2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
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3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
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5 * This file is part of Jalview.
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7 * Jalview is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License
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9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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11 * Jalview is distributed in the hope that it will be useful, but
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12 * WITHOUT ANY WARRANTY; without even the implied warranty
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13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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14 * PURPOSE. See the GNU General Public License for more details.
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16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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18 package jalview.appletgui;
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20 import jalview.analysis.AlignmentSorter;
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21 import jalview.analysis.Conservation;
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22 import jalview.api.SequenceStructureBinding;
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23 import jalview.bin.JalviewLite;
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24 import jalview.commands.CommandI;
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25 import jalview.commands.EditCommand;
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26 import jalview.commands.OrderCommand;
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27 import jalview.commands.RemoveGapColCommand;
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28 import jalview.commands.RemoveGapsCommand;
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29 import jalview.commands.SlideSequencesCommand;
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30 import jalview.commands.TrimRegionCommand;
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31 import jalview.datamodel.Alignment;
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32 import jalview.datamodel.AlignmentI;
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33 import jalview.datamodel.AlignmentOrder;
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34 import jalview.datamodel.ColumnSelection;
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35 import jalview.datamodel.PDBEntry;
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36 import jalview.datamodel.Sequence;
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37 import jalview.datamodel.SequenceCollectionI;
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38 import jalview.datamodel.SequenceGroup;
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39 import jalview.datamodel.SequenceI;
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40 import jalview.io.AnnotationFile;
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41 import jalview.io.AppletFormatAdapter;
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42 import jalview.io.FeaturesFile;
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43 import jalview.io.TCoffeeScoreFile;
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44 import jalview.schemes.Blosum62ColourScheme;
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45 import jalview.schemes.BuriedColourScheme;
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46 import jalview.schemes.ClustalxColourScheme;
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47 import jalview.schemes.ColourSchemeI;
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48 import jalview.schemes.HelixColourScheme;
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49 import jalview.schemes.HydrophobicColourScheme;
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50 import jalview.schemes.NucleotideColourScheme;
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51 import jalview.schemes.PIDColourScheme;
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52 import jalview.schemes.PurinePyrimidineColourScheme;
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53 import jalview.schemes.RNAHelicesColourChooser;
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54 import jalview.schemes.RNAInteractionColourScheme;
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55 import jalview.schemes.ResidueProperties;
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56 import jalview.schemes.StrandColourScheme;
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57 import jalview.schemes.TCoffeeColourScheme;
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58 import jalview.schemes.TaylorColourScheme;
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59 import jalview.schemes.TurnColourScheme;
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60 import jalview.schemes.ZappoColourScheme;
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61 import jalview.structure.StructureSelectionManager;
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63 import java.awt.BorderLayout;
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64 import java.awt.Canvas;
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65 import java.awt.CheckboxMenuItem;
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66 import java.awt.Color;
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67 import java.awt.Font;
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68 import java.awt.FontMetrics;
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69 import java.awt.Frame;
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70 import java.awt.Graphics;
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71 import java.awt.Label;
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72 import java.awt.Menu;
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73 import java.awt.MenuBar;
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74 import java.awt.MenuItem;
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75 import java.awt.event.ActionEvent;
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76 import java.awt.event.ActionListener;
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77 import java.awt.event.FocusEvent;
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78 import java.awt.event.FocusListener;
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79 import java.awt.event.ItemEvent;
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80 import java.awt.event.ItemListener;
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81 import java.awt.event.KeyEvent;
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82 import java.awt.event.KeyListener;
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83 import java.awt.event.WindowAdapter;
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84 import java.awt.event.WindowEvent;
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85 import java.io.IOException;
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86 import java.io.InputStreamReader;
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87 import java.net.URL;
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88 import java.net.URLEncoder;
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89 import java.util.Enumeration;
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90 import java.util.Hashtable;
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91 import java.util.List;
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92 import java.util.StringTokenizer;
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93 import java.util.Vector;
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95 import javax.xml.parsers.ParserConfigurationException;
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97 import org.xml.sax.SAXException;
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99 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
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100 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
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101 import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
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102 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
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104 public class AlignFrame extends EmbmenuFrame implements ActionListener,
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105 ItemListener, KeyListener
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107 public AlignmentPanel alignPanel;
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109 public AlignViewport viewport;
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111 int DEFAULT_WIDTH = 700;
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113 int DEFAULT_HEIGHT = 500;
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115 String jalviewServletURL;
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117 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
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118 String title, boolean embedded)
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120 if (applet != null)
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122 jalviewServletURL = applet.getParameter("APPLICATION_URL");
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128 } catch (Exception ex)
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130 ex.printStackTrace();
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133 viewport = new AlignViewport(al, applet);
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134 alignPanel = new AlignmentPanel(this, viewport);
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136 viewport.updateConservation(alignPanel);
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137 viewport.updateConsensus(alignPanel);
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139 annotationPanelMenuItem.setState(viewport.showAnnotation);
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140 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
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141 followMouseOverFlag.setState(viewport.getFollowHighlight());
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142 showGroupConsensus.setState(viewport.isShowGroupConsensus());
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143 showGroupConservation.setState(viewport.isShowGroupConservation());
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144 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
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145 showSequenceLogo.setState(viewport.isShowSequenceLogo());
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146 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
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148 seqLimits.setState(viewport.showJVSuffix);
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150 if (applet != null)
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152 String param = applet.getParameter("sortBy");
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155 if (param.equalsIgnoreCase("Id"))
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157 sortIDMenuItem_actionPerformed();
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159 else if (param.equalsIgnoreCase("Pairwise Identity"))
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161 sortPairwiseMenuItem_actionPerformed();
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163 else if (param.equalsIgnoreCase("Length"))
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165 sortLengthMenuItem_actionPerformed();
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169 param = applet.getParameter("wrap");
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172 if (param.equalsIgnoreCase("true"))
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174 wrapMenuItem.setState(true);
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175 wrapMenuItem_actionPerformed();
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178 param = applet.getParameter("centrecolumnlabels");
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181 centreColumnLabelFlag.setState(true);
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182 centreColumnLabelFlag_stateChanged();
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186 param = applet.getParameter("windowWidth");
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189 int width = Integer.parseInt(param);
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190 DEFAULT_WIDTH = width;
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192 param = applet.getParameter("windowHeight");
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195 int height = Integer.parseInt(param);
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196 DEFAULT_HEIGHT = height;
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198 } catch (Exception ex)
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203 if (viewport.getAlignment().isNucleotide())
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205 viewport.updateStrucConsensus(alignPanel);
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206 if (viewport.getAlignment().hasRNAStructure())
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208 RNAHelixColour.setEnabled(true);
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212 RNAHelixColour.setEnabled(false);
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217 RNAHelixColour.setEnabled(false);
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218 purinePyrimidineColour.setEnabled(false);
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221 // Some JVMS send keyevents to Top frame or lowest panel,
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222 // Havent worked out why yet. So add to both this frame and seqCanvas for
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224 this.addKeyListener(this);
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225 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
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226 alignPanel.idPanel.idCanvas.addKeyListener(this);
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227 alignPanel.scalePanel.addKeyListener(this);
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228 alignPanel.annotationPanel.addKeyListener(this);
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229 alignPanel.annotationPanelHolder.addKeyListener(this);
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230 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
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231 alignPanel.alabels.addKeyListener(this);
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232 createAlignFrameWindow(embedded, title);
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235 alignPanel.adjustAnnotationHeight();
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236 alignPanel.paintAlignment(true);
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239 public AlignViewport getAlignViewport()
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244 public SeqCanvas getSeqcanvas()
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246 return alignPanel.seqPanel.seqCanvas;
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250 * Load a features file onto the alignment
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253 * file URL, content, or other resolvable path
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255 * is protocol for accessing data referred to by file
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258 public boolean parseFeaturesFile(String file, String type)
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260 return parseFeaturesFile(file, type, true);
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264 * Load a features file onto the alignment
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267 * file URL, content, or other resolvable path
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269 * is protocol for accessing data referred to by file
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270 * @param autoenabledisplay
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271 * when true, display features flag will be automatically enabled if
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272 * features are loaded
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273 * @return true if data parsed as a features file
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275 public boolean parseFeaturesFile(String file, String type,
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276 boolean autoenabledisplay)
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278 // TODO: test if importing a features file onto an alignment which already
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279 // has features with links overwrites the original links.
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281 Hashtable featureLinks = new Hashtable();
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282 boolean featuresFile = false;
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285 featuresFile = new jalview.io.FeaturesFile(file, type)
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286 .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
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287 .getFeatureRenderer().featureColours, featureLinks,
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288 true, viewport.applet.getDefaultParameter(
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289 "relaxedidmatch", false));
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290 } catch (Exception ex)
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292 ex.printStackTrace();
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297 if (featureLinks.size() > 0)
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299 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
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301 if (autoenabledisplay)
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303 viewport.showSequenceFeatures = true;
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304 sequenceFeatures.setState(true);
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306 if (viewport.featureSettings != null)
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308 viewport.featureSettings.refreshTable();
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310 alignPanel.paintAlignment(true);
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311 statusBar.setText("Successfully added features to alignment.");
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313 return featuresFile;
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317 public void keyPressed(KeyEvent evt)
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319 if (viewport.cursorMode
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320 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
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321 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
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322 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
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323 && Character.isDigit(evt.getKeyChar()))
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324 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
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326 switch (evt.getKeyCode())
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328 case 27: // escape key
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329 deselectAllSequenceMenuItem_actionPerformed();
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331 alignPanel.alabels.cancelDrag();
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333 case KeyEvent.VK_X:
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334 if (evt.isControlDown() || evt.isMetaDown())
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336 cut_actionPerformed();
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339 case KeyEvent.VK_C:
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340 if (viewport.cursorMode && !evt.isControlDown())
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342 alignPanel.seqPanel.setCursorColumn();
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344 if (evt.isControlDown() || evt.isMetaDown())
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346 copy_actionPerformed();
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349 case KeyEvent.VK_V:
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350 if (evt.isControlDown())
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352 paste(evt.isShiftDown());
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355 case KeyEvent.VK_A:
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356 if (evt.isControlDown() || evt.isMetaDown())
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358 selectAllSequenceMenuItem_actionPerformed();
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361 case KeyEvent.VK_DOWN:
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362 if (viewport.cursorMode)
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364 alignPanel.seqPanel.moveCursor(0, 1);
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368 moveSelectedSequences(false);
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372 case KeyEvent.VK_UP:
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373 if (viewport.cursorMode)
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375 alignPanel.seqPanel.moveCursor(0, -1);
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379 moveSelectedSequences(true);
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383 case KeyEvent.VK_LEFT:
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384 if (evt.isAltDown() || !viewport.cursorMode)
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385 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
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387 alignPanel.seqPanel.moveCursor(-1, 0);
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390 case KeyEvent.VK_RIGHT:
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391 if (evt.isAltDown() || !viewport.cursorMode)
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392 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
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394 alignPanel.seqPanel.moveCursor(1, 0);
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397 case KeyEvent.VK_SPACE:
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398 if (viewport.cursorMode)
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400 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
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401 || evt.isShiftDown() || evt.isAltDown());
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405 case KeyEvent.VK_DELETE:
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406 case KeyEvent.VK_BACK_SPACE:
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407 if (viewport.cursorMode)
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409 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
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410 || evt.isShiftDown() || evt.isAltDown());
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414 cut_actionPerformed();
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415 alignPanel.seqPanel.seqCanvas.repaint();
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419 case KeyEvent.VK_S:
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420 if (viewport.cursorMode)
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422 alignPanel.seqPanel.setCursorRow();
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425 case KeyEvent.VK_P:
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426 if (viewport.cursorMode)
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428 alignPanel.seqPanel.setCursorPosition();
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432 case KeyEvent.VK_ENTER:
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433 case KeyEvent.VK_COMMA:
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434 if (viewport.cursorMode)
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436 alignPanel.seqPanel.setCursorRowAndColumn();
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440 case KeyEvent.VK_Q:
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441 if (viewport.cursorMode)
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443 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
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446 case KeyEvent.VK_M:
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447 if (viewport.cursorMode)
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449 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
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453 case KeyEvent.VK_F2:
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454 viewport.cursorMode = !viewport.cursorMode;
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455 statusBar.setText("Keyboard editing mode is "
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456 + (viewport.cursorMode ? "on" : "off"));
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457 if (viewport.cursorMode)
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459 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
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460 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
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464 case KeyEvent.VK_F:
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465 if (evt.isControlDown())
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467 findMenuItem_actionPerformed();
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471 case KeyEvent.VK_H:
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473 boolean toggleSeqs = !evt.isControlDown();
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474 boolean toggleCols = !evt.isShiftDown();
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475 toggleHiddenRegions(toggleSeqs, toggleCols);
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479 case KeyEvent.VK_PAGE_UP:
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480 if (viewport.wrapAlignment)
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482 alignPanel.scrollUp(true);
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486 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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487 - viewport.endSeq + viewport.startSeq);
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491 case KeyEvent.VK_PAGE_DOWN:
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492 if (viewport.wrapAlignment)
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494 alignPanel.scrollUp(false);
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498 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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499 + viewport.endSeq - viewport.startSeq);
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503 case KeyEvent.VK_Z:
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504 if (evt.isControlDown())
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506 undoMenuItem_actionPerformed();
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510 case KeyEvent.VK_Y:
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511 if (evt.isControlDown())
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513 redoMenuItem_actionPerformed();
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517 case KeyEvent.VK_L:
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518 if (evt.isControlDown())
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520 trimAlignment(true);
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524 case KeyEvent.VK_R:
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525 if (evt.isControlDown())
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527 trimAlignment(false);
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531 case KeyEvent.VK_E:
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532 if (evt.isControlDown())
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534 if (evt.isShiftDown())
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536 this.removeAllGapsMenuItem_actionPerformed();
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540 removeGappedColumnMenuItem_actionPerformed();
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544 case KeyEvent.VK_I:
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545 if (evt.isControlDown())
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547 if (evt.isAltDown())
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549 invertColSel_actionPerformed();
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553 invertSequenceMenuItem_actionPerformed();
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558 case KeyEvent.VK_U:
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559 if (evt.isControlDown())
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561 this.deleteGroups_actionPerformed();
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565 case KeyEvent.VK_T:
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566 if (evt.isControlDown())
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573 alignPanel.paintAlignment(true);
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577 * called by key handler and the hide all/show all menu items
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579 * @param toggleSeqs
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580 * @param toggleCols
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582 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
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584 boolean hide = false;
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585 SequenceGroup sg = viewport.getSelectionGroup();
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586 if (!toggleSeqs && !toggleCols)
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588 // Hide everything by the current selection - this is a hack - we do the
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589 // invert and then hide
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590 // first check that there will be visible columns after the invert.
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591 if ((viewport.getColumnSelection() != null
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592 && viewport.getColumnSelection().getSelected() != null && viewport
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593 .getColumnSelection().getSelected().size() > 0)
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594 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
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597 // now invert the sequence set, if required - empty selection implies
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598 // that no hiding is required.
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601 invertSequenceMenuItem_actionPerformed();
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602 sg = viewport.getSelectionGroup();
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606 viewport.expandColSelection(sg, true);
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607 // finally invert the column selection and get the new sequence
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608 // selection and indicate it should be hidden.
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609 invertColSel_actionPerformed();
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616 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
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619 viewport.hideAllSelectedSeqs();
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621 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
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624 viewport.showAllHiddenSeqs();
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630 if (viewport.getColumnSelection().getSelected().size() > 0)
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632 viewport.hideSelectedColumns();
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635 viewport.setSelectionGroup(sg);
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640 viewport.showAllHiddenColumns();
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646 public void keyReleased(KeyEvent evt)
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651 public void keyTyped(KeyEvent evt)
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656 public void itemStateChanged(ItemEvent evt)
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658 if (evt.getSource() == displayNonconservedMenuItem)
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660 displayNonconservedMenuItem_actionPerformed();
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662 else if (evt.getSource() == colourTextMenuItem)
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664 colourTextMenuItem_actionPerformed();
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666 else if (evt.getSource() == wrapMenuItem)
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668 wrapMenuItem_actionPerformed();
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670 else if (evt.getSource() == scaleAbove)
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672 viewport.setScaleAboveWrapped(scaleAbove.getState());
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674 else if (evt.getSource() == scaleLeft)
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676 viewport.setScaleLeftWrapped(scaleLeft.getState());
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678 else if (evt.getSource() == scaleRight)
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680 viewport.setScaleRightWrapped(scaleRight.getState());
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682 else if (evt.getSource() == seqLimits)
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684 seqLimits_itemStateChanged();
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686 else if (evt.getSource() == viewBoxesMenuItem)
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688 viewport.setShowBoxes(viewBoxesMenuItem.getState());
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690 else if (evt.getSource() == viewTextMenuItem)
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692 viewport.setShowText(viewTextMenuItem.getState());
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694 else if (evt.getSource() == renderGapsMenuItem)
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696 viewport.setRenderGaps(renderGapsMenuItem.getState());
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698 else if (evt.getSource() == annotationPanelMenuItem)
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700 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
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701 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
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703 else if (evt.getSource() == sequenceFeatures)
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705 viewport.showSequenceFeatures(sequenceFeatures.getState());
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706 alignPanel.seqPanel.seqCanvas.repaint();
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708 else if (evt.getSource() == conservationMenuItem)
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710 conservationMenuItem_actionPerformed();
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712 else if (evt.getSource() == abovePIDThreshold)
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714 abovePIDThreshold_actionPerformed();
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716 else if (evt.getSource() == applyToAllGroups)
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718 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
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720 else if (evt.getSource() == autoCalculate)
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722 viewport.autoCalculateConsensus = autoCalculate.getState();
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724 else if (evt.getSource() == sortByTree)
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726 viewport.sortByTree = sortByTree.getState();
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728 else if (evt.getSource() == this.centreColumnLabelFlag)
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730 centreColumnLabelFlag_stateChanged();
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732 else if (evt.getSource() == this.followMouseOverFlag)
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734 mouseOverFlag_stateChanged();
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736 else if (evt.getSource() == showGroupConsensus)
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738 showGroupConsensus_actionPerformed();
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740 else if (evt.getSource() == showGroupConservation)
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742 showGroupConservation_actionPerformed();
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744 else if (evt.getSource() == showSequenceLogo)
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746 showSequenceLogo_actionPerformed();
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748 else if (evt.getSource() == normSequenceLogo)
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750 normSequenceLogo_actionPerformed();
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752 else if (evt.getSource() == showConsensusHistogram)
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754 showConsensusHistogram_actionPerformed();
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756 else if (evt.getSource() == applyAutoAnnotationSettings)
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758 applyAutoAnnotationSettings_actionPerformed();
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760 alignPanel.paintAlignment(true);
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763 private void mouseOverFlag_stateChanged()
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765 viewport.followHighlight = followMouseOverFlag.getState();
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766 // TODO: could kick the scrollTo mechanism to reset view for current
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770 private void centreColumnLabelFlag_stateChanged()
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772 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
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773 this.alignPanel.annotationPanel.repaint();
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777 public void actionPerformed(ActionEvent evt)
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779 Object source = evt.getSource();
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781 if (source == inputText)
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783 inputText_actionPerformed();
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785 else if (source == loadTree)
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787 loadTree_actionPerformed();
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789 else if (source == loadApplication)
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791 launchFullApplication();
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793 else if (source == loadAnnotations)
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797 else if (source == outputAnnotations)
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799 outputAnnotations(true);
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801 else if (source == outputFeatures)
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803 outputFeatures(true, "Jalview");
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805 else if (source == closeMenuItem)
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807 closeMenuItem_actionPerformed();
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809 else if (source == copy)
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811 copy_actionPerformed();
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813 else if (source == undoMenuItem)
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815 undoMenuItem_actionPerformed();
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817 else if (source == redoMenuItem)
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819 redoMenuItem_actionPerformed();
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821 else if (source == inputText)
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823 inputText_actionPerformed();
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825 else if (source == closeMenuItem)
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827 closeMenuItem_actionPerformed();
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829 else if (source == undoMenuItem)
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831 undoMenuItem_actionPerformed();
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833 else if (source == redoMenuItem)
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835 redoMenuItem_actionPerformed();
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837 else if (source == copy)
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839 copy_actionPerformed();
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841 else if (source == pasteNew)
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843 pasteNew_actionPerformed();
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845 else if (source == pasteThis)
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847 pasteThis_actionPerformed();
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849 else if (source == cut)
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851 cut_actionPerformed();
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853 else if (source == delete)
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855 delete_actionPerformed();
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857 else if (source == grpsFromSelection)
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859 makeGrpsFromSelection_actionPerformed();
\r
861 else if (source == deleteGroups)
\r
863 deleteGroups_actionPerformed();
\r
865 else if (source == selectAllSequenceMenuItem)
\r
867 selectAllSequenceMenuItem_actionPerformed();
\r
869 else if (source == deselectAllSequenceMenuItem)
\r
871 deselectAllSequenceMenuItem_actionPerformed();
\r
873 else if (source == invertSequenceMenuItem)
\r
875 invertSequenceMenuItem_actionPerformed();
\r
877 else if (source == invertColSel)
\r
879 viewport.invertColumnSelection();
\r
880 alignPanel.paintAlignment(true);
\r
882 else if (source == remove2LeftMenuItem)
\r
884 trimAlignment(true);
\r
886 else if (source == remove2RightMenuItem)
\r
888 trimAlignment(false);
\r
890 else if (source == removeGappedColumnMenuItem)
\r
892 removeGappedColumnMenuItem_actionPerformed();
\r
894 else if (source == removeAllGapsMenuItem)
\r
896 removeAllGapsMenuItem_actionPerformed();
\r
898 else if (source == findMenuItem)
\r
900 findMenuItem_actionPerformed();
\r
902 else if (source == font)
\r
904 new FontChooser(alignPanel);
\r
906 else if (source == newView)
\r
910 else if (source == showColumns)
\r
912 viewport.showAllHiddenColumns();
\r
913 alignPanel.paintAlignment(true);
\r
915 else if (source == showSeqs)
\r
917 viewport.showAllHiddenSeqs();
\r
918 alignPanel.paintAlignment(true);
\r
920 else if (source == hideColumns)
\r
922 viewport.hideSelectedColumns();
\r
923 alignPanel.paintAlignment(true);
\r
925 else if (source == hideSequences
\r
926 && viewport.getSelectionGroup() != null)
\r
928 viewport.hideAllSelectedSeqs();
\r
929 alignPanel.paintAlignment(true);
\r
931 else if (source == hideAllButSelection)
\r
933 toggleHiddenRegions(false, false);
\r
934 alignPanel.paintAlignment(true);
\r
936 else if (source == hideAllSelection)
\r
938 SequenceGroup sg = viewport.getSelectionGroup();
\r
939 viewport.expandColSelection(sg, false);
\r
940 viewport.hideAllSelectedSeqs();
\r
941 viewport.hideSelectedColumns();
\r
942 alignPanel.paintAlignment(true);
\r
944 else if (source == showAllHidden)
\r
946 viewport.showAllHiddenColumns();
\r
947 viewport.showAllHiddenSeqs();
\r
948 alignPanel.paintAlignment(true);
\r
950 else if (source == showGroupConsensus)
\r
952 showGroupConsensus_actionPerformed();
\r
954 else if (source == showGroupConservation)
\r
956 showGroupConservation_actionPerformed();
\r
958 else if (source == showSequenceLogo)
\r
960 showSequenceLogo_actionPerformed();
\r
962 else if (source == normSequenceLogo)
\r
964 normSequenceLogo_actionPerformed();
\r
966 else if (source == showConsensusHistogram)
\r
968 showConsensusHistogram_actionPerformed();
\r
970 else if (source == applyAutoAnnotationSettings)
\r
972 applyAutoAnnotationSettings_actionPerformed();
\r
974 else if (source == featureSettings)
\r
976 new FeatureSettings(alignPanel);
\r
978 else if (source == alProperties)
\r
980 StringBuffer contents = new jalview.io.AlignmentProperties(
\r
981 viewport.getAlignment()).formatAsString();
\r
982 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
983 cap.setText(contents.toString());
\r
984 Frame frame = new Frame();
\r
986 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
\r
987 + getTitle(), 400, 250);
\r
989 else if (source == overviewMenuItem)
\r
991 overviewMenuItem_actionPerformed();
\r
993 else if (source == noColourmenuItem)
\r
995 changeColour(null);
\r
997 else if (source == clustalColour)
\r
999 abovePIDThreshold.setState(false);
\r
1000 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
\r
1002 else if (source == zappoColour)
\r
1004 changeColour(new ZappoColourScheme());
\r
1006 else if (source == taylorColour)
\r
1008 changeColour(new TaylorColourScheme());
\r
1010 else if (source == hydrophobicityColour)
\r
1012 changeColour(new HydrophobicColourScheme());
\r
1014 else if (source == helixColour)
\r
1016 changeColour(new HelixColourScheme());
\r
1018 else if (source == strandColour)
\r
1020 changeColour(new StrandColourScheme());
\r
1022 else if (source == turnColour)
\r
1024 changeColour(new TurnColourScheme());
\r
1026 else if (source == buriedColour)
\r
1028 changeColour(new BuriedColourScheme());
\r
1030 else if (source == nucleotideColour)
\r
1032 changeColour(new NucleotideColourScheme());
\r
1034 else if (source == purinePyrimidineColour)
\r
1036 changeColour(new PurinePyrimidineColourScheme());
\r
1039 else if (source == RNAHelixColour)
\r
1041 new RNAHelicesColourChooser(viewport, alignPanel);
\r
1043 else if (source == modifyPID)
\r
1045 modifyPID_actionPerformed();
\r
1047 else if (source == modifyConservation)
\r
1049 modifyConservation_actionPerformed();
\r
1051 else if (source == userDefinedColour)
\r
1053 new UserDefinedColours(alignPanel, null);
\r
1055 else if (source == PIDColour)
\r
1057 changeColour(new PIDColourScheme());
\r
1059 else if (source == BLOSUM62Colour)
\r
1061 changeColour(new Blosum62ColourScheme());
\r
1063 else if (source == tcoffeeColour)
\r
1065 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
\r
1067 else if (source == annotationColour)
\r
1069 new AnnotationColourChooser(viewport, alignPanel);
\r
1071 else if (source == sortPairwiseMenuItem)
\r
1073 sortPairwiseMenuItem_actionPerformed();
\r
1075 else if (source == sortIDMenuItem)
\r
1077 sortIDMenuItem_actionPerformed();
\r
1079 else if (source == sortLengthMenuItem)
\r
1081 sortLengthMenuItem_actionPerformed();
\r
1083 else if (source == sortGroupMenuItem)
\r
1085 sortGroupMenuItem_actionPerformed();
\r
1087 else if (source == removeRedundancyMenuItem)
\r
1089 removeRedundancyMenuItem_actionPerformed();
\r
1091 else if (source == pairwiseAlignmentMenuItem)
\r
1093 pairwiseAlignmentMenuItem_actionPerformed();
\r
1095 else if (source == PCAMenuItem)
\r
1097 PCAMenuItem_actionPerformed();
\r
1099 else if (source == averageDistanceTreeMenuItem)
\r
1101 averageDistanceTreeMenuItem_actionPerformed();
\r
1103 else if (source == neighbourTreeMenuItem)
\r
1105 neighbourTreeMenuItem_actionPerformed();
\r
1107 else if (source == njTreeBlosumMenuItem)
\r
1109 njTreeBlosumMenuItem_actionPerformed();
\r
1111 else if (source == avDistanceTreeBlosumMenuItem)
\r
1113 avTreeBlosumMenuItem_actionPerformed();
\r
1115 else if (source == documentation)
\r
1117 documentation_actionPerformed();
\r
1119 else if (source == about)
\r
1121 about_actionPerformed();
\r
1126 public void inputText_actionPerformed()
\r
1128 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1129 Frame frame = new Frame();
\r
1131 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
\r
1134 protected void outputText_actionPerformed(ActionEvent e)
\r
1136 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1137 Frame frame = new Frame();
\r
1139 jalview.bin.JalviewLite.addFrame(frame,
\r
1140 "Alignment output - " + e.getActionCommand(), 600, 500);
\r
1141 cap.setText(new AppletFormatAdapter().formatSequences(
\r
1142 e.getActionCommand(), viewport.getAlignment(),
\r
1143 viewport.showJVSuffix));
\r
1146 public void loadAnnotations()
\r
1148 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1149 cap.setText("Paste your features / annotations / T-coffee score file here.");
\r
1150 cap.setAnnotationImport();
\r
1151 Frame frame = new Frame();
\r
1153 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
\r
1157 public String outputAnnotations(boolean displayTextbox)
\r
1159 String annotation = new AnnotationFile().printAnnotations(
\r
1160 viewport.showAnnotation ? viewport.getAlignment()
\r
1161 .getAlignmentAnnotation() : null, viewport
\r
1162 .getAlignment().getGroups(), ((Alignment) viewport
\r
1163 .getAlignment()).alignmentProperties);
\r
1165 if (displayTextbox)
\r
1167 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
1168 Frame frame = new Frame();
\r
1170 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
\r
1171 cap.setText(annotation);
\r
1174 return annotation;
\r
1177 private Hashtable getDisplayedFeatureCols()
\r
1179 if (alignPanel.getFeatureRenderer() != null
\r
1180 && viewport.featuresDisplayed != null)
\r
1182 FeatureRenderer fr = alignPanel.getFeatureRenderer();
\r
1183 Hashtable fcols = new Hashtable();
\r
1184 Enumeration en = viewport.featuresDisplayed.keys();
\r
1185 while (en.hasMoreElements())
\r
1187 Object col = en.nextElement();
\r
1188 fcols.put(col, fr.featureColours.get(col));
\r
1195 public String outputFeatures(boolean displayTextbox, String format)
\r
1198 if (format.equalsIgnoreCase("Jalview"))
\r
1200 features = new FeaturesFile().printJalviewFormat(viewport
\r
1201 .getAlignment().getSequencesArray(),
\r
1202 getDisplayedFeatureCols());
\r
1206 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
\r
1207 .getSequencesArray(), getDisplayedFeatureCols());
\r
1210 if (displayTextbox)
\r
1212 boolean frimport = false;
\r
1213 if (features == null || features.equals("No Features Visible"))
\r
1215 features = "# No features visible - paste some and import them here.";
\r
1219 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
\r
1222 cap.setAnnotationImport();
\r
1224 Frame frame = new Frame();
\r
1226 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
\r
1227 cap.setText(features);
\r
1231 if (features == null)
\r
1238 void launchFullApplication()
\r
1240 StringBuffer url = new StringBuffer(jalviewServletURL);
\r
1242 url.append("?open="
\r
1243 + appendProtocol(viewport.applet.getParameter("file")));
\r
1245 if (viewport.applet.getParameter("features") != null)
\r
1247 url.append("&features=");
\r
1248 url.append(appendProtocol(viewport.applet.getParameter("features")));
\r
1251 if (viewport.applet.getParameter("annotations") != null)
\r
1253 url.append("&annotations=");
\r
1254 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
\r
1257 if (viewport.applet.getParameter("jnetfile") != null)
\r
1259 url.append("&annotations=");
\r
1260 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
\r
1263 if (viewport.applet.getParameter("defaultColour") != null)
\r
1265 url.append("&colour="
\r
1266 + removeWhiteSpace(viewport.applet
\r
1267 .getParameter("defaultColour")));
\r
1270 if (viewport.applet.getParameter("userDefinedColour") != null)
\r
1272 url.append("&colour="
\r
1273 + removeWhiteSpace(viewport.applet
\r
1274 .getParameter("userDefinedColour")));
\r
1276 if (viewport.applet.getParameter("tree") != null)
\r
1278 url.append("&tree="
\r
1279 + appendProtocol(viewport.applet.getParameter("tree")));
\r
1281 if (viewport.applet.getParameter("treeFile") != null)
\r
1283 url.append("&tree="
\r
1284 + appendProtocol(viewport.applet.getParameter("treeFile")));
\r
1287 showURL(url.toString(), "FULL_APP");
\r
1290 String removeWhiteSpace(String colour)
\r
1292 StringBuffer sb = new StringBuffer();
\r
1293 for (int i = 0; i < colour.length(); i++)
\r
1295 if (Character.isWhitespace(colour.charAt(i)))
\r
1301 sb.append(colour.charAt(i));
\r
1305 return sb.toString();
\r
1308 String appendProtocol(String url)
\r
1313 url = URLEncoder.encode(url);
\r
1316 * When we finally deprecate 1.1 compatibility, we can start to use
\r
1317 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
\r
1318 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
\r
1319 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
\r
1320 * ex.printStackTrace(); }
\r
1322 catch (java.net.MalformedURLException ex)
\r
1324 url = viewport.applet.getCodeBase() + url;
\r
1329 public void closeMenuItem_actionPerformed()
\r
1331 PaintRefresher.RemoveComponent(alignPanel);
\r
1332 if (alignPanel.seqPanel != null
\r
1333 && alignPanel.seqPanel.seqCanvas != null)
\r
1335 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
\r
1337 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
\r
1339 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
\r
1342 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
\r
1350 alignPanel = null;
\r
1357 void updateEditMenuBar()
\r
1360 if (viewport.historyList.size() > 0)
\r
1362 undoMenuItem.setEnabled(true);
\r
1363 CommandI command = (CommandI) viewport.historyList.peek();
\r
1364 undoMenuItem.setLabel("Undo " + command.getDescription());
\r
1368 undoMenuItem.setEnabled(false);
\r
1369 undoMenuItem.setLabel("Undo");
\r
1372 if (viewport.redoList.size() > 0)
\r
1374 redoMenuItem.setEnabled(true);
\r
1376 CommandI command = (CommandI) viewport.redoList.peek();
\r
1377 redoMenuItem.setLabel("Redo " + command.getDescription());
\r
1381 redoMenuItem.setEnabled(false);
\r
1382 redoMenuItem.setLabel("Redo");
\r
1389 public void addHistoryItem(CommandI command)
\r
1391 if (command.getSize() > 0)
\r
1393 viewport.historyList.push(command);
\r
1394 viewport.redoList.removeAllElements();
\r
1395 updateEditMenuBar();
\r
1396 viewport.updateHiddenColumns();
\r
1401 * TODO: JAL-1104 DOCUMENT ME!
\r
1406 protected void undoMenuItem_actionPerformed()
\r
1408 if (viewport.historyList.size() < 1)
\r
1413 CommandI command = (CommandI) viewport.historyList.pop();
\r
1414 viewport.redoList.push(command);
\r
1415 command.undoCommand(null);
\r
1417 AlignViewport originalSource = getOriginatingSource(command);
\r
1419 if (originalSource != viewport)
\r
1422 .println("Warning: Viewport object mismatch whilst undoing");
\r
1424 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
\r
1425 // viewport.getColumnSelection().getHiddenColumns()
\r
1427 updateEditMenuBar();
\r
1428 originalSource.firePropertyChange("alignment", null, originalSource
\r
1429 .getAlignment().getSequences());
\r
1433 * TODO: JAL-1104 DOCUMENT ME!
\r
1438 protected void redoMenuItem_actionPerformed()
\r
1440 if (viewport.redoList.size() < 1)
\r
1445 CommandI command = (CommandI) viewport.redoList.pop();
\r
1446 viewport.historyList.push(command);
\r
1447 command.doCommand(null);
\r
1449 AlignViewport originalSource = getOriginatingSource(command);
\r
1451 if (originalSource != viewport)
\r
1454 .println("Warning: Viewport object mismatch whilst re-doing");
\r
1456 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
\r
1457 // viewport.getColumnSelection().getHiddenColumns()
\r
1460 updateEditMenuBar();
\r
1461 originalSource.firePropertyChange("alignment", null, originalSource
\r
1462 .getAlignment().getSequences());
\r
1465 AlignViewport getOriginatingSource(CommandI command)
\r
1467 AlignViewport originalSource = null;
\r
1468 // For sequence removal and addition, we need to fire
\r
1469 // the property change event FROM the viewport where the
\r
1470 // original alignment was altered
\r
1471 AlignmentI al = null;
\r
1472 if (command instanceof EditCommand)
\r
1474 EditCommand editCommand = (EditCommand) command;
\r
1475 al = editCommand.getAlignment();
\r
1476 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
1477 .getSequenceSetId());
\r
1478 for (int i = 0; i < comps.size(); i++)
\r
1480 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
1482 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
\r
1484 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
\r
1491 if (originalSource == null)
\r
1493 // The original view is closed, we must validate
\r
1494 // the current view against the closed view first
\r
1497 PaintRefresher.validateSequences(al, viewport.getAlignment());
\r
1500 originalSource = viewport;
\r
1503 return originalSource;
\r
1506 public void moveSelectedSequences(boolean up)
\r
1508 SequenceGroup sg = viewport.getSelectionGroup();
\r
1513 viewport.getAlignment().moveSelectedSequencesByOne(sg,
\r
1514 up ? null : viewport.getHiddenRepSequences(), up);
\r
1515 alignPanel.paintAlignment(true);
\r
1518 synchronized void slideSequences(boolean right, int size)
\r
1520 List<SequenceI> sg = new Vector<SequenceI>();
\r
1521 if (viewport.cursorMode)
\r
1523 sg.add(viewport.getAlignment().getSequenceAt(
\r
1524 alignPanel.seqPanel.seqCanvas.cursorY));
\r
1526 else if (viewport.getSelectionGroup() != null
\r
1527 && viewport.getSelectionGroup().getSize() != viewport
\r
1528 .getAlignment().getHeight())
\r
1530 sg = viewport.getSelectionGroup().getSequences(
\r
1531 viewport.getHiddenRepSequences());
\r
1534 if (sg.size() < 1)
\r
1539 Vector<SequenceI> invertGroup = new Vector();
\r
1541 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
\r
1543 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
\r
1544 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
\r
1547 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
\r
1549 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
\r
1551 for (int i = 0; i < invertGroup.size(); i++)
\r
1552 seqs2[i] = invertGroup.elementAt(i);
\r
1554 SlideSequencesCommand ssc;
\r
1556 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
\r
1557 size, viewport.getGapCharacter());
\r
1559 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
\r
1560 size, viewport.getGapCharacter());
\r
1562 int groupAdjustment = 0;
\r
1563 if (ssc.getGapsInsertedBegin() && right)
\r
1565 if (viewport.cursorMode)
\r
1566 alignPanel.seqPanel.moveCursor(size, 0);
\r
1568 groupAdjustment = size;
\r
1570 else if (!ssc.getGapsInsertedBegin() && !right)
\r
1572 if (viewport.cursorMode)
\r
1573 alignPanel.seqPanel.moveCursor(-size, 0);
\r
1575 groupAdjustment = -size;
\r
1578 if (groupAdjustment != 0)
\r
1580 viewport.getSelectionGroup().setStartRes(
\r
1581 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
\r
1582 viewport.getSelectionGroup().setEndRes(
\r
1583 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
\r
1586 boolean appendHistoryItem = false;
\r
1587 if (viewport.historyList != null && viewport.historyList.size() > 0
\r
1588 && viewport.historyList.peek() instanceof SlideSequencesCommand)
\r
1590 appendHistoryItem = ssc
\r
1591 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
\r
1595 if (!appendHistoryItem)
\r
1596 addHistoryItem(ssc);
\r
1601 static StringBuffer copiedSequences;
\r
1603 static Vector copiedHiddenColumns;
\r
1605 protected void copy_actionPerformed()
\r
1607 if (viewport.getSelectionGroup() == null)
\r
1612 SequenceGroup sg = viewport.getSelectionGroup();
\r
1613 copiedSequences = new StringBuffer();
\r
1614 Hashtable orderedSeqs = new Hashtable();
\r
1615 for (int i = 0; i < sg.getSize(); i++)
\r
1617 SequenceI seq = sg.getSequenceAt(i);
\r
1618 int index = viewport.getAlignment().findIndex(seq);
\r
1619 orderedSeqs.put(index + "", seq);
\r
1622 int index = 0, startRes, endRes;
\r
1625 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
\r
1627 copiedHiddenColumns = new Vector();
\r
1628 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
\r
1629 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
\r
1632 int[] region = (int[]) viewport.getColumnSelection()
\r
1633 .getHiddenColumns().elementAt(i);
\r
1635 copiedHiddenColumns.addElement(new int[]
\r
1636 { region[0] - hiddenOffset, region[1] - hiddenOffset });
\r
1641 copiedHiddenColumns = null;
\r
1644 for (int i = 0; i < sg.getSize(); i++)
\r
1646 SequenceI seq = null;
\r
1648 while (seq == null)
\r
1650 if (orderedSeqs.containsKey(index + ""))
\r
1652 seq = (SequenceI) orderedSeqs.get(index + "");
\r
1664 // Returns residue following index if gap
\r
1665 startRes = seq.findPosition(sg.getStartRes());
\r
1668 // Need to find the residue preceeding index if gap
\r
1671 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
\r
1673 ch = seq.getCharAt(j);
\r
1674 if (!jalview.util.Comparison.isGap((ch)))
\r
1682 endRes += seq.getStart() - 1;
\r
1685 copiedSequences.append(seq.getName()
\r
1691 + seq.getSequenceAsString(sg.getStartRes(),
\r
1692 sg.getEndRes() + 1) + "\n");
\r
1697 protected void pasteNew_actionPerformed()
\r
1702 protected void pasteThis_actionPerformed()
\r
1707 void paste(boolean newAlignment)
\r
1712 if (copiedSequences == null)
\r
1717 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
1718 Vector seqs = new Vector();
\r
1719 while (st.hasMoreElements())
\r
1721 String name = st.nextToken();
\r
1722 int start = Integer.parseInt(st.nextToken());
\r
1723 int end = Integer.parseInt(st.nextToken());
\r
1724 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
\r
1726 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
1727 for (int i = 0; i < seqs.size(); i++)
\r
1729 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
1734 String newtitle = new String("Copied sequences");
\r
1735 if (getTitle().startsWith("Copied sequences"))
\r
1737 newtitle = getTitle();
\r
1741 newtitle = newtitle.concat("- from " + getTitle());
\r
1743 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
1744 viewport.applet, newtitle, false);
\r
1745 if (copiedHiddenColumns != null)
\r
1747 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
1749 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
1750 af.viewport.hideColumns(region[0], region[1]);
\r
1754 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
\r
1759 addSequences(newSeqs);
\r
1762 } catch (Exception ex)
\r
1764 } // could be anything being pasted in here
\r
1768 void addSequences(SequenceI[] seqs)
\r
1770 for (int i = 0; i < seqs.length; i++)
\r
1772 viewport.getAlignment().addSequence(seqs[i]);
\r
1776 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
\r
1777 seqs, 0, viewport.getAlignment().getWidth(),
\r
1778 viewport.getAlignment()));
\r
1780 viewport.setEndSeq(viewport.getAlignment().getHeight());
\r
1781 viewport.getAlignment().getWidth();
\r
1782 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1787 protected void cut_actionPerformed()
\r
1789 copy_actionPerformed();
\r
1790 delete_actionPerformed();
\r
1793 protected void delete_actionPerformed()
\r
1796 SequenceGroup sg = viewport.getSelectionGroup();
\r
1802 Vector seqs = new Vector();
\r
1804 for (int i = 0; i < sg.getSize(); i++)
\r
1806 seq = sg.getSequenceAt(i);
\r
1807 seqs.addElement(seq);
\r
1810 // If the cut affects all sequences, remove highlighted columns
\r
1811 if (sg.getSize() == viewport.getAlignment().getHeight())
\r
1813 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
1814 sg.getEndRes() + 1);
\r
1817 SequenceI[] cut = new SequenceI[seqs.size()];
\r
1818 for (int i = 0; i < seqs.size(); i++)
\r
1820 cut[i] = (SequenceI) seqs.elementAt(i);
\r
1824 * //ADD HISTORY ITEM
\r
1826 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
\r
1827 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
\r
1828 viewport.getAlignment()));
\r
1830 viewport.setSelectionGroup(null);
\r
1831 viewport.getAlignment().deleteGroup(sg);
\r
1833 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1836 if (viewport.getAlignment().getHeight() < 1)
\r
1838 this.setVisible(false);
\r
1840 viewport.sendSelection();
\r
1844 * group consensus toggled
\r
1847 protected void showGroupConsensus_actionPerformed()
\r
1849 viewport.setShowGroupConsensus(showGroupConsensus.getState());
\r
1850 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1855 * group conservation toggled.
\r
1857 protected void showGroupConservation_actionPerformed()
\r
1859 viewport.setShowGroupConservation(showGroupConservation.getState());
\r
1860 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1867 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
\r
1868 * .event.ActionEvent)
\r
1870 protected void showConsensusHistogram_actionPerformed()
\r
1872 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
\r
1873 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1880 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
\r
1881 * .event.ActionEvent)
\r
1883 protected void showSequenceLogo_actionPerformed()
\r
1885 viewport.setShowSequenceLogo(showSequenceLogo.getState());
\r
1886 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1889 protected void normSequenceLogo_actionPerformed()
\r
1891 showSequenceLogo.setState(true);
\r
1892 viewport.setShowSequenceLogo(true);
\r
1893 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
\r
1894 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1897 protected void applyAutoAnnotationSettings_actionPerformed()
\r
1899 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1902 protected void makeGrpsFromSelection_actionPerformed()
\r
1904 if (viewport.getSelectionGroup() != null)
\r
1906 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
\r
1907 viewport.getSequenceSelection(),
\r
1908 viewport.getAlignmentView(true).getSequenceStrings(
\r
1909 viewport.getGapCharacter()), viewport.getAlignment()
\r
1911 viewport.getAlignment().deleteAllGroups();
\r
1912 viewport.sequenceColours = null;
\r
1913 viewport.setSelectionGroup(null);
\r
1914 // set view properties for each group
\r
1915 for (int g = 0; g < gps.length; g++)
\r
1917 // gps[g].setShowunconserved(viewport.getShowUnconserved());
\r
1918 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
\r
1919 viewport.getAlignment().addGroup(gps[g]);
\r
1920 Color col = new Color((int) (Math.random() * 255),
\r
1921 (int) (Math.random() * 255), (int) (Math.random() * 255));
\r
1922 col = col.brighter();
\r
1923 for (SequenceI sq : gps[g].getSequences(null))
\r
1924 viewport.setSequenceColour(sq, col);
\r
1926 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
\r
1927 alignPanel.updateAnnotation();
\r
1928 alignPanel.paintAlignment(true);
\r
1932 protected void deleteGroups_actionPerformed()
\r
1934 viewport.getAlignment().deleteAllGroups();
\r
1935 viewport.sequenceColours = null;
\r
1936 viewport.setSelectionGroup(null);
\r
1938 alignPanel.paintAlignment(true);
\r
1941 public void selectAllSequenceMenuItem_actionPerformed()
\r
1943 SequenceGroup sg = new SequenceGroup();
\r
1944 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1946 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
1948 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
\r
1949 viewport.setSelectionGroup(sg);
\r
1950 alignPanel.paintAlignment(true);
\r
1951 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1952 viewport.sendSelection();
\r
1955 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1957 if (viewport.cursorMode)
\r
1959 alignPanel.seqPanel.keyboardNo1 = null;
\r
1960 alignPanel.seqPanel.keyboardNo2 = null;
\r
1962 viewport.setSelectionGroup(null);
\r
1963 viewport.getColumnSelection().clear();
\r
1964 viewport.setSelectionGroup(null);
\r
1965 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1966 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1967 alignPanel.paintAlignment(true);
\r
1968 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1969 viewport.sendSelection();
\r
1972 public void invertSequenceMenuItem_actionPerformed()
\r
1974 SequenceGroup sg = viewport.getSelectionGroup();
\r
1975 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1977 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1980 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1981 viewport.sendSelection();
\r
1984 public void invertColSel_actionPerformed()
\r
1986 viewport.invertColumnSelection();
\r
1987 alignPanel.paintAlignment(true);
\r
1988 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1989 viewport.sendSelection();
\r
1992 void trimAlignment(boolean trimLeft)
\r
1994 ColumnSelection colSel = viewport.getColumnSelection();
\r
1997 if (colSel.size() > 0)
\r
2001 column = colSel.getMin();
\r
2005 column = colSel.getMax();
\r
2009 if (viewport.getSelectionGroup() != null)
\r
2011 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2012 viewport.getHiddenRepSequences());
\r
2016 seqs = viewport.getAlignment().getSequencesArray();
\r
2019 TrimRegionCommand trimRegion;
\r
2022 trimRegion = new TrimRegionCommand("Remove Left",
\r
2023 TrimRegionCommand.TRIM_LEFT, seqs, column,
\r
2024 viewport.getAlignment(), viewport.getColumnSelection(),
\r
2025 viewport.getSelectionGroup());
\r
2026 viewport.setStartRes(0);
\r
2030 trimRegion = new TrimRegionCommand("Remove Right",
\r
2031 TrimRegionCommand.TRIM_RIGHT, seqs, column,
\r
2032 viewport.getAlignment(), viewport.getColumnSelection(),
\r
2033 viewport.getSelectionGroup());
\r
2036 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
\r
2038 addHistoryItem(trimRegion);
\r
2040 for (SequenceGroup sg : viewport.getAlignment().getGroups())
\r
2042 if ((trimLeft && !sg.adjustForRemoveLeft(column))
\r
2043 || (!trimLeft && !sg.adjustForRemoveRight(column)))
\r
2045 viewport.getAlignment().deleteGroup(sg);
\r
2049 viewport.firePropertyChange("alignment", null, viewport
\r
2050 .getAlignment().getSequences());
\r
2054 public void removeGappedColumnMenuItem_actionPerformed()
\r
2056 int start = 0, end = viewport.getAlignment().getWidth() - 1;
\r
2059 if (viewport.getSelectionGroup() != null)
\r
2061 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2062 viewport.getHiddenRepSequences());
\r
2063 start = viewport.getSelectionGroup().getStartRes();
\r
2064 end = viewport.getSelectionGroup().getEndRes();
\r
2068 seqs = viewport.getAlignment().getSequencesArray();
\r
2071 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
\r
2072 "Remove Gapped Columns", seqs, start, end,
\r
2073 viewport.getAlignment());
\r
2075 addHistoryItem(removeGapCols);
\r
2077 statusBar.setText("Removed " + removeGapCols.getSize()
\r
2078 + " empty columns.");
\r
2080 // This is to maintain viewport position on first residue
\r
2081 // of first sequence
\r
2082 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
\r
2083 int startRes = seq.findPosition(viewport.startRes);
\r
2084 // ShiftList shifts;
\r
2085 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
\r
2086 // edit.alColumnChanges=shifts.getInverse();
\r
2087 // if (viewport.hasHiddenColumns)
\r
2088 // viewport.getColumnSelection().compensateForEdits(shifts);
\r
2089 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
2090 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
2095 public void removeAllGapsMenuItem_actionPerformed()
\r
2097 int start = 0, end = viewport.getAlignment().getWidth() - 1;
\r
2100 if (viewport.getSelectionGroup() != null)
\r
2102 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2103 viewport.getHiddenRepSequences());
\r
2104 start = viewport.getSelectionGroup().getStartRes();
\r
2105 end = viewport.getSelectionGroup().getEndRes();
\r
2109 seqs = viewport.getAlignment().getSequencesArray();
\r
2112 // This is to maintain viewport position on first residue
\r
2113 // of first sequence
\r
2114 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
\r
2115 int startRes = seq.findPosition(viewport.startRes);
\r
2117 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
\r
2118 viewport.getAlignment()));
\r
2120 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
2122 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
2127 public void findMenuItem_actionPerformed()
\r
2129 new Finder(alignPanel);
\r
2133 * create a new view derived from the current view
\r
2135 * @param viewtitle
\r
2136 * @return frame for the new view
\r
2138 public AlignFrame newView(String viewtitle)
\r
2141 if (viewport.hasHiddenRows())
\r
2143 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
\r
2144 .getFullAlignment().getSequencesArray());
\r
2148 newal = new Alignment(viewport.getAlignment().getSequencesArray());
\r
2151 if (viewport.getAlignment().getAlignmentAnnotation() != null)
\r
2153 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
\r
2155 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
\r
2157 newal.addAnnotation(viewport.getAlignment()
\r
2158 .getAlignmentAnnotation()[i]);
\r
2163 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
\r
2165 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
\r
2166 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
\r
2167 PaintRefresher.Register(newaf.alignPanel,
\r
2168 newaf.alignPanel.av.getSequenceSetId());
\r
2170 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
\r
2171 newaf.alignPanel.av.getSequenceSetId());
\r
2172 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
\r
2173 newaf.alignPanel.av.getSequenceSetId());
\r
2175 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
2176 .getSequenceSetId());
\r
2177 int viewSize = -1;
\r
2178 for (int i = 0; i < comps.size(); i++)
\r
2180 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
2186 String title = new String(this.getTitle());
\r
2187 if (viewtitle != null)
\r
2189 title = viewtitle + " ( " + title + ")";
\r
2193 if (title.indexOf("(View") > -1)
\r
2195 title = title.substring(0, title.indexOf("(View"));
\r
2197 title += "(View " + viewSize + ")";
\r
2200 newaf.setTitle(title.toString());
\r
2202 newaf.viewport.historyList = viewport.historyList;
\r
2203 newaf.viewport.redoList = viewport.redoList;
\r
2209 * @return list of feature groups on the view
\r
2211 public String[] getFeatureGroups()
\r
2213 FeatureRenderer fr = null;
\r
2214 if (alignPanel != null
\r
2215 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2217 return fr.getGroups();
\r
2223 * get sequence feature groups that are hidden or shown
\r
2229 public String[] getFeatureGroupsOfState(boolean visible)
\r
2231 FeatureRenderer fr = null;
\r
2232 if (alignPanel != null
\r
2233 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2235 return fr.getGroups(visible);
\r
2241 * Change the display state for the given feature groups
\r
2244 * list of group strings
\r
2246 * visible or invisible
\r
2248 public void setFeatureGroupState(String[] groups, boolean state)
\r
2250 FeatureRenderer fr = null;
\r
2251 this.sequenceFeatures.setState(true);
\r
2252 viewport.showSequenceFeatures(true);
\r
2253 if (alignPanel != null
\r
2254 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2256 fr.setGroupState(groups, state);
\r
2257 alignPanel.seqPanel.seqCanvas.repaint();
\r
2258 if (alignPanel.overviewPanel != null)
\r
2260 alignPanel.overviewPanel.updateOverviewImage();
\r
2265 public void seqLimits_itemStateChanged()
\r
2267 viewport.setShowJVSuffix(seqLimits.getState());
\r
2268 alignPanel.fontChanged();
\r
2269 alignPanel.paintAlignment(true);
\r
2272 protected void colourTextMenuItem_actionPerformed()
\r
2274 viewport.setColourText(colourTextMenuItem.getState());
\r
2275 alignPanel.paintAlignment(true);
\r
2278 protected void displayNonconservedMenuItem_actionPerformed()
\r
2280 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
\r
2281 alignPanel.paintAlignment(true);
\r
2284 protected void wrapMenuItem_actionPerformed()
\r
2286 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
2287 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
2288 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
2289 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
2290 scaleRight.setEnabled(wrapMenuItem.getState());
\r
2291 alignPanel.paintAlignment(true);
\r
2294 public void overviewMenuItem_actionPerformed()
\r
2296 if (alignPanel.overviewPanel != null)
\r
2301 Frame frame = new Frame();
\r
2302 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
2303 frame.add(overview);
\r
2304 // +50 must allow for applet frame window
\r
2305 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
2306 overview.getPreferredSize().width,
\r
2307 overview.getPreferredSize().height + 50);
\r
2310 final AlignmentPanel ap = alignPanel;
\r
2311 frame.addWindowListener(new WindowAdapter()
\r
2314 public void windowClosing(WindowEvent e)
\r
2318 ap.setOverviewPanel(null);
\r
2323 alignPanel.setOverviewPanel(overview);
\r
2327 void changeColour(ColourSchemeI cs)
\r
2329 int threshold = 0;
\r
2333 if (viewport.getAbovePIDThreshold())
\r
2335 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
2338 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2340 viewport.setGlobalColourScheme(cs);
\r
2344 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2347 if (viewport.getConservationSelected())
\r
2350 Alignment al = (Alignment) viewport.getAlignment();
\r
2351 Conservation c = new Conservation("All",
\r
2352 ResidueProperties.propHash, 3, al.getSequences(), 0,
\r
2353 al.getWidth() - 1);
\r
2356 c.verdict(false, viewport.getConsPercGaps());
\r
2358 cs.setConservation(c);
\r
2360 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
\r
2361 cs, "Background"));
\r
2366 cs.setConservation(null);
\r
2369 cs.setConsensus(viewport.getSequenceConsensusHash());
\r
2372 viewport.setGlobalColourScheme(cs);
\r
2374 if (alignPanel.getOverviewPanel() != null)
\r
2376 alignPanel.getOverviewPanel().updateOverviewImage();
\r
2379 jalview.structure.StructureSelectionManager
\r
2380 .getStructureSelectionManager(viewport.applet)
\r
2381 .sequenceColoursChanged(alignPanel);
\r
2383 alignPanel.paintAlignment(true);
\r
2386 protected void modifyPID_actionPerformed()
\r
2388 if (viewport.getAbovePIDThreshold()
\r
2389 && viewport.getGlobalColourScheme() != null)
\r
2391 SliderPanel.setPIDSliderSource(alignPanel,
\r
2392 viewport.getGlobalColourScheme(), "Background");
\r
2393 SliderPanel.showPIDSlider();
\r
2397 protected void modifyConservation_actionPerformed()
\r
2399 if (viewport.getConservationSelected()
\r
2400 && viewport.getGlobalColourScheme() != null)
\r
2402 SliderPanel.setConservationSlider(alignPanel,
\r
2403 viewport.getGlobalColourScheme(), "Background");
\r
2404 SliderPanel.showConservationSlider();
\r
2408 protected void conservationMenuItem_actionPerformed()
\r
2410 viewport.setConservationSelected(conservationMenuItem.getState());
\r
2412 viewport.setAbovePIDThreshold(false);
\r
2413 abovePIDThreshold.setState(false);
\r
2415 changeColour(viewport.getGlobalColourScheme());
\r
2417 modifyConservation_actionPerformed();
\r
2420 public void abovePIDThreshold_actionPerformed()
\r
2422 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
2424 conservationMenuItem.setState(false);
\r
2425 viewport.setConservationSelected(false);
\r
2427 changeColour(viewport.getGlobalColourScheme());
\r
2429 modifyPID_actionPerformed();
\r
2432 public void sortPairwiseMenuItem_actionPerformed()
\r
2434 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2435 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
\r
2436 .getAlignment().getSequenceAt(0), null);
\r
2438 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
\r
2439 viewport.getAlignment()));
\r
2440 alignPanel.paintAlignment(true);
\r
2443 public void sortIDMenuItem_actionPerformed()
\r
2445 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2446 AlignmentSorter.sortByID(viewport.getAlignment());
\r
2447 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
\r
2448 viewport.getAlignment()));
\r
2449 alignPanel.paintAlignment(true);
\r
2452 public void sortLengthMenuItem_actionPerformed()
\r
2454 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2455 AlignmentSorter.sortByLength(viewport.getAlignment());
\r
2456 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
\r
2457 viewport.getAlignment()));
\r
2458 alignPanel.paintAlignment(true);
\r
2461 public void sortGroupMenuItem_actionPerformed()
\r
2463 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2464 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
2465 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
\r
2466 viewport.getAlignment()));
\r
2467 alignPanel.paintAlignment(true);
\r
2471 public void removeRedundancyMenuItem_actionPerformed()
\r
2473 new RedundancyPanel(alignPanel);
\r
2476 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
2478 if (viewport.getSelectionGroup() != null
\r
2479 && viewport.getSelectionGroup().getSize() > 1)
\r
2481 Frame frame = new Frame();
\r
2482 frame.add(new PairwiseAlignPanel(alignPanel));
\r
2483 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
\r
2488 public void PCAMenuItem_actionPerformed()
\r
2490 // are the sequences aligned?
\r
2491 if (!viewport.getAlignment().isAligned(false))
\r
2493 SequenceI current;
\r
2494 int Width = viewport.getAlignment().getWidth();
\r
2496 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2498 current = viewport.getAlignment().getSequenceAt(i);
\r
2500 if (current.getLength() < Width)
\r
2502 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2505 alignPanel.paintAlignment(true);
\r
2508 if ((viewport.getSelectionGroup() != null
\r
2509 && viewport.getSelectionGroup().getSize() < 4 && viewport
\r
2510 .getSelectionGroup().getSize() > 0)
\r
2511 || viewport.getAlignment().getHeight() < 4)
\r
2518 new PCAPanel(viewport);
\r
2519 } catch (java.lang.OutOfMemoryError ex)
\r
2525 public void averageDistanceTreeMenuItem_actionPerformed()
\r
2527 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
2530 public void neighbourTreeMenuItem_actionPerformed()
\r
2532 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
2535 protected void njTreeBlosumMenuItem_actionPerformed()
\r
2537 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2540 protected void avTreeBlosumMenuItem_actionPerformed()
\r
2542 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2545 void NewTreePanel(String type, String pwType, String title)
\r
2547 // are the sequences aligned?
\r
2548 if (!viewport.getAlignment().isAligned(false))
\r
2550 SequenceI current;
\r
2551 int Width = viewport.getAlignment().getWidth();
\r
2553 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2555 current = viewport.getAlignment().getSequenceAt(i);
\r
2557 if (current.getLength() < Width)
\r
2559 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2562 alignPanel.paintAlignment(true);
\r
2566 if ((viewport.getSelectionGroup() != null && viewport
\r
2567 .getSelectionGroup().getSize() > 1)
\r
2568 || (viewport.getAlignment().getHeight() > 1))
\r
2570 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
\r
2572 addTreeMenuItem(tp, title);
\r
2574 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
2578 void loadTree_actionPerformed()
\r
2580 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
2581 cap.setText("Paste your Newick tree file here.");
\r
2582 cap.setTreeImport();
\r
2583 Frame frame = new Frame();
\r
2585 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
2588 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
2590 TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
\r
2591 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
2592 addTreeMenuItem(tp, treeFile);
\r
2596 * sort the alignment using the given treePanel
\r
2598 * @param treePanel
\r
2599 * tree used to sort view
\r
2601 * string used for undo event name
\r
2603 public void sortByTree(TreePanel treePanel, String title)
\r
2605 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2607 .sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
2608 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2609 // HistoryItem.SORT));
\r
2610 addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
\r
2611 viewport.getAlignment()));
\r
2612 alignPanel.paintAlignment(true);
\r
2616 * Do any automatic reordering of the alignment and add the necessary bits to
\r
2617 * the menu structure for the new tree
\r
2619 * @param treePanel
\r
2622 protected void addTreeMenuItem(final TreePanel treePanel,
\r
2623 final String title)
\r
2625 final MenuItem item = new MenuItem(title);
\r
2626 sortByTreeMenu.add(item);
\r
2627 item.addActionListener(new java.awt.event.ActionListener()
\r
2630 public void actionPerformed(ActionEvent evt)
\r
2632 sortByTree(treePanel, title); // treePanel.getTitle());
\r
2636 treePanel.addWindowListener(new WindowAdapter()
\r
2639 public void windowOpened(WindowEvent e)
\r
2641 if (viewport.sortByTree)
\r
2643 sortByTree(treePanel, title);
\r
2645 super.windowOpened(e);
\r
2649 public void windowClosing(WindowEvent e)
\r
2651 sortByTreeMenu.remove(item);
\r
2656 public boolean sortBy(AlignmentOrder alorder, String undoname)
\r
2658 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2659 if (viewport.applet.debug)
\r
2661 System.err.println("Sorting " + alorder.getOrder().size()
\r
2662 + " in alignment '" + getTitle() + "'");
\r
2664 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
\r
2665 if (undoname != null)
\r
2667 addHistoryItem(new OrderCommand(undoname, oldOrder,
\r
2668 viewport.getAlignment()));
\r
2670 alignPanel.paintAlignment(true);
\r
2674 protected void documentation_actionPerformed()
\r
2676 alignPanel.av.applet.openJalviewHelpUrl();
\r
2679 protected void about_actionPerformed()
\r
2682 class AboutPanel extends Canvas
\r
2688 public AboutPanel(String version, String builddate)
\r
2690 this.version = version;
\r
2691 this.builddate = builddate;
\r
2695 public void paint(Graphics g)
\r
2697 g.setColor(Color.white);
\r
2698 g.fillRect(0, 0, getSize().width, getSize().height);
\r
2699 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2700 FontMetrics fm = g.getFontMetrics();
\r
2701 int fh = fm.getHeight();
\r
2703 g.setColor(Color.black);
\r
2704 // TODO: update this text for each release or centrally store it for
\r
2705 // lite and application
\r
2706 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
2707 g.drawString("JalviewLite - Release " + version, x, y += fh);
\r
2708 g.setFont(new Font("Helvetica", Font.BOLD, 12));
\r
2709 g.drawString("Build date: " + builddate, x, y += fh);
\r
2710 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2712 "Authors: Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui,",
\r
2713 x, y += fh * 1.5);
\r
2715 "Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.",
\r
2716 x + 50, y += fh + 8);
\r
2718 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
\r
2721 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
\r
2723 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
\r
2725 "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
\r
2728 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
\r
2730 g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
\r
2735 Frame frame = new Frame();
\r
2736 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
\r
2737 .getBuildDate()));
\r
2738 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
\r
2742 public void showURL(String url, String target)
\r
2744 if (viewport.applet == null)
\r
2746 System.out.println("Not running as applet - no browser available.");
\r
2750 viewport.applet.showURL(url, target);
\r
2754 // ////////////////////////////////////////////////////////////////////////////////
\r
2755 // JBuilder Graphics here
\r
2757 MenuBar alignFrameMenuBar = new MenuBar();
\r
2759 Menu fileMenu = new Menu("File");
\r
2761 MenuItem loadApplication = new MenuItem("View in Full Application");
\r
2763 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
\r
2765 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
\r
2767 MenuItem outputFeatures = new MenuItem("Export Features ...");
\r
2769 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
\r
2771 MenuItem closeMenuItem = new MenuItem("Close");
\r
2773 Menu editMenu = new Menu("Edit");
\r
2775 Menu viewMenu = new Menu("View");
\r
2777 Menu colourMenu = new Menu("Colour");
\r
2779 Menu calculateMenu = new Menu("Calculate");
\r
2781 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
2783 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
2785 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
2787 MenuItem remove2LeftMenuItem = new MenuItem();
\r
2789 MenuItem remove2RightMenuItem = new MenuItem();
\r
2791 MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
2793 MenuItem removeAllGapsMenuItem = new MenuItem();
\r
2795 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
2797 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
2799 MenuItem sortPairwiseMenuItem = new MenuItem();
\r
2801 MenuItem sortIDMenuItem = new MenuItem();
\r
2803 MenuItem sortLengthMenuItem = new MenuItem();
\r
2805 MenuItem sortGroupMenuItem = new MenuItem();
\r
2807 MenuItem removeRedundancyMenuItem = new MenuItem();
\r
2809 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
2811 MenuItem PCAMenuItem = new MenuItem();
\r
2813 MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
2815 MenuItem neighbourTreeMenuItem = new MenuItem();
\r
2817 BorderLayout borderLayout1 = new BorderLayout();
\r
2819 public Label statusBar = new Label();
\r
2821 Menu outputTextboxMenu = new Menu();
\r
2823 MenuItem clustalColour = new MenuItem();
\r
2825 MenuItem zappoColour = new MenuItem();
\r
2827 MenuItem taylorColour = new MenuItem();
\r
2829 MenuItem hydrophobicityColour = new MenuItem();
\r
2831 MenuItem helixColour = new MenuItem();
\r
2833 MenuItem strandColour = new MenuItem();
\r
2835 MenuItem turnColour = new MenuItem();
\r
2837 MenuItem buriedColour = new MenuItem();
\r
2839 MenuItem purinePyrimidineColour = new MenuItem();
\r
2841 MenuItem RNAInteractionColour = new MenuItem();
\r
2843 MenuItem RNAHelixColour = new MenuItem();
\r
2845 MenuItem userDefinedColour = new MenuItem();
\r
2847 MenuItem PIDColour = new MenuItem();
\r
2849 MenuItem BLOSUM62Colour = new MenuItem();
\r
2851 MenuItem tcoffeeColour = new MenuItem();
\r
2853 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
2855 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
2857 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
2859 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
2861 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
\r
2863 MenuItem alProperties = new MenuItem("Alignment Properties...");
\r
2865 MenuItem overviewMenuItem = new MenuItem();
\r
2867 MenuItem undoMenuItem = new MenuItem();
\r
2869 MenuItem redoMenuItem = new MenuItem();
\r
2871 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
2873 MenuItem noColourmenuItem = new MenuItem();
\r
2875 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
2877 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
2879 MenuItem findMenuItem = new MenuItem();
\r
2881 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
2883 MenuItem nucleotideColour = new MenuItem();
\r
2885 MenuItem deleteGroups = new MenuItem();
\r
2887 MenuItem grpsFromSelection = new MenuItem();
\r
2889 MenuItem delete = new MenuItem();
\r
2891 MenuItem copy = new MenuItem();
\r
2893 MenuItem cut = new MenuItem();
\r
2895 Menu pasteMenu = new Menu();
\r
2897 MenuItem pasteNew = new MenuItem();
\r
2899 MenuItem pasteThis = new MenuItem();
\r
2901 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
2903 MenuItem font = new MenuItem();
\r
2905 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
2907 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
2909 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
2911 MenuItem modifyPID = new MenuItem();
\r
2913 MenuItem modifyConservation = new MenuItem();
\r
2915 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
\r
2916 "Autocalculate Consensus", true);
\r
2918 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
\r
2919 "Sort Alignment With New Tree", true);
\r
2921 Menu sortByTreeMenu = new Menu();
\r
2923 Menu sort = new Menu();
\r
2925 Menu calculate = new Menu();
\r
2927 MenuItem inputText = new MenuItem();
\r
2929 Menu helpMenu = new Menu();
\r
2931 MenuItem documentation = new MenuItem();
\r
2933 MenuItem about = new MenuItem();
\r
2935 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
2937 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
\r
2939 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
\r
2941 Menu autoAnnMenu = new Menu();
\r
2943 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
\r
2945 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
\r
2947 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
\r
2949 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
\r
2951 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
\r
2953 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
\r
2955 private void jbInit() throws Exception
\r
2958 setMenuBar(alignFrameMenuBar);
\r
2962 // dynamically fill save as menu with available formats
\r
2963 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
2966 item = new MenuItem(
\r
2967 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
2969 item.addActionListener(new java.awt.event.ActionListener()
\r
2972 public void actionPerformed(ActionEvent e)
\r
2974 outputText_actionPerformed(e);
\r
2978 outputTextboxMenu.add(item);
\r
2980 closeMenuItem.addActionListener(this);
\r
2981 loadApplication.addActionListener(this);
\r
2983 loadTree.addActionListener(this);
\r
2984 loadAnnotations.addActionListener(this);
\r
2985 outputFeatures.addActionListener(this);
\r
2986 outputAnnotations.addActionListener(this);
\r
2987 selectAllSequenceMenuItem.addActionListener(this);
\r
2988 deselectAllSequenceMenuItem.addActionListener(this);
\r
2989 invertSequenceMenuItem.addActionListener(this);
\r
2990 remove2LeftMenuItem.setLabel("Remove Left");
\r
2991 remove2LeftMenuItem.addActionListener(this);
\r
2992 remove2RightMenuItem.setLabel("Remove Right");
\r
2993 remove2RightMenuItem.addActionListener(this);
\r
2994 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
2995 removeGappedColumnMenuItem.addActionListener(this);
\r
2996 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
2997 removeAllGapsMenuItem.addActionListener(this);
\r
2998 viewBoxesMenuItem.setLabel("Boxes");
\r
2999 viewBoxesMenuItem.setState(true);
\r
3000 viewBoxesMenuItem.addItemListener(this);
\r
3001 viewTextMenuItem.setLabel("Text");
\r
3002 viewTextMenuItem.setState(true);
\r
3003 viewTextMenuItem.addItemListener(this);
\r
3004 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
3005 sortPairwiseMenuItem.addActionListener(this);
\r
3006 sortIDMenuItem.setLabel("by ID");
\r
3007 sortIDMenuItem.addActionListener(this);
\r
3008 sortLengthMenuItem.setLabel("by Length");
\r
3009 sortLengthMenuItem.addActionListener(this);
\r
3010 sortGroupMenuItem.setLabel("by Group");
\r
3011 sortGroupMenuItem.addActionListener(this);
\r
3012 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
3013 removeRedundancyMenuItem.addActionListener(this);
\r
3014 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
3015 pairwiseAlignmentMenuItem.addActionListener(this);
\r
3016 PCAMenuItem.setLabel("Principal Component Analysis");
\r
3017 PCAMenuItem.addActionListener(this);
\r
3018 averageDistanceTreeMenuItem
\r
3019 .setLabel("Average Distance Using % Identity");
\r
3020 averageDistanceTreeMenuItem.addActionListener(this);
\r
3021 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
3022 neighbourTreeMenuItem.addActionListener(this);
\r
3023 statusBar.setBackground(Color.white);
\r
3024 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
3025 statusBar.setText("Status bar");
\r
3026 outputTextboxMenu.setLabel("Output to Textbox");
\r
3027 clustalColour.setLabel("Clustalx");
\r
3029 clustalColour.addActionListener(this);
\r
3030 zappoColour.setLabel("Zappo");
\r
3031 zappoColour.addActionListener(this);
\r
3032 taylorColour.setLabel("Taylor");
\r
3033 taylorColour.addActionListener(this);
\r
3034 hydrophobicityColour.setLabel("Hydrophobicity");
\r
3035 hydrophobicityColour.addActionListener(this);
\r
3036 helixColour.setLabel("Helix Propensity");
\r
3037 helixColour.addActionListener(this);
\r
3038 strandColour.setLabel("Strand Propensity");
\r
3039 strandColour.addActionListener(this);
\r
3040 turnColour.setLabel("Turn Propensity");
\r
3041 turnColour.addActionListener(this);
\r
3042 buriedColour.setLabel("Buried Index");
\r
3043 buriedColour.addActionListener(this);
\r
3044 purinePyrimidineColour.setLabel("Purine/Pyrimidine");
\r
3045 purinePyrimidineColour.addActionListener(this);
\r
3046 RNAInteractionColour.setLabel("Purine/Pyrimidine");
\r
3047 RNAInteractionColour.addActionListener(this);
\r
3048 RNAHelixColour.setLabel("by RNA Helices");
\r
3049 RNAHelixColour.addActionListener(this);
\r
3050 userDefinedColour.setLabel("User Defined...");
\r
3051 userDefinedColour.addActionListener(this);
\r
3052 PIDColour.setLabel("Percentage Identity");
\r
3053 PIDColour.addActionListener(this);
\r
3054 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
3055 BLOSUM62Colour.addActionListener(this);
\r
3056 tcoffeeColour.setLabel("T-Coffee Scores");
\r
3057 tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
\r
3059 tcoffeeColour.addActionListener(this);
\r
3060 avDistanceTreeBlosumMenuItem
\r
3061 .setLabel("Average Distance Using BLOSUM62");
\r
3062 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
3063 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
3064 njTreeBlosumMenuItem.addActionListener(this);
\r
3065 annotationPanelMenuItem.setLabel("Show Annotations");
\r
3066 annotationPanelMenuItem.addItemListener(this);
\r
3067 colourTextMenuItem.setLabel("Colour Text");
\r
3068 colourTextMenuItem.addItemListener(this);
\r
3069 displayNonconservedMenuItem.setLabel("Show nonconserved");
\r
3070 displayNonconservedMenuItem.addItemListener(this);
\r
3071 alProperties.addActionListener(this);
\r
3072 overviewMenuItem.setLabel("Overview Window");
\r
3073 overviewMenuItem.addActionListener(this);
\r
3074 undoMenuItem.setEnabled(false);
\r
3075 undoMenuItem.setLabel("Undo");
\r
3076 undoMenuItem.addActionListener(this);
\r
3077 redoMenuItem.setEnabled(false);
\r
3078 redoMenuItem.setLabel("Redo");
\r
3079 redoMenuItem.addActionListener(this);
\r
3080 conservationMenuItem.setLabel("by Conservation");
\r
3081 conservationMenuItem.addItemListener(this);
\r
3082 noColourmenuItem.setLabel("None");
\r
3083 noColourmenuItem.addActionListener(this);
\r
3084 wrapMenuItem.setLabel("Wrap");
\r
3085 wrapMenuItem.addItemListener(this);
\r
3086 renderGapsMenuItem.setLabel("Show Gaps");
\r
3087 renderGapsMenuItem.setState(true);
\r
3088 renderGapsMenuItem.addItemListener(this);
\r
3089 findMenuItem.setLabel("Find...");
\r
3090 findMenuItem.addActionListener(this);
\r
3091 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
3092 abovePIDThreshold.addItemListener(this);
\r
3093 nucleotideColour.setLabel("Nucleotide");
\r
3094 nucleotideColour.addActionListener(this);
\r
3095 deleteGroups.setLabel("Undefine Groups");
\r
3096 deleteGroups.addActionListener(this);
\r
3097 grpsFromSelection.setLabel("Make Groups for selection");
\r
3098 grpsFromSelection.addActionListener(this);
\r
3099 copy.setLabel("Copy");
\r
3100 copy.addActionListener(this);
\r
3101 cut.setLabel("Cut");
\r
3102 cut.addActionListener(this);
\r
3103 delete.setLabel("Delete");
\r
3104 delete.addActionListener(this);
\r
3105 pasteMenu.setLabel("Paste");
\r
3106 pasteNew.setLabel("To New Alignment");
\r
3107 pasteNew.addActionListener(this);
\r
3108 pasteThis.setLabel("Add To This Alignment");
\r
3109 pasteThis.addActionListener(this);
\r
3110 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
3111 applyToAllGroups.setState(true);
\r
3112 applyToAllGroups.addItemListener(this);
\r
3113 font.setLabel("Font...");
\r
3114 font.addActionListener(this);
\r
3115 scaleAbove.setLabel("Scale Above");
\r
3116 scaleAbove.setState(true);
\r
3117 scaleAbove.setEnabled(false);
\r
3118 scaleAbove.addItemListener(this);
\r
3119 scaleLeft.setEnabled(false);
\r
3120 scaleLeft.setState(true);
\r
3121 scaleLeft.setLabel("Scale Left");
\r
3122 scaleLeft.addItemListener(this);
\r
3123 scaleRight.setEnabled(false);
\r
3124 scaleRight.setState(true);
\r
3125 scaleRight.setLabel("Scale Right");
\r
3126 scaleRight.addItemListener(this);
\r
3127 modifyPID.setLabel("Modify Identity Threshold...");
\r
3128 modifyPID.addActionListener(this);
\r
3129 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
3130 modifyConservation.addActionListener(this);
\r
3131 sortByTreeMenu.setLabel("By Tree Order");
\r
3132 sort.setLabel("Sort");
\r
3133 calculate.setLabel("Calculate Tree");
\r
3134 autoCalculate.addItemListener(this);
\r
3135 sortByTree.addItemListener(this);
\r
3136 inputText.setLabel("Input from textbox");
\r
3137 inputText.addActionListener(this);
\r
3138 centreColumnLabelFlag.setLabel("Centre column labels");
\r
3139 centreColumnLabelFlag.addItemListener(this);
\r
3140 followMouseOverFlag.setLabel("Automatic Scrolling");
\r
3141 followMouseOverFlag.addItemListener(this);
\r
3142 helpMenu.setLabel("Help");
\r
3143 documentation.setLabel("Documentation");
\r
3144 documentation.addActionListener(this);
\r
3146 about.setLabel("About...");
\r
3147 about.addActionListener(this);
\r
3148 seqLimits.setState(true);
\r
3149 seqLimits.setLabel("Show Sequence Limits");
\r
3150 seqLimits.addItemListener(this);
\r
3151 featureSettings.setLabel("Feature Settings...");
\r
3152 featureSettings.addActionListener(this);
\r
3153 sequenceFeatures.setLabel("Sequence Features");
\r
3154 sequenceFeatures.addItemListener(this);
\r
3155 sequenceFeatures.setState(false);
\r
3156 annotationColour.setLabel("by Annotation...");
\r
3157 annotationColour.addActionListener(this);
\r
3158 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
3159 invertColSel.setLabel("Invert Column Selection");
\r
3160 menu1.setLabel("Show");
\r
3161 showColumns.setLabel("All Columns ");
\r
3162 showSeqs.setLabel("All Sequences");
\r
3163 menu2.setLabel("Hide");
\r
3164 hideColumns.setLabel("Selected Columns");
\r
3165 hideSequences.setLabel("Selected Sequences");
\r
3166 hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
\r
3167 hideAllSelection.setLabel("Selected Region");
\r
3168 showAllHidden.setLabel("All Sequences and Columns");
\r
3169 showGroupConsensus.setLabel("Group Consensus");
\r
3170 showGroupConservation.setLabel("Group Conservation");
\r
3171 showConsensusHistogram.setLabel("Show Consensus Histogram");
\r
3172 showSequenceLogo.setLabel("Show Consensus Logo");
\r
3173 normSequenceLogo.setLabel("Normalise Consensus Logo");
\r
3174 applyAutoAnnotationSettings.setLabel("Apply to all groups");
\r
3175 applyAutoAnnotationSettings.setState(true);
\r
3176 autoAnnMenu.setLabel("Autocalculated Annotation");
\r
3178 invertColSel.addActionListener(this);
\r
3179 showColumns.addActionListener(this);
\r
3180 showSeqs.addActionListener(this);
\r
3181 hideColumns.addActionListener(this);
\r
3182 hideSequences.addActionListener(this);
\r
3183 hideAllButSelection.addActionListener(this);
\r
3184 hideAllSelection.addActionListener(this);
\r
3185 showAllHidden.addActionListener(this);
\r
3186 showGroupConsensus.addItemListener(this);
\r
3187 showGroupConservation.addItemListener(this);
\r
3188 showConsensusHistogram.addItemListener(this);
\r
3189 showSequenceLogo.addItemListener(this);
\r
3190 applyAutoAnnotationSettings.addItemListener(this);
\r
3191 formatMenu.setLabel("Format");
\r
3192 selectMenu.setLabel("Select");
\r
3193 newView.setLabel("New View");
\r
3194 newView.addActionListener(this);
\r
3195 alignFrameMenuBar.add(fileMenu);
\r
3196 alignFrameMenuBar.add(editMenu);
\r
3197 alignFrameMenuBar.add(selectMenu);
\r
3198 alignFrameMenuBar.add(viewMenu);
\r
3199 alignFrameMenuBar.add(formatMenu);
\r
3200 alignFrameMenuBar.add(colourMenu);
\r
3201 alignFrameMenuBar.add(calculateMenu);
\r
3202 alignFrameMenuBar.add(helpMenu);
\r
3204 fileMenu.add(inputText);
\r
3205 fileMenu.add(loadTree);
\r
3206 fileMenu.add(loadAnnotations);
\r
3208 fileMenu.addSeparator();
\r
3209 fileMenu.add(outputTextboxMenu);
\r
3210 fileMenu.add(outputFeatures);
\r
3211 fileMenu.add(outputAnnotations);
\r
3213 if (jalviewServletURL != null)
\r
3215 fileMenu.add(loadApplication);
\r
3218 fileMenu.addSeparator();
\r
3219 fileMenu.add(closeMenuItem);
\r
3221 editMenu.add(undoMenuItem);
\r
3222 editMenu.add(redoMenuItem);
\r
3223 editMenu.add(cut);
\r
3224 editMenu.add(copy);
\r
3225 editMenu.add(pasteMenu);
\r
3226 editMenu.add(delete);
\r
3227 editMenu.addSeparator();
\r
3228 editMenu.add(remove2LeftMenuItem);
\r
3229 editMenu.add(remove2RightMenuItem);
\r
3230 editMenu.add(removeGappedColumnMenuItem);
\r
3231 editMenu.add(removeAllGapsMenuItem);
\r
3232 editMenu.add(removeRedundancyMenuItem);
\r
3233 viewMenu.add(newView);
\r
3234 viewMenu.addSeparator();
\r
3235 viewMenu.add(menu1);
\r
3236 viewMenu.add(menu2);
\r
3237 viewMenu.addSeparator();
\r
3238 viewMenu.add(followMouseOverFlag);
\r
3239 viewMenu.add(annotationPanelMenuItem);
\r
3240 autoAnnMenu.add(applyAutoAnnotationSettings);
\r
3241 autoAnnMenu.add(showConsensusHistogram);
\r
3242 autoAnnMenu.add(showSequenceLogo);
\r
3243 autoAnnMenu.add(normSequenceLogo);
\r
3244 autoAnnMenu.addSeparator();
\r
3245 autoAnnMenu.add(showGroupConservation);
\r
3246 autoAnnMenu.add(showGroupConsensus);
\r
3247 viewMenu.add(autoAnnMenu);
\r
3248 viewMenu.addSeparator();
\r
3249 viewMenu.add(sequenceFeatures);
\r
3250 viewMenu.add(featureSettings);
\r
3251 viewMenu.addSeparator();
\r
3252 viewMenu.add(alProperties);
\r
3253 viewMenu.addSeparator();
\r
3254 viewMenu.add(overviewMenuItem);
\r
3255 colourMenu.add(applyToAllGroups);
\r
3256 colourMenu.addSeparator();
\r
3257 colourMenu.add(noColourmenuItem);
\r
3258 colourMenu.add(clustalColour);
\r
3259 colourMenu.add(BLOSUM62Colour);
\r
3260 colourMenu.add(PIDColour);
\r
3261 colourMenu.add(zappoColour);
\r
3262 colourMenu.add(taylorColour);
\r
3263 colourMenu.add(hydrophobicityColour);
\r
3264 colourMenu.add(helixColour);
\r
3265 colourMenu.add(strandColour);
\r
3266 colourMenu.add(turnColour);
\r
3267 colourMenu.add(buriedColour);
\r
3268 colourMenu.add(nucleotideColour);
\r
3269 colourMenu.add(purinePyrimidineColour);
\r
3270 // colourMenu.add(RNAInteractionColour);
\r
3271 colourMenu.add(tcoffeeColour);
\r
3272 colourMenu.add(userDefinedColour);
\r
3273 colourMenu.addSeparator();
\r
3274 colourMenu.add(conservationMenuItem);
\r
3275 colourMenu.add(modifyConservation);
\r
3276 colourMenu.add(abovePIDThreshold);
\r
3277 colourMenu.add(modifyPID);
\r
3278 colourMenu.add(annotationColour);
\r
3279 colourMenu.add(RNAHelixColour);
\r
3280 calculateMenu.add(sort);
\r
3281 calculateMenu.add(calculate);
\r
3282 calculateMenu.addSeparator();
\r
3283 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
3284 calculateMenu.add(PCAMenuItem);
\r
3285 calculateMenu.add(autoCalculate);
\r
3286 calculateMenu.add(sortByTree);
\r
3287 this.add(statusBar, BorderLayout.SOUTH);
\r
3288 pasteMenu.add(pasteNew);
\r
3289 pasteMenu.add(pasteThis);
\r
3290 sort.add(sortIDMenuItem);
\r
3291 sort.add(sortLengthMenuItem);
\r
3292 sort.add(sortByTreeMenu);
\r
3293 sort.add(sortGroupMenuItem);
\r
3294 sort.add(sortPairwiseMenuItem);
\r
3295 calculate.add(averageDistanceTreeMenuItem);
\r
3296 calculate.add(neighbourTreeMenuItem);
\r
3297 calculate.add(avDistanceTreeBlosumMenuItem);
\r
3298 calculate.add(njTreeBlosumMenuItem);
\r
3299 helpMenu.add(documentation);
\r
3300 helpMenu.add(about);
\r
3301 menu1.add(showColumns);
\r
3302 menu1.add(showSeqs);
\r
3303 menu1.add(showAllHidden);
\r
3304 menu2.add(hideColumns);
\r
3305 menu2.add(hideSequences);
\r
3306 menu2.add(hideAllSelection);
\r
3307 menu2.add(hideAllButSelection);
\r
3308 formatMenu.add(font);
\r
3309 formatMenu.add(seqLimits);
\r
3310 formatMenu.add(wrapMenuItem);
\r
3311 formatMenu.add(scaleAbove);
\r
3312 formatMenu.add(scaleLeft);
\r
3313 formatMenu.add(scaleRight);
\r
3314 formatMenu.add(viewBoxesMenuItem);
\r
3315 formatMenu.add(viewTextMenuItem);
\r
3316 formatMenu.add(colourTextMenuItem);
\r
3317 formatMenu.add(displayNonconservedMenuItem);
\r
3318 formatMenu.add(renderGapsMenuItem);
\r
3319 formatMenu.add(centreColumnLabelFlag);
\r
3320 selectMenu.add(findMenuItem);
\r
3321 selectMenu.addSeparator();
\r
3322 selectMenu.add(selectAllSequenceMenuItem);
\r
3323 selectMenu.add(deselectAllSequenceMenuItem);
\r
3324 selectMenu.add(invertSequenceMenuItem);
\r
3325 selectMenu.add(invertColSel);
\r
3326 selectMenu.add(grpsFromSelection);
\r
3327 selectMenu.add(deleteGroups);
\r
3331 MenuItem featureSettings = new MenuItem();
\r
3333 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
3335 MenuItem annotationColour = new MenuItem();
\r
3337 MenuItem invertColSel = new MenuItem();
\r
3339 Menu menu1 = new Menu();
\r
3341 MenuItem showColumns = new MenuItem();
\r
3343 MenuItem showSeqs = new MenuItem();
\r
3345 Menu menu2 = new Menu();
\r
3347 MenuItem hideColumns = new MenuItem();
\r
3349 MenuItem hideSequences = new MenuItem();
\r
3351 MenuItem hideAllButSelection = new MenuItem();
\r
3353 MenuItem hideAllSelection = new MenuItem();
\r
3355 MenuItem showAllHidden = new MenuItem();
\r
3357 Menu formatMenu = new Menu();
\r
3359 Menu selectMenu = new Menu();
\r
3361 MenuItem newView = new MenuItem();
\r
3364 * Attach the alignFrame panels after embedding menus, if necessary. This used
\r
3365 * to be called setEmbedded, but is now creates the dropdown menus in a
\r
3366 * platform independent manner to avoid OSX/Mac menu appendage daftness.
\r
3368 * @param reallyEmbedded
\r
3369 * true to attach the view to the applet area on the page rather than
\r
3372 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
\r
3374 if (reallyEmbedded)
\r
3377 // Explicly build the embedded menu panel for the on-page applet
\r
3379 // view cannot be closed if its actually on the page
\r
3380 fileMenu.remove(closeMenuItem);
\r
3381 fileMenu.remove(3); // Remove Seperator
\r
3382 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
\r
3383 Font.PLAIN, 10, false); // use our own fonts.
\r
3384 // and actually add the components to the applet area
\r
3385 viewport.applet.setLayout(new BorderLayout());
\r
3386 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
\r
3387 viewport.applet.add(statusBar, BorderLayout.SOUTH);
\r
3388 alignPanel.setSize(viewport.applet.getSize().width,
\r
3389 viewport.applet.getSize().height - embeddedMenu.HEIGHT
\r
3390 - statusBar.HEIGHT);
\r
3391 viewport.applet.add(alignPanel, BorderLayout.CENTER);
\r
3392 final AlignFrame me = this;
\r
3393 viewport.applet.addFocusListener(new FocusListener()
\r
3397 public void focusLost(FocusEvent e)
\r
3399 if (me.viewport.applet.currentAlignFrame == me)
\r
3401 me.viewport.applet.currentAlignFrame = null;
\r
3406 public void focusGained(FocusEvent e)
\r
3408 me.viewport.applet.currentAlignFrame = me;
\r
3411 viewport.applet.validate();
\r
3416 // test and embed menu bar if necessary.
\r
3418 if (embedMenuIfNeeded(alignPanel))
\r
3420 // adjust for status bar height too
\r
3421 alignPanel.setSize(getSize().width, getSize().height
\r
3422 - statusBar.HEIGHT);
\r
3424 add(statusBar, BorderLayout.SOUTH);
\r
3425 add(alignPanel, BorderLayout.CENTER);
\r
3426 // and register with the applet so it can pass external API calls to us
\r
3427 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
\r
3433 * create a new binding between structures in an existing jmol viewer instance
\r
3434 * and an alignpanel with sequences that have existing PDBFile entries. Note,
\r
3435 * this does not open a new Jmol window, or modify the display of the
\r
3436 * structures in the original jmol window. Note This method doesn't work
\r
3437 * without an additional javascript library to exchange messages between the
\r
3438 * distinct applets. See http://issues.jalview.org/browse/JAL-621
\r
3441 * JmolViewer instance
\r
3442 * @param sequenceIds
\r
3443 * - sequence Ids to search for associations
\r
3445 public SequenceStructureBinding addStructureViewInstance(
\r
3446 Object jmolviewer, String[] sequenceIds)
\r
3448 org.jmol.api.JmolViewer viewer = null;
\r
3451 viewer = (org.jmol.api.JmolViewer) jmolviewer;
\r
3452 } catch (ClassCastException ex)
\r
3454 System.err.println("Unsupported viewer object :"
\r
3455 + jmolviewer.getClass());
\r
3457 if (viewer == null)
\r
3459 System.err.println("Can't use this object as a structure viewer:"
\r
3460 + jmolviewer.getClass());
\r
3463 SequenceI[] seqs = null;
\r
3464 if (sequenceIds == null || sequenceIds.length == 0)
\r
3466 seqs = viewport.getAlignment().getSequencesArray();
\r
3470 Vector sqi = new Vector();
\r
3471 AlignmentI al = viewport.getAlignment();
\r
3472 for (int sid = 0; sid < sequenceIds.length; sid++)
\r
3474 SequenceI sq = al.findName(sequenceIds[sid]);
\r
3477 sqi.addElement(sq);
\r
3480 if (sqi.size() > 0)
\r
3482 seqs = new SequenceI[sqi.size()];
\r
3483 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
\r
3485 seqs[sid] = (SequenceI) sqi.elementAt(sid);
\r
3493 ExtJmol jmv = null;
\r
3494 // TODO: search for a jmv that involves viewer
\r
3496 { // create a new viewer/jalview binding.
\r
3497 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
\r
3505 * bind a pdb file to a sequence in the current view
\r
3507 * @param sequenceId
\r
3508 * - sequenceId within the dataset.
\r
3509 * @param pdbEntryString
\r
3510 * - the short name for the PDB file
\r
3512 * - pdb file - either a URL or a valid PDB file.
\r
3513 * @return true if binding was as success TODO: consider making an exception
\r
3514 * structure for indicating when PDB parsing or sequenceId location
\r
3517 public boolean addPdbFile(String sequenceId, String pdbEntryString,
\r
3520 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
\r
3521 boolean needtoadd = false;
\r
3522 if (toaddpdb != null)
\r
3524 Vector pdbe = toaddpdb.getPDBId();
\r
3525 PDBEntry pdbentry = null;
\r
3526 if (pdbe != null && pdbe.size() > 0)
\r
3528 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
\r
3530 pdbentry = (PDBEntry) pdbe.elementAt(pe);
\r
3531 if (!pdbentry.getId().equals(pdbEntryString)
\r
3532 && !pdbentry.getFile().equals(pdbFile))
\r
3542 if (pdbentry == null)
\r
3544 pdbentry = new PDBEntry();
\r
3545 pdbentry.setId(pdbEntryString);
\r
3546 pdbentry.setFile(pdbFile);
\r
3547 needtoadd = true; // add this new entry to sequence.
\r
3549 // resolve data source
\r
3550 // TODO: this code should be a refactored to an io package
\r
3551 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
\r
3552 if (protocol == null)
\r
3558 // make a note of the access mode and add
\r
3559 if (pdbentry.getProperty() == null)
\r
3561 pdbentry.setProperty(new Hashtable());
\r
3563 pdbentry.getProperty().put("protocol", protocol);
\r
3564 toaddpdb.addPDBId(pdbentry);
\r
3570 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
\r
3574 Vector sequences = new Vector();
\r
3575 for (int i = 0; i < seqs.length; i++)
\r
3577 if (seqs[i] != null)
\r
3579 sequences.addElement(new Object[]
\r
3580 { seqs[i], (chains != null) ? chains[i] : null });
\r
3583 seqs = new SequenceI[sequences.size()];
\r
3584 chains = new String[sequences.size()];
\r
3585 for (int i = 0, isize = sequences.size(); i < isize; i++)
\r
3587 Object[] oj = (Object[]) sequences.elementAt(i);
\r
3589 seqs[i] = (SequenceI) oj[0];
\r
3590 chains[i] = (String) oj[1];
\r
3593 return new Object[]
\r
3598 public void newStructureView(JalviewLite applet, PDBEntry pdb,
\r
3599 SequenceI[] seqs, String[] chains, String protocol)
\r
3601 // Scrub any null sequences from the array
\r
3602 Object[] sqch = cleanSeqChainArrays(seqs, chains);
\r
3603 seqs = (SequenceI[]) sqch[0];
\r
3604 chains = (String[]) sqch[1];
\r
3605 if (seqs == null || seqs.length == 0)
\r
3608 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
\r
3610 if (protocol == null || protocol.trim().length() == 0
\r
3611 || protocol.equals("null"))
\r
3613 protocol = (String) pdb.getProperty().get("protocol");
\r
3614 if (protocol == null)
\r
3616 System.err.println("Couldn't work out protocol to open structure: "
\r
3621 if (applet.useXtrnalSviewer)
\r
3623 // register the association(s) and quit, don't create any windows.
\r
3624 if (StructureSelectionManager.getStructureSelectionManager(applet)
\r
3625 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
\r
3627 System.err.println("Failed to map " + pdb.getFile() + " ("
\r
3628 + protocol + ") to any sequences");
\r
3632 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
\r
3634 // can only do alignments with Jmol
\r
3635 // find the last jmol window assigned to this alignment
\r
3636 jalview.appletgui.AppletJmol ajm = null, tajm;
\r
3637 Vector jmols = applet
\r
3638 .getAppletWindow(jalview.appletgui.AppletJmol.class);
\r
3639 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
\r
3641 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
\r
3642 if (tajm.ap.alignFrame == this)
\r
3651 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
\r
3652 // try and add the pdb structure
\r
3657 // otherwise, create a new window
\r
3658 if (applet.jmolAvailable)
\r
3660 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
\r
3662 applet.lastFrameX += 40;
\r
3663 applet.lastFrameY += 40;
\r
3667 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
\r
3672 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
\r
3673 SequenceI[][] seqs, String[][] chains, String[] protocols)
\r
3675 // TODO Auto-generated method stub
\r
3676 System.err.println("Aligned Structure View: Not yet implemented.");
\r
3680 * modify the current selection, providing the user has not made a selection
\r
3684 * - sequences from this alignment
\r
3686 * - columns to be selected on the alignment
\r
3688 public void select(SequenceGroup sel, ColumnSelection csel)
\r
3690 alignPanel.seqPanel.selection(sel, csel, null);
\r
3693 public void scrollTo(int row, int column)
\r
3695 alignPanel.seqPanel.scrollTo(row, column);
\r
3698 public void scrollToRow(int row)
\r
3700 alignPanel.seqPanel.scrollToRow(row);
\r
3703 public void scrollToColumn(int column)
\r
3705 alignPanel.seqPanel.scrollToColumn(column);
\r
3709 * @return the alignments unique ID.
\r
3711 public String getSequenceSetId()
\r
3713 return viewport.getSequenceSetId();
\r
3717 * Load the (T-Coffee) score file from the specified url
\r
3720 * File/URL/T-COFFEE score file contents
\r
3721 * @throws IOException
\r
3722 * @return true if alignment was annotated with data from source
\r
3723 * @throws SAXException
\r
3724 * @throws ParserConfigurationException
\r
3725 * @throws ExceptionFileFormatOrSyntax
\r
3726 * @throws ExceptionLoadingFailed
\r
3727 * @throws ExceptionPermissionDenied
\r
3728 * @throws InterruptedException
\r
3729 * @throws ExceptionUnmatchedClosingParentheses
\r
3731 public boolean loadScoreFile(String source) throws Exception
\r
3734 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
\r
3735 AppletFormatAdapter.checkProtocol(source));
\r
3736 if (!file.isValid())
\r
3738 // TODO: raise dialog for gui
\r
3739 System.err.println("Problems parsing T-Coffee scores: "
\r
3740 + file.getWarningMessage());
\r
3741 System.err.println("Origin was:\n" + source);
\r
3746 * check that the score matrix matches the alignment dimensions
\r
3749 if ((aln = viewport.getAlignment()) != null
\r
3750 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
\r
3753 // TODO: raise a dialog box here rather than bomb out.
\r
3755 .println("The scores matrix does not match the alignment dimensions");
\r
3759 // TODO add parameter to indicate if matching should be done
\r
3760 if (file.annotateAlignment(alignPanel.getAlignment(), false))
\r
3762 alignPanel.fontChanged();
\r
3763 tcoffeeColour.setEnabled(true);
\r
3764 // switch to this color
\r
3765 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
\r
3770 System.err.println("Problems resolving T-Coffee scores:");
\r
3771 if (file.getWarningMessage() != null)
\r
3773 System.err.println(file.getWarningMessage());
\r