2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
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3 * Copyright (C) 2011 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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20 import jalview.analysis.AAFrequency;
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21 import jalview.analysis.AlignmentSorter;
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22 import jalview.analysis.Conservation;
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23 import jalview.api.SequenceStructureBinding;
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24 import jalview.bin.JalviewLite;
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25 import jalview.commands.CommandI;
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26 import jalview.commands.EditCommand;
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27 import jalview.commands.OrderCommand;
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28 import jalview.commands.RemoveGapColCommand;
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29 import jalview.commands.RemoveGapsCommand;
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30 import jalview.commands.SlideSequencesCommand;
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31 import jalview.commands.TrimRegionCommand;
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32 import jalview.datamodel.Alignment;
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33 import jalview.datamodel.AlignmentI;
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34 import jalview.datamodel.AlignmentOrder;
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35 import jalview.datamodel.ColumnSelection;
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36 import jalview.datamodel.PDBEntry;
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37 import jalview.datamodel.Sequence;
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38 import jalview.datamodel.SequenceGroup;
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39 import jalview.datamodel.SequenceI;
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40 import jalview.io.AnnotationFile;
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41 import jalview.io.AppletFormatAdapter;
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42 import jalview.io.FeaturesFile;
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43 import jalview.io.TCoffeeScoreFile;
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44 import jalview.schemes.Blosum62ColourScheme;
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45 import jalview.schemes.BuriedColourScheme;
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46 import jalview.schemes.ClustalxColourScheme;
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47 import jalview.schemes.ColourSchemeI;
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48 import jalview.schemes.HelixColourScheme;
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49 import jalview.schemes.HydrophobicColourScheme;
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50 import jalview.schemes.NucleotideColourScheme;
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51 import jalview.schemes.PIDColourScheme;
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52 import jalview.schemes.ResidueProperties;
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53 import jalview.schemes.StrandColourScheme;
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54 import jalview.schemes.TCoffeeColourScheme;
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55 import jalview.schemes.TaylorColourScheme;
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56 import jalview.schemes.TurnColourScheme;
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57 import jalview.schemes.ZappoColourScheme;
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58 import jalview.structure.StructureSelectionManager;
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60 import java.awt.BorderLayout;
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61 import java.awt.Canvas;
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62 import java.awt.CheckboxMenuItem;
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63 import java.awt.Color;
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64 import java.awt.Font;
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65 import java.awt.FontMetrics;
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66 import java.awt.Frame;
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67 import java.awt.Graphics;
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68 import java.awt.Label;
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69 import java.awt.Menu;
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70 import java.awt.MenuBar;
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71 import java.awt.MenuItem;
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72 import java.awt.event.ActionEvent;
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73 import java.awt.event.ActionListener;
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74 import java.awt.event.FocusEvent;
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75 import java.awt.event.FocusListener;
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76 import java.awt.event.ItemEvent;
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77 import java.awt.event.ItemListener;
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78 import java.awt.event.KeyEvent;
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79 import java.awt.event.KeyListener;
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80 import java.awt.event.WindowAdapter;
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81 import java.awt.event.WindowEvent;
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82 import java.io.IOException;
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83 import java.io.InputStreamReader;
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84 import java.net.URL;
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85 import java.net.URLEncoder;
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86 import java.util.Enumeration;
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87 import java.util.Hashtable;
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88 import java.util.StringTokenizer;
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89 import java.util.Vector;
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91 public class AlignFrame extends EmbmenuFrame implements ActionListener, ItemListener, KeyListener
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93 public AlignmentPanel alignPanel;
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95 public AlignViewport viewport;
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97 int DEFAULT_WIDTH = 700;
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99 int DEFAULT_HEIGHT = 500;
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101 String jalviewServletURL;
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103 TCoffeeScoreFile tcoffeeScoreFile;
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105 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title, boolean embedded)
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107 if (applet != null)
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109 jalviewServletURL = applet.getParameter("APPLICATION_URL");
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115 } catch (Exception ex)
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117 ex.printStackTrace();
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120 viewport = new AlignViewport(al, applet);
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121 alignPanel = new AlignmentPanel(this, viewport);
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123 viewport.updateConservation(alignPanel);
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124 viewport.updateConsensus(alignPanel);
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126 annotationPanelMenuItem.setState(viewport.showAnnotation);
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127 displayNonconservedMenuItem.setState(viewport.getShowunconserved());
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128 followMouseOverFlag.setState(viewport.getFollowHighlight());
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129 showGroupConsensus.setState(viewport.showGroupConsensus);
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130 showGroupConservation.setState(viewport.showGroupConservation);
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131 showConsensusHistogram.setState(viewport.showConsensusHistogram);
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132 showSequenceLogo.setState(viewport.showSequenceLogo);
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134 seqLimits.setState(viewport.showJVSuffix);
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136 if (applet != null)
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138 String param = applet.getParameter("sortBy");
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141 if (param.equalsIgnoreCase("Id"))
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143 sortIDMenuItem_actionPerformed();
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145 else if (param.equalsIgnoreCase("Pairwise Identity"))
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147 sortPairwiseMenuItem_actionPerformed();
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149 else if (param.equalsIgnoreCase("Length"))
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151 sortLengthMenuItem_actionPerformed();
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155 param = applet.getParameter("wrap");
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158 if (param.equalsIgnoreCase("true"))
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160 wrapMenuItem.setState(true);
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161 wrapMenuItem_actionPerformed();
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164 param = applet.getParameter("centrecolumnlabels");
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167 centreColumnLabelFlag.setState(true);
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168 centreColumnLabelFlag_stateChanged();
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172 param = applet.getParameter("windowWidth");
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175 int width = Integer.parseInt(param);
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176 DEFAULT_WIDTH = width;
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178 param = applet.getParameter("windowHeight");
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181 int height = Integer.parseInt(param);
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182 DEFAULT_HEIGHT = height;
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184 } catch (Exception ex)
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190 // Some JVMS send keyevents to Top frame or lowest panel,
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191 // Havent worked out why yet. So add to both this frame and seqCanvas for
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193 this.addKeyListener(this);
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194 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
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195 alignPanel.idPanel.idCanvas.addKeyListener(this);
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196 alignPanel.scalePanel.addKeyListener(this);
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197 alignPanel.annotationPanel.addKeyListener(this);
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198 alignPanel.annotationPanelHolder.addKeyListener(this);
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199 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
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200 alignPanel.alabels.addKeyListener(this);
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201 createAlignFrameWindow(embedded, title);
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204 alignPanel.adjustAnnotationHeight();
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205 alignPanel.paintAlignment(true);
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208 public AlignViewport getAlignViewport()
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213 public SeqCanvas getSeqcanvas()
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215 return alignPanel.seqPanel.seqCanvas;
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219 * Load a features file onto the alignment
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221 * @param file file URL, content, or other resolvable path
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222 * @param type is protocol for accessing data referred to by file
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225 public void parseFeaturesFile(String file, String type)
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227 parseFeaturesFile(file, type, true);
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231 * Load a features file onto the alignment
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233 * @param file file URL, content, or other resolvable path
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234 * @param type is protocol for accessing data referred to by file
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235 * @param autoenabledisplay when true, display features flag will be automatically enabled if features are loaded
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237 public void parseFeaturesFile(String file, String type, boolean autoenabledisplay)
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239 Hashtable featureLinks = new Hashtable();
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240 boolean featuresFile = false;
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243 featuresFile = new jalview.io.FeaturesFile(file, type)
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244 .parse(viewport.alignment,
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245 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
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246 featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));
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247 } catch (Exception ex)
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249 ex.printStackTrace();
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254 if (featureLinks.size() > 0)
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256 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
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258 if (autoenabledisplay)
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260 viewport.showSequenceFeatures = true;
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261 sequenceFeatures.setState(true);
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263 if (viewport.featureSettings != null)
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265 viewport.featureSettings.refreshTable();
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267 alignPanel.paintAlignment(true);
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272 public void keyPressed(KeyEvent evt)
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274 if (viewport.cursorMode
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275 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
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276 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
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277 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
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278 && Character.isDigit(evt.getKeyChar()))
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279 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
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281 switch (evt.getKeyCode())
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283 case 27: // escape key
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284 deselectAllSequenceMenuItem_actionPerformed();
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286 alignPanel.alabels.cancelDrag();
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288 case KeyEvent.VK_X:
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289 if (evt.isControlDown() || evt.isMetaDown())
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291 cut_actionPerformed();
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294 case KeyEvent.VK_C:
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295 if (viewport.cursorMode && !evt.isControlDown())
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297 alignPanel.seqPanel.setCursorColumn();
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299 if (evt.isControlDown() || evt.isMetaDown())
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301 copy_actionPerformed();
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304 case KeyEvent.VK_V:
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305 if (evt.isControlDown())
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307 paste(evt.isShiftDown());
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310 case KeyEvent.VK_A:
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311 if (evt.isControlDown() || evt.isMetaDown())
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313 selectAllSequenceMenuItem_actionPerformed();
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316 case KeyEvent.VK_DOWN:
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317 if (viewport.cursorMode)
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319 alignPanel.seqPanel.moveCursor(0, 1);
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323 moveSelectedSequences(false);
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327 case KeyEvent.VK_UP:
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328 if (viewport.cursorMode)
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330 alignPanel.seqPanel.moveCursor(0, -1);
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334 moveSelectedSequences(true);
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338 case KeyEvent.VK_LEFT:
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339 if (evt.isAltDown() || !viewport.cursorMode)
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340 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
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342 alignPanel.seqPanel.moveCursor(-1, 0);
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345 case KeyEvent.VK_RIGHT:
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346 if (evt.isAltDown() || !viewport.cursorMode)
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347 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
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349 alignPanel.seqPanel.moveCursor(1, 0);
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352 case KeyEvent.VK_SPACE:
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353 if (viewport.cursorMode)
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355 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
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356 || evt.isShiftDown() || evt.isAltDown());
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360 case KeyEvent.VK_DELETE:
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361 case KeyEvent.VK_BACK_SPACE:
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362 if (viewport.cursorMode)
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364 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
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365 || evt.isShiftDown() || evt.isAltDown());
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369 cut_actionPerformed();
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370 alignPanel.seqPanel.seqCanvas.repaint();
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374 case KeyEvent.VK_S:
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375 if (viewport.cursorMode)
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377 alignPanel.seqPanel.setCursorRow();
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380 case KeyEvent.VK_P:
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381 if (viewport.cursorMode)
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383 alignPanel.seqPanel.setCursorPosition();
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387 case KeyEvent.VK_ENTER:
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388 case KeyEvent.VK_COMMA:
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389 if (viewport.cursorMode)
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391 alignPanel.seqPanel.setCursorRowAndColumn();
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395 case KeyEvent.VK_Q:
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396 if (viewport.cursorMode)
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398 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
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401 case KeyEvent.VK_M:
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402 if (viewport.cursorMode)
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404 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
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408 case KeyEvent.VK_F2:
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409 viewport.cursorMode = !viewport.cursorMode;
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410 statusBar.setText("Keyboard editing mode is "
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411 + (viewport.cursorMode ? "on" : "off"));
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412 if (viewport.cursorMode)
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414 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
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415 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
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419 case KeyEvent.VK_F:
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420 if (evt.isControlDown())
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422 findMenuItem_actionPerformed();
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426 case KeyEvent.VK_H:
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428 boolean toggleSeqs = !evt.isControlDown();
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429 boolean toggleCols = !evt.isShiftDown();
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430 toggleHiddenRegions(toggleSeqs, toggleCols);
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434 case KeyEvent.VK_PAGE_UP:
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435 if (viewport.wrapAlignment)
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437 alignPanel.scrollUp(true);
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441 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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442 - viewport.endSeq + viewport.startSeq);
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446 case KeyEvent.VK_PAGE_DOWN:
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447 if (viewport.wrapAlignment)
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449 alignPanel.scrollUp(false);
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453 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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454 + viewport.endSeq - viewport.startSeq);
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458 case KeyEvent.VK_Z:
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459 if (evt.isControlDown())
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461 undoMenuItem_actionPerformed();
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465 case KeyEvent.VK_Y:
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466 if (evt.isControlDown())
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468 redoMenuItem_actionPerformed();
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472 case KeyEvent.VK_L:
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473 if (evt.isControlDown())
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475 trimAlignment(true);
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479 case KeyEvent.VK_R:
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480 if (evt.isControlDown())
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482 trimAlignment(false);
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486 case KeyEvent.VK_E:
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487 if (evt.isControlDown())
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489 if (evt.isShiftDown())
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491 this.removeAllGapsMenuItem_actionPerformed();
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495 removeGappedColumnMenuItem_actionPerformed();
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499 case KeyEvent.VK_I:
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500 if (evt.isControlDown())
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502 if (evt.isAltDown())
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504 invertColSel_actionPerformed();
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508 invertSequenceMenuItem_actionPerformed();
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513 case KeyEvent.VK_U:
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514 if (evt.isControlDown())
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516 this.deleteGroups_actionPerformed();
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520 case KeyEvent.VK_T:
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521 if (evt.isControlDown())
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528 alignPanel.paintAlignment(true);
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532 * called by key handler and the hide all/show all menu items
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534 * @param toggleSeqs
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535 * @param toggleCols
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537 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
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539 boolean hide = false;
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540 SequenceGroup sg = viewport.getSelectionGroup();
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541 if (!toggleSeqs && !toggleCols)
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543 // Hide everything by the current selection - this is a hack - we do the
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544 // invert and then hide
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545 // first check that there will be visible columns after the invert.
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546 if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
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547 .getSelected().size() > 0)
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548 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
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551 // now invert the sequence set, if required - empty selection implies
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552 // that no hiding is required.
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555 invertSequenceMenuItem_actionPerformed();
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556 sg = viewport.getSelectionGroup();
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560 viewport.expandColSelection(sg, true);
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561 // finally invert the column selection and get the new sequence
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562 // selection and indicate it should be hidden.
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563 invertColSel_actionPerformed();
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570 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
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573 viewport.hideAllSelectedSeqs();
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575 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
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577 viewport.showAllHiddenSeqs();
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583 if (viewport.colSel.getSelected().size() > 0)
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585 viewport.hideSelectedColumns();
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588 viewport.selectionGroup = sg;
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593 viewport.showAllHiddenColumns();
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598 public void keyReleased(KeyEvent evt)
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602 public void keyTyped(KeyEvent evt)
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606 public void itemStateChanged(ItemEvent evt)
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608 if (evt.getSource() == displayNonconservedMenuItem)
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610 displayNonconservedMenuItem_actionPerformed();
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612 else if (evt.getSource() == colourTextMenuItem)
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614 colourTextMenuItem_actionPerformed();
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616 else if (evt.getSource() == wrapMenuItem)
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618 wrapMenuItem_actionPerformed();
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620 else if (evt.getSource() == scaleAbove)
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622 viewport.setScaleAboveWrapped(scaleAbove.getState());
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624 else if (evt.getSource() == scaleLeft)
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626 viewport.setScaleLeftWrapped(scaleLeft.getState());
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628 else if (evt.getSource() == scaleRight)
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630 viewport.setScaleRightWrapped(scaleRight.getState());
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632 else if (evt.getSource() == seqLimits)
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634 seqLimits_itemStateChanged();
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636 else if (evt.getSource() == viewBoxesMenuItem)
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638 viewport.setShowBoxes(viewBoxesMenuItem.getState());
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640 else if (evt.getSource() == viewTextMenuItem)
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642 viewport.setShowText(viewTextMenuItem.getState());
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644 else if (evt.getSource() == renderGapsMenuItem)
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646 viewport.setRenderGaps(renderGapsMenuItem.getState());
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648 else if (evt.getSource() == annotationPanelMenuItem)
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650 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
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651 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
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653 else if (evt.getSource() == sequenceFeatures)
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655 viewport.showSequenceFeatures(sequenceFeatures.getState());
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656 alignPanel.seqPanel.seqCanvas.repaint();
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658 else if (evt.getSource() == conservationMenuItem)
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660 conservationMenuItem_actionPerformed();
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662 else if (evt.getSource() == abovePIDThreshold)
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664 abovePIDThreshold_actionPerformed();
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666 else if (evt.getSource() == applyToAllGroups)
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668 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
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670 else if (evt.getSource() == autoCalculate)
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672 viewport.autocalculateConsensus = autoCalculate.getState();
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674 else if (evt.getSource() == sortByTree)
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676 viewport.sortByTree = sortByTree.getState();
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678 else if (evt.getSource() == this.centreColumnLabelFlag)
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680 centreColumnLabelFlag_stateChanged();
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682 else if (evt.getSource() == this.followMouseOverFlag)
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684 mouseOverFlag_stateChanged();
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686 else if (evt.getSource() == showGroupConsensus)
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688 showGroupConsensus_actionPerformed();
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690 else if (evt.getSource() == showGroupConservation)
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692 showGroupConservation_actionPerformed();
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694 else if (evt.getSource() == showSequenceLogo)
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696 showSequenceLogo_actionPerformed();
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698 else if (evt.getSource() == showConsensusHistogram)
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700 showConsensusHistogram_actionPerformed();
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702 else if (evt.getSource() == applyAutoAnnotationSettings)
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704 applyAutoAnnotationSettings_actionPerformed();
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706 alignPanel.paintAlignment(true);
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709 private void mouseOverFlag_stateChanged()
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711 viewport.followHighlight = followMouseOverFlag.getState();
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712 // TODO: could kick the scrollTo mechanism to reset view for current
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716 private void centreColumnLabelFlag_stateChanged()
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718 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
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719 this.alignPanel.annotationPanel.repaint();
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722 public void actionPerformed(ActionEvent evt)
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724 Object source = evt.getSource();
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726 if (source == inputText)
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728 inputText_actionPerformed();
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730 else if (source == loadTree)
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732 loadTree_actionPerformed();
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734 else if (source == loadApplication)
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736 launchFullApplication();
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738 else if (source == loadAnnotations)
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742 else if( source == loadScores ) {
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745 else if (source == outputAnnotations)
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747 outputAnnotations(true);
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749 else if (source == outputFeatures)
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751 outputFeatures(true, "Jalview");
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753 else if (source == closeMenuItem)
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755 closeMenuItem_actionPerformed();
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757 else if (source == copy)
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759 copy_actionPerformed();
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761 else if (source == undoMenuItem)
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763 undoMenuItem_actionPerformed();
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765 else if (source == redoMenuItem)
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767 redoMenuItem_actionPerformed();
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769 else if (source == inputText)
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771 inputText_actionPerformed();
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773 else if (source == closeMenuItem)
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775 closeMenuItem_actionPerformed();
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777 else if (source == undoMenuItem)
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779 undoMenuItem_actionPerformed();
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781 else if (source == redoMenuItem)
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783 redoMenuItem_actionPerformed();
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785 else if (source == copy)
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787 copy_actionPerformed();
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789 else if (source == pasteNew)
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791 pasteNew_actionPerformed();
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793 else if (source == pasteThis)
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795 pasteThis_actionPerformed();
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797 else if (source == cut)
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799 cut_actionPerformed();
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801 else if (source == delete)
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803 delete_actionPerformed();
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805 else if (source == grpsFromSelection)
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807 makeGrpsFromSelection_actionPerformed();
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809 else if (source == deleteGroups)
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811 deleteGroups_actionPerformed();
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813 else if (source == selectAllSequenceMenuItem)
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815 selectAllSequenceMenuItem_actionPerformed();
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817 else if (source == deselectAllSequenceMenuItem)
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819 deselectAllSequenceMenuItem_actionPerformed();
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821 else if (source == invertSequenceMenuItem)
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823 invertSequenceMenuItem_actionPerformed();
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825 else if (source == invertColSel)
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827 viewport.invertColumnSelection();
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828 alignPanel.paintAlignment(true);
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830 else if (source == remove2LeftMenuItem)
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832 trimAlignment(true);
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834 else if (source == remove2RightMenuItem)
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836 trimAlignment(false);
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838 else if (source == removeGappedColumnMenuItem)
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840 removeGappedColumnMenuItem_actionPerformed();
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842 else if (source == removeAllGapsMenuItem)
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844 removeAllGapsMenuItem_actionPerformed();
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846 else if (source == findMenuItem)
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848 findMenuItem_actionPerformed();
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850 else if (source == font)
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852 new FontChooser(alignPanel);
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854 else if (source == newView)
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858 else if (source == showColumns)
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860 viewport.showAllHiddenColumns();
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861 alignPanel.paintAlignment(true);
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863 else if (source == showSeqs)
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865 viewport.showAllHiddenSeqs();
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866 alignPanel.paintAlignment(true);
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868 else if (source == hideColumns)
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870 viewport.hideSelectedColumns();
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871 alignPanel.paintAlignment(true);
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873 else if (source == hideSequences
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874 && viewport.getSelectionGroup() != null)
\r
876 viewport.hideAllSelectedSeqs();
\r
877 alignPanel.paintAlignment(true);
\r
879 else if (source == hideAllButSelection)
\r
881 toggleHiddenRegions(false, false);
\r
882 alignPanel.paintAlignment(true);
\r
884 else if (source == hideAllSelection)
\r
886 SequenceGroup sg = viewport.getSelectionGroup();
\r
887 viewport.expandColSelection(sg, false);
\r
888 viewport.hideAllSelectedSeqs();
\r
889 viewport.hideSelectedColumns();
\r
890 alignPanel.paintAlignment(true);
\r
892 else if (source == showAllHidden)
\r
894 viewport.showAllHiddenColumns();
\r
895 viewport.showAllHiddenSeqs();
\r
896 alignPanel.paintAlignment(true);
\r
898 else if (source == showGroupConsensus)
\r
900 showGroupConsensus_actionPerformed();
\r
902 else if (source == showGroupConservation)
\r
904 showGroupConservation_actionPerformed();
\r
906 else if (source == showSequenceLogo)
\r
908 showSequenceLogo_actionPerformed();
\r
910 else if (source == showConsensusHistogram)
\r
912 showConsensusHistogram_actionPerformed();
\r
914 else if (source == applyAutoAnnotationSettings)
\r
916 applyAutoAnnotationSettings_actionPerformed();
\r
918 else if (source == featureSettings)
\r
920 new FeatureSettings(alignPanel);
\r
922 else if (source == alProperties)
\r
924 StringBuffer contents = new jalview.io.AlignmentProperties(
\r
925 viewport.alignment).formatAsString();
\r
926 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
927 cap.setText(contents.toString());
\r
928 Frame frame = new Frame();
\r
930 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
\r
931 + getTitle(), 400, 250);
\r
933 else if (source == overviewMenuItem)
\r
935 overviewMenuItem_actionPerformed();
\r
937 else if (source == noColourmenuItem)
\r
939 changeColour(null);
\r
941 else if (source == clustalColour)
\r
943 abovePIDThreshold.setState(false);
\r
944 changeColour(new ClustalxColourScheme(
\r
945 viewport.alignment.getSequences(),
\r
946 viewport.alignment.getWidth()));
\r
948 else if (source == zappoColour)
\r
950 changeColour(new ZappoColourScheme());
\r
952 else if (source == taylorColour)
\r
954 changeColour(new TaylorColourScheme());
\r
956 else if (source == hydrophobicityColour)
\r
958 changeColour(new HydrophobicColourScheme());
\r
960 else if (source == helixColour)
\r
962 changeColour(new HelixColourScheme());
\r
964 else if (source == strandColour)
\r
966 changeColour(new StrandColourScheme());
\r
968 else if (source == turnColour)
\r
970 changeColour(new TurnColourScheme());
\r
972 else if (source == buriedColour)
\r
974 changeColour(new BuriedColourScheme());
\r
976 else if (source == nucleotideColour)
\r
978 changeColour(new NucleotideColourScheme());
\r
980 else if (source == modifyPID)
\r
982 modifyPID_actionPerformed();
\r
984 else if (source == modifyConservation)
\r
986 modifyConservation_actionPerformed();
\r
988 else if (source == userDefinedColour)
\r
990 new UserDefinedColours(alignPanel, null);
\r
992 else if (source == PIDColour)
\r
994 changeColour(new PIDColourScheme());
\r
996 else if (source == BLOSUM62Colour)
\r
998 changeColour(new Blosum62ColourScheme());
\r
1000 else if (source == tcoffeeColour) {
\r
1001 changeColour(new TCoffeeColourScheme(tcoffeeScoreFile));
\r
1003 else if (source == annotationColour)
\r
1005 new AnnotationColourChooser(viewport, alignPanel);
\r
1007 else if (source == sortPairwiseMenuItem)
\r
1009 sortPairwiseMenuItem_actionPerformed();
\r
1011 else if (source == sortIDMenuItem)
\r
1013 sortIDMenuItem_actionPerformed();
\r
1015 else if (source == sortLengthMenuItem)
\r
1017 sortLengthMenuItem_actionPerformed();
\r
1019 else if (source == sortGroupMenuItem)
\r
1021 sortGroupMenuItem_actionPerformed();
\r
1023 else if (source == removeRedundancyMenuItem)
\r
1025 removeRedundancyMenuItem_actionPerformed();
\r
1027 else if (source == pairwiseAlignmentMenuItem)
\r
1029 pairwiseAlignmentMenuItem_actionPerformed();
\r
1031 else if (source == PCAMenuItem)
\r
1033 PCAMenuItem_actionPerformed();
\r
1035 else if (source == averageDistanceTreeMenuItem)
\r
1037 averageDistanceTreeMenuItem_actionPerformed();
\r
1039 else if (source == neighbourTreeMenuItem)
\r
1041 neighbourTreeMenuItem_actionPerformed();
\r
1043 else if (source == njTreeBlosumMenuItem)
\r
1045 njTreeBlosumMenuItem_actionPerformed();
\r
1047 else if (source == avDistanceTreeBlosumMenuItem)
\r
1049 avTreeBlosumMenuItem_actionPerformed();
\r
1051 else if (source == documentation)
\r
1053 documentation_actionPerformed();
\r
1055 else if (source == about)
\r
1057 about_actionPerformed();
\r
1062 public void inputText_actionPerformed()
\r
1064 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1065 Frame frame = new Frame();
\r
1067 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
\r
1070 protected void outputText_actionPerformed(ActionEvent e)
\r
1072 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1073 Frame frame = new Frame();
\r
1075 jalview.bin.JalviewLite.addFrame(frame,
\r
1076 "Alignment output - " + e.getActionCommand(), 600, 500);
\r
1077 cap.setText(new AppletFormatAdapter().formatSequences(
\r
1078 e.getActionCommand(), viewport.getAlignment(),
\r
1079 viewport.showJVSuffix));
\r
1082 public void loadAnnotations()
\r
1084 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1085 cap.setText("Paste your features / annotations file here.");
\r
1086 cap.setAnnotationImport();
\r
1087 Frame frame = new Frame();
\r
1089 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
\r
1093 public void loadScores() {
\r
1098 public String outputAnnotations(boolean displayTextbox)
\r
1100 String annotation = new AnnotationFile().printAnnotations(
\r
1101 viewport.showAnnotation ? viewport.alignment
\r
1102 .getAlignmentAnnotation() : null, viewport.alignment
\r
1104 ((Alignment) viewport.alignment).alignmentProperties);
\r
1106 if (displayTextbox)
\r
1108 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
1109 Frame frame = new Frame();
\r
1111 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
\r
1112 cap.setText(annotation);
\r
1115 return annotation;
\r
1118 private Hashtable getDisplayedFeatureCols()
\r
1120 if (alignPanel.getFeatureRenderer() != null && viewport.featuresDisplayed!=null)
\r
1122 FeatureRenderer fr = alignPanel.getFeatureRenderer();
\r
1123 Hashtable fcols = new Hashtable();
\r
1124 Enumeration en = viewport.featuresDisplayed.keys();
\r
1125 while (en.hasMoreElements())
\r
1127 Object col = en.nextElement();
\r
1128 fcols.put(col, fr.featureColours.get(col));
\r
1135 public String outputFeatures(boolean displayTextbox, String format)
\r
1138 if (format.equalsIgnoreCase("Jalview"))
\r
1140 features = new FeaturesFile().printJalviewFormat(
\r
1141 viewport.alignment.getSequencesArray(),
\r
1142 getDisplayedFeatureCols());
\r
1146 features = new FeaturesFile().printGFFFormat(
\r
1147 viewport.alignment.getSequencesArray(),
\r
1148 getDisplayedFeatureCols());
\r
1151 if (displayTextbox)
\r
1153 boolean frimport=false;
\r
1154 if (features==null || features.equals("No Features Visible"))
\r
1156 features = "# No features visible - paste some and import them here.";
\r
1160 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
\r
1163 cap.setAnnotationImport();
\r
1165 Frame frame = new Frame();
\r
1167 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
\r
1168 cap.setText(features);
\r
1170 if (features==null)
\r
1177 void launchFullApplication()
\r
1179 StringBuffer url = new StringBuffer(jalviewServletURL);
\r
1181 url.append("?open="
\r
1182 + appendProtocol(viewport.applet.getParameter("file")));
\r
1184 if (viewport.applet.getParameter("features") != null)
\r
1186 url.append("&features=");
\r
1187 url.append(appendProtocol(viewport.applet.getParameter("features")));
\r
1190 if (viewport.applet.getParameter("annotations") != null)
\r
1192 url.append("&annotations=");
\r
1193 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
\r
1196 if (viewport.applet.getParameter("jnetfile") != null)
\r
1198 url.append("&annotations=");
\r
1199 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
\r
1202 if (viewport.applet.getParameter("defaultColour") != null)
\r
1204 url.append("&colour="
\r
1205 + removeWhiteSpace(viewport.applet
\r
1206 .getParameter("defaultColour")));
\r
1209 if (viewport.applet.getParameter("userDefinedColour") != null)
\r
1211 url.append("&colour="
\r
1212 + removeWhiteSpace(viewport.applet
\r
1213 .getParameter("userDefinedColour")));
\r
1215 if (viewport.applet.getParameter("tree") != null)
\r
1217 url.append("&tree="
\r
1218 + appendProtocol(viewport.applet.getParameter("tree")));
\r
1220 if (viewport.applet.getParameter("treeFile") != null)
\r
1222 url.append("&tree="
\r
1223 + appendProtocol(viewport.applet.getParameter("treeFile")));
\r
1226 showURL(url.toString(), "FULL_APP");
\r
1229 String removeWhiteSpace(String colour)
\r
1231 StringBuffer sb = new StringBuffer();
\r
1232 for (int i = 0; i < colour.length(); i++)
\r
1234 if (Character.isWhitespace(colour.charAt(i)))
\r
1240 sb.append(colour.charAt(i));
\r
1244 return sb.toString();
\r
1247 String appendProtocol(String url)
\r
1252 url = URLEncoder.encode(url);
\r
1255 * When we finally deprecate 1.1 compatibility, we can start to use
\r
1256 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
\r
1257 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
\r
1258 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
\r
1259 * ex.printStackTrace(); }
\r
1261 catch (java.net.MalformedURLException ex)
\r
1263 url = viewport.applet.getCodeBase() + url;
\r
1268 public void closeMenuItem_actionPerformed()
\r
1270 PaintRefresher.RemoveComponent(alignPanel);
\r
1271 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
\r
1272 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
\r
1274 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
\r
1280 alignPanel = null;
\r
1287 void updateEditMenuBar()
\r
1290 if (viewport.historyList.size() > 0)
\r
1292 undoMenuItem.setEnabled(true);
\r
1293 CommandI command = (CommandI) viewport.historyList.peek();
\r
1294 undoMenuItem.setLabel("Undo " + command.getDescription());
\r
1298 undoMenuItem.setEnabled(false);
\r
1299 undoMenuItem.setLabel("Undo");
\r
1302 if (viewport.redoList.size() > 0)
\r
1304 redoMenuItem.setEnabled(true);
\r
1306 CommandI command = (CommandI) viewport.redoList.peek();
\r
1307 redoMenuItem.setLabel("Redo " + command.getDescription());
\r
1311 redoMenuItem.setEnabled(false);
\r
1312 redoMenuItem.setLabel("Redo");
\r
1316 public void addHistoryItem(CommandI command)
\r
1318 if (command.getSize() > 0)
\r
1320 viewport.historyList.push(command);
\r
1321 viewport.redoList.removeAllElements();
\r
1322 updateEditMenuBar();
\r
1323 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
1333 protected void undoMenuItem_actionPerformed()
\r
1335 if (viewport.historyList.size() < 1)
\r
1340 CommandI command = (CommandI) viewport.historyList.pop();
\r
1341 viewport.redoList.push(command);
\r
1342 command.undoCommand(null);
\r
1344 AlignViewport originalSource = getOriginatingSource(command);
\r
1346 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
1347 updateEditMenuBar();
\r
1348 originalSource.firePropertyChange("alignment", null,
\r
1349 originalSource.alignment.getSequences());
\r
1358 protected void redoMenuItem_actionPerformed()
\r
1360 if (viewport.redoList.size() < 1)
\r
1365 CommandI command = (CommandI) viewport.redoList.pop();
\r
1366 viewport.historyList.push(command);
\r
1367 command.doCommand(null);
\r
1369 AlignViewport originalSource = getOriginatingSource(command);
\r
1370 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
1372 updateEditMenuBar();
\r
1373 originalSource.firePropertyChange("alignment", null,
\r
1374 originalSource.alignment.getSequences());
\r
1377 AlignViewport getOriginatingSource(CommandI command)
\r
1379 AlignViewport originalSource = null;
\r
1380 // For sequence removal and addition, we need to fire
\r
1381 // the property change event FROM the viewport where the
\r
1382 // original alignment was altered
\r
1383 AlignmentI al = null;
\r
1384 if (command instanceof EditCommand)
\r
1386 EditCommand editCommand = (EditCommand) command;
\r
1387 al = editCommand.getAlignment();
\r
1388 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
1389 .getSequenceSetId());
\r
1390 for (int i = 0; i < comps.size(); i++)
\r
1392 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
1394 if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
\r
1396 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
\r
1403 if (originalSource == null)
\r
1405 // The original view is closed, we must validate
\r
1406 // the current view against the closed view first
\r
1409 PaintRefresher.validateSequences(al, viewport.alignment);
\r
1412 originalSource = viewport;
\r
1415 return originalSource;
\r
1418 public void moveSelectedSequences(boolean up)
\r
1420 SequenceGroup sg = viewport.getSelectionGroup();
\r
1428 for (int i = 1; i < viewport.alignment.getHeight(); i++)
\r
1430 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
1431 if (!sg.getSequences(null).contains(seq))
\r
1436 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
\r
1437 if (sg.getSequences(null).contains(temp))
\r
1442 viewport.alignment.getSequences().setElementAt(temp, i);
\r
1443 viewport.alignment.getSequences().setElementAt(seq, i - 1);
\r
1448 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
\r
1450 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
1451 if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))
\r
1456 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
\r
1457 if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))
\r
1462 viewport.alignment.getSequences().setElementAt(temp, i);
\r
1463 viewport.alignment.getSequences().setElementAt(seq, i + 1);
\r
1467 alignPanel.paintAlignment(true);
\r
1470 synchronized void slideSequences(boolean right, int size)
\r
1472 Vector sg = new Vector();
\r
1473 if (viewport.cursorMode)
\r
1475 sg.addElement(viewport.alignment
\r
1476 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
\r
1478 else if (viewport.getSelectionGroup() != null
\r
1479 && viewport.getSelectionGroup().getSize() != viewport.alignment
\r
1482 sg = viewport.getSelectionGroup().getSequences(
\r
1483 viewport.hiddenRepSequences);
\r
1486 if (sg.size() < 1)
\r
1491 Vector invertGroup = new Vector();
\r
1493 for (int i = 0; i < viewport.alignment.getHeight(); i++)
\r
1495 if (!sg.contains(viewport.alignment.getSequenceAt(i)))
\r
1496 invertGroup.addElement(viewport.alignment.getSequenceAt(i));
\r
1499 SequenceI[] seqs1 = new SequenceI[sg.size()];
\r
1500 for (int i = 0; i < sg.size(); i++)
\r
1501 seqs1[i] = (SequenceI) sg.elementAt(i);
\r
1503 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
\r
1504 for (int i = 0; i < invertGroup.size(); i++)
\r
1505 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
\r
1507 SlideSequencesCommand ssc;
\r
1509 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
\r
1510 size, viewport.getGapCharacter());
\r
1512 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
\r
1513 size, viewport.getGapCharacter());
\r
1515 int groupAdjustment = 0;
\r
1516 if (ssc.getGapsInsertedBegin() && right)
\r
1518 if (viewport.cursorMode)
\r
1519 alignPanel.seqPanel.moveCursor(size, 0);
\r
1521 groupAdjustment = size;
\r
1523 else if (!ssc.getGapsInsertedBegin() && !right)
\r
1525 if (viewport.cursorMode)
\r
1526 alignPanel.seqPanel.moveCursor(-size, 0);
\r
1528 groupAdjustment = -size;
\r
1531 if (groupAdjustment != 0)
\r
1533 viewport.getSelectionGroup().setStartRes(
\r
1534 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
\r
1535 viewport.getSelectionGroup().setEndRes(
\r
1536 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
\r
1539 boolean appendHistoryItem = false;
\r
1540 if (viewport.historyList != null && viewport.historyList.size() > 0
\r
1541 && viewport.historyList.peek() instanceof SlideSequencesCommand)
\r
1543 appendHistoryItem = ssc
\r
1544 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
\r
1548 if (!appendHistoryItem)
\r
1549 addHistoryItem(ssc);
\r
1554 static StringBuffer copiedSequences;
\r
1556 static Vector copiedHiddenColumns;
\r
1558 protected void copy_actionPerformed()
\r
1560 if (viewport.getSelectionGroup() == null)
\r
1565 SequenceGroup sg = viewport.getSelectionGroup();
\r
1566 copiedSequences = new StringBuffer();
\r
1567 Hashtable orderedSeqs = new Hashtable();
\r
1568 for (int i = 0; i < sg.getSize(); i++)
\r
1570 SequenceI seq = sg.getSequenceAt(i);
\r
1571 int index = viewport.alignment.findIndex(seq);
\r
1572 orderedSeqs.put(index + "", seq);
\r
1575 int index = 0, startRes, endRes;
\r
1578 if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
\r
1580 copiedHiddenColumns = new Vector();
\r
1581 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
\r
1582 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
\r
1585 int[] region = (int[]) viewport.getColumnSelection()
\r
1586 .getHiddenColumns().elementAt(i);
\r
1588 copiedHiddenColumns.addElement(new int[]
\r
1589 { region[0] - hiddenOffset, region[1] - hiddenOffset });
\r
1594 copiedHiddenColumns = null;
\r
1597 for (int i = 0; i < sg.getSize(); i++)
\r
1599 SequenceI seq = null;
\r
1601 while (seq == null)
\r
1603 if (orderedSeqs.containsKey(index + ""))
\r
1605 seq = (SequenceI) orderedSeqs.get(index + "");
\r
1617 // Returns residue following index if gap
\r
1618 startRes = seq.findPosition(sg.getStartRes());
\r
1621 // Need to find the residue preceeding index if gap
\r
1624 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
\r
1626 ch = seq.getCharAt(j);
\r
1627 if (!jalview.util.Comparison.isGap((ch)))
\r
1635 endRes += seq.getStart() - 1;
\r
1638 copiedSequences.append(seq.getName()
\r
1644 + seq.getSequenceAsString(sg.getStartRes(),
\r
1645 sg.getEndRes() + 1) + "\n");
\r
1650 protected void pasteNew_actionPerformed()
\r
1655 protected void pasteThis_actionPerformed()
\r
1660 void paste(boolean newAlignment)
\r
1665 if (copiedSequences == null)
\r
1670 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
1671 Vector seqs = new Vector();
\r
1672 while (st.hasMoreElements())
\r
1674 String name = st.nextToken();
\r
1675 int start = Integer.parseInt(st.nextToken());
\r
1676 int end = Integer.parseInt(st.nextToken());
\r
1677 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
\r
1679 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
1680 for (int i = 0; i < seqs.size(); i++)
\r
1682 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
1687 String newtitle = new String("Copied sequences");
\r
1688 if (getTitle().startsWith("Copied sequences"))
\r
1690 newtitle = getTitle();
\r
1694 newtitle = newtitle.concat("- from " + getTitle());
\r
1696 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
1697 viewport.applet, newtitle, false);
\r
1698 if (copiedHiddenColumns != null)
\r
1700 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
1702 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
1703 af.viewport.hideColumns(region[0], region[1]);
\r
1707 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
\r
1712 addSequences(newSeqs);
\r
1715 } catch (Exception ex)
\r
1717 } // could be anything being pasted in here
\r
1721 void addSequences(SequenceI[] seqs)
\r
1723 for (int i = 0; i < seqs.length; i++)
\r
1725 viewport.alignment.addSequence(seqs[i]);
\r
1729 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
\r
1730 seqs, 0, viewport.alignment.getWidth(), viewport.alignment));
\r
1732 viewport.setEndSeq(viewport.alignment.getHeight());
\r
1733 viewport.alignment.getWidth();
\r
1734 viewport.firePropertyChange("alignment", null,
\r
1735 viewport.alignment.getSequences());
\r
1739 protected void cut_actionPerformed()
\r
1741 copy_actionPerformed();
\r
1742 delete_actionPerformed();
\r
1745 protected void delete_actionPerformed()
\r
1748 SequenceGroup sg = viewport.getSelectionGroup();
\r
1754 Vector seqs = new Vector();
\r
1756 for (int i = 0; i < sg.getSize(); i++)
\r
1758 seq = sg.getSequenceAt(i);
\r
1759 seqs.addElement(seq);
\r
1762 // If the cut affects all sequences, remove highlighted columns
\r
1763 if (sg.getSize() == viewport.alignment.getHeight())
\r
1765 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
1766 sg.getEndRes() + 1);
\r
1769 SequenceI[] cut = new SequenceI[seqs.size()];
\r
1770 for (int i = 0; i < seqs.size(); i++)
\r
1772 cut[i] = (SequenceI) seqs.elementAt(i);
\r
1776 * //ADD HISTORY ITEM
\r
1778 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
\r
1779 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
\r
1780 viewport.alignment));
\r
1782 viewport.setSelectionGroup(null);
\r
1783 viewport.alignment.deleteGroup(sg);
\r
1785 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1788 if (viewport.getAlignment().getHeight() < 1)
\r
1790 this.setVisible(false);
\r
1792 viewport.sendSelection();
\r
1796 * group consensus toggled
\r
1799 protected void showGroupConsensus_actionPerformed()
\r
1801 viewport.setShowGroupConsensus(showGroupConsensus.getState());
\r
1802 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1807 * group conservation toggled.
\r
1809 protected void showGroupConservation_actionPerformed()
\r
1811 viewport.setShowGroupConservation(showGroupConservation.getState());
\r
1812 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1819 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
\r
1820 * .event.ActionEvent)
\r
1822 protected void showConsensusHistogram_actionPerformed()
\r
1824 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
\r
1825 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1831 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
\r
1832 * .event.ActionEvent)
\r
1834 protected void showSequenceLogo_actionPerformed()
\r
1836 viewport.setShowSequenceLogo(showSequenceLogo.getState());
\r
1837 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1840 protected void applyAutoAnnotationSettings_actionPerformed()
\r
1842 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1845 protected void makeGrpsFromSelection_actionPerformed()
\r
1847 if (viewport.getSelectionGroup() != null)
\r
1849 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
\r
1850 viewport.getSequenceSelection(),
\r
1851 viewport.getAlignmentView(true).getSequenceStrings(
\r
1852 viewport.getGapCharacter()),
\r
1853 viewport.alignment.getGroups());
\r
1854 viewport.alignment.deleteAllGroups();
\r
1855 viewport.sequenceColours = null;
\r
1856 viewport.setSelectionGroup(null);
\r
1857 // set view properties for each group
\r
1858 for (int g = 0; g < gps.length; g++)
\r
1860 // gps[g].setShowunconserved(viewport.getShowUnconserved());
\r
1861 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
\r
1862 viewport.alignment.addGroup(gps[g]);
\r
1863 Color col = new Color((int) (Math.random() * 255),
\r
1864 (int) (Math.random() * 255), (int) (Math.random() * 255));
\r
1865 col = col.brighter();
\r
1866 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
\r
1867 .hasMoreElements(); viewport.setSequenceColour(
\r
1868 (SequenceI) sq.nextElement(), col))
\r
1871 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
\r
1872 alignPanel.updateAnnotation();
\r
1873 alignPanel.paintAlignment(true);
\r
1877 protected void deleteGroups_actionPerformed()
\r
1879 viewport.alignment.deleteAllGroups();
\r
1880 viewport.sequenceColours = null;
\r
1881 viewport.setSelectionGroup(null);
\r
1883 alignPanel.paintAlignment(true);
\r
1886 public void selectAllSequenceMenuItem_actionPerformed()
\r
1888 SequenceGroup sg = new SequenceGroup();
\r
1889 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1891 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
1893 sg.setEndRes(viewport.alignment.getWidth() - 1);
\r
1894 viewport.setSelectionGroup(sg);
\r
1895 alignPanel.paintAlignment(true);
\r
1896 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1897 viewport.sendSelection();
\r
1900 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1902 if (viewport.cursorMode)
\r
1904 alignPanel.seqPanel.keyboardNo1 = null;
\r
1905 alignPanel.seqPanel.keyboardNo2 = null;
\r
1907 viewport.setSelectionGroup(null);
\r
1908 viewport.getColumnSelection().clear();
\r
1909 viewport.setSelectionGroup(null);
\r
1910 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1911 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1912 alignPanel.paintAlignment(true);
\r
1913 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1914 viewport.sendSelection();
\r
1917 public void invertSequenceMenuItem_actionPerformed()
\r
1919 SequenceGroup sg = viewport.getSelectionGroup();
\r
1920 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1922 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1925 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1926 viewport.sendSelection();
\r
1929 public void invertColSel_actionPerformed()
\r
1931 viewport.invertColumnSelection();
\r
1932 alignPanel.paintAlignment(true);
\r
1933 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1934 viewport.sendSelection();
\r
1937 void trimAlignment(boolean trimLeft)
\r
1939 ColumnSelection colSel = viewport.getColumnSelection();
\r
1942 if (colSel.size() > 0)
\r
1946 column = colSel.getMin();
\r
1950 column = colSel.getMax();
\r
1954 if (viewport.getSelectionGroup() != null)
\r
1956 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
1957 viewport.hiddenRepSequences);
\r
1961 seqs = viewport.alignment.getSequencesArray();
\r
1964 TrimRegionCommand trimRegion;
\r
1967 trimRegion = new TrimRegionCommand("Remove Left",
\r
1968 TrimRegionCommand.TRIM_LEFT, seqs, column,
\r
1969 viewport.alignment, viewport.colSel,
\r
1970 viewport.selectionGroup);
\r
1971 viewport.setStartRes(0);
\r
1975 trimRegion = new TrimRegionCommand("Remove Right",
\r
1976 TrimRegionCommand.TRIM_RIGHT, seqs, column,
\r
1977 viewport.alignment, viewport.colSel,
\r
1978 viewport.selectionGroup);
\r
1981 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
\r
1983 addHistoryItem(trimRegion);
\r
1985 Vector groups = viewport.alignment.getGroups();
\r
1987 for (int i = 0; i < groups.size(); i++)
\r
1989 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1991 if ((trimLeft && !sg.adjustForRemoveLeft(column))
\r
1992 || (!trimLeft && !sg.adjustForRemoveRight(column)))
\r
1994 viewport.alignment.deleteGroup(sg);
\r
1998 viewport.firePropertyChange("alignment", null, viewport
\r
1999 .getAlignment().getSequences());
\r
2003 public void removeGappedColumnMenuItem_actionPerformed()
\r
2005 int start = 0, end = viewport.alignment.getWidth() - 1;
\r
2008 if (viewport.getSelectionGroup() != null)
\r
2010 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2011 viewport.hiddenRepSequences);
\r
2012 start = viewport.getSelectionGroup().getStartRes();
\r
2013 end = viewport.getSelectionGroup().getEndRes();
\r
2017 seqs = viewport.alignment.getSequencesArray();
\r
2020 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
\r
2021 "Remove Gapped Columns", seqs, start, end, viewport.alignment);
\r
2023 addHistoryItem(removeGapCols);
\r
2025 statusBar.setText("Removed " + removeGapCols.getSize()
\r
2026 + " empty columns.");
\r
2028 // This is to maintain viewport position on first residue
\r
2029 // of first sequence
\r
2030 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
2031 int startRes = seq.findPosition(viewport.startRes);
\r
2032 // ShiftList shifts;
\r
2033 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
\r
2034 // edit.alColumnChanges=shifts.getInverse();
\r
2035 // if (viewport.hasHiddenColumns)
\r
2036 // viewport.getColumnSelection().compensateForEdits(shifts);
\r
2037 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
2038 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
2043 public void removeAllGapsMenuItem_actionPerformed()
\r
2045 int start = 0, end = viewport.alignment.getWidth() - 1;
\r
2048 if (viewport.getSelectionGroup() != null)
\r
2050 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2051 viewport.hiddenRepSequences);
\r
2052 start = viewport.getSelectionGroup().getStartRes();
\r
2053 end = viewport.getSelectionGroup().getEndRes();
\r
2057 seqs = viewport.alignment.getSequencesArray();
\r
2060 // This is to maintain viewport position on first residue
\r
2061 // of first sequence
\r
2062 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
2063 int startRes = seq.findPosition(viewport.startRes);
\r
2065 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
\r
2066 viewport.alignment));
\r
2068 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
2070 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
2075 public void findMenuItem_actionPerformed()
\r
2077 new Finder(alignPanel);
\r
2081 * create a new view derived from the current view
\r
2083 * @param viewtitle
\r
2084 * @return frame for the new view
\r
2086 public AlignFrame newView(String viewtitle)
\r
2089 if (viewport.hasHiddenRows)
\r
2091 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
\r
2092 .getFullAlignment().getSequencesArray());
\r
2096 newal = new Alignment(viewport.alignment.getSequencesArray());
\r
2099 if (viewport.alignment.getAlignmentAnnotation() != null)
\r
2101 for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)
\r
2103 if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
\r
2105 newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);
\r
2110 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
\r
2112 newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
\r
2113 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
\r
2114 PaintRefresher.Register(newaf.alignPanel,
\r
2115 newaf.alignPanel.av.getSequenceSetId());
\r
2117 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
\r
2118 newaf.alignPanel.av.getSequenceSetId());
\r
2119 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
\r
2120 newaf.alignPanel.av.getSequenceSetId());
\r
2122 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
2123 .getSequenceSetId());
\r
2124 int viewSize = -1;
\r
2125 for (int i = 0; i < comps.size(); i++)
\r
2127 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
2133 String title = new String(this.getTitle());
\r
2134 if (viewtitle != null)
\r
2136 title = viewtitle + " ( " + title + ")";
\r
2140 if (title.indexOf("(View") > -1)
\r
2142 title = title.substring(0, title.indexOf("(View"));
\r
2144 title += "(View " + viewSize + ")";
\r
2147 newaf.setTitle(title.toString());
\r
2149 newaf.viewport.historyList = viewport.historyList;
\r
2150 newaf.viewport.redoList = viewport.redoList;
\r
2156 * @return list of feature groups on the view
\r
2158 public String[] getFeatureGroups()
\r
2160 FeatureRenderer fr = null;
\r
2161 if (alignPanel != null
\r
2162 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2164 return fr.getGroups();
\r
2170 * get sequence feature groups that are hidden or shown
\r
2176 public String[] getFeatureGroupsOfState(boolean visible)
\r
2178 FeatureRenderer fr = null;
\r
2179 if (alignPanel != null
\r
2180 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2182 return fr.getGroups(visible);
\r
2188 * Change the display state for the given feature groups
\r
2191 * list of group strings
\r
2193 * visible or invisible
\r
2195 public void setFeatureGroupState(String[] groups, boolean state)
\r
2197 FeatureRenderer fr = null;
\r
2198 this.sequenceFeatures.setState(true);
\r
2199 viewport.showSequenceFeatures(true);
\r
2200 if (alignPanel != null
\r
2201 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2203 fr.setGroupState(groups, state);
\r
2204 alignPanel.seqPanel.seqCanvas.repaint();
\r
2205 if (alignPanel.overviewPanel != null)
\r
2207 alignPanel.overviewPanel.updateOverviewImage();
\r
2212 public void seqLimits_itemStateChanged()
\r
2214 viewport.setShowJVSuffix(seqLimits.getState());
\r
2215 alignPanel.fontChanged();
\r
2216 alignPanel.paintAlignment(true);
\r
2219 protected void colourTextMenuItem_actionPerformed()
\r
2221 viewport.setColourText(colourTextMenuItem.getState());
\r
2222 alignPanel.paintAlignment(true);
\r
2225 protected void displayNonconservedMenuItem_actionPerformed()
\r
2227 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
\r
2228 alignPanel.paintAlignment(true);
\r
2231 protected void wrapMenuItem_actionPerformed()
\r
2233 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
2234 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
2235 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
2236 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
2237 scaleRight.setEnabled(wrapMenuItem.getState());
\r
2238 alignPanel.paintAlignment(true);
\r
2241 public void overviewMenuItem_actionPerformed()
\r
2243 if (alignPanel.overviewPanel != null)
\r
2248 Frame frame = new Frame();
\r
2249 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
2250 frame.add(overview);
\r
2251 // +50 must allow for applet frame window
\r
2252 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
2253 overview.getPreferredSize().width,
\r
2254 overview.getPreferredSize().height + 50);
\r
2257 frame.addWindowListener(new WindowAdapter()
\r
2259 public void windowClosing(WindowEvent e)
\r
2261 alignPanel.setOverviewPanel(null);
\r
2265 alignPanel.setOverviewPanel(overview);
\r
2269 void changeColour(ColourSchemeI cs)
\r
2271 int threshold = 0;
\r
2275 if (viewport.getAbovePIDThreshold())
\r
2277 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
2280 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2282 viewport.setGlobalColourScheme(cs);
\r
2286 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2289 if (viewport.getConservationSelected())
\r
2292 Alignment al = (Alignment) viewport.alignment;
\r
2293 Conservation c = new Conservation("All",
\r
2294 ResidueProperties.propHash, 3, al.getSequences(), 0,
\r
2295 al.getWidth() - 1);
\r
2298 c.verdict(false, viewport.ConsPercGaps);
\r
2300 cs.setConservation(c);
\r
2302 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
\r
2303 cs, "Background"));
\r
2308 cs.setConservation(null);
\r
2311 cs.setConsensus(viewport.hconsensus);
\r
2314 viewport.setGlobalColourScheme(cs);
\r
2316 if (viewport.getColourAppliesToAllGroups())
\r
2318 Vector groups = viewport.alignment.getGroups();
\r
2319 for (int i = 0; i < groups.size(); i++)
\r
2321 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
2328 if (cs instanceof ClustalxColourScheme)
\r
2330 sg.cs = new ClustalxColourScheme(
\r
2331 sg.getSequences(viewport.hiddenRepSequences),
\r
2338 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
2339 } catch (Exception ex)
\r
2341 ex.printStackTrace();
\r
2346 if (viewport.getAbovePIDThreshold()
\r
2347 || cs instanceof PIDColourScheme
\r
2348 || cs instanceof Blosum62ColourScheme)
\r
2350 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2351 sg.cs.setConsensus(AAFrequency.calculate(
\r
2352 sg.getSequences(viewport.hiddenRepSequences), 0,
\r
2357 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2360 if (viewport.getConservationSelected())
\r
2362 Conservation c = new Conservation("Group",
\r
2363 ResidueProperties.propHash, 3,
\r
2364 sg.getSequences(viewport.hiddenRepSequences), 0,
\r
2365 viewport.alignment.getWidth() - 1);
\r
2367 c.verdict(false, viewport.ConsPercGaps);
\r
2368 sg.cs.setConservation(c);
\r
2372 sg.cs.setConservation(null);
\r
2373 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2379 if (alignPanel.getOverviewPanel() != null)
\r
2381 alignPanel.getOverviewPanel().updateOverviewImage();
\r
2384 jalview.structure.StructureSelectionManager
\r
2385 .getStructureSelectionManager(viewport.applet).sequenceColoursChanged(
\r
2388 alignPanel.paintAlignment(true);
\r
2391 protected void modifyPID_actionPerformed()
\r
2393 if (viewport.getAbovePIDThreshold()
\r
2394 && viewport.globalColourScheme != null)
\r
2396 SliderPanel.setPIDSliderSource(alignPanel,
\r
2397 viewport.getGlobalColourScheme(), "Background");
\r
2398 SliderPanel.showPIDSlider();
\r
2402 protected void modifyConservation_actionPerformed()
\r
2404 if (viewport.getConservationSelected()
\r
2405 && viewport.globalColourScheme != null)
\r
2407 SliderPanel.setConservationSlider(alignPanel,
\r
2408 viewport.globalColourScheme, "Background");
\r
2409 SliderPanel.showConservationSlider();
\r
2413 protected void conservationMenuItem_actionPerformed()
\r
2415 viewport.setConservationSelected(conservationMenuItem.getState());
\r
2417 viewport.setAbovePIDThreshold(false);
\r
2418 abovePIDThreshold.setState(false);
\r
2420 changeColour(viewport.getGlobalColourScheme());
\r
2422 modifyConservation_actionPerformed();
\r
2425 public void abovePIDThreshold_actionPerformed()
\r
2427 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
2429 conservationMenuItem.setState(false);
\r
2430 viewport.setConservationSelected(false);
\r
2432 changeColour(viewport.getGlobalColourScheme());
\r
2434 modifyPID_actionPerformed();
\r
2437 public void sortPairwiseMenuItem_actionPerformed()
\r
2439 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2440 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
\r
2441 .getAlignment().getSequenceAt(0), null);
\r
2443 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
\r
2444 viewport.alignment));
\r
2445 alignPanel.paintAlignment(true);
\r
2448 public void sortIDMenuItem_actionPerformed()
\r
2450 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2451 AlignmentSorter.sortByID(viewport.getAlignment());
\r
2452 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
\r
2453 alignPanel.paintAlignment(true);
\r
2456 public void sortLengthMenuItem_actionPerformed()
\r
2458 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2459 AlignmentSorter.sortByLength(viewport.getAlignment());
\r
2460 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
\r
2461 viewport.alignment));
\r
2462 alignPanel.paintAlignment(true);
\r
2465 public void sortGroupMenuItem_actionPerformed()
\r
2467 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2468 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
2469 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
\r
2470 viewport.alignment));
\r
2471 alignPanel.paintAlignment(true);
\r
2475 public void removeRedundancyMenuItem_actionPerformed()
\r
2477 new RedundancyPanel(alignPanel);
\r
2480 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
2482 if (viewport.getSelectionGroup() != null
\r
2483 && viewport.getSelectionGroup().getSize() > 1)
\r
2485 Frame frame = new Frame();
\r
2486 frame.add(new PairwiseAlignPanel(alignPanel));
\r
2487 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
\r
2492 public void PCAMenuItem_actionPerformed()
\r
2494 // are the sequences aligned?
\r
2495 if (!viewport.alignment.isAligned(false))
\r
2497 SequenceI current;
\r
2498 int Width = viewport.getAlignment().getWidth();
\r
2500 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2502 current = viewport.getAlignment().getSequenceAt(i);
\r
2504 if (current.getLength() < Width)
\r
2506 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2509 alignPanel.paintAlignment(true);
\r
2512 if ((viewport.getSelectionGroup() != null
\r
2513 && viewport.getSelectionGroup().getSize() < 4 && viewport
\r
2514 .getSelectionGroup().getSize() > 0)
\r
2515 || viewport.getAlignment().getHeight() < 4)
\r
2522 new PCAPanel(viewport);
\r
2523 } catch (java.lang.OutOfMemoryError ex)
\r
2529 public void averageDistanceTreeMenuItem_actionPerformed()
\r
2531 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
2534 public void neighbourTreeMenuItem_actionPerformed()
\r
2536 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
2539 protected void njTreeBlosumMenuItem_actionPerformed()
\r
2541 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2544 protected void avTreeBlosumMenuItem_actionPerformed()
\r
2546 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2549 void NewTreePanel(String type, String pwType, String title)
\r
2551 // are the sequences aligned?
\r
2552 if (!viewport.alignment.isAligned(false))
\r
2554 SequenceI current;
\r
2555 int Width = viewport.getAlignment().getWidth();
\r
2557 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2559 current = viewport.getAlignment().getSequenceAt(i);
\r
2561 if (current.getLength() < Width)
\r
2563 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2566 alignPanel.paintAlignment(true);
\r
2570 if ((viewport.getSelectionGroup() != null && viewport
\r
2571 .getSelectionGroup().getSize() > 1)
\r
2572 || (viewport.getSelectionGroup() == null && viewport.alignment
\r
2573 .getHeight() > 1))
\r
2575 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
\r
2577 addTreeMenuItem(tp, title);
\r
2579 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
2583 void loadTree_actionPerformed()
\r
2585 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
2586 cap.setText("Paste your Newick tree file here.");
\r
2587 cap.setTreeImport();
\r
2588 Frame frame = new Frame();
\r
2590 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
2593 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
2595 TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
\r
2596 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
2597 addTreeMenuItem(tp, treeFile);
\r
2601 * sort the alignment using the given treePanel
\r
2603 * @param treePanel
\r
2604 * tree used to sort view
\r
2606 * string used for undo event name
\r
2608 public void sortByTree(TreePanel treePanel, String title)
\r
2610 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2612 .sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
2613 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2614 // HistoryItem.SORT));
\r
2615 addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
\r
2616 viewport.alignment));
\r
2617 alignPanel.paintAlignment(true);
\r
2621 * Do any automatic reordering of the alignment and add the necessary bits to
\r
2622 * the menu structure for the new tree
\r
2624 * @param treePanel
\r
2627 protected void addTreeMenuItem(final TreePanel treePanel,
\r
2628 final String title)
\r
2630 final MenuItem item = new MenuItem(title);
\r
2631 sortByTreeMenu.add(item);
\r
2632 item.addActionListener(new java.awt.event.ActionListener()
\r
2634 public void actionPerformed(ActionEvent evt)
\r
2636 sortByTree(treePanel, title); // treePanel.getTitle());
\r
2640 treePanel.addWindowListener(new WindowAdapter()
\r
2642 public void windowOpened(WindowEvent e)
\r
2644 if (viewport.sortByTree)
\r
2646 sortByTree(treePanel, title);
\r
2648 super.windowOpened(e);
\r
2651 public void windowClosing(WindowEvent e)
\r
2653 sortByTreeMenu.remove(item);
\r
2657 public boolean sortBy(AlignmentOrder alorder, String undoname)
\r
2659 SequenceI[] oldOrder = viewport.getAlignment()
\r
2660 .getSequencesArray();
\r
2661 if (viewport.applet.debug)
\r
2663 System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");
\r
2665 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
\r
2666 if (undoname!=null)
\r
2668 addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.alignment));
\r
2670 alignPanel.paintAlignment(true);
\r
2674 protected void documentation_actionPerformed()
\r
2676 alignPanel.av.applet.openJalviewHelpUrl();
\r
2679 protected void about_actionPerformed()
\r
2682 class AboutPanel extends Canvas
\r
2688 public AboutPanel(String version, String builddate)
\r
2690 this.version = version;
\r
2691 this.builddate = builddate;
\r
2694 public void paint(Graphics g)
\r
2696 g.setColor(Color.white);
\r
2697 g.fillRect(0, 0, getSize().width, getSize().height);
\r
2698 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2699 FontMetrics fm = g.getFontMetrics();
\r
2700 int fh = fm.getHeight();
\r
2702 g.setColor(Color.black);
\r
2703 // TODO: update this text for each release or centrally store it for
\r
2704 // lite and application
\r
2705 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
2706 g.drawString("JalviewLite - Release " + version, x, y += fh);
\r
2707 g.setFont(new Font("Helvetica", Font.BOLD, 12));
\r
2708 g.drawString("Build date: " + builddate, x, y += fh);
\r
2709 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2711 "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",
\r
2712 x, y += fh * 1.5);
\r
2713 g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
\r
2715 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
\r
2718 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
\r
2720 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
\r
2722 "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
\r
2725 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
\r
2727 g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
\r
2732 Frame frame = new Frame();
\r
2733 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
\r
2734 .getBuildDate()));
\r
2735 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
\r
2739 public void showURL(String url, String target)
\r
2741 if (viewport.applet == null)
\r
2743 System.out.println("Not running as applet - no browser available.");
\r
2747 viewport.applet.showURL(url, target);
\r
2751 // ////////////////////////////////////////////////////////////////////////////////
\r
2752 // JBuilder Graphics here
\r
2754 MenuBar alignFrameMenuBar = new MenuBar();
\r
2756 Menu fileMenu = new Menu("File");
\r
2758 MenuItem loadApplication = new MenuItem("View in Full Application");
\r
2760 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
\r
2762 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
\r
2764 MenuItem loadScores = new MenuItem("Load Associated T-Coffee scores ...");
\r
2766 MenuItem outputFeatures = new MenuItem("Export Features ...");
\r
2768 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
\r
2770 MenuItem closeMenuItem = new MenuItem("Close");
\r
2772 Menu editMenu = new Menu("Edit");
\r
2774 Menu viewMenu = new Menu("View");
\r
2776 Menu colourMenu = new Menu("Colour");
\r
2778 Menu calculateMenu = new Menu("Calculate");
\r
2780 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
2782 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
2784 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
2786 MenuItem remove2LeftMenuItem = new MenuItem();
\r
2788 MenuItem remove2RightMenuItem = new MenuItem();
\r
2790 MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
2792 MenuItem removeAllGapsMenuItem = new MenuItem();
\r
2794 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
2796 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
2798 MenuItem sortPairwiseMenuItem = new MenuItem();
\r
2800 MenuItem sortIDMenuItem = new MenuItem();
\r
2802 MenuItem sortLengthMenuItem = new MenuItem();
\r
2804 MenuItem sortGroupMenuItem = new MenuItem();
\r
2806 MenuItem removeRedundancyMenuItem = new MenuItem();
\r
2808 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
2810 MenuItem PCAMenuItem = new MenuItem();
\r
2812 MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
2814 MenuItem neighbourTreeMenuItem = new MenuItem();
\r
2816 BorderLayout borderLayout1 = new BorderLayout();
\r
2818 public Label statusBar = new Label();
\r
2820 Menu outputTextboxMenu = new Menu();
\r
2822 MenuItem clustalColour = new MenuItem();
\r
2824 MenuItem zappoColour = new MenuItem();
\r
2826 MenuItem taylorColour = new MenuItem();
\r
2828 MenuItem hydrophobicityColour = new MenuItem();
\r
2830 MenuItem helixColour = new MenuItem();
\r
2832 MenuItem strandColour = new MenuItem();
\r
2834 MenuItem turnColour = new MenuItem();
\r
2836 MenuItem buriedColour = new MenuItem();
\r
2838 MenuItem userDefinedColour = new MenuItem();
\r
2840 MenuItem PIDColour = new MenuItem();
\r
2842 MenuItem BLOSUM62Colour = new MenuItem();
\r
2844 MenuItem tcoffeeColour = new MenuItem();
\r
2846 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
2848 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
2850 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
2852 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
2854 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
\r
2856 MenuItem alProperties = new MenuItem("Alignment Properties...");
\r
2858 MenuItem overviewMenuItem = new MenuItem();
\r
2860 MenuItem undoMenuItem = new MenuItem();
\r
2862 MenuItem redoMenuItem = new MenuItem();
\r
2864 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
2866 MenuItem noColourmenuItem = new MenuItem();
\r
2868 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
2870 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
2872 MenuItem findMenuItem = new MenuItem();
\r
2874 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
2876 MenuItem nucleotideColour = new MenuItem();
\r
2878 MenuItem deleteGroups = new MenuItem();
\r
2880 MenuItem grpsFromSelection = new MenuItem();
\r
2882 MenuItem delete = new MenuItem();
\r
2884 MenuItem copy = new MenuItem();
\r
2886 MenuItem cut = new MenuItem();
\r
2888 Menu pasteMenu = new Menu();
\r
2890 MenuItem pasteNew = new MenuItem();
\r
2892 MenuItem pasteThis = new MenuItem();
\r
2894 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
2896 MenuItem font = new MenuItem();
\r
2898 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
2900 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
2902 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
2904 MenuItem modifyPID = new MenuItem();
\r
2906 MenuItem modifyConservation = new MenuItem();
\r
2908 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
\r
2909 "Autocalculate Consensus", true);
\r
2911 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
\r
2912 "Sort Alignment With New Tree", true);
\r
2914 Menu sortByTreeMenu = new Menu();
\r
2916 Menu sort = new Menu();
\r
2918 Menu calculate = new Menu();
\r
2920 MenuItem inputText = new MenuItem();
\r
2922 Menu helpMenu = new Menu();
\r
2924 MenuItem documentation = new MenuItem();
\r
2926 MenuItem about = new MenuItem();
\r
2928 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
2930 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
\r
2932 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
\r
2933 Menu autoAnnMenu=new Menu();
\r
2934 CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();
\r
2935 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
\r
2936 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
\r
2937 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
\r
2938 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
\r
2940 private void jbInit() throws Exception
\r
2943 setMenuBar(alignFrameMenuBar);
\r
2947 // dynamically fill save as menu with available formats
\r
2948 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
2951 item = new MenuItem(
\r
2952 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
2954 item.addActionListener(new java.awt.event.ActionListener()
\r
2956 public void actionPerformed(ActionEvent e)
\r
2958 outputText_actionPerformed(e);
\r
2962 outputTextboxMenu.add(item);
\r
2964 closeMenuItem.addActionListener(this);
\r
2965 loadApplication.addActionListener(this);
\r
2967 loadTree.addActionListener(this);
\r
2968 loadAnnotations.addActionListener(this);
\r
2969 loadScores.addActionListener(this);
\r
2970 outputFeatures.addActionListener(this);
\r
2971 outputAnnotations.addActionListener(this);
\r
2972 selectAllSequenceMenuItem.addActionListener(this);
\r
2973 deselectAllSequenceMenuItem.addActionListener(this);
\r
2974 invertSequenceMenuItem.addActionListener(this);
\r
2975 remove2LeftMenuItem.setLabel("Remove Left");
\r
2976 remove2LeftMenuItem.addActionListener(this);
\r
2977 remove2RightMenuItem.setLabel("Remove Right");
\r
2978 remove2RightMenuItem.addActionListener(this);
\r
2979 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
2980 removeGappedColumnMenuItem.addActionListener(this);
\r
2981 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
2982 removeAllGapsMenuItem.addActionListener(this);
\r
2983 viewBoxesMenuItem.setLabel("Boxes");
\r
2984 viewBoxesMenuItem.setState(true);
\r
2985 viewBoxesMenuItem.addItemListener(this);
\r
2986 viewTextMenuItem.setLabel("Text");
\r
2987 viewTextMenuItem.setState(true);
\r
2988 viewTextMenuItem.addItemListener(this);
\r
2989 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
2990 sortPairwiseMenuItem.addActionListener(this);
\r
2991 sortIDMenuItem.setLabel("by ID");
\r
2992 sortIDMenuItem.addActionListener(this);
\r
2993 sortLengthMenuItem.setLabel("by Length");
\r
2994 sortLengthMenuItem.addActionListener(this);
\r
2995 sortGroupMenuItem.setLabel("by Group");
\r
2996 sortGroupMenuItem.addActionListener(this);
\r
2997 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
2998 removeRedundancyMenuItem.addActionListener(this);
\r
2999 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
3000 pairwiseAlignmentMenuItem.addActionListener(this);
\r
3001 PCAMenuItem.setLabel("Principal Component Analysis");
\r
3002 PCAMenuItem.addActionListener(this);
\r
3003 averageDistanceTreeMenuItem
\r
3004 .setLabel("Average Distance Using % Identity");
\r
3005 averageDistanceTreeMenuItem.addActionListener(this);
\r
3006 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
3007 neighbourTreeMenuItem.addActionListener(this);
\r
3008 statusBar.setBackground(Color.white);
\r
3009 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
3010 statusBar.setText("Status bar");
\r
3011 outputTextboxMenu.setLabel("Output to Textbox");
\r
3012 clustalColour.setLabel("Clustalx");
\r
3014 clustalColour.addActionListener(this);
\r
3015 zappoColour.setLabel("Zappo");
\r
3016 zappoColour.addActionListener(this);
\r
3017 taylorColour.setLabel("Taylor");
\r
3018 taylorColour.addActionListener(this);
\r
3019 hydrophobicityColour.setLabel("Hydrophobicity");
\r
3020 hydrophobicityColour.addActionListener(this);
\r
3021 helixColour.setLabel("Helix Propensity");
\r
3022 helixColour.addActionListener(this);
\r
3023 strandColour.setLabel("Strand Propensity");
\r
3024 strandColour.addActionListener(this);
\r
3025 turnColour.setLabel("Turn Propensity");
\r
3026 turnColour.addActionListener(this);
\r
3027 buriedColour.setLabel("Buried Index");
\r
3028 buriedColour.addActionListener(this);
\r
3029 userDefinedColour.setLabel("User Defined...");
\r
3030 userDefinedColour.addActionListener(this);
\r
3031 PIDColour.setLabel("Percentage Identity");
\r
3032 PIDColour.addActionListener(this);
\r
3033 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
3034 BLOSUM62Colour.addActionListener(this);
\r
3035 tcoffeeColour.setLabel("T-Coffee Scores");
\r
3036 tcoffeeColour.setEnabled(false); // it will enabled only if a score file is provided
\r
3037 tcoffeeColour.addActionListener(this);
\r
3038 avDistanceTreeBlosumMenuItem .setLabel("Average Distance Using BLOSUM62");
\r
3039 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
3040 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
3041 njTreeBlosumMenuItem.addActionListener(this);
\r
3042 annotationPanelMenuItem.setLabel("Show Annotations");
\r
3043 annotationPanelMenuItem.addItemListener(this);
\r
3044 colourTextMenuItem.setLabel("Colour Text");
\r
3045 colourTextMenuItem.addItemListener(this);
\r
3046 displayNonconservedMenuItem.setLabel("Show nonconserved");
\r
3047 displayNonconservedMenuItem.addItemListener(this);
\r
3048 alProperties.addActionListener(this);
\r
3049 overviewMenuItem.setLabel("Overview Window");
\r
3050 overviewMenuItem.addActionListener(this);
\r
3051 undoMenuItem.setEnabled(false);
\r
3052 undoMenuItem.setLabel("Undo");
\r
3053 undoMenuItem.addActionListener(this);
\r
3054 redoMenuItem.setEnabled(false);
\r
3055 redoMenuItem.setLabel("Redo");
\r
3056 redoMenuItem.addActionListener(this);
\r
3057 conservationMenuItem.setLabel("by Conservation");
\r
3058 conservationMenuItem.addItemListener(this);
\r
3059 noColourmenuItem.setLabel("None");
\r
3060 noColourmenuItem.addActionListener(this);
\r
3061 wrapMenuItem.setLabel("Wrap");
\r
3062 wrapMenuItem.addItemListener(this);
\r
3063 renderGapsMenuItem.setLabel("Show Gaps");
\r
3064 renderGapsMenuItem.setState(true);
\r
3065 renderGapsMenuItem.addItemListener(this);
\r
3066 findMenuItem.setLabel("Find...");
\r
3067 findMenuItem.addActionListener(this);
\r
3068 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
3069 abovePIDThreshold.addItemListener(this);
\r
3070 nucleotideColour.setLabel("Nucleotide");
\r
3071 nucleotideColour.addActionListener(this);
\r
3072 deleteGroups.setLabel("Undefine Groups");
\r
3073 deleteGroups.addActionListener(this);
\r
3074 grpsFromSelection.setLabel("Make Groups for selection");
\r
3075 grpsFromSelection.addActionListener(this);
\r
3076 copy.setLabel("Copy");
\r
3077 copy.addActionListener(this);
\r
3078 cut.setLabel("Cut");
\r
3079 cut.addActionListener(this);
\r
3080 delete.setLabel("Delete");
\r
3081 delete.addActionListener(this);
\r
3082 pasteMenu.setLabel("Paste");
\r
3083 pasteNew.setLabel("To New Alignment");
\r
3084 pasteNew.addActionListener(this);
\r
3085 pasteThis.setLabel("Add To This Alignment");
\r
3086 pasteThis.addActionListener(this);
\r
3087 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
3088 applyToAllGroups.setState(true);
\r
3089 applyToAllGroups.addItemListener(this);
\r
3090 font.setLabel("Font...");
\r
3091 font.addActionListener(this);
\r
3092 scaleAbove.setLabel("Scale Above");
\r
3093 scaleAbove.setState(true);
\r
3094 scaleAbove.setEnabled(false);
\r
3095 scaleAbove.addItemListener(this);
\r
3096 scaleLeft.setEnabled(false);
\r
3097 scaleLeft.setState(true);
\r
3098 scaleLeft.setLabel("Scale Left");
\r
3099 scaleLeft.addItemListener(this);
\r
3100 scaleRight.setEnabled(false);
\r
3101 scaleRight.setState(true);
\r
3102 scaleRight.setLabel("Scale Right");
\r
3103 scaleRight.addItemListener(this);
\r
3104 modifyPID.setLabel("Modify Identity Threshold...");
\r
3105 modifyPID.addActionListener(this);
\r
3106 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
3107 modifyConservation.addActionListener(this);
\r
3108 sortByTreeMenu.setLabel("By Tree Order");
\r
3109 sort.setLabel("Sort");
\r
3110 calculate.setLabel("Calculate Tree");
\r
3111 autoCalculate.addItemListener(this);
\r
3112 sortByTree.addItemListener(this);
\r
3113 inputText.setLabel("Input from textbox");
\r
3114 inputText.addActionListener(this);
\r
3115 centreColumnLabelFlag.setLabel("Centre column labels");
\r
3116 centreColumnLabelFlag.addItemListener(this);
\r
3117 followMouseOverFlag.setLabel("Automatic Scrolling");
\r
3118 followMouseOverFlag.addItemListener(this);
\r
3119 helpMenu.setLabel("Help");
\r
3120 documentation.setLabel("Documentation");
\r
3121 documentation.addActionListener(this);
\r
3123 about.setLabel("About...");
\r
3124 about.addActionListener(this);
\r
3125 seqLimits.setState(true);
\r
3126 seqLimits.setLabel("Show Sequence Limits");
\r
3127 seqLimits.addItemListener(this);
\r
3128 featureSettings.setLabel("Feature Settings...");
\r
3129 featureSettings.addActionListener(this);
\r
3130 sequenceFeatures.setLabel("Sequence Features");
\r
3131 sequenceFeatures.addItemListener(this);
\r
3132 sequenceFeatures.setState(false);
\r
3133 annotationColour.setLabel("by Annotation...");
\r
3134 annotationColour.addActionListener(this);
\r
3135 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
3136 invertColSel.setLabel("Invert Column Selection");
\r
3137 menu1.setLabel("Show");
\r
3138 showColumns.setLabel("All Columns ");
\r
3139 showSeqs.setLabel("All Sequences");
\r
3140 menu2.setLabel("Hide");
\r
3141 hideColumns.setLabel("Selected Columns");
\r
3142 hideSequences.setLabel("Selected Sequences");
\r
3143 hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
\r
3144 hideAllSelection.setLabel("Selected Region");
\r
3145 showAllHidden.setLabel("All Sequences and Columns");
\r
3146 showGroupConsensus.setLabel("Group Consensus");
\r
3147 showGroupConservation.setLabel("Group Conservation");
\r
3148 showConsensusHistogram.setLabel("Show Consensus Histogram");
\r
3149 showSequenceLogo.setLabel("Show Consensus Logo");
\r
3150 applyAutoAnnotationSettings.setLabel("Apply to all groups");
\r
3151 applyAutoAnnotationSettings.setState(true);
\r
3152 autoAnnMenu.setLabel("Autocalculated Annotation");
\r
3154 invertColSel.addActionListener(this);
\r
3155 showColumns.addActionListener(this);
\r
3156 showSeqs.addActionListener(this);
\r
3157 hideColumns.addActionListener(this);
\r
3158 hideSequences.addActionListener(this);
\r
3159 hideAllButSelection.addActionListener(this);
\r
3160 hideAllSelection.addActionListener(this);
\r
3161 showAllHidden.addActionListener(this);
\r
3162 showGroupConsensus.addItemListener(this);
\r
3163 showGroupConservation.addItemListener(this);
\r
3164 showConsensusHistogram.addItemListener(this);
\r
3165 showSequenceLogo.addItemListener(this);
\r
3166 applyAutoAnnotationSettings.addItemListener(this);
\r
3167 formatMenu.setLabel("Format");
\r
3168 selectMenu.setLabel("Select");
\r
3169 newView.setLabel("New View");
\r
3170 newView.addActionListener(this);
\r
3171 alignFrameMenuBar.add(fileMenu);
\r
3172 alignFrameMenuBar.add(editMenu);
\r
3173 alignFrameMenuBar.add(selectMenu);
\r
3174 alignFrameMenuBar.add(viewMenu);
\r
3175 alignFrameMenuBar.add(formatMenu);
\r
3176 alignFrameMenuBar.add(colourMenu);
\r
3177 alignFrameMenuBar.add(calculateMenu);
\r
3178 alignFrameMenuBar.add(helpMenu);
\r
3180 fileMenu.add(inputText);
\r
3181 fileMenu.add(loadTree);
\r
3182 fileMenu.add(loadAnnotations);
\r
3183 fileMenu.add(loadScores);
\r
3185 fileMenu.addSeparator();
\r
3186 fileMenu.add(outputTextboxMenu);
\r
3187 fileMenu.add(outputFeatures);
\r
3188 fileMenu.add(outputAnnotations);
\r
3190 if (jalviewServletURL != null)
\r
3192 fileMenu.add(loadApplication);
\r
3195 fileMenu.addSeparator();
\r
3196 fileMenu.add(closeMenuItem);
\r
3198 editMenu.add(undoMenuItem);
\r
3199 editMenu.add(redoMenuItem);
\r
3200 editMenu.add(cut);
\r
3201 editMenu.add(copy);
\r
3202 editMenu.add(pasteMenu);
\r
3203 editMenu.add(delete);
\r
3204 editMenu.addSeparator();
\r
3205 editMenu.add(remove2LeftMenuItem);
\r
3206 editMenu.add(remove2RightMenuItem);
\r
3207 editMenu.add(removeGappedColumnMenuItem);
\r
3208 editMenu.add(removeAllGapsMenuItem);
\r
3209 editMenu.add(removeRedundancyMenuItem);
\r
3210 viewMenu.add(newView);
\r
3211 viewMenu.addSeparator();
\r
3212 viewMenu.add(menu1);
\r
3213 viewMenu.add(menu2);
\r
3214 viewMenu.addSeparator();
\r
3215 viewMenu.add(followMouseOverFlag);
\r
3216 viewMenu.add(annotationPanelMenuItem);
\r
3217 autoAnnMenu.add(applyAutoAnnotationSettings);
\r
3218 autoAnnMenu.add(showConsensusHistogram);
\r
3219 autoAnnMenu.add(showSequenceLogo);
\r
3220 autoAnnMenu.addSeparator();
\r
3221 autoAnnMenu.add(showGroupConservation);
\r
3222 autoAnnMenu.add(showGroupConsensus);
\r
3223 viewMenu.add(autoAnnMenu);
\r
3224 viewMenu.addSeparator();
\r
3225 viewMenu.add(sequenceFeatures);
\r
3226 viewMenu.add(featureSettings);
\r
3227 viewMenu.addSeparator();
\r
3228 viewMenu.add(alProperties);
\r
3229 viewMenu.addSeparator();
\r
3230 viewMenu.add(overviewMenuItem);
\r
3231 colourMenu.add(applyToAllGroups);
\r
3232 colourMenu.addSeparator();
\r
3233 colourMenu.add(noColourmenuItem);
\r
3234 colourMenu.add(clustalColour);
\r
3235 colourMenu.add(BLOSUM62Colour);
\r
3236 colourMenu.add(PIDColour);
\r
3237 colourMenu.add(zappoColour);
\r
3238 colourMenu.add(taylorColour);
\r
3239 colourMenu.add(hydrophobicityColour);
\r
3240 colourMenu.add(helixColour);
\r
3241 colourMenu.add(strandColour);
\r
3242 colourMenu.add(turnColour);
\r
3243 colourMenu.add(buriedColour);
\r
3244 colourMenu.add(nucleotideColour);
\r
3245 colourMenu.add(tcoffeeColour);
\r
3246 colourMenu.add(userDefinedColour);
\r
3247 colourMenu.addSeparator();
\r
3248 colourMenu.add(conservationMenuItem);
\r
3249 colourMenu.add(modifyConservation);
\r
3250 colourMenu.add(abovePIDThreshold);
\r
3251 colourMenu.add(modifyPID);
\r
3252 colourMenu.add(annotationColour);
\r
3253 calculateMenu.add(sort);
\r
3254 calculateMenu.add(calculate);
\r
3255 calculateMenu.addSeparator();
\r
3256 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
3257 calculateMenu.add(PCAMenuItem);
\r
3258 calculateMenu.add(autoCalculate);
\r
3259 calculateMenu.add(sortByTree);
\r
3260 this.add(statusBar, BorderLayout.SOUTH);
\r
3261 pasteMenu.add(pasteNew);
\r
3262 pasteMenu.add(pasteThis);
\r
3263 sort.add(sortIDMenuItem);
\r
3264 sort.add(sortLengthMenuItem);
\r
3265 sort.add(sortByTreeMenu);
\r
3266 sort.add(sortGroupMenuItem);
\r
3267 sort.add(sortPairwiseMenuItem);
\r
3268 calculate.add(averageDistanceTreeMenuItem);
\r
3269 calculate.add(neighbourTreeMenuItem);
\r
3270 calculate.add(avDistanceTreeBlosumMenuItem);
\r
3271 calculate.add(njTreeBlosumMenuItem);
\r
3272 helpMenu.add(documentation);
\r
3273 helpMenu.add(about);
\r
3274 menu1.add(showColumns);
\r
3275 menu1.add(showSeqs);
\r
3276 menu1.add(showAllHidden);
\r
3277 menu2.add(hideColumns);
\r
3278 menu2.add(hideSequences);
\r
3279 menu2.add(hideAllSelection);
\r
3280 menu2.add(hideAllButSelection);
\r
3281 formatMenu.add(font);
\r
3282 formatMenu.add(seqLimits);
\r
3283 formatMenu.add(wrapMenuItem);
\r
3284 formatMenu.add(scaleAbove);
\r
3285 formatMenu.add(scaleLeft);
\r
3286 formatMenu.add(scaleRight);
\r
3287 formatMenu.add(viewBoxesMenuItem);
\r
3288 formatMenu.add(viewTextMenuItem);
\r
3289 formatMenu.add(colourTextMenuItem);
\r
3290 formatMenu.add(displayNonconservedMenuItem);
\r
3291 formatMenu.add(renderGapsMenuItem);
\r
3292 formatMenu.add(centreColumnLabelFlag);
\r
3293 selectMenu.add(findMenuItem);
\r
3294 selectMenu.addSeparator();
\r
3295 selectMenu.add(selectAllSequenceMenuItem);
\r
3296 selectMenu.add(deselectAllSequenceMenuItem);
\r
3297 selectMenu.add(invertSequenceMenuItem);
\r
3298 selectMenu.add(invertColSel);
\r
3299 selectMenu.add(grpsFromSelection);
\r
3300 selectMenu.add(deleteGroups);
\r
3304 MenuItem featureSettings = new MenuItem();
\r
3306 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
3308 MenuItem annotationColour = new MenuItem();
\r
3310 MenuItem invertColSel = new MenuItem();
\r
3312 Menu menu1 = new Menu();
\r
3314 MenuItem showColumns = new MenuItem();
\r
3316 MenuItem showSeqs = new MenuItem();
\r
3318 Menu menu2 = new Menu();
\r
3320 MenuItem hideColumns = new MenuItem();
\r
3322 MenuItem hideSequences = new MenuItem();
\r
3324 MenuItem hideAllButSelection = new MenuItem();
\r
3326 MenuItem hideAllSelection = new MenuItem();
\r
3328 MenuItem showAllHidden = new MenuItem();
\r
3330 Menu formatMenu = new Menu();
\r
3332 Menu selectMenu = new Menu();
\r
3334 MenuItem newView = new MenuItem();
\r
3337 * Attach the alignFrame panels after embedding menus, if necessary. This used
\r
3338 * to be called setEmbedded, but is now creates the dropdown menus in a
\r
3339 * platform independent manner to avoid OSX/Mac menu appendage daftness.
\r
3341 * @param reallyEmbedded
\r
3342 * true to attach the view to the applet area on the page rather than
\r
3345 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
\r
3347 if (reallyEmbedded)
\r
3350 // Explicly build the embedded menu panel for the on-page applet
\r
3352 // view cannot be closed if its actually on the page
\r
3353 fileMenu.remove(closeMenuItem);
\r
3354 fileMenu.remove(3); // Remove Seperator
\r
3355 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
\r
3356 Font.PLAIN, 10, false); // use our own fonts.
\r
3357 // and actually add the components to the applet area
\r
3358 viewport.applet.setLayout(new BorderLayout());
\r
3359 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
\r
3360 viewport.applet.add(statusBar, BorderLayout.SOUTH);
\r
3361 alignPanel.setSize(viewport.applet.getSize().width,
\r
3362 viewport.applet.getSize().height - embeddedMenu.HEIGHT
\r
3363 - statusBar.HEIGHT);
\r
3364 viewport.applet.add(alignPanel, BorderLayout.CENTER);
\r
3365 final AlignFrame me = this;
\r
3366 viewport.applet.addFocusListener(new FocusListener()
\r
3370 public void focusLost(FocusEvent e)
\r
3372 if (me.viewport.applet.currentAlignFrame==me) {
\r
3373 me.viewport.applet.currentAlignFrame = null;
\r
3377 public void focusGained(FocusEvent e)
\r
3379 me.viewport.applet.currentAlignFrame = me;
\r
3382 viewport.applet.validate();
\r
3387 // test and embed menu bar if necessary.
\r
3389 if (embedMenuIfNeeded(alignPanel))
\r
3391 // adjust for status bar height too
\r
3392 alignPanel.setSize(getSize().width, getSize().height
\r
3393 - statusBar.HEIGHT);
\r
3395 add(statusBar, BorderLayout.SOUTH);
\r
3396 add(alignPanel, BorderLayout.CENTER);
\r
3397 // and register with the applet so it can pass external API calls to us
\r
3398 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
\r
3404 * create a new binding between structures in an existing jmol viewer instance
\r
3405 * and an alignpanel with sequences that have existing PDBFile entries. Note,
\r
3406 * this does not open a new Jmol window, or modify the display of the
\r
3407 * structures in the original jmol window. Note This method doesn't work
\r
3408 * without an additional javascript library to exchange messages between the
\r
3409 * distinct applets. See http://issues.jalview.org/browse/JAL-621
\r
3412 * JmolViewer instance
\r
3413 * @param sequenceIds
\r
3414 * - sequence Ids to search for associations
\r
3416 public SequenceStructureBinding addStructureViewInstance(
\r
3417 Object jmolviewer, String[] sequenceIds)
\r
3419 org.jmol.api.JmolViewer viewer = null;
\r
3422 viewer = (org.jmol.api.JmolViewer) jmolviewer;
\r
3423 } catch (ClassCastException ex)
\r
3425 System.err.println("Unsupported viewer object :"
\r
3426 + jmolviewer.getClass());
\r
3428 if (viewer == null)
\r
3430 System.err.println("Can't use this object as a structure viewer:"
\r
3431 + jmolviewer.getClass());
\r
3434 SequenceI[] seqs = null;
\r
3435 if (sequenceIds == null || sequenceIds.length == 0)
\r
3437 seqs = viewport.getAlignment().getSequencesArray();
\r
3441 Vector sqi = new Vector();
\r
3442 AlignmentI al = viewport.getAlignment();
\r
3443 for (int sid = 0; sid < sequenceIds.length; sid++)
\r
3445 SequenceI sq = al.findName(sequenceIds[sid]);
\r
3448 sqi.addElement(sq);
\r
3451 if (sqi.size() > 0)
\r
3453 seqs = new SequenceI[sqi.size()];
\r
3454 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
\r
3456 seqs[sid] = (SequenceI) sqi.elementAt(sid);
\r
3464 ExtJmol jmv = null;
\r
3465 // TODO: search for a jmv that involves viewer
\r
3467 { // create a new viewer/jalview binding.
\r
3468 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs});
\r
3474 * bind a pdb file to a sequence in the current view
\r
3476 * @param sequenceId
\r
3477 * - sequenceId within the dataset.
\r
3478 * @param pdbEntryString
\r
3479 * - the short name for the PDB file
\r
3481 * - pdb file - either a URL or a valid PDB file.
\r
3482 * @return true if binding was as success TODO: consider making an exception
\r
3483 * structure for indicating when PDB parsing or sequenceId location
\r
3486 public boolean addPdbFile(String sequenceId, String pdbEntryString,
\r
3489 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
\r
3490 boolean needtoadd = false;
\r
3491 if (toaddpdb != null)
\r
3493 Vector pdbe = toaddpdb.getPDBId();
\r
3494 PDBEntry pdbentry = null;
\r
3495 if (pdbe != null && pdbe.size() > 0)
\r
3497 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
\r
3499 pdbentry = (PDBEntry) pdbe.elementAt(pe);
\r
3500 if (!pdbentry.getId().equals(pdbEntryString)
\r
3501 && !pdbentry.getFile().equals(pdbFile))
\r
3511 if (pdbentry == null)
\r
3513 pdbentry = new PDBEntry();
\r
3514 pdbentry.setId(pdbEntryString);
\r
3515 pdbentry.setFile(pdbFile);
\r
3516 needtoadd = true; // add this new entry to sequence.
\r
3518 // resolve data source
\r
3519 // TODO: this code should be a refactored to an io package
\r
3520 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
\r
3521 if (protocol == null)
\r
3527 // make a note of the access mode and add
\r
3528 if (pdbentry.getProperty() == null)
\r
3530 pdbentry.setProperty(new Hashtable());
\r
3532 pdbentry.getProperty().put("protocol", protocol);
\r
3533 toaddpdb.addPDBId(pdbentry);
\r
3539 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
\r
3543 Vector sequences = new Vector();
\r
3544 for (int i = 0; i < seqs.length; i++)
\r
3546 if (seqs[i] != null)
\r
3548 sequences.addElement(new Object[]
\r
3549 { seqs[i], (chains != null) ? chains[i] : null });
\r
3552 seqs = new SequenceI[sequences.size()];
\r
3553 chains = new String[sequences.size()];
\r
3554 for (int i = 0, isize = sequences.size(); i < isize; i++)
\r
3556 Object[] oj = (Object[]) sequences.elementAt(i);
\r
3558 seqs[i] = (SequenceI) oj[0];
\r
3559 chains[i] = (String) oj[1];
\r
3562 return new Object[]
\r
3567 public void newStructureView(JalviewLite applet, PDBEntry pdb,
\r
3568 SequenceI[] seqs, String[] chains, String protocol)
\r
3570 // Scrub any null sequences from the array
\r
3571 Object[] sqch = cleanSeqChainArrays(seqs, chains);
\r
3572 seqs = (SequenceI[]) sqch[0];
\r
3573 chains = (String[]) sqch[1];
\r
3574 if (seqs == null || seqs.length == 0)
\r
3577 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
\r
3579 if (protocol == null || protocol.trim().length() == 0
\r
3580 || protocol.equals("null"))
\r
3582 protocol = (String) pdb.getProperty().get("protocol");
\r
3583 if (protocol == null)
\r
3585 System.err.println("Couldn't work out protocol to open structure: "
\r
3590 if (applet.useXtrnalSviewer)
\r
3592 // register the association(s) and quit, don't create any windows.
\r
3593 if (StructureSelectionManager.getStructureSelectionManager(applet).setMapping(seqs, chains, pdb.getFile(), protocol)==null) {
\r
3594 System.err.println("Failed to map "+pdb.getFile()+" ("+protocol+") to any sequences");
\r
3598 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
\r
3600 // can only do alignments with Jmol
\r
3601 // find the last jmol window assigned to this alignment
\r
3602 jalview.appletgui.AppletJmol ajm = null, tajm;
\r
3603 Vector jmols = applet
\r
3604 .getAppletWindow(jalview.appletgui.AppletJmol.class);
\r
3605 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
\r
3607 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
\r
3608 if (tajm.ap.alignFrame == this)
\r
3617 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
\r
3618 // try and add the pdb structure
\r
3623 // otherwise, create a new window
\r
3624 if (applet.jmolAvailable)
\r
3626 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
\r
3628 applet.lastFrameX += 40;
\r
3629 applet.lastFrameY += 40;
\r
3633 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
\r
3638 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
\r
3639 SequenceI[][] seqs, String[][] chains, String[] protocols)
\r
3641 // TODO Auto-generated method stub
\r
3642 System.err.println("Aligned Structure View: Not yet implemented.");
\r
3646 * modify the current selection, providing the user has not made a selection already.
\r
3647 * @param sel - sequences from this alignment
\r
3648 * @param csel - columns to be selected on the alignment
\r
3650 public void select(SequenceGroup sel, ColumnSelection csel)
\r
3652 alignPanel.seqPanel.selection(sel, csel, null);
\r
3655 public void scrollTo(int row, int column)
\r
3657 alignPanel.seqPanel.scrollTo(row, column);
\r
3659 public void scrollToRow(int row)
\r
3661 alignPanel.seqPanel.scrollToRow(row);
\r
3663 public void scrollToColumn(int column)
\r
3665 alignPanel.seqPanel.scrollToColumn(column);
\r
3668 * @return the alignments unique ID.
\r
3670 public String getSequenceSetId() {
\r
3671 return viewport.getSequenceSetId();
\r
3676 * Load the (T-Coffee) score file from the specified url
\r
3678 * @param url The absolute path from where download and read the score file
\r
3679 * @throws IOException
\r
3681 public void loadScoreFile( URL url ) throws IOException {
\r
3683 TCoffeeScoreFile file = TCoffeeScoreFile.load( new InputStreamReader( url.openStream() ) );
\r
3684 if( file == null ) {
\r
3685 throw new RuntimeException("The file provided does not match the T-Coffee scores file format");
\r
3688 tcoffeeColour.setEnabled(true);
\r
3689 tcoffeeScoreFile = file;
\r
3691 // switch to this color
\r
3692 changeColour(new TCoffeeColourScheme(tcoffeeScoreFile));
\r