2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
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3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
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5 * This file is part of Jalview.
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7 * Jalview is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License
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9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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11 * Jalview is distributed in the hope that it will be useful, but
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12 * WITHOUT ANY WARRANTY; without even the implied warranty
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13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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14 * PURPOSE. See the GNU General Public License for more details.
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16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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18 package jalview.appletgui;
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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.SequenceCollectionI;
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39 import jalview.datamodel.SequenceGroup;
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40 import jalview.datamodel.SequenceI;
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41 import jalview.io.AnnotationFile;
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42 import jalview.io.AppletFormatAdapter;
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43 import jalview.io.FeaturesFile;
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44 import jalview.io.TCoffeeScoreFile;
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45 import jalview.schemes.Blosum62ColourScheme;
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46 import jalview.schemes.BuriedColourScheme;
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47 import jalview.schemes.ClustalxColourScheme;
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48 import jalview.schemes.ColourSchemeI;
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49 import jalview.schemes.HelixColourScheme;
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50 import jalview.schemes.HydrophobicColourScheme;
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51 import jalview.schemes.NucleotideColourScheme;
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52 import jalview.schemes.PIDColourScheme;
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53 import jalview.schemes.PurinePyrimidineColourScheme;
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54 import jalview.schemes.RNAHelicesColourChooser;
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55 import jalview.schemes.ResidueProperties;
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56 import jalview.schemes.StrandColourScheme;
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57 import jalview.schemes.TCoffeeColourScheme;
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58 import jalview.schemes.TaylorColourScheme;
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59 import jalview.schemes.TurnColourScheme;
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60 import jalview.schemes.ZappoColourScheme;
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61 import jalview.structure.StructureSelectionManager;
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63 import java.awt.BorderLayout;
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64 import java.awt.Canvas;
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65 import java.awt.CheckboxMenuItem;
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66 import java.awt.Color;
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67 import java.awt.Font;
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68 import java.awt.FontMetrics;
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69 import java.awt.Frame;
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70 import java.awt.Graphics;
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71 import java.awt.Label;
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72 import java.awt.Menu;
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73 import java.awt.MenuBar;
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74 import java.awt.MenuItem;
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75 import java.awt.event.ActionEvent;
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76 import java.awt.event.ActionListener;
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77 import java.awt.event.FocusEvent;
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78 import java.awt.event.FocusListener;
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79 import java.awt.event.ItemEvent;
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80 import java.awt.event.ItemListener;
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81 import java.awt.event.KeyEvent;
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82 import java.awt.event.KeyListener;
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83 import java.awt.event.WindowAdapter;
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84 import java.awt.event.WindowEvent;
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85 import java.io.IOException;
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86 import java.io.InputStreamReader;
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87 import java.net.URL;
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88 import java.net.URLEncoder;
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89 import java.util.Enumeration;
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90 import java.util.Hashtable;
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91 import java.util.List;
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92 import java.util.StringTokenizer;
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93 import java.util.Vector;
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95 public class AlignFrame extends EmbmenuFrame implements ActionListener, ItemListener, KeyListener
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97 public AlignmentPanel alignPanel;
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99 public AlignViewport viewport;
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101 int DEFAULT_WIDTH = 700;
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103 int DEFAULT_HEIGHT = 500;
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105 String jalviewServletURL;
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108 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title, boolean embedded)
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110 if (applet != null)
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112 jalviewServletURL = applet.getParameter("APPLICATION_URL");
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118 } catch (Exception ex)
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120 ex.printStackTrace();
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123 viewport = new AlignViewport(al, applet);
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124 alignPanel = new AlignmentPanel(this, viewport);
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126 viewport.updateConservation(alignPanel);
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127 viewport.updateConsensus(alignPanel);
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129 annotationPanelMenuItem.setState(viewport.showAnnotation);
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130 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
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131 followMouseOverFlag.setState(viewport.getFollowHighlight());
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132 showGroupConsensus.setState(viewport.isShowGroupConsensus());
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133 showGroupConservation.setState(viewport.isShowGroupConservation());
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134 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
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135 showSequenceLogo.setState(viewport.isShowSequenceLogo());
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137 seqLimits.setState(viewport.showJVSuffix);
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139 if (applet != null)
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141 String param = applet.getParameter("sortBy");
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144 if (param.equalsIgnoreCase("Id"))
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146 sortIDMenuItem_actionPerformed();
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148 else if (param.equalsIgnoreCase("Pairwise Identity"))
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150 sortPairwiseMenuItem_actionPerformed();
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152 else if (param.equalsIgnoreCase("Length"))
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154 sortLengthMenuItem_actionPerformed();
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158 param = applet.getParameter("wrap");
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161 if (param.equalsIgnoreCase("true"))
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163 wrapMenuItem.setState(true);
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164 wrapMenuItem_actionPerformed();
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167 param = applet.getParameter("centrecolumnlabels");
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170 centreColumnLabelFlag.setState(true);
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171 centreColumnLabelFlag_stateChanged();
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175 param = applet.getParameter("windowWidth");
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178 int width = Integer.parseInt(param);
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179 DEFAULT_WIDTH = width;
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181 param = applet.getParameter("windowHeight");
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184 int height = Integer.parseInt(param);
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185 DEFAULT_HEIGHT = height;
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187 } catch (Exception ex)
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192 if (viewport.getAlignment().isNucleotide())
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194 viewport.updateStrucConsensus(alignPanel);
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195 if (viewport.getAlignment().hasRNAStructure())
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197 RNAHelixColour.setEnabled(true);
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200 RNAHelixColour.setEnabled(false);
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203 RNAHelixColour.setEnabled(false);
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204 purinePyrimidineColour.setEnabled(false);
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206 // Some JVMS send keyevents to Top frame or lowest panel,
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207 // Havent worked out why yet. So add to both this frame and seqCanvas for
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209 this.addKeyListener(this);
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210 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
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211 alignPanel.idPanel.idCanvas.addKeyListener(this);
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212 alignPanel.scalePanel.addKeyListener(this);
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213 alignPanel.annotationPanel.addKeyListener(this);
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214 alignPanel.annotationPanelHolder.addKeyListener(this);
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215 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
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216 alignPanel.alabels.addKeyListener(this);
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217 createAlignFrameWindow(embedded, title);
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220 alignPanel.adjustAnnotationHeight();
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221 alignPanel.paintAlignment(true);
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224 public AlignViewport getAlignViewport()
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229 public SeqCanvas getSeqcanvas()
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231 return alignPanel.seqPanel.seqCanvas;
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235 * Load a features file onto the alignment
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237 * @param file file URL, content, or other resolvable path
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238 * @param type is protocol for accessing data referred to by file
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241 public boolean parseFeaturesFile(String file, String type)
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243 return parseFeaturesFile(file, type, true);
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247 * Load a features file onto the alignment
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249 * @param file file URL, content, or other resolvable path
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250 * @param type is protocol for accessing data referred to by file
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251 * @param autoenabledisplay when true, display features flag will be automatically enabled if features are loaded
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252 * @return true if data parsed as a features file
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254 public boolean parseFeaturesFile(String file, String type, boolean autoenabledisplay)
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256 // TODO: test if importing a features file onto an alignment which already has features with links overwrites the original links.
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258 Hashtable featureLinks = new Hashtable();
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259 boolean featuresFile = false;
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262 featuresFile = new jalview.io.FeaturesFile(file, type)
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263 .parse(viewport.getAlignment(),
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264 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
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265 featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));
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266 } catch (Exception ex)
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268 ex.printStackTrace();
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273 if (featureLinks.size() > 0)
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275 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
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277 if (autoenabledisplay)
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279 viewport.showSequenceFeatures = true;
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280 sequenceFeatures.setState(true);
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282 if (viewport.featureSettings != null)
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284 viewport.featureSettings.refreshTable();
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286 alignPanel.paintAlignment(true);
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287 statusBar.setText("Successfully added features to alignment.");
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289 return featuresFile;
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292 public void keyPressed(KeyEvent evt)
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294 if (viewport.cursorMode
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295 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
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296 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
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297 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
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298 && Character.isDigit(evt.getKeyChar()))
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299 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
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301 switch (evt.getKeyCode())
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303 case 27: // escape key
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304 deselectAllSequenceMenuItem_actionPerformed();
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306 alignPanel.alabels.cancelDrag();
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308 case KeyEvent.VK_X:
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309 if (evt.isControlDown() || evt.isMetaDown())
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311 cut_actionPerformed();
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314 case KeyEvent.VK_C:
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315 if (viewport.cursorMode && !evt.isControlDown())
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317 alignPanel.seqPanel.setCursorColumn();
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319 if (evt.isControlDown() || evt.isMetaDown())
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321 copy_actionPerformed();
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324 case KeyEvent.VK_V:
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325 if (evt.isControlDown())
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327 paste(evt.isShiftDown());
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330 case KeyEvent.VK_A:
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331 if (evt.isControlDown() || evt.isMetaDown())
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333 selectAllSequenceMenuItem_actionPerformed();
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336 case KeyEvent.VK_DOWN:
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337 if (viewport.cursorMode)
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339 alignPanel.seqPanel.moveCursor(0, 1);
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343 moveSelectedSequences(false);
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347 case KeyEvent.VK_UP:
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348 if (viewport.cursorMode)
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350 alignPanel.seqPanel.moveCursor(0, -1);
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354 moveSelectedSequences(true);
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358 case KeyEvent.VK_LEFT:
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359 if (evt.isAltDown() || !viewport.cursorMode)
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360 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
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362 alignPanel.seqPanel.moveCursor(-1, 0);
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365 case KeyEvent.VK_RIGHT:
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366 if (evt.isAltDown() || !viewport.cursorMode)
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367 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
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369 alignPanel.seqPanel.moveCursor(1, 0);
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372 case KeyEvent.VK_SPACE:
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373 if (viewport.cursorMode)
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375 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
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376 || evt.isShiftDown() || evt.isAltDown());
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380 case KeyEvent.VK_DELETE:
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381 case KeyEvent.VK_BACK_SPACE:
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382 if (viewport.cursorMode)
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384 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
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385 || evt.isShiftDown() || evt.isAltDown());
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389 cut_actionPerformed();
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390 alignPanel.seqPanel.seqCanvas.repaint();
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394 case KeyEvent.VK_S:
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395 if (viewport.cursorMode)
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397 alignPanel.seqPanel.setCursorRow();
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400 case KeyEvent.VK_P:
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401 if (viewport.cursorMode)
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403 alignPanel.seqPanel.setCursorPosition();
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407 case KeyEvent.VK_ENTER:
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408 case KeyEvent.VK_COMMA:
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409 if (viewport.cursorMode)
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411 alignPanel.seqPanel.setCursorRowAndColumn();
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415 case KeyEvent.VK_Q:
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416 if (viewport.cursorMode)
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418 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
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421 case KeyEvent.VK_M:
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422 if (viewport.cursorMode)
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424 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
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428 case KeyEvent.VK_F2:
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429 viewport.cursorMode = !viewport.cursorMode;
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430 statusBar.setText("Keyboard editing mode is "
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431 + (viewport.cursorMode ? "on" : "off"));
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432 if (viewport.cursorMode)
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434 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
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435 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
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439 case KeyEvent.VK_F:
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440 if (evt.isControlDown())
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442 findMenuItem_actionPerformed();
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446 case KeyEvent.VK_H:
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448 boolean toggleSeqs = !evt.isControlDown();
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449 boolean toggleCols = !evt.isShiftDown();
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450 toggleHiddenRegions(toggleSeqs, toggleCols);
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454 case KeyEvent.VK_PAGE_UP:
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455 if (viewport.wrapAlignment)
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457 alignPanel.scrollUp(true);
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461 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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462 - viewport.endSeq + viewport.startSeq);
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466 case KeyEvent.VK_PAGE_DOWN:
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467 if (viewport.wrapAlignment)
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469 alignPanel.scrollUp(false);
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473 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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474 + viewport.endSeq - viewport.startSeq);
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478 case KeyEvent.VK_Z:
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479 if (evt.isControlDown())
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481 undoMenuItem_actionPerformed();
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485 case KeyEvent.VK_Y:
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486 if (evt.isControlDown())
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488 redoMenuItem_actionPerformed();
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492 case KeyEvent.VK_L:
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493 if (evt.isControlDown())
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495 trimAlignment(true);
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499 case KeyEvent.VK_R:
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500 if (evt.isControlDown())
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502 trimAlignment(false);
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506 case KeyEvent.VK_E:
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507 if (evt.isControlDown())
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509 if (evt.isShiftDown())
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511 this.removeAllGapsMenuItem_actionPerformed();
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515 removeGappedColumnMenuItem_actionPerformed();
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519 case KeyEvent.VK_I:
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520 if (evt.isControlDown())
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522 if (evt.isAltDown())
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524 invertColSel_actionPerformed();
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528 invertSequenceMenuItem_actionPerformed();
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533 case KeyEvent.VK_U:
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534 if (evt.isControlDown())
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536 this.deleteGroups_actionPerformed();
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540 case KeyEvent.VK_T:
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541 if (evt.isControlDown())
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548 alignPanel.paintAlignment(true);
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552 * called by key handler and the hide all/show all menu items
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554 * @param toggleSeqs
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555 * @param toggleCols
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557 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
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559 boolean hide = false;
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560 SequenceGroup sg = viewport.getSelectionGroup();
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561 if (!toggleSeqs && !toggleCols)
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563 // Hide everything by the current selection - this is a hack - we do the
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564 // invert and then hide
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565 // first check that there will be visible columns after the invert.
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566 if ((viewport.getColumnSelection() != null && viewport.getColumnSelection().getSelected() != null && viewport.getColumnSelection()
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567 .getSelected().size() > 0)
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568 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
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571 // now invert the sequence set, if required - empty selection implies
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572 // that no hiding is required.
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575 invertSequenceMenuItem_actionPerformed();
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576 sg = viewport.getSelectionGroup();
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580 viewport.expandColSelection(sg, true);
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581 // finally invert the column selection and get the new sequence
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582 // selection and indicate it should be hidden.
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583 invertColSel_actionPerformed();
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590 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
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593 viewport.hideAllSelectedSeqs();
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595 else if (!(toggleCols && viewport.getColumnSelection().getSelected().size() > 0))
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597 viewport.showAllHiddenSeqs();
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603 if (viewport.getColumnSelection().getSelected().size() > 0)
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605 viewport.hideSelectedColumns();
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608 viewport.setSelectionGroup(sg);
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613 viewport.showAllHiddenColumns();
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618 public void keyReleased(KeyEvent evt)
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622 public void keyTyped(KeyEvent evt)
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626 public void itemStateChanged(ItemEvent evt)
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628 if (evt.getSource() == displayNonconservedMenuItem)
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630 displayNonconservedMenuItem_actionPerformed();
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632 else if (evt.getSource() == colourTextMenuItem)
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634 colourTextMenuItem_actionPerformed();
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636 else if (evt.getSource() == wrapMenuItem)
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638 wrapMenuItem_actionPerformed();
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640 else if (evt.getSource() == scaleAbove)
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642 viewport.setScaleAboveWrapped(scaleAbove.getState());
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644 else if (evt.getSource() == scaleLeft)
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646 viewport.setScaleLeftWrapped(scaleLeft.getState());
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648 else if (evt.getSource() == scaleRight)
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650 viewport.setScaleRightWrapped(scaleRight.getState());
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652 else if (evt.getSource() == seqLimits)
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654 seqLimits_itemStateChanged();
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656 else if (evt.getSource() == viewBoxesMenuItem)
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658 viewport.setShowBoxes(viewBoxesMenuItem.getState());
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660 else if (evt.getSource() == viewTextMenuItem)
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662 viewport.setShowText(viewTextMenuItem.getState());
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664 else if (evt.getSource() == renderGapsMenuItem)
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666 viewport.setRenderGaps(renderGapsMenuItem.getState());
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668 else if (evt.getSource() == annotationPanelMenuItem)
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670 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
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671 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
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673 else if (evt.getSource() == sequenceFeatures)
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675 viewport.showSequenceFeatures(sequenceFeatures.getState());
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676 alignPanel.seqPanel.seqCanvas.repaint();
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678 else if (evt.getSource() == conservationMenuItem)
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680 conservationMenuItem_actionPerformed();
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682 else if (evt.getSource() == abovePIDThreshold)
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684 abovePIDThreshold_actionPerformed();
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686 else if (evt.getSource() == applyToAllGroups)
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688 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
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690 else if (evt.getSource() == autoCalculate)
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692 viewport.autoCalculateConsensus = autoCalculate.getState();
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694 else if (evt.getSource() == sortByTree)
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696 viewport.sortByTree = sortByTree.getState();
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698 else if (evt.getSource() == this.centreColumnLabelFlag)
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700 centreColumnLabelFlag_stateChanged();
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702 else if (evt.getSource() == this.followMouseOverFlag)
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704 mouseOverFlag_stateChanged();
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706 else if (evt.getSource() == showGroupConsensus)
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708 showGroupConsensus_actionPerformed();
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710 else if (evt.getSource() == showGroupConservation)
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712 showGroupConservation_actionPerformed();
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714 else if (evt.getSource() == showSequenceLogo)
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716 showSequenceLogo_actionPerformed();
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718 else if (evt.getSource() == showConsensusHistogram)
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720 showConsensusHistogram_actionPerformed();
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722 else if (evt.getSource() == applyAutoAnnotationSettings)
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724 applyAutoAnnotationSettings_actionPerformed();
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726 alignPanel.paintAlignment(true);
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729 private void mouseOverFlag_stateChanged()
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731 viewport.followHighlight = followMouseOverFlag.getState();
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732 // TODO: could kick the scrollTo mechanism to reset view for current
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736 private void centreColumnLabelFlag_stateChanged()
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738 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
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739 this.alignPanel.annotationPanel.repaint();
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742 public void actionPerformed(ActionEvent evt)
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744 Object source = evt.getSource();
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746 if (source == inputText)
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748 inputText_actionPerformed();
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750 else if (source == loadTree)
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752 loadTree_actionPerformed();
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754 else if (source == loadApplication)
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756 launchFullApplication();
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758 else if (source == loadAnnotations)
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762 else if (source == outputAnnotations)
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764 outputAnnotations(true);
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766 else if (source == outputFeatures)
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768 outputFeatures(true, "Jalview");
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770 else if (source == closeMenuItem)
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772 closeMenuItem_actionPerformed();
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774 else if (source == copy)
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776 copy_actionPerformed();
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778 else if (source == undoMenuItem)
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780 undoMenuItem_actionPerformed();
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782 else if (source == redoMenuItem)
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784 redoMenuItem_actionPerformed();
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786 else if (source == inputText)
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788 inputText_actionPerformed();
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790 else if (source == closeMenuItem)
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792 closeMenuItem_actionPerformed();
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794 else if (source == undoMenuItem)
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796 undoMenuItem_actionPerformed();
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798 else if (source == redoMenuItem)
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800 redoMenuItem_actionPerformed();
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802 else if (source == copy)
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804 copy_actionPerformed();
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806 else if (source == pasteNew)
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808 pasteNew_actionPerformed();
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810 else if (source == pasteThis)
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812 pasteThis_actionPerformed();
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814 else if (source == cut)
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816 cut_actionPerformed();
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818 else if (source == delete)
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820 delete_actionPerformed();
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822 else if (source == grpsFromSelection)
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824 makeGrpsFromSelection_actionPerformed();
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826 else if (source == deleteGroups)
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828 deleteGroups_actionPerformed();
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830 else if (source == selectAllSequenceMenuItem)
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832 selectAllSequenceMenuItem_actionPerformed();
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834 else if (source == deselectAllSequenceMenuItem)
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836 deselectAllSequenceMenuItem_actionPerformed();
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838 else if (source == invertSequenceMenuItem)
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840 invertSequenceMenuItem_actionPerformed();
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842 else if (source == invertColSel)
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844 viewport.invertColumnSelection();
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845 alignPanel.paintAlignment(true);
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847 else if (source == remove2LeftMenuItem)
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849 trimAlignment(true);
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851 else if (source == remove2RightMenuItem)
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853 trimAlignment(false);
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855 else if (source == removeGappedColumnMenuItem)
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857 removeGappedColumnMenuItem_actionPerformed();
\r
859 else if (source == removeAllGapsMenuItem)
\r
861 removeAllGapsMenuItem_actionPerformed();
\r
863 else if (source == findMenuItem)
\r
865 findMenuItem_actionPerformed();
\r
867 else if (source == font)
\r
869 new FontChooser(alignPanel);
\r
871 else if (source == newView)
\r
875 else if (source == showColumns)
\r
877 viewport.showAllHiddenColumns();
\r
878 alignPanel.paintAlignment(true);
\r
880 else if (source == showSeqs)
\r
882 viewport.showAllHiddenSeqs();
\r
883 alignPanel.paintAlignment(true);
\r
885 else if (source == hideColumns)
\r
887 viewport.hideSelectedColumns();
\r
888 alignPanel.paintAlignment(true);
\r
890 else if (source == hideSequences
\r
891 && viewport.getSelectionGroup() != null)
\r
893 viewport.hideAllSelectedSeqs();
\r
894 alignPanel.paintAlignment(true);
\r
896 else if (source == hideAllButSelection)
\r
898 toggleHiddenRegions(false, false);
\r
899 alignPanel.paintAlignment(true);
\r
901 else if (source == hideAllSelection)
\r
903 SequenceGroup sg = viewport.getSelectionGroup();
\r
904 viewport.expandColSelection(sg, false);
\r
905 viewport.hideAllSelectedSeqs();
\r
906 viewport.hideSelectedColumns();
\r
907 alignPanel.paintAlignment(true);
\r
909 else if (source == showAllHidden)
\r
911 viewport.showAllHiddenColumns();
\r
912 viewport.showAllHiddenSeqs();
\r
913 alignPanel.paintAlignment(true);
\r
915 else if (source == showGroupConsensus)
\r
917 showGroupConsensus_actionPerformed();
\r
919 else if (source == showGroupConservation)
\r
921 showGroupConservation_actionPerformed();
\r
923 else if (source == showSequenceLogo)
\r
925 showSequenceLogo_actionPerformed();
\r
927 else if (source == showConsensusHistogram)
\r
929 showConsensusHistogram_actionPerformed();
\r
931 else if (source == applyAutoAnnotationSettings)
\r
933 applyAutoAnnotationSettings_actionPerformed();
\r
935 else if (source == featureSettings)
\r
937 new FeatureSettings(alignPanel);
\r
939 else if (source == alProperties)
\r
941 StringBuffer contents = new jalview.io.AlignmentProperties(
\r
942 viewport.getAlignment()).formatAsString();
\r
943 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
944 cap.setText(contents.toString());
\r
945 Frame frame = new Frame();
\r
947 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
\r
948 + getTitle(), 400, 250);
\r
950 else if (source == overviewMenuItem)
\r
952 overviewMenuItem_actionPerformed();
\r
954 else if (source == noColourmenuItem)
\r
956 changeColour(null);
\r
958 else if (source == clustalColour)
\r
960 abovePIDThreshold.setState(false);
\r
961 changeColour(new ClustalxColourScheme(viewport.getAlignment(),null));
\r
963 else if (source == zappoColour)
\r
965 changeColour(new ZappoColourScheme());
\r
967 else if (source == taylorColour)
\r
969 changeColour(new TaylorColourScheme());
\r
971 else if (source == hydrophobicityColour)
\r
973 changeColour(new HydrophobicColourScheme());
\r
975 else if (source == helixColour)
\r
977 changeColour(new HelixColourScheme());
\r
979 else if (source == strandColour)
\r
981 changeColour(new StrandColourScheme());
\r
983 else if (source == turnColour)
\r
985 changeColour(new TurnColourScheme());
\r
987 else if (source == buriedColour)
\r
989 changeColour(new BuriedColourScheme());
\r
991 else if (source == nucleotideColour)
\r
993 changeColour(new NucleotideColourScheme());
\r
995 else if (source == purinePyrimidineColour)
\r
997 changeColour(new PurinePyrimidineColourScheme());
\r
999 else if (source == RNAHelixColour)
\r
1001 new RNAHelicesColourChooser(viewport, alignPanel);
\r
1003 else if (source == modifyPID)
\r
1005 modifyPID_actionPerformed();
\r
1007 else if (source == modifyConservation)
\r
1009 modifyConservation_actionPerformed();
\r
1011 else if (source == userDefinedColour)
\r
1013 new UserDefinedColours(alignPanel, null);
\r
1015 else if (source == PIDColour)
\r
1017 changeColour(new PIDColourScheme());
\r
1019 else if (source == BLOSUM62Colour)
\r
1021 changeColour(new Blosum62ColourScheme());
\r
1023 else if (source == tcoffeeColour) {
\r
1024 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
\r
1026 else if (source == annotationColour)
\r
1028 new AnnotationColourChooser(viewport, alignPanel);
\r
1030 else if (source == sortPairwiseMenuItem)
\r
1032 sortPairwiseMenuItem_actionPerformed();
\r
1034 else if (source == sortIDMenuItem)
\r
1036 sortIDMenuItem_actionPerformed();
\r
1038 else if (source == sortLengthMenuItem)
\r
1040 sortLengthMenuItem_actionPerformed();
\r
1042 else if (source == sortGroupMenuItem)
\r
1044 sortGroupMenuItem_actionPerformed();
\r
1046 else if (source == removeRedundancyMenuItem)
\r
1048 removeRedundancyMenuItem_actionPerformed();
\r
1050 else if (source == pairwiseAlignmentMenuItem)
\r
1052 pairwiseAlignmentMenuItem_actionPerformed();
\r
1054 else if (source == PCAMenuItem)
\r
1056 PCAMenuItem_actionPerformed();
\r
1058 else if (source == averageDistanceTreeMenuItem)
\r
1060 averageDistanceTreeMenuItem_actionPerformed();
\r
1062 else if (source == neighbourTreeMenuItem)
\r
1064 neighbourTreeMenuItem_actionPerformed();
\r
1066 else if (source == njTreeBlosumMenuItem)
\r
1068 njTreeBlosumMenuItem_actionPerformed();
\r
1070 else if (source == avDistanceTreeBlosumMenuItem)
\r
1072 avTreeBlosumMenuItem_actionPerformed();
\r
1074 else if (source == documentation)
\r
1076 documentation_actionPerformed();
\r
1078 else if (source == about)
\r
1080 about_actionPerformed();
\r
1085 public void inputText_actionPerformed()
\r
1087 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1088 Frame frame = new Frame();
\r
1090 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
\r
1093 protected void outputText_actionPerformed(ActionEvent e)
\r
1095 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1096 Frame frame = new Frame();
\r
1098 jalview.bin.JalviewLite.addFrame(frame,
\r
1099 "Alignment output - " + e.getActionCommand(), 600, 500);
\r
1100 cap.setText(new AppletFormatAdapter().formatSequences(
\r
1101 e.getActionCommand(), viewport.getAlignment(),
\r
1102 viewport.showJVSuffix));
\r
1105 public void loadAnnotations()
\r
1107 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1108 cap.setText("Paste your features / annotations / T-coffee score file here.");
\r
1109 cap.setAnnotationImport();
\r
1110 Frame frame = new Frame();
\r
1112 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
\r
1116 public String outputAnnotations(boolean displayTextbox)
\r
1118 String annotation = new AnnotationFile().printAnnotations(
\r
1119 viewport.showAnnotation ? viewport.getAlignment()
\r
1120 .getAlignmentAnnotation() : null, viewport.getAlignment()
\r
1122 ((Alignment) viewport.getAlignment()).alignmentProperties);
\r
1124 if (displayTextbox)
\r
1126 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
1127 Frame frame = new Frame();
\r
1129 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
\r
1130 cap.setText(annotation);
\r
1133 return annotation;
\r
1136 private Hashtable getDisplayedFeatureCols()
\r
1138 if (alignPanel.getFeatureRenderer() != null && viewport.featuresDisplayed!=null)
\r
1140 FeatureRenderer fr = alignPanel.getFeatureRenderer();
\r
1141 Hashtable fcols = new Hashtable();
\r
1142 Enumeration en = viewport.featuresDisplayed.keys();
\r
1143 while (en.hasMoreElements())
\r
1145 Object col = en.nextElement();
\r
1146 fcols.put(col, fr.featureColours.get(col));
\r
1153 public String outputFeatures(boolean displayTextbox, String format)
\r
1156 if (format.equalsIgnoreCase("Jalview"))
\r
1158 features = new FeaturesFile().printJalviewFormat(
\r
1159 viewport.getAlignment().getSequencesArray(),
\r
1160 getDisplayedFeatureCols());
\r
1164 features = new FeaturesFile().printGFFFormat(
\r
1165 viewport.getAlignment().getSequencesArray(),
\r
1166 getDisplayedFeatureCols());
\r
1169 if (displayTextbox)
\r
1171 boolean frimport=false;
\r
1172 if (features==null || features.equals("No Features Visible"))
\r
1174 features = "# No features visible - paste some and import them here.";
\r
1178 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
\r
1181 cap.setAnnotationImport();
\r
1183 Frame frame = new Frame();
\r
1185 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
\r
1186 cap.setText(features);
\r
1188 if (features==null)
\r
1195 void launchFullApplication()
\r
1197 StringBuffer url = new StringBuffer(jalviewServletURL);
\r
1199 url.append("?open="
\r
1200 + appendProtocol(viewport.applet.getParameter("file")));
\r
1202 if (viewport.applet.getParameter("features") != null)
\r
1204 url.append("&features=");
\r
1205 url.append(appendProtocol(viewport.applet.getParameter("features")));
\r
1208 if (viewport.applet.getParameter("annotations") != null)
\r
1210 url.append("&annotations=");
\r
1211 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
\r
1214 if (viewport.applet.getParameter("jnetfile") != null)
\r
1216 url.append("&annotations=");
\r
1217 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
\r
1220 if (viewport.applet.getParameter("defaultColour") != null)
\r
1222 url.append("&colour="
\r
1223 + removeWhiteSpace(viewport.applet
\r
1224 .getParameter("defaultColour")));
\r
1227 if (viewport.applet.getParameter("userDefinedColour") != null)
\r
1229 url.append("&colour="
\r
1230 + removeWhiteSpace(viewport.applet
\r
1231 .getParameter("userDefinedColour")));
\r
1233 if (viewport.applet.getParameter("tree") != null)
\r
1235 url.append("&tree="
\r
1236 + appendProtocol(viewport.applet.getParameter("tree")));
\r
1238 if (viewport.applet.getParameter("treeFile") != null)
\r
1240 url.append("&tree="
\r
1241 + appendProtocol(viewport.applet.getParameter("treeFile")));
\r
1244 showURL(url.toString(), "FULL_APP");
\r
1247 String removeWhiteSpace(String colour)
\r
1249 StringBuffer sb = new StringBuffer();
\r
1250 for (int i = 0; i < colour.length(); i++)
\r
1252 if (Character.isWhitespace(colour.charAt(i)))
\r
1258 sb.append(colour.charAt(i));
\r
1262 return sb.toString();
\r
1265 String appendProtocol(String url)
\r
1270 url = URLEncoder.encode(url);
\r
1273 * When we finally deprecate 1.1 compatibility, we can start to use
\r
1274 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
\r
1275 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
\r
1276 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
\r
1277 * ex.printStackTrace(); }
\r
1279 catch (java.net.MalformedURLException ex)
\r
1281 url = viewport.applet.getCodeBase() + url;
\r
1286 public void closeMenuItem_actionPerformed()
\r
1288 PaintRefresher.RemoveComponent(alignPanel);
\r
1289 if (alignPanel.seqPanel!=null && alignPanel.seqPanel.seqCanvas!=null)
\r
1291 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
\r
1293 if (alignPanel.idPanel!=null && alignPanel.idPanel.idCanvas!=null) {
\r
1294 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
\r
1297 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
\r
1303 alignPanel = null;
\r
1310 void updateEditMenuBar()
\r
1313 if (viewport.historyList.size() > 0)
\r
1315 undoMenuItem.setEnabled(true);
\r
1316 CommandI command = (CommandI) viewport.historyList.peek();
\r
1317 undoMenuItem.setLabel("Undo " + command.getDescription());
\r
1321 undoMenuItem.setEnabled(false);
\r
1322 undoMenuItem.setLabel("Undo");
\r
1325 if (viewport.redoList.size() > 0)
\r
1327 redoMenuItem.setEnabled(true);
\r
1329 CommandI command = (CommandI) viewport.redoList.peek();
\r
1330 redoMenuItem.setLabel("Redo " + command.getDescription());
\r
1334 redoMenuItem.setEnabled(false);
\r
1335 redoMenuItem.setLabel("Redo");
\r
1342 public void addHistoryItem(CommandI command)
\r
1344 if (command.getSize() > 0)
\r
1346 viewport.historyList.push(command);
\r
1347 viewport.redoList.removeAllElements();
\r
1348 updateEditMenuBar();
\r
1349 viewport.updateHiddenColumns();
\r
1360 protected void undoMenuItem_actionPerformed()
\r
1362 if (viewport.historyList.size() < 1)
\r
1367 CommandI command = (CommandI) viewport.historyList.pop();
\r
1368 viewport.redoList.push(command);
\r
1369 command.undoCommand(null);
\r
1371 AlignViewport originalSource = getOriginatingSource(command);
\r
1373 if (originalSource!=viewport) {
\r
1374 System.err.println("Warning: Viewport object mismatch whilst undoing");
\r
1376 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns = viewport.getColumnSelection().getHiddenColumns() != null;
\r
1377 updateEditMenuBar();
\r
1378 originalSource.firePropertyChange("alignment", null,
\r
1379 originalSource.getAlignment().getSequences());
\r
1389 protected void redoMenuItem_actionPerformed()
\r
1391 if (viewport.redoList.size() < 1)
\r
1396 CommandI command = (CommandI) viewport.redoList.pop();
\r
1397 viewport.historyList.push(command);
\r
1398 command.doCommand(null);
\r
1400 AlignViewport originalSource = getOriginatingSource(command);
\r
1402 if (originalSource!=viewport) {
\r
1403 System.err.println("Warning: Viewport object mismatch whilst re-doing");
\r
1405 originalSource.updateHiddenColumns(); //sethasHiddenColumns(); = viewport.getColumnSelection().getHiddenColumns() != null;
\r
1407 updateEditMenuBar();
\r
1408 originalSource.firePropertyChange("alignment", null,
\r
1409 originalSource.getAlignment().getSequences());
\r
1412 AlignViewport getOriginatingSource(CommandI command)
\r
1414 AlignViewport originalSource = null;
\r
1415 // For sequence removal and addition, we need to fire
\r
1416 // the property change event FROM the viewport where the
\r
1417 // original alignment was altered
\r
1418 AlignmentI al = null;
\r
1419 if (command instanceof EditCommand)
\r
1421 EditCommand editCommand = (EditCommand) command;
\r
1422 al = editCommand.getAlignment();
\r
1423 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
1424 .getSequenceSetId());
\r
1425 for (int i = 0; i < comps.size(); i++)
\r
1427 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
1429 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
\r
1431 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
\r
1438 if (originalSource == null)
\r
1440 // The original view is closed, we must validate
\r
1441 // the current view against the closed view first
\r
1444 PaintRefresher.validateSequences(al, viewport.getAlignment());
\r
1447 originalSource = viewport;
\r
1450 return originalSource;
\r
1453 public void moveSelectedSequences(boolean up)
\r
1455 SequenceGroup sg = viewport.getSelectionGroup();
\r
1463 for (int i = 1; i < viewport.getAlignment().getHeight(); i++)
\r
1465 SequenceI seq = viewport.getAlignment().getSequenceAt(i);
\r
1466 if (!sg.getSequences(null).contains(seq))
\r
1471 SequenceI temp = viewport.getAlignment().getSequenceAt(i - 1);
\r
1472 if (sg.getSequences(null).contains(temp))
\r
1477 viewport.getAlignment().getSequences().setElementAt(temp, i);
\r
1478 viewport.getAlignment().getSequences().setElementAt(seq, i - 1);
\r
1483 for (int i = viewport.getAlignment().getHeight() - 2; i > -1; i--)
\r
1485 SequenceI seq = viewport.getAlignment().getSequenceAt(i);
\r
1486 if (!sg.getSequences(viewport.getHiddenRepSequences()).contains(seq))
\r
1491 SequenceI temp = viewport.getAlignment().getSequenceAt(i + 1);
\r
1492 if (sg.getSequences(viewport.getHiddenRepSequences()).contains(temp))
\r
1497 viewport.getAlignment().getSequences().setElementAt(temp, i);
\r
1498 viewport.getAlignment().getSequences().setElementAt(seq, i + 1);
\r
1502 alignPanel.paintAlignment(true);
\r
1505 synchronized void slideSequences(boolean right, int size)
\r
1507 List<SequenceI>sg = new Vector<SequenceI>();
\r
1508 if (viewport.cursorMode)
\r
1510 sg.add(viewport.getAlignment()
\r
1511 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
\r
1513 else if (viewport.getSelectionGroup() != null
\r
1514 && viewport.getSelectionGroup().getSize() != viewport.getAlignment()
\r
1517 sg = viewport.getSelectionGroup().getSequences(
\r
1518 viewport.getHiddenRepSequences());
\r
1521 if (sg.size() < 1)
\r
1526 Vector<SequenceI> invertGroup = new Vector();
\r
1528 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
\r
1530 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
\r
1531 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
\r
1534 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
\r
1536 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup.size()]);
\r
1537 for (int i = 0; i < invertGroup.size(); i++)
\r
1538 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
\r
1540 SlideSequencesCommand ssc;
\r
1542 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
\r
1543 size, viewport.getGapCharacter());
\r
1545 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
\r
1546 size, viewport.getGapCharacter());
\r
1548 int groupAdjustment = 0;
\r
1549 if (ssc.getGapsInsertedBegin() && right)
\r
1551 if (viewport.cursorMode)
\r
1552 alignPanel.seqPanel.moveCursor(size, 0);
\r
1554 groupAdjustment = size;
\r
1556 else if (!ssc.getGapsInsertedBegin() && !right)
\r
1558 if (viewport.cursorMode)
\r
1559 alignPanel.seqPanel.moveCursor(-size, 0);
\r
1561 groupAdjustment = -size;
\r
1564 if (groupAdjustment != 0)
\r
1566 viewport.getSelectionGroup().setStartRes(
\r
1567 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
\r
1568 viewport.getSelectionGroup().setEndRes(
\r
1569 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
\r
1572 boolean appendHistoryItem = false;
\r
1573 if (viewport.historyList != null && viewport.historyList.size() > 0
\r
1574 && viewport.historyList.peek() instanceof SlideSequencesCommand)
\r
1576 appendHistoryItem = ssc
\r
1577 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
\r
1581 if (!appendHistoryItem)
\r
1582 addHistoryItem(ssc);
\r
1587 static StringBuffer copiedSequences;
\r
1589 static Vector copiedHiddenColumns;
\r
1591 protected void copy_actionPerformed()
\r
1593 if (viewport.getSelectionGroup() == null)
\r
1598 SequenceGroup sg = viewport.getSelectionGroup();
\r
1599 copiedSequences = new StringBuffer();
\r
1600 Hashtable orderedSeqs = new Hashtable();
\r
1601 for (int i = 0; i < sg.getSize(); i++)
\r
1603 SequenceI seq = sg.getSequenceAt(i);
\r
1604 int index = viewport.getAlignment().findIndex(seq);
\r
1605 orderedSeqs.put(index + "", seq);
\r
1608 int index = 0, startRes, endRes;
\r
1611 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
\r
1613 copiedHiddenColumns = new Vector();
\r
1614 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
\r
1615 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
\r
1618 int[] region = (int[]) viewport.getColumnSelection()
\r
1619 .getHiddenColumns().elementAt(i);
\r
1621 copiedHiddenColumns.addElement(new int[]
\r
1622 { region[0] - hiddenOffset, region[1] - hiddenOffset });
\r
1627 copiedHiddenColumns = null;
\r
1630 for (int i = 0; i < sg.getSize(); i++)
\r
1632 SequenceI seq = null;
\r
1634 while (seq == null)
\r
1636 if (orderedSeqs.containsKey(index + ""))
\r
1638 seq = (SequenceI) orderedSeqs.get(index + "");
\r
1650 // Returns residue following index if gap
\r
1651 startRes = seq.findPosition(sg.getStartRes());
\r
1654 // Need to find the residue preceeding index if gap
\r
1657 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
\r
1659 ch = seq.getCharAt(j);
\r
1660 if (!jalview.util.Comparison.isGap((ch)))
\r
1668 endRes += seq.getStart() - 1;
\r
1671 copiedSequences.append(seq.getName()
\r
1677 + seq.getSequenceAsString(sg.getStartRes(),
\r
1678 sg.getEndRes() + 1) + "\n");
\r
1683 protected void pasteNew_actionPerformed()
\r
1688 protected void pasteThis_actionPerformed()
\r
1693 void paste(boolean newAlignment)
\r
1698 if (copiedSequences == null)
\r
1703 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
1704 Vector seqs = new Vector();
\r
1705 while (st.hasMoreElements())
\r
1707 String name = st.nextToken();
\r
1708 int start = Integer.parseInt(st.nextToken());
\r
1709 int end = Integer.parseInt(st.nextToken());
\r
1710 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
\r
1712 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
1713 for (int i = 0; i < seqs.size(); i++)
\r
1715 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
1720 String newtitle = new String("Copied sequences");
\r
1721 if (getTitle().startsWith("Copied sequences"))
\r
1723 newtitle = getTitle();
\r
1727 newtitle = newtitle.concat("- from " + getTitle());
\r
1729 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
1730 viewport.applet, newtitle, false);
\r
1731 if (copiedHiddenColumns != null)
\r
1733 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
1735 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
1736 af.viewport.hideColumns(region[0], region[1]);
\r
1740 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
\r
1745 addSequences(newSeqs);
\r
1748 } catch (Exception ex)
\r
1750 } // could be anything being pasted in here
\r
1754 void addSequences(SequenceI[] seqs)
\r
1756 for (int i = 0; i < seqs.length; i++)
\r
1758 viewport.getAlignment().addSequence(seqs[i]);
\r
1762 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
\r
1763 seqs, 0, viewport.getAlignment().getWidth(), viewport.getAlignment()));
\r
1765 viewport.setEndSeq(viewport.getAlignment().getHeight());
\r
1766 viewport.getAlignment().getWidth();
\r
1767 viewport.firePropertyChange("alignment", null,
\r
1768 viewport.getAlignment().getSequences());
\r
1772 protected void cut_actionPerformed()
\r
1774 copy_actionPerformed();
\r
1775 delete_actionPerformed();
\r
1778 protected void delete_actionPerformed()
\r
1781 SequenceGroup sg = viewport.getSelectionGroup();
\r
1787 Vector seqs = new Vector();
\r
1789 for (int i = 0; i < sg.getSize(); i++)
\r
1791 seq = sg.getSequenceAt(i);
\r
1792 seqs.addElement(seq);
\r
1795 // If the cut affects all sequences, remove highlighted columns
\r
1796 if (sg.getSize() == viewport.getAlignment().getHeight())
\r
1798 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
1799 sg.getEndRes() + 1);
\r
1802 SequenceI[] cut = new SequenceI[seqs.size()];
\r
1803 for (int i = 0; i < seqs.size(); i++)
\r
1805 cut[i] = (SequenceI) seqs.elementAt(i);
\r
1809 * //ADD HISTORY ITEM
\r
1811 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
\r
1812 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
\r
1813 viewport.getAlignment()));
\r
1815 viewport.setSelectionGroup(null);
\r
1816 viewport.getAlignment().deleteGroup(sg);
\r
1818 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1821 if (viewport.getAlignment().getHeight() < 1)
\r
1823 this.setVisible(false);
\r
1825 viewport.sendSelection();
\r
1829 * group consensus toggled
\r
1832 protected void showGroupConsensus_actionPerformed()
\r
1834 viewport.setShowGroupConsensus(showGroupConsensus.getState());
\r
1835 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1840 * group conservation toggled.
\r
1842 protected void showGroupConservation_actionPerformed()
\r
1844 viewport.setShowGroupConservation(showGroupConservation.getState());
\r
1845 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1852 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
\r
1853 * .event.ActionEvent)
\r
1855 protected void showConsensusHistogram_actionPerformed()
\r
1857 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
\r
1858 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1864 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
\r
1865 * .event.ActionEvent)
\r
1867 protected void showSequenceLogo_actionPerformed()
\r
1869 viewport.setShowSequenceLogo(showSequenceLogo.getState());
\r
1870 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1873 protected void applyAutoAnnotationSettings_actionPerformed()
\r
1875 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1878 protected void makeGrpsFromSelection_actionPerformed()
\r
1880 if (viewport.getSelectionGroup() != null)
\r
1882 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
\r
1883 viewport.getSequenceSelection(),
\r
1884 viewport.getAlignmentView(true).getSequenceStrings(
\r
1885 viewport.getGapCharacter()),
\r
1886 viewport.getAlignment().getGroups());
\r
1887 viewport.getAlignment().deleteAllGroups();
\r
1888 viewport.sequenceColours = null;
\r
1889 viewport.setSelectionGroup(null);
\r
1890 // set view properties for each group
\r
1891 for (int g = 0; g < gps.length; g++)
\r
1893 // gps[g].setShowunconserved(viewport.getShowUnconserved());
\r
1894 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
\r
1895 viewport.getAlignment().addGroup(gps[g]);
\r
1896 Color col = new Color((int) (Math.random() * 255),
\r
1897 (int) (Math.random() * 255), (int) (Math.random() * 255));
\r
1898 col = col.brighter();
\r
1899 for (SequenceI sq : gps[g].getSequences(null))
\r
1900 viewport.setSequenceColour(
\r
1904 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
\r
1905 alignPanel.updateAnnotation();
\r
1906 alignPanel.paintAlignment(true);
\r
1910 protected void deleteGroups_actionPerformed()
\r
1912 viewport.getAlignment().deleteAllGroups();
\r
1913 viewport.sequenceColours = null;
\r
1914 viewport.setSelectionGroup(null);
\r
1916 alignPanel.paintAlignment(true);
\r
1919 public void selectAllSequenceMenuItem_actionPerformed()
\r
1921 SequenceGroup sg = new SequenceGroup();
\r
1922 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1924 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
1926 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
\r
1927 viewport.setSelectionGroup(sg);
\r
1928 alignPanel.paintAlignment(true);
\r
1929 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1930 viewport.sendSelection();
\r
1933 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1935 if (viewport.cursorMode)
\r
1937 alignPanel.seqPanel.keyboardNo1 = null;
\r
1938 alignPanel.seqPanel.keyboardNo2 = null;
\r
1940 viewport.setSelectionGroup(null);
\r
1941 viewport.getColumnSelection().clear();
\r
1942 viewport.setSelectionGroup(null);
\r
1943 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1944 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1945 alignPanel.paintAlignment(true);
\r
1946 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1947 viewport.sendSelection();
\r
1950 public void invertSequenceMenuItem_actionPerformed()
\r
1952 SequenceGroup sg = viewport.getSelectionGroup();
\r
1953 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1955 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1958 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1959 viewport.sendSelection();
\r
1962 public void invertColSel_actionPerformed()
\r
1964 viewport.invertColumnSelection();
\r
1965 alignPanel.paintAlignment(true);
\r
1966 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1967 viewport.sendSelection();
\r
1970 void trimAlignment(boolean trimLeft)
\r
1972 ColumnSelection colSel = viewport.getColumnSelection();
\r
1975 if (colSel.size() > 0)
\r
1979 column = colSel.getMin();
\r
1983 column = colSel.getMax();
\r
1987 if (viewport.getSelectionGroup() != null)
\r
1989 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
1990 viewport.getHiddenRepSequences());
\r
1994 seqs = viewport.getAlignment().getSequencesArray();
\r
1997 TrimRegionCommand trimRegion;
\r
2000 trimRegion = new TrimRegionCommand("Remove Left",
\r
2001 TrimRegionCommand.TRIM_LEFT, seqs, column,
\r
2002 viewport.getAlignment(), viewport.getColumnSelection(),
\r
2003 viewport.getSelectionGroup());
\r
2004 viewport.setStartRes(0);
\r
2008 trimRegion = new TrimRegionCommand("Remove Right",
\r
2009 TrimRegionCommand.TRIM_RIGHT, seqs, column,
\r
2010 viewport.getAlignment(), viewport.getColumnSelection(),
\r
2011 viewport.getSelectionGroup());
\r
2014 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
\r
2016 addHistoryItem(trimRegion);
\r
2020 for (SequenceGroup sg:viewport.getAlignment().getGroups())
\r
2022 if ((trimLeft && !sg.adjustForRemoveLeft(column))
\r
2023 || (!trimLeft && !sg.adjustForRemoveRight(column)))
\r
2025 viewport.getAlignment().deleteGroup(sg);
\r
2029 viewport.firePropertyChange("alignment", null, viewport
\r
2030 .getAlignment().getSequences());
\r
2034 public void removeGappedColumnMenuItem_actionPerformed()
\r
2036 int start = 0, end = viewport.getAlignment().getWidth() - 1;
\r
2039 if (viewport.getSelectionGroup() != null)
\r
2041 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2042 viewport.getHiddenRepSequences());
\r
2043 start = viewport.getSelectionGroup().getStartRes();
\r
2044 end = viewport.getSelectionGroup().getEndRes();
\r
2048 seqs = viewport.getAlignment().getSequencesArray();
\r
2051 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
\r
2052 "Remove Gapped Columns", seqs, start, end, viewport.getAlignment());
\r
2054 addHistoryItem(removeGapCols);
\r
2056 statusBar.setText("Removed " + removeGapCols.getSize()
\r
2057 + " empty columns.");
\r
2059 // This is to maintain viewport position on first residue
\r
2060 // of first sequence
\r
2061 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
\r
2062 int startRes = seq.findPosition(viewport.startRes);
\r
2063 // ShiftList shifts;
\r
2064 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
\r
2065 // edit.alColumnChanges=shifts.getInverse();
\r
2066 // if (viewport.hasHiddenColumns)
\r
2067 // viewport.getColumnSelection().compensateForEdits(shifts);
\r
2068 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
2069 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
2074 public void removeAllGapsMenuItem_actionPerformed()
\r
2076 int start = 0, end = viewport.getAlignment().getWidth() - 1;
\r
2079 if (viewport.getSelectionGroup() != null)
\r
2081 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2082 viewport.getHiddenRepSequences());
\r
2083 start = viewport.getSelectionGroup().getStartRes();
\r
2084 end = viewport.getSelectionGroup().getEndRes();
\r
2088 seqs = viewport.getAlignment().getSequencesArray();
\r
2091 // This is to maintain viewport position on first residue
\r
2092 // of first sequence
\r
2093 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
\r
2094 int startRes = seq.findPosition(viewport.startRes);
\r
2096 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
\r
2097 viewport.getAlignment()));
\r
2099 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
2101 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
2106 public void findMenuItem_actionPerformed()
\r
2108 new Finder(alignPanel);
\r
2112 * create a new view derived from the current view
\r
2114 * @param viewtitle
\r
2115 * @return frame for the new view
\r
2117 public AlignFrame newView(String viewtitle)
\r
2120 if (viewport.hasHiddenRows())
\r
2122 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
\r
2123 .getFullAlignment().getSequencesArray());
\r
2127 newal = new Alignment(viewport.getAlignment().getSequencesArray());
\r
2130 if (viewport.getAlignment().getAlignmentAnnotation() != null)
\r
2132 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
\r
2134 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
\r
2136 newal.addAnnotation(viewport.getAlignment().getAlignmentAnnotation()[i]);
\r
2141 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
\r
2143 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
\r
2144 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
\r
2145 PaintRefresher.Register(newaf.alignPanel,
\r
2146 newaf.alignPanel.av.getSequenceSetId());
\r
2148 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
\r
2149 newaf.alignPanel.av.getSequenceSetId());
\r
2150 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
\r
2151 newaf.alignPanel.av.getSequenceSetId());
\r
2153 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
2154 .getSequenceSetId());
\r
2155 int viewSize = -1;
\r
2156 for (int i = 0; i < comps.size(); i++)
\r
2158 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
2164 String title = new String(this.getTitle());
\r
2165 if (viewtitle != null)
\r
2167 title = viewtitle + " ( " + title + ")";
\r
2171 if (title.indexOf("(View") > -1)
\r
2173 title = title.substring(0, title.indexOf("(View"));
\r
2175 title += "(View " + viewSize + ")";
\r
2178 newaf.setTitle(title.toString());
\r
2180 newaf.viewport.historyList = viewport.historyList;
\r
2181 newaf.viewport.redoList = viewport.redoList;
\r
2187 * @return list of feature groups on the view
\r
2189 public String[] getFeatureGroups()
\r
2191 FeatureRenderer fr = null;
\r
2192 if (alignPanel != null
\r
2193 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2195 return fr.getGroups();
\r
2201 * get sequence feature groups that are hidden or shown
\r
2207 public String[] getFeatureGroupsOfState(boolean visible)
\r
2209 FeatureRenderer fr = null;
\r
2210 if (alignPanel != null
\r
2211 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2213 return fr.getGroups(visible);
\r
2219 * Change the display state for the given feature groups
\r
2222 * list of group strings
\r
2224 * visible or invisible
\r
2226 public void setFeatureGroupState(String[] groups, boolean state)
\r
2228 FeatureRenderer fr = null;
\r
2229 this.sequenceFeatures.setState(true);
\r
2230 viewport.showSequenceFeatures(true);
\r
2231 if (alignPanel != null
\r
2232 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2234 fr.setGroupState(groups, state);
\r
2235 alignPanel.seqPanel.seqCanvas.repaint();
\r
2236 if (alignPanel.overviewPanel != null)
\r
2238 alignPanel.overviewPanel.updateOverviewImage();
\r
2243 public void seqLimits_itemStateChanged()
\r
2245 viewport.setShowJVSuffix(seqLimits.getState());
\r
2246 alignPanel.fontChanged();
\r
2247 alignPanel.paintAlignment(true);
\r
2250 protected void colourTextMenuItem_actionPerformed()
\r
2252 viewport.setColourText(colourTextMenuItem.getState());
\r
2253 alignPanel.paintAlignment(true);
\r
2256 protected void displayNonconservedMenuItem_actionPerformed()
\r
2258 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
\r
2259 alignPanel.paintAlignment(true);
\r
2262 protected void wrapMenuItem_actionPerformed()
\r
2264 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
2265 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
2266 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
2267 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
2268 scaleRight.setEnabled(wrapMenuItem.getState());
\r
2269 alignPanel.paintAlignment(true);
\r
2272 public void overviewMenuItem_actionPerformed()
\r
2274 if (alignPanel.overviewPanel != null)
\r
2279 Frame frame = new Frame();
\r
2280 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
2281 frame.add(overview);
\r
2282 // +50 must allow for applet frame window
\r
2283 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
2284 overview.getPreferredSize().width,
\r
2285 overview.getPreferredSize().height + 50);
\r
2288 final AlignmentPanel ap=alignPanel;
\r
2289 frame.addWindowListener(new WindowAdapter()
\r
2291 public void windowClosing(WindowEvent e)
\r
2294 ap.setOverviewPanel(null);
\r
2299 alignPanel.setOverviewPanel(overview);
\r
2303 void changeColour(ColourSchemeI cs)
\r
2305 int threshold = 0;
\r
2309 if (viewport.getAbovePIDThreshold())
\r
2311 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
2314 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2316 viewport.setGlobalColourScheme(cs);
\r
2320 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2323 if (viewport.getConservationSelected())
\r
2326 Alignment al = (Alignment) viewport.getAlignment();
\r
2327 Conservation c = new Conservation("All",
\r
2328 ResidueProperties.propHash, 3, al.getSequences(), 0,
\r
2329 al.getWidth() - 1);
\r
2332 c.verdict(false, viewport.getConsPercGaps());
\r
2334 cs.setConservation(c);
\r
2336 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
\r
2337 cs, "Background"));
\r
2342 cs.setConservation(null);
\r
2345 cs.setConsensus(viewport.getSequenceConsensusHash());
\r
2348 viewport.setGlobalColourScheme(cs);
\r
2351 if (alignPanel.getOverviewPanel() != null)
\r
2353 alignPanel.getOverviewPanel().updateOverviewImage();
\r
2356 jalview.structure.StructureSelectionManager
\r
2357 .getStructureSelectionManager(viewport.applet).sequenceColoursChanged(
\r
2360 alignPanel.paintAlignment(true);
\r
2363 protected void modifyPID_actionPerformed()
\r
2365 if (viewport.getAbovePIDThreshold()
\r
2366 && viewport.getGlobalColourScheme() != null)
\r
2368 SliderPanel.setPIDSliderSource(alignPanel,
\r
2369 viewport.getGlobalColourScheme(), "Background");
\r
2370 SliderPanel.showPIDSlider();
\r
2374 protected void modifyConservation_actionPerformed()
\r
2376 if (viewport.getConservationSelected()
\r
2377 && viewport.getGlobalColourScheme() != null)
\r
2379 SliderPanel.setConservationSlider(alignPanel,
\r
2380 viewport.getGlobalColourScheme(), "Background");
\r
2381 SliderPanel.showConservationSlider();
\r
2385 protected void conservationMenuItem_actionPerformed()
\r
2387 viewport.setConservationSelected(conservationMenuItem.getState());
\r
2389 viewport.setAbovePIDThreshold(false);
\r
2390 abovePIDThreshold.setState(false);
\r
2392 changeColour(viewport.getGlobalColourScheme());
\r
2394 modifyConservation_actionPerformed();
\r
2397 public void abovePIDThreshold_actionPerformed()
\r
2399 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
2401 conservationMenuItem.setState(false);
\r
2402 viewport.setConservationSelected(false);
\r
2404 changeColour(viewport.getGlobalColourScheme());
\r
2406 modifyPID_actionPerformed();
\r
2409 public void sortPairwiseMenuItem_actionPerformed()
\r
2411 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2412 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
\r
2413 .getAlignment().getSequenceAt(0), null);
\r
2415 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
\r
2416 viewport.getAlignment()));
\r
2417 alignPanel.paintAlignment(true);
\r
2420 public void sortIDMenuItem_actionPerformed()
\r
2422 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2423 AlignmentSorter.sortByID(viewport.getAlignment());
\r
2424 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
\r
2425 alignPanel.paintAlignment(true);
\r
2428 public void sortLengthMenuItem_actionPerformed()
\r
2430 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2431 AlignmentSorter.sortByLength(viewport.getAlignment());
\r
2432 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
\r
2433 viewport.getAlignment()));
\r
2434 alignPanel.paintAlignment(true);
\r
2437 public void sortGroupMenuItem_actionPerformed()
\r
2439 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2440 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
2441 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
\r
2442 viewport.getAlignment()));
\r
2443 alignPanel.paintAlignment(true);
\r
2447 public void removeRedundancyMenuItem_actionPerformed()
\r
2449 new RedundancyPanel(alignPanel);
\r
2452 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
2454 if (viewport.getSelectionGroup() != null
\r
2455 && viewport.getSelectionGroup().getSize() > 1)
\r
2457 Frame frame = new Frame();
\r
2458 frame.add(new PairwiseAlignPanel(alignPanel));
\r
2459 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
\r
2464 public void PCAMenuItem_actionPerformed()
\r
2466 // are the sequences aligned?
\r
2467 if (!viewport.getAlignment().isAligned(false))
\r
2469 SequenceI current;
\r
2470 int Width = viewport.getAlignment().getWidth();
\r
2472 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2474 current = viewport.getAlignment().getSequenceAt(i);
\r
2476 if (current.getLength() < Width)
\r
2478 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2481 alignPanel.paintAlignment(true);
\r
2484 if ((viewport.getSelectionGroup() != null
\r
2485 && viewport.getSelectionGroup().getSize() < 4 && viewport
\r
2486 .getSelectionGroup().getSize() > 0)
\r
2487 || viewport.getAlignment().getHeight() < 4)
\r
2494 new PCAPanel(viewport);
\r
2495 } catch (java.lang.OutOfMemoryError ex)
\r
2501 public void averageDistanceTreeMenuItem_actionPerformed()
\r
2503 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
2506 public void neighbourTreeMenuItem_actionPerformed()
\r
2508 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
2511 protected void njTreeBlosumMenuItem_actionPerformed()
\r
2513 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2516 protected void avTreeBlosumMenuItem_actionPerformed()
\r
2518 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2521 void NewTreePanel(String type, String pwType, String title)
\r
2523 // are the sequences aligned?
\r
2524 if (!viewport.getAlignment().isAligned(false))
\r
2526 SequenceI current;
\r
2527 int Width = viewport.getAlignment().getWidth();
\r
2529 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2531 current = viewport.getAlignment().getSequenceAt(i);
\r
2533 if (current.getLength() < Width)
\r
2535 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2538 alignPanel.paintAlignment(true);
\r
2542 if ((viewport.getSelectionGroup() != null && viewport
\r
2543 .getSelectionGroup().getSize() > 1)
\r
2544 || (viewport.getSelectionGroup() == null && viewport.getAlignment()
\r
2545 .getHeight() > 1))
\r
2547 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
\r
2549 addTreeMenuItem(tp, title);
\r
2551 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
2555 void loadTree_actionPerformed()
\r
2557 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
2558 cap.setText("Paste your Newick tree file here.");
\r
2559 cap.setTreeImport();
\r
2560 Frame frame = new Frame();
\r
2562 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
2565 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
2567 TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
\r
2568 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
2569 addTreeMenuItem(tp, treeFile);
\r
2573 * sort the alignment using the given treePanel
\r
2575 * @param treePanel
\r
2576 * tree used to sort view
\r
2578 * string used for undo event name
\r
2580 public void sortByTree(TreePanel treePanel, String title)
\r
2582 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2584 .sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
2585 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2586 // HistoryItem.SORT));
\r
2587 addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
\r
2588 viewport.getAlignment()));
\r
2589 alignPanel.paintAlignment(true);
\r
2593 * Do any automatic reordering of the alignment and add the necessary bits to
\r
2594 * the menu structure for the new tree
\r
2596 * @param treePanel
\r
2599 protected void addTreeMenuItem(final TreePanel treePanel,
\r
2600 final String title)
\r
2602 final MenuItem item = new MenuItem(title);
\r
2603 sortByTreeMenu.add(item);
\r
2604 item.addActionListener(new java.awt.event.ActionListener()
\r
2606 public void actionPerformed(ActionEvent evt)
\r
2608 sortByTree(treePanel, title); // treePanel.getTitle());
\r
2612 treePanel.addWindowListener(new WindowAdapter()
\r
2614 public void windowOpened(WindowEvent e)
\r
2616 if (viewport.sortByTree)
\r
2618 sortByTree(treePanel, title);
\r
2620 super.windowOpened(e);
\r
2623 public void windowClosing(WindowEvent e)
\r
2625 sortByTreeMenu.remove(item);
\r
2629 public boolean sortBy(AlignmentOrder alorder, String undoname)
\r
2631 SequenceI[] oldOrder = viewport.getAlignment()
\r
2632 .getSequencesArray();
\r
2633 if (viewport.applet.debug)
\r
2635 System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");
\r
2637 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
\r
2638 if (undoname!=null)
\r
2640 addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.getAlignment()));
\r
2642 alignPanel.paintAlignment(true);
\r
2646 protected void documentation_actionPerformed()
\r
2648 alignPanel.av.applet.openJalviewHelpUrl();
\r
2651 protected void about_actionPerformed()
\r
2654 class AboutPanel extends Canvas
\r
2660 public AboutPanel(String version, String builddate)
\r
2662 this.version = version;
\r
2663 this.builddate = builddate;
\r
2666 public void paint(Graphics g)
\r
2668 g.setColor(Color.white);
\r
2669 g.fillRect(0, 0, getSize().width, getSize().height);
\r
2670 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2671 FontMetrics fm = g.getFontMetrics();
\r
2672 int fh = fm.getHeight();
\r
2674 g.setColor(Color.black);
\r
2675 // TODO: update this text for each release or centrally store it for
\r
2676 // lite and application
\r
2677 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
2678 g.drawString("JalviewLite - Release " + version, x, y += fh);
\r
2679 g.setFont(new Font("Helvetica", Font.BOLD, 12));
\r
2680 g.drawString("Build date: " + builddate, x, y += fh);
\r
2681 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2683 "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",
\r
2684 x, y += fh * 1.5);
\r
2685 g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
\r
2687 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
\r
2690 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
\r
2692 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
\r
2694 "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
\r
2697 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
\r
2699 g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
\r
2704 Frame frame = new Frame();
\r
2705 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
\r
2706 .getBuildDate()));
\r
2707 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
\r
2711 public void showURL(String url, String target)
\r
2713 if (viewport.applet == null)
\r
2715 System.out.println("Not running as applet - no browser available.");
\r
2719 viewport.applet.showURL(url, target);
\r
2723 // ////////////////////////////////////////////////////////////////////////////////
\r
2724 // JBuilder Graphics here
\r
2726 MenuBar alignFrameMenuBar = new MenuBar();
\r
2728 Menu fileMenu = new Menu("File");
\r
2730 MenuItem loadApplication = new MenuItem("View in Full Application");
\r
2732 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
\r
2734 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
\r
2736 MenuItem outputFeatures = new MenuItem("Export Features ...");
\r
2738 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
\r
2740 MenuItem closeMenuItem = new MenuItem("Close");
\r
2742 Menu editMenu = new Menu("Edit");
\r
2744 Menu viewMenu = new Menu("View");
\r
2746 Menu colourMenu = new Menu("Colour");
\r
2748 Menu calculateMenu = new Menu("Calculate");
\r
2750 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
2752 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
2754 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
2756 MenuItem remove2LeftMenuItem = new MenuItem();
\r
2758 MenuItem remove2RightMenuItem = new MenuItem();
\r
2760 MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
2762 MenuItem removeAllGapsMenuItem = new MenuItem();
\r
2764 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
2766 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
2768 MenuItem sortPairwiseMenuItem = new MenuItem();
\r
2770 MenuItem sortIDMenuItem = new MenuItem();
\r
2772 MenuItem sortLengthMenuItem = new MenuItem();
\r
2774 MenuItem sortGroupMenuItem = new MenuItem();
\r
2776 MenuItem removeRedundancyMenuItem = new MenuItem();
\r
2778 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
2780 MenuItem PCAMenuItem = new MenuItem();
\r
2782 MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
2784 MenuItem neighbourTreeMenuItem = new MenuItem();
\r
2786 BorderLayout borderLayout1 = new BorderLayout();
\r
2788 public Label statusBar = new Label();
\r
2790 Menu outputTextboxMenu = new Menu();
\r
2792 MenuItem clustalColour = new MenuItem();
\r
2794 MenuItem zappoColour = new MenuItem();
\r
2796 MenuItem taylorColour = new MenuItem();
\r
2798 MenuItem hydrophobicityColour = new MenuItem();
\r
2800 MenuItem helixColour = new MenuItem();
\r
2802 MenuItem strandColour = new MenuItem();
\r
2804 MenuItem turnColour = new MenuItem();
\r
2806 MenuItem buriedColour = new MenuItem();
\r
2808 MenuItem purinePyrimidineColour = new MenuItem();
\r
2809 MenuItem RNAHelixColour = new MenuItem();
\r
2811 MenuItem userDefinedColour = new MenuItem();
\r
2813 MenuItem PIDColour = new MenuItem();
\r
2815 MenuItem BLOSUM62Colour = new MenuItem();
\r
2817 MenuItem tcoffeeColour = new MenuItem();
\r
2819 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
2821 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
2823 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
2825 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
2827 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
\r
2829 MenuItem alProperties = new MenuItem("Alignment Properties...");
\r
2831 MenuItem overviewMenuItem = new MenuItem();
\r
2833 MenuItem undoMenuItem = new MenuItem();
\r
2835 MenuItem redoMenuItem = new MenuItem();
\r
2837 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
2839 MenuItem noColourmenuItem = new MenuItem();
\r
2841 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
2843 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
2845 MenuItem findMenuItem = new MenuItem();
\r
2847 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
2849 MenuItem nucleotideColour = new MenuItem();
\r
2851 MenuItem deleteGroups = new MenuItem();
\r
2853 MenuItem grpsFromSelection = new MenuItem();
\r
2855 MenuItem delete = new MenuItem();
\r
2857 MenuItem copy = new MenuItem();
\r
2859 MenuItem cut = new MenuItem();
\r
2861 Menu pasteMenu = new Menu();
\r
2863 MenuItem pasteNew = new MenuItem();
\r
2865 MenuItem pasteThis = new MenuItem();
\r
2867 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
2869 MenuItem font = new MenuItem();
\r
2871 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
2873 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
2875 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
2877 MenuItem modifyPID = new MenuItem();
\r
2879 MenuItem modifyConservation = new MenuItem();
\r
2881 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
\r
2882 "Autocalculate Consensus", true);
\r
2884 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
\r
2885 "Sort Alignment With New Tree", true);
\r
2887 Menu sortByTreeMenu = new Menu();
\r
2889 Menu sort = new Menu();
\r
2891 Menu calculate = new Menu();
\r
2893 MenuItem inputText = new MenuItem();
\r
2895 Menu helpMenu = new Menu();
\r
2897 MenuItem documentation = new MenuItem();
\r
2899 MenuItem about = new MenuItem();
\r
2901 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
2903 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
\r
2905 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
\r
2906 Menu autoAnnMenu=new Menu();
\r
2907 CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();
\r
2908 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
\r
2909 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
\r
2910 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
\r
2911 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
\r
2913 private void jbInit() throws Exception
\r
2916 setMenuBar(alignFrameMenuBar);
\r
2920 // dynamically fill save as menu with available formats
\r
2921 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
2924 item = new MenuItem(
\r
2925 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
2927 item.addActionListener(new java.awt.event.ActionListener()
\r
2929 public void actionPerformed(ActionEvent e)
\r
2931 outputText_actionPerformed(e);
\r
2935 outputTextboxMenu.add(item);
\r
2937 closeMenuItem.addActionListener(this);
\r
2938 loadApplication.addActionListener(this);
\r
2940 loadTree.addActionListener(this);
\r
2941 loadAnnotations.addActionListener(this);
\r
2942 outputFeatures.addActionListener(this);
\r
2943 outputAnnotations.addActionListener(this);
\r
2944 selectAllSequenceMenuItem.addActionListener(this);
\r
2945 deselectAllSequenceMenuItem.addActionListener(this);
\r
2946 invertSequenceMenuItem.addActionListener(this);
\r
2947 remove2LeftMenuItem.setLabel("Remove Left");
\r
2948 remove2LeftMenuItem.addActionListener(this);
\r
2949 remove2RightMenuItem.setLabel("Remove Right");
\r
2950 remove2RightMenuItem.addActionListener(this);
\r
2951 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
2952 removeGappedColumnMenuItem.addActionListener(this);
\r
2953 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
2954 removeAllGapsMenuItem.addActionListener(this);
\r
2955 viewBoxesMenuItem.setLabel("Boxes");
\r
2956 viewBoxesMenuItem.setState(true);
\r
2957 viewBoxesMenuItem.addItemListener(this);
\r
2958 viewTextMenuItem.setLabel("Text");
\r
2959 viewTextMenuItem.setState(true);
\r
2960 viewTextMenuItem.addItemListener(this);
\r
2961 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
2962 sortPairwiseMenuItem.addActionListener(this);
\r
2963 sortIDMenuItem.setLabel("by ID");
\r
2964 sortIDMenuItem.addActionListener(this);
\r
2965 sortLengthMenuItem.setLabel("by Length");
\r
2966 sortLengthMenuItem.addActionListener(this);
\r
2967 sortGroupMenuItem.setLabel("by Group");
\r
2968 sortGroupMenuItem.addActionListener(this);
\r
2969 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
2970 removeRedundancyMenuItem.addActionListener(this);
\r
2971 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
2972 pairwiseAlignmentMenuItem.addActionListener(this);
\r
2973 PCAMenuItem.setLabel("Principal Component Analysis");
\r
2974 PCAMenuItem.addActionListener(this);
\r
2975 averageDistanceTreeMenuItem
\r
2976 .setLabel("Average Distance Using % Identity");
\r
2977 averageDistanceTreeMenuItem.addActionListener(this);
\r
2978 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
2979 neighbourTreeMenuItem.addActionListener(this);
\r
2980 statusBar.setBackground(Color.white);
\r
2981 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
2982 statusBar.setText("Status bar");
\r
2983 outputTextboxMenu.setLabel("Output to Textbox");
\r
2984 clustalColour.setLabel("Clustalx");
\r
2986 clustalColour.addActionListener(this);
\r
2987 zappoColour.setLabel("Zappo");
\r
2988 zappoColour.addActionListener(this);
\r
2989 taylorColour.setLabel("Taylor");
\r
2990 taylorColour.addActionListener(this);
\r
2991 hydrophobicityColour.setLabel("Hydrophobicity");
\r
2992 hydrophobicityColour.addActionListener(this);
\r
2993 helixColour.setLabel("Helix Propensity");
\r
2994 helixColour.addActionListener(this);
\r
2995 strandColour.setLabel("Strand Propensity");
\r
2996 strandColour.addActionListener(this);
\r
2997 turnColour.setLabel("Turn Propensity");
\r
2998 turnColour.addActionListener(this);
\r
2999 buriedColour.setLabel("Buried Index");
\r
3000 buriedColour.addActionListener(this);
\r
3001 purinePyrimidineColour.setLabel("Purine/Pyrimidine");
\r
3002 purinePyrimidineColour.addActionListener(this);
\r
3003 RNAHelixColour.setLabel("by RNA Helices");
\r
3004 RNAHelixColour.addActionListener(this);
\r
3005 userDefinedColour.setLabel("User Defined...");
\r
3006 userDefinedColour.addActionListener(this);
\r
3007 PIDColour.setLabel("Percentage Identity");
\r
3008 PIDColour.addActionListener(this);
\r
3009 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
3010 BLOSUM62Colour.addActionListener(this);
\r
3011 tcoffeeColour.setLabel("T-Coffee Scores");
\r
3012 tcoffeeColour.setEnabled(false); // it will enabled only if a score file is provided
\r
3013 tcoffeeColour.addActionListener(this);
\r
3014 avDistanceTreeBlosumMenuItem .setLabel("Average Distance Using BLOSUM62");
\r
3015 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
3016 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
3017 njTreeBlosumMenuItem.addActionListener(this);
\r
3018 annotationPanelMenuItem.setLabel("Show Annotations");
\r
3019 annotationPanelMenuItem.addItemListener(this);
\r
3020 colourTextMenuItem.setLabel("Colour Text");
\r
3021 colourTextMenuItem.addItemListener(this);
\r
3022 displayNonconservedMenuItem.setLabel("Show nonconserved");
\r
3023 displayNonconservedMenuItem.addItemListener(this);
\r
3024 alProperties.addActionListener(this);
\r
3025 overviewMenuItem.setLabel("Overview Window");
\r
3026 overviewMenuItem.addActionListener(this);
\r
3027 undoMenuItem.setEnabled(false);
\r
3028 undoMenuItem.setLabel("Undo");
\r
3029 undoMenuItem.addActionListener(this);
\r
3030 redoMenuItem.setEnabled(false);
\r
3031 redoMenuItem.setLabel("Redo");
\r
3032 redoMenuItem.addActionListener(this);
\r
3033 conservationMenuItem.setLabel("by Conservation");
\r
3034 conservationMenuItem.addItemListener(this);
\r
3035 noColourmenuItem.setLabel("None");
\r
3036 noColourmenuItem.addActionListener(this);
\r
3037 wrapMenuItem.setLabel("Wrap");
\r
3038 wrapMenuItem.addItemListener(this);
\r
3039 renderGapsMenuItem.setLabel("Show Gaps");
\r
3040 renderGapsMenuItem.setState(true);
\r
3041 renderGapsMenuItem.addItemListener(this);
\r
3042 findMenuItem.setLabel("Find...");
\r
3043 findMenuItem.addActionListener(this);
\r
3044 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
3045 abovePIDThreshold.addItemListener(this);
\r
3046 nucleotideColour.setLabel("Nucleotide");
\r
3047 nucleotideColour.addActionListener(this);
\r
3048 deleteGroups.setLabel("Undefine Groups");
\r
3049 deleteGroups.addActionListener(this);
\r
3050 grpsFromSelection.setLabel("Make Groups for selection");
\r
3051 grpsFromSelection.addActionListener(this);
\r
3052 copy.setLabel("Copy");
\r
3053 copy.addActionListener(this);
\r
3054 cut.setLabel("Cut");
\r
3055 cut.addActionListener(this);
\r
3056 delete.setLabel("Delete");
\r
3057 delete.addActionListener(this);
\r
3058 pasteMenu.setLabel("Paste");
\r
3059 pasteNew.setLabel("To New Alignment");
\r
3060 pasteNew.addActionListener(this);
\r
3061 pasteThis.setLabel("Add To This Alignment");
\r
3062 pasteThis.addActionListener(this);
\r
3063 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
3064 applyToAllGroups.setState(true);
\r
3065 applyToAllGroups.addItemListener(this);
\r
3066 font.setLabel("Font...");
\r
3067 font.addActionListener(this);
\r
3068 scaleAbove.setLabel("Scale Above");
\r
3069 scaleAbove.setState(true);
\r
3070 scaleAbove.setEnabled(false);
\r
3071 scaleAbove.addItemListener(this);
\r
3072 scaleLeft.setEnabled(false);
\r
3073 scaleLeft.setState(true);
\r
3074 scaleLeft.setLabel("Scale Left");
\r
3075 scaleLeft.addItemListener(this);
\r
3076 scaleRight.setEnabled(false);
\r
3077 scaleRight.setState(true);
\r
3078 scaleRight.setLabel("Scale Right");
\r
3079 scaleRight.addItemListener(this);
\r
3080 modifyPID.setLabel("Modify Identity Threshold...");
\r
3081 modifyPID.addActionListener(this);
\r
3082 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
3083 modifyConservation.addActionListener(this);
\r
3084 sortByTreeMenu.setLabel("By Tree Order");
\r
3085 sort.setLabel("Sort");
\r
3086 calculate.setLabel("Calculate Tree");
\r
3087 autoCalculate.addItemListener(this);
\r
3088 sortByTree.addItemListener(this);
\r
3089 inputText.setLabel("Input from textbox");
\r
3090 inputText.addActionListener(this);
\r
3091 centreColumnLabelFlag.setLabel("Centre column labels");
\r
3092 centreColumnLabelFlag.addItemListener(this);
\r
3093 followMouseOverFlag.setLabel("Automatic Scrolling");
\r
3094 followMouseOverFlag.addItemListener(this);
\r
3095 helpMenu.setLabel("Help");
\r
3096 documentation.setLabel("Documentation");
\r
3097 documentation.addActionListener(this);
\r
3099 about.setLabel("About...");
\r
3100 about.addActionListener(this);
\r
3101 seqLimits.setState(true);
\r
3102 seqLimits.setLabel("Show Sequence Limits");
\r
3103 seqLimits.addItemListener(this);
\r
3104 featureSettings.setLabel("Feature Settings...");
\r
3105 featureSettings.addActionListener(this);
\r
3106 sequenceFeatures.setLabel("Sequence Features");
\r
3107 sequenceFeatures.addItemListener(this);
\r
3108 sequenceFeatures.setState(false);
\r
3109 annotationColour.setLabel("by Annotation...");
\r
3110 annotationColour.addActionListener(this);
\r
3111 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
3112 invertColSel.setLabel("Invert Column Selection");
\r
3113 menu1.setLabel("Show");
\r
3114 showColumns.setLabel("All Columns ");
\r
3115 showSeqs.setLabel("All Sequences");
\r
3116 menu2.setLabel("Hide");
\r
3117 hideColumns.setLabel("Selected Columns");
\r
3118 hideSequences.setLabel("Selected Sequences");
\r
3119 hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
\r
3120 hideAllSelection.setLabel("Selected Region");
\r
3121 showAllHidden.setLabel("All Sequences and Columns");
\r
3122 showGroupConsensus.setLabel("Group Consensus");
\r
3123 showGroupConservation.setLabel("Group Conservation");
\r
3124 showConsensusHistogram.setLabel("Show Consensus Histogram");
\r
3125 showSequenceLogo.setLabel("Show Consensus Logo");
\r
3126 applyAutoAnnotationSettings.setLabel("Apply to all groups");
\r
3127 applyAutoAnnotationSettings.setState(true);
\r
3128 autoAnnMenu.setLabel("Autocalculated Annotation");
\r
3130 invertColSel.addActionListener(this);
\r
3131 showColumns.addActionListener(this);
\r
3132 showSeqs.addActionListener(this);
\r
3133 hideColumns.addActionListener(this);
\r
3134 hideSequences.addActionListener(this);
\r
3135 hideAllButSelection.addActionListener(this);
\r
3136 hideAllSelection.addActionListener(this);
\r
3137 showAllHidden.addActionListener(this);
\r
3138 showGroupConsensus.addItemListener(this);
\r
3139 showGroupConservation.addItemListener(this);
\r
3140 showConsensusHistogram.addItemListener(this);
\r
3141 showSequenceLogo.addItemListener(this);
\r
3142 applyAutoAnnotationSettings.addItemListener(this);
\r
3143 formatMenu.setLabel("Format");
\r
3144 selectMenu.setLabel("Select");
\r
3145 newView.setLabel("New View");
\r
3146 newView.addActionListener(this);
\r
3147 alignFrameMenuBar.add(fileMenu);
\r
3148 alignFrameMenuBar.add(editMenu);
\r
3149 alignFrameMenuBar.add(selectMenu);
\r
3150 alignFrameMenuBar.add(viewMenu);
\r
3151 alignFrameMenuBar.add(formatMenu);
\r
3152 alignFrameMenuBar.add(colourMenu);
\r
3153 alignFrameMenuBar.add(calculateMenu);
\r
3154 alignFrameMenuBar.add(helpMenu);
\r
3156 fileMenu.add(inputText);
\r
3157 fileMenu.add(loadTree);
\r
3158 fileMenu.add(loadAnnotations);
\r
3160 fileMenu.addSeparator();
\r
3161 fileMenu.add(outputTextboxMenu);
\r
3162 fileMenu.add(outputFeatures);
\r
3163 fileMenu.add(outputAnnotations);
\r
3165 if (jalviewServletURL != null)
\r
3167 fileMenu.add(loadApplication);
\r
3170 fileMenu.addSeparator();
\r
3171 fileMenu.add(closeMenuItem);
\r
3173 editMenu.add(undoMenuItem);
\r
3174 editMenu.add(redoMenuItem);
\r
3175 editMenu.add(cut);
\r
3176 editMenu.add(copy);
\r
3177 editMenu.add(pasteMenu);
\r
3178 editMenu.add(delete);
\r
3179 editMenu.addSeparator();
\r
3180 editMenu.add(remove2LeftMenuItem);
\r
3181 editMenu.add(remove2RightMenuItem);
\r
3182 editMenu.add(removeGappedColumnMenuItem);
\r
3183 editMenu.add(removeAllGapsMenuItem);
\r
3184 editMenu.add(removeRedundancyMenuItem);
\r
3185 viewMenu.add(newView);
\r
3186 viewMenu.addSeparator();
\r
3187 viewMenu.add(menu1);
\r
3188 viewMenu.add(menu2);
\r
3189 viewMenu.addSeparator();
\r
3190 viewMenu.add(followMouseOverFlag);
\r
3191 viewMenu.add(annotationPanelMenuItem);
\r
3192 autoAnnMenu.add(applyAutoAnnotationSettings);
\r
3193 autoAnnMenu.add(showConsensusHistogram);
\r
3194 autoAnnMenu.add(showSequenceLogo);
\r
3195 autoAnnMenu.addSeparator();
\r
3196 autoAnnMenu.add(showGroupConservation);
\r
3197 autoAnnMenu.add(showGroupConsensus);
\r
3198 viewMenu.add(autoAnnMenu);
\r
3199 viewMenu.addSeparator();
\r
3200 viewMenu.add(sequenceFeatures);
\r
3201 viewMenu.add(featureSettings);
\r
3202 viewMenu.addSeparator();
\r
3203 viewMenu.add(alProperties);
\r
3204 viewMenu.addSeparator();
\r
3205 viewMenu.add(overviewMenuItem);
\r
3206 colourMenu.add(applyToAllGroups);
\r
3207 colourMenu.addSeparator();
\r
3208 colourMenu.add(noColourmenuItem);
\r
3209 colourMenu.add(clustalColour);
\r
3210 colourMenu.add(BLOSUM62Colour);
\r
3211 colourMenu.add(PIDColour);
\r
3212 colourMenu.add(zappoColour);
\r
3213 colourMenu.add(taylorColour);
\r
3214 colourMenu.add(hydrophobicityColour);
\r
3215 colourMenu.add(helixColour);
\r
3216 colourMenu.add(strandColour);
\r
3217 colourMenu.add(turnColour);
\r
3218 colourMenu.add(buriedColour);
\r
3219 colourMenu.add(nucleotideColour);
\r
3220 colourMenu.add(purinePyrimidineColour);
\r
3221 colourMenu.add(tcoffeeColour);
\r
3222 colourMenu.add(userDefinedColour);
\r
3223 colourMenu.addSeparator();
\r
3224 colourMenu.add(conservationMenuItem);
\r
3225 colourMenu.add(modifyConservation);
\r
3226 colourMenu.add(abovePIDThreshold);
\r
3227 colourMenu.add(modifyPID);
\r
3228 colourMenu.add(annotationColour);
\r
3229 colourMenu.add(RNAHelixColour);
\r
3230 calculateMenu.add(sort);
\r
3231 calculateMenu.add(calculate);
\r
3232 calculateMenu.addSeparator();
\r
3233 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
3234 calculateMenu.add(PCAMenuItem);
\r
3235 calculateMenu.add(autoCalculate);
\r
3236 calculateMenu.add(sortByTree);
\r
3237 this.add(statusBar, BorderLayout.SOUTH);
\r
3238 pasteMenu.add(pasteNew);
\r
3239 pasteMenu.add(pasteThis);
\r
3240 sort.add(sortIDMenuItem);
\r
3241 sort.add(sortLengthMenuItem);
\r
3242 sort.add(sortByTreeMenu);
\r
3243 sort.add(sortGroupMenuItem);
\r
3244 sort.add(sortPairwiseMenuItem);
\r
3245 calculate.add(averageDistanceTreeMenuItem);
\r
3246 calculate.add(neighbourTreeMenuItem);
\r
3247 calculate.add(avDistanceTreeBlosumMenuItem);
\r
3248 calculate.add(njTreeBlosumMenuItem);
\r
3249 helpMenu.add(documentation);
\r
3250 helpMenu.add(about);
\r
3251 menu1.add(showColumns);
\r
3252 menu1.add(showSeqs);
\r
3253 menu1.add(showAllHidden);
\r
3254 menu2.add(hideColumns);
\r
3255 menu2.add(hideSequences);
\r
3256 menu2.add(hideAllSelection);
\r
3257 menu2.add(hideAllButSelection);
\r
3258 formatMenu.add(font);
\r
3259 formatMenu.add(seqLimits);
\r
3260 formatMenu.add(wrapMenuItem);
\r
3261 formatMenu.add(scaleAbove);
\r
3262 formatMenu.add(scaleLeft);
\r
3263 formatMenu.add(scaleRight);
\r
3264 formatMenu.add(viewBoxesMenuItem);
\r
3265 formatMenu.add(viewTextMenuItem);
\r
3266 formatMenu.add(colourTextMenuItem);
\r
3267 formatMenu.add(displayNonconservedMenuItem);
\r
3268 formatMenu.add(renderGapsMenuItem);
\r
3269 formatMenu.add(centreColumnLabelFlag);
\r
3270 selectMenu.add(findMenuItem);
\r
3271 selectMenu.addSeparator();
\r
3272 selectMenu.add(selectAllSequenceMenuItem);
\r
3273 selectMenu.add(deselectAllSequenceMenuItem);
\r
3274 selectMenu.add(invertSequenceMenuItem);
\r
3275 selectMenu.add(invertColSel);
\r
3276 selectMenu.add(grpsFromSelection);
\r
3277 selectMenu.add(deleteGroups);
\r
3281 MenuItem featureSettings = new MenuItem();
\r
3283 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
3285 MenuItem annotationColour = new MenuItem();
\r
3287 MenuItem invertColSel = new MenuItem();
\r
3289 Menu menu1 = new Menu();
\r
3291 MenuItem showColumns = new MenuItem();
\r
3293 MenuItem showSeqs = new MenuItem();
\r
3295 Menu menu2 = new Menu();
\r
3297 MenuItem hideColumns = new MenuItem();
\r
3299 MenuItem hideSequences = new MenuItem();
\r
3301 MenuItem hideAllButSelection = new MenuItem();
\r
3303 MenuItem hideAllSelection = new MenuItem();
\r
3305 MenuItem showAllHidden = new MenuItem();
\r
3307 Menu formatMenu = new Menu();
\r
3309 Menu selectMenu = new Menu();
\r
3311 MenuItem newView = new MenuItem();
\r
3314 * Attach the alignFrame panels after embedding menus, if necessary. This used
\r
3315 * to be called setEmbedded, but is now creates the dropdown menus in a
\r
3316 * platform independent manner to avoid OSX/Mac menu appendage daftness.
\r
3318 * @param reallyEmbedded
\r
3319 * true to attach the view to the applet area on the page rather than
\r
3322 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
\r
3324 if (reallyEmbedded)
\r
3327 // Explicly build the embedded menu panel for the on-page applet
\r
3329 // view cannot be closed if its actually on the page
\r
3330 fileMenu.remove(closeMenuItem);
\r
3331 fileMenu.remove(3); // Remove Seperator
\r
3332 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
\r
3333 Font.PLAIN, 10, false); // use our own fonts.
\r
3334 // and actually add the components to the applet area
\r
3335 viewport.applet.setLayout(new BorderLayout());
\r
3336 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
\r
3337 viewport.applet.add(statusBar, BorderLayout.SOUTH);
\r
3338 alignPanel.setSize(viewport.applet.getSize().width,
\r
3339 viewport.applet.getSize().height - embeddedMenu.HEIGHT
\r
3340 - statusBar.HEIGHT);
\r
3341 viewport.applet.add(alignPanel, BorderLayout.CENTER);
\r
3342 final AlignFrame me = this;
\r
3343 viewport.applet.addFocusListener(new FocusListener()
\r
3347 public void focusLost(FocusEvent e)
\r
3349 if (me.viewport.applet.currentAlignFrame==me) {
\r
3350 me.viewport.applet.currentAlignFrame = null;
\r
3354 public void focusGained(FocusEvent e)
\r
3356 me.viewport.applet.currentAlignFrame = me;
\r
3359 viewport.applet.validate();
\r
3364 // test and embed menu bar if necessary.
\r
3366 if (embedMenuIfNeeded(alignPanel))
\r
3368 // adjust for status bar height too
\r
3369 alignPanel.setSize(getSize().width, getSize().height
\r
3370 - statusBar.HEIGHT);
\r
3372 add(statusBar, BorderLayout.SOUTH);
\r
3373 add(alignPanel, BorderLayout.CENTER);
\r
3374 // and register with the applet so it can pass external API calls to us
\r
3375 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
\r
3381 * create a new binding between structures in an existing jmol viewer instance
\r
3382 * and an alignpanel with sequences that have existing PDBFile entries. Note,
\r
3383 * this does not open a new Jmol window, or modify the display of the
\r
3384 * structures in the original jmol window. Note This method doesn't work
\r
3385 * without an additional javascript library to exchange messages between the
\r
3386 * distinct applets. See http://issues.jalview.org/browse/JAL-621
\r
3389 * JmolViewer instance
\r
3390 * @param sequenceIds
\r
3391 * - sequence Ids to search for associations
\r
3393 public SequenceStructureBinding addStructureViewInstance(
\r
3394 Object jmolviewer, String[] sequenceIds)
\r
3396 org.jmol.api.JmolViewer viewer = null;
\r
3399 viewer = (org.jmol.api.JmolViewer) jmolviewer;
\r
3400 } catch (ClassCastException ex)
\r
3402 System.err.println("Unsupported viewer object :"
\r
3403 + jmolviewer.getClass());
\r
3405 if (viewer == null)
\r
3407 System.err.println("Can't use this object as a structure viewer:"
\r
3408 + jmolviewer.getClass());
\r
3411 SequenceI[] seqs = null;
\r
3412 if (sequenceIds == null || sequenceIds.length == 0)
\r
3414 seqs = viewport.getAlignment().getSequencesArray();
\r
3418 Vector sqi = new Vector();
\r
3419 AlignmentI al = viewport.getAlignment();
\r
3420 for (int sid = 0; sid < sequenceIds.length; sid++)
\r
3422 SequenceI sq = al.findName(sequenceIds[sid]);
\r
3425 sqi.addElement(sq);
\r
3428 if (sqi.size() > 0)
\r
3430 seqs = new SequenceI[sqi.size()];
\r
3431 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
\r
3433 seqs[sid] = (SequenceI) sqi.elementAt(sid);
\r
3441 ExtJmol jmv = null;
\r
3442 // TODO: search for a jmv that involves viewer
\r
3444 { // create a new viewer/jalview binding.
\r
3445 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs});
\r
3451 * bind a pdb file to a sequence in the current view
\r
3453 * @param sequenceId
\r
3454 * - sequenceId within the dataset.
\r
3455 * @param pdbEntryString
\r
3456 * - the short name for the PDB file
\r
3458 * - pdb file - either a URL or a valid PDB file.
\r
3459 * @return true if binding was as success TODO: consider making an exception
\r
3460 * structure for indicating when PDB parsing or sequenceId location
\r
3463 public boolean addPdbFile(String sequenceId, String pdbEntryString,
\r
3466 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
\r
3467 boolean needtoadd = false;
\r
3468 if (toaddpdb != null)
\r
3470 Vector pdbe = toaddpdb.getPDBId();
\r
3471 PDBEntry pdbentry = null;
\r
3472 if (pdbe != null && pdbe.size() > 0)
\r
3474 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
\r
3476 pdbentry = (PDBEntry) pdbe.elementAt(pe);
\r
3477 if (!pdbentry.getId().equals(pdbEntryString)
\r
3478 && !pdbentry.getFile().equals(pdbFile))
\r
3488 if (pdbentry == null)
\r
3490 pdbentry = new PDBEntry();
\r
3491 pdbentry.setId(pdbEntryString);
\r
3492 pdbentry.setFile(pdbFile);
\r
3493 needtoadd = true; // add this new entry to sequence.
\r
3495 // resolve data source
\r
3496 // TODO: this code should be a refactored to an io package
\r
3497 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
\r
3498 if (protocol == null)
\r
3504 // make a note of the access mode and add
\r
3505 if (pdbentry.getProperty() == null)
\r
3507 pdbentry.setProperty(new Hashtable());
\r
3509 pdbentry.getProperty().put("protocol", protocol);
\r
3510 toaddpdb.addPDBId(pdbentry);
\r
3516 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
\r
3520 Vector sequences = new Vector();
\r
3521 for (int i = 0; i < seqs.length; i++)
\r
3523 if (seqs[i] != null)
\r
3525 sequences.addElement(new Object[]
\r
3526 { seqs[i], (chains != null) ? chains[i] : null });
\r
3529 seqs = new SequenceI[sequences.size()];
\r
3530 chains = new String[sequences.size()];
\r
3531 for (int i = 0, isize = sequences.size(); i < isize; i++)
\r
3533 Object[] oj = (Object[]) sequences.elementAt(i);
\r
3535 seqs[i] = (SequenceI) oj[0];
\r
3536 chains[i] = (String) oj[1];
\r
3539 return new Object[]
\r
3544 public void newStructureView(JalviewLite applet, PDBEntry pdb,
\r
3545 SequenceI[] seqs, String[] chains, String protocol)
\r
3547 // Scrub any null sequences from the array
\r
3548 Object[] sqch = cleanSeqChainArrays(seqs, chains);
\r
3549 seqs = (SequenceI[]) sqch[0];
\r
3550 chains = (String[]) sqch[1];
\r
3551 if (seqs == null || seqs.length == 0)
\r
3554 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
\r
3556 if (protocol == null || protocol.trim().length() == 0
\r
3557 || protocol.equals("null"))
\r
3559 protocol = (String) pdb.getProperty().get("protocol");
\r
3560 if (protocol == null)
\r
3562 System.err.println("Couldn't work out protocol to open structure: "
\r
3567 if (applet.useXtrnalSviewer)
\r
3569 // register the association(s) and quit, don't create any windows.
\r
3570 if (StructureSelectionManager.getStructureSelectionManager(applet).setMapping(seqs, chains, pdb.getFile(), protocol)==null) {
\r
3571 System.err.println("Failed to map "+pdb.getFile()+" ("+protocol+") to any sequences");
\r
3575 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
\r
3577 // can only do alignments with Jmol
\r
3578 // find the last jmol window assigned to this alignment
\r
3579 jalview.appletgui.AppletJmol ajm = null, tajm;
\r
3580 Vector jmols = applet
\r
3581 .getAppletWindow(jalview.appletgui.AppletJmol.class);
\r
3582 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
\r
3584 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
\r
3585 if (tajm.ap.alignFrame == this)
\r
3594 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
\r
3595 // try and add the pdb structure
\r
3600 // otherwise, create a new window
\r
3601 if (applet.jmolAvailable)
\r
3603 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
\r
3605 applet.lastFrameX += 40;
\r
3606 applet.lastFrameY += 40;
\r
3610 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
\r
3615 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
\r
3616 SequenceI[][] seqs, String[][] chains, String[] protocols)
\r
3618 // TODO Auto-generated method stub
\r
3619 System.err.println("Aligned Structure View: Not yet implemented.");
\r
3623 * modify the current selection, providing the user has not made a selection already.
\r
3624 * @param sel - sequences from this alignment
\r
3625 * @param csel - columns to be selected on the alignment
\r
3627 public void select(SequenceGroup sel, ColumnSelection csel)
\r
3629 alignPanel.seqPanel.selection(sel, csel, null);
\r
3632 public void scrollTo(int row, int column)
\r
3634 alignPanel.seqPanel.scrollTo(row, column);
\r
3636 public void scrollToRow(int row)
\r
3638 alignPanel.seqPanel.scrollToRow(row);
\r
3640 public void scrollToColumn(int column)
\r
3642 alignPanel.seqPanel.scrollToColumn(column);
\r
3645 * @return the alignments unique ID.
\r
3647 public String getSequenceSetId() {
\r
3648 return viewport.getSequenceSetId();
\r
3653 * Load the (T-Coffee) score file from the specified url
\r
3655 * @param source File/URL/T-COFFEE score file contents
\r
3656 * @throws IOException
\r
3657 * @return true if alignment was annotated with data from source
\r
3659 public boolean loadScoreFile( String source ) throws IOException {
\r
3661 TCoffeeScoreFile file = new TCoffeeScoreFile(source, AppletFormatAdapter.checkProtocol(source));
\r
3662 if( !file.isValid()) {
\r
3663 // TODO: raise dialog for gui
\r
3664 System.err.println("Problems parsing T-Coffee scores: "+file.getWarningMessage());
\r
3665 System.err.println("Origin was:\n"+source);
\r
3670 * check that the score matrix matches the alignment dimensions
\r
3673 if( (aln=viewport.getAlignment()) != null && (aln.getHeight() != file.getHeight() || aln.getWidth() != file.getWidth()) ) {
\r
3674 // TODO: raise a dialog box here rather than bomb out.
\r
3675 System.err.println("The scores matrix does not match the alignment dimensions");
\r
3679 // TODO add parameter to indicate if matching should be done
\r
3680 if (file.annotateAlignment(alignPanel.getAlignment(), false))
\r
3682 alignPanel.fontChanged();
\r
3683 tcoffeeColour.setEnabled(true);
\r
3684 // switch to this color
\r
3685 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
\r
3688 System.err.println("Problems resolving T-Coffee scores:");
\r
3689 if (file.getWarningMessage()!=null) {
\r
3690 System.err.println(file.getWarningMessage());
\r