2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
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3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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5 * This file is part of Jalview.
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7 * Jalview is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License
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9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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11 * Jalview is distributed in the hope that it will be useful, but
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12 * WITHOUT ANY WARRANTY; without even the implied warranty
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13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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14 * PURPOSE. See the GNU General Public License for more details.
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16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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18 package jalview.appletgui;
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24 import java.awt.event.*;
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26 import jalview.analysis.*;
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27 import jalview.api.SequenceStructureBinding;
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28 import jalview.bin.JalviewLite;
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29 import jalview.commands.*;
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30 import jalview.datamodel.*;
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31 import jalview.io.*;
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32 import jalview.schemes.*;
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33 import jalview.structure.StructureSelectionManager;
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35 public class AlignFrame extends EmbmenuFrame implements ActionListener,
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36 ItemListener, KeyListener
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38 public AlignmentPanel alignPanel;
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40 public AlignViewport viewport;
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42 int DEFAULT_WIDTH = 700;
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44 int DEFAULT_HEIGHT = 500;
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46 String jalviewServletURL;
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48 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
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49 String title, boolean embedded)
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54 jalviewServletURL = applet.getParameter("APPLICATION_URL");
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60 } catch (Exception ex)
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62 ex.printStackTrace();
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65 viewport = new AlignViewport(al, applet);
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66 alignPanel = new AlignmentPanel(this, viewport);
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68 viewport.updateConservation(alignPanel);
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69 viewport.updateConsensus(alignPanel);
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71 annotationPanelMenuItem.setState(viewport.showAnnotation);
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72 displayNonconservedMenuItem.setState(viewport.getShowunconserved());
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73 followMouseOverFlag.setState(viewport.getFollowHighlight());
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74 showGroupConsensus.setState(viewport.showGroupConsensus);
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75 showGroupConservation.setState(viewport.showGroupConservation);
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76 showConsensusHistogram.setState(viewport.showConsensusHistogram);
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77 showSequenceLogo.setState(viewport.showSequenceLogo);
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79 seqLimits.setState(viewport.showJVSuffix);
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83 String param = applet.getParameter("sortBy");
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86 if (param.equalsIgnoreCase("Id"))
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88 sortIDMenuItem_actionPerformed();
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90 else if (param.equalsIgnoreCase("Pairwise Identity"))
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92 sortPairwiseMenuItem_actionPerformed();
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94 else if (param.equalsIgnoreCase("Length"))
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96 sortLengthMenuItem_actionPerformed();
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100 param = applet.getParameter("wrap");
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103 if (param.equalsIgnoreCase("true"))
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105 wrapMenuItem.setState(true);
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106 wrapMenuItem_actionPerformed();
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109 param = applet.getParameter("centrecolumnlabels");
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112 centreColumnLabelFlag.setState(true);
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113 centreColumnLabelFlag_stateChanged();
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117 param = applet.getParameter("windowWidth");
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120 int width = Integer.parseInt(param);
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121 DEFAULT_WIDTH = width;
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123 param = applet.getParameter("windowHeight");
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126 int height = Integer.parseInt(param);
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127 DEFAULT_HEIGHT = height;
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129 } catch (Exception ex)
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135 // Some JVMS send keyevents to Top frame or lowest panel,
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136 // Havent worked out why yet. So add to both this frame and seqCanvas for
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138 this.addKeyListener(this);
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139 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
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140 alignPanel.idPanel.idCanvas.addKeyListener(this);
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141 alignPanel.scalePanel.addKeyListener(this);
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142 alignPanel.annotationPanel.addKeyListener(this);
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143 alignPanel.annotationPanelHolder.addKeyListener(this);
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144 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
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145 alignPanel.alabels.addKeyListener(this);
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146 createAlignFrameWindow(embedded, title);
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147 alignPanel.validate();
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148 alignPanel.adjustAnnotationHeight();
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149 alignPanel.paintAlignment(true);
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152 public AlignViewport getAlignViewport()
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157 public SeqCanvas getSeqcanvas()
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159 return alignPanel.seqPanel.seqCanvas;
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169 public void parseFeaturesFile(String file, String type)
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171 Hashtable featureLinks = new Hashtable();
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172 boolean featuresFile = false;
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175 featuresFile = new jalview.io.FeaturesFile(file, type)
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176 .parse(viewport.alignment,
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177 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
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178 featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));
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179 } catch (Exception ex)
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181 ex.printStackTrace();
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186 if (featureLinks.size() > 0)
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188 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
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190 viewport.showSequenceFeatures = true;
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191 sequenceFeatures.setState(true);
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192 if (viewport.featureSettings != null)
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194 viewport.featureSettings.refreshTable();
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196 alignPanel.paintAlignment(true);
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201 public void keyPressed(KeyEvent evt)
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203 if (viewport.cursorMode
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204 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
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205 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
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206 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
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207 && Character.isDigit(evt.getKeyChar()))
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208 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
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210 switch (evt.getKeyCode())
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212 case 27: // escape key
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213 deselectAllSequenceMenuItem_actionPerformed();
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215 alignPanel.alabels.cancelDrag();
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217 case KeyEvent.VK_X:
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218 if (evt.isControlDown() || evt.isMetaDown())
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220 cut_actionPerformed();
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223 case KeyEvent.VK_C:
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224 if (viewport.cursorMode && !evt.isControlDown())
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226 alignPanel.seqPanel.setCursorColumn();
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228 if (evt.isControlDown() || evt.isMetaDown())
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230 copy_actionPerformed();
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233 case KeyEvent.VK_V:
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234 if (evt.isControlDown())
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236 paste(evt.isShiftDown());
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239 case KeyEvent.VK_A:
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240 if (evt.isControlDown() || evt.isMetaDown())
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242 selectAllSequenceMenuItem_actionPerformed();
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245 case KeyEvent.VK_DOWN:
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246 if (viewport.cursorMode)
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248 alignPanel.seqPanel.moveCursor(0, 1);
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252 moveSelectedSequences(false);
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256 case KeyEvent.VK_UP:
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257 if (viewport.cursorMode)
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259 alignPanel.seqPanel.moveCursor(0, -1);
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263 moveSelectedSequences(true);
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267 case KeyEvent.VK_LEFT:
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268 if (evt.isAltDown() || !viewport.cursorMode)
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269 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
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271 alignPanel.seqPanel.moveCursor(-1, 0);
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274 case KeyEvent.VK_RIGHT:
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275 if (evt.isAltDown() || !viewport.cursorMode)
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276 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
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278 alignPanel.seqPanel.moveCursor(1, 0);
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281 case KeyEvent.VK_SPACE:
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282 if (viewport.cursorMode)
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284 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
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285 || evt.isShiftDown() || evt.isAltDown());
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289 case KeyEvent.VK_DELETE:
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290 case KeyEvent.VK_BACK_SPACE:
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291 if (viewport.cursorMode)
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293 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
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294 || evt.isShiftDown() || evt.isAltDown());
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298 cut_actionPerformed();
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299 alignPanel.seqPanel.seqCanvas.repaint();
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303 case KeyEvent.VK_S:
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304 if (viewport.cursorMode)
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306 alignPanel.seqPanel.setCursorRow();
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309 case KeyEvent.VK_P:
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310 if (viewport.cursorMode)
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312 alignPanel.seqPanel.setCursorPosition();
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316 case KeyEvent.VK_ENTER:
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317 case KeyEvent.VK_COMMA:
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318 if (viewport.cursorMode)
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320 alignPanel.seqPanel.setCursorRowAndColumn();
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324 case KeyEvent.VK_Q:
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325 if (viewport.cursorMode)
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327 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
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330 case KeyEvent.VK_M:
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331 if (viewport.cursorMode)
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333 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
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337 case KeyEvent.VK_F2:
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338 viewport.cursorMode = !viewport.cursorMode;
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339 statusBar.setText("Keyboard editing mode is "
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340 + (viewport.cursorMode ? "on" : "off"));
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341 if (viewport.cursorMode)
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343 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
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344 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
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348 case KeyEvent.VK_F:
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349 if (evt.isControlDown())
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351 findMenuItem_actionPerformed();
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355 case KeyEvent.VK_H:
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357 boolean toggleSeqs = !evt.isControlDown();
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358 boolean toggleCols = !evt.isShiftDown();
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359 toggleHiddenRegions(toggleSeqs, toggleCols);
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363 case KeyEvent.VK_PAGE_UP:
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364 if (viewport.wrapAlignment)
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366 alignPanel.scrollUp(true);
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370 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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371 - viewport.endSeq + viewport.startSeq);
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375 case KeyEvent.VK_PAGE_DOWN:
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376 if (viewport.wrapAlignment)
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378 alignPanel.scrollUp(false);
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382 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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383 + viewport.endSeq - viewport.startSeq);
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387 case KeyEvent.VK_Z:
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388 if (evt.isControlDown())
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390 undoMenuItem_actionPerformed();
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394 case KeyEvent.VK_Y:
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395 if (evt.isControlDown())
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397 redoMenuItem_actionPerformed();
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401 case KeyEvent.VK_L:
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402 if (evt.isControlDown())
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404 trimAlignment(true);
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408 case KeyEvent.VK_R:
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409 if (evt.isControlDown())
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411 trimAlignment(false);
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415 case KeyEvent.VK_E:
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416 if (evt.isControlDown())
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418 if (evt.isShiftDown())
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420 this.removeAllGapsMenuItem_actionPerformed();
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424 removeGappedColumnMenuItem_actionPerformed();
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428 case KeyEvent.VK_I:
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429 if (evt.isControlDown())
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431 if (evt.isAltDown())
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433 invertColSel_actionPerformed();
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437 invertSequenceMenuItem_actionPerformed();
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442 case KeyEvent.VK_U:
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443 if (evt.isControlDown())
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445 this.deleteGroups_actionPerformed();
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449 case KeyEvent.VK_T:
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450 if (evt.isControlDown())
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457 alignPanel.paintAlignment(true);
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461 * called by key handler and the hide all/show all menu items
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463 * @param toggleSeqs
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464 * @param toggleCols
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466 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
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468 boolean hide = false;
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469 SequenceGroup sg = viewport.getSelectionGroup();
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470 if (!toggleSeqs && !toggleCols)
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472 // Hide everything by the current selection - this is a hack - we do the
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473 // invert and then hide
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474 // first check that there will be visible columns after the invert.
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475 if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
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476 .getSelected().size() > 0)
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477 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
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480 // now invert the sequence set, if required - empty selection implies
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481 // that no hiding is required.
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484 invertSequenceMenuItem_actionPerformed();
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485 sg = viewport.getSelectionGroup();
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489 viewport.expandColSelection(sg, true);
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490 // finally invert the column selection and get the new sequence
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491 // selection and indicate it should be hidden.
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492 invertColSel_actionPerformed();
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499 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
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502 viewport.hideAllSelectedSeqs();
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504 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
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506 viewport.showAllHiddenSeqs();
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512 if (viewport.colSel.getSelected().size() > 0)
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514 viewport.hideSelectedColumns();
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517 viewport.selectionGroup = sg;
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522 viewport.showAllHiddenColumns();
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527 public void keyReleased(KeyEvent evt)
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531 public void keyTyped(KeyEvent evt)
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535 public void itemStateChanged(ItemEvent evt)
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537 if (evt.getSource() == displayNonconservedMenuItem)
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539 displayNonconservedMenuItem_actionPerformed();
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541 else if (evt.getSource() == colourTextMenuItem)
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543 colourTextMenuItem_actionPerformed();
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545 else if (evt.getSource() == wrapMenuItem)
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547 wrapMenuItem_actionPerformed();
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549 else if (evt.getSource() == scaleAbove)
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551 viewport.setScaleAboveWrapped(scaleAbove.getState());
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553 else if (evt.getSource() == scaleLeft)
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555 viewport.setScaleLeftWrapped(scaleLeft.getState());
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557 else if (evt.getSource() == scaleRight)
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559 viewport.setScaleRightWrapped(scaleRight.getState());
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561 else if (evt.getSource() == seqLimits)
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563 seqLimits_itemStateChanged();
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565 else if (evt.getSource() == viewBoxesMenuItem)
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567 viewport.setShowBoxes(viewBoxesMenuItem.getState());
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569 else if (evt.getSource() == viewTextMenuItem)
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571 viewport.setShowText(viewTextMenuItem.getState());
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573 else if (evt.getSource() == renderGapsMenuItem)
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575 viewport.setRenderGaps(renderGapsMenuItem.getState());
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577 else if (evt.getSource() == annotationPanelMenuItem)
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579 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
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580 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
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582 else if (evt.getSource() == sequenceFeatures)
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584 viewport.showSequenceFeatures(sequenceFeatures.getState());
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585 alignPanel.seqPanel.seqCanvas.repaint();
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587 else if (evt.getSource() == conservationMenuItem)
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589 conservationMenuItem_actionPerformed();
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591 else if (evt.getSource() == abovePIDThreshold)
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593 abovePIDThreshold_actionPerformed();
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595 else if (evt.getSource() == applyToAllGroups)
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597 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
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599 else if (evt.getSource() == autoCalculate)
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601 viewport.autocalculateConsensus = autoCalculate.getState();
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603 else if (evt.getSource() == this.centreColumnLabelFlag)
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605 centreColumnLabelFlag_stateChanged();
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607 else if (evt.getSource() == this.followMouseOverFlag)
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609 mouseOverFlag_stateChanged();
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611 else if (evt.getSource() == showGroupConsensus)
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613 showGroupConsensus_actionPerformed();
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615 else if (evt.getSource() == showGroupConservation)
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617 showGroupConservation_actionPerformed();
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619 else if (evt.getSource() == showSequenceLogo)
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621 showSequenceLogo_actionPerformed();
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623 else if (evt.getSource() == showConsensusHistogram)
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625 showConsensusHistogram_actionPerformed();
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627 else if (evt.getSource() == applyAutoAnnotationSettings)
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629 applyAutoAnnotationSettings_actionPerformed();
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631 alignPanel.paintAlignment(true);
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634 private void mouseOverFlag_stateChanged()
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636 viewport.followHighlight = followMouseOverFlag.getState();
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637 // TODO: could kick the scrollTo mechanism to reset view for current
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641 private void centreColumnLabelFlag_stateChanged()
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643 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
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644 this.alignPanel.annotationPanel.repaint();
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647 public void actionPerformed(ActionEvent evt)
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649 Object source = evt.getSource();
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651 if (source == inputText)
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653 inputText_actionPerformed();
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655 else if (source == loadTree)
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657 loadTree_actionPerformed();
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659 else if (source == loadApplication)
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661 launchFullApplication();
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663 else if (source == loadAnnotations)
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667 else if (source == outputAnnotations)
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669 outputAnnotations(true);
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671 else if (source == outputFeatures)
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673 outputFeatures(true, "Jalview");
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675 else if (source == closeMenuItem)
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677 closeMenuItem_actionPerformed();
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679 else if (source == copy)
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681 copy_actionPerformed();
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683 else if (source == undoMenuItem)
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685 undoMenuItem_actionPerformed();
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687 else if (source == redoMenuItem)
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689 redoMenuItem_actionPerformed();
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691 else if (source == inputText)
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693 inputText_actionPerformed();
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695 else if (source == closeMenuItem)
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697 closeMenuItem_actionPerformed();
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699 else if (source == undoMenuItem)
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701 undoMenuItem_actionPerformed();
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703 else if (source == redoMenuItem)
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705 redoMenuItem_actionPerformed();
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707 else if (source == copy)
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709 copy_actionPerformed();
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711 else if (source == pasteNew)
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713 pasteNew_actionPerformed();
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715 else if (source == pasteThis)
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717 pasteThis_actionPerformed();
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719 else if (source == cut)
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721 cut_actionPerformed();
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723 else if (source == delete)
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725 delete_actionPerformed();
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727 else if (source == grpsFromSelection)
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729 makeGrpsFromSelection_actionPerformed();
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731 else if (source == deleteGroups)
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733 deleteGroups_actionPerformed();
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735 else if (source == selectAllSequenceMenuItem)
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737 selectAllSequenceMenuItem_actionPerformed();
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739 else if (source == deselectAllSequenceMenuItem)
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741 deselectAllSequenceMenuItem_actionPerformed();
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743 else if (source == invertSequenceMenuItem)
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745 invertSequenceMenuItem_actionPerformed();
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747 else if (source == invertColSel)
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749 viewport.invertColumnSelection();
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750 alignPanel.paintAlignment(true);
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752 else if (source == remove2LeftMenuItem)
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754 trimAlignment(true);
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756 else if (source == remove2RightMenuItem)
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758 trimAlignment(false);
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760 else if (source == removeGappedColumnMenuItem)
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762 removeGappedColumnMenuItem_actionPerformed();
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764 else if (source == removeAllGapsMenuItem)
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766 removeAllGapsMenuItem_actionPerformed();
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768 else if (source == findMenuItem)
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770 findMenuItem_actionPerformed();
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772 else if (source == font)
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774 new FontChooser(alignPanel);
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776 else if (source == newView)
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780 else if (source == showColumns)
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782 viewport.showAllHiddenColumns();
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783 alignPanel.paintAlignment(true);
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785 else if (source == showSeqs)
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787 viewport.showAllHiddenSeqs();
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788 alignPanel.paintAlignment(true);
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790 else if (source == hideColumns)
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792 viewport.hideSelectedColumns();
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793 alignPanel.paintAlignment(true);
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795 else if (source == hideSequences
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796 && viewport.getSelectionGroup() != null)
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798 viewport.hideAllSelectedSeqs();
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799 alignPanel.paintAlignment(true);
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801 else if (source == hideAllButSelection)
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803 toggleHiddenRegions(false, false);
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804 alignPanel.paintAlignment(true);
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806 else if (source == hideAllSelection)
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808 SequenceGroup sg = viewport.getSelectionGroup();
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809 viewport.expandColSelection(sg, false);
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810 viewport.hideAllSelectedSeqs();
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811 viewport.hideSelectedColumns();
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812 alignPanel.paintAlignment(true);
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814 else if (source == showAllHidden)
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816 viewport.showAllHiddenColumns();
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817 viewport.showAllHiddenSeqs();
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818 alignPanel.paintAlignment(true);
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820 else if (source == showGroupConsensus)
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822 showGroupConsensus_actionPerformed();
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824 else if (source == showGroupConservation)
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826 showGroupConservation_actionPerformed();
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828 else if (source == showSequenceLogo)
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830 showSequenceLogo_actionPerformed();
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832 else if (source == showConsensusHistogram)
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834 showConsensusHistogram_actionPerformed();
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836 else if (source == applyAutoAnnotationSettings)
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838 applyAutoAnnotationSettings_actionPerformed();
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840 else if (source == featureSettings)
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842 new FeatureSettings(alignPanel);
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844 else if (source == alProperties)
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846 StringBuffer contents = new jalview.io.AlignmentProperties(
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847 viewport.alignment).formatAsString();
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848 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
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849 cap.setText(contents.toString());
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850 Frame frame = new Frame();
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852 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
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853 + getTitle(), 400, 250);
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855 else if (source == overviewMenuItem)
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857 overviewMenuItem_actionPerformed();
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859 else if (source == noColourmenuItem)
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861 changeColour(null);
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863 else if (source == clustalColour)
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865 abovePIDThreshold.setState(false);
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866 changeColour(new ClustalxColourScheme(
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867 viewport.alignment.getSequences(),
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868 viewport.alignment.getWidth()));
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870 else if (source == zappoColour)
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872 changeColour(new ZappoColourScheme());
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874 else if (source == taylorColour)
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876 changeColour(new TaylorColourScheme());
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878 else if (source == hydrophobicityColour)
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880 changeColour(new HydrophobicColourScheme());
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882 else if (source == helixColour)
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884 changeColour(new HelixColourScheme());
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886 else if (source == strandColour)
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888 changeColour(new StrandColourScheme());
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890 else if (source == turnColour)
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892 changeColour(new TurnColourScheme());
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894 else if (source == buriedColour)
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896 changeColour(new BuriedColourScheme());
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898 else if (source == nucleotideColour)
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900 changeColour(new NucleotideColourScheme());
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902 else if (source == modifyPID)
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904 modifyPID_actionPerformed();
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906 else if (source == modifyConservation)
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908 modifyConservation_actionPerformed();
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910 else if (source == userDefinedColour)
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912 new UserDefinedColours(alignPanel, null);
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914 else if (source == PIDColour)
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916 changeColour(new PIDColourScheme());
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918 else if (source == BLOSUM62Colour)
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920 changeColour(new Blosum62ColourScheme());
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922 else if (source == annotationColour)
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924 new AnnotationColourChooser(viewport, alignPanel);
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926 else if (source == sortPairwiseMenuItem)
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928 sortPairwiseMenuItem_actionPerformed();
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930 else if (source == sortIDMenuItem)
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932 sortIDMenuItem_actionPerformed();
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934 else if (source == sortLengthMenuItem)
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936 sortLengthMenuItem_actionPerformed();
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938 else if (source == sortGroupMenuItem)
\r
940 sortGroupMenuItem_actionPerformed();
\r
942 else if (source == removeRedundancyMenuItem)
\r
944 removeRedundancyMenuItem_actionPerformed();
\r
946 else if (source == pairwiseAlignmentMenuItem)
\r
948 pairwiseAlignmentMenuItem_actionPerformed();
\r
950 else if (source == PCAMenuItem)
\r
952 PCAMenuItem_actionPerformed();
\r
954 else if (source == averageDistanceTreeMenuItem)
\r
956 averageDistanceTreeMenuItem_actionPerformed();
\r
958 else if (source == neighbourTreeMenuItem)
\r
960 neighbourTreeMenuItem_actionPerformed();
\r
962 else if (source == njTreeBlosumMenuItem)
\r
964 njTreeBlosumMenuItem_actionPerformed();
\r
966 else if (source == avDistanceTreeBlosumMenuItem)
\r
968 avTreeBlosumMenuItem_actionPerformed();
\r
970 else if (source == documentation)
\r
972 documentation_actionPerformed();
\r
974 else if (source == about)
\r
976 about_actionPerformed();
\r
981 public void inputText_actionPerformed()
\r
983 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
984 Frame frame = new Frame();
\r
986 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
\r
989 protected void outputText_actionPerformed(ActionEvent e)
\r
991 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
992 Frame frame = new Frame();
\r
994 jalview.bin.JalviewLite.addFrame(frame,
\r
995 "Alignment output - " + e.getActionCommand(), 600, 500);
\r
996 cap.setText(new AppletFormatAdapter().formatSequences(
\r
997 e.getActionCommand(), viewport.getAlignment(),
\r
998 viewport.showJVSuffix));
\r
1001 public void loadAnnotations()
\r
1003 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1004 cap.setText("Paste your features / annotations file here.");
\r
1005 cap.setAnnotationImport();
\r
1006 Frame frame = new Frame();
\r
1008 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
\r
1012 public String outputAnnotations(boolean displayTextbox)
\r
1014 String annotation = new AnnotationFile().printAnnotations(
\r
1015 viewport.showAnnotation ? viewport.alignment
\r
1016 .getAlignmentAnnotation() : null, viewport.alignment
\r
1018 ((Alignment) viewport.alignment).alignmentProperties);
\r
1020 if (displayTextbox)
\r
1022 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
1023 Frame frame = new Frame();
\r
1025 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
\r
1026 cap.setText(annotation);
\r
1029 return annotation;
\r
1032 private Hashtable getDisplayedFeatureCols()
\r
1034 if (alignPanel.getFeatureRenderer() != null)
\r
1036 FeatureRenderer fr = alignPanel.getFeatureRenderer();
\r
1037 Hashtable fcols = new Hashtable();
\r
1038 Enumeration en = viewport.featuresDisplayed.keys();
\r
1039 while (en.hasMoreElements())
\r
1041 Object col = en.nextElement();
\r
1042 fcols.put(col, fr.featureColours.get(col));
\r
1049 public String outputFeatures(boolean displayTextbox, String format)
\r
1052 if (format.equalsIgnoreCase("Jalview"))
\r
1054 features = new FeaturesFile().printJalviewFormat(
\r
1055 viewport.alignment.getSequencesArray(),
\r
1056 getDisplayedFeatureCols());
\r
1060 features = new FeaturesFile().printGFFFormat(
\r
1061 viewport.alignment.getSequencesArray(),
\r
1062 getDisplayedFeatureCols());
\r
1065 if (displayTextbox)
\r
1067 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
1068 Frame frame = new Frame();
\r
1070 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
\r
1072 cap.setText(features);
\r
1078 void launchFullApplication()
\r
1080 StringBuffer url = new StringBuffer(jalviewServletURL);
\r
1082 url.append("?open="
\r
1083 + appendProtocol(viewport.applet.getParameter("file")));
\r
1085 if (viewport.applet.getParameter("features") != null)
\r
1087 url.append("&features=");
\r
1088 url.append(appendProtocol(viewport.applet.getParameter("features")));
\r
1091 if (viewport.applet.getParameter("annotations") != null)
\r
1093 url.append("&annotations=");
\r
1094 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
\r
1097 if (viewport.applet.getParameter("jnetfile") != null)
\r
1099 url.append("&annotations=");
\r
1100 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
\r
1103 if (viewport.applet.getParameter("defaultColour") != null)
\r
1105 url.append("&colour="
\r
1106 + removeWhiteSpace(viewport.applet
\r
1107 .getParameter("defaultColour")));
\r
1110 if (viewport.applet.getParameter("userDefinedColour") != null)
\r
1112 url.append("&colour="
\r
1113 + removeWhiteSpace(viewport.applet
\r
1114 .getParameter("userDefinedColour")));
\r
1116 if (viewport.applet.getParameter("tree") != null)
\r
1118 url.append("&tree="
\r
1119 + appendProtocol(viewport.applet.getParameter("tree")));
\r
1121 if (viewport.applet.getParameter("treeFile") != null)
\r
1123 url.append("&tree="
\r
1124 + appendProtocol(viewport.applet.getParameter("treeFile")));
\r
1127 showURL(url.toString(), "FULL_APP");
\r
1130 String removeWhiteSpace(String colour)
\r
1132 StringBuffer sb = new StringBuffer();
\r
1133 for (int i = 0; i < colour.length(); i++)
\r
1135 if (Character.isWhitespace(colour.charAt(i)))
\r
1141 sb.append(colour.charAt(i));
\r
1145 return sb.toString();
\r
1148 String appendProtocol(String url)
\r
1153 url = URLEncoder.encode(url);
\r
1156 * When we finally deprecate 1.1 compatibility, we can start to use
\r
1157 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
\r
1158 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
\r
1159 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
\r
1160 * ex.printStackTrace(); }
\r
1162 catch (java.net.MalformedURLException ex)
\r
1164 url = viewport.applet.getCodeBase() + url;
\r
1169 public void closeMenuItem_actionPerformed()
\r
1171 PaintRefresher.RemoveComponent(alignPanel);
\r
1172 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
\r
1173 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
\r
1175 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
\r
1181 alignPanel = null;
\r
1188 void updateEditMenuBar()
\r
1191 if (viewport.historyList.size() > 0)
\r
1193 undoMenuItem.setEnabled(true);
\r
1194 CommandI command = (CommandI) viewport.historyList.peek();
\r
1195 undoMenuItem.setLabel("Undo " + command.getDescription());
\r
1199 undoMenuItem.setEnabled(false);
\r
1200 undoMenuItem.setLabel("Undo");
\r
1203 if (viewport.redoList.size() > 0)
\r
1205 redoMenuItem.setEnabled(true);
\r
1207 CommandI command = (CommandI) viewport.redoList.peek();
\r
1208 redoMenuItem.setLabel("Redo " + command.getDescription());
\r
1212 redoMenuItem.setEnabled(false);
\r
1213 redoMenuItem.setLabel("Redo");
\r
1217 public void addHistoryItem(CommandI command)
\r
1219 if (command.getSize() > 0)
\r
1221 viewport.historyList.push(command);
\r
1222 viewport.redoList.removeAllElements();
\r
1223 updateEditMenuBar();
\r
1224 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
1234 protected void undoMenuItem_actionPerformed()
\r
1236 if (viewport.historyList.size() < 1)
\r
1241 CommandI command = (CommandI) viewport.historyList.pop();
\r
1242 viewport.redoList.push(command);
\r
1243 command.undoCommand(null);
\r
1245 AlignViewport originalSource = getOriginatingSource(command);
\r
1247 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
1248 updateEditMenuBar();
\r
1249 originalSource.firePropertyChange("alignment", null,
\r
1250 originalSource.alignment.getSequences());
\r
1259 protected void redoMenuItem_actionPerformed()
\r
1261 if (viewport.redoList.size() < 1)
\r
1266 CommandI command = (CommandI) viewport.redoList.pop();
\r
1267 viewport.historyList.push(command);
\r
1268 command.doCommand(null);
\r
1270 AlignViewport originalSource = getOriginatingSource(command);
\r
1271 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
1273 updateEditMenuBar();
\r
1274 originalSource.firePropertyChange("alignment", null,
\r
1275 originalSource.alignment.getSequences());
\r
1278 AlignViewport getOriginatingSource(CommandI command)
\r
1280 AlignViewport originalSource = null;
\r
1281 // For sequence removal and addition, we need to fire
\r
1282 // the property change event FROM the viewport where the
\r
1283 // original alignment was altered
\r
1284 AlignmentI al = null;
\r
1285 if (command instanceof EditCommand)
\r
1287 EditCommand editCommand = (EditCommand) command;
\r
1288 al = editCommand.getAlignment();
\r
1289 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
1290 .getSequenceSetId());
\r
1291 for (int i = 0; i < comps.size(); i++)
\r
1293 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
1295 if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
\r
1297 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
\r
1304 if (originalSource == null)
\r
1306 // The original view is closed, we must validate
\r
1307 // the current view against the closed view first
\r
1310 PaintRefresher.validateSequences(al, viewport.alignment);
\r
1313 originalSource = viewport;
\r
1316 return originalSource;
\r
1319 public void moveSelectedSequences(boolean up)
\r
1321 SequenceGroup sg = viewport.getSelectionGroup();
\r
1329 for (int i = 1; i < viewport.alignment.getHeight(); i++)
\r
1331 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
1332 if (!sg.getSequences(null).contains(seq))
\r
1337 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
\r
1338 if (sg.getSequences(null).contains(temp))
\r
1343 viewport.alignment.getSequences().setElementAt(temp, i);
\r
1344 viewport.alignment.getSequences().setElementAt(seq, i - 1);
\r
1349 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
\r
1351 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
1352 if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))
\r
1357 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
\r
1358 if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))
\r
1363 viewport.alignment.getSequences().setElementAt(temp, i);
\r
1364 viewport.alignment.getSequences().setElementAt(seq, i + 1);
\r
1368 alignPanel.paintAlignment(true);
\r
1371 synchronized void slideSequences(boolean right, int size)
\r
1373 Vector sg = new Vector();
\r
1374 if (viewport.cursorMode)
\r
1376 sg.addElement(viewport.alignment
\r
1377 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
\r
1379 else if (viewport.getSelectionGroup() != null
\r
1380 && viewport.getSelectionGroup().getSize() != viewport.alignment
\r
1383 sg = viewport.getSelectionGroup().getSequences(
\r
1384 viewport.hiddenRepSequences);
\r
1387 if (sg.size() < 1)
\r
1392 Vector invertGroup = new Vector();
\r
1394 for (int i = 0; i < viewport.alignment.getHeight(); i++)
\r
1396 if (!sg.contains(viewport.alignment.getSequenceAt(i)))
\r
1397 invertGroup.addElement(viewport.alignment.getSequenceAt(i));
\r
1400 SequenceI[] seqs1 = new SequenceI[sg.size()];
\r
1401 for (int i = 0; i < sg.size(); i++)
\r
1402 seqs1[i] = (SequenceI) sg.elementAt(i);
\r
1404 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
\r
1405 for (int i = 0; i < invertGroup.size(); i++)
\r
1406 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
\r
1408 SlideSequencesCommand ssc;
\r
1410 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
\r
1411 size, viewport.getGapCharacter());
\r
1413 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
\r
1414 size, viewport.getGapCharacter());
\r
1416 int groupAdjustment = 0;
\r
1417 if (ssc.getGapsInsertedBegin() && right)
\r
1419 if (viewport.cursorMode)
\r
1420 alignPanel.seqPanel.moveCursor(size, 0);
\r
1422 groupAdjustment = size;
\r
1424 else if (!ssc.getGapsInsertedBegin() && !right)
\r
1426 if (viewport.cursorMode)
\r
1427 alignPanel.seqPanel.moveCursor(-size, 0);
\r
1429 groupAdjustment = -size;
\r
1432 if (groupAdjustment != 0)
\r
1434 viewport.getSelectionGroup().setStartRes(
\r
1435 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
\r
1436 viewport.getSelectionGroup().setEndRes(
\r
1437 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
\r
1440 boolean appendHistoryItem = false;
\r
1441 if (viewport.historyList != null && viewport.historyList.size() > 0
\r
1442 && viewport.historyList.peek() instanceof SlideSequencesCommand)
\r
1444 appendHistoryItem = ssc
\r
1445 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
\r
1449 if (!appendHistoryItem)
\r
1450 addHistoryItem(ssc);
\r
1455 static StringBuffer copiedSequences;
\r
1457 static Vector copiedHiddenColumns;
\r
1459 protected void copy_actionPerformed()
\r
1461 if (viewport.getSelectionGroup() == null)
\r
1466 SequenceGroup sg = viewport.getSelectionGroup();
\r
1467 copiedSequences = new StringBuffer();
\r
1468 Hashtable orderedSeqs = new Hashtable();
\r
1469 for (int i = 0; i < sg.getSize(); i++)
\r
1471 SequenceI seq = sg.getSequenceAt(i);
\r
1472 int index = viewport.alignment.findIndex(seq);
\r
1473 orderedSeqs.put(index + "", seq);
\r
1476 int index = 0, startRes, endRes;
\r
1479 if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
\r
1481 copiedHiddenColumns = new Vector();
\r
1482 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
\r
1483 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
\r
1486 int[] region = (int[]) viewport.getColumnSelection()
\r
1487 .getHiddenColumns().elementAt(i);
\r
1489 copiedHiddenColumns.addElement(new int[]
\r
1490 { region[0] - hiddenOffset, region[1] - hiddenOffset });
\r
1495 copiedHiddenColumns = null;
\r
1498 for (int i = 0; i < sg.getSize(); i++)
\r
1500 SequenceI seq = null;
\r
1502 while (seq == null)
\r
1504 if (orderedSeqs.containsKey(index + ""))
\r
1506 seq = (SequenceI) orderedSeqs.get(index + "");
\r
1518 // Returns residue following index if gap
\r
1519 startRes = seq.findPosition(sg.getStartRes());
\r
1522 // Need to find the residue preceeding index if gap
\r
1525 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
\r
1527 ch = seq.getCharAt(j);
\r
1528 if (!jalview.util.Comparison.isGap((ch)))
\r
1536 endRes += seq.getStart() - 1;
\r
1539 copiedSequences.append(seq.getName()
\r
1545 + seq.getSequenceAsString(sg.getStartRes(),
\r
1546 sg.getEndRes() + 1) + "\n");
\r
1551 protected void pasteNew_actionPerformed()
\r
1556 protected void pasteThis_actionPerformed()
\r
1561 void paste(boolean newAlignment)
\r
1566 if (copiedSequences == null)
\r
1571 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
1572 Vector seqs = new Vector();
\r
1573 while (st.hasMoreElements())
\r
1575 String name = st.nextToken();
\r
1576 int start = Integer.parseInt(st.nextToken());
\r
1577 int end = Integer.parseInt(st.nextToken());
\r
1578 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
\r
1580 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
1581 for (int i = 0; i < seqs.size(); i++)
\r
1583 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
1588 String newtitle = new String("Copied sequences");
\r
1589 if (getTitle().startsWith("Copied sequences"))
\r
1591 newtitle = getTitle();
\r
1595 newtitle = newtitle.concat("- from " + getTitle());
\r
1597 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
1598 viewport.applet, newtitle, false);
\r
1599 if (copiedHiddenColumns != null)
\r
1601 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
1603 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
1604 af.viewport.hideColumns(region[0], region[1]);
\r
1608 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
\r
1613 addSequences(newSeqs);
\r
1616 } catch (Exception ex)
\r
1618 } // could be anything being pasted in here
\r
1622 void addSequences(SequenceI[] seqs)
\r
1624 for (int i = 0; i < seqs.length; i++)
\r
1626 viewport.alignment.addSequence(seqs[i]);
\r
1630 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
\r
1631 seqs, 0, viewport.alignment.getWidth(), viewport.alignment));
\r
1633 viewport.setEndSeq(viewport.alignment.getHeight());
\r
1634 viewport.alignment.getWidth();
\r
1635 viewport.firePropertyChange("alignment", null,
\r
1636 viewport.alignment.getSequences());
\r
1640 protected void cut_actionPerformed()
\r
1642 copy_actionPerformed();
\r
1643 delete_actionPerformed();
\r
1646 protected void delete_actionPerformed()
\r
1649 SequenceGroup sg = viewport.getSelectionGroup();
\r
1655 Vector seqs = new Vector();
\r
1657 for (int i = 0; i < sg.getSize(); i++)
\r
1659 seq = sg.getSequenceAt(i);
\r
1660 seqs.addElement(seq);
\r
1663 // If the cut affects all sequences, remove highlighted columns
\r
1664 if (sg.getSize() == viewport.alignment.getHeight())
\r
1666 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
1667 sg.getEndRes() + 1);
\r
1670 SequenceI[] cut = new SequenceI[seqs.size()];
\r
1671 for (int i = 0; i < seqs.size(); i++)
\r
1673 cut[i] = (SequenceI) seqs.elementAt(i);
\r
1677 * //ADD HISTORY ITEM
\r
1679 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
\r
1680 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
\r
1681 viewport.alignment));
\r
1683 viewport.setSelectionGroup(null);
\r
1684 viewport.alignment.deleteGroup(sg);
\r
1686 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1689 if (viewport.getAlignment().getHeight() < 1)
\r
1691 this.setVisible(false);
\r
1693 viewport.sendSelection();
\r
1697 * group consensus toggled
\r
1700 protected void showGroupConsensus_actionPerformed()
\r
1702 viewport.setShowGroupConsensus(showGroupConsensus.getState());
\r
1703 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1708 * group conservation toggled.
\r
1710 protected void showGroupConservation_actionPerformed()
\r
1712 viewport.setShowGroupConservation(showGroupConservation.getState());
\r
1713 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1720 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
\r
1721 * .event.ActionEvent)
\r
1723 protected void showConsensusHistogram_actionPerformed()
\r
1725 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
\r
1726 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1732 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
\r
1733 * .event.ActionEvent)
\r
1735 protected void showSequenceLogo_actionPerformed()
\r
1737 viewport.setShowSequenceLogo(showSequenceLogo.getState());
\r
1738 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1741 protected void applyAutoAnnotationSettings_actionPerformed()
\r
1743 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1746 protected void makeGrpsFromSelection_actionPerformed()
\r
1748 if (viewport.getSelectionGroup() != null)
\r
1750 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
\r
1751 viewport.getSequenceSelection(),
\r
1752 viewport.getAlignmentView(true).getSequenceStrings(
\r
1753 viewport.getGapCharacter()),
\r
1754 viewport.alignment.getGroups());
\r
1755 viewport.alignment.deleteAllGroups();
\r
1756 viewport.sequenceColours = null;
\r
1757 viewport.setSelectionGroup(null);
\r
1758 // set view properties for each group
\r
1759 for (int g = 0; g < gps.length; g++)
\r
1761 // gps[g].setShowunconserved(viewport.getShowUnconserved());
\r
1762 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
\r
1763 viewport.alignment.addGroup(gps[g]);
\r
1764 Color col = new Color((int) (Math.random() * 255),
\r
1765 (int) (Math.random() * 255), (int) (Math.random() * 255));
\r
1766 col = col.brighter();
\r
1767 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
\r
1768 .hasMoreElements(); viewport.setSequenceColour(
\r
1769 (SequenceI) sq.nextElement(), col))
\r
1772 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
\r
1773 alignPanel.updateAnnotation();
\r
1774 alignPanel.paintAlignment(true);
\r
1778 protected void deleteGroups_actionPerformed()
\r
1780 viewport.alignment.deleteAllGroups();
\r
1781 viewport.sequenceColours = null;
\r
1782 viewport.setSelectionGroup(null);
\r
1784 alignPanel.paintAlignment(true);
\r
1787 public void selectAllSequenceMenuItem_actionPerformed()
\r
1789 SequenceGroup sg = new SequenceGroup();
\r
1790 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1792 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
1794 sg.setEndRes(viewport.alignment.getWidth() - 1);
\r
1795 viewport.setSelectionGroup(sg);
\r
1796 alignPanel.paintAlignment(true);
\r
1797 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1798 viewport.sendSelection();
\r
1801 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1803 if (viewport.cursorMode)
\r
1805 alignPanel.seqPanel.keyboardNo1 = null;
\r
1806 alignPanel.seqPanel.keyboardNo2 = null;
\r
1808 viewport.setSelectionGroup(null);
\r
1809 viewport.getColumnSelection().clear();
\r
1810 viewport.setSelectionGroup(null);
\r
1811 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1812 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1813 alignPanel.paintAlignment(true);
\r
1814 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1815 viewport.sendSelection();
\r
1818 public void invertSequenceMenuItem_actionPerformed()
\r
1820 SequenceGroup sg = viewport.getSelectionGroup();
\r
1821 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1823 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1826 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1827 viewport.sendSelection();
\r
1830 public void invertColSel_actionPerformed()
\r
1832 viewport.invertColumnSelection();
\r
1833 alignPanel.paintAlignment(true);
\r
1834 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1835 viewport.sendSelection();
\r
1838 void trimAlignment(boolean trimLeft)
\r
1840 ColumnSelection colSel = viewport.getColumnSelection();
\r
1843 if (colSel.size() > 0)
\r
1847 column = colSel.getMin();
\r
1851 column = colSel.getMax();
\r
1855 if (viewport.getSelectionGroup() != null)
\r
1857 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
1858 viewport.hiddenRepSequences);
\r
1862 seqs = viewport.alignment.getSequencesArray();
\r
1865 TrimRegionCommand trimRegion;
\r
1868 trimRegion = new TrimRegionCommand("Remove Left",
\r
1869 TrimRegionCommand.TRIM_LEFT, seqs, column,
\r
1870 viewport.alignment, viewport.colSel,
\r
1871 viewport.selectionGroup);
\r
1872 viewport.setStartRes(0);
\r
1876 trimRegion = new TrimRegionCommand("Remove Right",
\r
1877 TrimRegionCommand.TRIM_RIGHT, seqs, column,
\r
1878 viewport.alignment, viewport.colSel,
\r
1879 viewport.selectionGroup);
\r
1882 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
\r
1884 addHistoryItem(trimRegion);
\r
1886 Vector groups = viewport.alignment.getGroups();
\r
1888 for (int i = 0; i < groups.size(); i++)
\r
1890 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1892 if ((trimLeft && !sg.adjustForRemoveLeft(column))
\r
1893 || (!trimLeft && !sg.adjustForRemoveRight(column)))
\r
1895 viewport.alignment.deleteGroup(sg);
\r
1899 viewport.firePropertyChange("alignment", null, viewport
\r
1900 .getAlignment().getSequences());
\r
1904 public void removeGappedColumnMenuItem_actionPerformed()
\r
1906 int start = 0, end = viewport.alignment.getWidth() - 1;
\r
1909 if (viewport.getSelectionGroup() != null)
\r
1911 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
1912 viewport.hiddenRepSequences);
\r
1913 start = viewport.getSelectionGroup().getStartRes();
\r
1914 end = viewport.getSelectionGroup().getEndRes();
\r
1918 seqs = viewport.alignment.getSequencesArray();
\r
1921 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
\r
1922 "Remove Gapped Columns", seqs, start, end, viewport.alignment);
\r
1924 addHistoryItem(removeGapCols);
\r
1926 statusBar.setText("Removed " + removeGapCols.getSize()
\r
1927 + " empty columns.");
\r
1929 // This is to maintain viewport position on first residue
\r
1930 // of first sequence
\r
1931 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1932 int startRes = seq.findPosition(viewport.startRes);
\r
1933 // ShiftList shifts;
\r
1934 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
\r
1935 // edit.alColumnChanges=shifts.getInverse();
\r
1936 // if (viewport.hasHiddenColumns)
\r
1937 // viewport.getColumnSelection().compensateForEdits(shifts);
\r
1938 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
1939 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1944 public void removeAllGapsMenuItem_actionPerformed()
\r
1946 int start = 0, end = viewport.alignment.getWidth() - 1;
\r
1949 if (viewport.getSelectionGroup() != null)
\r
1951 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
1952 viewport.hiddenRepSequences);
\r
1953 start = viewport.getSelectionGroup().getStartRes();
\r
1954 end = viewport.getSelectionGroup().getEndRes();
\r
1958 seqs = viewport.alignment.getSequencesArray();
\r
1961 // This is to maintain viewport position on first residue
\r
1962 // of first sequence
\r
1963 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1964 int startRes = seq.findPosition(viewport.startRes);
\r
1966 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
\r
1967 viewport.alignment));
\r
1969 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
1971 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1976 public void findMenuItem_actionPerformed()
\r
1978 new Finder(alignPanel);
\r
1982 * create a new view derived from the current view
\r
1984 * @param viewtitle
\r
1985 * @return frame for the new view
\r
1987 public AlignFrame newView(String viewtitle)
\r
1990 if (viewport.hasHiddenRows)
\r
1992 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
\r
1993 .getFullAlignment().getSequencesArray());
\r
1997 newal = new Alignment(viewport.alignment.getSequencesArray());
\r
2000 if (viewport.alignment.getAlignmentAnnotation() != null)
\r
2002 for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)
\r
2004 if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
\r
2006 newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);
\r
2011 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
\r
2013 newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
\r
2014 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
\r
2015 PaintRefresher.Register(newaf.alignPanel,
\r
2016 newaf.alignPanel.av.getSequenceSetId());
\r
2018 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
\r
2019 newaf.alignPanel.av.getSequenceSetId());
\r
2020 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
\r
2021 newaf.alignPanel.av.getSequenceSetId());
\r
2023 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
2024 .getSequenceSetId());
\r
2025 int viewSize = -1;
\r
2026 for (int i = 0; i < comps.size(); i++)
\r
2028 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
2034 String title = new String(this.getTitle());
\r
2035 if (viewtitle != null)
\r
2037 title = viewtitle + " ( " + title + ")";
\r
2041 if (title.indexOf("(View") > -1)
\r
2043 title = title.substring(0, title.indexOf("(View"));
\r
2045 title += "(View " + viewSize + ")";
\r
2048 newaf.setTitle(title.toString());
\r
2050 newaf.viewport.historyList = viewport.historyList;
\r
2051 newaf.viewport.redoList = viewport.redoList;
\r
2057 * @return list of feature groups on the view
\r
2059 public String[] getFeatureGroups()
\r
2061 FeatureRenderer fr = null;
\r
2062 if (alignPanel != null
\r
2063 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2065 return fr.getGroups();
\r
2071 * get sequence feature groups that are hidden or shown
\r
2077 public String[] getFeatureGroupsOfState(boolean visible)
\r
2079 FeatureRenderer fr = null;
\r
2080 if (alignPanel != null
\r
2081 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2083 return fr.getGroups(visible);
\r
2089 * Change the display state for the given feature groups
\r
2092 * list of group strings
\r
2094 * visible or invisible
\r
2096 public void setFeatureGroupState(String[] groups, boolean state)
\r
2098 FeatureRenderer fr = null;
\r
2099 this.sequenceFeatures.setState(true);
\r
2100 viewport.showSequenceFeatures(true);
\r
2101 if (alignPanel != null
\r
2102 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2104 fr.setGroupState(groups, state);
\r
2105 alignPanel.seqPanel.seqCanvas.repaint();
\r
2106 if (alignPanel.overviewPanel != null)
\r
2108 alignPanel.overviewPanel.updateOverviewImage();
\r
2113 public void seqLimits_itemStateChanged()
\r
2115 viewport.setShowJVSuffix(seqLimits.getState());
\r
2116 alignPanel.fontChanged();
\r
2117 alignPanel.paintAlignment(true);
\r
2120 protected void colourTextMenuItem_actionPerformed()
\r
2122 viewport.setColourText(colourTextMenuItem.getState());
\r
2123 alignPanel.paintAlignment(true);
\r
2126 protected void displayNonconservedMenuItem_actionPerformed()
\r
2128 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
\r
2129 alignPanel.paintAlignment(true);
\r
2132 protected void wrapMenuItem_actionPerformed()
\r
2134 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
2135 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
2136 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
2137 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
2138 scaleRight.setEnabled(wrapMenuItem.getState());
\r
2139 alignPanel.paintAlignment(true);
\r
2142 public void overviewMenuItem_actionPerformed()
\r
2144 if (alignPanel.overviewPanel != null)
\r
2149 Frame frame = new Frame();
\r
2150 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
2151 frame.add(overview);
\r
2152 // +50 must allow for applet frame window
\r
2153 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
2154 overview.getPreferredSize().width,
\r
2155 overview.getPreferredSize().height + 50);
\r
2158 frame.addWindowListener(new WindowAdapter()
\r
2160 public void windowClosing(WindowEvent e)
\r
2162 alignPanel.setOverviewPanel(null);
\r
2166 alignPanel.setOverviewPanel(overview);
\r
2170 void changeColour(ColourSchemeI cs)
\r
2172 int threshold = 0;
\r
2176 if (viewport.getAbovePIDThreshold())
\r
2178 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
2181 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2183 viewport.setGlobalColourScheme(cs);
\r
2187 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2190 if (viewport.getConservationSelected())
\r
2193 Alignment al = (Alignment) viewport.alignment;
\r
2194 Conservation c = new Conservation("All",
\r
2195 ResidueProperties.propHash, 3, al.getSequences(), 0,
\r
2196 al.getWidth() - 1);
\r
2199 c.verdict(false, viewport.ConsPercGaps);
\r
2201 cs.setConservation(c);
\r
2203 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
\r
2204 cs, "Background"));
\r
2209 cs.setConservation(null);
\r
2212 cs.setConsensus(viewport.hconsensus);
\r
2215 viewport.setGlobalColourScheme(cs);
\r
2217 if (viewport.getColourAppliesToAllGroups())
\r
2219 Vector groups = viewport.alignment.getGroups();
\r
2220 for (int i = 0; i < groups.size(); i++)
\r
2222 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
2229 if (cs instanceof ClustalxColourScheme)
\r
2231 sg.cs = new ClustalxColourScheme(
\r
2232 sg.getSequences(viewport.hiddenRepSequences),
\r
2239 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
2240 } catch (Exception ex)
\r
2242 ex.printStackTrace();
\r
2247 if (viewport.getAbovePIDThreshold()
\r
2248 || cs instanceof PIDColourScheme
\r
2249 || cs instanceof Blosum62ColourScheme)
\r
2251 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2252 sg.cs.setConsensus(AAFrequency.calculate(
\r
2253 sg.getSequences(viewport.hiddenRepSequences), 0,
\r
2258 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2261 if (viewport.getConservationSelected())
\r
2263 Conservation c = new Conservation("Group",
\r
2264 ResidueProperties.propHash, 3,
\r
2265 sg.getSequences(viewport.hiddenRepSequences), 0,
\r
2266 viewport.alignment.getWidth() - 1);
\r
2268 c.verdict(false, viewport.ConsPercGaps);
\r
2269 sg.cs.setConservation(c);
\r
2273 sg.cs.setConservation(null);
\r
2274 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2280 if (alignPanel.getOverviewPanel() != null)
\r
2282 alignPanel.getOverviewPanel().updateOverviewImage();
\r
2285 jalview.structure.StructureSelectionManager
\r
2286 .getStructureSelectionManager(viewport.applet).sequenceColoursChanged(
\r
2289 alignPanel.paintAlignment(true);
\r
2292 protected void modifyPID_actionPerformed()
\r
2294 if (viewport.getAbovePIDThreshold()
\r
2295 && viewport.globalColourScheme != null)
\r
2297 SliderPanel.setPIDSliderSource(alignPanel,
\r
2298 viewport.getGlobalColourScheme(), "Background");
\r
2299 SliderPanel.showPIDSlider();
\r
2303 protected void modifyConservation_actionPerformed()
\r
2305 if (viewport.getConservationSelected()
\r
2306 && viewport.globalColourScheme != null)
\r
2308 SliderPanel.setConservationSlider(alignPanel,
\r
2309 viewport.globalColourScheme, "Background");
\r
2310 SliderPanel.showConservationSlider();
\r
2314 protected void conservationMenuItem_actionPerformed()
\r
2316 viewport.setConservationSelected(conservationMenuItem.getState());
\r
2318 viewport.setAbovePIDThreshold(false);
\r
2319 abovePIDThreshold.setState(false);
\r
2321 changeColour(viewport.getGlobalColourScheme());
\r
2323 modifyConservation_actionPerformed();
\r
2326 public void abovePIDThreshold_actionPerformed()
\r
2328 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
2330 conservationMenuItem.setState(false);
\r
2331 viewport.setConservationSelected(false);
\r
2333 changeColour(viewport.getGlobalColourScheme());
\r
2335 modifyPID_actionPerformed();
\r
2338 public void sortPairwiseMenuItem_actionPerformed()
\r
2340 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2341 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
\r
2342 .getAlignment().getSequenceAt(0), null);
\r
2344 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
\r
2345 viewport.alignment));
\r
2346 alignPanel.paintAlignment(true);
\r
2349 public void sortIDMenuItem_actionPerformed()
\r
2351 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2352 AlignmentSorter.sortByID(viewport.getAlignment());
\r
2353 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
\r
2354 alignPanel.paintAlignment(true);
\r
2357 public void sortLengthMenuItem_actionPerformed()
\r
2359 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2360 AlignmentSorter.sortByLength(viewport.getAlignment());
\r
2361 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
\r
2362 viewport.alignment));
\r
2363 alignPanel.paintAlignment(true);
\r
2366 public void sortGroupMenuItem_actionPerformed()
\r
2368 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2369 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
2370 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
\r
2371 viewport.alignment));
\r
2372 alignPanel.paintAlignment(true);
\r
2376 public void removeRedundancyMenuItem_actionPerformed()
\r
2378 new RedundancyPanel(alignPanel);
\r
2381 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
2383 if (viewport.getSelectionGroup() != null
\r
2384 && viewport.getSelectionGroup().getSize() > 1)
\r
2386 Frame frame = new Frame();
\r
2387 frame.add(new PairwiseAlignPanel(alignPanel));
\r
2388 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
\r
2393 public void PCAMenuItem_actionPerformed()
\r
2395 // are the sequences aligned?
\r
2396 if (!viewport.alignment.isAligned(false))
\r
2398 SequenceI current;
\r
2399 int Width = viewport.getAlignment().getWidth();
\r
2401 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2403 current = viewport.getAlignment().getSequenceAt(i);
\r
2405 if (current.getLength() < Width)
\r
2407 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2410 alignPanel.paintAlignment(true);
\r
2413 if ((viewport.getSelectionGroup() != null
\r
2414 && viewport.getSelectionGroup().getSize() < 4 && viewport
\r
2415 .getSelectionGroup().getSize() > 0)
\r
2416 || viewport.getAlignment().getHeight() < 4)
\r
2423 new PCAPanel(viewport);
\r
2424 } catch (java.lang.OutOfMemoryError ex)
\r
2430 public void averageDistanceTreeMenuItem_actionPerformed()
\r
2432 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
2435 public void neighbourTreeMenuItem_actionPerformed()
\r
2437 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
2440 protected void njTreeBlosumMenuItem_actionPerformed()
\r
2442 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2445 protected void avTreeBlosumMenuItem_actionPerformed()
\r
2447 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2450 void NewTreePanel(String type, String pwType, String title)
\r
2452 // are the sequences aligned?
\r
2453 if (!viewport.alignment.isAligned(false))
\r
2455 SequenceI current;
\r
2456 int Width = viewport.getAlignment().getWidth();
\r
2458 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2460 current = viewport.getAlignment().getSequenceAt(i);
\r
2462 if (current.getLength() < Width)
\r
2464 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2467 alignPanel.paintAlignment(true);
\r
2471 if ((viewport.getSelectionGroup() != null && viewport
\r
2472 .getSelectionGroup().getSize() > 1)
\r
2473 || (viewport.getSelectionGroup() == null && viewport.alignment
\r
2474 .getHeight() > 1))
\r
2476 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
\r
2478 addTreeMenuItem(tp, title);
\r
2480 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
2484 void loadTree_actionPerformed()
\r
2486 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
2487 cap.setText("Paste your Newick tree file here.");
\r
2488 cap.setTreeImport();
\r
2489 Frame frame = new Frame();
\r
2491 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
2494 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
2496 TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
\r
2497 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
2498 addTreeMenuItem(tp, treeFile);
\r
2502 * sort the alignment using the given treePanel
\r
2504 * @param treePanel
\r
2505 * tree used to sort view
\r
2507 * string used for undo event name
\r
2509 public void sortByTree(TreePanel treePanel, String title)
\r
2511 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2513 .sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
2514 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2515 // HistoryItem.SORT));
\r
2516 addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
\r
2517 viewport.alignment));
\r
2518 alignPanel.paintAlignment(true);
\r
2522 * Do any automatic reordering of the alignment and add the necessary bits to
\r
2523 * the menu structure for the new tree
\r
2525 * @param treePanel
\r
2528 protected void addTreeMenuItem(final TreePanel treePanel,
\r
2529 final String title)
\r
2531 final MenuItem item = new MenuItem(title);
\r
2532 sortByTreeMenu.add(item);
\r
2533 item.addActionListener(new java.awt.event.ActionListener()
\r
2535 public void actionPerformed(ActionEvent evt)
\r
2537 sortByTree(treePanel, title); // treePanel.getTitle());
\r
2541 treePanel.addWindowListener(new WindowAdapter()
\r
2543 public void windowOpened(WindowEvent e)
\r
2545 if (viewport.sortByTree)
\r
2547 sortByTree(treePanel, title);
\r
2549 super.windowOpened(e);
\r
2552 public void windowClosing(WindowEvent e)
\r
2554 sortByTreeMenu.remove(item);
\r
2558 public boolean sortBy(AlignmentOrder alorder, String undoname)
\r
2560 SequenceI[] oldOrder = viewport.getAlignment()
\r
2561 .getSequencesArray();
\r
2562 if (viewport.applet.debug)
\r
2564 System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");
\r
2566 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
\r
2567 if (undoname!=null)
\r
2569 addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.alignment));
\r
2571 alignPanel.paintAlignment(true);
\r
2574 protected void documentation_actionPerformed()
\r
2576 showURL("http://www.jalview.org/help.html", "HELP");
\r
2579 protected void about_actionPerformed()
\r
2582 class AboutPanel extends Canvas
\r
2588 public AboutPanel(String version, String builddate)
\r
2590 this.version = version;
\r
2591 this.builddate = builddate;
\r
2594 public void paint(Graphics g)
\r
2596 g.setColor(Color.white);
\r
2597 g.fillRect(0, 0, getSize().width, getSize().height);
\r
2598 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2599 FontMetrics fm = g.getFontMetrics();
\r
2600 int fh = fm.getHeight();
\r
2602 g.setColor(Color.black);
\r
2603 // TODO: update this text for each release or centrally store it for
\r
2604 // lite and application
\r
2605 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
2606 g.drawString("JalviewLite - Release " + version, x, y += fh);
\r
2607 g.setFont(new Font("Helvetica", Font.BOLD, 12));
\r
2608 g.drawString("Build date: " + builddate, x, y += fh);
\r
2609 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2611 "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",
\r
2612 x, y += fh * 1.5);
\r
2613 g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
\r
2615 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
\r
2618 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
\r
2620 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
\r
2622 "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
\r
2625 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
\r
2627 g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
\r
2632 Frame frame = new Frame();
\r
2633 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
\r
2634 .getBuildDate()));
\r
2635 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
\r
2639 public void showURL(String url, String target)
\r
2641 if (viewport.applet == null)
\r
2643 System.out.println("Not running as applet - no browser available.");
\r
2649 if (url.indexOf(":") == -1)
\r
2651 // TODO: verify (Bas Vroling bug) prepend codebase or server URL to
\r
2653 // Should really use docbase, not codebase.
\r
2654 if (url.indexOf("/") == 0)
\r
2656 String codebase = viewport.applet.getCodeBase().toString();
\r
2657 url = codebase.substring(0, codebase.length()
\r
2658 - viewport.applet.getCodeBase().getFile().length())
\r
2663 url = viewport.applet.getCodeBase() + url;
\r
2665 System.out.println("Show url (prepended codebase): " + url);
\r
2669 System.out.println("Show url: " + url);
\r
2671 if (url.indexOf("javascript:") == 0)
\r
2673 // no target for the javascript context
\r
2674 viewport.applet.getAppletContext().showDocument(
\r
2675 new java.net.URL(url));
\r
2679 viewport.applet.getAppletContext().showDocument(
\r
2680 new java.net.URL(url), target);
\r
2682 } catch (Exception ex)
\r
2684 ex.printStackTrace();
\r
2689 // ////////////////////////////////////////////////////////////////////////////////
\r
2690 // JBuilder Graphics here
\r
2692 MenuBar alignFrameMenuBar = new MenuBar();
\r
2694 Menu fileMenu = new Menu("File");
\r
2696 MenuItem loadApplication = new MenuItem("View in Full Application");
\r
2698 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
\r
2700 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
\r
2702 MenuItem outputFeatures = new MenuItem("Export Features ...");
\r
2704 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
\r
2706 MenuItem closeMenuItem = new MenuItem("Close");
\r
2708 Menu editMenu = new Menu("Edit");
\r
2710 Menu viewMenu = new Menu("View");
\r
2712 Menu colourMenu = new Menu("Colour");
\r
2714 Menu calculateMenu = new Menu("Calculate");
\r
2716 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
2718 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
2720 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
2722 MenuItem remove2LeftMenuItem = new MenuItem();
\r
2724 MenuItem remove2RightMenuItem = new MenuItem();
\r
2726 MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
2728 MenuItem removeAllGapsMenuItem = new MenuItem();
\r
2730 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
2732 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
2734 MenuItem sortPairwiseMenuItem = new MenuItem();
\r
2736 MenuItem sortIDMenuItem = new MenuItem();
\r
2738 MenuItem sortLengthMenuItem = new MenuItem();
\r
2740 MenuItem sortGroupMenuItem = new MenuItem();
\r
2742 MenuItem removeRedundancyMenuItem = new MenuItem();
\r
2744 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
2746 MenuItem PCAMenuItem = new MenuItem();
\r
2748 MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
2750 MenuItem neighbourTreeMenuItem = new MenuItem();
\r
2752 BorderLayout borderLayout1 = new BorderLayout();
\r
2754 public Label statusBar = new Label();
\r
2756 Menu outputTextboxMenu = new Menu();
\r
2758 MenuItem clustalColour = new MenuItem();
\r
2760 MenuItem zappoColour = new MenuItem();
\r
2762 MenuItem taylorColour = new MenuItem();
\r
2764 MenuItem hydrophobicityColour = new MenuItem();
\r
2766 MenuItem helixColour = new MenuItem();
\r
2768 MenuItem strandColour = new MenuItem();
\r
2770 MenuItem turnColour = new MenuItem();
\r
2772 MenuItem buriedColour = new MenuItem();
\r
2774 MenuItem userDefinedColour = new MenuItem();
\r
2776 MenuItem PIDColour = new MenuItem();
\r
2778 MenuItem BLOSUM62Colour = new MenuItem();
\r
2780 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
2782 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
2784 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
2786 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
2788 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
\r
2790 MenuItem alProperties = new MenuItem("Alignment Properties...");
\r
2792 MenuItem overviewMenuItem = new MenuItem();
\r
2794 MenuItem undoMenuItem = new MenuItem();
\r
2796 MenuItem redoMenuItem = new MenuItem();
\r
2798 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
2800 MenuItem noColourmenuItem = new MenuItem();
\r
2802 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
2804 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
2806 MenuItem findMenuItem = new MenuItem();
\r
2808 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
2810 MenuItem nucleotideColour = new MenuItem();
\r
2812 MenuItem deleteGroups = new MenuItem();
\r
2814 MenuItem grpsFromSelection = new MenuItem();
\r
2816 MenuItem delete = new MenuItem();
\r
2818 MenuItem copy = new MenuItem();
\r
2820 MenuItem cut = new MenuItem();
\r
2822 Menu pasteMenu = new Menu();
\r
2824 MenuItem pasteNew = new MenuItem();
\r
2826 MenuItem pasteThis = new MenuItem();
\r
2828 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
2830 MenuItem font = new MenuItem();
\r
2832 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
2834 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
2836 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
2838 MenuItem modifyPID = new MenuItem();
\r
2840 MenuItem modifyConservation = new MenuItem();
\r
2842 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
\r
2843 "Autocalculate Consensus", true);
\r
2845 Menu sortByTreeMenu = new Menu();
\r
2847 Menu sort = new Menu();
\r
2849 Menu calculate = new Menu();
\r
2851 MenuItem inputText = new MenuItem();
\r
2853 Menu helpMenu = new Menu();
\r
2855 MenuItem documentation = new MenuItem();
\r
2857 MenuItem about = new MenuItem();
\r
2859 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
2861 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
\r
2863 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
\r
2864 Menu autoAnnMenu=new Menu();
\r
2865 CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();
\r
2866 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
\r
2867 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
\r
2868 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
\r
2869 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
\r
2871 private void jbInit() throws Exception
\r
2874 setMenuBar(alignFrameMenuBar);
\r
2878 // dynamically fill save as menu with available formats
\r
2879 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
2882 item = new MenuItem(
\r
2883 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
2885 item.addActionListener(new java.awt.event.ActionListener()
\r
2887 public void actionPerformed(ActionEvent e)
\r
2889 outputText_actionPerformed(e);
\r
2893 outputTextboxMenu.add(item);
\r
2895 closeMenuItem.addActionListener(this);
\r
2896 loadApplication.addActionListener(this);
\r
2898 loadTree.addActionListener(this);
\r
2899 loadAnnotations.addActionListener(this);
\r
2900 outputFeatures.addActionListener(this);
\r
2901 outputAnnotations.addActionListener(this);
\r
2902 selectAllSequenceMenuItem.addActionListener(this);
\r
2903 deselectAllSequenceMenuItem.addActionListener(this);
\r
2904 invertSequenceMenuItem.addActionListener(this);
\r
2905 remove2LeftMenuItem.setLabel("Remove Left");
\r
2906 remove2LeftMenuItem.addActionListener(this);
\r
2907 remove2RightMenuItem.setLabel("Remove Right");
\r
2908 remove2RightMenuItem.addActionListener(this);
\r
2909 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
2910 removeGappedColumnMenuItem.addActionListener(this);
\r
2911 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
2912 removeAllGapsMenuItem.addActionListener(this);
\r
2913 viewBoxesMenuItem.setLabel("Boxes");
\r
2914 viewBoxesMenuItem.setState(true);
\r
2915 viewBoxesMenuItem.addItemListener(this);
\r
2916 viewTextMenuItem.setLabel("Text");
\r
2917 viewTextMenuItem.setState(true);
\r
2918 viewTextMenuItem.addItemListener(this);
\r
2919 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
2920 sortPairwiseMenuItem.addActionListener(this);
\r
2921 sortIDMenuItem.setLabel("by ID");
\r
2922 sortIDMenuItem.addActionListener(this);
\r
2923 sortLengthMenuItem.setLabel("by Length");
\r
2924 sortLengthMenuItem.addActionListener(this);
\r
2925 sortGroupMenuItem.setLabel("by Group");
\r
2926 sortGroupMenuItem.addActionListener(this);
\r
2927 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
2928 removeRedundancyMenuItem.addActionListener(this);
\r
2929 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
2930 pairwiseAlignmentMenuItem.addActionListener(this);
\r
2931 PCAMenuItem.setLabel("Principal Component Analysis");
\r
2932 PCAMenuItem.addActionListener(this);
\r
2933 averageDistanceTreeMenuItem
\r
2934 .setLabel("Average Distance Using % Identity");
\r
2935 averageDistanceTreeMenuItem.addActionListener(this);
\r
2936 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
2937 neighbourTreeMenuItem.addActionListener(this);
\r
2938 statusBar.setBackground(Color.white);
\r
2939 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
2940 statusBar.setText("Status bar");
\r
2941 outputTextboxMenu.setLabel("Output to Textbox");
\r
2942 clustalColour.setLabel("Clustalx");
\r
2944 clustalColour.addActionListener(this);
\r
2945 zappoColour.setLabel("Zappo");
\r
2946 zappoColour.addActionListener(this);
\r
2947 taylorColour.setLabel("Taylor");
\r
2948 taylorColour.addActionListener(this);
\r
2949 hydrophobicityColour.setLabel("Hydrophobicity");
\r
2950 hydrophobicityColour.addActionListener(this);
\r
2951 helixColour.setLabel("Helix Propensity");
\r
2952 helixColour.addActionListener(this);
\r
2953 strandColour.setLabel("Strand Propensity");
\r
2954 strandColour.addActionListener(this);
\r
2955 turnColour.setLabel("Turn Propensity");
\r
2956 turnColour.addActionListener(this);
\r
2957 buriedColour.setLabel("Buried Index");
\r
2958 buriedColour.addActionListener(this);
\r
2959 userDefinedColour.setLabel("User Defined...");
\r
2960 userDefinedColour.addActionListener(this);
\r
2961 PIDColour.setLabel("Percentage Identity");
\r
2962 PIDColour.addActionListener(this);
\r
2963 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
2964 BLOSUM62Colour.addActionListener(this);
\r
2965 avDistanceTreeBlosumMenuItem
\r
2966 .setLabel("Average Distance Using BLOSUM62");
\r
2967 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
2968 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
2969 njTreeBlosumMenuItem.addActionListener(this);
\r
2970 annotationPanelMenuItem.setLabel("Show Annotations");
\r
2971 annotationPanelMenuItem.addItemListener(this);
\r
2972 colourTextMenuItem.setLabel("Colour Text");
\r
2973 colourTextMenuItem.addItemListener(this);
\r
2974 displayNonconservedMenuItem.setLabel("Show nonconserved");
\r
2975 displayNonconservedMenuItem.addItemListener(this);
\r
2976 alProperties.addActionListener(this);
\r
2977 overviewMenuItem.setLabel("Overview Window");
\r
2978 overviewMenuItem.addActionListener(this);
\r
2979 undoMenuItem.setEnabled(false);
\r
2980 undoMenuItem.setLabel("Undo");
\r
2981 undoMenuItem.addActionListener(this);
\r
2982 redoMenuItem.setEnabled(false);
\r
2983 redoMenuItem.setLabel("Redo");
\r
2984 redoMenuItem.addActionListener(this);
\r
2985 conservationMenuItem.setLabel("by Conservation");
\r
2986 conservationMenuItem.addItemListener(this);
\r
2987 noColourmenuItem.setLabel("None");
\r
2988 noColourmenuItem.addActionListener(this);
\r
2989 wrapMenuItem.setLabel("Wrap");
\r
2990 wrapMenuItem.addItemListener(this);
\r
2991 renderGapsMenuItem.setLabel("Show Gaps");
\r
2992 renderGapsMenuItem.setState(true);
\r
2993 renderGapsMenuItem.addItemListener(this);
\r
2994 findMenuItem.setLabel("Find...");
\r
2995 findMenuItem.addActionListener(this);
\r
2996 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
2997 abovePIDThreshold.addItemListener(this);
\r
2998 nucleotideColour.setLabel("Nucleotide");
\r
2999 nucleotideColour.addActionListener(this);
\r
3000 deleteGroups.setLabel("Undefine Groups");
\r
3001 deleteGroups.addActionListener(this);
\r
3002 grpsFromSelection.setLabel("Make Groups for selection");
\r
3003 grpsFromSelection.addActionListener(this);
\r
3004 copy.setLabel("Copy");
\r
3005 copy.addActionListener(this);
\r
3006 cut.setLabel("Cut");
\r
3007 cut.addActionListener(this);
\r
3008 delete.setLabel("Delete");
\r
3009 delete.addActionListener(this);
\r
3010 pasteMenu.setLabel("Paste");
\r
3011 pasteNew.setLabel("To New Alignment");
\r
3012 pasteNew.addActionListener(this);
\r
3013 pasteThis.setLabel("Add To This Alignment");
\r
3014 pasteThis.addActionListener(this);
\r
3015 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
3016 applyToAllGroups.setState(true);
\r
3017 applyToAllGroups.addItemListener(this);
\r
3018 font.setLabel("Font...");
\r
3019 font.addActionListener(this);
\r
3020 scaleAbove.setLabel("Scale Above");
\r
3021 scaleAbove.setState(true);
\r
3022 scaleAbove.setEnabled(false);
\r
3023 scaleAbove.addItemListener(this);
\r
3024 scaleLeft.setEnabled(false);
\r
3025 scaleLeft.setState(true);
\r
3026 scaleLeft.setLabel("Scale Left");
\r
3027 scaleLeft.addItemListener(this);
\r
3028 scaleRight.setEnabled(false);
\r
3029 scaleRight.setState(true);
\r
3030 scaleRight.setLabel("Scale Right");
\r
3031 scaleRight.addItemListener(this);
\r
3032 modifyPID.setLabel("Modify Identity Threshold...");
\r
3033 modifyPID.addActionListener(this);
\r
3034 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
3035 modifyConservation.addActionListener(this);
\r
3036 sortByTreeMenu.setLabel("By Tree Order");
\r
3037 sort.setLabel("Sort");
\r
3038 calculate.setLabel("Calculate Tree");
\r
3039 autoCalculate.addItemListener(this);
\r
3040 inputText.setLabel("Input from textbox");
\r
3041 inputText.addActionListener(this);
\r
3042 centreColumnLabelFlag.setLabel("Centre column labels");
\r
3043 centreColumnLabelFlag.addItemListener(this);
\r
3044 followMouseOverFlag.setLabel("Automatic Scrolling");
\r
3045 followMouseOverFlag.addItemListener(this);
\r
3046 helpMenu.setLabel("Help");
\r
3047 documentation.setLabel("Documentation");
\r
3048 documentation.addActionListener(this);
\r
3050 about.setLabel("About...");
\r
3051 about.addActionListener(this);
\r
3052 seqLimits.setState(true);
\r
3053 seqLimits.setLabel("Show Sequence Limits");
\r
3054 seqLimits.addItemListener(this);
\r
3055 featureSettings.setLabel("Feature Settings...");
\r
3056 featureSettings.addActionListener(this);
\r
3057 sequenceFeatures.setLabel("Sequence Features");
\r
3058 sequenceFeatures.addItemListener(this);
\r
3059 sequenceFeatures.setState(false);
\r
3060 annotationColour.setLabel("by Annotation...");
\r
3061 annotationColour.addActionListener(this);
\r
3062 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
3063 invertColSel.setLabel("Invert Column Selection");
\r
3064 menu1.setLabel("Show");
\r
3065 showColumns.setLabel("All Columns ");
\r
3066 showSeqs.setLabel("All Sequences");
\r
3067 menu2.setLabel("Hide");
\r
3068 hideColumns.setLabel("Selected Columns");
\r
3069 hideSequences.setLabel("Selected Sequences");
\r
3070 hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
\r
3071 hideAllSelection.setLabel("Selected Region");
\r
3072 showAllHidden.setLabel("All Sequences and Columns");
\r
3073 showGroupConsensus.setLabel("Group Consensus");
\r
3074 showGroupConservation.setLabel("Group Conservation");
\r
3075 showConsensusHistogram.setLabel("Show Consensus Histogram");
\r
3076 showSequenceLogo.setLabel("Show Consensus Logo");
\r
3077 applyAutoAnnotationSettings.setLabel("Apply to all groups");
\r
3078 applyAutoAnnotationSettings.setState(true);
\r
3079 autoAnnMenu.setLabel("Autocalculated Annotation");
\r
3081 invertColSel.addActionListener(this);
\r
3082 showColumns.addActionListener(this);
\r
3083 showSeqs.addActionListener(this);
\r
3084 hideColumns.addActionListener(this);
\r
3085 hideSequences.addActionListener(this);
\r
3086 hideAllButSelection.addActionListener(this);
\r
3087 hideAllSelection.addActionListener(this);
\r
3088 showAllHidden.addActionListener(this);
\r
3089 showGroupConsensus.addItemListener(this);
\r
3090 showGroupConservation.addItemListener(this);
\r
3091 showConsensusHistogram.addItemListener(this);
\r
3092 showSequenceLogo.addItemListener(this);
\r
3093 applyAutoAnnotationSettings.addItemListener(this);
\r
3094 formatMenu.setLabel("Format");
\r
3095 selectMenu.setLabel("Select");
\r
3096 newView.setLabel("New View");
\r
3097 newView.addActionListener(this);
\r
3098 alignFrameMenuBar.add(fileMenu);
\r
3099 alignFrameMenuBar.add(editMenu);
\r
3100 alignFrameMenuBar.add(selectMenu);
\r
3101 alignFrameMenuBar.add(viewMenu);
\r
3102 alignFrameMenuBar.add(formatMenu);
\r
3103 alignFrameMenuBar.add(colourMenu);
\r
3104 alignFrameMenuBar.add(calculateMenu);
\r
3105 alignFrameMenuBar.add(helpMenu);
\r
3107 fileMenu.add(inputText);
\r
3108 fileMenu.add(loadTree);
\r
3109 fileMenu.add(loadAnnotations);
\r
3111 fileMenu.addSeparator();
\r
3112 fileMenu.add(outputTextboxMenu);
\r
3113 fileMenu.add(outputFeatures);
\r
3114 fileMenu.add(outputAnnotations);
\r
3116 if (jalviewServletURL != null)
\r
3118 fileMenu.add(loadApplication);
\r
3121 fileMenu.addSeparator();
\r
3122 fileMenu.add(closeMenuItem);
\r
3124 editMenu.add(undoMenuItem);
\r
3125 editMenu.add(redoMenuItem);
\r
3126 editMenu.add(cut);
\r
3127 editMenu.add(copy);
\r
3128 editMenu.add(pasteMenu);
\r
3129 editMenu.add(delete);
\r
3130 editMenu.addSeparator();
\r
3131 editMenu.add(remove2LeftMenuItem);
\r
3132 editMenu.add(remove2RightMenuItem);
\r
3133 editMenu.add(removeGappedColumnMenuItem);
\r
3134 editMenu.add(removeAllGapsMenuItem);
\r
3135 editMenu.add(removeRedundancyMenuItem);
\r
3136 viewMenu.add(newView);
\r
3137 viewMenu.addSeparator();
\r
3138 viewMenu.add(menu1);
\r
3139 viewMenu.add(menu2);
\r
3140 viewMenu.addSeparator();
\r
3141 viewMenu.add(followMouseOverFlag);
\r
3142 viewMenu.add(annotationPanelMenuItem);
\r
3143 autoAnnMenu.add(applyAutoAnnotationSettings);
\r
3144 autoAnnMenu.add(showConsensusHistogram);
\r
3145 autoAnnMenu.add(showSequenceLogo);
\r
3146 autoAnnMenu.addSeparator();
\r
3147 autoAnnMenu.add(showGroupConservation);
\r
3148 autoAnnMenu.add(showGroupConsensus);
\r
3149 viewMenu.add(autoAnnMenu);
\r
3150 viewMenu.addSeparator();
\r
3151 viewMenu.add(sequenceFeatures);
\r
3152 viewMenu.add(featureSettings);
\r
3153 viewMenu.addSeparator();
\r
3154 viewMenu.add(alProperties);
\r
3155 viewMenu.addSeparator();
\r
3156 viewMenu.add(overviewMenuItem);
\r
3157 colourMenu.add(applyToAllGroups);
\r
3158 colourMenu.addSeparator();
\r
3159 colourMenu.add(noColourmenuItem);
\r
3160 colourMenu.add(clustalColour);
\r
3161 colourMenu.add(BLOSUM62Colour);
\r
3162 colourMenu.add(PIDColour);
\r
3163 colourMenu.add(zappoColour);
\r
3164 colourMenu.add(taylorColour);
\r
3165 colourMenu.add(hydrophobicityColour);
\r
3166 colourMenu.add(helixColour);
\r
3167 colourMenu.add(strandColour);
\r
3168 colourMenu.add(turnColour);
\r
3169 colourMenu.add(buriedColour);
\r
3170 colourMenu.add(nucleotideColour);
\r
3171 colourMenu.add(userDefinedColour);
\r
3172 colourMenu.addSeparator();
\r
3173 colourMenu.add(conservationMenuItem);
\r
3174 colourMenu.add(modifyConservation);
\r
3175 colourMenu.add(abovePIDThreshold);
\r
3176 colourMenu.add(modifyPID);
\r
3177 colourMenu.add(annotationColour);
\r
3178 calculateMenu.add(sort);
\r
3179 calculateMenu.add(calculate);
\r
3180 calculateMenu.addSeparator();
\r
3181 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
3182 calculateMenu.add(PCAMenuItem);
\r
3183 calculateMenu.add(autoCalculate);
\r
3184 this.add(statusBar, BorderLayout.SOUTH);
\r
3185 pasteMenu.add(pasteNew);
\r
3186 pasteMenu.add(pasteThis);
\r
3187 sort.add(sortIDMenuItem);
\r
3188 sort.add(sortLengthMenuItem);
\r
3189 sort.add(sortByTreeMenu);
\r
3190 sort.add(sortGroupMenuItem);
\r
3191 sort.add(sortPairwiseMenuItem);
\r
3192 calculate.add(averageDistanceTreeMenuItem);
\r
3193 calculate.add(neighbourTreeMenuItem);
\r
3194 calculate.add(avDistanceTreeBlosumMenuItem);
\r
3195 calculate.add(njTreeBlosumMenuItem);
\r
3196 helpMenu.add(documentation);
\r
3197 helpMenu.add(about);
\r
3198 menu1.add(showColumns);
\r
3199 menu1.add(showSeqs);
\r
3200 menu1.add(showAllHidden);
\r
3201 menu2.add(hideColumns);
\r
3202 menu2.add(hideSequences);
\r
3203 menu2.add(hideAllSelection);
\r
3204 menu2.add(hideAllButSelection);
\r
3205 formatMenu.add(font);
\r
3206 formatMenu.add(seqLimits);
\r
3207 formatMenu.add(wrapMenuItem);
\r
3208 formatMenu.add(scaleAbove);
\r
3209 formatMenu.add(scaleLeft);
\r
3210 formatMenu.add(scaleRight);
\r
3211 formatMenu.add(viewBoxesMenuItem);
\r
3212 formatMenu.add(viewTextMenuItem);
\r
3213 formatMenu.add(colourTextMenuItem);
\r
3214 formatMenu.add(displayNonconservedMenuItem);
\r
3215 formatMenu.add(renderGapsMenuItem);
\r
3216 formatMenu.add(centreColumnLabelFlag);
\r
3217 selectMenu.add(findMenuItem);
\r
3218 selectMenu.addSeparator();
\r
3219 selectMenu.add(selectAllSequenceMenuItem);
\r
3220 selectMenu.add(deselectAllSequenceMenuItem);
\r
3221 selectMenu.add(invertSequenceMenuItem);
\r
3222 selectMenu.add(invertColSel);
\r
3223 selectMenu.add(grpsFromSelection);
\r
3224 selectMenu.add(deleteGroups);
\r
3228 MenuItem featureSettings = new MenuItem();
\r
3230 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
3232 MenuItem annotationColour = new MenuItem();
\r
3234 MenuItem invertColSel = new MenuItem();
\r
3236 Menu menu1 = new Menu();
\r
3238 MenuItem showColumns = new MenuItem();
\r
3240 MenuItem showSeqs = new MenuItem();
\r
3242 Menu menu2 = new Menu();
\r
3244 MenuItem hideColumns = new MenuItem();
\r
3246 MenuItem hideSequences = new MenuItem();
\r
3248 MenuItem hideAllButSelection = new MenuItem();
\r
3250 MenuItem hideAllSelection = new MenuItem();
\r
3252 MenuItem showAllHidden = new MenuItem();
\r
3254 Menu formatMenu = new Menu();
\r
3256 Menu selectMenu = new Menu();
\r
3258 MenuItem newView = new MenuItem();
\r
3261 * Attach the alignFrame panels after embedding menus, if necessary. This used
\r
3262 * to be called setEmbedded, but is now creates the dropdown menus in a
\r
3263 * platform independent manner to avoid OSX/Mac menu appendage daftness.
\r
3265 * @param reallyEmbedded
\r
3266 * true to attach the view to the applet area on the page rather than
\r
3269 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
\r
3271 if (reallyEmbedded)
\r
3274 // Explicly build the embedded menu panel for the on-page applet
\r
3276 // view cannot be closed if its actually on the page
\r
3277 fileMenu.remove(closeMenuItem);
\r
3278 fileMenu.remove(3); // Remove Seperator
\r
3279 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
\r
3280 Font.PLAIN, 10, false); // use our own fonts.
\r
3281 // and actually add the components to the applet area
\r
3282 viewport.applet.setLayout(new BorderLayout());
\r
3283 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
\r
3284 viewport.applet.add(statusBar, BorderLayout.SOUTH);
\r
3285 alignPanel.setSize(viewport.applet.getSize().width,
\r
3286 viewport.applet.getSize().height - embeddedMenu.HEIGHT
\r
3287 - statusBar.HEIGHT);
\r
3288 viewport.applet.add(alignPanel, BorderLayout.CENTER);
\r
3289 final AlignFrame me = this;
\r
3290 viewport.applet.addFocusListener(new FocusListener()
\r
3294 public void focusLost(FocusEvent e)
\r
3296 if (me.viewport.applet.currentAlignFrame==me) {
\r
3297 me.viewport.applet.currentAlignFrame = null;
\r
3301 public void focusGained(FocusEvent e)
\r
3303 me.viewport.applet.currentAlignFrame = me;
\r
3306 viewport.applet.validate();
\r
3311 // test and embed menu bar if necessary.
\r
3313 if (embedMenuIfNeeded(alignPanel))
\r
3315 // adjust for status bar height too
\r
3316 alignPanel.setSize(getSize().width, getSize().height
\r
3317 - statusBar.HEIGHT);
\r
3319 add(statusBar, BorderLayout.SOUTH);
\r
3320 add(alignPanel, BorderLayout.CENTER);
\r
3321 // and register with the applet so it can pass external API calls to us
\r
3322 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
\r
3328 * create a new binding between structures in an existing jmol viewer instance
\r
3329 * and an alignpanel with sequences that have existing PDBFile entries. Note,
\r
3330 * this does not open a new Jmol window, or modify the display of the
\r
3331 * structures in the original jmol window. Note This method doesn't work
\r
3332 * without an additional javascript library to exchange messages between the
\r
3333 * distinct applets. See http://issues.jalview.org/browse/JAL-621
\r
3336 * JmolViewer instance
\r
3337 * @param sequenceIds
\r
3338 * - sequence Ids to search for associations
\r
3340 public SequenceStructureBinding addStructureViewInstance(
\r
3341 Object jmolviewer, String[] sequenceIds)
\r
3343 org.jmol.api.JmolViewer viewer = null;
\r
3346 viewer = (org.jmol.api.JmolViewer) jmolviewer;
\r
3347 } catch (ClassCastException ex)
\r
3349 System.err.println("Unsupported viewer object :"
\r
3350 + jmolviewer.getClass());
\r
3352 if (viewer == null)
\r
3354 System.err.println("Can't use this object as a structure viewer:"
\r
3355 + jmolviewer.getClass());
\r
3358 SequenceI[] seqs = null;
\r
3359 if (sequenceIds == null || sequenceIds.length == 0)
\r
3361 seqs = viewport.getAlignment().getSequencesArray();
\r
3365 Vector sqi = new Vector();
\r
3366 AlignmentI al = viewport.getAlignment();
\r
3367 for (int sid = 0; sid < sequenceIds.length; sid++)
\r
3369 SequenceI sq = al.findName(sequenceIds[sid]);
\r
3372 sqi.addElement(sq);
\r
3375 if (sqi.size() > 0)
\r
3377 seqs = new SequenceI[sqi.size()];
\r
3378 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
\r
3380 seqs[sid] = (SequenceI) sqi.elementAt(sid);
\r
3388 ExtJmol jmv = null;
\r
3389 // TODO: search for a jmv that involves viewer
\r
3391 { // create a new viewer/jalview binding.
\r
3392 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs});
\r
3398 * bind a pdb file to a sequence in the current view
\r
3400 * @param sequenceId
\r
3401 * - sequenceId within the dataset.
\r
3402 * @param pdbEntryString
\r
3403 * - the short name for the PDB file
\r
3405 * - pdb file - either a URL or a valid PDB file.
\r
3406 * @return true if binding was as success TODO: consider making an exception
\r
3407 * structure for indicating when PDB parsing or sequenceId location
\r
3410 public boolean addPdbFile(String sequenceId, String pdbEntryString,
\r
3413 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
\r
3414 boolean needtoadd = false;
\r
3415 if (toaddpdb != null)
\r
3417 Vector pdbe = toaddpdb.getPDBId();
\r
3418 PDBEntry pdbentry = null;
\r
3419 if (pdbe != null && pdbe.size() > 0)
\r
3421 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
\r
3423 pdbentry = (PDBEntry) pdbe.elementAt(pe);
\r
3424 if (!pdbentry.getId().equals(pdbEntryString)
\r
3425 && !pdbentry.getFile().equals(pdbFile))
\r
3435 if (pdbentry == null)
\r
3437 pdbentry = new PDBEntry();
\r
3438 pdbentry.setId(pdbEntryString);
\r
3439 pdbentry.setFile(pdbFile);
\r
3440 needtoadd = true; // add this new entry to sequence.
\r
3442 // resolve data source
\r
3443 // TODO: this code should be a refactored to an io package
\r
3444 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
\r
3445 if (protocol == null)
\r
3451 // make a note of the access mode and add
\r
3452 if (pdbentry.getProperty() == null)
\r
3454 pdbentry.setProperty(new Hashtable());
\r
3456 pdbentry.getProperty().put("protocol", protocol);
\r
3457 toaddpdb.addPDBId(pdbentry);
\r
3463 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
\r
3467 Vector sequences = new Vector();
\r
3468 for (int i = 0; i < seqs.length; i++)
\r
3470 if (seqs[i] != null)
\r
3472 sequences.addElement(new Object[]
\r
3473 { seqs[i], (chains != null) ? chains[i] : null });
\r
3476 seqs = new SequenceI[sequences.size()];
\r
3477 chains = new String[sequences.size()];
\r
3478 for (int i = 0, isize = sequences.size(); i < isize; i++)
\r
3480 Object[] oj = (Object[]) sequences.elementAt(i);
\r
3482 seqs[i] = (SequenceI) oj[0];
\r
3483 chains[i] = (String) oj[1];
\r
3486 return new Object[]
\r
3491 public void newStructureView(JalviewLite applet, PDBEntry pdb,
\r
3492 SequenceI[] seqs, String[] chains, String protocol)
\r
3494 // Scrub any null sequences from the array
\r
3495 Object[] sqch = cleanSeqChainArrays(seqs, chains);
\r
3496 seqs = (SequenceI[]) sqch[0];
\r
3497 chains = (String[]) sqch[1];
\r
3498 if (seqs == null || seqs.length == 0)
\r
3501 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
\r
3503 if (protocol == null || protocol.trim().length() == 0
\r
3504 || protocol.equals("null"))
\r
3506 protocol = (String) pdb.getProperty().get("protocol");
\r
3507 if (protocol == null)
\r
3509 System.err.println("Couldn't work out protocol to open structure: "
\r
3514 if (applet.useXtrnalSviewer)
\r
3516 // register the association(s) and quit, don't create any windows.
\r
3517 if (StructureSelectionManager.getStructureSelectionManager(applet).setMapping(seqs, chains, pdb.getFile(), protocol)==null) {
\r
3518 System.err.println("Failed to map "+pdb.getFile()+" ("+protocol+") to any sequences");
\r
3522 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
\r
3524 // can only do alignments with Jmol
\r
3525 // find the last jmol window assigned to this alignment
\r
3526 jalview.appletgui.AppletJmol ajm = null, tajm;
\r
3527 Vector jmols = applet
\r
3528 .getAppletWindow(jalview.appletgui.AppletJmol.class);
\r
3529 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
\r
3531 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
\r
3532 if (tajm.ap.alignFrame == this)
\r
3541 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
\r
3542 // try and add the pdb structure
\r
3547 // otherwise, create a new window
\r
3548 if (applet.jmolAvailable)
\r
3550 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
\r
3552 applet.lastFrameX += 40;
\r
3553 applet.lastFrameY += 40;
\r
3557 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
\r
3562 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
\r
3563 SequenceI[][] seqs, String[][] chains, String[] protocols)
\r
3565 // TODO Auto-generated method stub
\r
3566 System.err.println("Aligned Structure View: Not yet implemented.");
\r
3570 * modify the current selection, providing the user has not made a selection already.
\r
3571 * @param sel - sequences from this alignment
\r
3572 * @param csel - columns to be selected on the alignment
\r
3574 public void select(SequenceGroup sel, ColumnSelection csel)
\r
3576 alignPanel.seqPanel.selection(sel, csel, null);
\r
3579 public void scrollTo(int row, int column)
\r
3581 alignPanel.seqPanel.scrollTo(row, column);
\r