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.AAFrequency;
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21 import jalview.analysis.AlignmentSorter;
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22 import jalview.analysis.Conservation;
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23 import jalview.api.SequenceStructureBinding;
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24 import jalview.bin.JalviewLite;
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25 import jalview.commands.CommandI;
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26 import jalview.commands.EditCommand;
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27 import jalview.commands.OrderCommand;
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28 import jalview.commands.RemoveGapColCommand;
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29 import jalview.commands.RemoveGapsCommand;
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30 import jalview.commands.SlideSequencesCommand;
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31 import jalview.commands.TrimRegionCommand;
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32 import jalview.datamodel.Alignment;
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33 import jalview.datamodel.AlignmentI;
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34 import jalview.datamodel.AlignmentOrder;
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35 import jalview.datamodel.ColumnSelection;
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36 import jalview.datamodel.PDBEntry;
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37 import jalview.datamodel.Sequence;
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38 import jalview.datamodel.SequenceCollectionI;
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39 import jalview.datamodel.SequenceGroup;
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40 import jalview.datamodel.SequenceI;
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41 import jalview.io.AnnotationFile;
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42 import jalview.io.AppletFormatAdapter;
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43 import jalview.io.FeaturesFile;
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44 import jalview.io.TCoffeeScoreFile;
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45 import jalview.schemes.Blosum62ColourScheme;
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46 import jalview.schemes.BuriedColourScheme;
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47 import jalview.schemes.ClustalxColourScheme;
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48 import jalview.schemes.ColourSchemeI;
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49 import jalview.schemes.HelixColourScheme;
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50 import jalview.schemes.HydrophobicColourScheme;
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51 import jalview.schemes.NucleotideColourScheme;
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52 import jalview.schemes.PIDColourScheme;
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53 import jalview.schemes.PurinePyrimidineColourScheme;
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54 import jalview.schemes.RNAHelicesColourChooser;
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55 import jalview.schemes.RNAInteractionColourScheme;
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56 import jalview.schemes.ResidueProperties;
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57 import jalview.schemes.StrandColourScheme;
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58 import jalview.schemes.TCoffeeColourScheme;
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59 import jalview.schemes.TaylorColourScheme;
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60 import jalview.schemes.TurnColourScheme;
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61 import jalview.schemes.ZappoColourScheme;
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62 import jalview.structure.StructureSelectionManager;
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64 import java.awt.BorderLayout;
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65 import java.awt.Canvas;
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66 import java.awt.CheckboxMenuItem;
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67 import java.awt.Color;
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68 import java.awt.Font;
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69 import java.awt.FontMetrics;
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70 import java.awt.Frame;
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71 import java.awt.Graphics;
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72 import java.awt.Label;
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73 import java.awt.Menu;
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74 import java.awt.MenuBar;
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75 import java.awt.MenuItem;
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76 import java.awt.event.ActionEvent;
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77 import java.awt.event.ActionListener;
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78 import java.awt.event.FocusEvent;
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79 import java.awt.event.FocusListener;
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80 import java.awt.event.ItemEvent;
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81 import java.awt.event.ItemListener;
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82 import java.awt.event.KeyEvent;
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83 import java.awt.event.KeyListener;
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84 import java.awt.event.WindowAdapter;
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85 import java.awt.event.WindowEvent;
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86 import java.io.IOException;
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87 import java.net.URL;
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88 import java.net.URLEncoder;
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89 import java.util.Enumeration;
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90 import java.util.Hashtable;
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91 import java.util.List;
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92 import java.util.StringTokenizer;
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93 import java.util.Vector;
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96 public class AlignFrame extends EmbmenuFrame implements ActionListener,
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97 ItemListener, KeyListener
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99 public AlignmentPanel alignPanel;
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101 public AlignViewport viewport;
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103 int DEFAULT_WIDTH = 700;
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105 int DEFAULT_HEIGHT = 500;
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107 String jalviewServletURL;
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109 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
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110 String title, boolean embedded)
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112 if (applet != null)
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114 jalviewServletURL = applet.getParameter("APPLICATION_URL");
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120 } catch (Exception ex)
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122 ex.printStackTrace();
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125 viewport = new AlignViewport(al, applet);
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126 alignPanel = new AlignmentPanel(this, viewport);
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128 viewport.updateConservation(alignPanel);
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129 viewport.updateConsensus(alignPanel);
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131 annotationPanelMenuItem.setState(viewport.showAnnotation);
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132 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
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133 followMouseOverFlag.setState(viewport.getFollowHighlight());
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134 showGroupConsensus.setState(viewport.isShowGroupConsensus());
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135 showGroupConservation.setState(viewport.isShowGroupConservation());
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136 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
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137 showSequenceLogo.setState(viewport.isShowSequenceLogo());
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138 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
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140 seqLimits.setState(viewport.showJVSuffix);
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142 if (applet != null)
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144 String param = applet.getParameter("sortBy");
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147 if (param.equalsIgnoreCase("Id"))
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149 sortIDMenuItem_actionPerformed();
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151 else if (param.equalsIgnoreCase("Pairwise Identity"))
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153 sortPairwiseMenuItem_actionPerformed();
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155 else if (param.equalsIgnoreCase("Length"))
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157 sortLengthMenuItem_actionPerformed();
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161 param = applet.getParameter("wrap");
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164 if (param.equalsIgnoreCase("true"))
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166 wrapMenuItem.setState(true);
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167 wrapMenuItem_actionPerformed();
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170 param = applet.getParameter("centrecolumnlabels");
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173 centreColumnLabelFlag.setState(true);
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174 centreColumnLabelFlag_stateChanged();
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178 param = applet.getParameter("windowWidth");
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181 int width = Integer.parseInt(param);
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182 DEFAULT_WIDTH = width;
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184 param = applet.getParameter("windowHeight");
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187 int height = Integer.parseInt(param);
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188 DEFAULT_HEIGHT = height;
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190 } catch (Exception ex)
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195 if (viewport.getAlignment().isNucleotide())
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197 viewport.updateStrucConsensus(alignPanel);
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198 if (viewport.getAlignment().hasRNAStructure())
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200 RNAHelixColour.setEnabled(true);
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204 RNAHelixColour.setEnabled(false);
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209 RNAHelixColour.setEnabled(false);
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210 purinePyrimidineColour.setEnabled(false);
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213 // Some JVMS send keyevents to Top frame or lowest panel,
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214 // Havent worked out why yet. So add to both this frame and seqCanvas for
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216 this.addKeyListener(this);
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217 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
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218 alignPanel.idPanel.idCanvas.addKeyListener(this);
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219 alignPanel.scalePanel.addKeyListener(this);
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220 alignPanel.annotationPanel.addKeyListener(this);
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221 alignPanel.annotationPanelHolder.addKeyListener(this);
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222 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
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223 alignPanel.alabels.addKeyListener(this);
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224 createAlignFrameWindow(embedded, title);
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227 alignPanel.adjustAnnotationHeight();
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228 alignPanel.paintAlignment(true);
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231 public AlignViewport getAlignViewport()
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236 public SeqCanvas getSeqcanvas()
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238 return alignPanel.seqPanel.seqCanvas;
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242 * Load a features file onto the alignment
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245 * file URL, content, or other resolvable path
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247 * is protocol for accessing data referred to by file
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250 public boolean parseFeaturesFile(String file, String type)
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252 return parseFeaturesFile(file, type, true);
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256 * Load a features file onto the alignment
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259 * file URL, content, or other resolvable path
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261 * is protocol for accessing data referred to by file
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262 * @param autoenabledisplay
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263 * when true, display features flag will be automatically enabled if
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264 * features are loaded
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265 * @return true if data parsed as a features file
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267 public boolean parseFeaturesFile(String file, String type,
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268 boolean autoenabledisplay)
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270 // TODO: test if importing a features file onto an alignment which already
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271 // has features with links overwrites the original links.
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273 Hashtable featureLinks = new Hashtable();
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274 boolean featuresFile = false;
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277 featuresFile = new jalview.io.FeaturesFile(file, type)
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278 .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
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279 .getFeatureRenderer().featureColours, featureLinks,
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280 true, viewport.applet.getDefaultParameter(
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281 "relaxedidmatch", false));
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282 } catch (Exception ex)
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284 ex.printStackTrace();
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289 if (featureLinks.size() > 0)
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291 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
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293 if (autoenabledisplay)
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295 viewport.showSequenceFeatures = true;
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296 sequenceFeatures.setState(true);
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298 if (viewport.featureSettings != null)
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300 viewport.featureSettings.refreshTable();
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302 alignPanel.paintAlignment(true);
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303 statusBar.setText("Successfully added features to alignment.");
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305 return featuresFile;
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309 public void keyPressed(KeyEvent evt)
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311 if (viewport.cursorMode
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312 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
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313 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
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314 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
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315 && Character.isDigit(evt.getKeyChar()))
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316 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
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318 switch (evt.getKeyCode())
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320 case 27: // escape key
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321 deselectAllSequenceMenuItem_actionPerformed();
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323 alignPanel.alabels.cancelDrag();
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325 case KeyEvent.VK_X:
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326 if (evt.isControlDown() || evt.isMetaDown())
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328 cut_actionPerformed();
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331 case KeyEvent.VK_C:
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332 if (viewport.cursorMode && !evt.isControlDown())
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334 alignPanel.seqPanel.setCursorColumn();
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336 if (evt.isControlDown() || evt.isMetaDown())
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338 copy_actionPerformed();
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341 case KeyEvent.VK_V:
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342 if (evt.isControlDown())
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344 paste(evt.isShiftDown());
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347 case KeyEvent.VK_A:
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348 if (evt.isControlDown() || evt.isMetaDown())
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350 selectAllSequenceMenuItem_actionPerformed();
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353 case KeyEvent.VK_DOWN:
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354 if (viewport.cursorMode)
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356 alignPanel.seqPanel.moveCursor(0, 1);
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360 moveSelectedSequences(false);
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364 case KeyEvent.VK_UP:
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365 if (viewport.cursorMode)
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367 alignPanel.seqPanel.moveCursor(0, -1);
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371 moveSelectedSequences(true);
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375 case KeyEvent.VK_LEFT:
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376 if (evt.isAltDown() || !viewport.cursorMode)
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377 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
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379 alignPanel.seqPanel.moveCursor(-1, 0);
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382 case KeyEvent.VK_RIGHT:
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383 if (evt.isAltDown() || !viewport.cursorMode)
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384 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
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386 alignPanel.seqPanel.moveCursor(1, 0);
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389 case KeyEvent.VK_SPACE:
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390 if (viewport.cursorMode)
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392 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
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393 || evt.isShiftDown() || evt.isAltDown());
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397 case KeyEvent.VK_DELETE:
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398 case KeyEvent.VK_BACK_SPACE:
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399 if (viewport.cursorMode)
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401 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
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402 || evt.isShiftDown() || evt.isAltDown());
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406 cut_actionPerformed();
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407 alignPanel.seqPanel.seqCanvas.repaint();
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411 case KeyEvent.VK_S:
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412 if (viewport.cursorMode)
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414 alignPanel.seqPanel.setCursorRow();
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417 case KeyEvent.VK_P:
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418 if (viewport.cursorMode)
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420 alignPanel.seqPanel.setCursorPosition();
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424 case KeyEvent.VK_ENTER:
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425 case KeyEvent.VK_COMMA:
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426 if (viewport.cursorMode)
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428 alignPanel.seqPanel.setCursorRowAndColumn();
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432 case KeyEvent.VK_Q:
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433 if (viewport.cursorMode)
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435 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
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438 case KeyEvent.VK_M:
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439 if (viewport.cursorMode)
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441 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
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445 case KeyEvent.VK_F2:
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446 viewport.cursorMode = !viewport.cursorMode;
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447 statusBar.setText("Keyboard editing mode is "
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448 + (viewport.cursorMode ? "on" : "off"));
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449 if (viewport.cursorMode)
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451 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
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452 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
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456 case KeyEvent.VK_F:
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457 if (evt.isControlDown())
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459 findMenuItem_actionPerformed();
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463 case KeyEvent.VK_H:
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465 boolean toggleSeqs = !evt.isControlDown();
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466 boolean toggleCols = !evt.isShiftDown();
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467 toggleHiddenRegions(toggleSeqs, toggleCols);
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471 case KeyEvent.VK_PAGE_UP:
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472 if (viewport.wrapAlignment)
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474 alignPanel.scrollUp(true);
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478 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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479 - viewport.endSeq + viewport.startSeq);
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483 case KeyEvent.VK_PAGE_DOWN:
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484 if (viewport.wrapAlignment)
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486 alignPanel.scrollUp(false);
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490 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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491 + viewport.endSeq - viewport.startSeq);
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495 case KeyEvent.VK_Z:
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496 if (evt.isControlDown())
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498 undoMenuItem_actionPerformed();
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502 case KeyEvent.VK_Y:
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503 if (evt.isControlDown())
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505 redoMenuItem_actionPerformed();
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509 case KeyEvent.VK_L:
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510 if (evt.isControlDown())
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512 trimAlignment(true);
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516 case KeyEvent.VK_R:
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517 if (evt.isControlDown())
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519 trimAlignment(false);
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523 case KeyEvent.VK_E:
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524 if (evt.isControlDown())
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526 if (evt.isShiftDown())
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528 this.removeAllGapsMenuItem_actionPerformed();
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532 removeGappedColumnMenuItem_actionPerformed();
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536 case KeyEvent.VK_I:
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537 if (evt.isControlDown())
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539 if (evt.isAltDown())
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541 invertColSel_actionPerformed();
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545 invertSequenceMenuItem_actionPerformed();
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550 case KeyEvent.VK_U:
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551 if (evt.isControlDown())
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553 this.deleteGroups_actionPerformed();
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557 case KeyEvent.VK_T:
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558 if (evt.isControlDown())
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565 alignPanel.paintAlignment(true);
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569 * called by key handler and the hide all/show all menu items
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571 * @param toggleSeqs
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572 * @param toggleCols
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574 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
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576 boolean hide = false;
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577 SequenceGroup sg = viewport.getSelectionGroup();
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578 if (!toggleSeqs && !toggleCols)
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580 // Hide everything by the current selection - this is a hack - we do the
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581 // invert and then hide
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582 // first check that there will be visible columns after the invert.
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583 if ((viewport.getColumnSelection() != null
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584 && viewport.getColumnSelection().getSelected() != null && viewport
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585 .getColumnSelection().getSelected().size() > 0)
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586 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
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589 // now invert the sequence set, if required - empty selection implies
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590 // that no hiding is required.
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593 invertSequenceMenuItem_actionPerformed();
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594 sg = viewport.getSelectionGroup();
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598 viewport.expandColSelection(sg, true);
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599 // finally invert the column selection and get the new sequence
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600 // selection and indicate it should be hidden.
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601 invertColSel_actionPerformed();
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608 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
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611 viewport.hideAllSelectedSeqs();
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613 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
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616 viewport.showAllHiddenSeqs();
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622 if (viewport.getColumnSelection().getSelected().size() > 0)
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624 viewport.hideSelectedColumns();
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627 viewport.setSelectionGroup(sg);
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632 viewport.showAllHiddenColumns();
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638 public void keyReleased(KeyEvent evt)
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643 public void keyTyped(KeyEvent evt)
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648 public void itemStateChanged(ItemEvent evt)
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650 if (evt.getSource() == displayNonconservedMenuItem)
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652 displayNonconservedMenuItem_actionPerformed();
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654 else if (evt.getSource() == colourTextMenuItem)
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656 colourTextMenuItem_actionPerformed();
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658 else if (evt.getSource() == wrapMenuItem)
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660 wrapMenuItem_actionPerformed();
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662 else if (evt.getSource() == scaleAbove)
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664 viewport.setScaleAboveWrapped(scaleAbove.getState());
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666 else if (evt.getSource() == scaleLeft)
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668 viewport.setScaleLeftWrapped(scaleLeft.getState());
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670 else if (evt.getSource() == scaleRight)
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672 viewport.setScaleRightWrapped(scaleRight.getState());
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674 else if (evt.getSource() == seqLimits)
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676 seqLimits_itemStateChanged();
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678 else if (evt.getSource() == viewBoxesMenuItem)
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680 viewport.setShowBoxes(viewBoxesMenuItem.getState());
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682 else if (evt.getSource() == viewTextMenuItem)
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684 viewport.setShowText(viewTextMenuItem.getState());
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686 else if (evt.getSource() == renderGapsMenuItem)
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688 viewport.setRenderGaps(renderGapsMenuItem.getState());
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690 else if (evt.getSource() == annotationPanelMenuItem)
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692 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
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693 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
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695 else if (evt.getSource() == sequenceFeatures)
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697 viewport.showSequenceFeatures(sequenceFeatures.getState());
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698 alignPanel.seqPanel.seqCanvas.repaint();
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700 else if (evt.getSource() == conservationMenuItem)
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702 conservationMenuItem_actionPerformed();
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704 else if (evt.getSource() == abovePIDThreshold)
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706 abovePIDThreshold_actionPerformed();
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708 else if (evt.getSource() == applyToAllGroups)
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710 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
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712 else if (evt.getSource() == autoCalculate)
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714 viewport.autoCalculateConsensus = autoCalculate.getState();
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716 else if (evt.getSource() == sortByTree)
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718 viewport.sortByTree = sortByTree.getState();
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720 else if (evt.getSource() == this.centreColumnLabelFlag)
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722 centreColumnLabelFlag_stateChanged();
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724 else if (evt.getSource() == this.followMouseOverFlag)
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726 mouseOverFlag_stateChanged();
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728 else if (evt.getSource() == showGroupConsensus)
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730 showGroupConsensus_actionPerformed();
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732 else if (evt.getSource() == showGroupConservation)
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734 showGroupConservation_actionPerformed();
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736 else if (evt.getSource() == showSequenceLogo)
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738 showSequenceLogo_actionPerformed();
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740 else if (evt.getSource() == normSequenceLogo)
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742 normSequenceLogo_actionPerformed();
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744 else if (evt.getSource() == showConsensusHistogram)
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746 showConsensusHistogram_actionPerformed();
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748 else if (evt.getSource() == applyAutoAnnotationSettings)
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750 applyAutoAnnotationSettings_actionPerformed();
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752 alignPanel.paintAlignment(true);
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755 private void mouseOverFlag_stateChanged()
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757 viewport.followHighlight = followMouseOverFlag.getState();
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758 // TODO: could kick the scrollTo mechanism to reset view for current
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762 private void centreColumnLabelFlag_stateChanged()
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764 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
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765 this.alignPanel.annotationPanel.repaint();
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769 public void actionPerformed(ActionEvent evt)
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771 Object source = evt.getSource();
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773 if (source == inputText)
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775 inputText_actionPerformed();
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777 else if (source == loadTree)
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779 loadTree_actionPerformed();
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781 else if (source == loadApplication)
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783 launchFullApplication();
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785 else if (source == loadAnnotations)
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789 else if (source == outputAnnotations)
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791 outputAnnotations(true);
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793 else if (source == outputFeatures)
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795 outputFeatures(true, "Jalview");
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797 else if (source == closeMenuItem)
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799 closeMenuItem_actionPerformed();
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801 else if (source == copy)
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803 copy_actionPerformed();
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805 else if (source == undoMenuItem)
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807 undoMenuItem_actionPerformed();
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809 else if (source == redoMenuItem)
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811 redoMenuItem_actionPerformed();
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813 else if (source == inputText)
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815 inputText_actionPerformed();
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817 else if (source == closeMenuItem)
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819 closeMenuItem_actionPerformed();
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821 else if (source == undoMenuItem)
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823 undoMenuItem_actionPerformed();
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825 else if (source == redoMenuItem)
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827 redoMenuItem_actionPerformed();
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829 else if (source == copy)
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831 copy_actionPerformed();
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833 else if (source == pasteNew)
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835 pasteNew_actionPerformed();
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837 else if (source == pasteThis)
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839 pasteThis_actionPerformed();
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841 else if (source == cut)
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843 cut_actionPerformed();
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845 else if (source == delete)
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847 delete_actionPerformed();
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849 else if (source == grpsFromSelection)
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851 makeGrpsFromSelection_actionPerformed();
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853 else if (source == deleteGroups)
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855 deleteGroups_actionPerformed();
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857 else if (source == selectAllSequenceMenuItem)
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859 selectAllSequenceMenuItem_actionPerformed();
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861 else if (source == deselectAllSequenceMenuItem)
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863 deselectAllSequenceMenuItem_actionPerformed();
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865 else if (source == invertSequenceMenuItem)
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867 invertSequenceMenuItem_actionPerformed();
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869 else if (source == invertColSel)
\r
871 viewport.invertColumnSelection();
\r
872 alignPanel.paintAlignment(true);
\r
874 else if (source == remove2LeftMenuItem)
\r
876 trimAlignment(true);
\r
878 else if (source == remove2RightMenuItem)
\r
880 trimAlignment(false);
\r
882 else if (source == removeGappedColumnMenuItem)
\r
884 removeGappedColumnMenuItem_actionPerformed();
\r
886 else if (source == removeAllGapsMenuItem)
\r
888 removeAllGapsMenuItem_actionPerformed();
\r
890 else if (source == findMenuItem)
\r
892 findMenuItem_actionPerformed();
\r
894 else if (source == font)
\r
896 new FontChooser(alignPanel);
\r
898 else if (source == newView)
\r
902 else if (source == showColumns)
\r
904 viewport.showAllHiddenColumns();
\r
905 alignPanel.paintAlignment(true);
\r
907 else if (source == showSeqs)
\r
909 viewport.showAllHiddenSeqs();
\r
910 alignPanel.paintAlignment(true);
\r
912 else if (source == hideColumns)
\r
914 viewport.hideSelectedColumns();
\r
915 alignPanel.paintAlignment(true);
\r
917 else if (source == hideSequences
\r
918 && viewport.getSelectionGroup() != null)
\r
920 viewport.hideAllSelectedSeqs();
\r
921 alignPanel.paintAlignment(true);
\r
923 else if (source == hideAllButSelection)
\r
925 toggleHiddenRegions(false, false);
\r
926 alignPanel.paintAlignment(true);
\r
928 else if (source == hideAllSelection)
\r
930 SequenceGroup sg = viewport.getSelectionGroup();
\r
931 viewport.expandColSelection(sg, false);
\r
932 viewport.hideAllSelectedSeqs();
\r
933 viewport.hideSelectedColumns();
\r
934 alignPanel.paintAlignment(true);
\r
936 else if (source == showAllHidden)
\r
938 viewport.showAllHiddenColumns();
\r
939 viewport.showAllHiddenSeqs();
\r
940 alignPanel.paintAlignment(true);
\r
942 else if (source == showGroupConsensus)
\r
944 showGroupConsensus_actionPerformed();
\r
946 else if (source == showGroupConservation)
\r
948 showGroupConservation_actionPerformed();
\r
950 else if (source == showSequenceLogo)
\r
952 showSequenceLogo_actionPerformed();
\r
954 else if (source == normSequenceLogo)
\r
956 normSequenceLogo_actionPerformed();
\r
958 else if (source == showConsensusHistogram)
\r
960 showConsensusHistogram_actionPerformed();
\r
962 else if (source == applyAutoAnnotationSettings)
\r
964 applyAutoAnnotationSettings_actionPerformed();
\r
966 else if (source == featureSettings)
\r
968 new FeatureSettings(alignPanel);
\r
970 else if (source == alProperties)
\r
972 StringBuffer contents = new jalview.io.AlignmentProperties(
\r
973 viewport.getAlignment()).formatAsString();
\r
974 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
975 cap.setText(contents.toString());
\r
976 Frame frame = new Frame();
\r
978 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
\r
979 + getTitle(), 400, 250);
\r
981 else if (source == overviewMenuItem)
\r
983 overviewMenuItem_actionPerformed();
\r
985 else if (source == noColourmenuItem)
\r
987 changeColour(null);
\r
989 else if (source == clustalColour)
\r
991 abovePIDThreshold.setState(false);
\r
992 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
\r
994 else if (source == zappoColour)
\r
996 changeColour(new ZappoColourScheme());
\r
998 else if (source == taylorColour)
\r
1000 changeColour(new TaylorColourScheme());
\r
1002 else if (source == hydrophobicityColour)
\r
1004 changeColour(new HydrophobicColourScheme());
\r
1006 else if (source == helixColour)
\r
1008 changeColour(new HelixColourScheme());
\r
1010 else if (source == strandColour)
\r
1012 changeColour(new StrandColourScheme());
\r
1014 else if (source == turnColour)
\r
1016 changeColour(new TurnColourScheme());
\r
1018 else if (source == buriedColour)
\r
1020 changeColour(new BuriedColourScheme());
\r
1022 else if (source == nucleotideColour)
\r
1024 changeColour(new NucleotideColourScheme());
\r
1026 else if (source == purinePyrimidineColour)
\r
1028 changeColour(new PurinePyrimidineColourScheme());
\r
1030 else if (source == RNAInteractionColour)
\r
1032 changeColour(new RNAInteractionColourScheme());
\r
1034 else if (source == RNAHelixColour)
\r
1036 new RNAHelicesColourChooser(viewport, alignPanel);
\r
1038 else if (source == modifyPID)
\r
1040 modifyPID_actionPerformed();
\r
1042 else if (source == modifyConservation)
\r
1044 modifyConservation_actionPerformed();
\r
1046 else if (source == userDefinedColour)
\r
1048 new UserDefinedColours(alignPanel, null);
\r
1050 else if (source == PIDColour)
\r
1052 changeColour(new PIDColourScheme());
\r
1054 else if (source == BLOSUM62Colour)
\r
1056 changeColour(new Blosum62ColourScheme());
\r
1058 else if (source == tcoffeeColour)
\r
1060 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
\r
1062 else if (source == annotationColour)
\r
1064 new AnnotationColourChooser(viewport, alignPanel);
\r
1066 else if (source == sortPairwiseMenuItem)
\r
1068 sortPairwiseMenuItem_actionPerformed();
\r
1070 else if (source == sortIDMenuItem)
\r
1072 sortIDMenuItem_actionPerformed();
\r
1074 else if (source == sortLengthMenuItem)
\r
1076 sortLengthMenuItem_actionPerformed();
\r
1078 else if (source == sortGroupMenuItem)
\r
1080 sortGroupMenuItem_actionPerformed();
\r
1082 else if (source == removeRedundancyMenuItem)
\r
1084 removeRedundancyMenuItem_actionPerformed();
\r
1086 else if (source == pairwiseAlignmentMenuItem)
\r
1088 pairwiseAlignmentMenuItem_actionPerformed();
\r
1090 else if (source == PCAMenuItem)
\r
1092 PCAMenuItem_actionPerformed();
\r
1094 else if (source == averageDistanceTreeMenuItem)
\r
1096 averageDistanceTreeMenuItem_actionPerformed();
\r
1098 else if (source == neighbourTreeMenuItem)
\r
1100 neighbourTreeMenuItem_actionPerformed();
\r
1102 else if (source == njTreeBlosumMenuItem)
\r
1104 njTreeBlosumMenuItem_actionPerformed();
\r
1106 else if (source == avDistanceTreeBlosumMenuItem)
\r
1108 avTreeBlosumMenuItem_actionPerformed();
\r
1110 else if (source == documentation)
\r
1112 documentation_actionPerformed();
\r
1114 else if (source == about)
\r
1116 about_actionPerformed();
\r
1121 public void inputText_actionPerformed()
\r
1123 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1124 Frame frame = new Frame();
\r
1126 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
\r
1129 protected void outputText_actionPerformed(ActionEvent e)
\r
1131 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1132 Frame frame = new Frame();
\r
1134 jalview.bin.JalviewLite.addFrame(frame,
\r
1135 "Alignment output - " + e.getActionCommand(), 600, 500);
\r
1136 cap.setText(new AppletFormatAdapter().formatSequences(
\r
1137 e.getActionCommand(), viewport.getAlignment(),
\r
1138 viewport.showJVSuffix));
\r
1141 public void loadAnnotations()
\r
1143 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1144 cap.setText("Paste your features / annotations / T-coffee score file here.");
\r
1145 cap.setAnnotationImport();
\r
1146 Frame frame = new Frame();
\r
1148 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
\r
1152 public String outputAnnotations(boolean displayTextbox)
\r
1154 String annotation = new AnnotationFile().printAnnotations(
\r
1155 viewport.showAnnotation ? viewport.getAlignment()
\r
1156 .getAlignmentAnnotation() : null, viewport
\r
1157 .getAlignment().getGroups(), ((Alignment) viewport
\r
1158 .getAlignment()).alignmentProperties);
\r
1160 if (displayTextbox)
\r
1162 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
1163 Frame frame = new Frame();
\r
1165 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
\r
1166 cap.setText(annotation);
\r
1169 return annotation;
\r
1172 private Hashtable getDisplayedFeatureCols()
\r
1174 if (alignPanel.getFeatureRenderer() != null
\r
1175 && viewport.featuresDisplayed != null)
\r
1177 FeatureRenderer fr = alignPanel.getFeatureRenderer();
\r
1178 Hashtable fcols = new Hashtable();
\r
1179 Enumeration en = viewport.featuresDisplayed.keys();
\r
1180 while (en.hasMoreElements())
\r
1182 Object col = en.nextElement();
\r
1183 fcols.put(col, fr.featureColours.get(col));
\r
1190 public String outputFeatures(boolean displayTextbox, String format)
\r
1193 if (format.equalsIgnoreCase("Jalview"))
\r
1195 features = new FeaturesFile().printJalviewFormat(viewport
\r
1196 .getAlignment().getSequencesArray(),
\r
1197 getDisplayedFeatureCols());
\r
1201 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
\r
1202 .getSequencesArray(), getDisplayedFeatureCols());
\r
1205 if (displayTextbox)
\r
1207 boolean frimport = false;
\r
1208 if (features == null || features.equals("No Features Visible"))
\r
1210 features = "# No features visible - paste some and import them here.";
\r
1214 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
\r
1217 cap.setAnnotationImport();
\r
1219 Frame frame = new Frame();
\r
1221 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
\r
1222 cap.setText(features);
\r
1226 if (features == null)
\r
1233 void launchFullApplication()
\r
1235 StringBuffer url = new StringBuffer(jalviewServletURL);
\r
1237 url.append("?open="
\r
1238 + appendProtocol(viewport.applet.getParameter("file")));
\r
1240 if (viewport.applet.getParameter("features") != null)
\r
1242 url.append("&features=");
\r
1243 url.append(appendProtocol(viewport.applet.getParameter("features")));
\r
1246 if (viewport.applet.getParameter("annotations") != null)
\r
1248 url.append("&annotations=");
\r
1249 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
\r
1252 if (viewport.applet.getParameter("jnetfile") != null)
\r
1254 url.append("&annotations=");
\r
1255 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
\r
1258 if (viewport.applet.getParameter("defaultColour") != null)
\r
1260 url.append("&colour="
\r
1261 + removeWhiteSpace(viewport.applet
\r
1262 .getParameter("defaultColour")));
\r
1265 if (viewport.applet.getParameter("userDefinedColour") != null)
\r
1267 url.append("&colour="
\r
1268 + removeWhiteSpace(viewport.applet
\r
1269 .getParameter("userDefinedColour")));
\r
1271 if (viewport.applet.getParameter("tree") != null)
\r
1273 url.append("&tree="
\r
1274 + appendProtocol(viewport.applet.getParameter("tree")));
\r
1276 if (viewport.applet.getParameter("treeFile") != null)
\r
1278 url.append("&tree="
\r
1279 + appendProtocol(viewport.applet.getParameter("treeFile")));
\r
1282 showURL(url.toString(), "FULL_APP");
\r
1285 String removeWhiteSpace(String colour)
\r
1287 StringBuffer sb = new StringBuffer();
\r
1288 for (int i = 0; i < colour.length(); i++)
\r
1290 if (Character.isWhitespace(colour.charAt(i)))
\r
1296 sb.append(colour.charAt(i));
\r
1300 return sb.toString();
\r
1303 String appendProtocol(String url)
\r
1308 url = URLEncoder.encode(url);
\r
1311 * When we finally deprecate 1.1 compatibility, we can start to use
\r
1312 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
\r
1313 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
\r
1314 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
\r
1315 * ex.printStackTrace(); }
\r
1317 catch (java.net.MalformedURLException ex)
\r
1319 url = viewport.applet.getCodeBase() + url;
\r
1324 public void closeMenuItem_actionPerformed()
\r
1326 PaintRefresher.RemoveComponent(alignPanel);
\r
1327 if (alignPanel.seqPanel != null
\r
1328 && alignPanel.seqPanel.seqCanvas != null)
\r
1330 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
\r
1332 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
\r
1334 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
\r
1337 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
\r
1345 alignPanel = null;
\r
1352 void updateEditMenuBar()
\r
1355 if (viewport.historyList.size() > 0)
\r
1357 undoMenuItem.setEnabled(true);
\r
1358 CommandI command = (CommandI) viewport.historyList.peek();
\r
1359 undoMenuItem.setLabel("Undo " + command.getDescription());
\r
1363 undoMenuItem.setEnabled(false);
\r
1364 undoMenuItem.setLabel("Undo");
\r
1367 if (viewport.redoList.size() > 0)
\r
1369 redoMenuItem.setEnabled(true);
\r
1371 CommandI command = (CommandI) viewport.redoList.peek();
\r
1372 redoMenuItem.setLabel("Redo " + command.getDescription());
\r
1376 redoMenuItem.setEnabled(false);
\r
1377 redoMenuItem.setLabel("Redo");
\r
1384 public void addHistoryItem(CommandI command)
\r
1386 if (command.getSize() > 0)
\r
1388 viewport.historyList.push(command);
\r
1389 viewport.redoList.removeAllElements();
\r
1390 updateEditMenuBar();
\r
1391 viewport.updateHiddenColumns();
\r
1396 * TODO: JAL-1104 DOCUMENT ME!
\r
1401 protected void undoMenuItem_actionPerformed()
\r
1403 if (viewport.historyList.size() < 1)
\r
1408 CommandI command = (CommandI) viewport.historyList.pop();
\r
1409 viewport.redoList.push(command);
\r
1410 command.undoCommand(null);
\r
1412 AlignViewport originalSource = getOriginatingSource(command);
\r
1414 if (originalSource != viewport)
\r
1417 .println("Warning: Viewport object mismatch whilst undoing");
\r
1419 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
\r
1420 // viewport.getColumnSelection().getHiddenColumns()
\r
1422 updateEditMenuBar();
\r
1423 originalSource.firePropertyChange("alignment", null, originalSource
\r
1424 .getAlignment().getSequences());
\r
1428 * TODO: JAL-1104 DOCUMENT ME!
\r
1433 protected void redoMenuItem_actionPerformed()
\r
1435 if (viewport.redoList.size() < 1)
\r
1440 CommandI command = (CommandI) viewport.redoList.pop();
\r
1441 viewport.historyList.push(command);
\r
1442 command.doCommand(null);
\r
1444 AlignViewport originalSource = getOriginatingSource(command);
\r
1446 if (originalSource != viewport)
\r
1449 .println("Warning: Viewport object mismatch whilst re-doing");
\r
1451 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
\r
1452 // viewport.getColumnSelection().getHiddenColumns()
\r
1455 updateEditMenuBar();
\r
1456 originalSource.firePropertyChange("alignment", null, originalSource
\r
1457 .getAlignment().getSequences());
\r
1460 AlignViewport getOriginatingSource(CommandI command)
\r
1462 AlignViewport originalSource = null;
\r
1463 // For sequence removal and addition, we need to fire
\r
1464 // the property change event FROM the viewport where the
\r
1465 // original alignment was altered
\r
1466 AlignmentI al = null;
\r
1467 if (command instanceof EditCommand)
\r
1469 EditCommand editCommand = (EditCommand) command;
\r
1470 al = editCommand.getAlignment();
\r
1471 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
1472 .getSequenceSetId());
\r
1473 for (int i = 0; i < comps.size(); i++)
\r
1475 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
1477 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
\r
1479 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
\r
1486 if (originalSource == null)
\r
1488 // The original view is closed, we must validate
\r
1489 // the current view against the closed view first
\r
1492 PaintRefresher.validateSequences(al, viewport.getAlignment());
\r
1495 originalSource = viewport;
\r
1498 return originalSource;
\r
1501 public void moveSelectedSequences(boolean up)
\r
1503 SequenceGroup sg = viewport.getSelectionGroup();
\r
1508 viewport.getAlignment().moveSelectedSequencesByOne(sg,
\r
1509 up ? null : viewport.getHiddenRepSequences(), up);
\r
1510 alignPanel.paintAlignment(true);
\r
1513 synchronized void slideSequences(boolean right, int size)
\r
1515 List<SequenceI> sg = new Vector<SequenceI>();
\r
1516 if (viewport.cursorMode)
\r
1518 sg.add(viewport.getAlignment().getSequenceAt(
\r
1519 alignPanel.seqPanel.seqCanvas.cursorY));
\r
1521 else if (viewport.getSelectionGroup() != null
\r
1522 && viewport.getSelectionGroup().getSize() != viewport
\r
1523 .getAlignment().getHeight())
\r
1525 sg = viewport.getSelectionGroup().getSequences(
\r
1526 viewport.getHiddenRepSequences());
\r
1529 if (sg.size() < 1)
\r
1534 Vector<SequenceI> invertGroup = new Vector();
\r
1536 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
\r
1538 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
\r
1539 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
\r
1542 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
\r
1544 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
\r
1546 for (int i = 0; i < invertGroup.size(); i++)
\r
1547 seqs2[i] = invertGroup.elementAt(i);
\r
1549 SlideSequencesCommand ssc;
\r
1551 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
\r
1552 size, viewport.getGapCharacter());
\r
1554 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
\r
1555 size, viewport.getGapCharacter());
\r
1557 int groupAdjustment = 0;
\r
1558 if (ssc.getGapsInsertedBegin() && right)
\r
1560 if (viewport.cursorMode)
\r
1561 alignPanel.seqPanel.moveCursor(size, 0);
\r
1563 groupAdjustment = size;
\r
1565 else if (!ssc.getGapsInsertedBegin() && !right)
\r
1567 if (viewport.cursorMode)
\r
1568 alignPanel.seqPanel.moveCursor(-size, 0);
\r
1570 groupAdjustment = -size;
\r
1573 if (groupAdjustment != 0)
\r
1575 viewport.getSelectionGroup().setStartRes(
\r
1576 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
\r
1577 viewport.getSelectionGroup().setEndRes(
\r
1578 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
\r
1581 boolean appendHistoryItem = false;
\r
1582 if (viewport.historyList != null && viewport.historyList.size() > 0
\r
1583 && viewport.historyList.peek() instanceof SlideSequencesCommand)
\r
1585 appendHistoryItem = ssc
\r
1586 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
\r
1590 if (!appendHistoryItem)
\r
1591 addHistoryItem(ssc);
\r
1596 static StringBuffer copiedSequences;
\r
1598 static Vector copiedHiddenColumns;
\r
1600 protected void copy_actionPerformed()
\r
1602 if (viewport.getSelectionGroup() == null)
\r
1607 SequenceGroup sg = viewport.getSelectionGroup();
\r
1608 copiedSequences = new StringBuffer();
\r
1609 Hashtable orderedSeqs = new Hashtable();
\r
1610 for (int i = 0; i < sg.getSize(); i++)
\r
1612 SequenceI seq = sg.getSequenceAt(i);
\r
1613 int index = viewport.getAlignment().findIndex(seq);
\r
1614 orderedSeqs.put(index + "", seq);
\r
1617 int index = 0, startRes, endRes;
\r
1620 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
\r
1622 copiedHiddenColumns = new Vector();
\r
1623 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
\r
1624 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
\r
1627 int[] region = (int[]) viewport.getColumnSelection()
\r
1628 .getHiddenColumns().elementAt(i);
\r
1630 copiedHiddenColumns.addElement(new int[]
\r
1631 { region[0] - hiddenOffset, region[1] - hiddenOffset });
\r
1636 copiedHiddenColumns = null;
\r
1639 for (int i = 0; i < sg.getSize(); i++)
\r
1641 SequenceI seq = null;
\r
1643 while (seq == null)
\r
1645 if (orderedSeqs.containsKey(index + ""))
\r
1647 seq = (SequenceI) orderedSeqs.get(index + "");
\r
1659 // Returns residue following index if gap
\r
1660 startRes = seq.findPosition(sg.getStartRes());
\r
1663 // Need to find the residue preceeding index if gap
\r
1666 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
\r
1668 ch = seq.getCharAt(j);
\r
1669 if (!jalview.util.Comparison.isGap((ch)))
\r
1677 endRes += seq.getStart() - 1;
\r
1680 copiedSequences.append(seq.getName()
\r
1686 + seq.getSequenceAsString(sg.getStartRes(),
\r
1687 sg.getEndRes() + 1) + "\n");
\r
1692 protected void pasteNew_actionPerformed()
\r
1697 protected void pasteThis_actionPerformed()
\r
1702 void paste(boolean newAlignment)
\r
1707 if (copiedSequences == null)
\r
1712 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
1713 Vector seqs = new Vector();
\r
1714 while (st.hasMoreElements())
\r
1716 String name = st.nextToken();
\r
1717 int start = Integer.parseInt(st.nextToken());
\r
1718 int end = Integer.parseInt(st.nextToken());
\r
1719 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
\r
1721 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
1722 for (int i = 0; i < seqs.size(); i++)
\r
1724 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
1729 String newtitle = new String("Copied sequences");
\r
1730 if (getTitle().startsWith("Copied sequences"))
\r
1732 newtitle = getTitle();
\r
1736 newtitle = newtitle.concat("- from " + getTitle());
\r
1738 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
1739 viewport.applet, newtitle, false);
\r
1740 if (copiedHiddenColumns != null)
\r
1742 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
1744 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
1745 af.viewport.hideColumns(region[0], region[1]);
\r
1749 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
\r
1754 addSequences(newSeqs);
\r
1757 } catch (Exception ex)
\r
1759 } // could be anything being pasted in here
\r
1763 void addSequences(SequenceI[] seqs)
\r
1765 for (int i = 0; i < seqs.length; i++)
\r
1767 viewport.getAlignment().addSequence(seqs[i]);
\r
1771 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
\r
1772 seqs, 0, viewport.getAlignment().getWidth(),
\r
1773 viewport.getAlignment()));
\r
1775 viewport.setEndSeq(viewport.getAlignment().getHeight());
\r
1776 viewport.getAlignment().getWidth();
\r
1777 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1782 protected void cut_actionPerformed()
\r
1784 copy_actionPerformed();
\r
1785 delete_actionPerformed();
\r
1788 protected void delete_actionPerformed()
\r
1791 SequenceGroup sg = viewport.getSelectionGroup();
\r
1797 Vector seqs = new Vector();
\r
1799 for (int i = 0; i < sg.getSize(); i++)
\r
1801 seq = sg.getSequenceAt(i);
\r
1802 seqs.addElement(seq);
\r
1805 // If the cut affects all sequences, remove highlighted columns
\r
1806 if (sg.getSize() == viewport.getAlignment().getHeight())
\r
1808 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
1809 sg.getEndRes() + 1);
\r
1812 SequenceI[] cut = new SequenceI[seqs.size()];
\r
1813 for (int i = 0; i < seqs.size(); i++)
\r
1815 cut[i] = (SequenceI) seqs.elementAt(i);
\r
1819 * //ADD HISTORY ITEM
\r
1821 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
\r
1822 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
\r
1823 viewport.getAlignment()));
\r
1825 viewport.setSelectionGroup(null);
\r
1826 viewport.getAlignment().deleteGroup(sg);
\r
1828 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1831 if (viewport.getAlignment().getHeight() < 1)
\r
1833 this.setVisible(false);
\r
1835 viewport.sendSelection();
\r
1839 * group consensus toggled
\r
1842 protected void showGroupConsensus_actionPerformed()
\r
1844 viewport.setShowGroupConsensus(showGroupConsensus.getState());
\r
1845 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1850 * group conservation toggled.
\r
1852 protected void showGroupConservation_actionPerformed()
\r
1854 viewport.setShowGroupConservation(showGroupConservation.getState());
\r
1855 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1862 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
\r
1863 * .event.ActionEvent)
\r
1865 protected void showConsensusHistogram_actionPerformed()
\r
1867 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
\r
1868 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1875 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
\r
1876 * .event.ActionEvent)
\r
1878 protected void showSequenceLogo_actionPerformed()
\r
1880 viewport.setShowSequenceLogo(showSequenceLogo.getState());
\r
1881 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1884 protected void normSequenceLogo_actionPerformed()
\r
1886 showSequenceLogo.setState(true);
\r
1887 viewport.setShowSequenceLogo(true);
\r
1888 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
\r
1889 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1892 protected void applyAutoAnnotationSettings_actionPerformed()
\r
1894 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1897 protected void makeGrpsFromSelection_actionPerformed()
\r
1899 if (viewport.getSelectionGroup() != null)
\r
1901 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
\r
1902 viewport.getSequenceSelection(),
\r
1903 viewport.getAlignmentView(true).getSequenceStrings(
\r
1904 viewport.getGapCharacter()), viewport.getAlignment()
\r
1906 viewport.getAlignment().deleteAllGroups();
\r
1907 viewport.sequenceColours = null;
\r
1908 viewport.setSelectionGroup(null);
\r
1909 // set view properties for each group
\r
1910 for (int g = 0; g < gps.length; g++)
\r
1912 // gps[g].setShowunconserved(viewport.getShowUnconserved());
\r
1913 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
\r
1914 viewport.getAlignment().addGroup(gps[g]);
\r
1915 Color col = new Color((int) (Math.random() * 255),
\r
1916 (int) (Math.random() * 255), (int) (Math.random() * 255));
\r
1917 col = col.brighter();
\r
1918 for (SequenceI sq : gps[g].getSequences(null))
\r
1919 viewport.setSequenceColour(sq, col);
\r
1921 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
\r
1922 alignPanel.updateAnnotation();
\r
1923 alignPanel.paintAlignment(true);
\r
1927 protected void deleteGroups_actionPerformed()
\r
1929 viewport.getAlignment().deleteAllGroups();
\r
1930 viewport.sequenceColours = null;
\r
1931 viewport.setSelectionGroup(null);
\r
1933 alignPanel.paintAlignment(true);
\r
1936 public void selectAllSequenceMenuItem_actionPerformed()
\r
1938 SequenceGroup sg = new SequenceGroup();
\r
1939 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1941 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
1943 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
\r
1944 viewport.setSelectionGroup(sg);
\r
1945 alignPanel.paintAlignment(true);
\r
1946 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1947 viewport.sendSelection();
\r
1950 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1952 if (viewport.cursorMode)
\r
1954 alignPanel.seqPanel.keyboardNo1 = null;
\r
1955 alignPanel.seqPanel.keyboardNo2 = null;
\r
1957 viewport.setSelectionGroup(null);
\r
1958 viewport.getColumnSelection().clear();
\r
1959 viewport.setSelectionGroup(null);
\r
1960 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1961 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1962 alignPanel.paintAlignment(true);
\r
1963 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1964 viewport.sendSelection();
\r
1967 public void invertSequenceMenuItem_actionPerformed()
\r
1969 SequenceGroup sg = viewport.getSelectionGroup();
\r
1970 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1972 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1975 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1976 viewport.sendSelection();
\r
1979 public void invertColSel_actionPerformed()
\r
1981 viewport.invertColumnSelection();
\r
1982 alignPanel.paintAlignment(true);
\r
1983 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1984 viewport.sendSelection();
\r
1987 void trimAlignment(boolean trimLeft)
\r
1989 ColumnSelection colSel = viewport.getColumnSelection();
\r
1992 if (colSel.size() > 0)
\r
1996 column = colSel.getMin();
\r
2000 column = colSel.getMax();
\r
2004 if (viewport.getSelectionGroup() != null)
\r
2006 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2007 viewport.getHiddenRepSequences());
\r
2011 seqs = viewport.getAlignment().getSequencesArray();
\r
2014 TrimRegionCommand trimRegion;
\r
2017 trimRegion = new TrimRegionCommand("Remove Left",
\r
2018 TrimRegionCommand.TRIM_LEFT, seqs, column,
\r
2019 viewport.getAlignment(), viewport.getColumnSelection(),
\r
2020 viewport.getSelectionGroup());
\r
2021 viewport.setStartRes(0);
\r
2025 trimRegion = new TrimRegionCommand("Remove Right",
\r
2026 TrimRegionCommand.TRIM_RIGHT, seqs, column,
\r
2027 viewport.getAlignment(), viewport.getColumnSelection(),
\r
2028 viewport.getSelectionGroup());
\r
2031 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
\r
2033 addHistoryItem(trimRegion);
\r
2035 for (SequenceGroup sg : viewport.getAlignment().getGroups())
\r
2037 if ((trimLeft && !sg.adjustForRemoveLeft(column))
\r
2038 || (!trimLeft && !sg.adjustForRemoveRight(column)))
\r
2040 viewport.getAlignment().deleteGroup(sg);
\r
2044 viewport.firePropertyChange("alignment", null, viewport
\r
2045 .getAlignment().getSequences());
\r
2049 public void removeGappedColumnMenuItem_actionPerformed()
\r
2051 int start = 0, end = viewport.getAlignment().getWidth() - 1;
\r
2054 if (viewport.getSelectionGroup() != null)
\r
2056 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2057 viewport.getHiddenRepSequences());
\r
2058 start = viewport.getSelectionGroup().getStartRes();
\r
2059 end = viewport.getSelectionGroup().getEndRes();
\r
2063 seqs = viewport.getAlignment().getSequencesArray();
\r
2066 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
\r
2067 "Remove Gapped Columns", seqs, start, end,
\r
2068 viewport.getAlignment());
\r
2070 addHistoryItem(removeGapCols);
\r
2072 statusBar.setText("Removed " + removeGapCols.getSize()
\r
2073 + " empty columns.");
\r
2075 // This is to maintain viewport position on first residue
\r
2076 // of first sequence
\r
2077 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
\r
2078 int startRes = seq.findPosition(viewport.startRes);
\r
2079 // ShiftList shifts;
\r
2080 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
\r
2081 // edit.alColumnChanges=shifts.getInverse();
\r
2082 // if (viewport.hasHiddenColumns)
\r
2083 // viewport.getColumnSelection().compensateForEdits(shifts);
\r
2084 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
2085 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
2090 public void removeAllGapsMenuItem_actionPerformed()
\r
2092 int start = 0, end = viewport.getAlignment().getWidth() - 1;
\r
2095 if (viewport.getSelectionGroup() != null)
\r
2097 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2098 viewport.getHiddenRepSequences());
\r
2099 start = viewport.getSelectionGroup().getStartRes();
\r
2100 end = viewport.getSelectionGroup().getEndRes();
\r
2104 seqs = viewport.getAlignment().getSequencesArray();
\r
2107 // This is to maintain viewport position on first residue
\r
2108 // of first sequence
\r
2109 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
\r
2110 int startRes = seq.findPosition(viewport.startRes);
\r
2112 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
\r
2113 viewport.getAlignment()));
\r
2115 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
2117 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
2122 public void findMenuItem_actionPerformed()
\r
2124 new Finder(alignPanel);
\r
2128 * create a new view derived from the current view
\r
2130 * @param viewtitle
\r
2131 * @return frame for the new view
\r
2133 public AlignFrame newView(String viewtitle)
\r
2136 if (viewport.hasHiddenRows())
\r
2138 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
\r
2139 .getFullAlignment().getSequencesArray());
\r
2143 newal = new Alignment(viewport.getAlignment().getSequencesArray());
\r
2146 if (viewport.getAlignment().getAlignmentAnnotation() != null)
\r
2148 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
\r
2150 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
\r
2152 newal.addAnnotation(viewport.getAlignment()
\r
2153 .getAlignmentAnnotation()[i]);
\r
2158 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
\r
2160 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
\r
2161 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
\r
2162 PaintRefresher.Register(newaf.alignPanel,
\r
2163 newaf.alignPanel.av.getSequenceSetId());
\r
2165 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
\r
2166 newaf.alignPanel.av.getSequenceSetId());
\r
2167 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
\r
2168 newaf.alignPanel.av.getSequenceSetId());
\r
2170 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
2171 .getSequenceSetId());
\r
2172 int viewSize = -1;
\r
2173 for (int i = 0; i < comps.size(); i++)
\r
2175 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
2181 String title = new String(this.getTitle());
\r
2182 if (viewtitle != null)
\r
2184 title = viewtitle + " ( " + title + ")";
\r
2188 if (title.indexOf("(View") > -1)
\r
2190 title = title.substring(0, title.indexOf("(View"));
\r
2192 title += "(View " + viewSize + ")";
\r
2195 newaf.setTitle(title.toString());
\r
2197 newaf.viewport.historyList = viewport.historyList;
\r
2198 newaf.viewport.redoList = viewport.redoList;
\r
2204 * @return list of feature groups on the view
\r
2206 public String[] getFeatureGroups()
\r
2208 FeatureRenderer fr = null;
\r
2209 if (alignPanel != null
\r
2210 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2212 return fr.getGroups();
\r
2218 * get sequence feature groups that are hidden or shown
\r
2224 public String[] getFeatureGroupsOfState(boolean visible)
\r
2226 FeatureRenderer fr = null;
\r
2227 if (alignPanel != null
\r
2228 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2230 return fr.getGroups(visible);
\r
2236 * Change the display state for the given feature groups
\r
2239 * list of group strings
\r
2241 * visible or invisible
\r
2243 public void setFeatureGroupState(String[] groups, boolean state)
\r
2245 FeatureRenderer fr = null;
\r
2246 this.sequenceFeatures.setState(true);
\r
2247 viewport.showSequenceFeatures(true);
\r
2248 if (alignPanel != null
\r
2249 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2251 fr.setGroupState(groups, state);
\r
2252 alignPanel.seqPanel.seqCanvas.repaint();
\r
2253 if (alignPanel.overviewPanel != null)
\r
2255 alignPanel.overviewPanel.updateOverviewImage();
\r
2260 public void seqLimits_itemStateChanged()
\r
2262 viewport.setShowJVSuffix(seqLimits.getState());
\r
2263 alignPanel.fontChanged();
\r
2264 alignPanel.paintAlignment(true);
\r
2267 protected void colourTextMenuItem_actionPerformed()
\r
2269 viewport.setColourText(colourTextMenuItem.getState());
\r
2270 alignPanel.paintAlignment(true);
\r
2273 protected void displayNonconservedMenuItem_actionPerformed()
\r
2275 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
\r
2276 alignPanel.paintAlignment(true);
\r
2279 protected void wrapMenuItem_actionPerformed()
\r
2281 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
2282 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
2283 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
2284 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
2285 scaleRight.setEnabled(wrapMenuItem.getState());
\r
2286 alignPanel.paintAlignment(true);
\r
2289 public void overviewMenuItem_actionPerformed()
\r
2291 if (alignPanel.overviewPanel != null)
\r
2296 Frame frame = new Frame();
\r
2297 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
2298 frame.add(overview);
\r
2299 // +50 must allow for applet frame window
\r
2300 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
2301 overview.getPreferredSize().width,
\r
2302 overview.getPreferredSize().height + 50);
\r
2305 final AlignmentPanel ap = alignPanel;
\r
2306 frame.addWindowListener(new WindowAdapter()
\r
2309 public void windowClosing(WindowEvent e)
\r
2313 ap.setOverviewPanel(null);
\r
2318 alignPanel.setOverviewPanel(overview);
\r
2322 void changeColour(ColourSchemeI cs)
\r
2324 int threshold = 0;
\r
2328 if (viewport.getAbovePIDThreshold())
\r
2330 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
2333 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2335 viewport.setGlobalColourScheme(cs);
\r
2339 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2342 if (viewport.getConservationSelected())
\r
2345 Alignment al = (Alignment) viewport.getAlignment();
\r
2346 Conservation c = new Conservation("All",
\r
2347 ResidueProperties.propHash, 3, al.getSequences(), 0,
\r
2348 al.getWidth() - 1);
\r
2351 c.verdict(false, viewport.getConsPercGaps());
\r
2353 cs.setConservation(c);
\r
2355 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
\r
2356 cs, "Background"));
\r
2361 cs.setConservation(null);
\r
2364 cs.setConsensus(viewport.getSequenceConsensusHash());
\r
2367 viewport.setGlobalColourScheme(cs);
\r
2369 if (alignPanel.getOverviewPanel() != null)
\r
2371 alignPanel.getOverviewPanel().updateOverviewImage();
\r
2374 jalview.structure.StructureSelectionManager
\r
2375 .getStructureSelectionManager(viewport.applet)
\r
2376 .sequenceColoursChanged(alignPanel);
\r
2378 alignPanel.paintAlignment(true);
\r
2381 protected void modifyPID_actionPerformed()
\r
2383 if (viewport.getAbovePIDThreshold()
\r
2384 && viewport.getGlobalColourScheme() != null)
\r
2386 SliderPanel.setPIDSliderSource(alignPanel,
\r
2387 viewport.getGlobalColourScheme(), "Background");
\r
2388 SliderPanel.showPIDSlider();
\r
2392 protected void modifyConservation_actionPerformed()
\r
2394 if (viewport.getConservationSelected()
\r
2395 && viewport.getGlobalColourScheme() != null)
\r
2397 SliderPanel.setConservationSlider(alignPanel,
\r
2398 viewport.getGlobalColourScheme(), "Background");
\r
2399 SliderPanel.showConservationSlider();
\r
2403 protected void conservationMenuItem_actionPerformed()
\r
2405 viewport.setConservationSelected(conservationMenuItem.getState());
\r
2407 viewport.setAbovePIDThreshold(false);
\r
2408 abovePIDThreshold.setState(false);
\r
2410 changeColour(viewport.getGlobalColourScheme());
\r
2412 modifyConservation_actionPerformed();
\r
2415 public void abovePIDThreshold_actionPerformed()
\r
2417 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
2419 conservationMenuItem.setState(false);
\r
2420 viewport.setConservationSelected(false);
\r
2422 changeColour(viewport.getGlobalColourScheme());
\r
2424 modifyPID_actionPerformed();
\r
2427 public void sortPairwiseMenuItem_actionPerformed()
\r
2429 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2430 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
\r
2431 .getAlignment().getSequenceAt(0), null);
\r
2433 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
\r
2434 viewport.getAlignment()));
\r
2435 alignPanel.paintAlignment(true);
\r
2438 public void sortIDMenuItem_actionPerformed()
\r
2440 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2441 AlignmentSorter.sortByID(viewport.getAlignment());
\r
2442 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
\r
2443 viewport.getAlignment()));
\r
2444 alignPanel.paintAlignment(true);
\r
2447 public void sortLengthMenuItem_actionPerformed()
\r
2449 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2450 AlignmentSorter.sortByLength(viewport.getAlignment());
\r
2451 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
\r
2452 viewport.getAlignment()));
\r
2453 alignPanel.paintAlignment(true);
\r
2456 public void sortGroupMenuItem_actionPerformed()
\r
2458 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2459 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
2460 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
\r
2461 viewport.getAlignment()));
\r
2462 alignPanel.paintAlignment(true);
\r
2466 public void removeRedundancyMenuItem_actionPerformed()
\r
2468 new RedundancyPanel(alignPanel);
\r
2471 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
2473 if (viewport.getSelectionGroup() != null
\r
2474 && viewport.getSelectionGroup().getSize() > 1)
\r
2476 Frame frame = new Frame();
\r
2477 frame.add(new PairwiseAlignPanel(alignPanel));
\r
2478 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
\r
2483 public void PCAMenuItem_actionPerformed()
\r
2485 // are the sequences aligned?
\r
2486 if (!viewport.getAlignment().isAligned(false))
\r
2488 SequenceI current;
\r
2489 int Width = viewport.getAlignment().getWidth();
\r
2491 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2493 current = viewport.getAlignment().getSequenceAt(i);
\r
2495 if (current.getLength() < Width)
\r
2497 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2500 alignPanel.paintAlignment(true);
\r
2503 if ((viewport.getSelectionGroup() != null
\r
2504 && viewport.getSelectionGroup().getSize() < 4 && viewport
\r
2505 .getSelectionGroup().getSize() > 0)
\r
2506 || viewport.getAlignment().getHeight() < 4)
\r
2513 new PCAPanel(viewport);
\r
2514 } catch (java.lang.OutOfMemoryError ex)
\r
2520 public void averageDistanceTreeMenuItem_actionPerformed()
\r
2522 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
2525 public void neighbourTreeMenuItem_actionPerformed()
\r
2527 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
2530 protected void njTreeBlosumMenuItem_actionPerformed()
\r
2532 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2535 protected void avTreeBlosumMenuItem_actionPerformed()
\r
2537 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2540 void NewTreePanel(String type, String pwType, String title)
\r
2542 // are the sequences aligned?
\r
2543 if (!viewport.getAlignment().isAligned(false))
\r
2545 SequenceI current;
\r
2546 int Width = viewport.getAlignment().getWidth();
\r
2548 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2550 current = viewport.getAlignment().getSequenceAt(i);
\r
2552 if (current.getLength() < Width)
\r
2554 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2557 alignPanel.paintAlignment(true);
\r
2561 if ((viewport.getSelectionGroup() != null && viewport
\r
2562 .getSelectionGroup().getSize() > 1)
\r
2563 || (viewport.getAlignment().getHeight() > 1))
\r
2565 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
\r
2567 addTreeMenuItem(tp, title);
\r
2569 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
2573 void loadTree_actionPerformed()
\r
2575 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
2576 cap.setText("Paste your Newick tree file here.");
\r
2577 cap.setTreeImport();
\r
2578 Frame frame = new Frame();
\r
2580 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
2583 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
2585 TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
\r
2586 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
2587 addTreeMenuItem(tp, treeFile);
\r
2591 * sort the alignment using the given treePanel
\r
2593 * @param treePanel
\r
2594 * tree used to sort view
\r
2596 * string used for undo event name
\r
2598 public void sortByTree(TreePanel treePanel, String title)
\r
2600 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2602 .sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
2603 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2604 // HistoryItem.SORT));
\r
2605 addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
\r
2606 viewport.getAlignment()));
\r
2607 alignPanel.paintAlignment(true);
\r
2611 * Do any automatic reordering of the alignment and add the necessary bits to
\r
2612 * the menu structure for the new tree
\r
2614 * @param treePanel
\r
2617 protected void addTreeMenuItem(final TreePanel treePanel,
\r
2618 final String title)
\r
2620 final MenuItem item = new MenuItem(title);
\r
2621 sortByTreeMenu.add(item);
\r
2622 item.addActionListener(new java.awt.event.ActionListener()
\r
2625 public void actionPerformed(ActionEvent evt)
\r
2627 sortByTree(treePanel, title); // treePanel.getTitle());
\r
2631 treePanel.addWindowListener(new WindowAdapter()
\r
2634 public void windowOpened(WindowEvent e)
\r
2636 if (viewport.sortByTree)
\r
2638 sortByTree(treePanel, title);
\r
2640 super.windowOpened(e);
\r
2644 public void windowClosing(WindowEvent e)
\r
2646 sortByTreeMenu.remove(item);
\r
2651 public boolean sortBy(AlignmentOrder alorder, String undoname)
\r
2653 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2654 if (viewport.applet.debug)
\r
2656 System.err.println("Sorting " + alorder.getOrder().size()
\r
2657 + " in alignment '" + getTitle() + "'");
\r
2659 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
\r
2660 if (undoname != null)
\r
2662 addHistoryItem(new OrderCommand(undoname, oldOrder,
\r
2663 viewport.getAlignment()));
\r
2665 alignPanel.paintAlignment(true);
\r
2669 protected void documentation_actionPerformed()
\r
2671 alignPanel.av.applet.openJalviewHelpUrl();
\r
2674 protected void about_actionPerformed()
\r
2677 class AboutPanel extends Canvas
\r
2683 public AboutPanel(String version, String builddate)
\r
2685 this.version = version;
\r
2686 this.builddate = builddate;
\r
2690 public void paint(Graphics g)
\r
2692 g.setColor(Color.white);
\r
2693 g.fillRect(0, 0, getSize().width, getSize().height);
\r
2694 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2695 FontMetrics fm = g.getFontMetrics();
\r
2696 int fh = fm.getHeight();
\r
2698 g.setColor(Color.black);
\r
2699 // TODO: update this text for each release or centrally store it for
\r
2700 // lite and application
\r
2701 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
2702 g.drawString("JalviewLite - Release " + version, x, y += fh);
\r
2703 g.setFont(new Font("Helvetica", Font.BOLD, 12));
\r
2704 g.drawString("Build date: " + builddate, x, y += fh);
\r
2705 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2707 "Authors: Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui,",
\r
2708 x, y += fh * 1.5);
\r
2710 "Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.",
\r
2711 x + 50, y += fh + 8);
\r
2713 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
\r
2716 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
\r
2718 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
\r
2720 "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
\r
2723 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
\r
2725 g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
\r
2730 Frame frame = new Frame();
\r
2731 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
\r
2732 .getBuildDate()));
\r
2733 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
\r
2737 public void showURL(String url, String target)
\r
2739 if (viewport.applet == null)
\r
2741 System.out.println("Not running as applet - no browser available.");
\r
2745 viewport.applet.showURL(url, target);
\r
2749 // ////////////////////////////////////////////////////////////////////////////////
\r
2750 // JBuilder Graphics here
\r
2752 MenuBar alignFrameMenuBar = new MenuBar();
\r
2754 Menu fileMenu = new Menu("File");
\r
2756 MenuItem loadApplication = new MenuItem("View in Full Application");
\r
2758 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
\r
2760 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
\r
2762 MenuItem outputFeatures = new MenuItem("Export Features ...");
\r
2764 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
\r
2766 MenuItem closeMenuItem = new MenuItem("Close");
\r
2768 Menu editMenu = new Menu("Edit");
\r
2770 Menu viewMenu = new Menu("View");
\r
2772 Menu colourMenu = new Menu("Colour");
\r
2774 Menu calculateMenu = new Menu("Calculate");
\r
2776 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
2778 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
2780 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
2782 MenuItem remove2LeftMenuItem = new MenuItem();
\r
2784 MenuItem remove2RightMenuItem = new MenuItem();
\r
2786 MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
2788 MenuItem removeAllGapsMenuItem = new MenuItem();
\r
2790 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
2792 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
2794 MenuItem sortPairwiseMenuItem = new MenuItem();
\r
2796 MenuItem sortIDMenuItem = new MenuItem();
\r
2798 MenuItem sortLengthMenuItem = new MenuItem();
\r
2800 MenuItem sortGroupMenuItem = new MenuItem();
\r
2802 MenuItem removeRedundancyMenuItem = new MenuItem();
\r
2804 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
2806 MenuItem PCAMenuItem = new MenuItem();
\r
2808 MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
2810 MenuItem neighbourTreeMenuItem = new MenuItem();
\r
2812 BorderLayout borderLayout1 = new BorderLayout();
\r
2814 public Label statusBar = new Label();
\r
2816 Menu outputTextboxMenu = new Menu();
\r
2818 MenuItem clustalColour = new MenuItem();
\r
2820 MenuItem zappoColour = new MenuItem();
\r
2822 MenuItem taylorColour = new MenuItem();
\r
2824 MenuItem hydrophobicityColour = new MenuItem();
\r
2826 MenuItem helixColour = new MenuItem();
\r
2828 MenuItem strandColour = new MenuItem();
\r
2830 MenuItem turnColour = new MenuItem();
\r
2832 MenuItem buriedColour = new MenuItem();
\r
2834 MenuItem purinePyrimidineColour = new MenuItem();
\r
2836 MenuItem RNAInteractionColour = new MenuItem();
\r
2838 MenuItem RNAHelixColour = new MenuItem();
\r
2840 MenuItem userDefinedColour = new MenuItem();
\r
2842 MenuItem PIDColour = new MenuItem();
\r
2844 MenuItem BLOSUM62Colour = new MenuItem();
\r
2846 MenuItem tcoffeeColour = new MenuItem();
\r
2848 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
2850 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
2852 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
2854 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
2856 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
\r
2858 MenuItem alProperties = new MenuItem("Alignment Properties...");
\r
2860 MenuItem overviewMenuItem = new MenuItem();
\r
2862 MenuItem undoMenuItem = new MenuItem();
\r
2864 MenuItem redoMenuItem = new MenuItem();
\r
2866 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
2868 MenuItem noColourmenuItem = new MenuItem();
\r
2870 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
2872 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
2874 MenuItem findMenuItem = new MenuItem();
\r
2876 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
2878 MenuItem nucleotideColour = new MenuItem();
\r
2880 MenuItem deleteGroups = new MenuItem();
\r
2882 MenuItem grpsFromSelection = new MenuItem();
\r
2884 MenuItem delete = new MenuItem();
\r
2886 MenuItem copy = new MenuItem();
\r
2888 MenuItem cut = new MenuItem();
\r
2890 Menu pasteMenu = new Menu();
\r
2892 MenuItem pasteNew = new MenuItem();
\r
2894 MenuItem pasteThis = new MenuItem();
\r
2896 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
2898 MenuItem font = new MenuItem();
\r
2900 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
2902 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
2904 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
2906 MenuItem modifyPID = new MenuItem();
\r
2908 MenuItem modifyConservation = new MenuItem();
\r
2910 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
\r
2911 "Autocalculate Consensus", true);
\r
2913 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
\r
2914 "Sort Alignment With New Tree", true);
\r
2916 Menu sortByTreeMenu = new Menu();
\r
2918 Menu sort = new Menu();
\r
2920 Menu calculate = new Menu();
\r
2922 MenuItem inputText = new MenuItem();
\r
2924 Menu helpMenu = new Menu();
\r
2926 MenuItem documentation = new MenuItem();
\r
2928 MenuItem about = new MenuItem();
\r
2930 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
2932 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
\r
2934 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
\r
2936 Menu autoAnnMenu = new Menu();
\r
2938 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
\r
2940 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
\r
2942 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
\r
2944 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
\r
2946 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
\r
2948 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
\r
2950 private void jbInit() throws Exception
\r
2953 setMenuBar(alignFrameMenuBar);
\r
2957 // dynamically fill save as menu with available formats
\r
2958 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
2961 item = new MenuItem(
\r
2962 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
2964 item.addActionListener(new java.awt.event.ActionListener()
\r
2967 public void actionPerformed(ActionEvent e)
\r
2969 outputText_actionPerformed(e);
\r
2973 outputTextboxMenu.add(item);
\r
2975 closeMenuItem.addActionListener(this);
\r
2976 loadApplication.addActionListener(this);
\r
2978 loadTree.addActionListener(this);
\r
2979 loadAnnotations.addActionListener(this);
\r
2980 outputFeatures.addActionListener(this);
\r
2981 outputAnnotations.addActionListener(this);
\r
2982 selectAllSequenceMenuItem.addActionListener(this);
\r
2983 deselectAllSequenceMenuItem.addActionListener(this);
\r
2984 invertSequenceMenuItem.addActionListener(this);
\r
2985 remove2LeftMenuItem.setLabel("Remove Left");
\r
2986 remove2LeftMenuItem.addActionListener(this);
\r
2987 remove2RightMenuItem.setLabel("Remove Right");
\r
2988 remove2RightMenuItem.addActionListener(this);
\r
2989 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
2990 removeGappedColumnMenuItem.addActionListener(this);
\r
2991 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
2992 removeAllGapsMenuItem.addActionListener(this);
\r
2993 viewBoxesMenuItem.setLabel("Boxes");
\r
2994 viewBoxesMenuItem.setState(true);
\r
2995 viewBoxesMenuItem.addItemListener(this);
\r
2996 viewTextMenuItem.setLabel("Text");
\r
2997 viewTextMenuItem.setState(true);
\r
2998 viewTextMenuItem.addItemListener(this);
\r
2999 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
3000 sortPairwiseMenuItem.addActionListener(this);
\r
3001 sortIDMenuItem.setLabel("by ID");
\r
3002 sortIDMenuItem.addActionListener(this);
\r
3003 sortLengthMenuItem.setLabel("by Length");
\r
3004 sortLengthMenuItem.addActionListener(this);
\r
3005 sortGroupMenuItem.setLabel("by Group");
\r
3006 sortGroupMenuItem.addActionListener(this);
\r
3007 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
3008 removeRedundancyMenuItem.addActionListener(this);
\r
3009 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
3010 pairwiseAlignmentMenuItem.addActionListener(this);
\r
3011 PCAMenuItem.setLabel("Principal Component Analysis");
\r
3012 PCAMenuItem.addActionListener(this);
\r
3013 averageDistanceTreeMenuItem
\r
3014 .setLabel("Average Distance Using % Identity");
\r
3015 averageDistanceTreeMenuItem.addActionListener(this);
\r
3016 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
3017 neighbourTreeMenuItem.addActionListener(this);
\r
3018 statusBar.setBackground(Color.white);
\r
3019 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
3020 statusBar.setText("Status bar");
\r
3021 outputTextboxMenu.setLabel("Output to Textbox");
\r
3022 clustalColour.setLabel("Clustalx");
\r
3024 clustalColour.addActionListener(this);
\r
3025 zappoColour.setLabel("Zappo");
\r
3026 zappoColour.addActionListener(this);
\r
3027 taylorColour.setLabel("Taylor");
\r
3028 taylorColour.addActionListener(this);
\r
3029 hydrophobicityColour.setLabel("Hydrophobicity");
\r
3030 hydrophobicityColour.addActionListener(this);
\r
3031 helixColour.setLabel("Helix Propensity");
\r
3032 helixColour.addActionListener(this);
\r
3033 strandColour.setLabel("Strand Propensity");
\r
3034 strandColour.addActionListener(this);
\r
3035 turnColour.setLabel("Turn Propensity");
\r
3036 turnColour.addActionListener(this);
\r
3037 buriedColour.setLabel("Buried Index");
\r
3038 buriedColour.addActionListener(this);
\r
3039 purinePyrimidineColour.setLabel("Purine/Pyrimidine");
\r
3040 purinePyrimidineColour.addActionListener(this);
\r
3041 RNAInteractionColour.setLabel("Purine/Pyrimidine");
\r
3042 RNAInteractionColour.addActionListener(this);
\r
3043 RNAHelixColour.setLabel("by RNA Helices");
\r
3044 RNAHelixColour.addActionListener(this);
\r
3045 userDefinedColour.setLabel("User Defined...");
\r
3046 userDefinedColour.addActionListener(this);
\r
3047 PIDColour.setLabel("Percentage Identity");
\r
3048 PIDColour.addActionListener(this);
\r
3049 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
3050 BLOSUM62Colour.addActionListener(this);
\r
3051 tcoffeeColour.setLabel("T-Coffee Scores");
\r
3052 tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
\r
3054 tcoffeeColour.addActionListener(this);
\r
3055 avDistanceTreeBlosumMenuItem
\r
3056 .setLabel("Average Distance Using BLOSUM62");
\r
3057 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
3058 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
3059 njTreeBlosumMenuItem.addActionListener(this);
\r
3060 annotationPanelMenuItem.setLabel("Show Annotations");
\r
3061 annotationPanelMenuItem.addItemListener(this);
\r
3062 colourTextMenuItem.setLabel("Colour Text");
\r
3063 colourTextMenuItem.addItemListener(this);
\r
3064 displayNonconservedMenuItem.setLabel("Show nonconserved");
\r
3065 displayNonconservedMenuItem.addItemListener(this);
\r
3066 alProperties.addActionListener(this);
\r
3067 overviewMenuItem.setLabel("Overview Window");
\r
3068 overviewMenuItem.addActionListener(this);
\r
3069 undoMenuItem.setEnabled(false);
\r
3070 undoMenuItem.setLabel("Undo");
\r
3071 undoMenuItem.addActionListener(this);
\r
3072 redoMenuItem.setEnabled(false);
\r
3073 redoMenuItem.setLabel("Redo");
\r
3074 redoMenuItem.addActionListener(this);
\r
3075 conservationMenuItem.setLabel("by Conservation");
\r
3076 conservationMenuItem.addItemListener(this);
\r
3077 noColourmenuItem.setLabel("None");
\r
3078 noColourmenuItem.addActionListener(this);
\r
3079 wrapMenuItem.setLabel("Wrap");
\r
3080 wrapMenuItem.addItemListener(this);
\r
3081 renderGapsMenuItem.setLabel("Show Gaps");
\r
3082 renderGapsMenuItem.setState(true);
\r
3083 renderGapsMenuItem.addItemListener(this);
\r
3084 findMenuItem.setLabel("Find...");
\r
3085 findMenuItem.addActionListener(this);
\r
3086 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
3087 abovePIDThreshold.addItemListener(this);
\r
3088 nucleotideColour.setLabel("Nucleotide");
\r
3089 nucleotideColour.addActionListener(this);
\r
3090 deleteGroups.setLabel("Undefine Groups");
\r
3091 deleteGroups.addActionListener(this);
\r
3092 grpsFromSelection.setLabel("Make Groups for selection");
\r
3093 grpsFromSelection.addActionListener(this);
\r
3094 copy.setLabel("Copy");
\r
3095 copy.addActionListener(this);
\r
3096 cut.setLabel("Cut");
\r
3097 cut.addActionListener(this);
\r
3098 delete.setLabel("Delete");
\r
3099 delete.addActionListener(this);
\r
3100 pasteMenu.setLabel("Paste");
\r
3101 pasteNew.setLabel("To New Alignment");
\r
3102 pasteNew.addActionListener(this);
\r
3103 pasteThis.setLabel("Add To This Alignment");
\r
3104 pasteThis.addActionListener(this);
\r
3105 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
3106 applyToAllGroups.setState(true);
\r
3107 applyToAllGroups.addItemListener(this);
\r
3108 font.setLabel("Font...");
\r
3109 font.addActionListener(this);
\r
3110 scaleAbove.setLabel("Scale Above");
\r
3111 scaleAbove.setState(true);
\r
3112 scaleAbove.setEnabled(false);
\r
3113 scaleAbove.addItemListener(this);
\r
3114 scaleLeft.setEnabled(false);
\r
3115 scaleLeft.setState(true);
\r
3116 scaleLeft.setLabel("Scale Left");
\r
3117 scaleLeft.addItemListener(this);
\r
3118 scaleRight.setEnabled(false);
\r
3119 scaleRight.setState(true);
\r
3120 scaleRight.setLabel("Scale Right");
\r
3121 scaleRight.addItemListener(this);
\r
3122 modifyPID.setLabel("Modify Identity Threshold...");
\r
3123 modifyPID.addActionListener(this);
\r
3124 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
3125 modifyConservation.addActionListener(this);
\r
3126 sortByTreeMenu.setLabel("By Tree Order");
\r
3127 sort.setLabel("Sort");
\r
3128 calculate.setLabel("Calculate Tree");
\r
3129 autoCalculate.addItemListener(this);
\r
3130 sortByTree.addItemListener(this);
\r
3131 inputText.setLabel("Input from textbox");
\r
3132 inputText.addActionListener(this);
\r
3133 centreColumnLabelFlag.setLabel("Centre column labels");
\r
3134 centreColumnLabelFlag.addItemListener(this);
\r
3135 followMouseOverFlag.setLabel("Automatic Scrolling");
\r
3136 followMouseOverFlag.addItemListener(this);
\r
3137 helpMenu.setLabel("Help");
\r
3138 documentation.setLabel("Documentation");
\r
3139 documentation.addActionListener(this);
\r
3141 about.setLabel("About...");
\r
3142 about.addActionListener(this);
\r
3143 seqLimits.setState(true);
\r
3144 seqLimits.setLabel("Show Sequence Limits");
\r
3145 seqLimits.addItemListener(this);
\r
3146 featureSettings.setLabel("Feature Settings...");
\r
3147 featureSettings.addActionListener(this);
\r
3148 sequenceFeatures.setLabel("Sequence Features");
\r
3149 sequenceFeatures.addItemListener(this);
\r
3150 sequenceFeatures.setState(false);
\r
3151 annotationColour.setLabel("by Annotation...");
\r
3152 annotationColour.addActionListener(this);
\r
3153 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
3154 invertColSel.setLabel("Invert Column Selection");
\r
3155 menu1.setLabel("Show");
\r
3156 showColumns.setLabel("All Columns ");
\r
3157 showSeqs.setLabel("All Sequences");
\r
3158 menu2.setLabel("Hide");
\r
3159 hideColumns.setLabel("Selected Columns");
\r
3160 hideSequences.setLabel("Selected Sequences");
\r
3161 hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
\r
3162 hideAllSelection.setLabel("Selected Region");
\r
3163 showAllHidden.setLabel("All Sequences and Columns");
\r
3164 showGroupConsensus.setLabel("Group Consensus");
\r
3165 showGroupConservation.setLabel("Group Conservation");
\r
3166 showConsensusHistogram.setLabel("Show Consensus Histogram");
\r
3167 showSequenceLogo.setLabel("Show Consensus Logo");
\r
3168 normSequenceLogo.setLabel("Normalise Consensus Logo");
\r
3169 applyAutoAnnotationSettings.setLabel("Apply to all groups");
\r
3170 applyAutoAnnotationSettings.setState(true);
\r
3171 autoAnnMenu.setLabel("Autocalculated Annotation");
\r
3173 invertColSel.addActionListener(this);
\r
3174 showColumns.addActionListener(this);
\r
3175 showSeqs.addActionListener(this);
\r
3176 hideColumns.addActionListener(this);
\r
3177 hideSequences.addActionListener(this);
\r
3178 hideAllButSelection.addActionListener(this);
\r
3179 hideAllSelection.addActionListener(this);
\r
3180 showAllHidden.addActionListener(this);
\r
3181 showGroupConsensus.addItemListener(this);
\r
3182 showGroupConservation.addItemListener(this);
\r
3183 showConsensusHistogram.addItemListener(this);
\r
3184 showSequenceLogo.addItemListener(this);
\r
3185 applyAutoAnnotationSettings.addItemListener(this);
\r
3186 formatMenu.setLabel("Format");
\r
3187 selectMenu.setLabel("Select");
\r
3188 newView.setLabel("New View");
\r
3189 newView.addActionListener(this);
\r
3190 alignFrameMenuBar.add(fileMenu);
\r
3191 alignFrameMenuBar.add(editMenu);
\r
3192 alignFrameMenuBar.add(selectMenu);
\r
3193 alignFrameMenuBar.add(viewMenu);
\r
3194 alignFrameMenuBar.add(formatMenu);
\r
3195 alignFrameMenuBar.add(colourMenu);
\r
3196 alignFrameMenuBar.add(calculateMenu);
\r
3197 alignFrameMenuBar.add(helpMenu);
\r
3199 fileMenu.add(inputText);
\r
3200 fileMenu.add(loadTree);
\r
3201 fileMenu.add(loadAnnotations);
\r
3203 fileMenu.addSeparator();
\r
3204 fileMenu.add(outputTextboxMenu);
\r
3205 fileMenu.add(outputFeatures);
\r
3206 fileMenu.add(outputAnnotations);
\r
3208 if (jalviewServletURL != null)
\r
3210 fileMenu.add(loadApplication);
\r
3213 fileMenu.addSeparator();
\r
3214 fileMenu.add(closeMenuItem);
\r
3216 editMenu.add(undoMenuItem);
\r
3217 editMenu.add(redoMenuItem);
\r
3218 editMenu.add(cut);
\r
3219 editMenu.add(copy);
\r
3220 editMenu.add(pasteMenu);
\r
3221 editMenu.add(delete);
\r
3222 editMenu.addSeparator();
\r
3223 editMenu.add(remove2LeftMenuItem);
\r
3224 editMenu.add(remove2RightMenuItem);
\r
3225 editMenu.add(removeGappedColumnMenuItem);
\r
3226 editMenu.add(removeAllGapsMenuItem);
\r
3227 editMenu.add(removeRedundancyMenuItem);
\r
3228 viewMenu.add(newView);
\r
3229 viewMenu.addSeparator();
\r
3230 viewMenu.add(menu1);
\r
3231 viewMenu.add(menu2);
\r
3232 viewMenu.addSeparator();
\r
3233 viewMenu.add(followMouseOverFlag);
\r
3234 viewMenu.add(annotationPanelMenuItem);
\r
3235 autoAnnMenu.add(applyAutoAnnotationSettings);
\r
3236 autoAnnMenu.add(showConsensusHistogram);
\r
3237 autoAnnMenu.add(showSequenceLogo);
\r
3238 autoAnnMenu.add(normSequenceLogo);
\r
3239 autoAnnMenu.addSeparator();
\r
3240 autoAnnMenu.add(showGroupConservation);
\r
3241 autoAnnMenu.add(showGroupConsensus);
\r
3242 viewMenu.add(autoAnnMenu);
\r
3243 viewMenu.addSeparator();
\r
3244 viewMenu.add(sequenceFeatures);
\r
3245 viewMenu.add(featureSettings);
\r
3246 viewMenu.addSeparator();
\r
3247 viewMenu.add(alProperties);
\r
3248 viewMenu.addSeparator();
\r
3249 viewMenu.add(overviewMenuItem);
\r
3250 colourMenu.add(applyToAllGroups);
\r
3251 colourMenu.addSeparator();
\r
3252 colourMenu.add(noColourmenuItem);
\r
3253 colourMenu.add(clustalColour);
\r
3254 colourMenu.add(BLOSUM62Colour);
\r
3255 colourMenu.add(PIDColour);
\r
3256 colourMenu.add(zappoColour);
\r
3257 colourMenu.add(taylorColour);
\r
3258 colourMenu.add(hydrophobicityColour);
\r
3259 colourMenu.add(helixColour);
\r
3260 colourMenu.add(strandColour);
\r
3261 colourMenu.add(turnColour);
\r
3262 colourMenu.add(buriedColour);
\r
3263 colourMenu.add(nucleotideColour);
\r
3264 colourMenu.add(purinePyrimidineColour);
\r
3265 colourMenu.add(RNAInteractionColour);
\r
3266 colourMenu.add(tcoffeeColour);
\r
3267 colourMenu.add(userDefinedColour);
\r
3268 colourMenu.addSeparator();
\r
3269 colourMenu.add(conservationMenuItem);
\r
3270 colourMenu.add(modifyConservation);
\r
3271 colourMenu.add(abovePIDThreshold);
\r
3272 colourMenu.add(modifyPID);
\r
3273 colourMenu.add(annotationColour);
\r
3274 colourMenu.add(RNAHelixColour);
\r
3275 calculateMenu.add(sort);
\r
3276 calculateMenu.add(calculate);
\r
3277 calculateMenu.addSeparator();
\r
3278 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
3279 calculateMenu.add(PCAMenuItem);
\r
3280 calculateMenu.add(autoCalculate);
\r
3281 calculateMenu.add(sortByTree);
\r
3282 this.add(statusBar, BorderLayout.SOUTH);
\r
3283 pasteMenu.add(pasteNew);
\r
3284 pasteMenu.add(pasteThis);
\r
3285 sort.add(sortIDMenuItem);
\r
3286 sort.add(sortLengthMenuItem);
\r
3287 sort.add(sortByTreeMenu);
\r
3288 sort.add(sortGroupMenuItem);
\r
3289 sort.add(sortPairwiseMenuItem);
\r
3290 calculate.add(averageDistanceTreeMenuItem);
\r
3291 calculate.add(neighbourTreeMenuItem);
\r
3292 calculate.add(avDistanceTreeBlosumMenuItem);
\r
3293 calculate.add(njTreeBlosumMenuItem);
\r
3294 helpMenu.add(documentation);
\r
3295 helpMenu.add(about);
\r
3296 menu1.add(showColumns);
\r
3297 menu1.add(showSeqs);
\r
3298 menu1.add(showAllHidden);
\r
3299 menu2.add(hideColumns);
\r
3300 menu2.add(hideSequences);
\r
3301 menu2.add(hideAllSelection);
\r
3302 menu2.add(hideAllButSelection);
\r
3303 formatMenu.add(font);
\r
3304 formatMenu.add(seqLimits);
\r
3305 formatMenu.add(wrapMenuItem);
\r
3306 formatMenu.add(scaleAbove);
\r
3307 formatMenu.add(scaleLeft);
\r
3308 formatMenu.add(scaleRight);
\r
3309 formatMenu.add(viewBoxesMenuItem);
\r
3310 formatMenu.add(viewTextMenuItem);
\r
3311 formatMenu.add(colourTextMenuItem);
\r
3312 formatMenu.add(displayNonconservedMenuItem);
\r
3313 formatMenu.add(renderGapsMenuItem);
\r
3314 formatMenu.add(centreColumnLabelFlag);
\r
3315 selectMenu.add(findMenuItem);
\r
3316 selectMenu.addSeparator();
\r
3317 selectMenu.add(selectAllSequenceMenuItem);
\r
3318 selectMenu.add(deselectAllSequenceMenuItem);
\r
3319 selectMenu.add(invertSequenceMenuItem);
\r
3320 selectMenu.add(invertColSel);
\r
3321 selectMenu.add(grpsFromSelection);
\r
3322 selectMenu.add(deleteGroups);
\r
3326 MenuItem featureSettings = new MenuItem();
\r
3328 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
3330 MenuItem annotationColour = new MenuItem();
\r
3332 MenuItem invertColSel = new MenuItem();
\r
3334 Menu menu1 = new Menu();
\r
3336 MenuItem showColumns = new MenuItem();
\r
3338 MenuItem showSeqs = new MenuItem();
\r
3340 Menu menu2 = new Menu();
\r
3342 MenuItem hideColumns = new MenuItem();
\r
3344 MenuItem hideSequences = new MenuItem();
\r
3346 MenuItem hideAllButSelection = new MenuItem();
\r
3348 MenuItem hideAllSelection = new MenuItem();
\r
3350 MenuItem showAllHidden = new MenuItem();
\r
3352 Menu formatMenu = new Menu();
\r
3354 Menu selectMenu = new Menu();
\r
3356 MenuItem newView = new MenuItem();
\r
3359 * Attach the alignFrame panels after embedding menus, if necessary. This used
\r
3360 * to be called setEmbedded, but is now creates the dropdown menus in a
\r
3361 * platform independent manner to avoid OSX/Mac menu appendage daftness.
\r
3363 * @param reallyEmbedded
\r
3364 * true to attach the view to the applet area on the page rather than
\r
3367 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
\r
3369 if (reallyEmbedded)
\r
3372 // Explicly build the embedded menu panel for the on-page applet
\r
3374 // view cannot be closed if its actually on the page
\r
3375 fileMenu.remove(closeMenuItem);
\r
3376 fileMenu.remove(3); // Remove Seperator
\r
3377 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
\r
3378 Font.PLAIN, 10, false); // use our own fonts.
\r
3379 // and actually add the components to the applet area
\r
3380 viewport.applet.setLayout(new BorderLayout());
\r
3381 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
\r
3382 viewport.applet.add(statusBar, BorderLayout.SOUTH);
\r
3383 alignPanel.setSize(viewport.applet.getSize().width,
\r
3384 viewport.applet.getSize().height - embeddedMenu.HEIGHT
\r
3385 - statusBar.HEIGHT);
\r
3386 viewport.applet.add(alignPanel, BorderLayout.CENTER);
\r
3387 final AlignFrame me = this;
\r
3388 viewport.applet.addFocusListener(new FocusListener()
\r
3392 public void focusLost(FocusEvent e)
\r
3394 if (me.viewport.applet.currentAlignFrame == me)
\r
3396 me.viewport.applet.currentAlignFrame = null;
\r
3401 public void focusGained(FocusEvent e)
\r
3403 me.viewport.applet.currentAlignFrame = me;
\r
3406 viewport.applet.validate();
\r
3411 // test and embed menu bar if necessary.
\r
3413 if (embedMenuIfNeeded(alignPanel))
\r
3415 // adjust for status bar height too
\r
3416 alignPanel.setSize(getSize().width, getSize().height
\r
3417 - statusBar.HEIGHT);
\r
3419 add(statusBar, BorderLayout.SOUTH);
\r
3420 add(alignPanel, BorderLayout.CENTER);
\r
3421 // and register with the applet so it can pass external API calls to us
\r
3422 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
\r
3428 * create a new binding between structures in an existing jmol viewer instance
\r
3429 * and an alignpanel with sequences that have existing PDBFile entries. Note,
\r
3430 * this does not open a new Jmol window, or modify the display of the
\r
3431 * structures in the original jmol window. Note This method doesn't work
\r
3432 * without an additional javascript library to exchange messages between the
\r
3433 * distinct applets. See http://issues.jalview.org/browse/JAL-621
\r
3436 * JmolViewer instance
\r
3437 * @param sequenceIds
\r
3438 * - sequence Ids to search for associations
\r
3440 public SequenceStructureBinding addStructureViewInstance(
\r
3441 Object jmolviewer, String[] sequenceIds)
\r
3443 org.jmol.api.JmolViewer viewer = null;
\r
3446 viewer = (org.jmol.api.JmolViewer) jmolviewer;
\r
3447 } catch (ClassCastException ex)
\r
3449 System.err.println("Unsupported viewer object :"
\r
3450 + jmolviewer.getClass());
\r
3452 if (viewer == null)
\r
3454 System.err.println("Can't use this object as a structure viewer:"
\r
3455 + jmolviewer.getClass());
\r
3458 SequenceI[] seqs = null;
\r
3459 if (sequenceIds == null || sequenceIds.length == 0)
\r
3461 seqs = viewport.getAlignment().getSequencesArray();
\r
3465 Vector sqi = new Vector();
\r
3466 AlignmentI al = viewport.getAlignment();
\r
3467 for (int sid = 0; sid < sequenceIds.length; sid++)
\r
3469 SequenceI sq = al.findName(sequenceIds[sid]);
\r
3472 sqi.addElement(sq);
\r
3475 if (sqi.size() > 0)
\r
3477 seqs = new SequenceI[sqi.size()];
\r
3478 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
\r
3480 seqs[sid] = (SequenceI) sqi.elementAt(sid);
\r
3488 ExtJmol jmv = null;
\r
3489 // TODO: search for a jmv that involves viewer
\r
3491 { // create a new viewer/jalview binding.
\r
3492 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
\r
3500 * bind a pdb file to a sequence in the current view
\r
3502 * @param sequenceId
\r
3503 * - sequenceId within the dataset.
\r
3504 * @param pdbEntryString
\r
3505 * - the short name for the PDB file
\r
3507 * - pdb file - either a URL or a valid PDB file.
\r
3508 * @return true if binding was as success TODO: consider making an exception
\r
3509 * structure for indicating when PDB parsing or sequenceId location
\r
3512 public boolean addPdbFile(String sequenceId, String pdbEntryString,
\r
3515 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
\r
3516 boolean needtoadd = false;
\r
3517 if (toaddpdb != null)
\r
3519 Vector pdbe = toaddpdb.getPDBId();
\r
3520 PDBEntry pdbentry = null;
\r
3521 if (pdbe != null && pdbe.size() > 0)
\r
3523 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
\r
3525 pdbentry = (PDBEntry) pdbe.elementAt(pe);
\r
3526 if (!pdbentry.getId().equals(pdbEntryString)
\r
3527 && !pdbentry.getFile().equals(pdbFile))
\r
3537 if (pdbentry == null)
\r
3539 pdbentry = new PDBEntry();
\r
3540 pdbentry.setId(pdbEntryString);
\r
3541 pdbentry.setFile(pdbFile);
\r
3542 needtoadd = true; // add this new entry to sequence.
\r
3544 // resolve data source
\r
3545 // TODO: this code should be a refactored to an io package
\r
3546 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
\r
3547 if (protocol == null)
\r
3553 // make a note of the access mode and add
\r
3554 if (pdbentry.getProperty() == null)
\r
3556 pdbentry.setProperty(new Hashtable());
\r
3558 pdbentry.getProperty().put("protocol", protocol);
\r
3559 toaddpdb.addPDBId(pdbentry);
\r
3565 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
\r
3569 Vector sequences = new Vector();
\r
3570 for (int i = 0; i < seqs.length; i++)
\r
3572 if (seqs[i] != null)
\r
3574 sequences.addElement(new Object[]
\r
3575 { seqs[i], (chains != null) ? chains[i] : null });
\r
3578 seqs = new SequenceI[sequences.size()];
\r
3579 chains = new String[sequences.size()];
\r
3580 for (int i = 0, isize = sequences.size(); i < isize; i++)
\r
3582 Object[] oj = (Object[]) sequences.elementAt(i);
\r
3584 seqs[i] = (SequenceI) oj[0];
\r
3585 chains[i] = (String) oj[1];
\r
3588 return new Object[]
\r
3593 public void newStructureView(JalviewLite applet, PDBEntry pdb,
\r
3594 SequenceI[] seqs, String[] chains, String protocol)
\r
3596 // Scrub any null sequences from the array
\r
3597 Object[] sqch = cleanSeqChainArrays(seqs, chains);
\r
3598 seqs = (SequenceI[]) sqch[0];
\r
3599 chains = (String[]) sqch[1];
\r
3600 if (seqs == null || seqs.length == 0)
\r
3603 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
\r
3605 if (protocol == null || protocol.trim().length() == 0
\r
3606 || protocol.equals("null"))
\r
3608 protocol = (String) pdb.getProperty().get("protocol");
\r
3609 if (protocol == null)
\r
3611 System.err.println("Couldn't work out protocol to open structure: "
\r
3616 if (applet.useXtrnalSviewer)
\r
3618 // register the association(s) and quit, don't create any windows.
\r
3619 if (StructureSelectionManager.getStructureSelectionManager(applet)
\r
3620 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
\r
3622 System.err.println("Failed to map " + pdb.getFile() + " ("
\r
3623 + protocol + ") to any sequences");
\r
3627 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
\r
3629 // can only do alignments with Jmol
\r
3630 // find the last jmol window assigned to this alignment
\r
3631 jalview.appletgui.AppletJmol ajm = null, tajm;
\r
3632 Vector jmols = applet
\r
3633 .getAppletWindow(jalview.appletgui.AppletJmol.class);
\r
3634 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
\r
3636 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
\r
3637 if (tajm.ap.alignFrame == this)
\r
3646 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
\r
3647 // try and add the pdb structure
\r
3652 // otherwise, create a new window
\r
3653 if (applet.jmolAvailable)
\r
3655 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
\r
3657 applet.lastFrameX += 40;
\r
3658 applet.lastFrameY += 40;
\r
3662 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
\r
3667 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
\r
3668 SequenceI[][] seqs, String[][] chains, String[] protocols)
\r
3670 // TODO Auto-generated method stub
\r
3671 System.err.println("Aligned Structure View: Not yet implemented.");
\r
3675 * modify the current selection, providing the user has not made a selection
\r
3679 * - sequences from this alignment
\r
3681 * - columns to be selected on the alignment
\r
3683 public void select(SequenceGroup sel, ColumnSelection csel)
\r
3685 alignPanel.seqPanel.selection(sel, csel, null);
\r
3688 public void scrollTo(int row, int column)
\r
3690 alignPanel.seqPanel.scrollTo(row, column);
\r
3693 public void scrollToRow(int row)
\r
3695 alignPanel.seqPanel.scrollToRow(row);
\r
3698 public void scrollToColumn(int column)
\r
3700 alignPanel.seqPanel.scrollToColumn(column);
\r
3704 * @return the alignments unique ID.
\r
3706 public String getSequenceSetId()
\r
3708 return viewport.getSequenceSetId();
\r
3712 * Load the (T-Coffee) score file from the specified url
\r
3715 * File/URL/T-COFFEE score file contents
\r
3716 * @throws IOException
\r
3717 * @return true if alignment was annotated with data from source
\r
3719 public boolean loadScoreFile(String source) throws IOException
\r
3722 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
\r
3723 AppletFormatAdapter.checkProtocol(source));
\r
3724 if (!file.isValid())
\r
3726 // TODO: raise dialog for gui
\r
3727 System.err.println("Problems parsing T-Coffee scores: "
\r
3728 + file.getWarningMessage());
\r
3729 System.err.println("Origin was:\n" + source);
\r
3734 * check that the score matrix matches the alignment dimensions
\r
3737 if ((aln = viewport.getAlignment()) != null
\r
3738 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
\r
3741 // TODO: raise a dialog box here rather than bomb out.
\r
3743 .println("The scores matrix does not match the alignment dimensions");
\r
3747 // TODO add parameter to indicate if matching should be done
\r
3748 if (file.annotateAlignment(alignPanel.getAlignment(), false))
\r
3750 alignPanel.fontChanged();
\r
3751 tcoffeeColour.setEnabled(true);
\r
3752 // switch to this color
\r
3753 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
\r
3758 System.err.println("Problems resolving T-Coffee scores:");
\r
3759 if (file.getWarningMessage() != null)
\r
3761 System.err.println(file.getWarningMessage());
\r