2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
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3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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.AlignmentSorter;
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21 import jalview.analysis.Conservation;
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22 import jalview.api.SequenceStructureBinding;
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23 import jalview.bin.JalviewLite;
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24 import jalview.commands.CommandI;
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25 import jalview.commands.EditCommand;
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26 import jalview.commands.OrderCommand;
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27 import jalview.commands.RemoveGapColCommand;
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28 import jalview.commands.RemoveGapsCommand;
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29 import jalview.commands.SlideSequencesCommand;
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30 import jalview.commands.TrimRegionCommand;
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31 import jalview.datamodel.Alignment;
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32 import jalview.datamodel.AlignmentI;
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33 import jalview.datamodel.AlignmentOrder;
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34 import jalview.datamodel.ColumnSelection;
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35 import jalview.datamodel.PDBEntry;
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36 import jalview.datamodel.Sequence;
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37 import jalview.datamodel.SequenceCollectionI;
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38 import jalview.datamodel.SequenceGroup;
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39 import jalview.datamodel.SequenceI;
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40 import jalview.io.AnnotationFile;
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41 import jalview.io.AppletFormatAdapter;
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42 import jalview.io.FeaturesFile;
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43 import jalview.io.TCoffeeScoreFile;
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44 import jalview.schemes.Blosum62ColourScheme;
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45 import jalview.schemes.BuriedColourScheme;
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46 import jalview.schemes.ClustalxColourScheme;
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47 import jalview.schemes.ColourSchemeI;
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48 import jalview.schemes.HelixColourScheme;
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49 import jalview.schemes.HydrophobicColourScheme;
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50 import jalview.schemes.NucleotideColourScheme;
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51 import jalview.schemes.PIDColourScheme;
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52 import jalview.schemes.PurinePyrimidineColourScheme;
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53 import jalview.schemes.RNAHelicesColourChooser;
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54 import jalview.schemes.RNAInteractionColourScheme;
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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.net.URL;
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87 import java.net.URLEncoder;
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88 import java.util.Enumeration;
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89 import java.util.Hashtable;
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90 import java.util.List;
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91 import java.util.StringTokenizer;
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92 import java.util.Vector;
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94 public class AlignFrame extends EmbmenuFrame implements ActionListener,
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95 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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107 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
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108 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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136 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
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138 seqLimits.setState(viewport.showJVSuffix);
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140 if (applet != null)
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142 String param = applet.getParameter("sortBy");
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145 if (param.equalsIgnoreCase("Id"))
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147 sortIDMenuItem_actionPerformed();
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149 else if (param.equalsIgnoreCase("Pairwise Identity"))
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151 sortPairwiseMenuItem_actionPerformed();
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153 else if (param.equalsIgnoreCase("Length"))
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155 sortLengthMenuItem_actionPerformed();
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159 param = applet.getParameter("wrap");
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162 if (param.equalsIgnoreCase("true"))
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164 wrapMenuItem.setState(true);
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165 wrapMenuItem_actionPerformed();
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168 param = applet.getParameter("centrecolumnlabels");
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171 centreColumnLabelFlag.setState(true);
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172 centreColumnLabelFlag_stateChanged();
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176 param = applet.getParameter("windowWidth");
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179 int width = Integer.parseInt(param);
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180 DEFAULT_WIDTH = width;
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182 param = applet.getParameter("windowHeight");
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185 int height = Integer.parseInt(param);
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186 DEFAULT_HEIGHT = height;
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188 } catch (Exception ex)
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193 if (viewport.getAlignment().isNucleotide())
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195 viewport.updateStrucConsensus(alignPanel);
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196 if (viewport.getAlignment().hasRNAStructure())
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198 RNAHelixColour.setEnabled(true);
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202 RNAHelixColour.setEnabled(false);
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207 RNAHelixColour.setEnabled(false);
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208 purinePyrimidineColour.setEnabled(false);
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211 // Some JVMS send keyevents to Top frame or lowest panel,
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212 // Havent worked out why yet. So add to both this frame and seqCanvas for
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214 this.addKeyListener(this);
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215 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
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216 alignPanel.idPanel.idCanvas.addKeyListener(this);
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217 alignPanel.scalePanel.addKeyListener(this);
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218 alignPanel.annotationPanel.addKeyListener(this);
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219 alignPanel.annotationPanelHolder.addKeyListener(this);
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220 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
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221 alignPanel.alabels.addKeyListener(this);
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222 createAlignFrameWindow(embedded, title);
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225 alignPanel.adjustAnnotationHeight();
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226 alignPanel.paintAlignment(true);
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229 public AlignViewport getAlignViewport()
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234 public SeqCanvas getSeqcanvas()
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236 return alignPanel.seqPanel.seqCanvas;
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240 * Load a features file onto the alignment
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243 * file URL, content, or other resolvable path
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245 * is protocol for accessing data referred to by file
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248 public boolean parseFeaturesFile(String file, String type)
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250 return parseFeaturesFile(file, type, true);
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254 * Load a features file onto the alignment
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257 * file URL, content, or other resolvable path
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259 * is protocol for accessing data referred to by file
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260 * @param autoenabledisplay
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261 * when true, display features flag will be automatically enabled if
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262 * features are loaded
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263 * @return true if data parsed as a features file
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265 public boolean parseFeaturesFile(String file, String type,
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266 boolean autoenabledisplay)
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268 // TODO: test if importing a features file onto an alignment which already
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269 // has features with links overwrites the original links.
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271 Hashtable featureLinks = new Hashtable();
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272 boolean featuresFile = false;
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275 featuresFile = new jalview.io.FeaturesFile(file, type)
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276 .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
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277 .getFeatureRenderer().featureColours, featureLinks,
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278 true, viewport.applet.getDefaultParameter(
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279 "relaxedidmatch", false));
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280 } catch (Exception ex)
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282 ex.printStackTrace();
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287 if (featureLinks.size() > 0)
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289 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
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291 if (autoenabledisplay)
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293 viewport.showSequenceFeatures = true;
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294 sequenceFeatures.setState(true);
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296 if (viewport.featureSettings != null)
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298 viewport.featureSettings.refreshTable();
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300 alignPanel.paintAlignment(true);
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301 statusBar.setText("Successfully added features to alignment.");
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303 return featuresFile;
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307 public void keyPressed(KeyEvent evt)
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309 if (viewport.cursorMode
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310 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
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311 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
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312 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
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313 && Character.isDigit(evt.getKeyChar()))
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314 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
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316 switch (evt.getKeyCode())
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318 case 27: // escape key
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319 deselectAllSequenceMenuItem_actionPerformed();
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321 alignPanel.alabels.cancelDrag();
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323 case KeyEvent.VK_X:
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324 if (evt.isControlDown() || evt.isMetaDown())
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326 cut_actionPerformed();
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329 case KeyEvent.VK_C:
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330 if (viewport.cursorMode && !evt.isControlDown())
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332 alignPanel.seqPanel.setCursorColumn();
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334 if (evt.isControlDown() || evt.isMetaDown())
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336 copy_actionPerformed();
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339 case KeyEvent.VK_V:
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340 if (evt.isControlDown())
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342 paste(evt.isShiftDown());
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345 case KeyEvent.VK_A:
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346 if (evt.isControlDown() || evt.isMetaDown())
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348 selectAllSequenceMenuItem_actionPerformed();
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351 case KeyEvent.VK_DOWN:
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352 if (viewport.cursorMode)
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354 alignPanel.seqPanel.moveCursor(0, 1);
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358 moveSelectedSequences(false);
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362 case KeyEvent.VK_UP:
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363 if (viewport.cursorMode)
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365 alignPanel.seqPanel.moveCursor(0, -1);
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369 moveSelectedSequences(true);
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373 case KeyEvent.VK_LEFT:
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374 if (evt.isAltDown() || !viewport.cursorMode)
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375 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
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377 alignPanel.seqPanel.moveCursor(-1, 0);
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380 case KeyEvent.VK_RIGHT:
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381 if (evt.isAltDown() || !viewport.cursorMode)
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382 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
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384 alignPanel.seqPanel.moveCursor(1, 0);
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387 case KeyEvent.VK_SPACE:
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388 if (viewport.cursorMode)
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390 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
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391 || evt.isShiftDown() || evt.isAltDown());
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395 case KeyEvent.VK_DELETE:
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396 case KeyEvent.VK_BACK_SPACE:
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397 if (viewport.cursorMode)
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399 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
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400 || evt.isShiftDown() || evt.isAltDown());
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404 cut_actionPerformed();
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405 alignPanel.seqPanel.seqCanvas.repaint();
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409 case KeyEvent.VK_S:
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410 if (viewport.cursorMode)
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412 alignPanel.seqPanel.setCursorRow();
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415 case KeyEvent.VK_P:
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416 if (viewport.cursorMode)
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418 alignPanel.seqPanel.setCursorPosition();
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422 case KeyEvent.VK_ENTER:
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423 case KeyEvent.VK_COMMA:
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424 if (viewport.cursorMode)
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426 alignPanel.seqPanel.setCursorRowAndColumn();
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430 case KeyEvent.VK_Q:
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431 if (viewport.cursorMode)
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433 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
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436 case KeyEvent.VK_M:
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437 if (viewport.cursorMode)
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439 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
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443 case KeyEvent.VK_F2:
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444 viewport.cursorMode = !viewport.cursorMode;
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445 statusBar.setText("Keyboard editing mode is "
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446 + (viewport.cursorMode ? "on" : "off"));
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447 if (viewport.cursorMode)
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449 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
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450 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
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454 case KeyEvent.VK_F:
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455 if (evt.isControlDown())
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457 findMenuItem_actionPerformed();
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461 case KeyEvent.VK_H:
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463 boolean toggleSeqs = !evt.isControlDown();
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464 boolean toggleCols = !evt.isShiftDown();
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465 toggleHiddenRegions(toggleSeqs, toggleCols);
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469 case KeyEvent.VK_PAGE_UP:
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470 if (viewport.wrapAlignment)
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472 alignPanel.scrollUp(true);
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476 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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477 - viewport.endSeq + viewport.startSeq);
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481 case KeyEvent.VK_PAGE_DOWN:
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482 if (viewport.wrapAlignment)
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484 alignPanel.scrollUp(false);
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488 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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489 + viewport.endSeq - viewport.startSeq);
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493 case KeyEvent.VK_Z:
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494 if (evt.isControlDown())
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496 undoMenuItem_actionPerformed();
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500 case KeyEvent.VK_Y:
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501 if (evt.isControlDown())
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503 redoMenuItem_actionPerformed();
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507 case KeyEvent.VK_L:
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508 if (evt.isControlDown())
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510 trimAlignment(true);
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514 case KeyEvent.VK_R:
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515 if (evt.isControlDown())
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517 trimAlignment(false);
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521 case KeyEvent.VK_E:
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522 if (evt.isControlDown())
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524 if (evt.isShiftDown())
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526 this.removeAllGapsMenuItem_actionPerformed();
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530 removeGappedColumnMenuItem_actionPerformed();
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534 case KeyEvent.VK_I:
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535 if (evt.isControlDown())
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537 if (evt.isAltDown())
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539 invertColSel_actionPerformed();
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543 invertSequenceMenuItem_actionPerformed();
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548 case KeyEvent.VK_U:
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549 if (evt.isControlDown())
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551 this.deleteGroups_actionPerformed();
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555 case KeyEvent.VK_T:
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556 if (evt.isControlDown())
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563 alignPanel.paintAlignment(true);
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567 * called by key handler and the hide all/show all menu items
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569 * @param toggleSeqs
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570 * @param toggleCols
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572 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
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574 boolean hide = false;
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575 SequenceGroup sg = viewport.getSelectionGroup();
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576 if (!toggleSeqs && !toggleCols)
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578 // Hide everything by the current selection - this is a hack - we do the
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579 // invert and then hide
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580 // first check that there will be visible columns after the invert.
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581 if ((viewport.getColumnSelection() != null
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582 && viewport.getColumnSelection().getSelected() != null && viewport
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583 .getColumnSelection().getSelected().size() > 0)
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584 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
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587 // now invert the sequence set, if required - empty selection implies
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588 // that no hiding is required.
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591 invertSequenceMenuItem_actionPerformed();
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592 sg = viewport.getSelectionGroup();
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596 viewport.expandColSelection(sg, true);
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597 // finally invert the column selection and get the new sequence
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598 // selection and indicate it should be hidden.
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599 invertColSel_actionPerformed();
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606 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
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609 viewport.hideAllSelectedSeqs();
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611 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
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614 viewport.showAllHiddenSeqs();
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620 if (viewport.getColumnSelection().getSelected().size() > 0)
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622 viewport.hideSelectedColumns();
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625 viewport.setSelectionGroup(sg);
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630 viewport.showAllHiddenColumns();
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636 public void keyReleased(KeyEvent evt)
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641 public void keyTyped(KeyEvent evt)
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646 public void itemStateChanged(ItemEvent evt)
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648 if (evt.getSource() == displayNonconservedMenuItem)
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650 displayNonconservedMenuItem_actionPerformed();
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652 else if (evt.getSource() == colourTextMenuItem)
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654 colourTextMenuItem_actionPerformed();
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656 else if (evt.getSource() == wrapMenuItem)
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658 wrapMenuItem_actionPerformed();
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660 else if (evt.getSource() == scaleAbove)
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662 viewport.setScaleAboveWrapped(scaleAbove.getState());
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664 else if (evt.getSource() == scaleLeft)
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666 viewport.setScaleLeftWrapped(scaleLeft.getState());
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668 else if (evt.getSource() == scaleRight)
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670 viewport.setScaleRightWrapped(scaleRight.getState());
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672 else if (evt.getSource() == seqLimits)
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674 seqLimits_itemStateChanged();
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676 else if (evt.getSource() == viewBoxesMenuItem)
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678 viewport.setShowBoxes(viewBoxesMenuItem.getState());
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680 else if (evt.getSource() == viewTextMenuItem)
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682 viewport.setShowText(viewTextMenuItem.getState());
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684 else if (evt.getSource() == renderGapsMenuItem)
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686 viewport.setRenderGaps(renderGapsMenuItem.getState());
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688 else if (evt.getSource() == annotationPanelMenuItem)
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690 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
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691 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
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693 else if (evt.getSource() == sequenceFeatures)
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695 viewport.showSequenceFeatures(sequenceFeatures.getState());
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696 alignPanel.seqPanel.seqCanvas.repaint();
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698 else if (evt.getSource() == conservationMenuItem)
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700 conservationMenuItem_actionPerformed();
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702 else if (evt.getSource() == abovePIDThreshold)
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704 abovePIDThreshold_actionPerformed();
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706 else if (evt.getSource() == applyToAllGroups)
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708 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
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710 else if (evt.getSource() == autoCalculate)
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712 viewport.autoCalculateConsensus = autoCalculate.getState();
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714 else if (evt.getSource() == sortByTree)
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716 viewport.sortByTree = sortByTree.getState();
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718 else if (evt.getSource() == this.centreColumnLabelFlag)
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720 centreColumnLabelFlag_stateChanged();
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722 else if (evt.getSource() == this.followMouseOverFlag)
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724 mouseOverFlag_stateChanged();
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726 else if (evt.getSource() == showGroupConsensus)
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728 showGroupConsensus_actionPerformed();
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730 else if (evt.getSource() == showGroupConservation)
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732 showGroupConservation_actionPerformed();
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734 else if (evt.getSource() == showSequenceLogo)
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736 showSequenceLogo_actionPerformed();
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738 else if (evt.getSource() == normSequenceLogo)
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740 normSequenceLogo_actionPerformed();
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742 else if (evt.getSource() == showConsensusHistogram)
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744 showConsensusHistogram_actionPerformed();
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746 else if (evt.getSource() == applyAutoAnnotationSettings)
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748 applyAutoAnnotationSettings_actionPerformed();
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750 alignPanel.paintAlignment(true);
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753 private void mouseOverFlag_stateChanged()
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755 viewport.followHighlight = followMouseOverFlag.getState();
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756 // TODO: could kick the scrollTo mechanism to reset view for current
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760 private void centreColumnLabelFlag_stateChanged()
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762 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
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763 this.alignPanel.annotationPanel.repaint();
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767 public void actionPerformed(ActionEvent evt)
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769 Object source = evt.getSource();
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771 if (source == inputText)
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773 inputText_actionPerformed();
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775 else if (source == loadTree)
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777 loadTree_actionPerformed();
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779 else if (source == loadApplication)
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781 launchFullApplication();
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783 else if (source == loadAnnotations)
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787 else if (source == outputAnnotations)
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789 outputAnnotations(true);
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791 else if (source == outputFeatures)
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793 outputFeatures(true, "Jalview");
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795 else if (source == closeMenuItem)
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797 closeMenuItem_actionPerformed();
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799 else if (source == copy)
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801 copy_actionPerformed();
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803 else if (source == undoMenuItem)
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805 undoMenuItem_actionPerformed();
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807 else if (source == redoMenuItem)
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809 redoMenuItem_actionPerformed();
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811 else if (source == inputText)
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813 inputText_actionPerformed();
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815 else if (source == closeMenuItem)
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817 closeMenuItem_actionPerformed();
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819 else if (source == undoMenuItem)
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821 undoMenuItem_actionPerformed();
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823 else if (source == redoMenuItem)
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825 redoMenuItem_actionPerformed();
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827 else if (source == copy)
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829 copy_actionPerformed();
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831 else if (source == pasteNew)
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833 pasteNew_actionPerformed();
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835 else if (source == pasteThis)
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837 pasteThis_actionPerformed();
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839 else if (source == cut)
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841 cut_actionPerformed();
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843 else if (source == delete)
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845 delete_actionPerformed();
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847 else if (source == grpsFromSelection)
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849 makeGrpsFromSelection_actionPerformed();
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851 else if (source == deleteGroups)
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853 deleteGroups_actionPerformed();
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855 else if (source == selectAllSequenceMenuItem)
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857 selectAllSequenceMenuItem_actionPerformed();
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859 else if (source == deselectAllSequenceMenuItem)
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861 deselectAllSequenceMenuItem_actionPerformed();
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863 else if (source == invertSequenceMenuItem)
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865 invertSequenceMenuItem_actionPerformed();
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867 else if (source == invertColSel)
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869 viewport.invertColumnSelection();
\r
870 alignPanel.paintAlignment(true);
\r
872 else if (source == remove2LeftMenuItem)
\r
874 trimAlignment(true);
\r
876 else if (source == remove2RightMenuItem)
\r
878 trimAlignment(false);
\r
880 else if (source == removeGappedColumnMenuItem)
\r
882 removeGappedColumnMenuItem_actionPerformed();
\r
884 else if (source == removeAllGapsMenuItem)
\r
886 removeAllGapsMenuItem_actionPerformed();
\r
888 else if (source == findMenuItem)
\r
890 findMenuItem_actionPerformed();
\r
892 else if (source == font)
\r
894 new FontChooser(alignPanel);
\r
896 else if (source == newView)
\r
900 else if (source == showColumns)
\r
902 viewport.showAllHiddenColumns();
\r
903 alignPanel.paintAlignment(true);
\r
905 else if (source == showSeqs)
\r
907 viewport.showAllHiddenSeqs();
\r
908 alignPanel.paintAlignment(true);
\r
910 else if (source == hideColumns)
\r
912 viewport.hideSelectedColumns();
\r
913 alignPanel.paintAlignment(true);
\r
915 else if (source == hideSequences
\r
916 && viewport.getSelectionGroup() != null)
\r
918 viewport.hideAllSelectedSeqs();
\r
919 alignPanel.paintAlignment(true);
\r
921 else if (source == hideAllButSelection)
\r
923 toggleHiddenRegions(false, false);
\r
924 alignPanel.paintAlignment(true);
\r
926 else if (source == hideAllSelection)
\r
928 SequenceGroup sg = viewport.getSelectionGroup();
\r
929 viewport.expandColSelection(sg, false);
\r
930 viewport.hideAllSelectedSeqs();
\r
931 viewport.hideSelectedColumns();
\r
932 alignPanel.paintAlignment(true);
\r
934 else if (source == showAllHidden)
\r
936 viewport.showAllHiddenColumns();
\r
937 viewport.showAllHiddenSeqs();
\r
938 alignPanel.paintAlignment(true);
\r
940 else if (source == showGroupConsensus)
\r
942 showGroupConsensus_actionPerformed();
\r
944 else if (source == showGroupConservation)
\r
946 showGroupConservation_actionPerformed();
\r
948 else if (source == showSequenceLogo)
\r
950 showSequenceLogo_actionPerformed();
\r
952 else if (source == normSequenceLogo)
\r
954 normSequenceLogo_actionPerformed();
\r
956 else if (source == showConsensusHistogram)
\r
958 showConsensusHistogram_actionPerformed();
\r
960 else if (source == applyAutoAnnotationSettings)
\r
962 applyAutoAnnotationSettings_actionPerformed();
\r
964 else if (source == featureSettings)
\r
966 new FeatureSettings(alignPanel);
\r
968 else if (source == alProperties)
\r
970 StringBuffer contents = new jalview.io.AlignmentProperties(
\r
971 viewport.getAlignment()).formatAsString();
\r
972 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
973 cap.setText(contents.toString());
\r
974 Frame frame = new Frame();
\r
976 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
\r
977 + getTitle(), 400, 250);
\r
979 else if (source == overviewMenuItem)
\r
981 overviewMenuItem_actionPerformed();
\r
983 else if (source == noColourmenuItem)
\r
985 changeColour(null);
\r
987 else if (source == clustalColour)
\r
989 abovePIDThreshold.setState(false);
\r
990 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
\r
992 else if (source == zappoColour)
\r
994 changeColour(new ZappoColourScheme());
\r
996 else if (source == taylorColour)
\r
998 changeColour(new TaylorColourScheme());
\r
1000 else if (source == hydrophobicityColour)
\r
1002 changeColour(new HydrophobicColourScheme());
\r
1004 else if (source == helixColour)
\r
1006 changeColour(new HelixColourScheme());
\r
1008 else if (source == strandColour)
\r
1010 changeColour(new StrandColourScheme());
\r
1012 else if (source == turnColour)
\r
1014 changeColour(new TurnColourScheme());
\r
1016 else if (source == buriedColour)
\r
1018 changeColour(new BuriedColourScheme());
\r
1020 else if (source == nucleotideColour)
\r
1022 changeColour(new NucleotideColourScheme());
\r
1024 else if (source == purinePyrimidineColour)
\r
1026 changeColour(new PurinePyrimidineColourScheme());
\r
1029 else if (source == RNAHelixColour)
\r
1031 new RNAHelicesColourChooser(viewport, alignPanel);
\r
1033 else if (source == modifyPID)
\r
1035 modifyPID_actionPerformed();
\r
1037 else if (source == modifyConservation)
\r
1039 modifyConservation_actionPerformed();
\r
1041 else if (source == userDefinedColour)
\r
1043 new UserDefinedColours(alignPanel, null);
\r
1045 else if (source == PIDColour)
\r
1047 changeColour(new PIDColourScheme());
\r
1049 else if (source == BLOSUM62Colour)
\r
1051 changeColour(new Blosum62ColourScheme());
\r
1053 else if (source == tcoffeeColour)
\r
1055 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
\r
1057 else if (source == annotationColour)
\r
1059 new AnnotationColourChooser(viewport, alignPanel);
\r
1061 else if (source == sortPairwiseMenuItem)
\r
1063 sortPairwiseMenuItem_actionPerformed();
\r
1065 else if (source == sortIDMenuItem)
\r
1067 sortIDMenuItem_actionPerformed();
\r
1069 else if (source == sortLengthMenuItem)
\r
1071 sortLengthMenuItem_actionPerformed();
\r
1073 else if (source == sortGroupMenuItem)
\r
1075 sortGroupMenuItem_actionPerformed();
\r
1077 else if (source == removeRedundancyMenuItem)
\r
1079 removeRedundancyMenuItem_actionPerformed();
\r
1081 else if (source == pairwiseAlignmentMenuItem)
\r
1083 pairwiseAlignmentMenuItem_actionPerformed();
\r
1085 else if (source == PCAMenuItem)
\r
1087 PCAMenuItem_actionPerformed();
\r
1089 else if (source == averageDistanceTreeMenuItem)
\r
1091 averageDistanceTreeMenuItem_actionPerformed();
\r
1093 else if (source == neighbourTreeMenuItem)
\r
1095 neighbourTreeMenuItem_actionPerformed();
\r
1097 else if (source == njTreeBlosumMenuItem)
\r
1099 njTreeBlosumMenuItem_actionPerformed();
\r
1101 else if (source == avDistanceTreeBlosumMenuItem)
\r
1103 avTreeBlosumMenuItem_actionPerformed();
\r
1105 else if (source == documentation)
\r
1107 documentation_actionPerformed();
\r
1109 else if (source == about)
\r
1111 about_actionPerformed();
\r
1116 public void inputText_actionPerformed()
\r
1118 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1119 Frame frame = new Frame();
\r
1121 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
\r
1124 protected void outputText_actionPerformed(ActionEvent e)
\r
1126 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1127 Frame frame = new Frame();
\r
1129 jalview.bin.JalviewLite.addFrame(frame,
\r
1130 "Alignment output - " + e.getActionCommand(), 600, 500);
\r
1131 cap.setText(new AppletFormatAdapter().formatSequences(
\r
1132 e.getActionCommand(), viewport.getAlignment(),
\r
1133 viewport.showJVSuffix));
\r
1136 public void loadAnnotations()
\r
1138 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1139 cap.setText("Paste your features / annotations / T-coffee score file here.");
\r
1140 cap.setAnnotationImport();
\r
1141 Frame frame = new Frame();
\r
1143 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
\r
1147 public String outputAnnotations(boolean displayTextbox)
\r
1149 String annotation = new AnnotationFile().printAnnotations(
\r
1150 viewport.showAnnotation ? viewport.getAlignment()
\r
1151 .getAlignmentAnnotation() : null, viewport
\r
1152 .getAlignment().getGroups(), ((Alignment) viewport
\r
1153 .getAlignment()).alignmentProperties);
\r
1155 if (displayTextbox)
\r
1157 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
1158 Frame frame = new Frame();
\r
1160 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
\r
1161 cap.setText(annotation);
\r
1164 return annotation;
\r
1167 private Hashtable getDisplayedFeatureCols()
\r
1169 if (alignPanel.getFeatureRenderer() != null
\r
1170 && viewport.featuresDisplayed != null)
\r
1172 FeatureRenderer fr = alignPanel.getFeatureRenderer();
\r
1173 Hashtable fcols = new Hashtable();
\r
1174 Enumeration en = viewport.featuresDisplayed.keys();
\r
1175 while (en.hasMoreElements())
\r
1177 Object col = en.nextElement();
\r
1178 fcols.put(col, fr.featureColours.get(col));
\r
1185 public String outputFeatures(boolean displayTextbox, String format)
\r
1188 if (format.equalsIgnoreCase("Jalview"))
\r
1190 features = new FeaturesFile().printJalviewFormat(viewport
\r
1191 .getAlignment().getSequencesArray(),
\r
1192 getDisplayedFeatureCols());
\r
1196 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
\r
1197 .getSequencesArray(), getDisplayedFeatureCols());
\r
1200 if (displayTextbox)
\r
1202 boolean frimport = false;
\r
1203 if (features == null || features.equals("No Features Visible"))
\r
1205 features = "# No features visible - paste some and import them here.";
\r
1209 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
\r
1212 cap.setAnnotationImport();
\r
1214 Frame frame = new Frame();
\r
1216 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
\r
1217 cap.setText(features);
\r
1221 if (features == null)
\r
1228 void launchFullApplication()
\r
1230 StringBuffer url = new StringBuffer(jalviewServletURL);
\r
1232 url.append("?open="
\r
1233 + appendProtocol(viewport.applet.getParameter("file")));
\r
1235 if (viewport.applet.getParameter("features") != null)
\r
1237 url.append("&features=");
\r
1238 url.append(appendProtocol(viewport.applet.getParameter("features")));
\r
1241 if (viewport.applet.getParameter("annotations") != null)
\r
1243 url.append("&annotations=");
\r
1244 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
\r
1247 if (viewport.applet.getParameter("jnetfile") != null)
\r
1249 url.append("&annotations=");
\r
1250 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
\r
1253 if (viewport.applet.getParameter("defaultColour") != null)
\r
1255 url.append("&colour="
\r
1256 + removeWhiteSpace(viewport.applet
\r
1257 .getParameter("defaultColour")));
\r
1260 if (viewport.applet.getParameter("userDefinedColour") != null)
\r
1262 url.append("&colour="
\r
1263 + removeWhiteSpace(viewport.applet
\r
1264 .getParameter("userDefinedColour")));
\r
1266 if (viewport.applet.getParameter("tree") != null)
\r
1268 url.append("&tree="
\r
1269 + appendProtocol(viewport.applet.getParameter("tree")));
\r
1271 if (viewport.applet.getParameter("treeFile") != null)
\r
1273 url.append("&tree="
\r
1274 + appendProtocol(viewport.applet.getParameter("treeFile")));
\r
1277 showURL(url.toString(), "FULL_APP");
\r
1280 String removeWhiteSpace(String colour)
\r
1282 StringBuffer sb = new StringBuffer();
\r
1283 for (int i = 0; i < colour.length(); i++)
\r
1285 if (Character.isWhitespace(colour.charAt(i)))
\r
1291 sb.append(colour.charAt(i));
\r
1295 return sb.toString();
\r
1298 String appendProtocol(String url)
\r
1303 url = URLEncoder.encode(url);
\r
1306 * When we finally deprecate 1.1 compatibility, we can start to use
\r
1307 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
\r
1308 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
\r
1309 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
\r
1310 * ex.printStackTrace(); }
\r
1312 catch (java.net.MalformedURLException ex)
\r
1314 url = viewport.applet.getCodeBase() + url;
\r
1319 public void closeMenuItem_actionPerformed()
\r
1321 PaintRefresher.RemoveComponent(alignPanel);
\r
1322 if (alignPanel.seqPanel != null
\r
1323 && alignPanel.seqPanel.seqCanvas != null)
\r
1325 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
\r
1327 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
\r
1329 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
\r
1332 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
\r
1340 alignPanel = null;
\r
1347 void updateEditMenuBar()
\r
1350 if (viewport.historyList.size() > 0)
\r
1352 undoMenuItem.setEnabled(true);
\r
1353 CommandI command = (CommandI) viewport.historyList.peek();
\r
1354 undoMenuItem.setLabel("Undo " + command.getDescription());
\r
1358 undoMenuItem.setEnabled(false);
\r
1359 undoMenuItem.setLabel("Undo");
\r
1362 if (viewport.redoList.size() > 0)
\r
1364 redoMenuItem.setEnabled(true);
\r
1366 CommandI command = (CommandI) viewport.redoList.peek();
\r
1367 redoMenuItem.setLabel("Redo " + command.getDescription());
\r
1371 redoMenuItem.setEnabled(false);
\r
1372 redoMenuItem.setLabel("Redo");
\r
1379 public void addHistoryItem(CommandI command)
\r
1381 if (command.getSize() > 0)
\r
1383 viewport.historyList.push(command);
\r
1384 viewport.redoList.removeAllElements();
\r
1385 updateEditMenuBar();
\r
1386 viewport.updateHiddenColumns();
\r
1391 * TODO: JAL-1104 DOCUMENT ME!
\r
1396 protected void undoMenuItem_actionPerformed()
\r
1398 if (viewport.historyList.size() < 1)
\r
1403 CommandI command = (CommandI) viewport.historyList.pop();
\r
1404 viewport.redoList.push(command);
\r
1405 command.undoCommand(null);
\r
1407 AlignViewport originalSource = getOriginatingSource(command);
\r
1409 if (originalSource != viewport)
\r
1412 .println("Warning: Viewport object mismatch whilst undoing");
\r
1414 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
\r
1415 // viewport.getColumnSelection().getHiddenColumns()
\r
1417 updateEditMenuBar();
\r
1418 originalSource.firePropertyChange("alignment", null, originalSource
\r
1419 .getAlignment().getSequences());
\r
1423 * TODO: JAL-1104 DOCUMENT ME!
\r
1428 protected void redoMenuItem_actionPerformed()
\r
1430 if (viewport.redoList.size() < 1)
\r
1435 CommandI command = (CommandI) viewport.redoList.pop();
\r
1436 viewport.historyList.push(command);
\r
1437 command.doCommand(null);
\r
1439 AlignViewport originalSource = getOriginatingSource(command);
\r
1441 if (originalSource != viewport)
\r
1444 .println("Warning: Viewport object mismatch whilst re-doing");
\r
1446 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
\r
1447 // viewport.getColumnSelection().getHiddenColumns()
\r
1450 updateEditMenuBar();
\r
1451 originalSource.firePropertyChange("alignment", null, originalSource
\r
1452 .getAlignment().getSequences());
\r
1455 AlignViewport getOriginatingSource(CommandI command)
\r
1457 AlignViewport originalSource = null;
\r
1458 // For sequence removal and addition, we need to fire
\r
1459 // the property change event FROM the viewport where the
\r
1460 // original alignment was altered
\r
1461 AlignmentI al = null;
\r
1462 if (command instanceof EditCommand)
\r
1464 EditCommand editCommand = (EditCommand) command;
\r
1465 al = editCommand.getAlignment();
\r
1466 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
1467 .getSequenceSetId());
\r
1468 for (int i = 0; i < comps.size(); i++)
\r
1470 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
1472 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
\r
1474 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
\r
1481 if (originalSource == null)
\r
1483 // The original view is closed, we must validate
\r
1484 // the current view against the closed view first
\r
1487 PaintRefresher.validateSequences(al, viewport.getAlignment());
\r
1490 originalSource = viewport;
\r
1493 return originalSource;
\r
1496 public void moveSelectedSequences(boolean up)
\r
1498 SequenceGroup sg = viewport.getSelectionGroup();
\r
1503 viewport.getAlignment().moveSelectedSequencesByOne(sg,
\r
1504 up ? null : viewport.getHiddenRepSequences(), up);
\r
1505 alignPanel.paintAlignment(true);
\r
1508 synchronized void slideSequences(boolean right, int size)
\r
1510 List<SequenceI> sg = new Vector<SequenceI>();
\r
1511 if (viewport.cursorMode)
\r
1513 sg.add(viewport.getAlignment().getSequenceAt(
\r
1514 alignPanel.seqPanel.seqCanvas.cursorY));
\r
1516 else if (viewport.getSelectionGroup() != null
\r
1517 && viewport.getSelectionGroup().getSize() != viewport
\r
1518 .getAlignment().getHeight())
\r
1520 sg = viewport.getSelectionGroup().getSequences(
\r
1521 viewport.getHiddenRepSequences());
\r
1524 if (sg.size() < 1)
\r
1529 Vector<SequenceI> invertGroup = new Vector();
\r
1531 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
\r
1533 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
\r
1534 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
\r
1537 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
\r
1539 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
\r
1541 for (int i = 0; i < invertGroup.size(); i++)
\r
1542 seqs2[i] = invertGroup.elementAt(i);
\r
1544 SlideSequencesCommand ssc;
\r
1546 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
\r
1547 size, viewport.getGapCharacter());
\r
1549 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
\r
1550 size, viewport.getGapCharacter());
\r
1552 int groupAdjustment = 0;
\r
1553 if (ssc.getGapsInsertedBegin() && right)
\r
1555 if (viewport.cursorMode)
\r
1556 alignPanel.seqPanel.moveCursor(size, 0);
\r
1558 groupAdjustment = size;
\r
1560 else if (!ssc.getGapsInsertedBegin() && !right)
\r
1562 if (viewport.cursorMode)
\r
1563 alignPanel.seqPanel.moveCursor(-size, 0);
\r
1565 groupAdjustment = -size;
\r
1568 if (groupAdjustment != 0)
\r
1570 viewport.getSelectionGroup().setStartRes(
\r
1571 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
\r
1572 viewport.getSelectionGroup().setEndRes(
\r
1573 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
\r
1576 boolean appendHistoryItem = false;
\r
1577 if (viewport.historyList != null && viewport.historyList.size() > 0
\r
1578 && viewport.historyList.peek() instanceof SlideSequencesCommand)
\r
1580 appendHistoryItem = ssc
\r
1581 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
\r
1585 if (!appendHistoryItem)
\r
1586 addHistoryItem(ssc);
\r
1591 static StringBuffer copiedSequences;
\r
1593 static Vector copiedHiddenColumns;
\r
1595 protected void copy_actionPerformed()
\r
1597 if (viewport.getSelectionGroup() == null)
\r
1602 SequenceGroup sg = viewport.getSelectionGroup();
\r
1603 copiedSequences = new StringBuffer();
\r
1604 Hashtable orderedSeqs = new Hashtable();
\r
1605 for (int i = 0; i < sg.getSize(); i++)
\r
1607 SequenceI seq = sg.getSequenceAt(i);
\r
1608 int index = viewport.getAlignment().findIndex(seq);
\r
1609 orderedSeqs.put(index + "", seq);
\r
1612 int index = 0, startRes, endRes;
\r
1615 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
\r
1617 copiedHiddenColumns = new Vector();
\r
1618 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
\r
1619 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
\r
1622 int[] region = (int[]) viewport.getColumnSelection()
\r
1623 .getHiddenColumns().elementAt(i);
\r
1625 copiedHiddenColumns.addElement(new int[]
\r
1626 { region[0] - hiddenOffset, region[1] - hiddenOffset });
\r
1631 copiedHiddenColumns = null;
\r
1634 for (int i = 0; i < sg.getSize(); i++)
\r
1636 SequenceI seq = null;
\r
1638 while (seq == null)
\r
1640 if (orderedSeqs.containsKey(index + ""))
\r
1642 seq = (SequenceI) orderedSeqs.get(index + "");
\r
1654 // Returns residue following index if gap
\r
1655 startRes = seq.findPosition(sg.getStartRes());
\r
1658 // Need to find the residue preceeding index if gap
\r
1661 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
\r
1663 ch = seq.getCharAt(j);
\r
1664 if (!jalview.util.Comparison.isGap((ch)))
\r
1672 endRes += seq.getStart() - 1;
\r
1675 copiedSequences.append(seq.getName()
\r
1681 + seq.getSequenceAsString(sg.getStartRes(),
\r
1682 sg.getEndRes() + 1) + "\n");
\r
1687 protected void pasteNew_actionPerformed()
\r
1692 protected void pasteThis_actionPerformed()
\r
1697 void paste(boolean newAlignment)
\r
1702 if (copiedSequences == null)
\r
1707 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
1708 Vector seqs = new Vector();
\r
1709 while (st.hasMoreElements())
\r
1711 String name = st.nextToken();
\r
1712 int start = Integer.parseInt(st.nextToken());
\r
1713 int end = Integer.parseInt(st.nextToken());
\r
1714 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
\r
1716 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
1717 for (int i = 0; i < seqs.size(); i++)
\r
1719 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
1724 String newtitle = new String("Copied sequences");
\r
1725 if (getTitle().startsWith("Copied sequences"))
\r
1727 newtitle = getTitle();
\r
1731 newtitle = newtitle.concat("- from " + getTitle());
\r
1733 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
1734 viewport.applet, newtitle, false);
\r
1735 if (copiedHiddenColumns != null)
\r
1737 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
1739 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
1740 af.viewport.hideColumns(region[0], region[1]);
\r
1744 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
\r
1749 addSequences(newSeqs);
\r
1752 } catch (Exception ex)
\r
1754 } // could be anything being pasted in here
\r
1758 void addSequences(SequenceI[] seqs)
\r
1760 for (int i = 0; i < seqs.length; i++)
\r
1762 viewport.getAlignment().addSequence(seqs[i]);
\r
1766 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
\r
1767 seqs, 0, viewport.getAlignment().getWidth(),
\r
1768 viewport.getAlignment()));
\r
1770 viewport.setEndSeq(viewport.getAlignment().getHeight());
\r
1771 viewport.getAlignment().getWidth();
\r
1772 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1777 protected void cut_actionPerformed()
\r
1779 copy_actionPerformed();
\r
1780 delete_actionPerformed();
\r
1783 protected void delete_actionPerformed()
\r
1786 SequenceGroup sg = viewport.getSelectionGroup();
\r
1792 Vector seqs = new Vector();
\r
1794 for (int i = 0; i < sg.getSize(); i++)
\r
1796 seq = sg.getSequenceAt(i);
\r
1797 seqs.addElement(seq);
\r
1800 // If the cut affects all sequences, remove highlighted columns
\r
1801 if (sg.getSize() == viewport.getAlignment().getHeight())
\r
1803 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
1804 sg.getEndRes() + 1);
\r
1807 SequenceI[] cut = new SequenceI[seqs.size()];
\r
1808 for (int i = 0; i < seqs.size(); i++)
\r
1810 cut[i] = (SequenceI) seqs.elementAt(i);
\r
1814 * //ADD HISTORY ITEM
\r
1816 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
\r
1817 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
\r
1818 viewport.getAlignment()));
\r
1820 viewport.setSelectionGroup(null);
\r
1821 viewport.getAlignment().deleteGroup(sg);
\r
1823 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1826 if (viewport.getAlignment().getHeight() < 1)
\r
1828 this.setVisible(false);
\r
1830 viewport.sendSelection();
\r
1834 * group consensus toggled
\r
1837 protected void showGroupConsensus_actionPerformed()
\r
1839 viewport.setShowGroupConsensus(showGroupConsensus.getState());
\r
1840 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1845 * group conservation toggled.
\r
1847 protected void showGroupConservation_actionPerformed()
\r
1849 viewport.setShowGroupConservation(showGroupConservation.getState());
\r
1850 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1857 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
\r
1858 * .event.ActionEvent)
\r
1860 protected void showConsensusHistogram_actionPerformed()
\r
1862 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
\r
1863 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1870 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
\r
1871 * .event.ActionEvent)
\r
1873 protected void showSequenceLogo_actionPerformed()
\r
1875 viewport.setShowSequenceLogo(showSequenceLogo.getState());
\r
1876 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1879 protected void normSequenceLogo_actionPerformed()
\r
1881 showSequenceLogo.setState(true);
\r
1882 viewport.setShowSequenceLogo(true);
\r
1883 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
\r
1884 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1887 protected void applyAutoAnnotationSettings_actionPerformed()
\r
1889 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1892 protected void makeGrpsFromSelection_actionPerformed()
\r
1894 if (viewport.getSelectionGroup() != null)
\r
1896 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
\r
1897 viewport.getSequenceSelection(),
\r
1898 viewport.getAlignmentView(true).getSequenceStrings(
\r
1899 viewport.getGapCharacter()), viewport.getAlignment()
\r
1901 viewport.getAlignment().deleteAllGroups();
\r
1902 viewport.sequenceColours = null;
\r
1903 viewport.setSelectionGroup(null);
\r
1904 // set view properties for each group
\r
1905 for (int g = 0; g < gps.length; g++)
\r
1907 // gps[g].setShowunconserved(viewport.getShowUnconserved());
\r
1908 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
\r
1909 viewport.getAlignment().addGroup(gps[g]);
\r
1910 Color col = new Color((int) (Math.random() * 255),
\r
1911 (int) (Math.random() * 255), (int) (Math.random() * 255));
\r
1912 col = col.brighter();
\r
1913 for (SequenceI sq : gps[g].getSequences(null))
\r
1914 viewport.setSequenceColour(sq, col);
\r
1916 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
\r
1917 alignPanel.updateAnnotation();
\r
1918 alignPanel.paintAlignment(true);
\r
1922 protected void deleteGroups_actionPerformed()
\r
1924 viewport.getAlignment().deleteAllGroups();
\r
1925 viewport.sequenceColours = null;
\r
1926 viewport.setSelectionGroup(null);
\r
1928 alignPanel.paintAlignment(true);
\r
1931 public void selectAllSequenceMenuItem_actionPerformed()
\r
1933 SequenceGroup sg = new SequenceGroup();
\r
1934 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1936 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
1938 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
\r
1939 viewport.setSelectionGroup(sg);
\r
1940 alignPanel.paintAlignment(true);
\r
1941 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1942 viewport.sendSelection();
\r
1945 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1947 if (viewport.cursorMode)
\r
1949 alignPanel.seqPanel.keyboardNo1 = null;
\r
1950 alignPanel.seqPanel.keyboardNo2 = null;
\r
1952 viewport.setSelectionGroup(null);
\r
1953 viewport.getColumnSelection().clear();
\r
1954 viewport.setSelectionGroup(null);
\r
1955 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1956 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1957 alignPanel.paintAlignment(true);
\r
1958 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1959 viewport.sendSelection();
\r
1962 public void invertSequenceMenuItem_actionPerformed()
\r
1964 SequenceGroup sg = viewport.getSelectionGroup();
\r
1965 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1967 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1970 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1971 viewport.sendSelection();
\r
1974 public void invertColSel_actionPerformed()
\r
1976 viewport.invertColumnSelection();
\r
1977 alignPanel.paintAlignment(true);
\r
1978 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1979 viewport.sendSelection();
\r
1982 void trimAlignment(boolean trimLeft)
\r
1984 ColumnSelection colSel = viewport.getColumnSelection();
\r
1987 if (colSel.size() > 0)
\r
1991 column = colSel.getMin();
\r
1995 column = colSel.getMax();
\r
1999 if (viewport.getSelectionGroup() != null)
\r
2001 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2002 viewport.getHiddenRepSequences());
\r
2006 seqs = viewport.getAlignment().getSequencesArray();
\r
2009 TrimRegionCommand trimRegion;
\r
2012 trimRegion = new TrimRegionCommand("Remove Left",
\r
2013 TrimRegionCommand.TRIM_LEFT, seqs, column,
\r
2014 viewport.getAlignment(), viewport.getColumnSelection(),
\r
2015 viewport.getSelectionGroup());
\r
2016 viewport.setStartRes(0);
\r
2020 trimRegion = new TrimRegionCommand("Remove Right",
\r
2021 TrimRegionCommand.TRIM_RIGHT, seqs, column,
\r
2022 viewport.getAlignment(), viewport.getColumnSelection(),
\r
2023 viewport.getSelectionGroup());
\r
2026 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
\r
2028 addHistoryItem(trimRegion);
\r
2030 for (SequenceGroup sg : viewport.getAlignment().getGroups())
\r
2032 if ((trimLeft && !sg.adjustForRemoveLeft(column))
\r
2033 || (!trimLeft && !sg.adjustForRemoveRight(column)))
\r
2035 viewport.getAlignment().deleteGroup(sg);
\r
2039 viewport.firePropertyChange("alignment", null, viewport
\r
2040 .getAlignment().getSequences());
\r
2044 public void removeGappedColumnMenuItem_actionPerformed()
\r
2046 int start = 0, end = viewport.getAlignment().getWidth() - 1;
\r
2049 if (viewport.getSelectionGroup() != null)
\r
2051 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2052 viewport.getHiddenRepSequences());
\r
2053 start = viewport.getSelectionGroup().getStartRes();
\r
2054 end = viewport.getSelectionGroup().getEndRes();
\r
2058 seqs = viewport.getAlignment().getSequencesArray();
\r
2061 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
\r
2062 "Remove Gapped Columns", seqs, start, end,
\r
2063 viewport.getAlignment());
\r
2065 addHistoryItem(removeGapCols);
\r
2067 statusBar.setText("Removed " + removeGapCols.getSize()
\r
2068 + " empty columns.");
\r
2070 // This is to maintain viewport position on first residue
\r
2071 // of first sequence
\r
2072 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
\r
2073 int startRes = seq.findPosition(viewport.startRes);
\r
2074 // ShiftList shifts;
\r
2075 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
\r
2076 // edit.alColumnChanges=shifts.getInverse();
\r
2077 // if (viewport.hasHiddenColumns)
\r
2078 // viewport.getColumnSelection().compensateForEdits(shifts);
\r
2079 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
2080 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
2085 public void removeAllGapsMenuItem_actionPerformed()
\r
2087 int start = 0, end = viewport.getAlignment().getWidth() - 1;
\r
2090 if (viewport.getSelectionGroup() != null)
\r
2092 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2093 viewport.getHiddenRepSequences());
\r
2094 start = viewport.getSelectionGroup().getStartRes();
\r
2095 end = viewport.getSelectionGroup().getEndRes();
\r
2099 seqs = viewport.getAlignment().getSequencesArray();
\r
2102 // This is to maintain viewport position on first residue
\r
2103 // of first sequence
\r
2104 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
\r
2105 int startRes = seq.findPosition(viewport.startRes);
\r
2107 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
\r
2108 viewport.getAlignment()));
\r
2110 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
2112 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
2117 public void findMenuItem_actionPerformed()
\r
2119 new Finder(alignPanel);
\r
2123 * create a new view derived from the current view
\r
2125 * @param viewtitle
\r
2126 * @return frame for the new view
\r
2128 public AlignFrame newView(String viewtitle)
\r
2131 if (viewport.hasHiddenRows())
\r
2133 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
\r
2134 .getFullAlignment().getSequencesArray());
\r
2138 newal = new Alignment(viewport.getAlignment().getSequencesArray());
\r
2141 if (viewport.getAlignment().getAlignmentAnnotation() != null)
\r
2143 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
\r
2145 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
\r
2147 newal.addAnnotation(viewport.getAlignment()
\r
2148 .getAlignmentAnnotation()[i]);
\r
2153 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
\r
2155 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
\r
2156 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
\r
2157 PaintRefresher.Register(newaf.alignPanel,
\r
2158 newaf.alignPanel.av.getSequenceSetId());
\r
2160 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
\r
2161 newaf.alignPanel.av.getSequenceSetId());
\r
2162 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
\r
2163 newaf.alignPanel.av.getSequenceSetId());
\r
2165 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
2166 .getSequenceSetId());
\r
2167 int viewSize = -1;
\r
2168 for (int i = 0; i < comps.size(); i++)
\r
2170 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
2176 String title = new String(this.getTitle());
\r
2177 if (viewtitle != null)
\r
2179 title = viewtitle + " ( " + title + ")";
\r
2183 if (title.indexOf("(View") > -1)
\r
2185 title = title.substring(0, title.indexOf("(View"));
\r
2187 title += "(View " + viewSize + ")";
\r
2190 newaf.setTitle(title.toString());
\r
2192 newaf.viewport.historyList = viewport.historyList;
\r
2193 newaf.viewport.redoList = viewport.redoList;
\r
2199 * @return list of feature groups on the view
\r
2201 public String[] getFeatureGroups()
\r
2203 FeatureRenderer fr = null;
\r
2204 if (alignPanel != null
\r
2205 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2207 return fr.getGroups();
\r
2213 * get sequence feature groups that are hidden or shown
\r
2219 public String[] getFeatureGroupsOfState(boolean visible)
\r
2221 FeatureRenderer fr = null;
\r
2222 if (alignPanel != null
\r
2223 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2225 return fr.getGroups(visible);
\r
2231 * Change the display state for the given feature groups
\r
2234 * list of group strings
\r
2236 * visible or invisible
\r
2238 public void setFeatureGroupState(String[] groups, boolean state)
\r
2240 FeatureRenderer fr = null;
\r
2241 this.sequenceFeatures.setState(true);
\r
2242 viewport.showSequenceFeatures(true);
\r
2243 if (alignPanel != null
\r
2244 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2246 fr.setGroupState(groups, state);
\r
2247 alignPanel.seqPanel.seqCanvas.repaint();
\r
2248 if (alignPanel.overviewPanel != null)
\r
2250 alignPanel.overviewPanel.updateOverviewImage();
\r
2255 public void seqLimits_itemStateChanged()
\r
2257 viewport.setShowJVSuffix(seqLimits.getState());
\r
2258 alignPanel.fontChanged();
\r
2259 alignPanel.paintAlignment(true);
\r
2262 protected void colourTextMenuItem_actionPerformed()
\r
2264 viewport.setColourText(colourTextMenuItem.getState());
\r
2265 alignPanel.paintAlignment(true);
\r
2268 protected void displayNonconservedMenuItem_actionPerformed()
\r
2270 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
\r
2271 alignPanel.paintAlignment(true);
\r
2274 protected void wrapMenuItem_actionPerformed()
\r
2276 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
2277 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
2278 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
2279 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
2280 scaleRight.setEnabled(wrapMenuItem.getState());
\r
2281 alignPanel.paintAlignment(true);
\r
2284 public void overviewMenuItem_actionPerformed()
\r
2286 if (alignPanel.overviewPanel != null)
\r
2291 Frame frame = new Frame();
\r
2292 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
2293 frame.add(overview);
\r
2294 // +50 must allow for applet frame window
\r
2295 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
2296 overview.getPreferredSize().width,
\r
2297 overview.getPreferredSize().height + 50);
\r
2300 final AlignmentPanel ap = alignPanel;
\r
2301 frame.addWindowListener(new WindowAdapter()
\r
2304 public void windowClosing(WindowEvent e)
\r
2308 ap.setOverviewPanel(null);
\r
2313 alignPanel.setOverviewPanel(overview);
\r
2317 void changeColour(ColourSchemeI cs)
\r
2319 int threshold = 0;
\r
2323 if (viewport.getAbovePIDThreshold())
\r
2325 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
2328 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2330 viewport.setGlobalColourScheme(cs);
\r
2334 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2337 if (viewport.getConservationSelected())
\r
2340 Alignment al = (Alignment) viewport.getAlignment();
\r
2341 Conservation c = new Conservation("All",
\r
2342 ResidueProperties.propHash, 3, al.getSequences(), 0,
\r
2343 al.getWidth() - 1);
\r
2346 c.verdict(false, viewport.getConsPercGaps());
\r
2348 cs.setConservation(c);
\r
2350 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
\r
2351 cs, "Background"));
\r
2356 cs.setConservation(null);
\r
2359 cs.setConsensus(viewport.getSequenceConsensusHash());
\r
2362 viewport.setGlobalColourScheme(cs);
\r
2364 if (alignPanel.getOverviewPanel() != null)
\r
2366 alignPanel.getOverviewPanel().updateOverviewImage();
\r
2369 jalview.structure.StructureSelectionManager
\r
2370 .getStructureSelectionManager(viewport.applet)
\r
2371 .sequenceColoursChanged(alignPanel);
\r
2373 alignPanel.paintAlignment(true);
\r
2376 protected void modifyPID_actionPerformed()
\r
2378 if (viewport.getAbovePIDThreshold()
\r
2379 && viewport.getGlobalColourScheme() != null)
\r
2381 SliderPanel.setPIDSliderSource(alignPanel,
\r
2382 viewport.getGlobalColourScheme(), "Background");
\r
2383 SliderPanel.showPIDSlider();
\r
2387 protected void modifyConservation_actionPerformed()
\r
2389 if (viewport.getConservationSelected()
\r
2390 && viewport.getGlobalColourScheme() != null)
\r
2392 SliderPanel.setConservationSlider(alignPanel,
\r
2393 viewport.getGlobalColourScheme(), "Background");
\r
2394 SliderPanel.showConservationSlider();
\r
2398 protected void conservationMenuItem_actionPerformed()
\r
2400 viewport.setConservationSelected(conservationMenuItem.getState());
\r
2402 viewport.setAbovePIDThreshold(false);
\r
2403 abovePIDThreshold.setState(false);
\r
2405 changeColour(viewport.getGlobalColourScheme());
\r
2407 modifyConservation_actionPerformed();
\r
2410 public void abovePIDThreshold_actionPerformed()
\r
2412 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
2414 conservationMenuItem.setState(false);
\r
2415 viewport.setConservationSelected(false);
\r
2417 changeColour(viewport.getGlobalColourScheme());
\r
2419 modifyPID_actionPerformed();
\r
2422 public void sortPairwiseMenuItem_actionPerformed()
\r
2424 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2425 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
\r
2426 .getAlignment().getSequenceAt(0), null);
\r
2428 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
\r
2429 viewport.getAlignment()));
\r
2430 alignPanel.paintAlignment(true);
\r
2433 public void sortIDMenuItem_actionPerformed()
\r
2435 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2436 AlignmentSorter.sortByID(viewport.getAlignment());
\r
2437 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
\r
2438 viewport.getAlignment()));
\r
2439 alignPanel.paintAlignment(true);
\r
2442 public void sortLengthMenuItem_actionPerformed()
\r
2444 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2445 AlignmentSorter.sortByLength(viewport.getAlignment());
\r
2446 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
\r
2447 viewport.getAlignment()));
\r
2448 alignPanel.paintAlignment(true);
\r
2451 public void sortGroupMenuItem_actionPerformed()
\r
2453 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2454 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
2455 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
\r
2456 viewport.getAlignment()));
\r
2457 alignPanel.paintAlignment(true);
\r
2461 public void removeRedundancyMenuItem_actionPerformed()
\r
2463 new RedundancyPanel(alignPanel);
\r
2466 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
2468 if (viewport.getSelectionGroup() != null
\r
2469 && viewport.getSelectionGroup().getSize() > 1)
\r
2471 Frame frame = new Frame();
\r
2472 frame.add(new PairwiseAlignPanel(alignPanel));
\r
2473 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
\r
2478 public void PCAMenuItem_actionPerformed()
\r
2480 // are the sequences aligned?
\r
2481 if (!viewport.getAlignment().isAligned(false))
\r
2483 SequenceI current;
\r
2484 int Width = viewport.getAlignment().getWidth();
\r
2486 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2488 current = viewport.getAlignment().getSequenceAt(i);
\r
2490 if (current.getLength() < Width)
\r
2492 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2495 alignPanel.paintAlignment(true);
\r
2498 if ((viewport.getSelectionGroup() != null
\r
2499 && viewport.getSelectionGroup().getSize() < 4 && viewport
\r
2500 .getSelectionGroup().getSize() > 0)
\r
2501 || viewport.getAlignment().getHeight() < 4)
\r
2508 new PCAPanel(viewport);
\r
2509 } catch (java.lang.OutOfMemoryError ex)
\r
2515 public void averageDistanceTreeMenuItem_actionPerformed()
\r
2517 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
2520 public void neighbourTreeMenuItem_actionPerformed()
\r
2522 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
2525 protected void njTreeBlosumMenuItem_actionPerformed()
\r
2527 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2530 protected void avTreeBlosumMenuItem_actionPerformed()
\r
2532 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2535 void NewTreePanel(String type, String pwType, String title)
\r
2537 // are the sequences aligned?
\r
2538 if (!viewport.getAlignment().isAligned(false))
\r
2540 SequenceI current;
\r
2541 int Width = viewport.getAlignment().getWidth();
\r
2543 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2545 current = viewport.getAlignment().getSequenceAt(i);
\r
2547 if (current.getLength() < Width)
\r
2549 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2552 alignPanel.paintAlignment(true);
\r
2556 if ((viewport.getSelectionGroup() != null && viewport
\r
2557 .getSelectionGroup().getSize() > 1)
\r
2558 || (viewport.getAlignment().getHeight() > 1))
\r
2560 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
\r
2562 addTreeMenuItem(tp, title);
\r
2564 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
2568 void loadTree_actionPerformed()
\r
2570 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
2571 cap.setText("Paste your Newick tree file here.");
\r
2572 cap.setTreeImport();
\r
2573 Frame frame = new Frame();
\r
2575 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
2578 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
2580 TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
\r
2581 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
2582 addTreeMenuItem(tp, treeFile);
\r
2586 * sort the alignment using the given treePanel
\r
2588 * @param treePanel
\r
2589 * tree used to sort view
\r
2591 * string used for undo event name
\r
2593 public void sortByTree(TreePanel treePanel, String title)
\r
2595 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2597 .sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
2598 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2599 // HistoryItem.SORT));
\r
2600 addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
\r
2601 viewport.getAlignment()));
\r
2602 alignPanel.paintAlignment(true);
\r
2606 * Do any automatic reordering of the alignment and add the necessary bits to
\r
2607 * the menu structure for the new tree
\r
2609 * @param treePanel
\r
2612 protected void addTreeMenuItem(final TreePanel treePanel,
\r
2613 final String title)
\r
2615 final MenuItem item = new MenuItem(title);
\r
2616 sortByTreeMenu.add(item);
\r
2617 item.addActionListener(new java.awt.event.ActionListener()
\r
2620 public void actionPerformed(ActionEvent evt)
\r
2622 sortByTree(treePanel, title); // treePanel.getTitle());
\r
2626 treePanel.addWindowListener(new WindowAdapter()
\r
2629 public void windowOpened(WindowEvent e)
\r
2631 if (viewport.sortByTree)
\r
2633 sortByTree(treePanel, title);
\r
2635 super.windowOpened(e);
\r
2639 public void windowClosing(WindowEvent e)
\r
2641 sortByTreeMenu.remove(item);
\r
2646 public boolean sortBy(AlignmentOrder alorder, String undoname)
\r
2648 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2649 if (viewport.applet.debug)
\r
2651 System.err.println("Sorting " + alorder.getOrder().size()
\r
2652 + " in alignment '" + getTitle() + "'");
\r
2654 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
\r
2655 if (undoname != null)
\r
2657 addHistoryItem(new OrderCommand(undoname, oldOrder,
\r
2658 viewport.getAlignment()));
\r
2660 alignPanel.paintAlignment(true);
\r
2664 protected void documentation_actionPerformed()
\r
2666 alignPanel.av.applet.openJalviewHelpUrl();
\r
2669 protected void about_actionPerformed()
\r
2672 class AboutPanel extends Canvas
\r
2678 public AboutPanel(String version, String builddate)
\r
2680 this.version = version;
\r
2681 this.builddate = builddate;
\r
2685 public void paint(Graphics g)
\r
2687 g.setColor(Color.white);
\r
2688 g.fillRect(0, 0, getSize().width, getSize().height);
\r
2689 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2690 FontMetrics fm = g.getFontMetrics();
\r
2691 int fh = fm.getHeight();
\r
2693 g.setColor(Color.black);
\r
2694 // TODO: update this text for each release or centrally store it for
\r
2695 // lite and application
\r
2696 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
2697 g.drawString("JalviewLite - Release " + version, x, y += fh);
\r
2698 g.setFont(new Font("Helvetica", Font.BOLD, 12));
\r
2699 g.drawString("Build date: " + builddate, x, y += fh);
\r
2700 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2702 "Authors: Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui,",
\r
2703 x, y += fh * 1.5);
\r
2705 "Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.",
\r
2706 x + 50, y += fh + 8);
\r
2708 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
\r
2711 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
\r
2713 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
\r
2715 "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
\r
2718 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
\r
2720 g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
\r
2725 Frame frame = new Frame();
\r
2726 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
\r
2727 .getBuildDate()));
\r
2728 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
\r
2732 public void showURL(String url, String target)
\r
2734 if (viewport.applet == null)
\r
2736 System.out.println("Not running as applet - no browser available.");
\r
2740 viewport.applet.showURL(url, target);
\r
2744 // ////////////////////////////////////////////////////////////////////////////////
\r
2745 // JBuilder Graphics here
\r
2747 MenuBar alignFrameMenuBar = new MenuBar();
\r
2749 Menu fileMenu = new Menu("File");
\r
2751 MenuItem loadApplication = new MenuItem("View in Full Application");
\r
2753 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
\r
2755 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
\r
2757 MenuItem outputFeatures = new MenuItem("Export Features ...");
\r
2759 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
\r
2761 MenuItem closeMenuItem = new MenuItem("Close");
\r
2763 Menu editMenu = new Menu("Edit");
\r
2765 Menu viewMenu = new Menu("View");
\r
2767 Menu colourMenu = new Menu("Colour");
\r
2769 Menu calculateMenu = new Menu("Calculate");
\r
2771 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
2773 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
2775 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
2777 MenuItem remove2LeftMenuItem = new MenuItem();
\r
2779 MenuItem remove2RightMenuItem = new MenuItem();
\r
2781 MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
2783 MenuItem removeAllGapsMenuItem = new MenuItem();
\r
2785 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
2787 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
2789 MenuItem sortPairwiseMenuItem = new MenuItem();
\r
2791 MenuItem sortIDMenuItem = new MenuItem();
\r
2793 MenuItem sortLengthMenuItem = new MenuItem();
\r
2795 MenuItem sortGroupMenuItem = new MenuItem();
\r
2797 MenuItem removeRedundancyMenuItem = new MenuItem();
\r
2799 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
2801 MenuItem PCAMenuItem = new MenuItem();
\r
2803 MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
2805 MenuItem neighbourTreeMenuItem = new MenuItem();
\r
2807 BorderLayout borderLayout1 = new BorderLayout();
\r
2809 public Label statusBar = new Label();
\r
2811 Menu outputTextboxMenu = new Menu();
\r
2813 MenuItem clustalColour = new MenuItem();
\r
2815 MenuItem zappoColour = new MenuItem();
\r
2817 MenuItem taylorColour = new MenuItem();
\r
2819 MenuItem hydrophobicityColour = new MenuItem();
\r
2821 MenuItem helixColour = new MenuItem();
\r
2823 MenuItem strandColour = new MenuItem();
\r
2825 MenuItem turnColour = new MenuItem();
\r
2827 MenuItem buriedColour = new MenuItem();
\r
2829 MenuItem purinePyrimidineColour = new MenuItem();
\r
2831 MenuItem RNAInteractionColour = new MenuItem();
\r
2833 MenuItem RNAHelixColour = new MenuItem();
\r
2835 MenuItem userDefinedColour = new MenuItem();
\r
2837 MenuItem PIDColour = new MenuItem();
\r
2839 MenuItem BLOSUM62Colour = new MenuItem();
\r
2841 MenuItem tcoffeeColour = new MenuItem();
\r
2843 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
2845 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
2847 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
2849 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
2851 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
\r
2853 MenuItem alProperties = new MenuItem("Alignment Properties...");
\r
2855 MenuItem overviewMenuItem = new MenuItem();
\r
2857 MenuItem undoMenuItem = new MenuItem();
\r
2859 MenuItem redoMenuItem = new MenuItem();
\r
2861 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
2863 MenuItem noColourmenuItem = new MenuItem();
\r
2865 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
2867 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
2869 MenuItem findMenuItem = new MenuItem();
\r
2871 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
2873 MenuItem nucleotideColour = new MenuItem();
\r
2875 MenuItem deleteGroups = new MenuItem();
\r
2877 MenuItem grpsFromSelection = new MenuItem();
\r
2879 MenuItem delete = new MenuItem();
\r
2881 MenuItem copy = new MenuItem();
\r
2883 MenuItem cut = new MenuItem();
\r
2885 Menu pasteMenu = new Menu();
\r
2887 MenuItem pasteNew = new MenuItem();
\r
2889 MenuItem pasteThis = new MenuItem();
\r
2891 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
2893 MenuItem font = new MenuItem();
\r
2895 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
2897 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
2899 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
2901 MenuItem modifyPID = new MenuItem();
\r
2903 MenuItem modifyConservation = new MenuItem();
\r
2905 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
\r
2906 "Autocalculate Consensus", true);
\r
2908 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
\r
2909 "Sort Alignment With New Tree", true);
\r
2911 Menu sortByTreeMenu = new Menu();
\r
2913 Menu sort = new Menu();
\r
2915 Menu calculate = new Menu();
\r
2917 MenuItem inputText = new MenuItem();
\r
2919 Menu helpMenu = new Menu();
\r
2921 MenuItem documentation = new MenuItem();
\r
2923 MenuItem about = new MenuItem();
\r
2925 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
2927 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
\r
2929 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
\r
2931 Menu autoAnnMenu = new Menu();
\r
2933 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
\r
2935 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
\r
2937 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
\r
2939 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
\r
2941 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
\r
2943 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
\r
2945 private void jbInit() throws Exception
\r
2948 setMenuBar(alignFrameMenuBar);
\r
2952 // dynamically fill save as menu with available formats
\r
2953 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
2956 item = new MenuItem(
\r
2957 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
2959 item.addActionListener(new java.awt.event.ActionListener()
\r
2962 public void actionPerformed(ActionEvent e)
\r
2964 outputText_actionPerformed(e);
\r
2968 outputTextboxMenu.add(item);
\r
2970 closeMenuItem.addActionListener(this);
\r
2971 loadApplication.addActionListener(this);
\r
2973 loadTree.addActionListener(this);
\r
2974 loadAnnotations.addActionListener(this);
\r
2975 outputFeatures.addActionListener(this);
\r
2976 outputAnnotations.addActionListener(this);
\r
2977 selectAllSequenceMenuItem.addActionListener(this);
\r
2978 deselectAllSequenceMenuItem.addActionListener(this);
\r
2979 invertSequenceMenuItem.addActionListener(this);
\r
2980 remove2LeftMenuItem.setLabel("Remove Left");
\r
2981 remove2LeftMenuItem.addActionListener(this);
\r
2982 remove2RightMenuItem.setLabel("Remove Right");
\r
2983 remove2RightMenuItem.addActionListener(this);
\r
2984 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
2985 removeGappedColumnMenuItem.addActionListener(this);
\r
2986 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
2987 removeAllGapsMenuItem.addActionListener(this);
\r
2988 viewBoxesMenuItem.setLabel("Boxes");
\r
2989 viewBoxesMenuItem.setState(true);
\r
2990 viewBoxesMenuItem.addItemListener(this);
\r
2991 viewTextMenuItem.setLabel("Text");
\r
2992 viewTextMenuItem.setState(true);
\r
2993 viewTextMenuItem.addItemListener(this);
\r
2994 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
2995 sortPairwiseMenuItem.addActionListener(this);
\r
2996 sortIDMenuItem.setLabel("by ID");
\r
2997 sortIDMenuItem.addActionListener(this);
\r
2998 sortLengthMenuItem.setLabel("by Length");
\r
2999 sortLengthMenuItem.addActionListener(this);
\r
3000 sortGroupMenuItem.setLabel("by Group");
\r
3001 sortGroupMenuItem.addActionListener(this);
\r
3002 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
3003 removeRedundancyMenuItem.addActionListener(this);
\r
3004 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
3005 pairwiseAlignmentMenuItem.addActionListener(this);
\r
3006 PCAMenuItem.setLabel("Principal Component Analysis");
\r
3007 PCAMenuItem.addActionListener(this);
\r
3008 averageDistanceTreeMenuItem
\r
3009 .setLabel("Average Distance Using % Identity");
\r
3010 averageDistanceTreeMenuItem.addActionListener(this);
\r
3011 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
3012 neighbourTreeMenuItem.addActionListener(this);
\r
3013 statusBar.setBackground(Color.white);
\r
3014 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
3015 statusBar.setText("Status bar");
\r
3016 outputTextboxMenu.setLabel("Output to Textbox");
\r
3017 clustalColour.setLabel("Clustalx");
\r
3019 clustalColour.addActionListener(this);
\r
3020 zappoColour.setLabel("Zappo");
\r
3021 zappoColour.addActionListener(this);
\r
3022 taylorColour.setLabel("Taylor");
\r
3023 taylorColour.addActionListener(this);
\r
3024 hydrophobicityColour.setLabel("Hydrophobicity");
\r
3025 hydrophobicityColour.addActionListener(this);
\r
3026 helixColour.setLabel("Helix Propensity");
\r
3027 helixColour.addActionListener(this);
\r
3028 strandColour.setLabel("Strand Propensity");
\r
3029 strandColour.addActionListener(this);
\r
3030 turnColour.setLabel("Turn Propensity");
\r
3031 turnColour.addActionListener(this);
\r
3032 buriedColour.setLabel("Buried Index");
\r
3033 buriedColour.addActionListener(this);
\r
3034 purinePyrimidineColour.setLabel("Purine/Pyrimidine");
\r
3035 purinePyrimidineColour.addActionListener(this);
\r
3036 RNAInteractionColour.setLabel("Purine/Pyrimidine");
\r
3037 RNAInteractionColour.addActionListener(this);
\r
3038 RNAHelixColour.setLabel("by RNA Helices");
\r
3039 RNAHelixColour.addActionListener(this);
\r
3040 userDefinedColour.setLabel("User Defined...");
\r
3041 userDefinedColour.addActionListener(this);
\r
3042 PIDColour.setLabel("Percentage Identity");
\r
3043 PIDColour.addActionListener(this);
\r
3044 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
3045 BLOSUM62Colour.addActionListener(this);
\r
3046 tcoffeeColour.setLabel("T-Coffee Scores");
\r
3047 tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
\r
3049 tcoffeeColour.addActionListener(this);
\r
3050 avDistanceTreeBlosumMenuItem
\r
3051 .setLabel("Average Distance Using BLOSUM62");
\r
3052 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
3053 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
3054 njTreeBlosumMenuItem.addActionListener(this);
\r
3055 annotationPanelMenuItem.setLabel("Show Annotations");
\r
3056 annotationPanelMenuItem.addItemListener(this);
\r
3057 colourTextMenuItem.setLabel("Colour Text");
\r
3058 colourTextMenuItem.addItemListener(this);
\r
3059 displayNonconservedMenuItem.setLabel("Show nonconserved");
\r
3060 displayNonconservedMenuItem.addItemListener(this);
\r
3061 alProperties.addActionListener(this);
\r
3062 overviewMenuItem.setLabel("Overview Window");
\r
3063 overviewMenuItem.addActionListener(this);
\r
3064 undoMenuItem.setEnabled(false);
\r
3065 undoMenuItem.setLabel("Undo");
\r
3066 undoMenuItem.addActionListener(this);
\r
3067 redoMenuItem.setEnabled(false);
\r
3068 redoMenuItem.setLabel("Redo");
\r
3069 redoMenuItem.addActionListener(this);
\r
3070 conservationMenuItem.setLabel("by Conservation");
\r
3071 conservationMenuItem.addItemListener(this);
\r
3072 noColourmenuItem.setLabel("None");
\r
3073 noColourmenuItem.addActionListener(this);
\r
3074 wrapMenuItem.setLabel("Wrap");
\r
3075 wrapMenuItem.addItemListener(this);
\r
3076 renderGapsMenuItem.setLabel("Show Gaps");
\r
3077 renderGapsMenuItem.setState(true);
\r
3078 renderGapsMenuItem.addItemListener(this);
\r
3079 findMenuItem.setLabel("Find...");
\r
3080 findMenuItem.addActionListener(this);
\r
3081 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
3082 abovePIDThreshold.addItemListener(this);
\r
3083 nucleotideColour.setLabel("Nucleotide");
\r
3084 nucleotideColour.addActionListener(this);
\r
3085 deleteGroups.setLabel("Undefine Groups");
\r
3086 deleteGroups.addActionListener(this);
\r
3087 grpsFromSelection.setLabel("Make Groups for selection");
\r
3088 grpsFromSelection.addActionListener(this);
\r
3089 copy.setLabel("Copy");
\r
3090 copy.addActionListener(this);
\r
3091 cut.setLabel("Cut");
\r
3092 cut.addActionListener(this);
\r
3093 delete.setLabel("Delete");
\r
3094 delete.addActionListener(this);
\r
3095 pasteMenu.setLabel("Paste");
\r
3096 pasteNew.setLabel("To New Alignment");
\r
3097 pasteNew.addActionListener(this);
\r
3098 pasteThis.setLabel("Add To This Alignment");
\r
3099 pasteThis.addActionListener(this);
\r
3100 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
3101 applyToAllGroups.setState(true);
\r
3102 applyToAllGroups.addItemListener(this);
\r
3103 font.setLabel("Font...");
\r
3104 font.addActionListener(this);
\r
3105 scaleAbove.setLabel("Scale Above");
\r
3106 scaleAbove.setState(true);
\r
3107 scaleAbove.setEnabled(false);
\r
3108 scaleAbove.addItemListener(this);
\r
3109 scaleLeft.setEnabled(false);
\r
3110 scaleLeft.setState(true);
\r
3111 scaleLeft.setLabel("Scale Left");
\r
3112 scaleLeft.addItemListener(this);
\r
3113 scaleRight.setEnabled(false);
\r
3114 scaleRight.setState(true);
\r
3115 scaleRight.setLabel("Scale Right");
\r
3116 scaleRight.addItemListener(this);
\r
3117 modifyPID.setLabel("Modify Identity Threshold...");
\r
3118 modifyPID.addActionListener(this);
\r
3119 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
3120 modifyConservation.addActionListener(this);
\r
3121 sortByTreeMenu.setLabel("By Tree Order");
\r
3122 sort.setLabel("Sort");
\r
3123 calculate.setLabel("Calculate Tree");
\r
3124 autoCalculate.addItemListener(this);
\r
3125 sortByTree.addItemListener(this);
\r
3126 inputText.setLabel("Input from textbox");
\r
3127 inputText.addActionListener(this);
\r
3128 centreColumnLabelFlag.setLabel("Centre column labels");
\r
3129 centreColumnLabelFlag.addItemListener(this);
\r
3130 followMouseOverFlag.setLabel("Automatic Scrolling");
\r
3131 followMouseOverFlag.addItemListener(this);
\r
3132 helpMenu.setLabel("Help");
\r
3133 documentation.setLabel("Documentation");
\r
3134 documentation.addActionListener(this);
\r
3136 about.setLabel("About...");
\r
3137 about.addActionListener(this);
\r
3138 seqLimits.setState(true);
\r
3139 seqLimits.setLabel("Show Sequence Limits");
\r
3140 seqLimits.addItemListener(this);
\r
3141 featureSettings.setLabel("Feature Settings...");
\r
3142 featureSettings.addActionListener(this);
\r
3143 sequenceFeatures.setLabel("Sequence Features");
\r
3144 sequenceFeatures.addItemListener(this);
\r
3145 sequenceFeatures.setState(false);
\r
3146 annotationColour.setLabel("by Annotation...");
\r
3147 annotationColour.addActionListener(this);
\r
3148 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
3149 invertColSel.setLabel("Invert Column Selection");
\r
3150 menu1.setLabel("Show");
\r
3151 showColumns.setLabel("All Columns ");
\r
3152 showSeqs.setLabel("All Sequences");
\r
3153 menu2.setLabel("Hide");
\r
3154 hideColumns.setLabel("Selected Columns");
\r
3155 hideSequences.setLabel("Selected Sequences");
\r
3156 hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
\r
3157 hideAllSelection.setLabel("Selected Region");
\r
3158 showAllHidden.setLabel("All Sequences and Columns");
\r
3159 showGroupConsensus.setLabel("Group Consensus");
\r
3160 showGroupConservation.setLabel("Group Conservation");
\r
3161 showConsensusHistogram.setLabel("Show Consensus Histogram");
\r
3162 showSequenceLogo.setLabel("Show Consensus Logo");
\r
3163 normSequenceLogo.setLabel("Normalise Consensus Logo");
\r
3164 applyAutoAnnotationSettings.setLabel("Apply to all groups");
\r
3165 applyAutoAnnotationSettings.setState(true);
\r
3166 autoAnnMenu.setLabel("Autocalculated Annotation");
\r
3168 invertColSel.addActionListener(this);
\r
3169 showColumns.addActionListener(this);
\r
3170 showSeqs.addActionListener(this);
\r
3171 hideColumns.addActionListener(this);
\r
3172 hideSequences.addActionListener(this);
\r
3173 hideAllButSelection.addActionListener(this);
\r
3174 hideAllSelection.addActionListener(this);
\r
3175 showAllHidden.addActionListener(this);
\r
3176 showGroupConsensus.addItemListener(this);
\r
3177 showGroupConservation.addItemListener(this);
\r
3178 showConsensusHistogram.addItemListener(this);
\r
3179 showSequenceLogo.addItemListener(this);
\r
3180 applyAutoAnnotationSettings.addItemListener(this);
\r
3181 formatMenu.setLabel("Format");
\r
3182 selectMenu.setLabel("Select");
\r
3183 newView.setLabel("New View");
\r
3184 newView.addActionListener(this);
\r
3185 alignFrameMenuBar.add(fileMenu);
\r
3186 alignFrameMenuBar.add(editMenu);
\r
3187 alignFrameMenuBar.add(selectMenu);
\r
3188 alignFrameMenuBar.add(viewMenu);
\r
3189 alignFrameMenuBar.add(formatMenu);
\r
3190 alignFrameMenuBar.add(colourMenu);
\r
3191 alignFrameMenuBar.add(calculateMenu);
\r
3192 alignFrameMenuBar.add(helpMenu);
\r
3194 fileMenu.add(inputText);
\r
3195 fileMenu.add(loadTree);
\r
3196 fileMenu.add(loadAnnotations);
\r
3198 fileMenu.addSeparator();
\r
3199 fileMenu.add(outputTextboxMenu);
\r
3200 fileMenu.add(outputFeatures);
\r
3201 fileMenu.add(outputAnnotations);
\r
3203 if (jalviewServletURL != null)
\r
3205 fileMenu.add(loadApplication);
\r
3208 fileMenu.addSeparator();
\r
3209 fileMenu.add(closeMenuItem);
\r
3211 editMenu.add(undoMenuItem);
\r
3212 editMenu.add(redoMenuItem);
\r
3213 editMenu.add(cut);
\r
3214 editMenu.add(copy);
\r
3215 editMenu.add(pasteMenu);
\r
3216 editMenu.add(delete);
\r
3217 editMenu.addSeparator();
\r
3218 editMenu.add(remove2LeftMenuItem);
\r
3219 editMenu.add(remove2RightMenuItem);
\r
3220 editMenu.add(removeGappedColumnMenuItem);
\r
3221 editMenu.add(removeAllGapsMenuItem);
\r
3222 editMenu.add(removeRedundancyMenuItem);
\r
3223 viewMenu.add(newView);
\r
3224 viewMenu.addSeparator();
\r
3225 viewMenu.add(menu1);
\r
3226 viewMenu.add(menu2);
\r
3227 viewMenu.addSeparator();
\r
3228 viewMenu.add(followMouseOverFlag);
\r
3229 viewMenu.add(annotationPanelMenuItem);
\r
3230 autoAnnMenu.add(applyAutoAnnotationSettings);
\r
3231 autoAnnMenu.add(showConsensusHistogram);
\r
3232 autoAnnMenu.add(showSequenceLogo);
\r
3233 autoAnnMenu.add(normSequenceLogo);
\r
3234 autoAnnMenu.addSeparator();
\r
3235 autoAnnMenu.add(showGroupConservation);
\r
3236 autoAnnMenu.add(showGroupConsensus);
\r
3237 viewMenu.add(autoAnnMenu);
\r
3238 viewMenu.addSeparator();
\r
3239 viewMenu.add(sequenceFeatures);
\r
3240 viewMenu.add(featureSettings);
\r
3241 viewMenu.addSeparator();
\r
3242 viewMenu.add(alProperties);
\r
3243 viewMenu.addSeparator();
\r
3244 viewMenu.add(overviewMenuItem);
\r
3245 colourMenu.add(applyToAllGroups);
\r
3246 colourMenu.addSeparator();
\r
3247 colourMenu.add(noColourmenuItem);
\r
3248 colourMenu.add(clustalColour);
\r
3249 colourMenu.add(BLOSUM62Colour);
\r
3250 colourMenu.add(PIDColour);
\r
3251 colourMenu.add(zappoColour);
\r
3252 colourMenu.add(taylorColour);
\r
3253 colourMenu.add(hydrophobicityColour);
\r
3254 colourMenu.add(helixColour);
\r
3255 colourMenu.add(strandColour);
\r
3256 colourMenu.add(turnColour);
\r
3257 colourMenu.add(buriedColour);
\r
3258 colourMenu.add(nucleotideColour);
\r
3259 colourMenu.add(purinePyrimidineColour);
\r
3260 // colourMenu.add(RNAInteractionColour);
\r
3261 colourMenu.add(tcoffeeColour);
\r
3262 colourMenu.add(userDefinedColour);
\r
3263 colourMenu.addSeparator();
\r
3264 colourMenu.add(conservationMenuItem);
\r
3265 colourMenu.add(modifyConservation);
\r
3266 colourMenu.add(abovePIDThreshold);
\r
3267 colourMenu.add(modifyPID);
\r
3268 colourMenu.add(annotationColour);
\r
3269 colourMenu.add(RNAHelixColour);
\r
3270 calculateMenu.add(sort);
\r
3271 calculateMenu.add(calculate);
\r
3272 calculateMenu.addSeparator();
\r
3273 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
3274 calculateMenu.add(PCAMenuItem);
\r
3275 calculateMenu.add(autoCalculate);
\r
3276 calculateMenu.add(sortByTree);
\r
3277 this.add(statusBar, BorderLayout.SOUTH);
\r
3278 pasteMenu.add(pasteNew);
\r
3279 pasteMenu.add(pasteThis);
\r
3280 sort.add(sortIDMenuItem);
\r
3281 sort.add(sortLengthMenuItem);
\r
3282 sort.add(sortByTreeMenu);
\r
3283 sort.add(sortGroupMenuItem);
\r
3284 sort.add(sortPairwiseMenuItem);
\r
3285 calculate.add(averageDistanceTreeMenuItem);
\r
3286 calculate.add(neighbourTreeMenuItem);
\r
3287 calculate.add(avDistanceTreeBlosumMenuItem);
\r
3288 calculate.add(njTreeBlosumMenuItem);
\r
3289 helpMenu.add(documentation);
\r
3290 helpMenu.add(about);
\r
3291 menu1.add(showColumns);
\r
3292 menu1.add(showSeqs);
\r
3293 menu1.add(showAllHidden);
\r
3294 menu2.add(hideColumns);
\r
3295 menu2.add(hideSequences);
\r
3296 menu2.add(hideAllSelection);
\r
3297 menu2.add(hideAllButSelection);
\r
3298 formatMenu.add(font);
\r
3299 formatMenu.add(seqLimits);
\r
3300 formatMenu.add(wrapMenuItem);
\r
3301 formatMenu.add(scaleAbove);
\r
3302 formatMenu.add(scaleLeft);
\r
3303 formatMenu.add(scaleRight);
\r
3304 formatMenu.add(viewBoxesMenuItem);
\r
3305 formatMenu.add(viewTextMenuItem);
\r
3306 formatMenu.add(colourTextMenuItem);
\r
3307 formatMenu.add(displayNonconservedMenuItem);
\r
3308 formatMenu.add(renderGapsMenuItem);
\r
3309 formatMenu.add(centreColumnLabelFlag);
\r
3310 selectMenu.add(findMenuItem);
\r
3311 selectMenu.addSeparator();
\r
3312 selectMenu.add(selectAllSequenceMenuItem);
\r
3313 selectMenu.add(deselectAllSequenceMenuItem);
\r
3314 selectMenu.add(invertSequenceMenuItem);
\r
3315 selectMenu.add(invertColSel);
\r
3316 selectMenu.add(grpsFromSelection);
\r
3317 selectMenu.add(deleteGroups);
\r
3321 MenuItem featureSettings = new MenuItem();
\r
3323 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
3325 MenuItem annotationColour = new MenuItem();
\r
3327 MenuItem invertColSel = new MenuItem();
\r
3329 Menu menu1 = new Menu();
\r
3331 MenuItem showColumns = new MenuItem();
\r
3333 MenuItem showSeqs = new MenuItem();
\r
3335 Menu menu2 = new Menu();
\r
3337 MenuItem hideColumns = new MenuItem();
\r
3339 MenuItem hideSequences = new MenuItem();
\r
3341 MenuItem hideAllButSelection = new MenuItem();
\r
3343 MenuItem hideAllSelection = new MenuItem();
\r
3345 MenuItem showAllHidden = new MenuItem();
\r
3347 Menu formatMenu = new Menu();
\r
3349 Menu selectMenu = new Menu();
\r
3351 MenuItem newView = new MenuItem();
\r
3354 * Attach the alignFrame panels after embedding menus, if necessary. This used
\r
3355 * to be called setEmbedded, but is now creates the dropdown menus in a
\r
3356 * platform independent manner to avoid OSX/Mac menu appendage daftness.
\r
3358 * @param reallyEmbedded
\r
3359 * true to attach the view to the applet area on the page rather than
\r
3362 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
\r
3364 if (reallyEmbedded)
\r
3367 // Explicly build the embedded menu panel for the on-page applet
\r
3369 // view cannot be closed if its actually on the page
\r
3370 fileMenu.remove(closeMenuItem);
\r
3371 fileMenu.remove(3); // Remove Seperator
\r
3372 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
\r
3373 Font.PLAIN, 10, false); // use our own fonts.
\r
3374 // and actually add the components to the applet area
\r
3375 viewport.applet.setLayout(new BorderLayout());
\r
3376 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
\r
3377 viewport.applet.add(statusBar, BorderLayout.SOUTH);
\r
3378 alignPanel.setSize(viewport.applet.getSize().width,
\r
3379 viewport.applet.getSize().height - embeddedMenu.HEIGHT
\r
3380 - statusBar.HEIGHT);
\r
3381 viewport.applet.add(alignPanel, BorderLayout.CENTER);
\r
3382 final AlignFrame me = this;
\r
3383 viewport.applet.addFocusListener(new FocusListener()
\r
3387 public void focusLost(FocusEvent e)
\r
3389 if (me.viewport.applet.currentAlignFrame == me)
\r
3391 me.viewport.applet.currentAlignFrame = null;
\r
3396 public void focusGained(FocusEvent e)
\r
3398 me.viewport.applet.currentAlignFrame = me;
\r
3401 viewport.applet.validate();
\r
3406 // test and embed menu bar if necessary.
\r
3408 if (embedMenuIfNeeded(alignPanel))
\r
3410 // adjust for status bar height too
\r
3411 alignPanel.setSize(getSize().width, getSize().height
\r
3412 - statusBar.HEIGHT);
\r
3414 add(statusBar, BorderLayout.SOUTH);
\r
3415 add(alignPanel, BorderLayout.CENTER);
\r
3416 // and register with the applet so it can pass external API calls to us
\r
3417 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
\r
3423 * create a new binding between structures in an existing jmol viewer instance
\r
3424 * and an alignpanel with sequences that have existing PDBFile entries. Note,
\r
3425 * this does not open a new Jmol window, or modify the display of the
\r
3426 * structures in the original jmol window. Note This method doesn't work
\r
3427 * without an additional javascript library to exchange messages between the
\r
3428 * distinct applets. See http://issues.jalview.org/browse/JAL-621
\r
3431 * JmolViewer instance
\r
3432 * @param sequenceIds
\r
3433 * - sequence Ids to search for associations
\r
3435 public SequenceStructureBinding addStructureViewInstance(
\r
3436 Object jmolviewer, String[] sequenceIds)
\r
3438 org.jmol.api.JmolViewer viewer = null;
\r
3441 viewer = (org.jmol.api.JmolViewer) jmolviewer;
\r
3442 } catch (ClassCastException ex)
\r
3444 System.err.println("Unsupported viewer object :"
\r
3445 + jmolviewer.getClass());
\r
3447 if (viewer == null)
\r
3449 System.err.println("Can't use this object as a structure viewer:"
\r
3450 + jmolviewer.getClass());
\r
3453 SequenceI[] seqs = null;
\r
3454 if (sequenceIds == null || sequenceIds.length == 0)
\r
3456 seqs = viewport.getAlignment().getSequencesArray();
\r
3460 Vector sqi = new Vector();
\r
3461 AlignmentI al = viewport.getAlignment();
\r
3462 for (int sid = 0; sid < sequenceIds.length; sid++)
\r
3464 SequenceI sq = al.findName(sequenceIds[sid]);
\r
3467 sqi.addElement(sq);
\r
3470 if (sqi.size() > 0)
\r
3472 seqs = new SequenceI[sqi.size()];
\r
3473 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
\r
3475 seqs[sid] = (SequenceI) sqi.elementAt(sid);
\r
3483 ExtJmol jmv = null;
\r
3484 // TODO: search for a jmv that involves viewer
\r
3486 { // create a new viewer/jalview binding.
\r
3487 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
\r
3495 * bind a pdb file to a sequence in the current view
\r
3497 * @param sequenceId
\r
3498 * - sequenceId within the dataset.
\r
3499 * @param pdbEntryString
\r
3500 * - the short name for the PDB file
\r
3502 * - pdb file - either a URL or a valid PDB file.
\r
3503 * @return true if binding was as success TODO: consider making an exception
\r
3504 * structure for indicating when PDB parsing or sequenceId location
\r
3507 public boolean addPdbFile(String sequenceId, String pdbEntryString,
\r
3510 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
\r
3511 boolean needtoadd = false;
\r
3512 if (toaddpdb != null)
\r
3514 Vector pdbe = toaddpdb.getPDBId();
\r
3515 PDBEntry pdbentry = null;
\r
3516 if (pdbe != null && pdbe.size() > 0)
\r
3518 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
\r
3520 pdbentry = (PDBEntry) pdbe.elementAt(pe);
\r
3521 if (!pdbentry.getId().equals(pdbEntryString)
\r
3522 && !pdbentry.getFile().equals(pdbFile))
\r
3532 if (pdbentry == null)
\r
3534 pdbentry = new PDBEntry();
\r
3535 pdbentry.setId(pdbEntryString);
\r
3536 pdbentry.setFile(pdbFile);
\r
3537 needtoadd = true; // add this new entry to sequence.
\r
3539 // resolve data source
\r
3540 // TODO: this code should be a refactored to an io package
\r
3541 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
\r
3542 if (protocol == null)
\r
3548 // make a note of the access mode and add
\r
3549 if (pdbentry.getProperty() == null)
\r
3551 pdbentry.setProperty(new Hashtable());
\r
3553 pdbentry.getProperty().put("protocol", protocol);
\r
3554 toaddpdb.addPDBId(pdbentry);
\r
3560 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
\r
3564 Vector sequences = new Vector();
\r
3565 for (int i = 0; i < seqs.length; i++)
\r
3567 if (seqs[i] != null)
\r
3569 sequences.addElement(new Object[]
\r
3570 { seqs[i], (chains != null) ? chains[i] : null });
\r
3573 seqs = new SequenceI[sequences.size()];
\r
3574 chains = new String[sequences.size()];
\r
3575 for (int i = 0, isize = sequences.size(); i < isize; i++)
\r
3577 Object[] oj = (Object[]) sequences.elementAt(i);
\r
3579 seqs[i] = (SequenceI) oj[0];
\r
3580 chains[i] = (String) oj[1];
\r
3583 return new Object[]
\r
3588 public void newStructureView(JalviewLite applet, PDBEntry pdb,
\r
3589 SequenceI[] seqs, String[] chains, String protocol)
\r
3591 // Scrub any null sequences from the array
\r
3592 Object[] sqch = cleanSeqChainArrays(seqs, chains);
\r
3593 seqs = (SequenceI[]) sqch[0];
\r
3594 chains = (String[]) sqch[1];
\r
3595 if (seqs == null || seqs.length == 0)
\r
3598 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
\r
3600 if (protocol == null || protocol.trim().length() == 0
\r
3601 || protocol.equals("null"))
\r
3603 protocol = (String) pdb.getProperty().get("protocol");
\r
3604 if (protocol == null)
\r
3606 System.err.println("Couldn't work out protocol to open structure: "
\r
3611 if (applet.useXtrnalSviewer)
\r
3613 // register the association(s) and quit, don't create any windows.
\r
3614 if (StructureSelectionManager.getStructureSelectionManager(applet)
\r
3615 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
\r
3617 System.err.println("Failed to map " + pdb.getFile() + " ("
\r
3618 + protocol + ") to any sequences");
\r
3622 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
\r
3624 // can only do alignments with Jmol
\r
3625 // find the last jmol window assigned to this alignment
\r
3626 jalview.appletgui.AppletJmol ajm = null, tajm;
\r
3627 Vector jmols = applet
\r
3628 .getAppletWindow(jalview.appletgui.AppletJmol.class);
\r
3629 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
\r
3631 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
\r
3632 if (tajm.ap.alignFrame == this)
\r
3641 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
\r
3642 // try and add the pdb structure
\r
3647 // otherwise, create a new window
\r
3648 if (applet.jmolAvailable)
\r
3650 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
\r
3652 applet.lastFrameX += 40;
\r
3653 applet.lastFrameY += 40;
\r
3657 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
\r
3662 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
\r
3663 SequenceI[][] seqs, String[][] chains, String[] protocols)
\r
3665 // TODO Auto-generated method stub
\r
3666 System.err.println("Aligned Structure View: Not yet implemented.");
\r
3670 * modify the current selection, providing the user has not made a selection
\r
3674 * - sequences from this alignment
\r
3676 * - columns to be selected on the alignment
\r
3678 public void select(SequenceGroup sel, ColumnSelection csel)
\r
3680 alignPanel.seqPanel.selection(sel, csel, null);
\r
3683 public void scrollTo(int row, int column)
\r
3685 alignPanel.seqPanel.scrollTo(row, column);
\r
3688 public void scrollToRow(int row)
\r
3690 alignPanel.seqPanel.scrollToRow(row);
\r
3693 public void scrollToColumn(int column)
\r
3695 alignPanel.seqPanel.scrollToColumn(column);
\r
3699 * @return the alignments unique ID.
\r
3701 public String getSequenceSetId()
\r
3703 return viewport.getSequenceSetId();
\r
3707 * Load the (T-Coffee) score file from the specified url
\r
3710 * File/URL/T-COFFEE score file contents
\r
3711 * @throws IOException
\r
3712 * @return true if alignment was annotated with data from source
\r
3714 public boolean loadScoreFile(String source) throws IOException
\r
3717 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
\r
3718 AppletFormatAdapter.checkProtocol(source));
\r
3719 if (!file.isValid())
\r
3721 // TODO: raise dialog for gui
\r
3722 System.err.println("Problems parsing T-Coffee scores: "
\r
3723 + file.getWarningMessage());
\r
3724 System.err.println("Origin was:\n" + source);
\r
3729 * check that the score matrix matches the alignment dimensions
\r
3732 if ((aln = viewport.getAlignment()) != null
\r
3733 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
\r
3736 // TODO: raise a dialog box here rather than bomb out.
\r
3738 .println("The scores matrix does not match the alignment dimensions");
\r
3742 // TODO add parameter to indicate if matching should be done
\r
3743 if (file.annotateAlignment(alignPanel.getAlignment(), false))
\r
3745 alignPanel.fontChanged();
\r
3746 tcoffeeColour.setEnabled(true);
\r
3747 // switch to this color
\r
3748 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
\r
3753 System.err.println("Problems resolving T-Coffee scores:");
\r
3754 if (file.getWarningMessage() != null)
\r
3756 System.err.println(file.getWarningMessage());
\r