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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293 public void keyPressed(KeyEvent evt)
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295 if (viewport.cursorMode
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296 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
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297 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
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298 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
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299 && Character.isDigit(evt.getKeyChar()))
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300 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
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302 switch (evt.getKeyCode())
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304 case 27: // escape key
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305 deselectAllSequenceMenuItem_actionPerformed();
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307 alignPanel.alabels.cancelDrag();
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309 case KeyEvent.VK_X:
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310 if (evt.isControlDown() || evt.isMetaDown())
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312 cut_actionPerformed();
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315 case KeyEvent.VK_C:
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316 if (viewport.cursorMode && !evt.isControlDown())
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318 alignPanel.seqPanel.setCursorColumn();
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320 if (evt.isControlDown() || evt.isMetaDown())
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322 copy_actionPerformed();
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325 case KeyEvent.VK_V:
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326 if (evt.isControlDown())
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328 paste(evt.isShiftDown());
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331 case KeyEvent.VK_A:
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332 if (evt.isControlDown() || evt.isMetaDown())
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334 selectAllSequenceMenuItem_actionPerformed();
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337 case KeyEvent.VK_DOWN:
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338 if (viewport.cursorMode)
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340 alignPanel.seqPanel.moveCursor(0, 1);
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344 moveSelectedSequences(false);
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348 case KeyEvent.VK_UP:
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349 if (viewport.cursorMode)
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351 alignPanel.seqPanel.moveCursor(0, -1);
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355 moveSelectedSequences(true);
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359 case KeyEvent.VK_LEFT:
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360 if (evt.isAltDown() || !viewport.cursorMode)
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361 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
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363 alignPanel.seqPanel.moveCursor(-1, 0);
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366 case KeyEvent.VK_RIGHT:
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367 if (evt.isAltDown() || !viewport.cursorMode)
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368 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
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370 alignPanel.seqPanel.moveCursor(1, 0);
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373 case KeyEvent.VK_SPACE:
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374 if (viewport.cursorMode)
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376 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
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377 || evt.isShiftDown() || evt.isAltDown());
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381 case KeyEvent.VK_DELETE:
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382 case KeyEvent.VK_BACK_SPACE:
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383 if (viewport.cursorMode)
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385 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
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386 || evt.isShiftDown() || evt.isAltDown());
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390 cut_actionPerformed();
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391 alignPanel.seqPanel.seqCanvas.repaint();
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395 case KeyEvent.VK_S:
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396 if (viewport.cursorMode)
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398 alignPanel.seqPanel.setCursorRow();
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401 case KeyEvent.VK_P:
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402 if (viewport.cursorMode)
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404 alignPanel.seqPanel.setCursorPosition();
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408 case KeyEvent.VK_ENTER:
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409 case KeyEvent.VK_COMMA:
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410 if (viewport.cursorMode)
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412 alignPanel.seqPanel.setCursorRowAndColumn();
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416 case KeyEvent.VK_Q:
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417 if (viewport.cursorMode)
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419 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
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422 case KeyEvent.VK_M:
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423 if (viewport.cursorMode)
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425 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
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429 case KeyEvent.VK_F2:
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430 viewport.cursorMode = !viewport.cursorMode;
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431 statusBar.setText("Keyboard editing mode is "
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432 + (viewport.cursorMode ? "on" : "off"));
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433 if (viewport.cursorMode)
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435 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
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436 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
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440 case KeyEvent.VK_F:
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441 if (evt.isControlDown())
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443 findMenuItem_actionPerformed();
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447 case KeyEvent.VK_H:
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449 boolean toggleSeqs = !evt.isControlDown();
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450 boolean toggleCols = !evt.isShiftDown();
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451 toggleHiddenRegions(toggleSeqs, toggleCols);
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455 case KeyEvent.VK_PAGE_UP:
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456 if (viewport.wrapAlignment)
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458 alignPanel.scrollUp(true);
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462 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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463 - viewport.endSeq + viewport.startSeq);
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467 case KeyEvent.VK_PAGE_DOWN:
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468 if (viewport.wrapAlignment)
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470 alignPanel.scrollUp(false);
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474 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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475 + viewport.endSeq - viewport.startSeq);
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479 case KeyEvent.VK_Z:
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480 if (evt.isControlDown())
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482 undoMenuItem_actionPerformed();
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486 case KeyEvent.VK_Y:
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487 if (evt.isControlDown())
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489 redoMenuItem_actionPerformed();
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493 case KeyEvent.VK_L:
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494 if (evt.isControlDown())
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496 trimAlignment(true);
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500 case KeyEvent.VK_R:
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501 if (evt.isControlDown())
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503 trimAlignment(false);
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507 case KeyEvent.VK_E:
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508 if (evt.isControlDown())
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510 if (evt.isShiftDown())
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512 this.removeAllGapsMenuItem_actionPerformed();
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516 removeGappedColumnMenuItem_actionPerformed();
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520 case KeyEvent.VK_I:
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521 if (evt.isControlDown())
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523 if (evt.isAltDown())
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525 invertColSel_actionPerformed();
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529 invertSequenceMenuItem_actionPerformed();
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534 case KeyEvent.VK_U:
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535 if (evt.isControlDown())
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537 this.deleteGroups_actionPerformed();
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541 case KeyEvent.VK_T:
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542 if (evt.isControlDown())
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549 alignPanel.paintAlignment(true);
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553 * called by key handler and the hide all/show all menu items
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555 * @param toggleSeqs
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556 * @param toggleCols
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558 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
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560 boolean hide = false;
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561 SequenceGroup sg = viewport.getSelectionGroup();
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562 if (!toggleSeqs && !toggleCols)
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564 // Hide everything by the current selection - this is a hack - we do the
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565 // invert and then hide
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566 // first check that there will be visible columns after the invert.
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567 if ((viewport.getColumnSelection() != null && viewport.getColumnSelection().getSelected() != null && viewport.getColumnSelection()
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568 .getSelected().size() > 0)
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569 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
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572 // now invert the sequence set, if required - empty selection implies
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573 // that no hiding is required.
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576 invertSequenceMenuItem_actionPerformed();
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577 sg = viewport.getSelectionGroup();
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581 viewport.expandColSelection(sg, true);
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582 // finally invert the column selection and get the new sequence
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583 // selection and indicate it should be hidden.
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584 invertColSel_actionPerformed();
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591 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
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594 viewport.hideAllSelectedSeqs();
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596 else if (!(toggleCols && viewport.getColumnSelection().getSelected().size() > 0))
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598 viewport.showAllHiddenSeqs();
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604 if (viewport.getColumnSelection().getSelected().size() > 0)
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606 viewport.hideSelectedColumns();
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609 viewport.setSelectionGroup(sg);
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614 viewport.showAllHiddenColumns();
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620 public void keyReleased(KeyEvent evt)
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625 public void keyTyped(KeyEvent evt)
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630 public void itemStateChanged(ItemEvent evt)
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632 if (evt.getSource() == displayNonconservedMenuItem)
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634 displayNonconservedMenuItem_actionPerformed();
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636 else if (evt.getSource() == colourTextMenuItem)
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638 colourTextMenuItem_actionPerformed();
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640 else if (evt.getSource() == wrapMenuItem)
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642 wrapMenuItem_actionPerformed();
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644 else if (evt.getSource() == scaleAbove)
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646 viewport.setScaleAboveWrapped(scaleAbove.getState());
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648 else if (evt.getSource() == scaleLeft)
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650 viewport.setScaleLeftWrapped(scaleLeft.getState());
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652 else if (evt.getSource() == scaleRight)
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654 viewport.setScaleRightWrapped(scaleRight.getState());
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656 else if (evt.getSource() == seqLimits)
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658 seqLimits_itemStateChanged();
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660 else if (evt.getSource() == viewBoxesMenuItem)
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662 viewport.setShowBoxes(viewBoxesMenuItem.getState());
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664 else if (evt.getSource() == viewTextMenuItem)
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666 viewport.setShowText(viewTextMenuItem.getState());
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668 else if (evt.getSource() == renderGapsMenuItem)
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670 viewport.setRenderGaps(renderGapsMenuItem.getState());
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672 else if (evt.getSource() == annotationPanelMenuItem)
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674 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
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675 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
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677 else if (evt.getSource() == sequenceFeatures)
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679 viewport.showSequenceFeatures(sequenceFeatures.getState());
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680 alignPanel.seqPanel.seqCanvas.repaint();
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682 else if (evt.getSource() == conservationMenuItem)
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684 conservationMenuItem_actionPerformed();
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686 else if (evt.getSource() == abovePIDThreshold)
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688 abovePIDThreshold_actionPerformed();
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690 else if (evt.getSource() == applyToAllGroups)
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692 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
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694 else if (evt.getSource() == autoCalculate)
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696 viewport.autoCalculateConsensus = autoCalculate.getState();
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698 else if (evt.getSource() == sortByTree)
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700 viewport.sortByTree = sortByTree.getState();
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702 else if (evt.getSource() == this.centreColumnLabelFlag)
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704 centreColumnLabelFlag_stateChanged();
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706 else if (evt.getSource() == this.followMouseOverFlag)
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708 mouseOverFlag_stateChanged();
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710 else if (evt.getSource() == showGroupConsensus)
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712 showGroupConsensus_actionPerformed();
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714 else if (evt.getSource() == showGroupConservation)
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716 showGroupConservation_actionPerformed();
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718 else if (evt.getSource() == showSequenceLogo)
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720 showSequenceLogo_actionPerformed();
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722 else if (evt.getSource() == showConsensusHistogram)
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724 showConsensusHistogram_actionPerformed();
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726 else if (evt.getSource() == applyAutoAnnotationSettings)
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728 applyAutoAnnotationSettings_actionPerformed();
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730 alignPanel.paintAlignment(true);
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733 private void mouseOverFlag_stateChanged()
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735 viewport.followHighlight = followMouseOverFlag.getState();
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736 // TODO: could kick the scrollTo mechanism to reset view for current
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740 private void centreColumnLabelFlag_stateChanged()
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742 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
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743 this.alignPanel.annotationPanel.repaint();
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747 public void actionPerformed(ActionEvent evt)
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749 Object source = evt.getSource();
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751 if (source == inputText)
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753 inputText_actionPerformed();
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755 else if (source == loadTree)
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757 loadTree_actionPerformed();
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759 else if (source == loadApplication)
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761 launchFullApplication();
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763 else if (source == loadAnnotations)
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767 else if (source == outputAnnotations)
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769 outputAnnotations(true);
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771 else if (source == outputFeatures)
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773 outputFeatures(true, "Jalview");
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775 else if (source == closeMenuItem)
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777 closeMenuItem_actionPerformed();
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779 else if (source == copy)
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781 copy_actionPerformed();
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783 else if (source == undoMenuItem)
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785 undoMenuItem_actionPerformed();
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787 else if (source == redoMenuItem)
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789 redoMenuItem_actionPerformed();
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791 else if (source == inputText)
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793 inputText_actionPerformed();
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795 else if (source == closeMenuItem)
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797 closeMenuItem_actionPerformed();
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799 else if (source == undoMenuItem)
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801 undoMenuItem_actionPerformed();
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803 else if (source == redoMenuItem)
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805 redoMenuItem_actionPerformed();
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807 else if (source == copy)
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809 copy_actionPerformed();
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811 else if (source == pasteNew)
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813 pasteNew_actionPerformed();
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815 else if (source == pasteThis)
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817 pasteThis_actionPerformed();
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819 else if (source == cut)
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821 cut_actionPerformed();
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823 else if (source == delete)
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825 delete_actionPerformed();
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827 else if (source == grpsFromSelection)
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829 makeGrpsFromSelection_actionPerformed();
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831 else if (source == deleteGroups)
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833 deleteGroups_actionPerformed();
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835 else if (source == selectAllSequenceMenuItem)
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837 selectAllSequenceMenuItem_actionPerformed();
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839 else if (source == deselectAllSequenceMenuItem)
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841 deselectAllSequenceMenuItem_actionPerformed();
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843 else if (source == invertSequenceMenuItem)
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845 invertSequenceMenuItem_actionPerformed();
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847 else if (source == invertColSel)
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849 viewport.invertColumnSelection();
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850 alignPanel.paintAlignment(true);
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852 else if (source == remove2LeftMenuItem)
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854 trimAlignment(true);
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856 else if (source == remove2RightMenuItem)
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858 trimAlignment(false);
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860 else if (source == removeGappedColumnMenuItem)
\r
862 removeGappedColumnMenuItem_actionPerformed();
\r
864 else if (source == removeAllGapsMenuItem)
\r
866 removeAllGapsMenuItem_actionPerformed();
\r
868 else if (source == findMenuItem)
\r
870 findMenuItem_actionPerformed();
\r
872 else if (source == font)
\r
874 new FontChooser(alignPanel);
\r
876 else if (source == newView)
\r
880 else if (source == showColumns)
\r
882 viewport.showAllHiddenColumns();
\r
883 alignPanel.paintAlignment(true);
\r
885 else if (source == showSeqs)
\r
887 viewport.showAllHiddenSeqs();
\r
888 alignPanel.paintAlignment(true);
\r
890 else if (source == hideColumns)
\r
892 viewport.hideSelectedColumns();
\r
893 alignPanel.paintAlignment(true);
\r
895 else if (source == hideSequences
\r
896 && viewport.getSelectionGroup() != null)
\r
898 viewport.hideAllSelectedSeqs();
\r
899 alignPanel.paintAlignment(true);
\r
901 else if (source == hideAllButSelection)
\r
903 toggleHiddenRegions(false, false);
\r
904 alignPanel.paintAlignment(true);
\r
906 else if (source == hideAllSelection)
\r
908 SequenceGroup sg = viewport.getSelectionGroup();
\r
909 viewport.expandColSelection(sg, false);
\r
910 viewport.hideAllSelectedSeqs();
\r
911 viewport.hideSelectedColumns();
\r
912 alignPanel.paintAlignment(true);
\r
914 else if (source == showAllHidden)
\r
916 viewport.showAllHiddenColumns();
\r
917 viewport.showAllHiddenSeqs();
\r
918 alignPanel.paintAlignment(true);
\r
920 else if (source == showGroupConsensus)
\r
922 showGroupConsensus_actionPerformed();
\r
924 else if (source == showGroupConservation)
\r
926 showGroupConservation_actionPerformed();
\r
928 else if (source == showSequenceLogo)
\r
930 showSequenceLogo_actionPerformed();
\r
932 else if (source == showConsensusHistogram)
\r
934 showConsensusHistogram_actionPerformed();
\r
936 else if (source == applyAutoAnnotationSettings)
\r
938 applyAutoAnnotationSettings_actionPerformed();
\r
940 else if (source == featureSettings)
\r
942 new FeatureSettings(alignPanel);
\r
944 else if (source == alProperties)
\r
946 StringBuffer contents = new jalview.io.AlignmentProperties(
\r
947 viewport.getAlignment()).formatAsString();
\r
948 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
949 cap.setText(contents.toString());
\r
950 Frame frame = new Frame();
\r
952 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
\r
953 + getTitle(), 400, 250);
\r
955 else if (source == overviewMenuItem)
\r
957 overviewMenuItem_actionPerformed();
\r
959 else if (source == noColourmenuItem)
\r
961 changeColour(null);
\r
963 else if (source == clustalColour)
\r
965 abovePIDThreshold.setState(false);
\r
966 changeColour(new ClustalxColourScheme(viewport.getAlignment(),null));
\r
968 else if (source == zappoColour)
\r
970 changeColour(new ZappoColourScheme());
\r
972 else if (source == taylorColour)
\r
974 changeColour(new TaylorColourScheme());
\r
976 else if (source == hydrophobicityColour)
\r
978 changeColour(new HydrophobicColourScheme());
\r
980 else if (source == helixColour)
\r
982 changeColour(new HelixColourScheme());
\r
984 else if (source == strandColour)
\r
986 changeColour(new StrandColourScheme());
\r
988 else if (source == turnColour)
\r
990 changeColour(new TurnColourScheme());
\r
992 else if (source == buriedColour)
\r
994 changeColour(new BuriedColourScheme());
\r
996 else if (source == nucleotideColour)
\r
998 changeColour(new NucleotideColourScheme());
\r
1000 else if (source == purinePyrimidineColour)
\r
1002 changeColour(new PurinePyrimidineColourScheme());
\r
1004 else if (source == RNAHelixColour)
\r
1006 new RNAHelicesColourChooser(viewport, alignPanel);
\r
1008 else if (source == modifyPID)
\r
1010 modifyPID_actionPerformed();
\r
1012 else if (source == modifyConservation)
\r
1014 modifyConservation_actionPerformed();
\r
1016 else if (source == userDefinedColour)
\r
1018 new UserDefinedColours(alignPanel, null);
\r
1020 else if (source == PIDColour)
\r
1022 changeColour(new PIDColourScheme());
\r
1024 else if (source == BLOSUM62Colour)
\r
1026 changeColour(new Blosum62ColourScheme());
\r
1028 else if (source == tcoffeeColour) {
\r
1029 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
\r
1031 else if (source == annotationColour)
\r
1033 new AnnotationColourChooser(viewport, alignPanel);
\r
1035 else if (source == sortPairwiseMenuItem)
\r
1037 sortPairwiseMenuItem_actionPerformed();
\r
1039 else if (source == sortIDMenuItem)
\r
1041 sortIDMenuItem_actionPerformed();
\r
1043 else if (source == sortLengthMenuItem)
\r
1045 sortLengthMenuItem_actionPerformed();
\r
1047 else if (source == sortGroupMenuItem)
\r
1049 sortGroupMenuItem_actionPerformed();
\r
1051 else if (source == removeRedundancyMenuItem)
\r
1053 removeRedundancyMenuItem_actionPerformed();
\r
1055 else if (source == pairwiseAlignmentMenuItem)
\r
1057 pairwiseAlignmentMenuItem_actionPerformed();
\r
1059 else if (source == PCAMenuItem)
\r
1061 PCAMenuItem_actionPerformed();
\r
1063 else if (source == averageDistanceTreeMenuItem)
\r
1065 averageDistanceTreeMenuItem_actionPerformed();
\r
1067 else if (source == neighbourTreeMenuItem)
\r
1069 neighbourTreeMenuItem_actionPerformed();
\r
1071 else if (source == njTreeBlosumMenuItem)
\r
1073 njTreeBlosumMenuItem_actionPerformed();
\r
1075 else if (source == avDistanceTreeBlosumMenuItem)
\r
1077 avTreeBlosumMenuItem_actionPerformed();
\r
1079 else if (source == documentation)
\r
1081 documentation_actionPerformed();
\r
1083 else if (source == about)
\r
1085 about_actionPerformed();
\r
1090 public void inputText_actionPerformed()
\r
1092 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1093 Frame frame = new Frame();
\r
1095 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
\r
1098 protected void outputText_actionPerformed(ActionEvent e)
\r
1100 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1101 Frame frame = new Frame();
\r
1103 jalview.bin.JalviewLite.addFrame(frame,
\r
1104 "Alignment output - " + e.getActionCommand(), 600, 500);
\r
1105 cap.setText(new AppletFormatAdapter().formatSequences(
\r
1106 e.getActionCommand(), viewport.getAlignment(),
\r
1107 viewport.showJVSuffix));
\r
1110 public void loadAnnotations()
\r
1112 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1113 cap.setText("Paste your features / annotations / T-coffee score file here.");
\r
1114 cap.setAnnotationImport();
\r
1115 Frame frame = new Frame();
\r
1117 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
\r
1121 public String outputAnnotations(boolean displayTextbox)
\r
1123 String annotation = new AnnotationFile().printAnnotations(
\r
1124 viewport.showAnnotation ? viewport.getAlignment()
\r
1125 .getAlignmentAnnotation() : null, viewport.getAlignment()
\r
1127 ((Alignment) viewport.getAlignment()).alignmentProperties);
\r
1129 if (displayTextbox)
\r
1131 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
1132 Frame frame = new Frame();
\r
1134 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
\r
1135 cap.setText(annotation);
\r
1138 return annotation;
\r
1141 private Hashtable getDisplayedFeatureCols()
\r
1143 if (alignPanel.getFeatureRenderer() != null && viewport.featuresDisplayed!=null)
\r
1145 FeatureRenderer fr = alignPanel.getFeatureRenderer();
\r
1146 Hashtable fcols = new Hashtable();
\r
1147 Enumeration en = viewport.featuresDisplayed.keys();
\r
1148 while (en.hasMoreElements())
\r
1150 Object col = en.nextElement();
\r
1151 fcols.put(col, fr.featureColours.get(col));
\r
1158 public String outputFeatures(boolean displayTextbox, String format)
\r
1161 if (format.equalsIgnoreCase("Jalview"))
\r
1163 features = new FeaturesFile().printJalviewFormat(
\r
1164 viewport.getAlignment().getSequencesArray(),
\r
1165 getDisplayedFeatureCols());
\r
1169 features = new FeaturesFile().printGFFFormat(
\r
1170 viewport.getAlignment().getSequencesArray(),
\r
1171 getDisplayedFeatureCols());
\r
1174 if (displayTextbox)
\r
1176 boolean frimport=false;
\r
1177 if (features==null || features.equals("No Features Visible"))
\r
1179 features = "# No features visible - paste some and import them here.";
\r
1183 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
\r
1186 cap.setAnnotationImport();
\r
1188 Frame frame = new Frame();
\r
1190 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
\r
1191 cap.setText(features);
\r
1193 if (features==null)
\r
1200 void launchFullApplication()
\r
1202 StringBuffer url = new StringBuffer(jalviewServletURL);
\r
1204 url.append("?open="
\r
1205 + appendProtocol(viewport.applet.getParameter("file")));
\r
1207 if (viewport.applet.getParameter("features") != null)
\r
1209 url.append("&features=");
\r
1210 url.append(appendProtocol(viewport.applet.getParameter("features")));
\r
1213 if (viewport.applet.getParameter("annotations") != null)
\r
1215 url.append("&annotations=");
\r
1216 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
\r
1219 if (viewport.applet.getParameter("jnetfile") != null)
\r
1221 url.append("&annotations=");
\r
1222 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
\r
1225 if (viewport.applet.getParameter("defaultColour") != null)
\r
1227 url.append("&colour="
\r
1228 + removeWhiteSpace(viewport.applet
\r
1229 .getParameter("defaultColour")));
\r
1232 if (viewport.applet.getParameter("userDefinedColour") != null)
\r
1234 url.append("&colour="
\r
1235 + removeWhiteSpace(viewport.applet
\r
1236 .getParameter("userDefinedColour")));
\r
1238 if (viewport.applet.getParameter("tree") != null)
\r
1240 url.append("&tree="
\r
1241 + appendProtocol(viewport.applet.getParameter("tree")));
\r
1243 if (viewport.applet.getParameter("treeFile") != null)
\r
1245 url.append("&tree="
\r
1246 + appendProtocol(viewport.applet.getParameter("treeFile")));
\r
1249 showURL(url.toString(), "FULL_APP");
\r
1252 String removeWhiteSpace(String colour)
\r
1254 StringBuffer sb = new StringBuffer();
\r
1255 for (int i = 0; i < colour.length(); i++)
\r
1257 if (Character.isWhitespace(colour.charAt(i)))
\r
1263 sb.append(colour.charAt(i));
\r
1267 return sb.toString();
\r
1270 String appendProtocol(String url)
\r
1275 url = URLEncoder.encode(url);
\r
1278 * When we finally deprecate 1.1 compatibility, we can start to use
\r
1279 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
\r
1280 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
\r
1281 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
\r
1282 * ex.printStackTrace(); }
\r
1284 catch (java.net.MalformedURLException ex)
\r
1286 url = viewport.applet.getCodeBase() + url;
\r
1291 public void closeMenuItem_actionPerformed()
\r
1293 PaintRefresher.RemoveComponent(alignPanel);
\r
1294 if (alignPanel.seqPanel!=null && alignPanel.seqPanel.seqCanvas!=null)
\r
1296 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
\r
1298 if (alignPanel.idPanel!=null && alignPanel.idPanel.idCanvas!=null) {
\r
1299 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
\r
1302 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
\r
1308 alignPanel = null;
\r
1315 void updateEditMenuBar()
\r
1318 if (viewport.historyList.size() > 0)
\r
1320 undoMenuItem.setEnabled(true);
\r
1321 CommandI command = (CommandI) viewport.historyList.peek();
\r
1322 undoMenuItem.setLabel("Undo " + command.getDescription());
\r
1326 undoMenuItem.setEnabled(false);
\r
1327 undoMenuItem.setLabel("Undo");
\r
1330 if (viewport.redoList.size() > 0)
\r
1332 redoMenuItem.setEnabled(true);
\r
1334 CommandI command = (CommandI) viewport.redoList.peek();
\r
1335 redoMenuItem.setLabel("Redo " + command.getDescription());
\r
1339 redoMenuItem.setEnabled(false);
\r
1340 redoMenuItem.setLabel("Redo");
\r
1347 public void addHistoryItem(CommandI command)
\r
1349 if (command.getSize() > 0)
\r
1351 viewport.historyList.push(command);
\r
1352 viewport.redoList.removeAllElements();
\r
1353 updateEditMenuBar();
\r
1354 viewport.updateHiddenColumns();
\r
1365 protected void undoMenuItem_actionPerformed()
\r
1367 if (viewport.historyList.size() < 1)
\r
1372 CommandI command = (CommandI) viewport.historyList.pop();
\r
1373 viewport.redoList.push(command);
\r
1374 command.undoCommand(null);
\r
1376 AlignViewport originalSource = getOriginatingSource(command);
\r
1378 if (originalSource!=viewport) {
\r
1379 System.err.println("Warning: Viewport object mismatch whilst undoing");
\r
1381 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns = viewport.getColumnSelection().getHiddenColumns() != null;
\r
1382 updateEditMenuBar();
\r
1383 originalSource.firePropertyChange("alignment", null,
\r
1384 originalSource.getAlignment().getSequences());
\r
1394 protected void redoMenuItem_actionPerformed()
\r
1396 if (viewport.redoList.size() < 1)
\r
1401 CommandI command = (CommandI) viewport.redoList.pop();
\r
1402 viewport.historyList.push(command);
\r
1403 command.doCommand(null);
\r
1405 AlignViewport originalSource = getOriginatingSource(command);
\r
1407 if (originalSource!=viewport) {
\r
1408 System.err.println("Warning: Viewport object mismatch whilst re-doing");
\r
1410 originalSource.updateHiddenColumns(); //sethasHiddenColumns(); = viewport.getColumnSelection().getHiddenColumns() != null;
\r
1412 updateEditMenuBar();
\r
1413 originalSource.firePropertyChange("alignment", null,
\r
1414 originalSource.getAlignment().getSequences());
\r
1417 AlignViewport getOriginatingSource(CommandI command)
\r
1419 AlignViewport originalSource = null;
\r
1420 // For sequence removal and addition, we need to fire
\r
1421 // the property change event FROM the viewport where the
\r
1422 // original alignment was altered
\r
1423 AlignmentI al = null;
\r
1424 if (command instanceof EditCommand)
\r
1426 EditCommand editCommand = (EditCommand) command;
\r
1427 al = editCommand.getAlignment();
\r
1428 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
1429 .getSequenceSetId());
\r
1430 for (int i = 0; i < comps.size(); i++)
\r
1432 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
1434 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
\r
1436 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
\r
1443 if (originalSource == null)
\r
1445 // The original view is closed, we must validate
\r
1446 // the current view against the closed view first
\r
1449 PaintRefresher.validateSequences(al, viewport.getAlignment());
\r
1452 originalSource = viewport;
\r
1455 return originalSource;
\r
1458 public void moveSelectedSequences(boolean up)
\r
1460 SequenceGroup sg = viewport.getSelectionGroup();
\r
1465 viewport.getAlignment().moveSelectedSequencesByOne(sg, up ? null : viewport.getHiddenRepSequences(), up);
\r
1466 alignPanel.paintAlignment(true);
\r
1469 synchronized void slideSequences(boolean right, int size)
\r
1471 List<SequenceI>sg = new Vector<SequenceI>();
\r
1472 if (viewport.cursorMode)
\r
1474 sg.add(viewport.getAlignment()
\r
1475 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
\r
1477 else if (viewport.getSelectionGroup() != null
\r
1478 && viewport.getSelectionGroup().getSize() != viewport.getAlignment()
\r
1481 sg = viewport.getSelectionGroup().getSequences(
\r
1482 viewport.getHiddenRepSequences());
\r
1485 if (sg.size() < 1)
\r
1490 Vector<SequenceI> invertGroup = new Vector();
\r
1492 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
\r
1494 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
\r
1495 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
\r
1498 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
\r
1500 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup.size()]);
\r
1501 for (int i = 0; i < invertGroup.size(); i++)
\r
1502 seqs2[i] = invertGroup.elementAt(i);
\r
1504 SlideSequencesCommand ssc;
\r
1506 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
\r
1507 size, viewport.getGapCharacter());
\r
1509 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
\r
1510 size, viewport.getGapCharacter());
\r
1512 int groupAdjustment = 0;
\r
1513 if (ssc.getGapsInsertedBegin() && right)
\r
1515 if (viewport.cursorMode)
\r
1516 alignPanel.seqPanel.moveCursor(size, 0);
\r
1518 groupAdjustment = size;
\r
1520 else if (!ssc.getGapsInsertedBegin() && !right)
\r
1522 if (viewport.cursorMode)
\r
1523 alignPanel.seqPanel.moveCursor(-size, 0);
\r
1525 groupAdjustment = -size;
\r
1528 if (groupAdjustment != 0)
\r
1530 viewport.getSelectionGroup().setStartRes(
\r
1531 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
\r
1532 viewport.getSelectionGroup().setEndRes(
\r
1533 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
\r
1536 boolean appendHistoryItem = false;
\r
1537 if (viewport.historyList != null && viewport.historyList.size() > 0
\r
1538 && viewport.historyList.peek() instanceof SlideSequencesCommand)
\r
1540 appendHistoryItem = ssc
\r
1541 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
\r
1545 if (!appendHistoryItem)
\r
1546 addHistoryItem(ssc);
\r
1551 static StringBuffer copiedSequences;
\r
1553 static Vector copiedHiddenColumns;
\r
1555 protected void copy_actionPerformed()
\r
1557 if (viewport.getSelectionGroup() == null)
\r
1562 SequenceGroup sg = viewport.getSelectionGroup();
\r
1563 copiedSequences = new StringBuffer();
\r
1564 Hashtable orderedSeqs = new Hashtable();
\r
1565 for (int i = 0; i < sg.getSize(); i++)
\r
1567 SequenceI seq = sg.getSequenceAt(i);
\r
1568 int index = viewport.getAlignment().findIndex(seq);
\r
1569 orderedSeqs.put(index + "", seq);
\r
1572 int index = 0, startRes, endRes;
\r
1575 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
\r
1577 copiedHiddenColumns = new Vector();
\r
1578 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
\r
1579 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
\r
1582 int[] region = (int[]) viewport.getColumnSelection()
\r
1583 .getHiddenColumns().elementAt(i);
\r
1585 copiedHiddenColumns.addElement(new int[]
\r
1586 { region[0] - hiddenOffset, region[1] - hiddenOffset });
\r
1591 copiedHiddenColumns = null;
\r
1594 for (int i = 0; i < sg.getSize(); i++)
\r
1596 SequenceI seq = null;
\r
1598 while (seq == null)
\r
1600 if (orderedSeqs.containsKey(index + ""))
\r
1602 seq = (SequenceI) orderedSeqs.get(index + "");
\r
1614 // Returns residue following index if gap
\r
1615 startRes = seq.findPosition(sg.getStartRes());
\r
1618 // Need to find the residue preceeding index if gap
\r
1621 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
\r
1623 ch = seq.getCharAt(j);
\r
1624 if (!jalview.util.Comparison.isGap((ch)))
\r
1632 endRes += seq.getStart() - 1;
\r
1635 copiedSequences.append(seq.getName()
\r
1641 + seq.getSequenceAsString(sg.getStartRes(),
\r
1642 sg.getEndRes() + 1) + "\n");
\r
1647 protected void pasteNew_actionPerformed()
\r
1652 protected void pasteThis_actionPerformed()
\r
1657 void paste(boolean newAlignment)
\r
1662 if (copiedSequences == null)
\r
1667 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
1668 Vector seqs = new Vector();
\r
1669 while (st.hasMoreElements())
\r
1671 String name = st.nextToken();
\r
1672 int start = Integer.parseInt(st.nextToken());
\r
1673 int end = Integer.parseInt(st.nextToken());
\r
1674 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
\r
1676 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
1677 for (int i = 0; i < seqs.size(); i++)
\r
1679 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
1684 String newtitle = new String("Copied sequences");
\r
1685 if (getTitle().startsWith("Copied sequences"))
\r
1687 newtitle = getTitle();
\r
1691 newtitle = newtitle.concat("- from " + getTitle());
\r
1693 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
1694 viewport.applet, newtitle, false);
\r
1695 if (copiedHiddenColumns != null)
\r
1697 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
1699 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
1700 af.viewport.hideColumns(region[0], region[1]);
\r
1704 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
\r
1709 addSequences(newSeqs);
\r
1712 } catch (Exception ex)
\r
1714 } // could be anything being pasted in here
\r
1718 void addSequences(SequenceI[] seqs)
\r
1720 for (int i = 0; i < seqs.length; i++)
\r
1722 viewport.getAlignment().addSequence(seqs[i]);
\r
1726 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
\r
1727 seqs, 0, viewport.getAlignment().getWidth(), viewport.getAlignment()));
\r
1729 viewport.setEndSeq(viewport.getAlignment().getHeight());
\r
1730 viewport.getAlignment().getWidth();
\r
1731 viewport.firePropertyChange("alignment", null,
\r
1732 viewport.getAlignment().getSequences());
\r
1736 protected void cut_actionPerformed()
\r
1738 copy_actionPerformed();
\r
1739 delete_actionPerformed();
\r
1742 protected void delete_actionPerformed()
\r
1745 SequenceGroup sg = viewport.getSelectionGroup();
\r
1751 Vector seqs = new Vector();
\r
1753 for (int i = 0; i < sg.getSize(); i++)
\r
1755 seq = sg.getSequenceAt(i);
\r
1756 seqs.addElement(seq);
\r
1759 // If the cut affects all sequences, remove highlighted columns
\r
1760 if (sg.getSize() == viewport.getAlignment().getHeight())
\r
1762 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
1763 sg.getEndRes() + 1);
\r
1766 SequenceI[] cut = new SequenceI[seqs.size()];
\r
1767 for (int i = 0; i < seqs.size(); i++)
\r
1769 cut[i] = (SequenceI) seqs.elementAt(i);
\r
1773 * //ADD HISTORY ITEM
\r
1775 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
\r
1776 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
\r
1777 viewport.getAlignment()));
\r
1779 viewport.setSelectionGroup(null);
\r
1780 viewport.getAlignment().deleteGroup(sg);
\r
1782 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1785 if (viewport.getAlignment().getHeight() < 1)
\r
1787 this.setVisible(false);
\r
1789 viewport.sendSelection();
\r
1793 * group consensus toggled
\r
1796 protected void showGroupConsensus_actionPerformed()
\r
1798 viewport.setShowGroupConsensus(showGroupConsensus.getState());
\r
1799 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1804 * group conservation toggled.
\r
1806 protected void showGroupConservation_actionPerformed()
\r
1808 viewport.setShowGroupConservation(showGroupConservation.getState());
\r
1809 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1816 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
\r
1817 * .event.ActionEvent)
\r
1819 protected void showConsensusHistogram_actionPerformed()
\r
1821 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
\r
1822 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1828 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
\r
1829 * .event.ActionEvent)
\r
1831 protected void showSequenceLogo_actionPerformed()
\r
1833 viewport.setShowSequenceLogo(showSequenceLogo.getState());
\r
1834 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1837 protected void applyAutoAnnotationSettings_actionPerformed()
\r
1839 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1842 protected void makeGrpsFromSelection_actionPerformed()
\r
1844 if (viewport.getSelectionGroup() != null)
\r
1846 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
\r
1847 viewport.getSequenceSelection(),
\r
1848 viewport.getAlignmentView(true).getSequenceStrings(
\r
1849 viewport.getGapCharacter()),
\r
1850 viewport.getAlignment().getGroups());
\r
1851 viewport.getAlignment().deleteAllGroups();
\r
1852 viewport.sequenceColours = null;
\r
1853 viewport.setSelectionGroup(null);
\r
1854 // set view properties for each group
\r
1855 for (int g = 0; g < gps.length; g++)
\r
1857 // gps[g].setShowunconserved(viewport.getShowUnconserved());
\r
1858 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
\r
1859 viewport.getAlignment().addGroup(gps[g]);
\r
1860 Color col = new Color((int) (Math.random() * 255),
\r
1861 (int) (Math.random() * 255), (int) (Math.random() * 255));
\r
1862 col = col.brighter();
\r
1863 for (SequenceI sq : gps[g].getSequences(null))
\r
1864 viewport.setSequenceColour(
\r
1868 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
\r
1869 alignPanel.updateAnnotation();
\r
1870 alignPanel.paintAlignment(true);
\r
1874 protected void deleteGroups_actionPerformed()
\r
1876 viewport.getAlignment().deleteAllGroups();
\r
1877 viewport.sequenceColours = null;
\r
1878 viewport.setSelectionGroup(null);
\r
1880 alignPanel.paintAlignment(true);
\r
1883 public void selectAllSequenceMenuItem_actionPerformed()
\r
1885 SequenceGroup sg = new SequenceGroup();
\r
1886 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1888 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
1890 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
\r
1891 viewport.setSelectionGroup(sg);
\r
1892 alignPanel.paintAlignment(true);
\r
1893 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1894 viewport.sendSelection();
\r
1897 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1899 if (viewport.cursorMode)
\r
1901 alignPanel.seqPanel.keyboardNo1 = null;
\r
1902 alignPanel.seqPanel.keyboardNo2 = null;
\r
1904 viewport.setSelectionGroup(null);
\r
1905 viewport.getColumnSelection().clear();
\r
1906 viewport.setSelectionGroup(null);
\r
1907 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1908 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1909 alignPanel.paintAlignment(true);
\r
1910 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1911 viewport.sendSelection();
\r
1914 public void invertSequenceMenuItem_actionPerformed()
\r
1916 SequenceGroup sg = viewport.getSelectionGroup();
\r
1917 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1919 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1922 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1923 viewport.sendSelection();
\r
1926 public void invertColSel_actionPerformed()
\r
1928 viewport.invertColumnSelection();
\r
1929 alignPanel.paintAlignment(true);
\r
1930 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1931 viewport.sendSelection();
\r
1934 void trimAlignment(boolean trimLeft)
\r
1936 ColumnSelection colSel = viewport.getColumnSelection();
\r
1939 if (colSel.size() > 0)
\r
1943 column = colSel.getMin();
\r
1947 column = colSel.getMax();
\r
1951 if (viewport.getSelectionGroup() != null)
\r
1953 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
1954 viewport.getHiddenRepSequences());
\r
1958 seqs = viewport.getAlignment().getSequencesArray();
\r
1961 TrimRegionCommand trimRegion;
\r
1964 trimRegion = new TrimRegionCommand("Remove Left",
\r
1965 TrimRegionCommand.TRIM_LEFT, seqs, column,
\r
1966 viewport.getAlignment(), viewport.getColumnSelection(),
\r
1967 viewport.getSelectionGroup());
\r
1968 viewport.setStartRes(0);
\r
1972 trimRegion = new TrimRegionCommand("Remove Right",
\r
1973 TrimRegionCommand.TRIM_RIGHT, seqs, column,
\r
1974 viewport.getAlignment(), viewport.getColumnSelection(),
\r
1975 viewport.getSelectionGroup());
\r
1978 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
\r
1980 addHistoryItem(trimRegion);
\r
1984 for (SequenceGroup sg:viewport.getAlignment().getGroups())
\r
1986 if ((trimLeft && !sg.adjustForRemoveLeft(column))
\r
1987 || (!trimLeft && !sg.adjustForRemoveRight(column)))
\r
1989 viewport.getAlignment().deleteGroup(sg);
\r
1993 viewport.firePropertyChange("alignment", null, viewport
\r
1994 .getAlignment().getSequences());
\r
1998 public void removeGappedColumnMenuItem_actionPerformed()
\r
2000 int start = 0, end = viewport.getAlignment().getWidth() - 1;
\r
2003 if (viewport.getSelectionGroup() != null)
\r
2005 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2006 viewport.getHiddenRepSequences());
\r
2007 start = viewport.getSelectionGroup().getStartRes();
\r
2008 end = viewport.getSelectionGroup().getEndRes();
\r
2012 seqs = viewport.getAlignment().getSequencesArray();
\r
2015 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
\r
2016 "Remove Gapped Columns", seqs, start, end, viewport.getAlignment());
\r
2018 addHistoryItem(removeGapCols);
\r
2020 statusBar.setText("Removed " + removeGapCols.getSize()
\r
2021 + " empty columns.");
\r
2023 // This is to maintain viewport position on first residue
\r
2024 // of first sequence
\r
2025 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
\r
2026 int startRes = seq.findPosition(viewport.startRes);
\r
2027 // ShiftList shifts;
\r
2028 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
\r
2029 // edit.alColumnChanges=shifts.getInverse();
\r
2030 // if (viewport.hasHiddenColumns)
\r
2031 // viewport.getColumnSelection().compensateForEdits(shifts);
\r
2032 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
2033 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
2038 public void removeAllGapsMenuItem_actionPerformed()
\r
2040 int start = 0, end = viewport.getAlignment().getWidth() - 1;
\r
2043 if (viewport.getSelectionGroup() != null)
\r
2045 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2046 viewport.getHiddenRepSequences());
\r
2047 start = viewport.getSelectionGroup().getStartRes();
\r
2048 end = viewport.getSelectionGroup().getEndRes();
\r
2052 seqs = viewport.getAlignment().getSequencesArray();
\r
2055 // This is to maintain viewport position on first residue
\r
2056 // of first sequence
\r
2057 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
\r
2058 int startRes = seq.findPosition(viewport.startRes);
\r
2060 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
\r
2061 viewport.getAlignment()));
\r
2063 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
2065 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
2070 public void findMenuItem_actionPerformed()
\r
2072 new Finder(alignPanel);
\r
2076 * create a new view derived from the current view
\r
2078 * @param viewtitle
\r
2079 * @return frame for the new view
\r
2081 public AlignFrame newView(String viewtitle)
\r
2084 if (viewport.hasHiddenRows())
\r
2086 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
\r
2087 .getFullAlignment().getSequencesArray());
\r
2091 newal = new Alignment(viewport.getAlignment().getSequencesArray());
\r
2094 if (viewport.getAlignment().getAlignmentAnnotation() != null)
\r
2096 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
\r
2098 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
\r
2100 newal.addAnnotation(viewport.getAlignment().getAlignmentAnnotation()[i]);
\r
2105 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
\r
2107 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
\r
2108 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
\r
2109 PaintRefresher.Register(newaf.alignPanel,
\r
2110 newaf.alignPanel.av.getSequenceSetId());
\r
2112 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
\r
2113 newaf.alignPanel.av.getSequenceSetId());
\r
2114 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
\r
2115 newaf.alignPanel.av.getSequenceSetId());
\r
2117 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
2118 .getSequenceSetId());
\r
2119 int viewSize = -1;
\r
2120 for (int i = 0; i < comps.size(); i++)
\r
2122 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
2128 String title = new String(this.getTitle());
\r
2129 if (viewtitle != null)
\r
2131 title = viewtitle + " ( " + title + ")";
\r
2135 if (title.indexOf("(View") > -1)
\r
2137 title = title.substring(0, title.indexOf("(View"));
\r
2139 title += "(View " + viewSize + ")";
\r
2142 newaf.setTitle(title.toString());
\r
2144 newaf.viewport.historyList = viewport.historyList;
\r
2145 newaf.viewport.redoList = viewport.redoList;
\r
2151 * @return list of feature groups on the view
\r
2153 public String[] getFeatureGroups()
\r
2155 FeatureRenderer fr = null;
\r
2156 if (alignPanel != null
\r
2157 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2159 return fr.getGroups();
\r
2165 * get sequence feature groups that are hidden or shown
\r
2171 public String[] getFeatureGroupsOfState(boolean visible)
\r
2173 FeatureRenderer fr = null;
\r
2174 if (alignPanel != null
\r
2175 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2177 return fr.getGroups(visible);
\r
2183 * Change the display state for the given feature groups
\r
2186 * list of group strings
\r
2188 * visible or invisible
\r
2190 public void setFeatureGroupState(String[] groups, boolean state)
\r
2192 FeatureRenderer fr = null;
\r
2193 this.sequenceFeatures.setState(true);
\r
2194 viewport.showSequenceFeatures(true);
\r
2195 if (alignPanel != null
\r
2196 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2198 fr.setGroupState(groups, state);
\r
2199 alignPanel.seqPanel.seqCanvas.repaint();
\r
2200 if (alignPanel.overviewPanel != null)
\r
2202 alignPanel.overviewPanel.updateOverviewImage();
\r
2207 public void seqLimits_itemStateChanged()
\r
2209 viewport.setShowJVSuffix(seqLimits.getState());
\r
2210 alignPanel.fontChanged();
\r
2211 alignPanel.paintAlignment(true);
\r
2214 protected void colourTextMenuItem_actionPerformed()
\r
2216 viewport.setColourText(colourTextMenuItem.getState());
\r
2217 alignPanel.paintAlignment(true);
\r
2220 protected void displayNonconservedMenuItem_actionPerformed()
\r
2222 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
\r
2223 alignPanel.paintAlignment(true);
\r
2226 protected void wrapMenuItem_actionPerformed()
\r
2228 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
2229 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
2230 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
2231 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
2232 scaleRight.setEnabled(wrapMenuItem.getState());
\r
2233 alignPanel.paintAlignment(true);
\r
2236 public void overviewMenuItem_actionPerformed()
\r
2238 if (alignPanel.overviewPanel != null)
\r
2243 Frame frame = new Frame();
\r
2244 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
2245 frame.add(overview);
\r
2246 // +50 must allow for applet frame window
\r
2247 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
2248 overview.getPreferredSize().width,
\r
2249 overview.getPreferredSize().height + 50);
\r
2252 final AlignmentPanel ap=alignPanel;
\r
2253 frame.addWindowListener(new WindowAdapter()
\r
2256 public void windowClosing(WindowEvent e)
\r
2259 ap.setOverviewPanel(null);
\r
2264 alignPanel.setOverviewPanel(overview);
\r
2268 void changeColour(ColourSchemeI cs)
\r
2270 int threshold = 0;
\r
2274 if (viewport.getAbovePIDThreshold())
\r
2276 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
2279 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2281 viewport.setGlobalColourScheme(cs);
\r
2285 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2288 if (viewport.getConservationSelected())
\r
2291 Alignment al = (Alignment) viewport.getAlignment();
\r
2292 Conservation c = new Conservation("All",
\r
2293 ResidueProperties.propHash, 3, al.getSequences(), 0,
\r
2294 al.getWidth() - 1);
\r
2297 c.verdict(false, viewport.getConsPercGaps());
\r
2299 cs.setConservation(c);
\r
2301 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
\r
2302 cs, "Background"));
\r
2307 cs.setConservation(null);
\r
2310 cs.setConsensus(viewport.getSequenceConsensusHash());
\r
2313 viewport.setGlobalColourScheme(cs);
\r
2316 if (alignPanel.getOverviewPanel() != null)
\r
2318 alignPanel.getOverviewPanel().updateOverviewImage();
\r
2321 jalview.structure.StructureSelectionManager
\r
2322 .getStructureSelectionManager(viewport.applet).sequenceColoursChanged(
\r
2325 alignPanel.paintAlignment(true);
\r
2328 protected void modifyPID_actionPerformed()
\r
2330 if (viewport.getAbovePIDThreshold()
\r
2331 && viewport.getGlobalColourScheme() != null)
\r
2333 SliderPanel.setPIDSliderSource(alignPanel,
\r
2334 viewport.getGlobalColourScheme(), "Background");
\r
2335 SliderPanel.showPIDSlider();
\r
2339 protected void modifyConservation_actionPerformed()
\r
2341 if (viewport.getConservationSelected()
\r
2342 && viewport.getGlobalColourScheme() != null)
\r
2344 SliderPanel.setConservationSlider(alignPanel,
\r
2345 viewport.getGlobalColourScheme(), "Background");
\r
2346 SliderPanel.showConservationSlider();
\r
2350 protected void conservationMenuItem_actionPerformed()
\r
2352 viewport.setConservationSelected(conservationMenuItem.getState());
\r
2354 viewport.setAbovePIDThreshold(false);
\r
2355 abovePIDThreshold.setState(false);
\r
2357 changeColour(viewport.getGlobalColourScheme());
\r
2359 modifyConservation_actionPerformed();
\r
2362 public void abovePIDThreshold_actionPerformed()
\r
2364 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
2366 conservationMenuItem.setState(false);
\r
2367 viewport.setConservationSelected(false);
\r
2369 changeColour(viewport.getGlobalColourScheme());
\r
2371 modifyPID_actionPerformed();
\r
2374 public void sortPairwiseMenuItem_actionPerformed()
\r
2376 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2377 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
\r
2378 .getAlignment().getSequenceAt(0), null);
\r
2380 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
\r
2381 viewport.getAlignment()));
\r
2382 alignPanel.paintAlignment(true);
\r
2385 public void sortIDMenuItem_actionPerformed()
\r
2387 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2388 AlignmentSorter.sortByID(viewport.getAlignment());
\r
2389 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
\r
2390 alignPanel.paintAlignment(true);
\r
2393 public void sortLengthMenuItem_actionPerformed()
\r
2395 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2396 AlignmentSorter.sortByLength(viewport.getAlignment());
\r
2397 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
\r
2398 viewport.getAlignment()));
\r
2399 alignPanel.paintAlignment(true);
\r
2402 public void sortGroupMenuItem_actionPerformed()
\r
2404 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2405 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
2406 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
\r
2407 viewport.getAlignment()));
\r
2408 alignPanel.paintAlignment(true);
\r
2412 public void removeRedundancyMenuItem_actionPerformed()
\r
2414 new RedundancyPanel(alignPanel);
\r
2417 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
2419 if (viewport.getSelectionGroup() != null
\r
2420 && viewport.getSelectionGroup().getSize() > 1)
\r
2422 Frame frame = new Frame();
\r
2423 frame.add(new PairwiseAlignPanel(alignPanel));
\r
2424 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
\r
2429 public void PCAMenuItem_actionPerformed()
\r
2431 // are the sequences aligned?
\r
2432 if (!viewport.getAlignment().isAligned(false))
\r
2434 SequenceI current;
\r
2435 int Width = viewport.getAlignment().getWidth();
\r
2437 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2439 current = viewport.getAlignment().getSequenceAt(i);
\r
2441 if (current.getLength() < Width)
\r
2443 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2446 alignPanel.paintAlignment(true);
\r
2449 if ((viewport.getSelectionGroup() != null
\r
2450 && viewport.getSelectionGroup().getSize() < 4 && viewport
\r
2451 .getSelectionGroup().getSize() > 0)
\r
2452 || viewport.getAlignment().getHeight() < 4)
\r
2459 new PCAPanel(viewport);
\r
2460 } catch (java.lang.OutOfMemoryError ex)
\r
2466 public void averageDistanceTreeMenuItem_actionPerformed()
\r
2468 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
2471 public void neighbourTreeMenuItem_actionPerformed()
\r
2473 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
2476 protected void njTreeBlosumMenuItem_actionPerformed()
\r
2478 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2481 protected void avTreeBlosumMenuItem_actionPerformed()
\r
2483 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2486 void NewTreePanel(String type, String pwType, String title)
\r
2488 // are the sequences aligned?
\r
2489 if (!viewport.getAlignment().isAligned(false))
\r
2491 SequenceI current;
\r
2492 int Width = viewport.getAlignment().getWidth();
\r
2494 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2496 current = viewport.getAlignment().getSequenceAt(i);
\r
2498 if (current.getLength() < Width)
\r
2500 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2503 alignPanel.paintAlignment(true);
\r
2507 if ((viewport.getSelectionGroup() != null && viewport
\r
2508 .getSelectionGroup().getSize() > 1)
\r
2509 || (viewport.getSelectionGroup() == null && viewport.getAlignment()
\r
2510 .getHeight() > 1))
\r
2512 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
\r
2514 addTreeMenuItem(tp, title);
\r
2516 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
2520 void loadTree_actionPerformed()
\r
2522 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
2523 cap.setText("Paste your Newick tree file here.");
\r
2524 cap.setTreeImport();
\r
2525 Frame frame = new Frame();
\r
2527 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
2530 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
2532 TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
\r
2533 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
2534 addTreeMenuItem(tp, treeFile);
\r
2538 * sort the alignment using the given treePanel
\r
2540 * @param treePanel
\r
2541 * tree used to sort view
\r
2543 * string used for undo event name
\r
2545 public void sortByTree(TreePanel treePanel, String title)
\r
2547 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2549 .sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
2550 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2551 // HistoryItem.SORT));
\r
2552 addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
\r
2553 viewport.getAlignment()));
\r
2554 alignPanel.paintAlignment(true);
\r
2558 * Do any automatic reordering of the alignment and add the necessary bits to
\r
2559 * the menu structure for the new tree
\r
2561 * @param treePanel
\r
2564 protected void addTreeMenuItem(final TreePanel treePanel,
\r
2565 final String title)
\r
2567 final MenuItem item = new MenuItem(title);
\r
2568 sortByTreeMenu.add(item);
\r
2569 item.addActionListener(new java.awt.event.ActionListener()
\r
2572 public void actionPerformed(ActionEvent evt)
\r
2574 sortByTree(treePanel, title); // treePanel.getTitle());
\r
2578 treePanel.addWindowListener(new WindowAdapter()
\r
2581 public void windowOpened(WindowEvent e)
\r
2583 if (viewport.sortByTree)
\r
2585 sortByTree(treePanel, title);
\r
2587 super.windowOpened(e);
\r
2591 public void windowClosing(WindowEvent e)
\r
2593 sortByTreeMenu.remove(item);
\r
2597 public boolean sortBy(AlignmentOrder alorder, String undoname)
\r
2599 SequenceI[] oldOrder = viewport.getAlignment()
\r
2600 .getSequencesArray();
\r
2601 if (viewport.applet.debug)
\r
2603 System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");
\r
2605 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
\r
2606 if (undoname!=null)
\r
2608 addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.getAlignment()));
\r
2610 alignPanel.paintAlignment(true);
\r
2614 protected void documentation_actionPerformed()
\r
2616 alignPanel.av.applet.openJalviewHelpUrl();
\r
2619 protected void about_actionPerformed()
\r
2622 class AboutPanel extends Canvas
\r
2628 public AboutPanel(String version, String builddate)
\r
2630 this.version = version;
\r
2631 this.builddate = builddate;
\r
2635 public void paint(Graphics g)
\r
2637 g.setColor(Color.white);
\r
2638 g.fillRect(0, 0, getSize().width, getSize().height);
\r
2639 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2640 FontMetrics fm = g.getFontMetrics();
\r
2641 int fh = fm.getHeight();
\r
2643 g.setColor(Color.black);
\r
2644 // TODO: update this text for each release or centrally store it for
\r
2645 // lite and application
\r
2646 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
2647 g.drawString("JalviewLite - Release " + version, x, y += fh);
\r
2648 g.setFont(new Font("Helvetica", Font.BOLD, 12));
\r
2649 g.drawString("Build date: " + builddate, x, y += fh);
\r
2650 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2652 "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",
\r
2653 x, y += fh * 1.5);
\r
2654 g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
\r
2656 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
\r
2659 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
\r
2661 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
\r
2663 "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
\r
2666 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
\r
2668 g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
\r
2673 Frame frame = new Frame();
\r
2674 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
\r
2675 .getBuildDate()));
\r
2676 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
\r
2680 public void showURL(String url, String target)
\r
2682 if (viewport.applet == null)
\r
2684 System.out.println("Not running as applet - no browser available.");
\r
2688 viewport.applet.showURL(url, target);
\r
2692 // ////////////////////////////////////////////////////////////////////////////////
\r
2693 // JBuilder Graphics here
\r
2695 MenuBar alignFrameMenuBar = new MenuBar();
\r
2697 Menu fileMenu = new Menu("File");
\r
2699 MenuItem loadApplication = new MenuItem("View in Full Application");
\r
2701 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
\r
2703 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
\r
2705 MenuItem outputFeatures = new MenuItem("Export Features ...");
\r
2707 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
\r
2709 MenuItem closeMenuItem = new MenuItem("Close");
\r
2711 Menu editMenu = new Menu("Edit");
\r
2713 Menu viewMenu = new Menu("View");
\r
2715 Menu colourMenu = new Menu("Colour");
\r
2717 Menu calculateMenu = new Menu("Calculate");
\r
2719 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
2721 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
2723 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
2725 MenuItem remove2LeftMenuItem = new MenuItem();
\r
2727 MenuItem remove2RightMenuItem = new MenuItem();
\r
2729 MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
2731 MenuItem removeAllGapsMenuItem = new MenuItem();
\r
2733 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
2735 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
2737 MenuItem sortPairwiseMenuItem = new MenuItem();
\r
2739 MenuItem sortIDMenuItem = new MenuItem();
\r
2741 MenuItem sortLengthMenuItem = new MenuItem();
\r
2743 MenuItem sortGroupMenuItem = new MenuItem();
\r
2745 MenuItem removeRedundancyMenuItem = new MenuItem();
\r
2747 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
2749 MenuItem PCAMenuItem = new MenuItem();
\r
2751 MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
2753 MenuItem neighbourTreeMenuItem = new MenuItem();
\r
2755 BorderLayout borderLayout1 = new BorderLayout();
\r
2757 public Label statusBar = new Label();
\r
2759 Menu outputTextboxMenu = new Menu();
\r
2761 MenuItem clustalColour = new MenuItem();
\r
2763 MenuItem zappoColour = new MenuItem();
\r
2765 MenuItem taylorColour = new MenuItem();
\r
2767 MenuItem hydrophobicityColour = new MenuItem();
\r
2769 MenuItem helixColour = new MenuItem();
\r
2771 MenuItem strandColour = new MenuItem();
\r
2773 MenuItem turnColour = new MenuItem();
\r
2775 MenuItem buriedColour = new MenuItem();
\r
2777 MenuItem purinePyrimidineColour = new MenuItem();
\r
2778 MenuItem RNAHelixColour = new MenuItem();
\r
2780 MenuItem userDefinedColour = new MenuItem();
\r
2782 MenuItem PIDColour = new MenuItem();
\r
2784 MenuItem BLOSUM62Colour = new MenuItem();
\r
2786 MenuItem tcoffeeColour = new MenuItem();
\r
2788 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
2790 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
2792 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
2794 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
2796 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
\r
2798 MenuItem alProperties = new MenuItem("Alignment Properties...");
\r
2800 MenuItem overviewMenuItem = new MenuItem();
\r
2802 MenuItem undoMenuItem = new MenuItem();
\r
2804 MenuItem redoMenuItem = new MenuItem();
\r
2806 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
2808 MenuItem noColourmenuItem = new MenuItem();
\r
2810 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
2812 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
2814 MenuItem findMenuItem = new MenuItem();
\r
2816 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
2818 MenuItem nucleotideColour = new MenuItem();
\r
2820 MenuItem deleteGroups = new MenuItem();
\r
2822 MenuItem grpsFromSelection = new MenuItem();
\r
2824 MenuItem delete = new MenuItem();
\r
2826 MenuItem copy = new MenuItem();
\r
2828 MenuItem cut = new MenuItem();
\r
2830 Menu pasteMenu = new Menu();
\r
2832 MenuItem pasteNew = new MenuItem();
\r
2834 MenuItem pasteThis = new MenuItem();
\r
2836 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
2838 MenuItem font = new MenuItem();
\r
2840 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
2842 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
2844 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
2846 MenuItem modifyPID = new MenuItem();
\r
2848 MenuItem modifyConservation = new MenuItem();
\r
2850 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
\r
2851 "Autocalculate Consensus", true);
\r
2853 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
\r
2854 "Sort Alignment With New Tree", true);
\r
2856 Menu sortByTreeMenu = new Menu();
\r
2858 Menu sort = new Menu();
\r
2860 Menu calculate = new Menu();
\r
2862 MenuItem inputText = new MenuItem();
\r
2864 Menu helpMenu = new Menu();
\r
2866 MenuItem documentation = new MenuItem();
\r
2868 MenuItem about = new MenuItem();
\r
2870 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
2872 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
\r
2874 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
\r
2875 Menu autoAnnMenu=new Menu();
\r
2876 CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();
\r
2877 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
\r
2878 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
\r
2879 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
\r
2880 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
\r
2882 private void jbInit() throws Exception
\r
2885 setMenuBar(alignFrameMenuBar);
\r
2889 // dynamically fill save as menu with available formats
\r
2890 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
2893 item = new MenuItem(
\r
2894 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
2896 item.addActionListener(new java.awt.event.ActionListener()
\r
2899 public void actionPerformed(ActionEvent e)
\r
2901 outputText_actionPerformed(e);
\r
2905 outputTextboxMenu.add(item);
\r
2907 closeMenuItem.addActionListener(this);
\r
2908 loadApplication.addActionListener(this);
\r
2910 loadTree.addActionListener(this);
\r
2911 loadAnnotations.addActionListener(this);
\r
2912 outputFeatures.addActionListener(this);
\r
2913 outputAnnotations.addActionListener(this);
\r
2914 selectAllSequenceMenuItem.addActionListener(this);
\r
2915 deselectAllSequenceMenuItem.addActionListener(this);
\r
2916 invertSequenceMenuItem.addActionListener(this);
\r
2917 remove2LeftMenuItem.setLabel("Remove Left");
\r
2918 remove2LeftMenuItem.addActionListener(this);
\r
2919 remove2RightMenuItem.setLabel("Remove Right");
\r
2920 remove2RightMenuItem.addActionListener(this);
\r
2921 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
2922 removeGappedColumnMenuItem.addActionListener(this);
\r
2923 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
2924 removeAllGapsMenuItem.addActionListener(this);
\r
2925 viewBoxesMenuItem.setLabel("Boxes");
\r
2926 viewBoxesMenuItem.setState(true);
\r
2927 viewBoxesMenuItem.addItemListener(this);
\r
2928 viewTextMenuItem.setLabel("Text");
\r
2929 viewTextMenuItem.setState(true);
\r
2930 viewTextMenuItem.addItemListener(this);
\r
2931 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
2932 sortPairwiseMenuItem.addActionListener(this);
\r
2933 sortIDMenuItem.setLabel("by ID");
\r
2934 sortIDMenuItem.addActionListener(this);
\r
2935 sortLengthMenuItem.setLabel("by Length");
\r
2936 sortLengthMenuItem.addActionListener(this);
\r
2937 sortGroupMenuItem.setLabel("by Group");
\r
2938 sortGroupMenuItem.addActionListener(this);
\r
2939 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
2940 removeRedundancyMenuItem.addActionListener(this);
\r
2941 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
2942 pairwiseAlignmentMenuItem.addActionListener(this);
\r
2943 PCAMenuItem.setLabel("Principal Component Analysis");
\r
2944 PCAMenuItem.addActionListener(this);
\r
2945 averageDistanceTreeMenuItem
\r
2946 .setLabel("Average Distance Using % Identity");
\r
2947 averageDistanceTreeMenuItem.addActionListener(this);
\r
2948 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
2949 neighbourTreeMenuItem.addActionListener(this);
\r
2950 statusBar.setBackground(Color.white);
\r
2951 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
2952 statusBar.setText("Status bar");
\r
2953 outputTextboxMenu.setLabel("Output to Textbox");
\r
2954 clustalColour.setLabel("Clustalx");
\r
2956 clustalColour.addActionListener(this);
\r
2957 zappoColour.setLabel("Zappo");
\r
2958 zappoColour.addActionListener(this);
\r
2959 taylorColour.setLabel("Taylor");
\r
2960 taylorColour.addActionListener(this);
\r
2961 hydrophobicityColour.setLabel("Hydrophobicity");
\r
2962 hydrophobicityColour.addActionListener(this);
\r
2963 helixColour.setLabel("Helix Propensity");
\r
2964 helixColour.addActionListener(this);
\r
2965 strandColour.setLabel("Strand Propensity");
\r
2966 strandColour.addActionListener(this);
\r
2967 turnColour.setLabel("Turn Propensity");
\r
2968 turnColour.addActionListener(this);
\r
2969 buriedColour.setLabel("Buried Index");
\r
2970 buriedColour.addActionListener(this);
\r
2971 purinePyrimidineColour.setLabel("Purine/Pyrimidine");
\r
2972 purinePyrimidineColour.addActionListener(this);
\r
2973 RNAHelixColour.setLabel("by RNA Helices");
\r
2974 RNAHelixColour.addActionListener(this);
\r
2975 userDefinedColour.setLabel("User Defined...");
\r
2976 userDefinedColour.addActionListener(this);
\r
2977 PIDColour.setLabel("Percentage Identity");
\r
2978 PIDColour.addActionListener(this);
\r
2979 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
2980 BLOSUM62Colour.addActionListener(this);
\r
2981 tcoffeeColour.setLabel("T-Coffee Scores");
\r
2982 tcoffeeColour.setEnabled(false); // it will enabled only if a score file is provided
\r
2983 tcoffeeColour.addActionListener(this);
\r
2984 avDistanceTreeBlosumMenuItem .setLabel("Average Distance Using BLOSUM62");
\r
2985 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
2986 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
2987 njTreeBlosumMenuItem.addActionListener(this);
\r
2988 annotationPanelMenuItem.setLabel("Show Annotations");
\r
2989 annotationPanelMenuItem.addItemListener(this);
\r
2990 colourTextMenuItem.setLabel("Colour Text");
\r
2991 colourTextMenuItem.addItemListener(this);
\r
2992 displayNonconservedMenuItem.setLabel("Show nonconserved");
\r
2993 displayNonconservedMenuItem.addItemListener(this);
\r
2994 alProperties.addActionListener(this);
\r
2995 overviewMenuItem.setLabel("Overview Window");
\r
2996 overviewMenuItem.addActionListener(this);
\r
2997 undoMenuItem.setEnabled(false);
\r
2998 undoMenuItem.setLabel("Undo");
\r
2999 undoMenuItem.addActionListener(this);
\r
3000 redoMenuItem.setEnabled(false);
\r
3001 redoMenuItem.setLabel("Redo");
\r
3002 redoMenuItem.addActionListener(this);
\r
3003 conservationMenuItem.setLabel("by Conservation");
\r
3004 conservationMenuItem.addItemListener(this);
\r
3005 noColourmenuItem.setLabel("None");
\r
3006 noColourmenuItem.addActionListener(this);
\r
3007 wrapMenuItem.setLabel("Wrap");
\r
3008 wrapMenuItem.addItemListener(this);
\r
3009 renderGapsMenuItem.setLabel("Show Gaps");
\r
3010 renderGapsMenuItem.setState(true);
\r
3011 renderGapsMenuItem.addItemListener(this);
\r
3012 findMenuItem.setLabel("Find...");
\r
3013 findMenuItem.addActionListener(this);
\r
3014 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
3015 abovePIDThreshold.addItemListener(this);
\r
3016 nucleotideColour.setLabel("Nucleotide");
\r
3017 nucleotideColour.addActionListener(this);
\r
3018 deleteGroups.setLabel("Undefine Groups");
\r
3019 deleteGroups.addActionListener(this);
\r
3020 grpsFromSelection.setLabel("Make Groups for selection");
\r
3021 grpsFromSelection.addActionListener(this);
\r
3022 copy.setLabel("Copy");
\r
3023 copy.addActionListener(this);
\r
3024 cut.setLabel("Cut");
\r
3025 cut.addActionListener(this);
\r
3026 delete.setLabel("Delete");
\r
3027 delete.addActionListener(this);
\r
3028 pasteMenu.setLabel("Paste");
\r
3029 pasteNew.setLabel("To New Alignment");
\r
3030 pasteNew.addActionListener(this);
\r
3031 pasteThis.setLabel("Add To This Alignment");
\r
3032 pasteThis.addActionListener(this);
\r
3033 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
3034 applyToAllGroups.setState(true);
\r
3035 applyToAllGroups.addItemListener(this);
\r
3036 font.setLabel("Font...");
\r
3037 font.addActionListener(this);
\r
3038 scaleAbove.setLabel("Scale Above");
\r
3039 scaleAbove.setState(true);
\r
3040 scaleAbove.setEnabled(false);
\r
3041 scaleAbove.addItemListener(this);
\r
3042 scaleLeft.setEnabled(false);
\r
3043 scaleLeft.setState(true);
\r
3044 scaleLeft.setLabel("Scale Left");
\r
3045 scaleLeft.addItemListener(this);
\r
3046 scaleRight.setEnabled(false);
\r
3047 scaleRight.setState(true);
\r
3048 scaleRight.setLabel("Scale Right");
\r
3049 scaleRight.addItemListener(this);
\r
3050 modifyPID.setLabel("Modify Identity Threshold...");
\r
3051 modifyPID.addActionListener(this);
\r
3052 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
3053 modifyConservation.addActionListener(this);
\r
3054 sortByTreeMenu.setLabel("By Tree Order");
\r
3055 sort.setLabel("Sort");
\r
3056 calculate.setLabel("Calculate Tree");
\r
3057 autoCalculate.addItemListener(this);
\r
3058 sortByTree.addItemListener(this);
\r
3059 inputText.setLabel("Input from textbox");
\r
3060 inputText.addActionListener(this);
\r
3061 centreColumnLabelFlag.setLabel("Centre column labels");
\r
3062 centreColumnLabelFlag.addItemListener(this);
\r
3063 followMouseOverFlag.setLabel("Automatic Scrolling");
\r
3064 followMouseOverFlag.addItemListener(this);
\r
3065 helpMenu.setLabel("Help");
\r
3066 documentation.setLabel("Documentation");
\r
3067 documentation.addActionListener(this);
\r
3069 about.setLabel("About...");
\r
3070 about.addActionListener(this);
\r
3071 seqLimits.setState(true);
\r
3072 seqLimits.setLabel("Show Sequence Limits");
\r
3073 seqLimits.addItemListener(this);
\r
3074 featureSettings.setLabel("Feature Settings...");
\r
3075 featureSettings.addActionListener(this);
\r
3076 sequenceFeatures.setLabel("Sequence Features");
\r
3077 sequenceFeatures.addItemListener(this);
\r
3078 sequenceFeatures.setState(false);
\r
3079 annotationColour.setLabel("by Annotation...");
\r
3080 annotationColour.addActionListener(this);
\r
3081 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
3082 invertColSel.setLabel("Invert Column Selection");
\r
3083 menu1.setLabel("Show");
\r
3084 showColumns.setLabel("All Columns ");
\r
3085 showSeqs.setLabel("All Sequences");
\r
3086 menu2.setLabel("Hide");
\r
3087 hideColumns.setLabel("Selected Columns");
\r
3088 hideSequences.setLabel("Selected Sequences");
\r
3089 hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
\r
3090 hideAllSelection.setLabel("Selected Region");
\r
3091 showAllHidden.setLabel("All Sequences and Columns");
\r
3092 showGroupConsensus.setLabel("Group Consensus");
\r
3093 showGroupConservation.setLabel("Group Conservation");
\r
3094 showConsensusHistogram.setLabel("Show Consensus Histogram");
\r
3095 showSequenceLogo.setLabel("Show Consensus Logo");
\r
3096 applyAutoAnnotationSettings.setLabel("Apply to all groups");
\r
3097 applyAutoAnnotationSettings.setState(true);
\r
3098 autoAnnMenu.setLabel("Autocalculated Annotation");
\r
3100 invertColSel.addActionListener(this);
\r
3101 showColumns.addActionListener(this);
\r
3102 showSeqs.addActionListener(this);
\r
3103 hideColumns.addActionListener(this);
\r
3104 hideSequences.addActionListener(this);
\r
3105 hideAllButSelection.addActionListener(this);
\r
3106 hideAllSelection.addActionListener(this);
\r
3107 showAllHidden.addActionListener(this);
\r
3108 showGroupConsensus.addItemListener(this);
\r
3109 showGroupConservation.addItemListener(this);
\r
3110 showConsensusHistogram.addItemListener(this);
\r
3111 showSequenceLogo.addItemListener(this);
\r
3112 applyAutoAnnotationSettings.addItemListener(this);
\r
3113 formatMenu.setLabel("Format");
\r
3114 selectMenu.setLabel("Select");
\r
3115 newView.setLabel("New View");
\r
3116 newView.addActionListener(this);
\r
3117 alignFrameMenuBar.add(fileMenu);
\r
3118 alignFrameMenuBar.add(editMenu);
\r
3119 alignFrameMenuBar.add(selectMenu);
\r
3120 alignFrameMenuBar.add(viewMenu);
\r
3121 alignFrameMenuBar.add(formatMenu);
\r
3122 alignFrameMenuBar.add(colourMenu);
\r
3123 alignFrameMenuBar.add(calculateMenu);
\r
3124 alignFrameMenuBar.add(helpMenu);
\r
3126 fileMenu.add(inputText);
\r
3127 fileMenu.add(loadTree);
\r
3128 fileMenu.add(loadAnnotations);
\r
3130 fileMenu.addSeparator();
\r
3131 fileMenu.add(outputTextboxMenu);
\r
3132 fileMenu.add(outputFeatures);
\r
3133 fileMenu.add(outputAnnotations);
\r
3135 if (jalviewServletURL != null)
\r
3137 fileMenu.add(loadApplication);
\r
3140 fileMenu.addSeparator();
\r
3141 fileMenu.add(closeMenuItem);
\r
3143 editMenu.add(undoMenuItem);
\r
3144 editMenu.add(redoMenuItem);
\r
3145 editMenu.add(cut);
\r
3146 editMenu.add(copy);
\r
3147 editMenu.add(pasteMenu);
\r
3148 editMenu.add(delete);
\r
3149 editMenu.addSeparator();
\r
3150 editMenu.add(remove2LeftMenuItem);
\r
3151 editMenu.add(remove2RightMenuItem);
\r
3152 editMenu.add(removeGappedColumnMenuItem);
\r
3153 editMenu.add(removeAllGapsMenuItem);
\r
3154 editMenu.add(removeRedundancyMenuItem);
\r
3155 viewMenu.add(newView);
\r
3156 viewMenu.addSeparator();
\r
3157 viewMenu.add(menu1);
\r
3158 viewMenu.add(menu2);
\r
3159 viewMenu.addSeparator();
\r
3160 viewMenu.add(followMouseOverFlag);
\r
3161 viewMenu.add(annotationPanelMenuItem);
\r
3162 autoAnnMenu.add(applyAutoAnnotationSettings);
\r
3163 autoAnnMenu.add(showConsensusHistogram);
\r
3164 autoAnnMenu.add(showSequenceLogo);
\r
3165 autoAnnMenu.addSeparator();
\r
3166 autoAnnMenu.add(showGroupConservation);
\r
3167 autoAnnMenu.add(showGroupConsensus);
\r
3168 viewMenu.add(autoAnnMenu);
\r
3169 viewMenu.addSeparator();
\r
3170 viewMenu.add(sequenceFeatures);
\r
3171 viewMenu.add(featureSettings);
\r
3172 viewMenu.addSeparator();
\r
3173 viewMenu.add(alProperties);
\r
3174 viewMenu.addSeparator();
\r
3175 viewMenu.add(overviewMenuItem);
\r
3176 colourMenu.add(applyToAllGroups);
\r
3177 colourMenu.addSeparator();
\r
3178 colourMenu.add(noColourmenuItem);
\r
3179 colourMenu.add(clustalColour);
\r
3180 colourMenu.add(BLOSUM62Colour);
\r
3181 colourMenu.add(PIDColour);
\r
3182 colourMenu.add(zappoColour);
\r
3183 colourMenu.add(taylorColour);
\r
3184 colourMenu.add(hydrophobicityColour);
\r
3185 colourMenu.add(helixColour);
\r
3186 colourMenu.add(strandColour);
\r
3187 colourMenu.add(turnColour);
\r
3188 colourMenu.add(buriedColour);
\r
3189 colourMenu.add(nucleotideColour);
\r
3190 colourMenu.add(purinePyrimidineColour);
\r
3191 colourMenu.add(tcoffeeColour);
\r
3192 colourMenu.add(userDefinedColour);
\r
3193 colourMenu.addSeparator();
\r
3194 colourMenu.add(conservationMenuItem);
\r
3195 colourMenu.add(modifyConservation);
\r
3196 colourMenu.add(abovePIDThreshold);
\r
3197 colourMenu.add(modifyPID);
\r
3198 colourMenu.add(annotationColour);
\r
3199 colourMenu.add(RNAHelixColour);
\r
3200 calculateMenu.add(sort);
\r
3201 calculateMenu.add(calculate);
\r
3202 calculateMenu.addSeparator();
\r
3203 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
3204 calculateMenu.add(PCAMenuItem);
\r
3205 calculateMenu.add(autoCalculate);
\r
3206 calculateMenu.add(sortByTree);
\r
3207 this.add(statusBar, BorderLayout.SOUTH);
\r
3208 pasteMenu.add(pasteNew);
\r
3209 pasteMenu.add(pasteThis);
\r
3210 sort.add(sortIDMenuItem);
\r
3211 sort.add(sortLengthMenuItem);
\r
3212 sort.add(sortByTreeMenu);
\r
3213 sort.add(sortGroupMenuItem);
\r
3214 sort.add(sortPairwiseMenuItem);
\r
3215 calculate.add(averageDistanceTreeMenuItem);
\r
3216 calculate.add(neighbourTreeMenuItem);
\r
3217 calculate.add(avDistanceTreeBlosumMenuItem);
\r
3218 calculate.add(njTreeBlosumMenuItem);
\r
3219 helpMenu.add(documentation);
\r
3220 helpMenu.add(about);
\r
3221 menu1.add(showColumns);
\r
3222 menu1.add(showSeqs);
\r
3223 menu1.add(showAllHidden);
\r
3224 menu2.add(hideColumns);
\r
3225 menu2.add(hideSequences);
\r
3226 menu2.add(hideAllSelection);
\r
3227 menu2.add(hideAllButSelection);
\r
3228 formatMenu.add(font);
\r
3229 formatMenu.add(seqLimits);
\r
3230 formatMenu.add(wrapMenuItem);
\r
3231 formatMenu.add(scaleAbove);
\r
3232 formatMenu.add(scaleLeft);
\r
3233 formatMenu.add(scaleRight);
\r
3234 formatMenu.add(viewBoxesMenuItem);
\r
3235 formatMenu.add(viewTextMenuItem);
\r
3236 formatMenu.add(colourTextMenuItem);
\r
3237 formatMenu.add(displayNonconservedMenuItem);
\r
3238 formatMenu.add(renderGapsMenuItem);
\r
3239 formatMenu.add(centreColumnLabelFlag);
\r
3240 selectMenu.add(findMenuItem);
\r
3241 selectMenu.addSeparator();
\r
3242 selectMenu.add(selectAllSequenceMenuItem);
\r
3243 selectMenu.add(deselectAllSequenceMenuItem);
\r
3244 selectMenu.add(invertSequenceMenuItem);
\r
3245 selectMenu.add(invertColSel);
\r
3246 selectMenu.add(grpsFromSelection);
\r
3247 selectMenu.add(deleteGroups);
\r
3251 MenuItem featureSettings = new MenuItem();
\r
3253 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
3255 MenuItem annotationColour = new MenuItem();
\r
3257 MenuItem invertColSel = new MenuItem();
\r
3259 Menu menu1 = new Menu();
\r
3261 MenuItem showColumns = new MenuItem();
\r
3263 MenuItem showSeqs = new MenuItem();
\r
3265 Menu menu2 = new Menu();
\r
3267 MenuItem hideColumns = new MenuItem();
\r
3269 MenuItem hideSequences = new MenuItem();
\r
3271 MenuItem hideAllButSelection = new MenuItem();
\r
3273 MenuItem hideAllSelection = new MenuItem();
\r
3275 MenuItem showAllHidden = new MenuItem();
\r
3277 Menu formatMenu = new Menu();
\r
3279 Menu selectMenu = new Menu();
\r
3281 MenuItem newView = new MenuItem();
\r
3284 * Attach the alignFrame panels after embedding menus, if necessary. This used
\r
3285 * to be called setEmbedded, but is now creates the dropdown menus in a
\r
3286 * platform independent manner to avoid OSX/Mac menu appendage daftness.
\r
3288 * @param reallyEmbedded
\r
3289 * true to attach the view to the applet area on the page rather than
\r
3292 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
\r
3294 if (reallyEmbedded)
\r
3297 // Explicly build the embedded menu panel for the on-page applet
\r
3299 // view cannot be closed if its actually on the page
\r
3300 fileMenu.remove(closeMenuItem);
\r
3301 fileMenu.remove(3); // Remove Seperator
\r
3302 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
\r
3303 Font.PLAIN, 10, false); // use our own fonts.
\r
3304 // and actually add the components to the applet area
\r
3305 viewport.applet.setLayout(new BorderLayout());
\r
3306 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
\r
3307 viewport.applet.add(statusBar, BorderLayout.SOUTH);
\r
3308 alignPanel.setSize(viewport.applet.getSize().width,
\r
3309 viewport.applet.getSize().height - embeddedMenu.HEIGHT
\r
3310 - statusBar.HEIGHT);
\r
3311 viewport.applet.add(alignPanel, BorderLayout.CENTER);
\r
3312 final AlignFrame me = this;
\r
3313 viewport.applet.addFocusListener(new FocusListener()
\r
3317 public void focusLost(FocusEvent e)
\r
3319 if (me.viewport.applet.currentAlignFrame==me) {
\r
3320 me.viewport.applet.currentAlignFrame = null;
\r
3324 public void focusGained(FocusEvent e)
\r
3326 me.viewport.applet.currentAlignFrame = me;
\r
3329 viewport.applet.validate();
\r
3334 // test and embed menu bar if necessary.
\r
3336 if (embedMenuIfNeeded(alignPanel))
\r
3338 // adjust for status bar height too
\r
3339 alignPanel.setSize(getSize().width, getSize().height
\r
3340 - statusBar.HEIGHT);
\r
3342 add(statusBar, BorderLayout.SOUTH);
\r
3343 add(alignPanel, BorderLayout.CENTER);
\r
3344 // and register with the applet so it can pass external API calls to us
\r
3345 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
\r
3351 * create a new binding between structures in an existing jmol viewer instance
\r
3352 * and an alignpanel with sequences that have existing PDBFile entries. Note,
\r
3353 * this does not open a new Jmol window, or modify the display of the
\r
3354 * structures in the original jmol window. Note This method doesn't work
\r
3355 * without an additional javascript library to exchange messages between the
\r
3356 * distinct applets. See http://issues.jalview.org/browse/JAL-621
\r
3359 * JmolViewer instance
\r
3360 * @param sequenceIds
\r
3361 * - sequence Ids to search for associations
\r
3363 public SequenceStructureBinding addStructureViewInstance(
\r
3364 Object jmolviewer, String[] sequenceIds)
\r
3366 org.jmol.api.JmolViewer viewer = null;
\r
3369 viewer = (org.jmol.api.JmolViewer) jmolviewer;
\r
3370 } catch (ClassCastException ex)
\r
3372 System.err.println("Unsupported viewer object :"
\r
3373 + jmolviewer.getClass());
\r
3375 if (viewer == null)
\r
3377 System.err.println("Can't use this object as a structure viewer:"
\r
3378 + jmolviewer.getClass());
\r
3381 SequenceI[] seqs = null;
\r
3382 if (sequenceIds == null || sequenceIds.length == 0)
\r
3384 seqs = viewport.getAlignment().getSequencesArray();
\r
3388 Vector sqi = new Vector();
\r
3389 AlignmentI al = viewport.getAlignment();
\r
3390 for (int sid = 0; sid < sequenceIds.length; sid++)
\r
3392 SequenceI sq = al.findName(sequenceIds[sid]);
\r
3395 sqi.addElement(sq);
\r
3398 if (sqi.size() > 0)
\r
3400 seqs = new SequenceI[sqi.size()];
\r
3401 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
\r
3403 seqs[sid] = (SequenceI) sqi.elementAt(sid);
\r
3411 ExtJmol jmv = null;
\r
3412 // TODO: search for a jmv that involves viewer
\r
3414 { // create a new viewer/jalview binding.
\r
3415 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs});
\r
3421 * bind a pdb file to a sequence in the current view
\r
3423 * @param sequenceId
\r
3424 * - sequenceId within the dataset.
\r
3425 * @param pdbEntryString
\r
3426 * - the short name for the PDB file
\r
3428 * - pdb file - either a URL or a valid PDB file.
\r
3429 * @return true if binding was as success TODO: consider making an exception
\r
3430 * structure for indicating when PDB parsing or sequenceId location
\r
3433 public boolean addPdbFile(String sequenceId, String pdbEntryString,
\r
3436 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
\r
3437 boolean needtoadd = false;
\r
3438 if (toaddpdb != null)
\r
3440 Vector pdbe = toaddpdb.getPDBId();
\r
3441 PDBEntry pdbentry = null;
\r
3442 if (pdbe != null && pdbe.size() > 0)
\r
3444 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
\r
3446 pdbentry = (PDBEntry) pdbe.elementAt(pe);
\r
3447 if (!pdbentry.getId().equals(pdbEntryString)
\r
3448 && !pdbentry.getFile().equals(pdbFile))
\r
3458 if (pdbentry == null)
\r
3460 pdbentry = new PDBEntry();
\r
3461 pdbentry.setId(pdbEntryString);
\r
3462 pdbentry.setFile(pdbFile);
\r
3463 needtoadd = true; // add this new entry to sequence.
\r
3465 // resolve data source
\r
3466 // TODO: this code should be a refactored to an io package
\r
3467 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
\r
3468 if (protocol == null)
\r
3474 // make a note of the access mode and add
\r
3475 if (pdbentry.getProperty() == null)
\r
3477 pdbentry.setProperty(new Hashtable());
\r
3479 pdbentry.getProperty().put("protocol", protocol);
\r
3480 toaddpdb.addPDBId(pdbentry);
\r
3486 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
\r
3490 Vector sequences = new Vector();
\r
3491 for (int i = 0; i < seqs.length; i++)
\r
3493 if (seqs[i] != null)
\r
3495 sequences.addElement(new Object[]
\r
3496 { seqs[i], (chains != null) ? chains[i] : null });
\r
3499 seqs = new SequenceI[sequences.size()];
\r
3500 chains = new String[sequences.size()];
\r
3501 for (int i = 0, isize = sequences.size(); i < isize; i++)
\r
3503 Object[] oj = (Object[]) sequences.elementAt(i);
\r
3505 seqs[i] = (SequenceI) oj[0];
\r
3506 chains[i] = (String) oj[1];
\r
3509 return new Object[]
\r
3514 public void newStructureView(JalviewLite applet, PDBEntry pdb,
\r
3515 SequenceI[] seqs, String[] chains, String protocol)
\r
3517 // Scrub any null sequences from the array
\r
3518 Object[] sqch = cleanSeqChainArrays(seqs, chains);
\r
3519 seqs = (SequenceI[]) sqch[0];
\r
3520 chains = (String[]) sqch[1];
\r
3521 if (seqs == null || seqs.length == 0)
\r
3524 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
\r
3526 if (protocol == null || protocol.trim().length() == 0
\r
3527 || protocol.equals("null"))
\r
3529 protocol = (String) pdb.getProperty().get("protocol");
\r
3530 if (protocol == null)
\r
3532 System.err.println("Couldn't work out protocol to open structure: "
\r
3537 if (applet.useXtrnalSviewer)
\r
3539 // register the association(s) and quit, don't create any windows.
\r
3540 if (StructureSelectionManager.getStructureSelectionManager(applet).setMapping(seqs, chains, pdb.getFile(), protocol)==null) {
\r
3541 System.err.println("Failed to map "+pdb.getFile()+" ("+protocol+") to any sequences");
\r
3545 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
\r
3547 // can only do alignments with Jmol
\r
3548 // find the last jmol window assigned to this alignment
\r
3549 jalview.appletgui.AppletJmol ajm = null, tajm;
\r
3550 Vector jmols = applet
\r
3551 .getAppletWindow(jalview.appletgui.AppletJmol.class);
\r
3552 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
\r
3554 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
\r
3555 if (tajm.ap.alignFrame == this)
\r
3564 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
\r
3565 // try and add the pdb structure
\r
3570 // otherwise, create a new window
\r
3571 if (applet.jmolAvailable)
\r
3573 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
\r
3575 applet.lastFrameX += 40;
\r
3576 applet.lastFrameY += 40;
\r
3580 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
\r
3585 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
\r
3586 SequenceI[][] seqs, String[][] chains, String[] protocols)
\r
3588 // TODO Auto-generated method stub
\r
3589 System.err.println("Aligned Structure View: Not yet implemented.");
\r
3593 * modify the current selection, providing the user has not made a selection already.
\r
3594 * @param sel - sequences from this alignment
\r
3595 * @param csel - columns to be selected on the alignment
\r
3597 public void select(SequenceGroup sel, ColumnSelection csel)
\r
3599 alignPanel.seqPanel.selection(sel, csel, null);
\r
3602 public void scrollTo(int row, int column)
\r
3604 alignPanel.seqPanel.scrollTo(row, column);
\r
3606 public void scrollToRow(int row)
\r
3608 alignPanel.seqPanel.scrollToRow(row);
\r
3610 public void scrollToColumn(int column)
\r
3612 alignPanel.seqPanel.scrollToColumn(column);
\r
3615 * @return the alignments unique ID.
\r
3617 public String getSequenceSetId() {
\r
3618 return viewport.getSequenceSetId();
\r
3623 * Load the (T-Coffee) score file from the specified url
\r
3625 * @param source File/URL/T-COFFEE score file contents
\r
3626 * @throws IOException
\r
3627 * @return true if alignment was annotated with data from source
\r
3629 public boolean loadScoreFile( String source ) throws IOException {
\r
3631 TCoffeeScoreFile file = new TCoffeeScoreFile(source, AppletFormatAdapter.checkProtocol(source));
\r
3632 if( !file.isValid()) {
\r
3633 // TODO: raise dialog for gui
\r
3634 System.err.println("Problems parsing T-Coffee scores: "+file.getWarningMessage());
\r
3635 System.err.println("Origin was:\n"+source);
\r
3640 * check that the score matrix matches the alignment dimensions
\r
3643 if( (aln=viewport.getAlignment()) != null && (aln.getHeight() != file.getHeight() || aln.getWidth() != file.getWidth()) ) {
\r
3644 // TODO: raise a dialog box here rather than bomb out.
\r
3645 System.err.println("The scores matrix does not match the alignment dimensions");
\r
3649 // TODO add parameter to indicate if matching should be done
\r
3650 if (file.annotateAlignment(alignPanel.getAlignment(), false))
\r
3652 alignPanel.fontChanged();
\r
3653 tcoffeeColour.setEnabled(true);
\r
3654 // switch to this color
\r
3655 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
\r
3658 System.err.println("Problems resolving T-Coffee scores:");
\r
3659 if (file.getWarningMessage()!=null) {
\r
3660 System.err.println(file.getWarningMessage());
\r