r
2944 zappoColour.setLabel("Zappo");
\r
2945 zappoColour.addActionListener(this);
\r
2946 taylorColour.setLabel("Taylor");
\r
2947 taylorColour.addActionListener(this);
\r
2948 hydrophobicityColour.setLabel("Hydrophobicity");
\r
2949 hydrophobicityColour.addActionListener(this);
\r
2950 helixColour.setLabel("Helix Propensity");
\r
2951 helixColour.addActionListener(this);
\r
2952 strandColour.setLabel("Strand Propensity");
\r
2953 strandColour.addActionListener(this);
\r
2954 turnColour.setLabel("Turn Propensity");
\r
2955 turnColour.addActionListener(this);
\r
2956 buriedColour.setLabel("Buried Index");
\r
2957 buriedColour.addActionListener(this);
\r
2958 userDefinedColour.setLabel("User Defined...");
\r
2959 userDefinedColour.addActionListener(this);
\r
2960 PIDColour.setLabel("Percentage Identity");
\r
2961 PIDColour.addActionListener(this);
\r
2962 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
2963 BLOSUM62Colour.addActionListener(this);
\r
2964 avDistanceTreeBlosumMenuItem
\r
2965 .setLabel("Average Distance Using BLOSUM62");
\r
2966 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
2967 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
2968 njTreeBlosumMenuItem.addActionListener(this);
\r
2969 annotationPanelMenuItem.setLabel("Show Annotations");
\r
2970 annotationPanelMenuItem.addItemListener(this);
\r
2971 colourTextMenuItem.setLabel("Colour Text");
\r
2972 colourTextMenuItem.addItemListener(this);
\r
2973 displayNonconservedMenuItem.setLabel("Show nonconserved");
\r
2974 displayNonconservedMenuItem.addItemListener(this);
\r
2975 alProperties.addActionListener(this);
\r
2976 overviewMenuItem.setLabel("Overview Window");
\r
2977 overviewMenuItem.addActionListener(this);
\r
2978 undoMenuItem.setEnabled(false);
\r
2979 undoMenuItem.setLabel("Undo");
\r
2980 undoMenuItem.addActionListener(this);
\r
2981 redoMenuItem.setEnabled(false);
\r
2982 redoMenuItem.setLabel("Redo");
\r
2983 redoMenuItem.addActionListener(this);
\r
2984 conservationMenuItem.setLabel("by Conservation");
\r
2985 conservationMenuItem.addItemListener(this);
\r
2986 noColourmenuItem.setLabel("None");
\r
2987 noColourmenuItem.addActionListener(this);
\r
2988 wrapMenuItem.setLabel("Wrap");
\r
2989 wrapMenuItem.addItemListener(this);
\r
2990 renderGapsMenuItem.setLabel("Show Gaps");
\r
2991 renderGapsMenuItem.setState(true);
\r
2992 renderGapsMenuItem.addItemListener(this);
\r
2993 findMenuItem.setLabel("Find...");
\r
2994 findMenuItem.addActionListener(this);
\r
2995 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
2996 abovePIDThreshold.addItemListener(this);
\r
2997 nucleotideColour.setLabel("Nucleotide");
\r
2998 nucleotideColour.addActionListener(this);
\r
2999 deleteGroups.setLabel("Undefine Groups");
\r
3000 deleteGroups.addActionListener(this);
\r
3001 grpsFromSelection.setLabel("Make Groups for selection");
\r
3002 grpsFromSelection.addActionListener(this);
\r
3003 copy.setLabel("Copy");
\r
3004 copy.addActionListener(this);
\r
3005 cut.setLabel("Cut");
\r
3006 cut.addActionListener(this);
\r
3007 delete.setLabel("Delete");
\r
3008 delete.addActionListener(this);
\r
3009 pasteMenu.setLabel("Paste");
\r
3010 pasteNew.setLabel("To New Alignment");
\r
3011 pasteNew.addActionListener(this);
\r
3012 pasteThis.setLabel("Add To This Alignment");
\r
3013 pasteThis.addActionListener(this);
\r
3014 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
3015 applyToAllGroups.setState(true);
\r
3016 applyToAllGroups.addItemListener(this);
\r
3017 font.setLabel("Font...");
\r
3018 font.addActionListener(this);
\r
3019 scaleAbove.setLabel("Scale Above");
\r
3020 scaleAbove.setState(true);
\r
3021 scaleAbove.setEnabled(false);
\r
3022 scaleAbove.addItemListener(this);
\r
3023 scaleLeft.setEnabled(false);
\r
3024 scaleLeft.setState(true);
\r
3025 scaleLeft.setLabel("Scale Left");
\r
3026 scaleLeft.addItemListener(this);
\r
3027 scaleRight.setEnabled(false);
\r
3028 scaleRight.setState(true);
\r
3029 scaleRight.setLabel("Scale Right");
\r
3030 scaleRight.addItemListener(this);
\r
3031 modifyPID.setLabel("Modify Identity Threshold...");
\r
3032 modifyPID.addActionListener(this);
\r
3033 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
3034 modifyConservation.addActionListener(this);
\r
3035 sortByTreeMenu.setLabel("By Tree Order");
\r
3036 sort.setLabel("Sort");
\r
3037 calculate.setLabel("Calculate Tree");
\r
3038 autoCalculate.addItemListener(this);
\r
3039 sortByTree.addItemListener(this);
\r
3040 inputText.setLabel("Input from textbox");
\r
3041 inputText.addActionListener(this);
\r
3042 centreColumnLabelFlag.setLabel("Centre column labels");
\r
3043 centreColumnLabelFlag.addItemListener(this);
\r
3044 followMouseOverFlag.setLabel("Automatic Scrolling");
\r
3045 followMouseOverFlag.addItemListener(this);
\r
3046 helpMenu.setLabel("Help");
\r
3047 documentation.setLabel("Documentation");
\r
3048 documentation.addActionListener(this);
\r
3050 about.setLabel("About...");
\r
3051 about.addActionListener(this);
\r
3052 seqLimits.setState(true);
\r
3053 seqLimits.setLabel("Show Sequence Limits");
\r
3054 seqLimits.addItemListener(this);
\r
3055 featureSettings.setLabel("Feature Settings...");
\r
3056 featureSettings.addActionListener(this);
\r
3057 sequenceFeatures.setLabel("Sequence Features");
\r
3058 sequenceFeatures.addItemListener(this);
\r
3059 sequenceFeatures.setState(false);
\r
3060 annotationColour.setLabel("by Annotation...");
\r
3061 annotationColour.addActionListener(this);
\r
3062 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
3063 invertColSel.setLabel("Invert Column Selection");
\r
3064 menu1.setLabel("Show");
\r
3065 showColumns.setLabel("All Columns ");
\r
3066 showSeqs.setLabel("All Sequences");
\r
3067 menu2.setLabel("Hide");
\r
3068 hideColumns.setLabel("Selected Columns");
\r
3069 hideSequences.setLabel("Selected Sequences");
\r
3070 hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
\r
3071 hideAllSelection.setLabel("Selected Region");
\r
3072 showAllHidden.setLabel("All Sequences and Columns");
\r
3073 showGroupConsensus.setLabel("Group Consensus");
\r
3074 showGroupConservation.setLabel("Group Conservation");
\r
3075 showConsensusHistogram.setLabel("Show Consensus Histogram");
\r
3076 showSequenceLogo.setLabel("Show Consensus Logo");
\r
3077 applyAutoAnnotationSettings.setLabel("Apply to all groups");
\r
3078 applyAutoAnnotationSettings.setState(true);
\r
3079 autoAnnMenu.setLabel("Autocalculated Annotation");
\r
3081 invertColSel.addActionListener(this);
\r
3082 showColumns.addActionListener(this);
\r
3083 showSeqs.addActionListener(this);
\r
3084 hideColumns.addActionListener(this);
\r
3085 hideSequences.addActionListener(this);
\r
3086 hideAllButSelection.addActionListener(this);
\r
3087 hideAllSelection.addActionListener(this);
\r
3088 showAllHidden.addActionListener(this);
\r
3089 showGroupConsensus.addItemListener(this);
\r
3090 showGroupConservation.addItemListener(this);
\r
3091 showConsensusHistogram.addItemListener(this);
\r
3092 showSequenceLogo.addItemListener(this);
\r
3093 applyAutoAnnotationSettings.addItemListener(this);
\r
3094 formatMenu.setLabel("Format");
\r
3095 selectMenu.setLabel("Select");
\r
3096 newView.setLabel("New View");
\r
3097 newView.addActionListener(this);
\r
3098 alignFrameMenuBar.add(fileMenu);
\r
3099 alignFrameMenuBar.add(editMenu);
\r
3100 alignFrameMenuBar.add(selectMenu);
\r
3101 alignFrameMenuBar.add(viewMenu);
\r
3102 alignFrameMenuBar.add(formatMenu);
\r
3103 alignFrameMenuBar.add(colourMenu);
\r
3104 alignFrameMenuBar.add(calculateMenu);
\r
3105 alignFrameMenuBar.add(helpMenu);
\r
3107 fileMenu.add(inputText);
\r
3108 fileMenu.add(loadTree);
\r
3109 fileMenu.add(loadAnnotations);
\r
3111 fileMenu.addSeparator();
\r
3112 fileMenu.add(outputTextboxMenu);
\r
3113 fileMenu.add(outputFeatures);
\r
3114 fileMenu.add(outputAnnotations);
\r
3116 if (jalviewServletURL != null)
\r
3118 fileMenu.add(loadApplication);
\r
3121 fileMenu.addSeparator();
\r
3122 fileMenu.add(closeMenuItem);
\r
3124 editMenu.add(undoMenuItem);
\r
3125 editMenu.add(redoMenuItem);
\r
3126 editMenu.add(cut);
\r
3127 editMenu.add(copy);
\r
3128 editMenu.add(pasteMenu);
\r
3129 editMenu.add(delete);
\r
3130 editMenu.addSeparator();
\r
3131 editMenu.add(remove2LeftMenuItem);
\r
3132 editMenu.add(remove2RightMenuItem);
\r
3133 editMenu.add(removeGappedColumnMenuItem);
\r
3134 editMenu.add(removeAllGapsMenuItem);
\r
3135 editMenu.add(removeRedundancyMenuItem);
\r
3136 viewMenu.add(newView);
\r
3137 viewMenu.addSeparator();
\r
3138 viewMenu.add(menu1);
\r
3139 viewMenu.add(menu2);
\r
3140 viewMenu.addSeparator();
\r
3141 viewMenu.add(followMouseOverFlag);
\r
3142 viewMenu.add(annotationPanelMenuItem);
\r
3143 autoAnnMenu.add(applyAutoAnnotationSettings);
\r
3144 autoAnnMenu.add(showConsensusHistogram);
\r
3145 autoAnnMenu.add(showSequenceLogo);
\r
3146 autoAnnMenu.addSeparator();
\r
3147 autoAnnMenu.add(showGroupConservation);
\r
3148 autoAnnMenu.add(showGroupConsensus);
\r
3149 viewMenu.add(autoAnnMenu);
\r
3150 viewMenu.addSeparator();
\r
3151 viewMenu.add(sequenceFeatures);
\r
3152 viewMenu.add(featureSettings);
\r
3153 viewMenu.addSeparator();
\r
3154 viewMenu.add(alProperties);
\r
3155 viewMenu.addSeparator();
\r
3156 viewMenu.add(overviewMenuItem);
\r
3157 colourMenu.add(applyToAllGroups);
\r
3158 colourMenu.addSeparator();
\r
3159 colourMenu.add(noColourmenuItem);
\r
3160 colourMenu.add(clustalColour);
\r
3161 colourMenu.add(BLOSUM62Colour);
\r
3162 colourMenu.add(PIDColour);
\r
3163 colourMenu.add(zappoColour);
\r
3164 colourMenu.add(taylorColour);
\r
3165 colourMenu.add(hydrophobicityColour);
\r
3166 colourMenu.add(helixColour);
\r
3167 colourMenu.add(strandColour);
\r
3168 colourMenu.add(turnColour);
\r
3169 colourMenu.add(buriedColour);
\r
3170 colourMenu.add(nucleotideColour);
\r
3171 colourMenu.add(userDefinedColour);
\r
3172 colourMenu.addSeparator();
\r
3173 colourMenu.add(conservationMenuItem);
\r
3174 colourMenu.add(modifyConservation);
\r
3175 colourMenu.add(abovePIDThreshold);
\r
3176 colourMenu.add(modifyPID);
\r
3177 colourMenu.add(annotationColour);
\r
3178 calculateMenu.add(sort);
\r
3179 calculateMenu.add(calculate);
\r
3180 calculateMenu.addSeparator();
\r
3181 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
3182 calculateMenu.add(PCAMenuItem);
\r
3183 calculateMenu.add(autoCalculate);
\r
3184 calculateMenu.add(sortByTree);
\r
3185 this.add(statusBar, BorderLayout.SOUTH);
\r
3186 pasteMenu.add(pasteNew);
\r
3187 pasteMenu.add(pasteThis);
\r
3188 sort.add(sortIDMenuItem);
\r
3189 sort.add(sortLengthMenuItem);
\r
3190 sort.add(sortByTreeMenu);
\r
3191 sort.add(sortGroupMenuItem);
\r
3192 sort.add(sortPairwiseMenuItem);
\r
3193 calculate.add(averageDistanceTreeMenuItem);
\r
3194 calculate.add(neighbourTreeMenuItem);
\r
3195 calculate.add(avDistanceTreeBlosumMenuItem);
\r
3196 calculate.add(njTreeBlosumMenuItem);
\r
3197 helpMenu.add(documentation);
\r
3198 helpMenu.add(about);
\r
3199 menu1.add(showColumns);
\r
3200 menu1.add(showSeqs);
\r
3201 menu1.add(showAllHidden);
\r
3202 menu2.add(hideColumns);
\r
3203 menu2.add(hideSequences);
\r
3204 menu2.add(hideAllSelection);
\r
3205 menu2.add(hideAllButSelection);
\r
3206 formatMenu.add(font);
\r
3207 formatMenu.add(seqLimits);
\r
3208 formatMenu.add(wrapMenuItem);
\r
3209 formatMenu.add(scaleAbove);
\r
3210 formatMenu.add(scaleLeft);
\r
3211 formatMenu.add(scaleRight);
\r
3212 formatMenu.add(viewBoxesMenuItem);
\r
3213 formatMenu.add(viewTextMenuItem);
\r
3214 formatMenu.add(colourTextMenuItem);
\r
3215 formatMenu.add(displayNonconservedMenuItem);
\r
3216 formatMenu.add(renderGapsMenuItem);
\r
3217 formatMenu.add(centreColumnLabelFlag);
\r
3218 selectMenu.add(findMenuItem);
\r
3219 selectMenu.addSeparator();
\r
3220 selectMenu.add(selectAllSequenceMenuItem);
\r
3221 selectMenu.add(deselectAllSequenceMenuItem);
\r
3222 selectMenu.add(invertSequenceMenuItem);
\r
3223 selectMenu.add(invertColSel);
\r
3224 selectMenu.add(grpsFromSelection);
\r
3225 selectMenu.add(deleteGroups);
\r
3229 MenuItem featureSettings = new MenuItem();
\r
3231 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
3233 MenuItem annotationColour = new MenuItem();
\r
3235 MenuItem invertColSel = new MenuItem();
\r
3237 Menu menu1 = new Menu();
\r
3239 MenuItem showColumns = new MenuItem();
\r
3241 MenuItem showSeqs = new MenuItem();
\r
3243 Menu menu2 = new Menu();
\r
3245 MenuItem hideColumns = new MenuItem();
\r
3247 MenuItem hideSequences = new MenuItem();
\r
3249 MenuItem hideAllButSelection = new MenuItem();
\r
3251 MenuItem hideAllSelection = new MenuItem();
\r
3253 MenuItem showAllHidden = new MenuItem();
\r
3255 Menu formatMenu = new Menu();
\r
3257 Menu selectMenu = new Menu();
\r
3259 MenuItem newView = new MenuItem();
\r
3262 * Attach the alignFrame panels after embedding menus, if necessary. This used
\r
3263 * to be called setEmbedded, but is now creates the dropdown menus in a
\r
3264 * platform independent manner to avoid OSX/Mac menu appendage daftness.
\r
3266 * @param reallyEmbedded
\r
3267 * true to attach the view to the applet area on the page rather than
\r
3270 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
\r
3272 if (reallyEmbedded)
\r
3275 // Explicly build the embedded menu panel for the on-page applet
\r
3277 // view cannot be closed if its actually on the page
\r
3278 fileMenu.remove(closeMenuItem);
\r
3279 fileMenu.remove(3); // Remove Seperator
\r
3280 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
\r
3281 Font.PLAIN, 10, false); // use our own fonts.
\r
3282 // and actually add the components to the applet area
\r
3283 viewport.applet.setLayout(new BorderLayout());
\r
3284 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
\r
3285 viewport.applet.add(statusBar, BorderLayout.SOUTH);
\r
3286 alignPanel.setSize(viewport.applet.getSize().width,
\r
3287 viewport.applet.getSize().height - embeddedMenu.HEIGHT
\r
3288 - statusBar.HEIGHT);
\r
3289 viewport.applet.add(alignPanel, BorderLayout.CENTER);
\r
3290 final AlignFrame me = this;
\r
3291 viewport.applet.addFocusListener(new FocusListener()
\r
3295 public void focusLost(FocusEvent e)
\r
3297 if (me.viewport.applet.currentAlignFrame==me) {
\r
3298 me.viewport.applet.currentAlignFrame = null;
\r
3302 public void focusGained(FocusEvent e)
\r
3304 me.viewport.applet.currentAlignFrame = me;
\r
3307 viewport.applet.validate();
\r
3312 // test and embed menu bar if necessary.
\r
3314 if (embedMenuIfNeeded(alignPanel))
\r
3316 // adjust for status bar height too
\r
3317 alignPanel.setSize(getSize().width, getSize().height
\r
3318 - statusBar.HEIGHT);
\r
3320 add(statusBar, BorderLayout.SOUTH);
\r
3321 add(alignPanel, BorderLayout.CENTER);
\r
3322 // and register with the applet so it can pass external API calls to us
\r
3323 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
\r
3329 * create a new binding between structures in an existing jmol viewer instance
\r
3330 * and an alignpanel with sequences that have existing PDBFile entries. Note,
\r
3331 * this does not open a new Jmol window, or modify the display of the
\r
3332 * structures in the original jmol window. Note This method doesn't work
\r
3333 * without an additional javascript library to exchange messages between the
\r
3334 * distinct applets. See http://issues.jalview.org/browse/JAL-621
\r
3337 * JmolViewer instance
\r
3338 * @param sequenceIds
\r
3339 * - sequence Ids to search for associations
\r
3341 public SequenceStructureBinding addStructureViewInstance(
\r
3342 Object jmolviewer, String[] sequenceIds)
\r
3344 org.jmol.api.JmolViewer viewer = null;
\r
3347 viewer = (org.jmol.api.JmolViewer) jmolviewer;
\r
3348 } catch (ClassCastException ex)
\r
3350 System.err.println("Unsupported viewer object :"
\r
3351 + jmolviewer.getClass());
\r
3353 if (viewer == null)
\r
3355 System.err.println("Can't use this object as a structure viewer:"
\r
3356 + jmolviewer.getClass());
\r
3359 SequenceI[] seqs = null;
\r
3360 if (sequenceIds == null || sequenceIds.length == 0)
\r
3362 seqs = viewport.getAlignment().getSequencesArray();
\r
3366 Vector sqi = new Vector();
\r
3367 AlignmentI al = viewport.getAlignment();
\r
3368 for (int sid = 0; sid < sequenceIds.length; sid++)
\r
3370 SequenceI sq = al.findName(sequenceIds[sid]);
\r
3373 sqi.addElement(sq);
\r
3376 if (sqi.size() > 0)
\r
3378 seqs = new SequenceI[sqi.size()];
\r
3379 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
\r
3381 seqs[sid] = (SequenceI) sqi.elementAt(sid);
\r
3389 ExtJmol jmv = null;
\r
3390 // TODO: search for a jmv that involves viewer
\r
3392 { // create a new viewer/jalview binding.
\r
3393 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs});
\r
3399 * bind a pdb file to a sequence in the current view
\r
3401 * @param sequenceId
\r
3402 * - sequenceId within the dataset.
\r
3403 * @param pdbEntryString
\r
3404 * - the short name for the PDB file
\r
3406 * - pdb file - either a URL or a valid PDB file.
\r
3407 * @return true if binding was as success TODO: consider making an exception
\r
3408 * structure for indicating when PDB parsing or sequenceId location
\r
3411 public boolean addPdbFile(String sequenceId, String pdbEntryString,
\r
3414 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
\r
3415 boolean needtoadd = false;
\r
3416 if (toaddpdb != null)
\r
3418 Vector pdbe = toaddpdb.getPDBId();
\r
3419 PDBEntry pdbentry = null;
\r
3420 if (pdbe != null && pdbe.size() > 0)
\r
3422 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
\r
3424 pdbentry = (PDBEntry) pdbe.elementAt(pe);
\r
3425 if (!pdbentry.getId().equals(pdbEntryString)
\r
3426 && !pdbentry.getFile().equals(pdbFile))
\r
3436 if (pdbentry == null)
\r
3438 pdbentry = new PDBEntry();
\r
3439 pdbentry.setId(pdbEntryString);
\r
3440 pdbentry.setFile(pdbFile);
\r
3441 needtoadd = true; // add this new entry to sequence.
\r
3443 // resolve data source
\r
3444 // TODO: this code should be a refactored to an io package
\r
3445 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
\r
3446 if (protocol == null)
\r
3452 // make a note of the access mode and add
\r
3453 if (pdbentry.getProperty() == null)
\r
3455 pdbentry.setProperty(new Hashtable());
\r
3457 pdbentry.getProperty().put("protocol", protocol);
\r
3458 toaddpdb.addPDBId(pdbentry);
\r
3464 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
\r
3468 Vector sequences = new Vector();
\r
3469 for (int i = 0; i < seqs.length; i++)
\r
3471 if (seqs[i] != null)
\r
3473 sequences.addElement(new Object[]
\r
3474 { seqs[i], (chains != null) ? chains[i] : null });
\r
3477 seqs = new SequenceI[sequences.size()];
\r
3478 chains = new String[sequences.size()];
\r
3479 for (int i = 0, isize = sequences.size(); i < isize; i++)
\r
3481 Object[] oj = (Object[]) sequences.elementAt(i);
\r
3483 seqs[i] = (SequenceI) oj[0];
\r
3484 chains[i] = (String) oj[1];
\r
3487 return new Object[]
\r
3492 public void newStructureView(JalviewLite applet, PDBEntry pdb,
\r
3493 SequenceI[] seqs, String[] chains, String protocol)
\r
3495 // Scrub any null sequences from the array
\r
3496 Object[] sqch = cleanSeqChainArrays(seqs, chains);
\r
3497 seqs = (SequenceI[]) sqch[0];
\r
3498 chains = (String[]) sqch[1];
\r
3499 if (seqs == null || seqs.length == 0)
\r
3502 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
\r
3504 if (protocol == null || protocol.trim().length() == 0
\r
3505 || protocol.equals("null"))
\r
3507 protocol = (String) pdb.getProperty().get("protocol");
\r
3508 if (protocol == null)
\r
3510 System.err.println("Couldn't work out protocol to open structure: "
\r
3515 if (applet.useXtrnalSviewer)
\r
3517 // register the association(s) and quit, don't create any windows.
\r
3518 if (StructureSelectionManager.getStructureSelectionManager(applet).setMapping(seqs, chains, pdb.getFile(), protocol)==null) {
\r
3519 System.err.println("Failed to map "+pdb.getFile()+" ("+protocol+") to any sequences");
\r
3523 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
\r
3525 // can only do alignments with Jmol
\r
3526 // find the last jmol window assigned to this alignment
\r
3527 jalview.appletgui.AppletJmol ajm = null, tajm;
\r
3528 Vector jmols = applet
\r
3529 .getAppletWindow(jalview.appletgui.AppletJmol.class);
\r
3530 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
\r
3532 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
\r
3533 if (tajm.ap.alignFrame == this)
\r
3542 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
\r
3543 // try and add the pdb structure
\r
3548 // otherwise, create a new window
\r
3549 if (applet.jmolAvailable)
\r
3551 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
\r
3553 applet.lastFrameX += 40;
\r
3554 applet.lastFrameY += 40;
\r
3558 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
\r
3563 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
\r
3564 SequenceI[][] seqs, String[][] chains, String[] protocols)
\r
3566 // TODO Auto-generated method stub
\r
3567 System.err.println("Aligned Structure View: Not yet implemented.");
\r
3571 * modify the current selection, providing the user has not made a selection already.
\r
3572 * @param sel - sequences from this alignment
\r
3573 * @param csel - columns to be selected on the alignment
\r
3575 public void select(SequenceGroup sel, ColumnSelection csel)
\r
3577 alignPanel.seqPanel.selection(sel, csel, null);
\r
3580 public void scrollTo(int row, int column)
\r
3582 alignPanel.seqPanel.scrollTo(row, column);
\r
3584 public void scrollToRow(int row)
\r
3586 alignPanel.seqPanel.scrollToRow(row);
\r
3588 public void scrollToColumn(int column)
\r
3590 alignPanel.seqPanel.scrollToColumn(column);
\r
3593 * @return the alignments unique ID.
\r
3595 public String getSequenceSetId() {
\r
3596 return viewport.getSequenceSetId();
\r