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.isShowGroupConsensus());
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75 showGroupConservation.setState(viewport.isShowGroupConservation());
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76 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
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77 showSequenceLogo.setState(viewport.isShowSequenceLogo());
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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.getAlignment(),
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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.getColumnSelection() != null && viewport.getColumnSelection().getSelected() != null && viewport.getColumnSelection()
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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.getAlignment().getHeight())
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518 viewport.hideAllSelectedSeqs();
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520 else if (!(toggleCols && viewport.getColumnSelection().getSelected().size() > 0))
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522 viewport.showAllHiddenSeqs();
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528 if (viewport.getColumnSelection().getSelected().size() > 0)
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530 viewport.hideSelectedColumns();
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533 viewport.setSelectionGroup(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.getAlignment()).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.getAlignment().getSequences(),
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888 viewport.getAlignment().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();
\r
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.getAlignment()
\r
1036 .getAlignmentAnnotation() : null, viewport.getAlignment()
\r
1038 ((Alignment) viewport.getAlignment()).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.getAlignment().getSequencesArray(),
\r
1076 getDisplayedFeatureCols());
\r
1080 features = new FeaturesFile().printGFFFormat(
\r
1081 viewport.getAlignment().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.updateHiddenColumns();
\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 if (originalSource!=viewport) {
\r
1281 System.err.println("Warning: Viewport object mismatch whilst undoing");
\r
1283 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns = viewport.getColumnSelection().getHiddenColumns() != null;
\r
1284 updateEditMenuBar();
\r
1285 originalSource.firePropertyChange("alignment", null,
\r
1286 originalSource.getAlignment().getSequences());
\r
1295 protected void redoMenuItem_actionPerformed()
\r
1297 if (viewport.redoList.size() < 1)
\r
1302 CommandI command = (CommandI) viewport.redoList.pop();
\r
1303 viewport.historyList.push(command);
\r
1304 command.doCommand(null);
\r
1306 AlignViewport originalSource = getOriginatingSource(command);
\r
1308 if (originalSource!=viewport) {
\r
1309 System.err.println("Warning: Viewport object mismatch whilst re-doing");
\r
1311 originalSource.updateHiddenColumns(); //sethasHiddenColumns(); = viewport.getColumnSelection().getHiddenColumns() != null;
\r
1313 updateEditMenuBar();
\r
1314 originalSource.firePropertyChange("alignment", null,
\r
1315 originalSource.getAlignment().getSequences());
\r
1318 AlignViewport getOriginatingSource(CommandI command)
\r
1320 AlignViewport originalSource = null;
\r
1321 // For sequence removal and addition, we need to fire
\r
1322 // the property change event FROM the viewport where the
\r
1323 // original alignment was altered
\r
1324 AlignmentI al = null;
\r
1325 if (command instanceof EditCommand)
\r
1327 EditCommand editCommand = (EditCommand) command;
\r
1328 al = editCommand.getAlignment();
\r
1329 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
1330 .getSequenceSetId());
\r
1331 for (int i = 0; i < comps.size(); i++)
\r
1333 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
1335 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
\r
1337 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
\r
1344 if (originalSource == null)
\r
1346 // The original view is closed, we must validate
\r
1347 // the current view against the closed view first
\r
1350 PaintRefresher.validateSequences(al, viewport.getAlignment());
\r
1353 originalSource = viewport;
\r
1356 return originalSource;
\r
1359 public void moveSelectedSequences(boolean up)
\r
1361 SequenceGroup sg = viewport.getSelectionGroup();
\r
1369 for (int i = 1; i < viewport.getAlignment().getHeight(); i++)
\r
1371 SequenceI seq = viewport.getAlignment().getSequenceAt(i);
\r
1372 if (!sg.getSequences(null).contains(seq))
\r
1377 SequenceI temp = viewport.getAlignment().getSequenceAt(i - 1);
\r
1378 if (sg.getSequences(null).contains(temp))
\r
1383 viewport.getAlignment().getSequences().setElementAt(temp, i);
\r
1384 viewport.getAlignment().getSequences().setElementAt(seq, i - 1);
\r
1389 for (int i = viewport.getAlignment().getHeight() - 2; i > -1; i--)
\r
1391 SequenceI seq = viewport.getAlignment().getSequenceAt(i);
\r
1392 if (!sg.getSequences(viewport.getHiddenRepSequences()).contains(seq))
\r
1397 SequenceI temp = viewport.getAlignment().getSequenceAt(i + 1);
\r
1398 if (sg.getSequences(viewport.getHiddenRepSequences()).contains(temp))
\r
1403 viewport.getAlignment().getSequences().setElementAt(temp, i);
\r
1404 viewport.getAlignment().getSequences().setElementAt(seq, i + 1);
\r
1408 alignPanel.paintAlignment(true);
\r
1411 synchronized void slideSequences(boolean right, int size)
\r
1413 Vector sg = new Vector();
\r
1414 if (viewport.cursorMode)
\r
1416 sg.addElement(viewport.getAlignment()
\r
1417 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
\r
1419 else if (viewport.getSelectionGroup() != null
\r
1420 && viewport.getSelectionGroup().getSize() != viewport.getAlignment()
\r
1423 sg = viewport.getSelectionGroup().getSequences(
\r
1424 viewport.getHiddenRepSequences());
\r
1427 if (sg.size() < 1)
\r
1432 Vector invertGroup = new Vector();
\r
1434 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
\r
1436 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
\r
1437 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
\r
1440 SequenceI[] seqs1 = new SequenceI[sg.size()];
\r
1441 for (int i = 0; i < sg.size(); i++)
\r
1442 seqs1[i] = (SequenceI) sg.elementAt(i);
\r
1444 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
\r
1445 for (int i = 0; i < invertGroup.size(); i++)
\r
1446 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
\r
1448 SlideSequencesCommand ssc;
\r
1450 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
\r
1451 size, viewport.getGapCharacter());
\r
1453 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
\r
1454 size, viewport.getGapCharacter());
\r
1456 int groupAdjustment = 0;
\r
1457 if (ssc.getGapsInsertedBegin() && right)
\r
1459 if (viewport.cursorMode)
\r
1460 alignPanel.seqPanel.moveCursor(size, 0);
\r
1462 groupAdjustment = size;
\r
1464 else if (!ssc.getGapsInsertedBegin() && !right)
\r
1466 if (viewport.cursorMode)
\r
1467 alignPanel.seqPanel.moveCursor(-size, 0);
\r
1469 groupAdjustment = -size;
\r
1472 if (groupAdjustment != 0)
\r
1474 viewport.getSelectionGroup().setStartRes(
\r
1475 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
\r
1476 viewport.getSelectionGroup().setEndRes(
\r
1477 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
\r
1480 boolean appendHistoryItem = false;
\r
1481 if (viewport.historyList != null && viewport.historyList.size() > 0
\r
1482 && viewport.historyList.peek() instanceof SlideSequencesCommand)
\r
1484 appendHistoryItem = ssc
\r
1485 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
\r
1489 if (!appendHistoryItem)
\r
1490 addHistoryItem(ssc);
\r
1495 static StringBuffer copiedSequences;
\r
1497 static Vector copiedHiddenColumns;
\r
1499 protected void copy_actionPerformed()
\r
1501 if (viewport.getSelectionGroup() == null)
\r
1506 SequenceGroup sg = viewport.getSelectionGroup();
\r
1507 copiedSequences = new StringBuffer();
\r
1508 Hashtable orderedSeqs = new Hashtable();
\r
1509 for (int i = 0; i < sg.getSize(); i++)
\r
1511 SequenceI seq = sg.getSequenceAt(i);
\r
1512 int index = viewport.getAlignment().findIndex(seq);
\r
1513 orderedSeqs.put(index + "", seq);
\r
1516 int index = 0, startRes, endRes;
\r
1519 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
\r
1521 copiedHiddenColumns = new Vector();
\r
1522 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
\r
1523 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
\r
1526 int[] region = (int[]) viewport.getColumnSelection()
\r
1527 .getHiddenColumns().elementAt(i);
\r
1529 copiedHiddenColumns.addElement(new int[]
\r
1530 { region[0] - hiddenOffset, region[1] - hiddenOffset });
\r
1535 copiedHiddenColumns = null;
\r
1538 for (int i = 0; i < sg.getSize(); i++)
\r
1540 SequenceI seq = null;
\r
1542 while (seq == null)
\r
1544 if (orderedSeqs.containsKey(index + ""))
\r
1546 seq = (SequenceI) orderedSeqs.get(index + "");
\r
1558 // Returns residue following index if gap
\r
1559 startRes = seq.findPosition(sg.getStartRes());
\r
1562 // Need to find the residue preceeding index if gap
\r
1565 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
\r
1567 ch = seq.getCharAt(j);
\r
1568 if (!jalview.util.Comparison.isGap((ch)))
\r
1576 endRes += seq.getStart() - 1;
\r
1579 copiedSequences.append(seq.getName()
\r
1585 + seq.getSequenceAsString(sg.getStartRes(),
\r
1586 sg.getEndRes() + 1) + "\n");
\r
1591 protected void pasteNew_actionPerformed()
\r
1596 protected void pasteThis_actionPerformed()
\r
1601 void paste(boolean newAlignment)
\r
1606 if (copiedSequences == null)
\r
1611 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
1612 Vector seqs = new Vector();
\r
1613 while (st.hasMoreElements())
\r
1615 String name = st.nextToken();
\r
1616 int start = Integer.parseInt(st.nextToken());
\r
1617 int end = Integer.parseInt(st.nextToken());
\r
1618 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
\r
1620 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
1621 for (int i = 0; i < seqs.size(); i++)
\r
1623 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
1628 String newtitle = new String("Copied sequences");
\r
1629 if (getTitle().startsWith("Copied sequences"))
\r
1631 newtitle = getTitle();
\r
1635 newtitle = newtitle.concat("- from " + getTitle());
\r
1637 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
1638 viewport.applet, newtitle, false);
\r
1639 if (copiedHiddenColumns != null)
\r
1641 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
1643 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
1644 af.viewport.hideColumns(region[0], region[1]);
\r
1648 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
\r
1653 addSequences(newSeqs);
\r
1656 } catch (Exception ex)
\r
1658 } // could be anything being pasted in here
\r
1662 void addSequences(SequenceI[] seqs)
\r
1664 for (int i = 0; i < seqs.length; i++)
\r
1666 viewport.getAlignment().addSequence(seqs[i]);
\r
1670 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
\r
1671 seqs, 0, viewport.getAlignment().getWidth(), viewport.getAlignment()));
\r
1673 viewport.setEndSeq(viewport.getAlignment().getHeight());
\r
1674 viewport.getAlignment().getWidth();
\r
1675 viewport.firePropertyChange("alignment", null,
\r
1676 viewport.getAlignment().getSequences());
\r
1680 protected void cut_actionPerformed()
\r
1682 copy_actionPerformed();
\r
1683 delete_actionPerformed();
\r
1686 protected void delete_actionPerformed()
\r
1689 SequenceGroup sg = viewport.getSelectionGroup();
\r
1695 Vector seqs = new Vector();
\r
1697 for (int i = 0; i < sg.getSize(); i++)
\r
1699 seq = sg.getSequenceAt(i);
\r
1700 seqs.addElement(seq);
\r
1703 // If the cut affects all sequences, remove highlighted columns
\r
1704 if (sg.getSize() == viewport.getAlignment().getHeight())
\r
1706 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
1707 sg.getEndRes() + 1);
\r
1710 SequenceI[] cut = new SequenceI[seqs.size()];
\r
1711 for (int i = 0; i < seqs.size(); i++)
\r
1713 cut[i] = (SequenceI) seqs.elementAt(i);
\r
1717 * //ADD HISTORY ITEM
\r
1719 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
\r
1720 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
\r
1721 viewport.getAlignment()));
\r
1723 viewport.setSelectionGroup(null);
\r
1724 viewport.getAlignment().deleteGroup(sg);
\r
1726 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1729 if (viewport.getAlignment().getHeight() < 1)
\r
1731 this.setVisible(false);
\r
1733 viewport.sendSelection();
\r
1737 * group consensus toggled
\r
1740 protected void showGroupConsensus_actionPerformed()
\r
1742 viewport.setShowGroupConsensus(showGroupConsensus.getState());
\r
1743 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1748 * group conservation toggled.
\r
1750 protected void showGroupConservation_actionPerformed()
\r
1752 viewport.setShowGroupConservation(showGroupConservation.getState());
\r
1753 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1760 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
\r
1761 * .event.ActionEvent)
\r
1763 protected void showConsensusHistogram_actionPerformed()
\r
1765 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
\r
1766 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1772 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
\r
1773 * .event.ActionEvent)
\r
1775 protected void showSequenceLogo_actionPerformed()
\r
1777 viewport.setShowSequenceLogo(showSequenceLogo.getState());
\r
1778 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1781 protected void applyAutoAnnotationSettings_actionPerformed()
\r
1783 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1786 protected void makeGrpsFromSelection_actionPerformed()
\r
1788 if (viewport.getSelectionGroup() != null)
\r
1790 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
\r
1791 viewport.getSequenceSelection(),
\r
1792 viewport.getAlignmentView(true).getSequenceStrings(
\r
1793 viewport.getGapCharacter()),
\r
1794 viewport.getAlignment().getGroups());
\r
1795 viewport.getAlignment().deleteAllGroups();
\r
1796 viewport.sequenceColours = null;
\r
1797 viewport.setSelectionGroup(null);
\r
1798 // set view properties for each group
\r
1799 for (int g = 0; g < gps.length; g++)
\r
1801 // gps[g].setShowunconserved(viewport.getShowUnconserved());
\r
1802 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
\r
1803 viewport.getAlignment().addGroup(gps[g]);
\r
1804 Color col = new Color((int) (Math.random() * 255),
\r
1805 (int) (Math.random() * 255), (int) (Math.random() * 255));
\r
1806 col = col.brighter();
\r
1807 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
\r
1808 .hasMoreElements(); viewport.setSequenceColour(
\r
1809 (SequenceI) sq.nextElement(), col))
\r
1812 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
\r
1813 alignPanel.updateAnnotation();
\r
1814 alignPanel.paintAlignment(true);
\r
1818 protected void deleteGroups_actionPerformed()
\r
1820 viewport.getAlignment().deleteAllGroups();
\r
1821 viewport.sequenceColours = null;
\r
1822 viewport.setSelectionGroup(null);
\r
1824 alignPanel.paintAlignment(true);
\r
1827 public void selectAllSequenceMenuItem_actionPerformed()
\r
1829 SequenceGroup sg = new SequenceGroup();
\r
1830 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1832 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
1834 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
\r
1835 viewport.setSelectionGroup(sg);
\r
1836 alignPanel.paintAlignment(true);
\r
1837 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1838 viewport.sendSelection();
\r
1841 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1843 if (viewport.cursorMode)
\r
1845 alignPanel.seqPanel.keyboardNo1 = null;
\r
1846 alignPanel.seqPanel.keyboardNo2 = null;
\r
1848 viewport.setSelectionGroup(null);
\r
1849 viewport.getColumnSelection().clear();
\r
1850 viewport.setSelectionGroup(null);
\r
1851 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1852 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1853 alignPanel.paintAlignment(true);
\r
1854 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1855 viewport.sendSelection();
\r
1858 public void invertSequenceMenuItem_actionPerformed()
\r
1860 SequenceGroup sg = viewport.getSelectionGroup();
\r
1861 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1863 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1866 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1867 viewport.sendSelection();
\r
1870 public void invertColSel_actionPerformed()
\r
1872 viewport.invertColumnSelection();
\r
1873 alignPanel.paintAlignment(true);
\r
1874 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1875 viewport.sendSelection();
\r
1878 void trimAlignment(boolean trimLeft)
\r
1880 ColumnSelection colSel = viewport.getColumnSelection();
\r
1883 if (colSel.size() > 0)
\r
1887 column = colSel.getMin();
\r
1891 column = colSel.getMax();
\r
1895 if (viewport.getSelectionGroup() != null)
\r
1897 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
1898 viewport.getHiddenRepSequences());
\r
1902 seqs = viewport.getAlignment().getSequencesArray();
\r
1905 TrimRegionCommand trimRegion;
\r
1908 trimRegion = new TrimRegionCommand("Remove Left",
\r
1909 TrimRegionCommand.TRIM_LEFT, seqs, column,
\r
1910 viewport.getAlignment(), viewport.getColumnSelection(),
\r
1911 viewport.getSelectionGroup());
\r
1912 viewport.setStartRes(0);
\r
1916 trimRegion = new TrimRegionCommand("Remove Right",
\r
1917 TrimRegionCommand.TRIM_RIGHT, seqs, column,
\r
1918 viewport.getAlignment(), viewport.getColumnSelection(),
\r
1919 viewport.getSelectionGroup());
\r
1922 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
\r
1924 addHistoryItem(trimRegion);
\r
1926 Vector groups = viewport.getAlignment().getGroups();
\r
1928 for (int i = 0; i < groups.size(); i++)
\r
1930 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1932 if ((trimLeft && !sg.adjustForRemoveLeft(column))
\r
1933 || (!trimLeft && !sg.adjustForRemoveRight(column)))
\r
1935 viewport.getAlignment().deleteGroup(sg);
\r
1939 viewport.firePropertyChange("alignment", null, viewport
\r
1940 .getAlignment().getSequences());
\r
1944 public void removeGappedColumnMenuItem_actionPerformed()
\r
1946 int start = 0, end = viewport.getAlignment().getWidth() - 1;
\r
1949 if (viewport.getSelectionGroup() != null)
\r
1951 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
1952 viewport.getHiddenRepSequences());
\r
1953 start = viewport.getSelectionGroup().getStartRes();
\r
1954 end = viewport.getSelectionGroup().getEndRes();
\r
1958 seqs = viewport.getAlignment().getSequencesArray();
\r
1961 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
\r
1962 "Remove Gapped Columns", seqs, start, end, viewport.getAlignment());
\r
1964 addHistoryItem(removeGapCols);
\r
1966 statusBar.setText("Removed " + removeGapCols.getSize()
\r
1967 + " empty columns.");
\r
1969 // This is to maintain viewport position on first residue
\r
1970 // of first sequence
\r
1971 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
\r
1972 int startRes = seq.findPosition(viewport.startRes);
\r
1973 // ShiftList shifts;
\r
1974 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
\r
1975 // edit.alColumnChanges=shifts.getInverse();
\r
1976 // if (viewport.hasHiddenColumns)
\r
1977 // viewport.getColumnSelection().compensateForEdits(shifts);
\r
1978 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
1979 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1984 public void removeAllGapsMenuItem_actionPerformed()
\r
1986 int start = 0, end = viewport.getAlignment().getWidth() - 1;
\r
1989 if (viewport.getSelectionGroup() != null)
\r
1991 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
1992 viewport.getHiddenRepSequences());
\r
1993 start = viewport.getSelectionGroup().getStartRes();
\r
1994 end = viewport.getSelectionGroup().getEndRes();
\r
1998 seqs = viewport.getAlignment().getSequencesArray();
\r
2001 // This is to maintain viewport position on first residue
\r
2002 // of first sequence
\r
2003 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
\r
2004 int startRes = seq.findPosition(viewport.startRes);
\r
2006 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
\r
2007 viewport.getAlignment()));
\r
2009 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
2011 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
2016 public void findMenuItem_actionPerformed()
\r
2018 new Finder(alignPanel);
\r
2022 * create a new view derived from the current view
\r
2024 * @param viewtitle
\r
2025 * @return frame for the new view
\r
2027 public AlignFrame newView(String viewtitle)
\r
2030 if (viewport.hasHiddenRows())
\r
2032 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
\r
2033 .getFullAlignment().getSequencesArray());
\r
2037 newal = new Alignment(viewport.getAlignment().getSequencesArray());
\r
2040 if (viewport.getAlignment().getAlignmentAnnotation() != null)
\r
2042 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
\r
2044 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
\r
2046 newal.addAnnotation(viewport.getAlignment().getAlignmentAnnotation()[i]);
\r
2051 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
\r
2053 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
\r
2054 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
\r
2055 PaintRefresher.Register(newaf.alignPanel,
\r
2056 newaf.alignPanel.av.getSequenceSetId());
\r
2058 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
\r
2059 newaf.alignPanel.av.getSequenceSetId());
\r
2060 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
\r
2061 newaf.alignPanel.av.getSequenceSetId());
\r
2063 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
2064 .getSequenceSetId());
\r
2065 int viewSize = -1;
\r
2066 for (int i = 0; i < comps.size(); i++)
\r
2068 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
2074 String title = new String(this.getTitle());
\r
2075 if (viewtitle != null)
\r
2077 title = viewtitle + " ( " + title + ")";
\r
2081 if (title.indexOf("(View") > -1)
\r
2083 title = title.substring(0, title.indexOf("(View"));
\r
2085 title += "(View " + viewSize + ")";
\r
2088 newaf.setTitle(title.toString());
\r
2090 newaf.viewport.historyList = viewport.historyList;
\r
2091 newaf.viewport.redoList = viewport.redoList;
\r
2097 * @return list of feature groups on the view
\r
2099 public String[] getFeatureGroups()
\r
2101 FeatureRenderer fr = null;
\r
2102 if (alignPanel != null
\r
2103 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2105 return fr.getGroups();
\r
2111 * get sequence feature groups that are hidden or shown
\r
2117 public String[] getFeatureGroupsOfState(boolean visible)
\r
2119 FeatureRenderer fr = null;
\r
2120 if (alignPanel != null
\r
2121 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2123 return fr.getGroups(visible);
\r
2129 * Change the display state for the given feature groups
\r
2132 * list of group strings
\r
2134 * visible or invisible
\r
2136 public void setFeatureGroupState(String[] groups, boolean state)
\r
2138 FeatureRenderer fr = null;
\r
2139 this.sequenceFeatures.setState(true);
\r
2140 viewport.showSequenceFeatures(true);
\r
2141 if (alignPanel != null
\r
2142 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2144 fr.setGroupState(groups, state);
\r
2145 alignPanel.seqPanel.seqCanvas.repaint();
\r
2146 if (alignPanel.overviewPanel != null)
\r
2148 alignPanel.overviewPanel.updateOverviewImage();
\r
2153 public void seqLimits_itemStateChanged()
\r
2155 viewport.setShowJVSuffix(seqLimits.getState());
\r
2156 alignPanel.fontChanged();
\r
2157 alignPanel.paintAlignment(true);
\r
2160 protected void colourTextMenuItem_actionPerformed()
\r
2162 viewport.setColourText(colourTextMenuItem.getState());
\r
2163 alignPanel.paintAlignment(true);
\r
2166 protected void displayNonconservedMenuItem_actionPerformed()
\r
2168 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
\r
2169 alignPanel.paintAlignment(true);
\r
2172 protected void wrapMenuItem_actionPerformed()
\r
2174 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
2175 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
2176 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
2177 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
2178 scaleRight.setEnabled(wrapMenuItem.getState());
\r
2179 alignPanel.paintAlignment(true);
\r
2182 public void overviewMenuItem_actionPerformed()
\r
2184 if (alignPanel.overviewPanel != null)
\r
2189 Frame frame = new Frame();
\r
2190 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
2191 frame.add(overview);
\r
2192 // +50 must allow for applet frame window
\r
2193 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
2194 overview.getPreferredSize().width,
\r
2195 overview.getPreferredSize().height + 50);
\r
2198 frame.addWindowListener(new WindowAdapter()
\r
2200 public void windowClosing(WindowEvent e)
\r
2202 alignPanel.setOverviewPanel(null);
\r
2206 alignPanel.setOverviewPanel(overview);
\r
2210 void changeColour(ColourSchemeI cs)
\r
2212 int threshold = 0;
\r
2216 if (viewport.getAbovePIDThreshold())
\r
2218 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
2221 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2223 viewport.setGlobalColourScheme(cs);
\r
2227 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2230 if (viewport.getConservationSelected())
\r
2233 Alignment al = (Alignment) viewport.getAlignment();
\r
2234 Conservation c = new Conservation("All",
\r
2235 ResidueProperties.propHash, 3, al.getSequences(), 0,
\r
2236 al.getWidth() - 1);
\r
2239 c.verdict(false, viewport.getConsPercGaps());
\r
2241 cs.setConservation(c);
\r
2243 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
\r
2244 cs, "Background"));
\r
2249 cs.setConservation(null);
\r
2252 cs.setConsensus(viewport.getSequenceConsensusHash());
\r
2255 viewport.setGlobalColourScheme(cs);
\r
2257 if (viewport.getColourAppliesToAllGroups())
\r
2259 Vector groups = viewport.getAlignment().getGroups();
\r
2260 for (int i = 0; i < groups.size(); i++)
\r
2262 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
2269 if (cs instanceof ClustalxColourScheme)
\r
2271 sg.cs = new ClustalxColourScheme(
\r
2272 sg.getSequences(viewport.getHiddenRepSequences()),
\r
2279 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
2280 } catch (Exception ex)
\r
2282 ex.printStackTrace();
\r
2287 if (viewport.getAbovePIDThreshold()
\r
2288 || cs instanceof PIDColourScheme
\r
2289 || cs instanceof Blosum62ColourScheme)
\r
2291 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2292 sg.cs.setConsensus(AAFrequency.calculate(
\r
2293 sg.getSequences(viewport.getHiddenRepSequences()), 0,
\r
2298 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2301 if (viewport.getConservationSelected())
\r
2303 Conservation c = new Conservation("Group",
\r
2304 ResidueProperties.propHash, 3,
\r
2305 sg.getSequences(viewport.getHiddenRepSequences()), 0,
\r
2306 viewport.getAlignment().getWidth() - 1);
\r
2308 c.verdict(false, viewport.getConsPercGaps());
\r
2309 sg.cs.setConservation(c);
\r
2313 sg.cs.setConservation(null);
\r
2314 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2320 if (alignPanel.getOverviewPanel() != null)
\r
2322 alignPanel.getOverviewPanel().updateOverviewImage();
\r
2325 jalview.structure.StructureSelectionManager
\r
2326 .getStructureSelectionManager(viewport.applet).sequenceColoursChanged(
\r
2329 alignPanel.paintAlignment(true);
\r
2332 protected void modifyPID_actionPerformed()
\r
2334 if (viewport.getAbovePIDThreshold()
\r
2335 && viewport.getGlobalColourScheme() != null)
\r
2337 SliderPanel.setPIDSliderSource(alignPanel,
\r
2338 viewport.getGlobalColourScheme(), "Background");
\r
2339 SliderPanel.showPIDSlider();
\r
2343 protected void modifyConservation_actionPerformed()
\r
2345 if (viewport.getConservationSelected()
\r
2346 && viewport.getGlobalColourScheme() != null)
\r
2348 SliderPanel.setConservationSlider(alignPanel,
\r
2349 viewport.getGlobalColourScheme(), "Background");
\r
2350 SliderPanel.showConservationSlider();
\r
2354 protected void conservationMenuItem_actionPerformed()
\r
2356 viewport.setConservationSelected(conservationMenuItem.getState());
\r
2358 viewport.setAbovePIDThreshold(false);
\r
2359 abovePIDThreshold.setState(false);
\r
2361 changeColour(viewport.getGlobalColourScheme());
\r
2363 modifyConservation_actionPerformed();
\r
2366 public void abovePIDThreshold_actionPerformed()
\r
2368 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
2370 conservationMenuItem.setState(false);
\r
2371 viewport.setConservationSelected(false);
\r
2373 changeColour(viewport.getGlobalColourScheme());
\r
2375 modifyPID_actionPerformed();
\r
2378 public void sortPairwiseMenuItem_actionPerformed()
\r
2380 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2381 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
\r
2382 .getAlignment().getSequenceAt(0), null);
\r
2384 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
\r
2385 viewport.getAlignment()));
\r
2386 alignPanel.paintAlignment(true);
\r
2389 public void sortIDMenuItem_actionPerformed()
\r
2391 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2392 AlignmentSorter.sortByID(viewport.getAlignment());
\r
2393 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
\r
2394 alignPanel.paintAlignment(true);
\r
2397 public void sortLengthMenuItem_actionPerformed()
\r
2399 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2400 AlignmentSorter.sortByLength(viewport.getAlignment());
\r
2401 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
\r
2402 viewport.getAlignment()));
\r
2403 alignPanel.paintAlignment(true);
\r
2406 public void sortGroupMenuItem_actionPerformed()
\r
2408 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2409 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
2410 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
\r
2411 viewport.getAlignment()));
\r
2412 alignPanel.paintAlignment(true);
\r
2416 public void removeRedundancyMenuItem_actionPerformed()
\r
2418 new RedundancyPanel(alignPanel);
\r
2421 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
2423 if (viewport.getSelectionGroup() != null
\r
2424 && viewport.getSelectionGroup().getSize() > 1)
\r
2426 Frame frame = new Frame();
\r
2427 frame.add(new PairwiseAlignPanel(alignPanel));
\r
2428 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
\r
2433 public void PCAMenuItem_actionPerformed()
\r
2435 // are the sequences aligned?
\r
2436 if (!viewport.getAlignment().isAligned(false))
\r
2438 SequenceI current;
\r
2439 int Width = viewport.getAlignment().getWidth();
\r
2441 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2443 current = viewport.getAlignment().getSequenceAt(i);
\r
2445 if (current.getLength() < Width)
\r
2447 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2450 alignPanel.paintAlignment(true);
\r
2453 if ((viewport.getSelectionGroup() != null
\r
2454 && viewport.getSelectionGroup().getSize() < 4 && viewport
\r
2455 .getSelectionGroup().getSize() > 0)
\r
2456 || viewport.getAlignment().getHeight() < 4)
\r
2463 new PCAPanel(viewport);
\r
2464 } catch (java.lang.OutOfMemoryError ex)
\r
2470 public void averageDistanceTreeMenuItem_actionPerformed()
\r
2472 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
2475 public void neighbourTreeMenuItem_actionPerformed()
\r
2477 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
2480 protected void njTreeBlosumMenuItem_actionPerformed()
\r
2482 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2485 protected void avTreeBlosumMenuItem_actionPerformed()
\r
2487 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2490 void NewTreePanel(String type, String pwType, String title)
\r
2492 // are the sequences aligned?
\r
2493 if (!viewport.getAlignment().isAligned(false))
\r
2495 SequenceI current;
\r
2496 int Width = viewport.getAlignment().getWidth();
\r
2498 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2500 current = viewport.getAlignment().getSequenceAt(i);
\r
2502 if (current.getLength() < Width)
\r
2504 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2507 alignPanel.paintAlignment(true);
\r
2511 if ((viewport.getSelectionGroup() != null && viewport
\r
2512 .getSelectionGroup().getSize() > 1)
\r
2513 || (viewport.getSelectionGroup() == null && viewport.getAlignment()
\r
2514 .getHeight() > 1))
\r
2516 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
\r
2518 addTreeMenuItem(tp, title);
\r
2520 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
2524 void loadTree_actionPerformed()
\r
2526 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
2527 cap.setText("Paste your Newick tree file here.");
\r
2528 cap.setTreeImport();
\r
2529 Frame frame = new Frame();
\r
2531 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
2534 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
2536 TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
\r
2537 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
2538 addTreeMenuItem(tp, treeFile);
\r
2542 * sort the alignment using the given treePanel
\r
2544 * @param treePanel
\r
2545 * tree used to sort view
\r
2547 * string used for undo event name
\r
2549 public void sortByTree(TreePanel treePanel, String title)
\r
2551 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2553 .sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
2554 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2555 // HistoryItem.SORT));
\r
2556 addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
\r
2557 viewport.getAlignment()));
\r
2558 alignPanel.paintAlignment(true);
\r
2562 * Do any automatic reordering of the alignment and add the necessary bits to
\r
2563 * the menu structure for the new tree
\r
2565 * @param treePanel
\r
2568 protected void addTreeMenuItem(final TreePanel treePanel,
\r
2569 final String title)
\r
2571 final MenuItem item = new MenuItem(title);
\r
2572 sortByTreeMenu.add(item);
\r
2573 item.addActionListener(new java.awt.event.ActionListener()
\r
2575 public void actionPerformed(ActionEvent evt)
\r
2577 sortByTree(treePanel, title); // treePanel.getTitle());
\r
2581 treePanel.addWindowListener(new WindowAdapter()
\r
2583 public void windowOpened(WindowEvent e)
\r
2585 if (viewport.sortByTree)
\r
2587 sortByTree(treePanel, title);
\r
2589 super.windowOpened(e);
\r
2592 public void windowClosing(WindowEvent e)
\r
2594 sortByTreeMenu.remove(item);
\r
2598 public boolean sortBy(AlignmentOrder alorder, String undoname)
\r
2600 SequenceI[] oldOrder = viewport.getAlignment()
\r
2601 .getSequencesArray();
\r
2602 if (viewport.applet.debug)
\r
2604 System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");
\r
2606 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
\r
2607 if (undoname!=null)
\r
2609 addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.getAlignment()));
\r
2611 alignPanel.paintAlignment(true);
\r
2615 protected void documentation_actionPerformed()
\r
2617 alignPanel.av.applet.openJalviewHelpUrl();
\r
2620 protected void about_actionPerformed()
\r
2623 class AboutPanel extends Canvas
\r
2629 public AboutPanel(String version, String builddate)
\r
2631 this.version = version;
\r
2632 this.builddate = builddate;
\r
2635 public void paint(Graphics g)
\r
2637 g.setColor(Color.white);
\r
2638 g.fillRect(0, 0, getSize().width, getSize().height);
\r
2639 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2640 FontMetrics fm = g.getFontMetrics();
\r
2641 int fh = fm.getHeight();
\r
2643 g.setColor(Color.black);
\r
2644 // TODO: update this text for each release or centrally store it for
\r
2645 // lite and application
\r
2646 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
2647 g.drawString("JalviewLite - Release " + version, x, y += fh);
\r
2648 g.setFont(new Font("Helvetica", Font.BOLD, 12));
\r
2649 g.drawString("Build date: " + builddate, x, y += fh);
\r
2650 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2652 "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",
\r
2653 x, y += fh * 1.5);
\r
2654 g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
\r
2656 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
\r
2659 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
\r
2661 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
\r
2663 "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
\r
2666 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
\r
2668 g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
\r
2673 Frame frame = new Frame();
\r
2674 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
\r
2675 .getBuildDate()));
\r
2676 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
\r
2680 public void showURL(String url, String target)
\r
2682 if (viewport.applet == null)
\r
2684 System.out.println("Not running as applet - no browser available.");
\r
2688 viewport.applet.showURL(url, target);
\r
2692 // ////////////////////////////////////////////////////////////////////////////////
\r
2693 // JBuilder Graphics here
\r
2695 MenuBar alignFrameMenuBar = new MenuBar();
\r
2697 Menu fileMenu = new Menu("File");
\r
2699 MenuItem loadApplication = new MenuItem("View in Full Application");
\r
2701 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
\r
2703 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
\r
2705 MenuItem outputFeatures = new MenuItem("Export Features ...");
\r
2707 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
\r
2709 MenuItem closeMenuItem = new MenuItem("Close");
\r
2711 Menu editMenu = new Menu("Edit");
\r
2713 Menu viewMenu = new Menu("View");
\r
2715 Menu colourMenu = new Menu("Colour");
\r
2717 Menu calculateMenu = new Menu("Calculate");
\r
2719 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
2721 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
2723 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
2725 MenuItem remove2LeftMenuItem = new MenuItem();
\r
2727 MenuItem remove2RightMenuItem = new MenuItem();
\r
2729 MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
2731 MenuItem removeAllGapsMenuItem = new MenuItem();
\r
2733 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
2735 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
2737 MenuItem sortPairwiseMenuItem = new MenuItem();
\r
2739 MenuItem sortIDMenuItem = new MenuItem();
\r
2741 MenuItem sortLengthMenuItem = new MenuItem();
\r
2743 MenuItem sortGroupMenuItem = new MenuItem();
\r
2745 MenuItem removeRedundancyMenuItem = new MenuItem();
\r
2747 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
2749 MenuItem PCAMenuItem = new MenuItem();
\r
2751 MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
2753 MenuItem neighbourTreeMenuItem = new MenuItem();
\r
2755 BorderLayout borderLayout1 = new BorderLayout();
\r
2757 public Label statusBar = new Label();
\r
2759 Menu outputTextboxMenu = new Menu();
\r
2761 MenuItem clustalColour = new MenuItem();
\r
2763 MenuItem zappoColour = new MenuItem();
\r
2765 MenuItem taylorColour = new MenuItem();
\r
2767 MenuItem hydrophobicityColour = new MenuItem();
\r
2769 MenuItem helixColour = new MenuItem();
\r
2771 MenuItem strandColour = new MenuItem();
\r
2773 MenuItem turnColour = new MenuItem();
\r
2775 MenuItem buriedColour = new MenuItem();
\r
2777 MenuItem userDefinedColour = new MenuItem();
\r
2779 MenuItem PIDColour = new MenuItem();
\r
2781 MenuItem BLOSUM62Colour = new MenuItem();
\r
2783 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
2785 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
2787 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
2789 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
2791 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
\r
2793 MenuItem alProperties = new MenuItem("Alignment Properties...");
\r
2795 MenuItem overviewMenuItem = new MenuItem();
\r
2797 MenuItem undoMenuItem = new MenuItem();
\r
2799 MenuItem redoMenuItem = new MenuItem();
\r
2801 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
2803 MenuItem noColourmenuItem = new MenuItem();
\r
2805 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
2807 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
2809 MenuItem findMenuItem = new MenuItem();
\r
2811 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
2813 MenuItem nucleotideColour = new MenuItem();
\r
2815 MenuItem deleteGroups = new MenuItem();
\r
2817 MenuItem grpsFromSelection = new MenuItem();
\r
2819 MenuItem delete = new MenuItem();
\r
2821 MenuItem copy = new MenuItem();
\r
2823 MenuItem cut = new MenuItem();
\r
2825 Menu pasteMenu = new Menu();
\r
2827 MenuItem pasteNew = new MenuItem();
\r
2829 MenuItem pasteThis = new MenuItem();
\r
2831 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
2833 MenuItem font = new MenuItem();
\r
2835 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
2837 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
2839 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
2841 MenuItem modifyPID = new MenuItem();
\r
2843 MenuItem modifyConservation = new MenuItem();
\r
2845 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
\r
2846 "Autocalculate Consensus", true);
\r
2848 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
\r
2849 "Sort Alignment With New Tree", true);
\r
2851 Menu sortByTreeMenu = new Menu();
\r
2853 Menu sort = new Menu();
\r
2855 Menu calculate = new Menu();
\r
2857 MenuItem inputText = new MenuItem();
\r
2859 Menu helpMenu = new Menu();
\r
2861 MenuItem documentation = new MenuItem();
\r
2863 MenuItem about = new MenuItem();
\r
2865 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
2867 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
\r
2869 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
\r
2870 Menu autoAnnMenu=new Menu();
\r
2871 CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();
\r
2872 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
\r
2873 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
\r
2874 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
\r
2875 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
\r
2877 private void jbInit() throws Exception
\r
2880 setMenuBar(alignFrameMenuBar);
\r
2884 // dynamically fill save as menu with available formats
\r
2885 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
2888 item = new MenuItem(
\r
2889 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
2891 item.addActionListener(new java.awt.event.ActionListener()
\r
2893 public void actionPerformed(ActionEvent e)
\r
2895 outputText_actionPerformed(e);
\r
2899 outputTextboxMenu.add(item);
\r
2901 closeMenuItem.addActionListener(this);
\r
2902 loadApplication.addActionListener(this);
\r
2904 loadTree.addActionListener(this);
\r
2905 loadAnnotations.addActionListener(this);
\r
2906 outputFeatures.addActionListener(this);
\r
2907 outputAnnotations.addActionListener(this);
\r
2908 selectAllSequenceMenuItem.addActionListener(this);
\r
2909 deselectAllSequenceMenuItem.addActionListener(this);
\r
2910 invertSequenceMenuItem.addActionListener(this);
\r
2911 remove2LeftMenuItem.setLabel("Remove Left");
\r
2912 remove2LeftMenuItem.addActionListener(this);
\r
2913 remove2RightMenuItem.setLabel("Remove Right");
\r
2914 remove2RightMenuItem.addActionListener(this);
\r
2915 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
2916 removeGappedColumnMenuItem.addActionListener(this);
\r
2917 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
2918 removeAllGapsMenuItem.addActionListener(this);
\r
2919 viewBoxesMenuItem.setLabel("Boxes");
\r
2920 viewBoxesMenuItem.setState(true);
\r
2921 viewBoxesMenuItem.addItemListener(this);
\r
2922 viewTextMenuItem.setLabel("Text");
\r
2923 viewTextMenuItem.setState(true);
\r
2924 viewTextMenuItem.addItemListener(this);
\r
2925 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
2926 sortPairwiseMenuItem.addActionListener(this);
\r
2927 sortIDMenuItem.setLabel("by ID");
\r
2928 sortIDMenuItem.addActionListener(this);
\r
2929 sortLengthMenuItem.setLabel("by Length");
\r
2930 sortLengthMenuItem.addActionListener(this);
\r
2931 sortGroupMenuItem.setLabel("by Group");
\r
2932 sortGroupMenuItem.addActionListener(this);
\r
2933 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
2934 removeRedundancyMenuItem.addActionListener(this);
\r
2935 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
2936 pairwiseAlignmentMenuItem.addActionListener(this);
\r
2937 PCAMenuItem.setLabel("Principal Component Analysis");
\r
2938 PCAMenuItem.addActionListener(this);
\r
2939 averageDistanceTreeMenuItem
\r
2940 .setLabel("Average Distance Using % Identity");
\r
2941 averageDistanceTreeMenuItem.addActionListener(this);
\r
2942 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
2943 neighbourTreeMenuItem.addActionListener(this);
\r
2944 statusBar.setBackground(Color.white);
\r
2945 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
2946 statusBar.setText("Status bar");
\r
2947 outputTextboxMenu.setLabel("Output to Textbox");
\r
2948 clustalColour.setLabel("Clustalx");
\r
2950 clustalColour.addActionListener(this);
\r
2951 zappoColour.setLabel("Zappo");
\r
2952 zappoColour.addActionListener(this);
\r
2953 taylorColour.setLabel("Taylor");
\r
2954 taylorColour.addActionListener(this);
\r
2955 hydrophobicityColour.setLabel("Hydrophobicity");
\r
2956 hydrophobicityColour.addActionListener(this);
\r
2957 helixColour.setLabel("Helix Propensity");
\r
2958 helixColour.addActionListener(this);
\r
2959 strandColour.setLabel("Strand Propensity");
\r
2960 strandColour.addActionListener(this);
\r
2961 turnColour.setLabel("Turn Propensity");
\r
2962 turnColour.addActionListener(this);
\r
2963 buriedColour.setLabel("Buried Index");
\r
2964 buriedColour.addActionListener(this);
\r
2965 userDefinedColour.setLabel("User Defined...");
\r
2966 userDefinedColour.addActionListener(this);
\r
2967 PIDColour.setLabel("Percentage Identity");
\r
2968 PIDColour.addActionListener(this);
\r
2969 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
2970 BLOSUM62Colour.addActionListener(this);
\r
2971 avDistanceTreeBlosumMenuItem
\r
2972 .setLabel("Average Distance Using BLOSUM62");
\r
2973 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
2974 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
2975 njTreeBlosumMenuItem.addActionListener(this);
\r
2976 annotationPanelMenuItem.setLabel("Show Annotations");
\r
2977 annotationPanelMenuItem.addItemListener(this);
\r
2978 colourTextMenuItem.setLabel("Colour Text");
\r
2979 colourTextMenuItem.addItemListener(this);
\r
2980 displayNonconservedMenuItem.setLabel("Show nonconserved");
\r
2981 displayNonconservedMenuItem.addItemListener(this);
\r
2982 alProperties.addActionListener(this);
\r
2983 overviewMenuItem.setLabel("Overview Window");
\r
2984 overviewMenuItem.addActionListener(this);
\r
2985 undoMenuItem.setEnabled(false);
\r
2986 undoMenuItem.setLabel("Undo");
\r
2987 undoMenuItem.addActionListener(this);
\r
2988 redoMenuItem.setEnabled(false);
\r
2989 redoMenuItem.setLabel("Redo");
\r
2990 redoMenuItem.addActionListener(this);
\r
2991 conservationMenuItem.setLabel("by Conservation");
\r
2992 conservationMenuItem.addItemListener(this);
\r
2993 noColourmenuItem.setLabel("None");
\r
2994 noColourmenuItem.addActionListener(this);
\r
2995 wrapMenuItem.setLabel("Wrap");
\r
2996 wrapMenuItem.addItemListener(this);
\r
2997 renderGapsMenuItem.setLabel("Show Gaps");
\r
2998 renderGapsMenuItem.setState(true);
\r
2999 renderGapsMenuItem.addItemListener(this);
\r
3000 findMenuItem.setLabel("Find...");
\r
3001 findMenuItem.addActionListener(this);
\r
3002 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
3003 abovePIDThreshold.addItemListener(this);
\r
3004 nucleotideColour.setLabel("Nucleotide");
\r
3005 nucleotideColour.addActionListener(this);
\r
3006 deleteGroups.setLabel("Undefine Groups");
\r
3007 deleteGroups.addActionListener(this);
\r
3008 grpsFromSelection.setLabel("Make Groups for selection");
\r
3009 grpsFromSelection.addActionListener(this);
\r
3010 copy.setLabel("Copy");
\r
3011 copy.addActionListener(this);
\r
3012 cut.setLabel("Cut");
\r
3013 cut.addActionListener(this);
\r
3014 delete.setLabel("Delete");
\r
3015 delete.addActionListener(this);
\r
3016 pasteMenu.setLabel("Paste");
\r
3017 pasteNew.setLabel("To New Alignment");
\r
3018 pasteNew.addActionListener(this);
\r
3019 pasteThis.setLabel("Add To This Alignment");
\r
3020 pasteThis.addActionListener(this);
\r
3021 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
3022 applyToAllGroups.setState(true);
\r
3023 applyToAllGroups.addItemListener(this);
\r
3024 font.setLabel("Font...");
\r
3025 font.addActionListener(this);
\r
3026 scaleAbove.setLabel("Scale Above");
\r
3027 scaleAbove.setState(true);
\r
3028 scaleAbove.setEnabled(false);
\r
3029 scaleAbove.addItemListener(this);
\r
3030 scaleLeft.setEnabled(false);
\r
3031 scaleLeft.setState(true);
\r
3032 scaleLeft.setLabel("Scale Left");
\r
3033 scaleLeft.addItemListener(this);
\r
3034 scaleRight.setEnabled(false);
\r
3035 scaleRight.setState(true);
\r
3036 scaleRight.setLabel("Scale Right");
\r
3037 scaleRight.addItemListener(this);
\r
3038 modifyPID.setLabel("Modify Identity Threshold...");
\r
3039 modifyPID.addActionListener(this);
\r
3040 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
3041 modifyConservation.addActionListener(this);
\r
3042 sortByTreeMenu.setLabel("By Tree Order");
\r
3043 sort.setLabel("Sort");
\r
3044 calculate.setLabel("Calculate Tree");
\r
3045 autoCalculate.addItemListener(this);
\r
3046 sortByTree.addItemListener(this);
\r
3047 inputText.setLabel("Input from textbox");
\r
3048 inputText.addActionListener(this);
\r
3049 centreColumnLabelFlag.setLabel("Centre column labels");
\r
3050 centreColumnLabelFlag.addItemListener(this);
\r
3051 followMouseOverFlag.setLabel("Automatic Scrolling");
\r
3052 followMouseOverFlag.addItemListener(this);
\r
3053 helpMenu.setLabel("Help");
\r
3054 documentation.setLabel("Documentation");
\r
3055 documentation.addActionListener(this);
\r
3057 about.setLabel("About...");
\r
3058 about.addActionListener(this);
\r
3059 seqLimits.setState(true);
\r
3060 seqLimits.setLabel("Show Sequence Limits");
\r
3061 seqLimits.addItemListener(this);
\r
3062 featureSettings.setLabel("Feature Settings...");
\r
3063 featureSettings.addActionListener(this);
\r
3064 sequenceFeatures.setLabel("Sequence Features");
\r
3065 sequenceFeatures.addItemListener(this);
\r
3066 sequenceFeatures.setState(false);
\r
3067 annotationColour.setLabel("by Annotation...");
\r
3068 annotationColour.addActionListener(this);
\r
3069 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
3070 invertColSel.setLabel("Invert Column Selection");
\r
3071 menu1.setLabel("Show");
\r
3072 showColumns.setLabel("All Columns ");
\r
3073 showSeqs.setLabel("All Sequences");
\r
3074 menu2.setLabel("Hide");
\r
3075 hideColumns.setLabel("Selected Columns");
\r
3076 hideSequences.setLabel("Selected Sequences");
\r
3077 hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
\r
3078 hideAllSelection.setLabel("Selected Region");
\r
3079 showAllHidden.setLabel("All Sequences and Columns");
\r
3080 showGroupConsensus.setLabel("Group Consensus");
\r
3081 showGroupConservation.setLabel("Group Conservation");
\r
3082 showConsensusHistogram.setLabel("Show Consensus Histogram");
\r
3083 showSequenceLogo.setLabel("Show Consensus Logo");
\r
3084 applyAutoAnnotationSettings.setLabel("Apply to all groups");
\r
3085 applyAutoAnnotationSettings.setState(true);
\r
3086 autoAnnMenu.setLabel("Autocalculated Annotation");
\r
3088 invertColSel.addActionListener(this);
\r
3089 showColumns.addActionListener(this);
\r
3090 showSeqs.addActionListener(this);
\r
3091 hideColumns.addActionListener(this);
\r
3092 hideSequences.addActionListener(this);
\r
3093 hideAllButSelection.addActionListener(this);
\r
3094 hideAllSelection.addActionListener(this);
\r
3095 showAllHidden.addActionListener(this);
\r
3096 showGroupConsensus.addItemListener(this);
\r
3097 showGroupConservation.addItemListener(this);
\r
3098 showConsensusHistogram.addItemListener(this);
\r
3099 showSequenceLogo.addItemListener(this);
\r
3100 applyAutoAnnotationSettings.addItemListener(this);
\r
3101 formatMenu.setLabel("Format");
\r
3102 selectMenu.setLabel("Select");
\r
3103 newView.setLabel("New View");
\r
3104 newView.addActionListener(this);
\r
3105 alignFrameMenuBar.add(fileMenu);
\r
3106 alignFrameMenuBar.add(editMenu);
\r
3107 alignFrameMenuBar.add(selectMenu);
\r
3108 alignFrameMenuBar.add(viewMenu);
\r
3109 alignFrameMenuBar.add(formatMenu);
\r
3110 alignFrameMenuBar.add(colourMenu);
\r
3111 alignFrameMenuBar.add(calculateMenu);
\r
3112 alignFrameMenuBar.add(helpMenu);
\r
3114 fileMenu.add(inputText);
\r
3115 fileMenu.add(loadTree);
\r
3116 fileMenu.add(loadAnnotations);
\r
3118 fileMenu.addSeparator();
\r
3119 fileMenu.add(outputTextboxMenu);
\r
3120 fileMenu.add(outputFeatures);
\r
3121 fileMenu.add(outputAnnotations);
\r
3123 if (jalviewServletURL != null)
\r
3125 fileMenu.add(loadApplication);
\r
3128 fileMenu.addSeparator();
\r
3129 fileMenu.add(closeMenuItem);
\r
3131 editMenu.add(undoMenuItem);
\r
3132 editMenu.add(redoMenuItem);
\r
3133 editMenu.add(cut);
\r
3134 editMenu.add(copy);
\r
3135 editMenu.add(pasteMenu);
\r
3136 editMenu.add(delete);
\r
3137 editMenu.addSeparator();
\r
3138 editMenu.add(remove2LeftMenuItem);
\r
3139 editMenu.add(remove2RightMenuItem);
\r
3140 editMenu.add(removeGappedColumnMenuItem);
\r
3141 editMenu.add(removeAllGapsMenuItem);
\r
3142 editMenu.add(removeRedundancyMenuItem);
\r
3143 viewMenu.add(newView);
\r
3144 viewMenu.addSeparator();
\r
3145 viewMenu.add(menu1);
\r
3146 viewMenu.add(menu2);
\r
3147 viewMenu.addSeparator();
\r
3148 viewMenu.add(followMouseOverFlag);
\r
3149 viewMenu.add(annotationPanelMenuItem);
\r
3150 autoAnnMenu.add(applyAutoAnnotationSettings);
\r
3151 autoAnnMenu.add(showConsensusHistogram);
\r
3152 autoAnnMenu.add(showSequenceLogo);
\r
3153 autoAnnMenu.addSeparator();
\r
3154 autoAnnMenu.add(showGroupConservation);
\r
3155 autoAnnMenu.add(showGroupConsensus);
\r
3156 viewMenu.add(autoAnnMenu);
\r
3157 viewMenu.addSeparator();
\r
3158 viewMenu.add(sequenceFeatures);
\r
3159 viewMenu.add(featureSettings);
\r
3160 viewMenu.addSeparator();
\r
3161 viewMenu.add(alProperties);
\r
3162 viewMenu.addSeparator();
\r
3163 viewMenu.add(overviewMenuItem);
\r
3164 colourMenu.add(applyToAllGroups);
\r
3165 colourMenu.addSeparator();
\r
3166 colourMenu.add(noColourmenuItem);
\r
3167 colourMenu.add(clustalColour);
\r
3168 colourMenu.add(BLOSUM62Colour);
\r
3169 colourMenu.add(PIDColour);
\r
3170 colourMenu.add(zappoColour);
\r
3171 colourMenu.add(taylorColour);
\r
3172 colourMenu.add(hydrophobicityColour);
\r
3173 colourMenu.add(helixColour);
\r
3174 colourMenu.add(strandColour);
\r
3175 colourMenu.add(turnColour);
\r
3176 colourMenu.add(buriedColour);
\r
3177 colourMenu.add(nucleotideColour);
\r
3178 colourMenu.add(userDefinedColour);
\r
3179 colourMenu.addSeparator();
\r
3180 colourMenu.add(conservationMenuItem);
\r
3181 colourMenu.add(modifyConservation);
\r
3182 colourMenu.add(abovePIDThreshold);
\r
3183 colourMenu.add(modifyPID);
\r
3184 colourMenu.add(annotationColour);
\r
3185 calculateMenu.add(sort);
\r
3186 calculateMenu.add(calculate);
\r
3187 calculateMenu.addSeparator();
\r
3188 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
3189 calculateMenu.add(PCAMenuItem);
\r
3190 calculateMenu.add(autoCalculate);
\r
3191 calculateMenu.add(sortByTree);
\r
3192 this.add(statusBar, BorderLayout.SOUTH);
\r
3193 pasteMenu.add(pasteNew);
\r
3194 pasteMenu.add(pasteThis);
\r
3195 sort.add(sortIDMenuItem);
\r
3196 sort.add(sortLengthMenuItem);
\r
3197 sort.add(sortByTreeMenu);
\r
3198 sort.add(sortGroupMenuItem);
\r
3199 sort.add(sortPairwiseMenuItem);
\r
3200 calculate.add(averageDistanceTreeMenuItem);
\r
3201 calculate.add(neighbourTreeMenuItem);
\r
3202 calculate.add(avDistanceTreeBlosumMenuItem);
\r
3203 calculate.add(njTreeBlosumMenuItem);
\r
3204 helpMenu.add(documentation);
\r
3205 helpMenu.add(about);
\r
3206 menu1.add(showColumns);
\r
3207 menu1.add(showSeqs);
\r
3208 menu1.add(showAllHidden);
\r
3209 menu2.add(hideColumns);
\r
3210 menu2.add(hideSequences);
\r
3211 menu2.add(hideAllSelection);
\r
3212 menu2.add(hideAllButSelection);
\r
3213 formatMenu.add(font);
\r
3214 formatMenu.add(seqLimits);
\r
3215 formatMenu.add(wrapMenuItem);
\r
3216 formatMenu.add(scaleAbove);
\r
3217 formatMenu.add(scaleLeft);
\r
3218 formatMenu.add(scaleRight);
\r
3219 formatMenu.add(viewBoxesMenuItem);
\r
3220 formatMenu.add(viewTextMenuItem);
\r
3221 formatMenu.add(colourTextMenuItem);
\r
3222 formatMenu.add(displayNonconservedMenuItem);
\r
3223 formatMenu.add(renderGapsMenuItem);
\r
3224 formatMenu.add(centreColumnLabelFlag);
\r
3225 selectMenu.add(findMenuItem);
\r
3226 selectMenu.addSeparator();
\r
3227 selectMenu.add(selectAllSequenceMenuItem);
\r
3228 selectMenu.add(deselectAllSequenceMenuItem);
\r
3229 selectMenu.add(invertSequenceMenuItem);
\r
3230 selectMenu.add(invertColSel);
\r
3231 selectMenu.add(grpsFromSelection);
\r
3232 selectMenu.add(deleteGroups);
\r
3236 MenuItem featureSettings = new MenuItem();
\r
3238 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
3240 MenuItem annotationColour = new MenuItem();
\r
3242 MenuItem invertColSel = new MenuItem();
\r
3244 Menu menu1 = new Menu();
\r
3246 MenuItem showColumns = new MenuItem();
\r
3248 MenuItem showSeqs = new MenuItem();
\r
3250 Menu menu2 = new Menu();
\r
3252 MenuItem hideColumns = new MenuItem();
\r
3254 MenuItem hideSequences = new MenuItem();
\r
3256 MenuItem hideAllButSelection = new MenuItem();
\r
3258 MenuItem hideAllSelection = new MenuItem();
\r
3260 MenuItem showAllHidden = new MenuItem();
\r
3262 Menu formatMenu = new Menu();
\r
3264 Menu selectMenu = new Menu();
\r
3266 MenuItem newView = new MenuItem();
\r
3269 * Attach the alignFrame panels after embedding menus, if necessary. This used
\r
3270 * to be called setEmbedded, but is now creates the dropdown menus in a
\r
3271 * platform independent manner to avoid OSX/Mac menu appendage daftness.
\r
3273 * @param reallyEmbedded
\r
3274 * true to attach the view to the applet area on the page rather than
\r
3277 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
\r
3279 if (reallyEmbedded)
\r
3282 // Explicly build the embedded menu panel for the on-page applet
\r
3284 // view cannot be closed if its actually on the page
\r
3285 fileMenu.remove(closeMenuItem);
\r
3286 fileMenu.remove(3); // Remove Seperator
\r
3287 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
\r
3288 Font.PLAIN, 10, false); // use our own fonts.
\r
3289 // and actually add the components to the applet area
\r
3290 viewport.applet.setLayout(new BorderLayout());
\r
3291 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
\r
3292 viewport.applet.add(statusBar, BorderLayout.SOUTH);
\r
3293 alignPanel.setSize(viewport.applet.getSize().width,
\r
3294 viewport.applet.getSize().height - embeddedMenu.HEIGHT
\r
3295 - statusBar.HEIGHT);
\r
3296 viewport.applet.add(alignPanel, BorderLayout.CENTER);
\r
3297 final AlignFrame me = this;
\r
3298 viewport.applet.addFocusListener(new FocusListener()
\r
3302 public void focusLost(FocusEvent e)
\r
3304 if (me.viewport.applet.currentAlignFrame==me) {
\r
3305 me.viewport.applet.currentAlignFrame = null;
\r
3309 public void focusGained(FocusEvent e)
\r
3311 me.viewport.applet.currentAlignFrame = me;
\r
3314 viewport.applet.validate();
\r
3319 // test and embed menu bar if necessary.
\r
3321 if (embedMenuIfNeeded(alignPanel))
\r
3323 // adjust for status bar height too
\r
3324 alignPanel.setSize(getSize().width, getSize().height
\r
3325 - statusBar.HEIGHT);
\r
3327 add(statusBar, BorderLayout.SOUTH);
\r
3328 add(alignPanel, BorderLayout.CENTER);
\r
3329 // and register with the applet so it can pass external API calls to us
\r
3330 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
\r
3336 * create a new binding between structures in an existing jmol viewer instance
\r
3337 * and an alignpanel with sequences that have existing PDBFile entries. Note,
\r
3338 * this does not open a new Jmol window, or modify the display of the
\r
3339 * structures in the original jmol window. Note This method doesn't work
\r
3340 * without an additional javascript library to exchange messages between the
\r
3341 * distinct applets. See http://issues.jalview.org/browse/JAL-621
\r
3344 * JmolViewer instance
\r
3345 * @param sequenceIds
\r
3346 * - sequence Ids to search for associations
\r
3348 public SequenceStructureBinding addStructureViewInstance(
\r
3349 Object jmolviewer, String[] sequenceIds)
\r
3351 org.jmol.api.JmolViewer viewer = null;
\r
3354 viewer = (org.jmol.api.JmolViewer) jmolviewer;
\r
3355 } catch (ClassCastException ex)
\r
3357 System.err.println("Unsupported viewer object :"
\r
3358 + jmolviewer.getClass());
\r
3360 if (viewer == null)
\r
3362 System.err.println("Can't use this object as a structure viewer:"
\r
3363 + jmolviewer.getClass());
\r
3366 SequenceI[] seqs = null;
\r
3367 if (sequenceIds == null || sequenceIds.length == 0)
\r
3369 seqs = viewport.getAlignment().getSequencesArray();
\r
3373 Vector sqi = new Vector();
\r
3374 AlignmentI al = viewport.getAlignment();
\r
3375 for (int sid = 0; sid < sequenceIds.length; sid++)
\r
3377 SequenceI sq = al.findName(sequenceIds[sid]);
\r
3380 sqi.addElement(sq);
\r
3383 if (sqi.size() > 0)
\r
3385 seqs = new SequenceI[sqi.size()];
\r
3386 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
\r
3388 seqs[sid] = (SequenceI) sqi.elementAt(sid);
\r
3396 ExtJmol jmv = null;
\r
3397 // TODO: search for a jmv that involves viewer
\r
3399 { // create a new viewer/jalview binding.
\r
3400 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs});
\r
3406 * bind a pdb file to a sequence in the current view
\r
3408 * @param sequenceId
\r
3409 * - sequenceId within the dataset.
\r
3410 * @param pdbEntryString
\r
3411 * - the short name for the PDB file
\r
3413 * - pdb file - either a URL or a valid PDB file.
\r
3414 * @return true if binding was as success TODO: consider making an exception
\r
3415 * structure for indicating when PDB parsing or sequenceId location
\r
3418 public boolean addPdbFile(String sequenceId, String pdbEntryString,
\r
3421 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
\r
3422 boolean needtoadd = false;
\r
3423 if (toaddpdb != null)
\r
3425 Vector pdbe = toaddpdb.getPDBId();
\r
3426 PDBEntry pdbentry = null;
\r
3427 if (pdbe != null && pdbe.size() > 0)
\r
3429 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
\r
3431 pdbentry = (PDBEntry) pdbe.elementAt(pe);
\r
3432 if (!pdbentry.getId().equals(pdbEntryString)
\r
3433 && !pdbentry.getFile().equals(pdbFile))
\r
3443 if (pdbentry == null)
\r
3445 pdbentry = new PDBEntry();
\r
3446 pdbentry.setId(pdbEntryString);
\r
3447 pdbentry.setFile(pdbFile);
\r
3448 needtoadd = true; // add this new entry to sequence.
\r
3450 // resolve data source
\r
3451 // TODO: this code should be a refactored to an io package
\r
3452 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
\r
3453 if (protocol == null)
\r
3459 // make a note of the access mode and add
\r
3460 if (pdbentry.getProperty() == null)
\r
3462 pdbentry.setProperty(new Hashtable());
\r
3464 pdbentry.getProperty().put("protocol", protocol);
\r
3465 toaddpdb.addPDBId(pdbentry);
\r
3471 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
\r
3475 Vector sequences = new Vector();
\r
3476 for (int i = 0; i < seqs.length; i++)
\r
3478 if (seqs[i] != null)
\r
3480 sequences.addElement(new Object[]
\r
3481 { seqs[i], (chains != null) ? chains[i] : null });
\r
3484 seqs = new SequenceI[sequences.size()];
\r
3485 chains = new String[sequences.size()];
\r
3486 for (int i = 0, isize = sequences.size(); i < isize; i++)
\r
3488 Object[] oj = (Object[]) sequences.elementAt(i);
\r
3490 seqs[i] = (SequenceI) oj[0];
\r
3491 chains[i] = (String) oj[1];
\r
3494 return new Object[]
\r
3499 public void newStructureView(JalviewLite applet, PDBEntry pdb,
\r
3500 SequenceI[] seqs, String[] chains, String protocol)
\r
3502 // Scrub any null sequences from the array
\r
3503 Object[] sqch = cleanSeqChainArrays(seqs, chains);
\r
3504 seqs = (SequenceI[]) sqch[0];
\r
3505 chains = (String[]) sqch[1];
\r
3506 if (seqs == null || seqs.length == 0)
\r
3509 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
\r
3511 if (protocol == null || protocol.trim().length() == 0
\r
3512 || protocol.equals("null"))
\r
3514 protocol = (String) pdb.getProperty().get("protocol");
\r
3515 if (protocol == null)
\r
3517 System.err.println("Couldn't work out protocol to open structure: "
\r
3522 if (applet.useXtrnalSviewer)
\r
3524 // register the association(s) and quit, don't create any windows.
\r
3525 if (StructureSelectionManager.getStructureSelectionManager(applet).setMapping(seqs, chains, pdb.getFile(), protocol)==null) {
\r
3526 System.err.println("Failed to map "+pdb.getFile()+" ("+protocol+") to any sequences");
\r
3530 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
\r
3532 // can only do alignments with Jmol
\r
3533 // find the last jmol window assigned to this alignment
\r
3534 jalview.appletgui.AppletJmol ajm = null, tajm;
\r
3535 Vector jmols = applet
\r
3536 .getAppletWindow(jalview.appletgui.AppletJmol.class);
\r
3537 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
\r
3539 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
\r
3540 if (tajm.ap.alignFrame == this)
\r
3549 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
\r
3550 // try and add the pdb structure
\r
3555 // otherwise, create a new window
\r
3556 if (applet.jmolAvailable)
\r
3558 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
\r
3560 applet.lastFrameX += 40;
\r
3561 applet.lastFrameY += 40;
\r
3565 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
\r
3570 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
\r
3571 SequenceI[][] seqs, String[][] chains, String[] protocols)
\r
3573 // TODO Auto-generated method stub
\r
3574 System.err.println("Aligned Structure View: Not yet implemented.");
\r
3578 * modify the current selection, providing the user has not made a selection already.
\r
3579 * @param sel - sequences from this alignment
\r
3580 * @param csel - columns to be selected on the alignment
\r
3582 public void select(SequenceGroup sel, ColumnSelection csel)
\r
3584 alignPanel.seqPanel.selection(sel, csel, null);
\r
3587 public void scrollTo(int row, int column)
\r
3589 alignPanel.seqPanel.scrollTo(row, column);
\r
3591 public void scrollToRow(int row)
\r
3593 alignPanel.seqPanel.scrollToRow(row);
\r
3595 public void scrollToColumn(int column)
\r
3597 alignPanel.seqPanel.scrollToColumn(column);
\r
3600 * @return the alignments unique ID.
\r
3602 public String getSequenceSetId() {
\r
3603 return viewport.getSequenceSetId();
\r