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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104 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title, boolean embedded)
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106 if (applet != null)
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108 jalviewServletURL = applet.getParameter("APPLICATION_URL");
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114 } catch (Exception ex)
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116 ex.printStackTrace();
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119 viewport = new AlignViewport(al, applet);
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120 alignPanel = new AlignmentPanel(this, viewport);
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122 viewport.updateConservation(alignPanel);
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123 viewport.updateConsensus(alignPanel);
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125 annotationPanelMenuItem.setState(viewport.showAnnotation);
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126 displayNonconservedMenuItem.setState(viewport.getShowunconserved());
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127 followMouseOverFlag.setState(viewport.getFollowHighlight());
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128 showGroupConsensus.setState(viewport.showGroupConsensus);
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129 showGroupConservation.setState(viewport.showGroupConservation);
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130 showConsensusHistogram.setState(viewport.showConsensusHistogram);
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131 showSequenceLogo.setState(viewport.showSequenceLogo);
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133 seqLimits.setState(viewport.showJVSuffix);
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135 if (applet != null)
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137 String param = applet.getParameter("sortBy");
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140 if (param.equalsIgnoreCase("Id"))
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142 sortIDMenuItem_actionPerformed();
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144 else if (param.equalsIgnoreCase("Pairwise Identity"))
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146 sortPairwiseMenuItem_actionPerformed();
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148 else if (param.equalsIgnoreCase("Length"))
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150 sortLengthMenuItem_actionPerformed();
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154 param = applet.getParameter("wrap");
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157 if (param.equalsIgnoreCase("true"))
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159 wrapMenuItem.setState(true);
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160 wrapMenuItem_actionPerformed();
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163 param = applet.getParameter("centrecolumnlabels");
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166 centreColumnLabelFlag.setState(true);
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167 centreColumnLabelFlag_stateChanged();
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171 param = applet.getParameter("windowWidth");
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174 int width = Integer.parseInt(param);
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175 DEFAULT_WIDTH = width;
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177 param = applet.getParameter("windowHeight");
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180 int height = Integer.parseInt(param);
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181 DEFAULT_HEIGHT = height;
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183 } catch (Exception ex)
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189 // Some JVMS send keyevents to Top frame or lowest panel,
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190 // Havent worked out why yet. So add to both this frame and seqCanvas for
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192 this.addKeyListener(this);
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193 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
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194 alignPanel.idPanel.idCanvas.addKeyListener(this);
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195 alignPanel.scalePanel.addKeyListener(this);
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196 alignPanel.annotationPanel.addKeyListener(this);
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197 alignPanel.annotationPanelHolder.addKeyListener(this);
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198 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
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199 alignPanel.alabels.addKeyListener(this);
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200 createAlignFrameWindow(embedded, title);
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203 alignPanel.adjustAnnotationHeight();
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204 alignPanel.paintAlignment(true);
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207 public AlignViewport getAlignViewport()
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212 public SeqCanvas getSeqcanvas()
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214 return alignPanel.seqPanel.seqCanvas;
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218 * Load a features file onto the alignment
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220 * @param file file URL, content, or other resolvable path
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221 * @param type is protocol for accessing data referred to by file
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224 public void parseFeaturesFile(String file, String type)
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226 parseFeaturesFile(file, type, true);
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230 * Load a features file onto the alignment
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232 * @param file file URL, content, or other resolvable path
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233 * @param type is protocol for accessing data referred to by file
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234 * @param autoenabledisplay when true, display features flag will be automatically enabled if features are loaded
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236 public void parseFeaturesFile(String file, String type, boolean autoenabledisplay)
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238 Hashtable featureLinks = new Hashtable();
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239 boolean featuresFile = false;
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242 featuresFile = new jalview.io.FeaturesFile(file, type)
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243 .parse(viewport.alignment,
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244 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
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245 featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));
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246 } catch (Exception ex)
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248 ex.printStackTrace();
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253 if (featureLinks.size() > 0)
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255 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
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257 if (autoenabledisplay)
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259 viewport.showSequenceFeatures = true;
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260 sequenceFeatures.setState(true);
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262 if (viewport.featureSettings != null)
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264 viewport.featureSettings.refreshTable();
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266 alignPanel.paintAlignment(true);
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271 public void keyPressed(KeyEvent evt)
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273 if (viewport.cursorMode
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274 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
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275 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
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276 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
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277 && Character.isDigit(evt.getKeyChar()))
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278 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
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280 switch (evt.getKeyCode())
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282 case 27: // escape key
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283 deselectAllSequenceMenuItem_actionPerformed();
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285 alignPanel.alabels.cancelDrag();
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287 case KeyEvent.VK_X:
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288 if (evt.isControlDown() || evt.isMetaDown())
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290 cut_actionPerformed();
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293 case KeyEvent.VK_C:
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294 if (viewport.cursorMode && !evt.isControlDown())
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296 alignPanel.seqPanel.setCursorColumn();
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298 if (evt.isControlDown() || evt.isMetaDown())
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300 copy_actionPerformed();
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303 case KeyEvent.VK_V:
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304 if (evt.isControlDown())
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306 paste(evt.isShiftDown());
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309 case KeyEvent.VK_A:
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310 if (evt.isControlDown() || evt.isMetaDown())
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312 selectAllSequenceMenuItem_actionPerformed();
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315 case KeyEvent.VK_DOWN:
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316 if (viewport.cursorMode)
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318 alignPanel.seqPanel.moveCursor(0, 1);
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322 moveSelectedSequences(false);
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326 case KeyEvent.VK_UP:
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327 if (viewport.cursorMode)
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329 alignPanel.seqPanel.moveCursor(0, -1);
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333 moveSelectedSequences(true);
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337 case KeyEvent.VK_LEFT:
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338 if (evt.isAltDown() || !viewport.cursorMode)
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339 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
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341 alignPanel.seqPanel.moveCursor(-1, 0);
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344 case KeyEvent.VK_RIGHT:
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345 if (evt.isAltDown() || !viewport.cursorMode)
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346 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
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348 alignPanel.seqPanel.moveCursor(1, 0);
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351 case KeyEvent.VK_SPACE:
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352 if (viewport.cursorMode)
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354 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
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355 || evt.isShiftDown() || evt.isAltDown());
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359 case KeyEvent.VK_DELETE:
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360 case KeyEvent.VK_BACK_SPACE:
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361 if (viewport.cursorMode)
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363 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
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364 || evt.isShiftDown() || evt.isAltDown());
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368 cut_actionPerformed();
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369 alignPanel.seqPanel.seqCanvas.repaint();
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373 case KeyEvent.VK_S:
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374 if (viewport.cursorMode)
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376 alignPanel.seqPanel.setCursorRow();
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379 case KeyEvent.VK_P:
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380 if (viewport.cursorMode)
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382 alignPanel.seqPanel.setCursorPosition();
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386 case KeyEvent.VK_ENTER:
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387 case KeyEvent.VK_COMMA:
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388 if (viewport.cursorMode)
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390 alignPanel.seqPanel.setCursorRowAndColumn();
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394 case KeyEvent.VK_Q:
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395 if (viewport.cursorMode)
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397 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
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400 case KeyEvent.VK_M:
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401 if (viewport.cursorMode)
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403 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
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407 case KeyEvent.VK_F2:
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408 viewport.cursorMode = !viewport.cursorMode;
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409 statusBar.setText("Keyboard editing mode is "
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410 + (viewport.cursorMode ? "on" : "off"));
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411 if (viewport.cursorMode)
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413 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
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414 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
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418 case KeyEvent.VK_F:
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419 if (evt.isControlDown())
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421 findMenuItem_actionPerformed();
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425 case KeyEvent.VK_H:
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427 boolean toggleSeqs = !evt.isControlDown();
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428 boolean toggleCols = !evt.isShiftDown();
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429 toggleHiddenRegions(toggleSeqs, toggleCols);
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433 case KeyEvent.VK_PAGE_UP:
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434 if (viewport.wrapAlignment)
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436 alignPanel.scrollUp(true);
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440 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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441 - viewport.endSeq + viewport.startSeq);
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445 case KeyEvent.VK_PAGE_DOWN:
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446 if (viewport.wrapAlignment)
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448 alignPanel.scrollUp(false);
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452 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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453 + viewport.endSeq - viewport.startSeq);
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457 case KeyEvent.VK_Z:
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458 if (evt.isControlDown())
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460 undoMenuItem_actionPerformed();
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464 case KeyEvent.VK_Y:
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465 if (evt.isControlDown())
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467 redoMenuItem_actionPerformed();
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471 case KeyEvent.VK_L:
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472 if (evt.isControlDown())
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474 trimAlignment(true);
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478 case KeyEvent.VK_R:
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479 if (evt.isControlDown())
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481 trimAlignment(false);
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485 case KeyEvent.VK_E:
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486 if (evt.isControlDown())
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488 if (evt.isShiftDown())
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490 this.removeAllGapsMenuItem_actionPerformed();
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494 removeGappedColumnMenuItem_actionPerformed();
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498 case KeyEvent.VK_I:
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499 if (evt.isControlDown())
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501 if (evt.isAltDown())
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503 invertColSel_actionPerformed();
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507 invertSequenceMenuItem_actionPerformed();
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512 case KeyEvent.VK_U:
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513 if (evt.isControlDown())
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515 this.deleteGroups_actionPerformed();
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519 case KeyEvent.VK_T:
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520 if (evt.isControlDown())
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527 alignPanel.paintAlignment(true);
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531 * called by key handler and the hide all/show all menu items
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533 * @param toggleSeqs
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534 * @param toggleCols
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536 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
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538 boolean hide = false;
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539 SequenceGroup sg = viewport.getSelectionGroup();
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540 if (!toggleSeqs && !toggleCols)
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542 // Hide everything by the current selection - this is a hack - we do the
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543 // invert and then hide
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544 // first check that there will be visible columns after the invert.
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545 if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
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546 .getSelected().size() > 0)
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547 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
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550 // now invert the sequence set, if required - empty selection implies
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551 // that no hiding is required.
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554 invertSequenceMenuItem_actionPerformed();
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555 sg = viewport.getSelectionGroup();
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559 viewport.expandColSelection(sg, true);
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560 // finally invert the column selection and get the new sequence
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561 // selection and indicate it should be hidden.
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562 invertColSel_actionPerformed();
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569 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
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572 viewport.hideAllSelectedSeqs();
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574 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
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576 viewport.showAllHiddenSeqs();
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582 if (viewport.colSel.getSelected().size() > 0)
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584 viewport.hideSelectedColumns();
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587 viewport.selectionGroup = sg;
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592 viewport.showAllHiddenColumns();
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597 public void keyReleased(KeyEvent evt)
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601 public void keyTyped(KeyEvent evt)
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605 public void itemStateChanged(ItemEvent evt)
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607 if (evt.getSource() == displayNonconservedMenuItem)
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609 displayNonconservedMenuItem_actionPerformed();
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611 else if (evt.getSource() == colourTextMenuItem)
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613 colourTextMenuItem_actionPerformed();
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615 else if (evt.getSource() == wrapMenuItem)
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617 wrapMenuItem_actionPerformed();
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619 else if (evt.getSource() == scaleAbove)
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621 viewport.setScaleAboveWrapped(scaleAbove.getState());
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623 else if (evt.getSource() == scaleLeft)
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625 viewport.setScaleLeftWrapped(scaleLeft.getState());
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627 else if (evt.getSource() == scaleRight)
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629 viewport.setScaleRightWrapped(scaleRight.getState());
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631 else if (evt.getSource() == seqLimits)
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633 seqLimits_itemStateChanged();
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635 else if (evt.getSource() == viewBoxesMenuItem)
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637 viewport.setShowBoxes(viewBoxesMenuItem.getState());
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639 else if (evt.getSource() == viewTextMenuItem)
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641 viewport.setShowText(viewTextMenuItem.getState());
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643 else if (evt.getSource() == renderGapsMenuItem)
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645 viewport.setRenderGaps(renderGapsMenuItem.getState());
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647 else if (evt.getSource() == annotationPanelMenuItem)
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649 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
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650 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
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652 else if (evt.getSource() == sequenceFeatures)
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654 viewport.showSequenceFeatures(sequenceFeatures.getState());
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655 alignPanel.seqPanel.seqCanvas.repaint();
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657 else if (evt.getSource() == conservationMenuItem)
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659 conservationMenuItem_actionPerformed();
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661 else if (evt.getSource() == abovePIDThreshold)
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663 abovePIDThreshold_actionPerformed();
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665 else if (evt.getSource() == applyToAllGroups)
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667 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
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669 else if (evt.getSource() == autoCalculate)
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671 viewport.autocalculateConsensus = autoCalculate.getState();
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673 else if (evt.getSource() == sortByTree)
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675 viewport.sortByTree = sortByTree.getState();
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677 else if (evt.getSource() == this.centreColumnLabelFlag)
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679 centreColumnLabelFlag_stateChanged();
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681 else if (evt.getSource() == this.followMouseOverFlag)
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683 mouseOverFlag_stateChanged();
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685 else if (evt.getSource() == showGroupConsensus)
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687 showGroupConsensus_actionPerformed();
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689 else if (evt.getSource() == showGroupConservation)
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691 showGroupConservation_actionPerformed();
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693 else if (evt.getSource() == showSequenceLogo)
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695 showSequenceLogo_actionPerformed();
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697 else if (evt.getSource() == showConsensusHistogram)
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699 showConsensusHistogram_actionPerformed();
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701 else if (evt.getSource() == applyAutoAnnotationSettings)
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703 applyAutoAnnotationSettings_actionPerformed();
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705 alignPanel.paintAlignment(true);
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708 private void mouseOverFlag_stateChanged()
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710 viewport.followHighlight = followMouseOverFlag.getState();
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711 // TODO: could kick the scrollTo mechanism to reset view for current
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715 private void centreColumnLabelFlag_stateChanged()
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717 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
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718 this.alignPanel.annotationPanel.repaint();
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721 public void actionPerformed(ActionEvent evt)
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723 Object source = evt.getSource();
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725 if (source == inputText)
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727 inputText_actionPerformed();
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729 else if (source == loadTree)
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731 loadTree_actionPerformed();
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733 else if (source == loadApplication)
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735 launchFullApplication();
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737 else if (source == loadAnnotations)
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741 else if( source == loadScores ) {
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744 else if (source == outputAnnotations)
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746 outputAnnotations(true);
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748 else if (source == outputFeatures)
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750 outputFeatures(true, "Jalview");
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752 else if (source == closeMenuItem)
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754 closeMenuItem_actionPerformed();
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756 else if (source == copy)
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758 copy_actionPerformed();
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760 else if (source == undoMenuItem)
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762 undoMenuItem_actionPerformed();
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764 else if (source == redoMenuItem)
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766 redoMenuItem_actionPerformed();
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768 else if (source == inputText)
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770 inputText_actionPerformed();
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772 else if (source == closeMenuItem)
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774 closeMenuItem_actionPerformed();
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776 else if (source == undoMenuItem)
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778 undoMenuItem_actionPerformed();
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780 else if (source == redoMenuItem)
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782 redoMenuItem_actionPerformed();
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784 else if (source == copy)
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786 copy_actionPerformed();
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788 else if (source == pasteNew)
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790 pasteNew_actionPerformed();
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792 else if (source == pasteThis)
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794 pasteThis_actionPerformed();
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796 else if (source == cut)
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798 cut_actionPerformed();
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800 else if (source == delete)
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802 delete_actionPerformed();
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804 else if (source == grpsFromSelection)
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806 makeGrpsFromSelection_actionPerformed();
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808 else if (source == deleteGroups)
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810 deleteGroups_actionPerformed();
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812 else if (source == selectAllSequenceMenuItem)
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814 selectAllSequenceMenuItem_actionPerformed();
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816 else if (source == deselectAllSequenceMenuItem)
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818 deselectAllSequenceMenuItem_actionPerformed();
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820 else if (source == invertSequenceMenuItem)
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822 invertSequenceMenuItem_actionPerformed();
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824 else if (source == invertColSel)
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826 viewport.invertColumnSelection();
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827 alignPanel.paintAlignment(true);
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829 else if (source == remove2LeftMenuItem)
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831 trimAlignment(true);
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833 else if (source == remove2RightMenuItem)
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835 trimAlignment(false);
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837 else if (source == removeGappedColumnMenuItem)
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839 removeGappedColumnMenuItem_actionPerformed();
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841 else if (source == removeAllGapsMenuItem)
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843 removeAllGapsMenuItem_actionPerformed();
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845 else if (source == findMenuItem)
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847 findMenuItem_actionPerformed();
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849 else if (source == font)
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851 new FontChooser(alignPanel);
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853 else if (source == newView)
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857 else if (source == showColumns)
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859 viewport.showAllHiddenColumns();
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860 alignPanel.paintAlignment(true);
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862 else if (source == showSeqs)
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864 viewport.showAllHiddenSeqs();
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865 alignPanel.paintAlignment(true);
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867 else if (source == hideColumns)
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869 viewport.hideSelectedColumns();
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870 alignPanel.paintAlignment(true);
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872 else if (source == hideSequences
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873 && viewport.getSelectionGroup() != null)
\r
875 viewport.hideAllSelectedSeqs();
\r
876 alignPanel.paintAlignment(true);
\r
878 else if (source == hideAllButSelection)
\r
880 toggleHiddenRegions(false, false);
\r
881 alignPanel.paintAlignment(true);
\r
883 else if (source == hideAllSelection)
\r
885 SequenceGroup sg = viewport.getSelectionGroup();
\r
886 viewport.expandColSelection(sg, false);
\r
887 viewport.hideAllSelectedSeqs();
\r
888 viewport.hideSelectedColumns();
\r
889 alignPanel.paintAlignment(true);
\r
891 else if (source == showAllHidden)
\r
893 viewport.showAllHiddenColumns();
\r
894 viewport.showAllHiddenSeqs();
\r
895 alignPanel.paintAlignment(true);
\r
897 else if (source == showGroupConsensus)
\r
899 showGroupConsensus_actionPerformed();
\r
901 else if (source == showGroupConservation)
\r
903 showGroupConservation_actionPerformed();
\r
905 else if (source == showSequenceLogo)
\r
907 showSequenceLogo_actionPerformed();
\r
909 else if (source == showConsensusHistogram)
\r
911 showConsensusHistogram_actionPerformed();
\r
913 else if (source == applyAutoAnnotationSettings)
\r
915 applyAutoAnnotationSettings_actionPerformed();
\r
917 else if (source == featureSettings)
\r
919 new FeatureSettings(alignPanel);
\r
921 else if (source == alProperties)
\r
923 StringBuffer contents = new jalview.io.AlignmentProperties(
\r
924 viewport.alignment).formatAsString();
\r
925 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
926 cap.setText(contents.toString());
\r
927 Frame frame = new Frame();
\r
929 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
\r
930 + getTitle(), 400, 250);
\r
932 else if (source == overviewMenuItem)
\r
934 overviewMenuItem_actionPerformed();
\r
936 else if (source == noColourmenuItem)
\r
938 changeColour(null);
\r
940 else if (source == clustalColour)
\r
942 abovePIDThreshold.setState(false);
\r
943 changeColour(new ClustalxColourScheme(
\r
944 viewport.alignment.getSequences(),
\r
945 viewport.alignment.getWidth()));
\r
947 else if (source == zappoColour)
\r
949 changeColour(new ZappoColourScheme());
\r
951 else if (source == taylorColour)
\r
953 changeColour(new TaylorColourScheme());
\r
955 else if (source == hydrophobicityColour)
\r
957 changeColour(new HydrophobicColourScheme());
\r
959 else if (source == helixColour)
\r
961 changeColour(new HelixColourScheme());
\r
963 else if (source == strandColour)
\r
965 changeColour(new StrandColourScheme());
\r
967 else if (source == turnColour)
\r
969 changeColour(new TurnColourScheme());
\r
971 else if (source == buriedColour)
\r
973 changeColour(new BuriedColourScheme());
\r
975 else if (source == nucleotideColour)
\r
977 changeColour(new NucleotideColourScheme());
\r
979 else if (source == modifyPID)
\r
981 modifyPID_actionPerformed();
\r
983 else if (source == modifyConservation)
\r
985 modifyConservation_actionPerformed();
\r
987 else if (source == userDefinedColour)
\r
989 new UserDefinedColours(alignPanel, null);
\r
991 else if (source == PIDColour)
\r
993 changeColour(new PIDColourScheme());
\r
995 else if (source == BLOSUM62Colour)
\r
997 changeColour(new Blosum62ColourScheme());
\r
999 else if (source == tcoffeeColour) {
\r
1000 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
\r
1002 else if (source == annotationColour)
\r
1004 new AnnotationColourChooser(viewport, alignPanel);
\r
1006 else if (source == sortPairwiseMenuItem)
\r
1008 sortPairwiseMenuItem_actionPerformed();
\r
1010 else if (source == sortIDMenuItem)
\r
1012 sortIDMenuItem_actionPerformed();
\r
1014 else if (source == sortLengthMenuItem)
\r
1016 sortLengthMenuItem_actionPerformed();
\r
1018 else if (source == sortGroupMenuItem)
\r
1020 sortGroupMenuItem_actionPerformed();
\r
1022 else if (source == removeRedundancyMenuItem)
\r
1024 removeRedundancyMenuItem_actionPerformed();
\r
1026 else if (source == pairwiseAlignmentMenuItem)
\r
1028 pairwiseAlignmentMenuItem_actionPerformed();
\r
1030 else if (source == PCAMenuItem)
\r
1032 PCAMenuItem_actionPerformed();
\r
1034 else if (source == averageDistanceTreeMenuItem)
\r
1036 averageDistanceTreeMenuItem_actionPerformed();
\r
1038 else if (source == neighbourTreeMenuItem)
\r
1040 neighbourTreeMenuItem_actionPerformed();
\r
1042 else if (source == njTreeBlosumMenuItem)
\r
1044 njTreeBlosumMenuItem_actionPerformed();
\r
1046 else if (source == avDistanceTreeBlosumMenuItem)
\r
1048 avTreeBlosumMenuItem_actionPerformed();
\r
1050 else if (source == documentation)
\r
1052 documentation_actionPerformed();
\r
1054 else if (source == about)
\r
1056 about_actionPerformed();
\r
1061 public void inputText_actionPerformed()
\r
1063 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1064 Frame frame = new Frame();
\r
1066 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
\r
1069 protected void outputText_actionPerformed(ActionEvent e)
\r
1071 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1072 Frame frame = new Frame();
\r
1074 jalview.bin.JalviewLite.addFrame(frame,
\r
1075 "Alignment output - " + e.getActionCommand(), 600, 500);
\r
1076 cap.setText(new AppletFormatAdapter().formatSequences(
\r
1077 e.getActionCommand(), viewport.getAlignment(),
\r
1078 viewport.showJVSuffix));
\r
1081 public void loadAnnotations()
\r
1083 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1084 cap.setText("Paste your features / annotations file here.");
\r
1085 cap.setAnnotationImport();
\r
1086 Frame frame = new Frame();
\r
1088 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
\r
1092 public void loadScores() {
\r
1097 public String outputAnnotations(boolean displayTextbox)
\r
1099 String annotation = new AnnotationFile().printAnnotations(
\r
1100 viewport.showAnnotation ? viewport.alignment
\r
1101 .getAlignmentAnnotation() : null, viewport.alignment
\r
1103 ((Alignment) viewport.alignment).alignmentProperties);
\r
1105 if (displayTextbox)
\r
1107 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
1108 Frame frame = new Frame();
\r
1110 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
\r
1111 cap.setText(annotation);
\r
1114 return annotation;
\r
1117 private Hashtable getDisplayedFeatureCols()
\r
1119 if (alignPanel.getFeatureRenderer() != null && viewport.featuresDisplayed!=null)
\r
1121 FeatureRenderer fr = alignPanel.getFeatureRenderer();
\r
1122 Hashtable fcols = new Hashtable();
\r
1123 Enumeration en = viewport.featuresDisplayed.keys();
\r
1124 while (en.hasMoreElements())
\r
1126 Object col = en.nextElement();
\r
1127 fcols.put(col, fr.featureColours.get(col));
\r
1134 public String outputFeatures(boolean displayTextbox, String format)
\r
1137 if (format.equalsIgnoreCase("Jalview"))
\r
1139 features = new FeaturesFile().printJalviewFormat(
\r
1140 viewport.alignment.getSequencesArray(),
\r
1141 getDisplayedFeatureCols());
\r
1145 features = new FeaturesFile().printGFFFormat(
\r
1146 viewport.alignment.getSequencesArray(),
\r
1147 getDisplayedFeatureCols());
\r
1150 if (displayTextbox)
\r
1152 boolean frimport=false;
\r
1153 if (features==null || features.equals("No Features Visible"))
\r
1155 features = "# No features visible - paste some and import them here.";
\r
1159 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
\r
1162 cap.setAnnotationImport();
\r
1164 Frame frame = new Frame();
\r
1166 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
\r
1167 cap.setText(features);
\r
1169 if (features==null)
\r
1176 void launchFullApplication()
\r
1178 StringBuffer url = new StringBuffer(jalviewServletURL);
\r
1180 url.append("?open="
\r
1181 + appendProtocol(viewport.applet.getParameter("file")));
\r
1183 if (viewport.applet.getParameter("features") != null)
\r
1185 url.append("&features=");
\r
1186 url.append(appendProtocol(viewport.applet.getParameter("features")));
\r
1189 if (viewport.applet.getParameter("annotations") != null)
\r
1191 url.append("&annotations=");
\r
1192 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
\r
1195 if (viewport.applet.getParameter("jnetfile") != null)
\r
1197 url.append("&annotations=");
\r
1198 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
\r
1201 if (viewport.applet.getParameter("defaultColour") != null)
\r
1203 url.append("&colour="
\r
1204 + removeWhiteSpace(viewport.applet
\r
1205 .getParameter("defaultColour")));
\r
1208 if (viewport.applet.getParameter("userDefinedColour") != null)
\r
1210 url.append("&colour="
\r
1211 + removeWhiteSpace(viewport.applet
\r
1212 .getParameter("userDefinedColour")));
\r
1214 if (viewport.applet.getParameter("tree") != null)
\r
1216 url.append("&tree="
\r
1217 + appendProtocol(viewport.applet.getParameter("tree")));
\r
1219 if (viewport.applet.getParameter("treeFile") != null)
\r
1221 url.append("&tree="
\r
1222 + appendProtocol(viewport.applet.getParameter("treeFile")));
\r
1225 showURL(url.toString(), "FULL_APP");
\r
1228 String removeWhiteSpace(String colour)
\r
1230 StringBuffer sb = new StringBuffer();
\r
1231 for (int i = 0; i < colour.length(); i++)
\r
1233 if (Character.isWhitespace(colour.charAt(i)))
\r
1239 sb.append(colour.charAt(i));
\r
1243 return sb.toString();
\r
1246 String appendProtocol(String url)
\r
1251 url = URLEncoder.encode(url);
\r
1254 * When we finally deprecate 1.1 compatibility, we can start to use
\r
1255 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
\r
1256 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
\r
1257 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
\r
1258 * ex.printStackTrace(); }
\r
1260 catch (java.net.MalformedURLException ex)
\r
1262 url = viewport.applet.getCodeBase() + url;
\r
1267 public void closeMenuItem_actionPerformed()
\r
1269 PaintRefresher.RemoveComponent(alignPanel);
\r
1270 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
\r
1271 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
\r
1273 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
\r
1279 alignPanel = null;
\r
1286 void updateEditMenuBar()
\r
1289 if (viewport.historyList.size() > 0)
\r
1291 undoMenuItem.setEnabled(true);
\r
1292 CommandI command = (CommandI) viewport.historyList.peek();
\r
1293 undoMenuItem.setLabel("Undo " + command.getDescription());
\r
1297 undoMenuItem.setEnabled(false);
\r
1298 undoMenuItem.setLabel("Undo");
\r
1301 if (viewport.redoList.size() > 0)
\r
1303 redoMenuItem.setEnabled(true);
\r
1305 CommandI command = (CommandI) viewport.redoList.peek();
\r
1306 redoMenuItem.setLabel("Redo " + command.getDescription());
\r
1310 redoMenuItem.setEnabled(false);
\r
1311 redoMenuItem.setLabel("Redo");
\r
1315 public void addHistoryItem(CommandI command)
\r
1317 if (command.getSize() > 0)
\r
1319 viewport.historyList.push(command);
\r
1320 viewport.redoList.removeAllElements();
\r
1321 updateEditMenuBar();
\r
1322 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
1332 protected void undoMenuItem_actionPerformed()
\r
1334 if (viewport.historyList.size() < 1)
\r
1339 CommandI command = (CommandI) viewport.historyList.pop();
\r
1340 viewport.redoList.push(command);
\r
1341 command.undoCommand(null);
\r
1343 AlignViewport originalSource = getOriginatingSource(command);
\r
1345 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
1346 updateEditMenuBar();
\r
1347 originalSource.firePropertyChange("alignment", null,
\r
1348 originalSource.alignment.getSequences());
\r
1357 protected void redoMenuItem_actionPerformed()
\r
1359 if (viewport.redoList.size() < 1)
\r
1364 CommandI command = (CommandI) viewport.redoList.pop();
\r
1365 viewport.historyList.push(command);
\r
1366 command.doCommand(null);
\r
1368 AlignViewport originalSource = getOriginatingSource(command);
\r
1369 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
1371 updateEditMenuBar();
\r
1372 originalSource.firePropertyChange("alignment", null,
\r
1373 originalSource.alignment.getSequences());
\r
1376 AlignViewport getOriginatingSource(CommandI command)
\r
1378 AlignViewport originalSource = null;
\r
1379 // For sequence removal and addition, we need to fire
\r
1380 // the property change event FROM the viewport where the
\r
1381 // original alignment was altered
\r
1382 AlignmentI al = null;
\r
1383 if (command instanceof EditCommand)
\r
1385 EditCommand editCommand = (EditCommand) command;
\r
1386 al = editCommand.getAlignment();
\r
1387 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
1388 .getSequenceSetId());
\r
1389 for (int i = 0; i < comps.size(); i++)
\r
1391 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
1393 if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
\r
1395 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
\r
1402 if (originalSource == null)
\r
1404 // The original view is closed, we must validate
\r
1405 // the current view against the closed view first
\r
1408 PaintRefresher.validateSequences(al, viewport.alignment);
\r
1411 originalSource = viewport;
\r
1414 return originalSource;
\r
1417 public void moveSelectedSequences(boolean up)
\r
1419 SequenceGroup sg = viewport.getSelectionGroup();
\r
1427 for (int i = 1; i < viewport.alignment.getHeight(); i++)
\r
1429 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
1430 if (!sg.getSequences(null).contains(seq))
\r
1435 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
\r
1436 if (sg.getSequences(null).contains(temp))
\r
1441 viewport.alignment.getSequences().setElementAt(temp, i);
\r
1442 viewport.alignment.getSequences().setElementAt(seq, i - 1);
\r
1447 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
\r
1449 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
1450 if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))
\r
1455 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
\r
1456 if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))
\r
1461 viewport.alignment.getSequences().setElementAt(temp, i);
\r
1462 viewport.alignment.getSequences().setElementAt(seq, i + 1);
\r
1466 alignPanel.paintAlignment(true);
\r
1469 synchronized void slideSequences(boolean right, int size)
\r
1471 Vector sg = new Vector();
\r
1472 if (viewport.cursorMode)
\r
1474 sg.addElement(viewport.alignment
\r
1475 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
\r
1477 else if (viewport.getSelectionGroup() != null
\r
1478 && viewport.getSelectionGroup().getSize() != viewport.alignment
\r
1481 sg = viewport.getSelectionGroup().getSequences(
\r
1482 viewport.hiddenRepSequences);
\r
1485 if (sg.size() < 1)
\r
1490 Vector invertGroup = new Vector();
\r
1492 for (int i = 0; i < viewport.alignment.getHeight(); i++)
\r
1494 if (!sg.contains(viewport.alignment.getSequenceAt(i)))
\r
1495 invertGroup.addElement(viewport.alignment.getSequenceAt(i));
\r
1498 SequenceI[] seqs1 = new SequenceI[sg.size()];
\r
1499 for (int i = 0; i < sg.size(); i++)
\r
1500 seqs1[i] = (SequenceI) sg.elementAt(i);
\r
1502 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
\r
1503 for (int i = 0; i < invertGroup.size(); i++)
\r
1504 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
\r
1506 SlideSequencesCommand ssc;
\r
1508 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
\r
1509 size, viewport.getGapCharacter());
\r
1511 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
\r
1512 size, viewport.getGapCharacter());
\r
1514 int groupAdjustment = 0;
\r
1515 if (ssc.getGapsInsertedBegin() && right)
\r
1517 if (viewport.cursorMode)
\r
1518 alignPanel.seqPanel.moveCursor(size, 0);
\r
1520 groupAdjustment = size;
\r
1522 else if (!ssc.getGapsInsertedBegin() && !right)
\r
1524 if (viewport.cursorMode)
\r
1525 alignPanel.seqPanel.moveCursor(-size, 0);
\r
1527 groupAdjustment = -size;
\r
1530 if (groupAdjustment != 0)
\r
1532 viewport.getSelectionGroup().setStartRes(
\r
1533 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
\r
1534 viewport.getSelectionGroup().setEndRes(
\r
1535 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
\r
1538 boolean appendHistoryItem = false;
\r
1539 if (viewport.historyList != null && viewport.historyList.size() > 0
\r
1540 && viewport.historyList.peek() instanceof SlideSequencesCommand)
\r
1542 appendHistoryItem = ssc
\r
1543 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
\r
1547 if (!appendHistoryItem)
\r
1548 addHistoryItem(ssc);
\r
1553 static StringBuffer copiedSequences;
\r
1555 static Vector copiedHiddenColumns;
\r
1557 protected void copy_actionPerformed()
\r
1559 if (viewport.getSelectionGroup() == null)
\r
1564 SequenceGroup sg = viewport.getSelectionGroup();
\r
1565 copiedSequences = new StringBuffer();
\r
1566 Hashtable orderedSeqs = new Hashtable();
\r
1567 for (int i = 0; i < sg.getSize(); i++)
\r
1569 SequenceI seq = sg.getSequenceAt(i);
\r
1570 int index = viewport.alignment.findIndex(seq);
\r
1571 orderedSeqs.put(index + "", seq);
\r
1574 int index = 0, startRes, endRes;
\r
1577 if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
\r
1579 copiedHiddenColumns = new Vector();
\r
1580 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
\r
1581 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
\r
1584 int[] region = (int[]) viewport.getColumnSelection()
\r
1585 .getHiddenColumns().elementAt(i);
\r
1587 copiedHiddenColumns.addElement(new int[]
\r
1588 { region[0] - hiddenOffset, region[1] - hiddenOffset });
\r
1593 copiedHiddenColumns = null;
\r
1596 for (int i = 0; i < sg.getSize(); i++)
\r
1598 SequenceI seq = null;
\r
1600 while (seq == null)
\r
1602 if (orderedSeqs.containsKey(index + ""))
\r
1604 seq = (SequenceI) orderedSeqs.get(index + "");
\r
1616 // Returns residue following index if gap
\r
1617 startRes = seq.findPosition(sg.getStartRes());
\r
1620 // Need to find the residue preceeding index if gap
\r
1623 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
\r
1625 ch = seq.getCharAt(j);
\r
1626 if (!jalview.util.Comparison.isGap((ch)))
\r
1634 endRes += seq.getStart() - 1;
\r
1637 copiedSequences.append(seq.getName()
\r
1643 + seq.getSequenceAsString(sg.getStartRes(),
\r
1644 sg.getEndRes() + 1) + "\n");
\r
1649 protected void pasteNew_actionPerformed()
\r
1654 protected void pasteThis_actionPerformed()
\r
1659 void paste(boolean newAlignment)
\r
1664 if (copiedSequences == null)
\r
1669 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
1670 Vector seqs = new Vector();
\r
1671 while (st.hasMoreElements())
\r
1673 String name = st.nextToken();
\r
1674 int start = Integer.parseInt(st.nextToken());
\r
1675 int end = Integer.parseInt(st.nextToken());
\r
1676 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
\r
1678 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
1679 for (int i = 0; i < seqs.size(); i++)
\r
1681 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
1686 String newtitle = new String("Copied sequences");
\r
1687 if (getTitle().startsWith("Copied sequences"))
\r
1689 newtitle = getTitle();
\r
1693 newtitle = newtitle.concat("- from " + getTitle());
\r
1695 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
1696 viewport.applet, newtitle, false);
\r
1697 if (copiedHiddenColumns != null)
\r
1699 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
1701 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
1702 af.viewport.hideColumns(region[0], region[1]);
\r
1706 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
\r
1711 addSequences(newSeqs);
\r
1714 } catch (Exception ex)
\r
1716 } // could be anything being pasted in here
\r
1720 void addSequences(SequenceI[] seqs)
\r
1722 for (int i = 0; i < seqs.length; i++)
\r
1724 viewport.alignment.addSequence(seqs[i]);
\r
1728 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
\r
1729 seqs, 0, viewport.alignment.getWidth(), viewport.alignment));
\r
1731 viewport.setEndSeq(viewport.alignment.getHeight());
\r
1732 viewport.alignment.getWidth();
\r
1733 viewport.firePropertyChange("alignment", null,
\r
1734 viewport.alignment.getSequences());
\r
1738 protected void cut_actionPerformed()
\r
1740 copy_actionPerformed();
\r
1741 delete_actionPerformed();
\r
1744 protected void delete_actionPerformed()
\r
1747 SequenceGroup sg = viewport.getSelectionGroup();
\r
1753 Vector seqs = new Vector();
\r
1755 for (int i = 0; i < sg.getSize(); i++)
\r
1757 seq = sg.getSequenceAt(i);
\r
1758 seqs.addElement(seq);
\r
1761 // If the cut affects all sequences, remove highlighted columns
\r
1762 if (sg.getSize() == viewport.alignment.getHeight())
\r
1764 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
1765 sg.getEndRes() + 1);
\r
1768 SequenceI[] cut = new SequenceI[seqs.size()];
\r
1769 for (int i = 0; i < seqs.size(); i++)
\r
1771 cut[i] = (SequenceI) seqs.elementAt(i);
\r
1775 * //ADD HISTORY ITEM
\r
1777 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
\r
1778 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
\r
1779 viewport.alignment));
\r
1781 viewport.setSelectionGroup(null);
\r
1782 viewport.alignment.deleteGroup(sg);
\r
1784 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1787 if (viewport.getAlignment().getHeight() < 1)
\r
1789 this.setVisible(false);
\r
1791 viewport.sendSelection();
\r
1795 * group consensus toggled
\r
1798 protected void showGroupConsensus_actionPerformed()
\r
1800 viewport.setShowGroupConsensus(showGroupConsensus.getState());
\r
1801 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1806 * group conservation toggled.
\r
1808 protected void showGroupConservation_actionPerformed()
\r
1810 viewport.setShowGroupConservation(showGroupConservation.getState());
\r
1811 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1818 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
\r
1819 * .event.ActionEvent)
\r
1821 protected void showConsensusHistogram_actionPerformed()
\r
1823 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
\r
1824 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1830 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
\r
1831 * .event.ActionEvent)
\r
1833 protected void showSequenceLogo_actionPerformed()
\r
1835 viewport.setShowSequenceLogo(showSequenceLogo.getState());
\r
1836 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1839 protected void applyAutoAnnotationSettings_actionPerformed()
\r
1841 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1844 protected void makeGrpsFromSelection_actionPerformed()
\r
1846 if (viewport.getSelectionGroup() != null)
\r
1848 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
\r
1849 viewport.getSequenceSelection(),
\r
1850 viewport.getAlignmentView(true).getSequenceStrings(
\r
1851 viewport.getGapCharacter()),
\r
1852 viewport.alignment.getGroups());
\r
1853 viewport.alignment.deleteAllGroups();
\r
1854 viewport.sequenceColours = null;
\r
1855 viewport.setSelectionGroup(null);
\r
1856 // set view properties for each group
\r
1857 for (int g = 0; g < gps.length; g++)
\r
1859 // gps[g].setShowunconserved(viewport.getShowUnconserved());
\r
1860 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
\r
1861 viewport.alignment.addGroup(gps[g]);
\r
1862 Color col = new Color((int) (Math.random() * 255),
\r
1863 (int) (Math.random() * 255), (int) (Math.random() * 255));
\r
1864 col = col.brighter();
\r
1865 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
\r
1866 .hasMoreElements(); viewport.setSequenceColour(
\r
1867 (SequenceI) sq.nextElement(), col))
\r
1870 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
\r
1871 alignPanel.updateAnnotation();
\r
1872 alignPanel.paintAlignment(true);
\r
1876 protected void deleteGroups_actionPerformed()
\r
1878 viewport.alignment.deleteAllGroups();
\r
1879 viewport.sequenceColours = null;
\r
1880 viewport.setSelectionGroup(null);
\r
1882 alignPanel.paintAlignment(true);
\r
1885 public void selectAllSequenceMenuItem_actionPerformed()
\r
1887 SequenceGroup sg = new SequenceGroup();
\r
1888 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1890 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
1892 sg.setEndRes(viewport.alignment.getWidth() - 1);
\r
1893 viewport.setSelectionGroup(sg);
\r
1894 alignPanel.paintAlignment(true);
\r
1895 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1896 viewport.sendSelection();
\r
1899 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1901 if (viewport.cursorMode)
\r
1903 alignPanel.seqPanel.keyboardNo1 = null;
\r
1904 alignPanel.seqPanel.keyboardNo2 = null;
\r
1906 viewport.setSelectionGroup(null);
\r
1907 viewport.getColumnSelection().clear();
\r
1908 viewport.setSelectionGroup(null);
\r
1909 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1910 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1911 alignPanel.paintAlignment(true);
\r
1912 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1913 viewport.sendSelection();
\r
1916 public void invertSequenceMenuItem_actionPerformed()
\r
1918 SequenceGroup sg = viewport.getSelectionGroup();
\r
1919 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1921 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1924 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1925 viewport.sendSelection();
\r
1928 public void invertColSel_actionPerformed()
\r
1930 viewport.invertColumnSelection();
\r
1931 alignPanel.paintAlignment(true);
\r
1932 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1933 viewport.sendSelection();
\r
1936 void trimAlignment(boolean trimLeft)
\r
1938 ColumnSelection colSel = viewport.getColumnSelection();
\r
1941 if (colSel.size() > 0)
\r
1945 column = colSel.getMin();
\r
1949 column = colSel.getMax();
\r
1953 if (viewport.getSelectionGroup() != null)
\r
1955 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
1956 viewport.hiddenRepSequences);
\r
1960 seqs = viewport.alignment.getSequencesArray();
\r
1963 TrimRegionCommand trimRegion;
\r
1966 trimRegion = new TrimRegionCommand("Remove Left",
\r
1967 TrimRegionCommand.TRIM_LEFT, seqs, column,
\r
1968 viewport.alignment, viewport.colSel,
\r
1969 viewport.selectionGroup);
\r
1970 viewport.setStartRes(0);
\r
1974 trimRegion = new TrimRegionCommand("Remove Right",
\r
1975 TrimRegionCommand.TRIM_RIGHT, seqs, column,
\r
1976 viewport.alignment, viewport.colSel,
\r
1977 viewport.selectionGroup);
\r
1980 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
\r
1982 addHistoryItem(trimRegion);
\r
1984 Vector groups = viewport.alignment.getGroups();
\r
1986 for (int i = 0; i < groups.size(); i++)
\r
1988 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1990 if ((trimLeft && !sg.adjustForRemoveLeft(column))
\r
1991 || (!trimLeft && !sg.adjustForRemoveRight(column)))
\r
1993 viewport.alignment.deleteGroup(sg);
\r
1997 viewport.firePropertyChange("alignment", null, viewport
\r
1998 .getAlignment().getSequences());
\r
2002 public void removeGappedColumnMenuItem_actionPerformed()
\r
2004 int start = 0, end = viewport.alignment.getWidth() - 1;
\r
2007 if (viewport.getSelectionGroup() != null)
\r
2009 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2010 viewport.hiddenRepSequences);
\r
2011 start = viewport.getSelectionGroup().getStartRes();
\r
2012 end = viewport.getSelectionGroup().getEndRes();
\r
2016 seqs = viewport.alignment.getSequencesArray();
\r
2019 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
\r
2020 "Remove Gapped Columns", seqs, start, end, viewport.alignment);
\r
2022 addHistoryItem(removeGapCols);
\r
2024 statusBar.setText("Removed " + removeGapCols.getSize()
\r
2025 + " empty columns.");
\r
2027 // This is to maintain viewport position on first residue
\r
2028 // of first sequence
\r
2029 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
2030 int startRes = seq.findPosition(viewport.startRes);
\r
2031 // ShiftList shifts;
\r
2032 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
\r
2033 // edit.alColumnChanges=shifts.getInverse();
\r
2034 // if (viewport.hasHiddenColumns)
\r
2035 // viewport.getColumnSelection().compensateForEdits(shifts);
\r
2036 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
2037 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
2042 public void removeAllGapsMenuItem_actionPerformed()
\r
2044 int start = 0, end = viewport.alignment.getWidth() - 1;
\r
2047 if (viewport.getSelectionGroup() != null)
\r
2049 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2050 viewport.hiddenRepSequences);
\r
2051 start = viewport.getSelectionGroup().getStartRes();
\r
2052 end = viewport.getSelectionGroup().getEndRes();
\r
2056 seqs = viewport.alignment.getSequencesArray();
\r
2059 // This is to maintain viewport position on first residue
\r
2060 // of first sequence
\r
2061 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
2062 int startRes = seq.findPosition(viewport.startRes);
\r
2064 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
\r
2065 viewport.alignment));
\r
2067 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
2069 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
2074 public void findMenuItem_actionPerformed()
\r
2076 new Finder(alignPanel);
\r
2080 * create a new view derived from the current view
\r
2082 * @param viewtitle
\r
2083 * @return frame for the new view
\r
2085 public AlignFrame newView(String viewtitle)
\r
2088 if (viewport.hasHiddenRows)
\r
2090 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
\r
2091 .getFullAlignment().getSequencesArray());
\r
2095 newal = new Alignment(viewport.alignment.getSequencesArray());
\r
2098 if (viewport.alignment.getAlignmentAnnotation() != null)
\r
2100 for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)
\r
2102 if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
\r
2104 newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);
\r
2109 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
\r
2111 newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
\r
2112 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
\r
2113 PaintRefresher.Register(newaf.alignPanel,
\r
2114 newaf.alignPanel.av.getSequenceSetId());
\r
2116 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
\r
2117 newaf.alignPanel.av.getSequenceSetId());
\r
2118 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
\r
2119 newaf.alignPanel.av.getSequenceSetId());
\r
2121 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
2122 .getSequenceSetId());
\r
2123 int viewSize = -1;
\r
2124 for (int i = 0; i < comps.size(); i++)
\r
2126 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
2132 String title = new String(this.getTitle());
\r
2133 if (viewtitle != null)
\r
2135 title = viewtitle + " ( " + title + ")";
\r
2139 if (title.indexOf("(View") > -1)
\r
2141 title = title.substring(0, title.indexOf("(View"));
\r
2143 title += "(View " + viewSize + ")";
\r
2146 newaf.setTitle(title.toString());
\r
2148 newaf.viewport.historyList = viewport.historyList;
\r
2149 newaf.viewport.redoList = viewport.redoList;
\r
2155 * @return list of feature groups on the view
\r
2157 public String[] getFeatureGroups()
\r
2159 FeatureRenderer fr = null;
\r
2160 if (alignPanel != null
\r
2161 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2163 return fr.getGroups();
\r
2169 * get sequence feature groups that are hidden or shown
\r
2175 public String[] getFeatureGroupsOfState(boolean visible)
\r
2177 FeatureRenderer fr = null;
\r
2178 if (alignPanel != null
\r
2179 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2181 return fr.getGroups(visible);
\r
2187 * Change the display state for the given feature groups
\r
2190 * list of group strings
\r
2192 * visible or invisible
\r
2194 public void setFeatureGroupState(String[] groups, boolean state)
\r
2196 FeatureRenderer fr = null;
\r
2197 this.sequenceFeatures.setState(true);
\r
2198 viewport.showSequenceFeatures(true);
\r
2199 if (alignPanel != null
\r
2200 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2202 fr.setGroupState(groups, state);
\r
2203 alignPanel.seqPanel.seqCanvas.repaint();
\r
2204 if (alignPanel.overviewPanel != null)
\r
2206 alignPanel.overviewPanel.updateOverviewImage();
\r
2211 public void seqLimits_itemStateChanged()
\r
2213 viewport.setShowJVSuffix(seqLimits.getState());
\r
2214 alignPanel.fontChanged();
\r
2215 alignPanel.paintAlignment(true);
\r
2218 protected void colourTextMenuItem_actionPerformed()
\r
2220 viewport.setColourText(colourTextMenuItem.getState());
\r
2221 alignPanel.paintAlignment(true);
\r
2224 protected void displayNonconservedMenuItem_actionPerformed()
\r
2226 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
\r
2227 alignPanel.paintAlignment(true);
\r
2230 protected void wrapMenuItem_actionPerformed()
\r
2232 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
2233 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
2234 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
2235 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
2236 scaleRight.setEnabled(wrapMenuItem.getState());
\r
2237 alignPanel.paintAlignment(true);
\r
2240 public void overviewMenuItem_actionPerformed()
\r
2242 if (alignPanel.overviewPanel != null)
\r
2247 Frame frame = new Frame();
\r
2248 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
2249 frame.add(overview);
\r
2250 // +50 must allow for applet frame window
\r
2251 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
2252 overview.getPreferredSize().width,
\r
2253 overview.getPreferredSize().height + 50);
\r
2256 frame.addWindowListener(new WindowAdapter()
\r
2258 public void windowClosing(WindowEvent e)
\r
2260 alignPanel.setOverviewPanel(null);
\r
2264 alignPanel.setOverviewPanel(overview);
\r
2268 void changeColour(ColourSchemeI cs)
\r
2270 int threshold = 0;
\r
2274 if (viewport.getAbovePIDThreshold())
\r
2276 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
2279 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2281 viewport.setGlobalColourScheme(cs);
\r
2285 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2288 if (viewport.getConservationSelected())
\r
2291 Alignment al = (Alignment) viewport.alignment;
\r
2292 Conservation c = new Conservation("All",
\r
2293 ResidueProperties.propHash, 3, al.getSequences(), 0,
\r
2294 al.getWidth() - 1);
\r
2297 c.verdict(false, viewport.ConsPercGaps);
\r
2299 cs.setConservation(c);
\r
2301 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
\r
2302 cs, "Background"));
\r
2307 cs.setConservation(null);
\r
2310 cs.setConsensus(viewport.hconsensus);
\r
2313 viewport.setGlobalColourScheme(cs);
\r
2315 if (viewport.getColourAppliesToAllGroups())
\r
2317 Vector groups = viewport.alignment.getGroups();
\r
2318 for (int i = 0; i < groups.size(); i++)
\r
2320 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
2327 if (cs instanceof ClustalxColourScheme)
\r
2329 sg.cs = new ClustalxColourScheme(
\r
2330 sg.getSequences(viewport.hiddenRepSequences),
\r
2337 sg.cs = cs.getClass().newInstance();
\r
2338 } catch (Exception ex)
\r
2340 ex.printStackTrace();
\r
2345 if (viewport.getAbovePIDThreshold()
\r
2346 || cs instanceof PIDColourScheme
\r
2347 || cs instanceof Blosum62ColourScheme)
\r
2349 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2350 sg.cs.setConsensus(AAFrequency.calculate(
\r
2351 sg.getSequences(viewport.hiddenRepSequences), 0,
\r
2356 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2359 if (viewport.getConservationSelected())
\r
2361 Conservation c = new Conservation("Group",
\r
2362 ResidueProperties.propHash, 3,
\r
2363 sg.getSequences(viewport.hiddenRepSequences), 0,
\r
2364 viewport.alignment.getWidth() - 1);
\r
2366 c.verdict(false, viewport.ConsPercGaps);
\r
2367 sg.cs.setConservation(c);
\r
2371 sg.cs.setConservation(null);
\r
2372 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2378 if (alignPanel.getOverviewPanel() != null)
\r
2380 alignPanel.getOverviewPanel().updateOverviewImage();
\r
2383 jalview.structure.StructureSelectionManager
\r
2384 .getStructureSelectionManager(viewport.applet).sequenceColoursChanged(
\r
2387 alignPanel.paintAlignment(true);
\r
2390 protected void modifyPID_actionPerformed()
\r
2392 if (viewport.getAbovePIDThreshold()
\r
2393 && viewport.globalColourScheme != null)
\r
2395 SliderPanel.setPIDSliderSource(alignPanel,
\r
2396 viewport.getGlobalColourScheme(), "Background");
\r
2397 SliderPanel.showPIDSlider();
\r
2401 protected void modifyConservation_actionPerformed()
\r
2403 if (viewport.getConservationSelected()
\r
2404 && viewport.globalColourScheme != null)
\r
2406 SliderPanel.setConservationSlider(alignPanel,
\r
2407 viewport.globalColourScheme, "Background");
\r
2408 SliderPanel.showConservationSlider();
\r
2412 protected void conservationMenuItem_actionPerformed()
\r
2414 viewport.setConservationSelected(conservationMenuItem.getState());
\r
2416 viewport.setAbovePIDThreshold(false);
\r
2417 abovePIDThreshold.setState(false);
\r
2419 changeColour(viewport.getGlobalColourScheme());
\r
2421 modifyConservation_actionPerformed();
\r
2424 public void abovePIDThreshold_actionPerformed()
\r
2426 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
2428 conservationMenuItem.setState(false);
\r
2429 viewport.setConservationSelected(false);
\r
2431 changeColour(viewport.getGlobalColourScheme());
\r
2433 modifyPID_actionPerformed();
\r
2436 public void sortPairwiseMenuItem_actionPerformed()
\r
2438 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2439 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
\r
2440 .getAlignment().getSequenceAt(0), null);
\r
2442 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
\r
2443 viewport.alignment));
\r
2444 alignPanel.paintAlignment(true);
\r
2447 public void sortIDMenuItem_actionPerformed()
\r
2449 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2450 AlignmentSorter.sortByID(viewport.getAlignment());
\r
2451 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
\r
2452 alignPanel.paintAlignment(true);
\r
2455 public void sortLengthMenuItem_actionPerformed()
\r
2457 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2458 AlignmentSorter.sortByLength(viewport.getAlignment());
\r
2459 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
\r
2460 viewport.alignment));
\r
2461 alignPanel.paintAlignment(true);
\r
2464 public void sortGroupMenuItem_actionPerformed()
\r
2466 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2467 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
2468 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
\r
2469 viewport.alignment));
\r
2470 alignPanel.paintAlignment(true);
\r
2474 public void removeRedundancyMenuItem_actionPerformed()
\r
2476 new RedundancyPanel(alignPanel);
\r
2479 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
2481 if (viewport.getSelectionGroup() != null
\r
2482 && viewport.getSelectionGroup().getSize() > 1)
\r
2484 Frame frame = new Frame();
\r
2485 frame.add(new PairwiseAlignPanel(alignPanel));
\r
2486 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
\r
2491 public void PCAMenuItem_actionPerformed()
\r
2493 // are the sequences aligned?
\r
2494 if (!viewport.alignment.isAligned(false))
\r
2496 SequenceI current;
\r
2497 int Width = viewport.getAlignment().getWidth();
\r
2499 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2501 current = viewport.getAlignment().getSequenceAt(i);
\r
2503 if (current.getLength() < Width)
\r
2505 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2508 alignPanel.paintAlignment(true);
\r
2511 if ((viewport.getSelectionGroup() != null
\r
2512 && viewport.getSelectionGroup().getSize() < 4 && viewport
\r
2513 .getSelectionGroup().getSize() > 0)
\r
2514 || viewport.getAlignment().getHeight() < 4)
\r
2521 new PCAPanel(viewport);
\r
2522 } catch (java.lang.OutOfMemoryError ex)
\r
2528 public void averageDistanceTreeMenuItem_actionPerformed()
\r
2530 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
2533 public void neighbourTreeMenuItem_actionPerformed()
\r
2535 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
2538 protected void njTreeBlosumMenuItem_actionPerformed()
\r
2540 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2543 protected void avTreeBlosumMenuItem_actionPerformed()
\r
2545 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2548 void NewTreePanel(String type, String pwType, String title)
\r
2550 // are the sequences aligned?
\r
2551 if (!viewport.alignment.isAligned(false))
\r
2553 SequenceI current;
\r
2554 int Width = viewport.getAlignment().getWidth();
\r
2556 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2558 current = viewport.getAlignment().getSequenceAt(i);
\r
2560 if (current.getLength() < Width)
\r
2562 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2565 alignPanel.paintAlignment(true);
\r
2569 if ((viewport.getSelectionGroup() != null && viewport
\r
2570 .getSelectionGroup().getSize() > 1)
\r
2571 || (viewport.getSelectionGroup() == null && viewport.alignment
\r
2572 .getHeight() > 1))
\r
2574 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
\r
2576 addTreeMenuItem(tp, title);
\r
2578 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
2582 void loadTree_actionPerformed()
\r
2584 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
2585 cap.setText("Paste your Newick tree file here.");
\r
2586 cap.setTreeImport();
\r
2587 Frame frame = new Frame();
\r
2589 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
2592 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
2594 TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
\r
2595 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
2596 addTreeMenuItem(tp, treeFile);
\r
2600 * sort the alignment using the given treePanel
\r
2602 * @param treePanel
\r
2603 * tree used to sort view
\r
2605 * string used for undo event name
\r
2607 public void sortByTree(TreePanel treePanel, String title)
\r
2609 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2611 .sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
2612 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2613 // HistoryItem.SORT));
\r
2614 addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
\r
2615 viewport.alignment));
\r
2616 alignPanel.paintAlignment(true);
\r
2620 * Do any automatic reordering of the alignment and add the necessary bits to
\r
2621 * the menu structure for the new tree
\r
2623 * @param treePanel
\r
2626 protected void addTreeMenuItem(final TreePanel treePanel,
\r
2627 final String title)
\r
2629 final MenuItem item = new MenuItem(title);
\r
2630 sortByTreeMenu.add(item);
\r
2631 item.addActionListener(new java.awt.event.ActionListener()
\r
2633 public void actionPerformed(ActionEvent evt)
\r
2635 sortByTree(treePanel, title); // treePanel.getTitle());
\r
2639 treePanel.addWindowListener(new WindowAdapter()
\r
2641 public void windowOpened(WindowEvent e)
\r
2643 if (viewport.sortByTree)
\r
2645 sortByTree(treePanel, title);
\r
2647 super.windowOpened(e);
\r
2650 public void windowClosing(WindowEvent e)
\r
2652 sortByTreeMenu.remove(item);
\r
2656 public boolean sortBy(AlignmentOrder alorder, String undoname)
\r
2658 SequenceI[] oldOrder = viewport.getAlignment()
\r
2659 .getSequencesArray();
\r
2660 if (viewport.applet.debug)
\r
2662 System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");
\r
2664 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
\r
2665 if (undoname!=null)
\r
2667 addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.alignment));
\r
2669 alignPanel.paintAlignment(true);
\r
2673 protected void documentation_actionPerformed()
\r
2675 alignPanel.av.applet.openJalviewHelpUrl();
\r
2678 protected void about_actionPerformed()
\r
2681 class AboutPanel extends Canvas
\r
2687 public AboutPanel(String version, String builddate)
\r
2689 this.version = version;
\r
2690 this.builddate = builddate;
\r
2693 public void paint(Graphics g)
\r
2695 g.setColor(Color.white);
\r
2696 g.fillRect(0, 0, getSize().width, getSize().height);
\r
2697 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2698 FontMetrics fm = g.getFontMetrics();
\r
2699 int fh = fm.getHeight();
\r
2701 g.setColor(Color.black);
\r
2702 // TODO: update this text for each release or centrally store it for
\r
2703 // lite and application
\r
2704 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
2705 g.drawString("JalviewLite - Release " + version, x, y += fh);
\r
2706 g.setFont(new Font("Helvetica", Font.BOLD, 12));
\r
2707 g.drawString("Build date: " + builddate, x, y += fh);
\r
2708 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2710 "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",
\r
2711 x, y += fh * 1.5);
\r
2712 g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
\r
2714 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
\r
2717 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
\r
2719 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
\r
2721 "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
\r
2724 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
\r
2726 g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
\r
2731 Frame frame = new Frame();
\r
2732 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
\r
2733 .getBuildDate()));
\r
2734 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
\r
2738 public void showURL(String url, String target)
\r
2740 if (viewport.applet == null)
\r
2742 System.out.println("Not running as applet - no browser available.");
\r
2746 viewport.applet.showURL(url, target);
\r
2750 // ////////////////////////////////////////////////////////////////////////////////
\r
2751 // JBuilder Graphics here
\r
2753 MenuBar alignFrameMenuBar = new MenuBar();
\r
2755 Menu fileMenu = new Menu("File");
\r
2757 MenuItem loadApplication = new MenuItem("View in Full Application");
\r
2759 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
\r
2761 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
\r
2763 MenuItem loadScores = new MenuItem("Load Associated T-Coffee scores ...");
\r
2765 MenuItem outputFeatures = new MenuItem("Export Features ...");
\r
2767 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
\r
2769 MenuItem closeMenuItem = new MenuItem("Close");
\r
2771 Menu editMenu = new Menu("Edit");
\r
2773 Menu viewMenu = new Menu("View");
\r
2775 Menu colourMenu = new Menu("Colour");
\r
2777 Menu calculateMenu = new Menu("Calculate");
\r
2779 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
2781 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
2783 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
2785 MenuItem remove2LeftMenuItem = new MenuItem();
\r
2787 MenuItem remove2RightMenuItem = new MenuItem();
\r
2789 MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
2791 MenuItem removeAllGapsMenuItem = new MenuItem();
\r
2793 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
2795 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
2797 MenuItem sortPairwiseMenuItem = new MenuItem();
\r
2799 MenuItem sortIDMenuItem = new MenuItem();
\r
2801 MenuItem sortLengthMenuItem = new MenuItem();
\r
2803 MenuItem sortGroupMenuItem = new MenuItem();
\r
2805 MenuItem removeRedundancyMenuItem = new MenuItem();
\r
2807 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
2809 MenuItem PCAMenuItem = new MenuItem();
\r
2811 MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
2813 MenuItem neighbourTreeMenuItem = new MenuItem();
\r
2815 BorderLayout borderLayout1 = new BorderLayout();
\r
2817 public Label statusBar = new Label();
\r
2819 Menu outputTextboxMenu = new Menu();
\r
2821 MenuItem clustalColour = new MenuItem();
\r
2823 MenuItem zappoColour = new MenuItem();
\r
2825 MenuItem taylorColour = new MenuItem();
\r
2827 MenuItem hydrophobicityColour = new MenuItem();
\r
2829 MenuItem helixColour = new MenuItem();
\r
2831 MenuItem strandColour = new MenuItem();
\r
2833 MenuItem turnColour = new MenuItem();
\r
2835 MenuItem buriedColour = new MenuItem();
\r
2837 MenuItem userDefinedColour = new MenuItem();
\r
2839 MenuItem PIDColour = new MenuItem();
\r
2841 MenuItem BLOSUM62Colour = new MenuItem();
\r
2843 MenuItem tcoffeeColour = new MenuItem();
\r
2845 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
2847 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
2849 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
2851 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
2853 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
\r
2855 MenuItem alProperties = new MenuItem("Alignment Properties...");
\r
2857 MenuItem overviewMenuItem = new MenuItem();
\r
2859 MenuItem undoMenuItem = new MenuItem();
\r
2861 MenuItem redoMenuItem = new MenuItem();
\r
2863 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
2865 MenuItem noColourmenuItem = new MenuItem();
\r
2867 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
2869 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
2871 MenuItem findMenuItem = new MenuItem();
\r
2873 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
2875 MenuItem nucleotideColour = new MenuItem();
\r
2877 MenuItem deleteGroups = new MenuItem();
\r
2879 MenuItem grpsFromSelection = new MenuItem();
\r
2881 MenuItem delete = new MenuItem();
\r
2883 MenuItem copy = new MenuItem();
\r
2885 MenuItem cut = new MenuItem();
\r
2887 Menu pasteMenu = new Menu();
\r
2889 MenuItem pasteNew = new MenuItem();
\r
2891 MenuItem pasteThis = new MenuItem();
\r
2893 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
2895 MenuItem font = new MenuItem();
\r
2897 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
2899 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
2901 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
2903 MenuItem modifyPID = new MenuItem();
\r
2905 MenuItem modifyConservation = new MenuItem();
\r
2907 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
\r
2908 "Autocalculate Consensus", true);
\r
2910 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
\r
2911 "Sort Alignment With New Tree", true);
\r
2913 Menu sortByTreeMenu = new Menu();
\r
2915 Menu sort = new Menu();
\r
2917 Menu calculate = new Menu();
\r
2919 MenuItem inputText = new MenuItem();
\r
2921 Menu helpMenu = new Menu();
\r
2923 MenuItem documentation = new MenuItem();
\r
2925 MenuItem about = new MenuItem();
\r
2927 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
2929 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
\r
2931 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
\r
2932 Menu autoAnnMenu=new Menu();
\r
2933 CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();
\r
2934 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
\r
2935 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
\r
2936 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
\r
2937 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
\r
2939 private void jbInit() throws Exception
\r
2942 setMenuBar(alignFrameMenuBar);
\r
2946 // dynamically fill save as menu with available formats
\r
2947 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
2950 item = new MenuItem(
\r
2951 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
2953 item.addActionListener(new java.awt.event.ActionListener()
\r
2955 public void actionPerformed(ActionEvent e)
\r
2957 outputText_actionPerformed(e);
\r
2961 outputTextboxMenu.add(item);
\r
2963 closeMenuItem.addActionListener(this);
\r
2964 loadApplication.addActionListener(this);
\r
2966 loadTree.addActionListener(this);
\r
2967 loadAnnotations.addActionListener(this);
\r
2968 loadScores.addActionListener(this);
\r
2969 outputFeatures.addActionListener(this);
\r
2970 outputAnnotations.addActionListener(this);
\r
2971 selectAllSequenceMenuItem.addActionListener(this);
\r
2972 deselectAllSequenceMenuItem.addActionListener(this);
\r
2973 invertSequenceMenuItem.addActionListener(this);
\r
2974 remove2LeftMenuItem.setLabel("Remove Left");
\r
2975 remove2LeftMenuItem.addActionListener(this);
\r
2976 remove2RightMenuItem.setLabel("Remove Right");
\r
2977 remove2RightMenuItem.addActionListener(this);
\r
2978 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
2979 removeGappedColumnMenuItem.addActionListener(this);
\r
2980 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
2981 removeAllGapsMenuItem.addActionListener(this);
\r
2982 viewBoxesMenuItem.setLabel("Boxes");
\r
2983 viewBoxesMenuItem.setState(true);
\r
2984 viewBoxesMenuItem.addItemListener(this);
\r
2985 viewTextMenuItem.setLabel("Text");
\r
2986 viewTextMenuItem.setState(true);
\r
2987 viewTextMenuItem.addItemListener(this);
\r
2988 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
2989 sortPairwiseMenuItem.addActionListener(this);
\r
2990 sortIDMenuItem.setLabel("by ID");
\r
2991 sortIDMenuItem.addActionListener(this);
\r
2992 sortLengthMenuItem.setLabel("by Length");
\r
2993 sortLengthMenuItem.addActionListener(this);
\r
2994 sortGroupMenuItem.setLabel("by Group");
\r
2995 sortGroupMenuItem.addActionListener(this);
\r
2996 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
2997 removeRedundancyMenuItem.addActionListener(this);
\r
2998 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
2999 pairwiseAlignmentMenuItem.addActionListener(this);
\r
3000 PCAMenuItem.setLabel("Principal Component Analysis");
\r
3001 PCAMenuItem.addActionListener(this);
\r
3002 averageDistanceTreeMenuItem
\r
3003 .setLabel("Average Distance Using % Identity");
\r
3004 averageDistanceTreeMenuItem.addActionListener(this);
\r
3005 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
3006 neighbourTreeMenuItem.addActionListener(this);
\r
3007 statusBar.setBackground(Color.white);
\r
3008 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
3009 statusBar.setText("Status bar");
\r
3010 outputTextboxMenu.setLabel("Output to Textbox");
\r
3011 clustalColour.setLabel("Clustalx");
\r
3013 clustalColour.addActionListener(this);
\r
3014 zappoColour.setLabel("Zappo");
\r
3015 zappoColour.addActionListener(this);
\r
3016 taylorColour.setLabel("Taylor");
\r
3017 taylorColour.addActionListener(this);
\r
3018 hydrophobicityColour.setLabel("Hydrophobicity");
\r
3019 hydrophobicityColour.addActionListener(this);
\r
3020 helixColour.setLabel("Helix Propensity");
\r
3021 helixColour.addActionListener(this);
\r
3022 strandColour.setLabel("Strand Propensity");
\r
3023 strandColour.addActionListener(this);
\r
3024 turnColour.setLabel("Turn Propensity");
\r
3025 turnColour.addActionListener(this);
\r
3026 buriedColour.setLabel("Buried Index");
\r
3027 buriedColour.addActionListener(this);
\r
3028 userDefinedColour.setLabel("User Defined...");
\r
3029 userDefinedColour.addActionListener(this);
\r
3030 PIDColour.setLabel("Percentage Identity");
\r
3031 PIDColour.addActionListener(this);
\r
3032 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
3033 BLOSUM62Colour.addActionListener(this);
\r
3034 tcoffeeColour.setLabel("T-Coffee Scores");
\r
3035 tcoffeeColour.setEnabled(false); // it will enabled only if a score file is provided
\r
3036 tcoffeeColour.addActionListener(this);
\r
3037 avDistanceTreeBlosumMenuItem .setLabel("Average Distance Using BLOSUM62");
\r
3038 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
3039 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
3040 njTreeBlosumMenuItem.addActionListener(this);
\r
3041 annotationPanelMenuItem.setLabel("Show Annotations");
\r
3042 annotationPanelMenuItem.addItemListener(this);
\r
3043 colourTextMenuItem.setLabel("Colour Text");
\r
3044 colourTextMenuItem.addItemListener(this);
\r
3045 displayNonconservedMenuItem.setLabel("Show nonconserved");
\r
3046 displayNonconservedMenuItem.addItemListener(this);
\r
3047 alProperties.addActionListener(this);
\r
3048 overviewMenuItem.setLabel("Overview Window");
\r
3049 overviewMenuItem.addActionListener(this);
\r
3050 undoMenuItem.setEnabled(false);
\r
3051 undoMenuItem.setLabel("Undo");
\r
3052 undoMenuItem.addActionListener(this);
\r
3053 redoMenuItem.setEnabled(false);
\r
3054 redoMenuItem.setLabel("Redo");
\r
3055 redoMenuItem.addActionListener(this);
\r
3056 conservationMenuItem.setLabel("by Conservation");
\r
3057 conservationMenuItem.addItemListener(this);
\r
3058 noColourmenuItem.setLabel("None");
\r
3059 noColourmenuItem.addActionListener(this);
\r
3060 wrapMenuItem.setLabel("Wrap");
\r
3061 wrapMenuItem.addItemListener(this);
\r
3062 renderGapsMenuItem.setLabel("Show Gaps");
\r
3063 renderGapsMenuItem.setState(true);
\r
3064 renderGapsMenuItem.addItemListener(this);
\r
3065 findMenuItem.setLabel("Find...");
\r
3066 findMenuItem.addActionListener(this);
\r
3067 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
3068 abovePIDThreshold.addItemListener(this);
\r
3069 nucleotideColour.setLabel("Nucleotide");
\r
3070 nucleotideColour.addActionListener(this);
\r
3071 deleteGroups.setLabel("Undefine Groups");
\r
3072 deleteGroups.addActionListener(this);
\r
3073 grpsFromSelection.setLabel("Make Groups for selection");
\r
3074 grpsFromSelection.addActionListener(this);
\r
3075 copy.setLabel("Copy");
\r
3076 copy.addActionListener(this);
\r
3077 cut.setLabel("Cut");
\r
3078 cut.addActionListener(this);
\r
3079 delete.setLabel("Delete");
\r
3080 delete.addActionListener(this);
\r
3081 pasteMenu.setLabel("Paste");
\r
3082 pasteNew.setLabel("To New Alignment");
\r
3083 pasteNew.addActionListener(this);
\r
3084 pasteThis.setLabel("Add To This Alignment");
\r
3085 pasteThis.addActionListener(this);
\r
3086 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
3087 applyToAllGroups.setState(true);
\r
3088 applyToAllGroups.addItemListener(this);
\r
3089 font.setLabel("Font...");
\r
3090 font.addActionListener(this);
\r
3091 scaleAbove.setLabel("Scale Above");
\r
3092 scaleAbove.setState(true);
\r
3093 scaleAbove.setEnabled(false);
\r
3094 scaleAbove.addItemListener(this);
\r
3095 scaleLeft.setEnabled(false);
\r
3096 scaleLeft.setState(true);
\r
3097 scaleLeft.setLabel("Scale Left");
\r
3098 scaleLeft.addItemListener(this);
\r
3099 scaleRight.setEnabled(false);
\r
3100 scaleRight.setState(true);
\r
3101 scaleRight.setLabel("Scale Right");
\r
3102 scaleRight.addItemListener(this);
\r
3103 modifyPID.setLabel("Modify Identity Threshold...");
\r
3104 modifyPID.addActionListener(this);
\r
3105 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
3106 modifyConservation.addActionListener(this);
\r
3107 sortByTreeMenu.setLabel("By Tree Order");
\r
3108 sort.setLabel("Sort");
\r
3109 calculate.setLabel("Calculate Tree");
\r
3110 autoCalculate.addItemListener(this);
\r
3111 sortByTree.addItemListener(this);
\r
3112 inputText.setLabel("Input from textbox");
\r
3113 inputText.addActionListener(this);
\r
3114 centreColumnLabelFlag.setLabel("Centre column labels");
\r
3115 centreColumnLabelFlag.addItemListener(this);
\r
3116 followMouseOverFlag.setLabel("Automatic Scrolling");
\r
3117 followMouseOverFlag.addItemListener(this);
\r
3118 helpMenu.setLabel("Help");
\r
3119 documentation.setLabel("Documentation");
\r
3120 documentation.addActionListener(this);
\r
3122 about.setLabel("About...");
\r
3123 about.addActionListener(this);
\r
3124 seqLimits.setState(true);
\r
3125 seqLimits.setLabel("Show Sequence Limits");
\r
3126 seqLimits.addItemListener(this);
\r
3127 featureSettings.setLabel("Feature Settings...");
\r
3128 featureSettings.addActionListener(this);
\r
3129 sequenceFeatures.setLabel("Sequence Features");
\r
3130 sequenceFeatures.addItemListener(this);
\r
3131 sequenceFeatures.setState(false);
\r
3132 annotationColour.setLabel("by Annotation...");
\r
3133 annotationColour.addActionListener(this);
\r
3134 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
3135 invertColSel.setLabel("Invert Column Selection");
\r
3136 menu1.setLabel("Show");
\r
3137 showColumns.setLabel("All Columns ");
\r
3138 showSeqs.setLabel("All Sequences");
\r
3139 menu2.setLabel("Hide");
\r
3140 hideColumns.setLabel("Selected Columns");
\r
3141 hideSequences.setLabel("Selected Sequences");
\r
3142 hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
\r
3143 hideAllSelection.setLabel("Selected Region");
\r
3144 showAllHidden.setLabel("All Sequences and Columns");
\r
3145 showGroupConsensus.setLabel("Group Consensus");
\r
3146 showGroupConservation.setLabel("Group Conservation");
\r
3147 showConsensusHistogram.setLabel("Show Consensus Histogram");
\r
3148 showSequenceLogo.setLabel("Show Consensus Logo");
\r
3149 applyAutoAnnotationSettings.setLabel("Apply to all groups");
\r
3150 applyAutoAnnotationSettings.setState(true);
\r
3151 autoAnnMenu.setLabel("Autocalculated Annotation");
\r
3153 invertColSel.addActionListener(this);
\r
3154 showColumns.addActionListener(this);
\r
3155 showSeqs.addActionListener(this);
\r
3156 hideColumns.addActionListener(this);
\r
3157 hideSequences.addActionListener(this);
\r
3158 hideAllButSelection.addActionListener(this);
\r
3159 hideAllSelection.addActionListener(this);
\r
3160 showAllHidden.addActionListener(this);
\r
3161 showGroupConsensus.addItemListener(this);
\r
3162 showGroupConservation.addItemListener(this);
\r
3163 showConsensusHistogram.addItemListener(this);
\r
3164 showSequenceLogo.addItemListener(this);
\r
3165 applyAutoAnnotationSettings.addItemListener(this);
\r
3166 formatMenu.setLabel("Format");
\r
3167 selectMenu.setLabel("Select");
\r
3168 newView.setLabel("New View");
\r
3169 newView.addActionListener(this);
\r
3170 alignFrameMenuBar.add(fileMenu);
\r
3171 alignFrameMenuBar.add(editMenu);
\r
3172 alignFrameMenuBar.add(selectMenu);
\r
3173 alignFrameMenuBar.add(viewMenu);
\r
3174 alignFrameMenuBar.add(formatMenu);
\r
3175 alignFrameMenuBar.add(colourMenu);
\r
3176 alignFrameMenuBar.add(calculateMenu);
\r
3177 alignFrameMenuBar.add(helpMenu);
\r
3179 fileMenu.add(inputText);
\r
3180 fileMenu.add(loadTree);
\r
3181 fileMenu.add(loadAnnotations);
\r
3182 fileMenu.add(loadScores);
\r
3184 fileMenu.addSeparator();
\r
3185 fileMenu.add(outputTextboxMenu);
\r
3186 fileMenu.add(outputFeatures);
\r
3187 fileMenu.add(outputAnnotations);
\r
3189 if (jalviewServletURL != null)
\r
3191 fileMenu.add(loadApplication);
\r
3194 fileMenu.addSeparator();
\r
3195 fileMenu.add(closeMenuItem);
\r
3197 editMenu.add(undoMenuItem);
\r
3198 editMenu.add(redoMenuItem);
\r
3199 editMenu.add(cut);
\r
3200 editMenu.add(copy);
\r
3201 editMenu.add(pasteMenu);
\r
3202 editMenu.add(delete);
\r
3203 editMenu.addSeparator();
\r
3204 editMenu.add(remove2LeftMenuItem);
\r
3205 editMenu.add(remove2RightMenuItem);
\r
3206 editMenu.add(removeGappedColumnMenuItem);
\r
3207 editMenu.add(removeAllGapsMenuItem);
\r
3208 editMenu.add(removeRedundancyMenuItem);
\r
3209 viewMenu.add(newView);
\r
3210 viewMenu.addSeparator();
\r
3211 viewMenu.add(menu1);
\r
3212 viewMenu.add(menu2);
\r
3213 viewMenu.addSeparator();
\r
3214 viewMenu.add(followMouseOverFlag);
\r
3215 viewMenu.add(annotationPanelMenuItem);
\r
3216 autoAnnMenu.add(applyAutoAnnotationSettings);
\r
3217 autoAnnMenu.add(showConsensusHistogram);
\r
3218 autoAnnMenu.add(showSequenceLogo);
\r
3219 autoAnnMenu.addSeparator();
\r
3220 autoAnnMenu.add(showGroupConservation);
\r
3221 autoAnnMenu.add(showGroupConsensus);
\r
3222 viewMenu.add(autoAnnMenu);
\r
3223 viewMenu.addSeparator();
\r
3224 viewMenu.add(sequenceFeatures);
\r
3225 viewMenu.add(featureSettings);
\r
3226 viewMenu.addSeparator();
\r
3227 viewMenu.add(alProperties);
\r
3228 viewMenu.addSeparator();
\r
3229 viewMenu.add(overviewMenuItem);
\r
3230 colourMenu.add(applyToAllGroups);
\r
3231 colourMenu.addSeparator();
\r
3232 colourMenu.add(noColourmenuItem);
\r
3233 colourMenu.add(clustalColour);
\r
3234 colourMenu.add(BLOSUM62Colour);
\r
3235 colourMenu.add(PIDColour);
\r
3236 colourMenu.add(zappoColour);
\r
3237 colourMenu.add(taylorColour);
\r
3238 colourMenu.add(hydrophobicityColour);
\r
3239 colourMenu.add(helixColour);
\r
3240 colourMenu.add(strandColour);
\r
3241 colourMenu.add(turnColour);
\r
3242 colourMenu.add(buriedColour);
\r
3243 colourMenu.add(nucleotideColour);
\r
3244 colourMenu.add(tcoffeeColour);
\r
3245 colourMenu.add(userDefinedColour);
\r
3246 colourMenu.addSeparator();
\r
3247 colourMenu.add(conservationMenuItem);
\r
3248 colourMenu.add(modifyConservation);
\r
3249 colourMenu.add(abovePIDThreshold);
\r
3250 colourMenu.add(modifyPID);
\r
3251 colourMenu.add(annotationColour);
\r
3252 calculateMenu.add(sort);
\r
3253 calculateMenu.add(calculate);
\r
3254 calculateMenu.addSeparator();
\r
3255 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
3256 calculateMenu.add(PCAMenuItem);
\r
3257 calculateMenu.add(autoCalculate);
\r
3258 calculateMenu.add(sortByTree);
\r
3259 this.add(statusBar, BorderLayout.SOUTH);
\r
3260 pasteMenu.add(pasteNew);
\r
3261 pasteMenu.add(pasteThis);
\r
3262 sort.add(sortIDMenuItem);
\r
3263 sort.add(sortLengthMenuItem);
\r
3264 sort.add(sortByTreeMenu);
\r
3265 sort.add(sortGroupMenuItem);
\r
3266 sort.add(sortPairwiseMenuItem);
\r
3267 calculate.add(averageDistanceTreeMenuItem);
\r
3268 calculate.add(neighbourTreeMenuItem);
\r
3269 calculate.add(avDistanceTreeBlosumMenuItem);
\r
3270 calculate.add(njTreeBlosumMenuItem);
\r
3271 helpMenu.add(documentation);
\r
3272 helpMenu.add(about);
\r
3273 menu1.add(showColumns);
\r
3274 menu1.add(showSeqs);
\r
3275 menu1.add(showAllHidden);
\r
3276 menu2.add(hideColumns);
\r
3277 menu2.add(hideSequences);
\r
3278 menu2.add(hideAllSelection);
\r
3279 menu2.add(hideAllButSelection);
\r
3280 formatMenu.add(font);
\r
3281 formatMenu.add(seqLimits);
\r
3282 formatMenu.add(wrapMenuItem);
\r
3283 formatMenu.add(scaleAbove);
\r
3284 formatMenu.add(scaleLeft);
\r
3285 formatMenu.add(scaleRight);
\r
3286 formatMenu.add(viewBoxesMenuItem);
\r
3287 formatMenu.add(viewTextMenuItem);
\r
3288 formatMenu.add(colourTextMenuItem);
\r
3289 formatMenu.add(displayNonconservedMenuItem);
\r
3290 formatMenu.add(renderGapsMenuItem);
\r
3291 formatMenu.add(centreColumnLabelFlag);
\r
3292 selectMenu.add(findMenuItem);
\r
3293 selectMenu.addSeparator();
\r
3294 selectMenu.add(selectAllSequenceMenuItem);
\r
3295 selectMenu.add(deselectAllSequenceMenuItem);
\r
3296 selectMenu.add(invertSequenceMenuItem);
\r
3297 selectMenu.add(invertColSel);
\r
3298 selectMenu.add(grpsFromSelection);
\r
3299 selectMenu.add(deleteGroups);
\r
3303 MenuItem featureSettings = new MenuItem();
\r
3305 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
3307 MenuItem annotationColour = new MenuItem();
\r
3309 MenuItem invertColSel = new MenuItem();
\r
3311 Menu menu1 = new Menu();
\r
3313 MenuItem showColumns = new MenuItem();
\r
3315 MenuItem showSeqs = new MenuItem();
\r
3317 Menu menu2 = new Menu();
\r
3319 MenuItem hideColumns = new MenuItem();
\r
3321 MenuItem hideSequences = new MenuItem();
\r
3323 MenuItem hideAllButSelection = new MenuItem();
\r
3325 MenuItem hideAllSelection = new MenuItem();
\r
3327 MenuItem showAllHidden = new MenuItem();
\r
3329 Menu formatMenu = new Menu();
\r
3331 Menu selectMenu = new Menu();
\r
3333 MenuItem newView = new MenuItem();
\r
3336 * Attach the alignFrame panels after embedding menus, if necessary. This used
\r
3337 * to be called setEmbedded, but is now creates the dropdown menus in a
\r
3338 * platform independent manner to avoid OSX/Mac menu appendage daftness.
\r
3340 * @param reallyEmbedded
\r
3341 * true to attach the view to the applet area on the page rather than
\r
3344 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
\r
3346 if (reallyEmbedded)
\r
3349 // Explicly build the embedded menu panel for the on-page applet
\r
3351 // view cannot be closed if its actually on the page
\r
3352 fileMenu.remove(closeMenuItem);
\r
3353 fileMenu.remove(3); // Remove Seperator
\r
3354 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
\r
3355 Font.PLAIN, 10, false); // use our own fonts.
\r
3356 // and actually add the components to the applet area
\r
3357 viewport.applet.setLayout(new BorderLayout());
\r
3358 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
\r
3359 viewport.applet.add(statusBar, BorderLayout.SOUTH);
\r
3360 alignPanel.setSize(viewport.applet.getSize().width,
\r
3361 viewport.applet.getSize().height - embeddedMenu.HEIGHT
\r
3362 - statusBar.HEIGHT);
\r
3363 viewport.applet.add(alignPanel, BorderLayout.CENTER);
\r
3364 final AlignFrame me = this;
\r
3365 viewport.applet.addFocusListener(new FocusListener()
\r
3369 public void focusLost(FocusEvent e)
\r
3371 if (me.viewport.applet.currentAlignFrame==me) {
\r
3372 me.viewport.applet.currentAlignFrame = null;
\r
3376 public void focusGained(FocusEvent e)
\r
3378 me.viewport.applet.currentAlignFrame = me;
\r
3381 viewport.applet.validate();
\r
3386 // test and embed menu bar if necessary.
\r
3388 if (embedMenuIfNeeded(alignPanel))
\r
3390 // adjust for status bar height too
\r
3391 alignPanel.setSize(getSize().width, getSize().height
\r
3392 - statusBar.HEIGHT);
\r
3394 add(statusBar, BorderLayout.SOUTH);
\r
3395 add(alignPanel, BorderLayout.CENTER);
\r
3396 // and register with the applet so it can pass external API calls to us
\r
3397 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
\r
3403 * create a new binding between structures in an existing jmol viewer instance
\r
3404 * and an alignpanel with sequences that have existing PDBFile entries. Note,
\r
3405 * this does not open a new Jmol window, or modify the display of the
\r
3406 * structures in the original jmol window. Note This method doesn't work
\r
3407 * without an additional javascript library to exchange messages between the
\r
3408 * distinct applets. See http://issues.jalview.org/browse/JAL-621
\r
3411 * JmolViewer instance
\r
3412 * @param sequenceIds
\r
3413 * - sequence Ids to search for associations
\r
3415 public SequenceStructureBinding addStructureViewInstance(
\r
3416 Object jmolviewer, String[] sequenceIds)
\r
3418 org.jmol.api.JmolViewer viewer = null;
\r
3421 viewer = (org.jmol.api.JmolViewer) jmolviewer;
\r
3422 } catch (ClassCastException ex)
\r
3424 System.err.println("Unsupported viewer object :"
\r
3425 + jmolviewer.getClass());
\r
3427 if (viewer == null)
\r
3429 System.err.println("Can't use this object as a structure viewer:"
\r
3430 + jmolviewer.getClass());
\r
3433 SequenceI[] seqs = null;
\r
3434 if (sequenceIds == null || sequenceIds.length == 0)
\r
3436 seqs = viewport.getAlignment().getSequencesArray();
\r
3440 Vector sqi = new Vector();
\r
3441 AlignmentI al = viewport.getAlignment();
\r
3442 for (int sid = 0; sid < sequenceIds.length; sid++)
\r
3444 SequenceI sq = al.findName(sequenceIds[sid]);
\r
3447 sqi.addElement(sq);
\r
3450 if (sqi.size() > 0)
\r
3452 seqs = new SequenceI[sqi.size()];
\r
3453 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
\r
3455 seqs[sid] = (SequenceI) sqi.elementAt(sid);
\r
3463 ExtJmol jmv = null;
\r
3464 // TODO: search for a jmv that involves viewer
\r
3466 { // create a new viewer/jalview binding.
\r
3467 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs});
\r
3473 * bind a pdb file to a sequence in the current view
\r
3475 * @param sequenceId
\r
3476 * - sequenceId within the dataset.
\r
3477 * @param pdbEntryString
\r
3478 * - the short name for the PDB file
\r
3480 * - pdb file - either a URL or a valid PDB file.
\r
3481 * @return true if binding was as success TODO: consider making an exception
\r
3482 * structure for indicating when PDB parsing or sequenceId location
\r
3485 public boolean addPdbFile(String sequenceId, String pdbEntryString,
\r
3488 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
\r
3489 boolean needtoadd = false;
\r
3490 if (toaddpdb != null)
\r
3492 Vector pdbe = toaddpdb.getPDBId();
\r
3493 PDBEntry pdbentry = null;
\r
3494 if (pdbe != null && pdbe.size() > 0)
\r
3496 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
\r
3498 pdbentry = (PDBEntry) pdbe.elementAt(pe);
\r
3499 if (!pdbentry.getId().equals(pdbEntryString)
\r
3500 && !pdbentry.getFile().equals(pdbFile))
\r
3510 if (pdbentry == null)
\r
3512 pdbentry = new PDBEntry();
\r
3513 pdbentry.setId(pdbEntryString);
\r
3514 pdbentry.setFile(pdbFile);
\r
3515 needtoadd = true; // add this new entry to sequence.
\r
3517 // resolve data source
\r
3518 // TODO: this code should be a refactored to an io package
\r
3519 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
\r
3520 if (protocol == null)
\r
3526 // make a note of the access mode and add
\r
3527 if (pdbentry.getProperty() == null)
\r
3529 pdbentry.setProperty(new Hashtable());
\r
3531 pdbentry.getProperty().put("protocol", protocol);
\r
3532 toaddpdb.addPDBId(pdbentry);
\r
3538 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
\r
3542 Vector sequences = new Vector();
\r
3543 for (int i = 0; i < seqs.length; i++)
\r
3545 if (seqs[i] != null)
\r
3547 sequences.addElement(new Object[]
\r
3548 { seqs[i], (chains != null) ? chains[i] : null });
\r
3551 seqs = new SequenceI[sequences.size()];
\r
3552 chains = new String[sequences.size()];
\r
3553 for (int i = 0, isize = sequences.size(); i < isize; i++)
\r
3555 Object[] oj = (Object[]) sequences.elementAt(i);
\r
3557 seqs[i] = (SequenceI) oj[0];
\r
3558 chains[i] = (String) oj[1];
\r
3561 return new Object[]
\r
3566 public void newStructureView(JalviewLite applet, PDBEntry pdb,
\r
3567 SequenceI[] seqs, String[] chains, String protocol)
\r
3569 // Scrub any null sequences from the array
\r
3570 Object[] sqch = cleanSeqChainArrays(seqs, chains);
\r
3571 seqs = (SequenceI[]) sqch[0];
\r
3572 chains = (String[]) sqch[1];
\r
3573 if (seqs == null || seqs.length == 0)
\r
3576 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
\r
3578 if (protocol == null || protocol.trim().length() == 0
\r
3579 || protocol.equals("null"))
\r
3581 protocol = (String) pdb.getProperty().get("protocol");
\r
3582 if (protocol == null)
\r
3584 System.err.println("Couldn't work out protocol to open structure: "
\r
3589 if (applet.useXtrnalSviewer)
\r
3591 // register the association(s) and quit, don't create any windows.
\r
3592 if (StructureSelectionManager.getStructureSelectionManager(applet).setMapping(seqs, chains, pdb.getFile(), protocol)==null) {
\r
3593 System.err.println("Failed to map "+pdb.getFile()+" ("+protocol+") to any sequences");
\r
3597 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
\r
3599 // can only do alignments with Jmol
\r
3600 // find the last jmol window assigned to this alignment
\r
3601 jalview.appletgui.AppletJmol ajm = null, tajm;
\r
3602 Vector jmols = applet
\r
3603 .getAppletWindow(jalview.appletgui.AppletJmol.class);
\r
3604 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
\r
3606 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
\r
3607 if (tajm.ap.alignFrame == this)
\r
3616 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
\r
3617 // try and add the pdb structure
\r
3622 // otherwise, create a new window
\r
3623 if (applet.jmolAvailable)
\r
3625 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
\r
3627 applet.lastFrameX += 40;
\r
3628 applet.lastFrameY += 40;
\r
3632 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
\r
3637 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
\r
3638 SequenceI[][] seqs, String[][] chains, String[] protocols)
\r
3640 // TODO Auto-generated method stub
\r
3641 System.err.println("Aligned Structure View: Not yet implemented.");
\r
3645 * modify the current selection, providing the user has not made a selection already.
\r
3646 * @param sel - sequences from this alignment
\r
3647 * @param csel - columns to be selected on the alignment
\r
3649 public void select(SequenceGroup sel, ColumnSelection csel)
\r
3651 alignPanel.seqPanel.selection(sel, csel, null);
\r
3654 public void scrollTo(int row, int column)
\r
3656 alignPanel.seqPanel.scrollTo(row, column);
\r
3658 public void scrollToRow(int row)
\r
3660 alignPanel.seqPanel.scrollToRow(row);
\r
3662 public void scrollToColumn(int column)
\r
3664 alignPanel.seqPanel.scrollToColumn(column);
\r
3667 * @return the alignments unique ID.
\r
3669 public String getSequenceSetId() {
\r
3670 return viewport.getSequenceSetId();
\r
3675 * Load the (T-Coffee) score file from the specified url
\r
3677 * @param url The absolute path from where download and read the score file
\r
3678 * @throws IOException
\r
3680 public void loadScoreFile( URL url ) throws IOException {
\r
3682 TCoffeeScoreFile file = TCoffeeScoreFile.load( new InputStreamReader( url.openStream() ) );
\r
3683 if( file == null ) {
\r
3684 // TODO: raise a dialog box here rather than bomb out.
\r
3686 throw new RuntimeException("The file provided does not match the T-Coffee scores file format");
\r
3690 * check that the score matrix matches the alignment dimensions
\r
3693 if( (aln=viewport.alignment) != null && (aln.getHeight() != file.getHeight() || aln.getWidth() != file.getWidth()) ) {
\r
3694 // TODO: raise a dialog box here rather than bomb out.
\r
3695 throw new RuntimeException("The scores matrix does not match the alignment dimensions");
\r
3699 // TODO add parameter to indicate if matching should be done
\r
3700 if (file.annotateAlignment(alignPanel.getAlignment(), false))
\r
3702 tcoffeeColour.setEnabled(true);
\r
3703 // switch to this color
\r
3704 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
\r