2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
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3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
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5 * This file is part of Jalview.
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7 * Jalview is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License
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9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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11 * Jalview is distributed in the hope that it will be useful, but
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12 * WITHOUT ANY WARRANTY; without even the implied warranty
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13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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14 * PURPOSE. See the GNU General Public License for more details.
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16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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18 package jalview.appletgui;
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20 import jalview.analysis.AAFrequency;
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21 import jalview.analysis.AlignmentSorter;
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22 import jalview.analysis.Conservation;
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23 import jalview.api.SequenceStructureBinding;
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24 import jalview.bin.JalviewLite;
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25 import jalview.commands.CommandI;
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26 import jalview.commands.EditCommand;
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27 import jalview.commands.OrderCommand;
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28 import jalview.commands.RemoveGapColCommand;
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29 import jalview.commands.RemoveGapsCommand;
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30 import jalview.commands.SlideSequencesCommand;
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31 import jalview.commands.TrimRegionCommand;
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32 import jalview.datamodel.Alignment;
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33 import jalview.datamodel.AlignmentI;
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34 import jalview.datamodel.AlignmentOrder;
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35 import jalview.datamodel.ColumnSelection;
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36 import jalview.datamodel.PDBEntry;
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37 import jalview.datamodel.Sequence;
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38 import jalview.datamodel.SequenceCollectionI;
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39 import jalview.datamodel.SequenceGroup;
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40 import jalview.datamodel.SequenceI;
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41 import jalview.io.AnnotationFile;
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42 import jalview.io.AppletFormatAdapter;
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43 import jalview.io.FeaturesFile;
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44 import jalview.io.TCoffeeScoreFile;
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45 import jalview.schemes.Blosum62ColourScheme;
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46 import jalview.schemes.BuriedColourScheme;
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47 import jalview.schemes.ClustalxColourScheme;
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48 import jalview.schemes.ColourSchemeI;
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49 import jalview.schemes.HelixColourScheme;
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50 import jalview.schemes.HydrophobicColourScheme;
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51 import jalview.schemes.NucleotideColourScheme;
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52 import jalview.schemes.PIDColourScheme;
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53 import jalview.schemes.PurinePyrimidineColourScheme;
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54 import jalview.schemes.RNAHelicesColourChooser;
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55 import jalview.schemes.RNAInteractionColourScheme;
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56 import jalview.schemes.ResidueProperties;
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57 import jalview.schemes.StrandColourScheme;
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58 import jalview.schemes.TCoffeeColourScheme;
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59 import jalview.schemes.TaylorColourScheme;
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60 import jalview.schemes.TurnColourScheme;
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61 import jalview.schemes.ZappoColourScheme;
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62 import jalview.structure.StructureSelectionManager;
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64 import java.awt.BorderLayout;
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65 import java.awt.Canvas;
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66 import java.awt.CheckboxMenuItem;
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67 import java.awt.Color;
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68 import java.awt.Font;
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69 import java.awt.FontMetrics;
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70 import java.awt.Frame;
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71 import java.awt.Graphics;
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72 import java.awt.Label;
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73 import java.awt.Menu;
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74 import java.awt.MenuBar;
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75 import java.awt.MenuItem;
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76 import java.awt.event.ActionEvent;
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77 import java.awt.event.ActionListener;
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78 import java.awt.event.FocusEvent;
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79 import java.awt.event.FocusListener;
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80 import java.awt.event.ItemEvent;
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81 import java.awt.event.ItemListener;
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82 import java.awt.event.KeyEvent;
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83 import java.awt.event.KeyListener;
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84 import java.awt.event.WindowAdapter;
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85 import java.awt.event.WindowEvent;
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86 import java.io.IOException;
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87 import java.io.InputStreamReader;
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88 import java.net.URL;
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89 import java.net.URLEncoder;
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90 import java.util.Enumeration;
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91 import java.util.Hashtable;
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92 import java.util.List;
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93 import java.util.StringTokenizer;
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94 import java.util.Vector;
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96 import javax.xml.parsers.ParserConfigurationException;
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98 import org.xml.sax.SAXException;
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100 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
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101 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
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102 import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
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103 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
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105 public class AlignFrame extends EmbmenuFrame implements ActionListener,
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106 ItemListener, KeyListener
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108 public AlignmentPanel alignPanel;
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110 public AlignViewport viewport;
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112 int DEFAULT_WIDTH = 700;
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114 int DEFAULT_HEIGHT = 500;
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116 String jalviewServletURL;
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118 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
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119 String title, boolean embedded)
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121 if (applet != null)
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123 jalviewServletURL = applet.getParameter("APPLICATION_URL");
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129 } catch (Exception ex)
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131 ex.printStackTrace();
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134 viewport = new AlignViewport(al, applet);
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135 alignPanel = new AlignmentPanel(this, viewport);
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137 viewport.updateConservation(alignPanel);
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138 viewport.updateConsensus(alignPanel);
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140 annotationPanelMenuItem.setState(viewport.showAnnotation);
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141 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
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142 followMouseOverFlag.setState(viewport.getFollowHighlight());
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143 showGroupConsensus.setState(viewport.isShowGroupConsensus());
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144 showGroupConservation.setState(viewport.isShowGroupConservation());
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145 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
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146 showSequenceLogo.setState(viewport.isShowSequenceLogo());
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147 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
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149 seqLimits.setState(viewport.showJVSuffix);
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151 if (applet != null)
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153 String param = applet.getParameter("sortBy");
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156 if (param.equalsIgnoreCase("Id"))
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158 sortIDMenuItem_actionPerformed();
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160 else if (param.equalsIgnoreCase("Pairwise Identity"))
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162 sortPairwiseMenuItem_actionPerformed();
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164 else if (param.equalsIgnoreCase("Length"))
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166 sortLengthMenuItem_actionPerformed();
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170 param = applet.getParameter("wrap");
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173 if (param.equalsIgnoreCase("true"))
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175 wrapMenuItem.setState(true);
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176 wrapMenuItem_actionPerformed();
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179 param = applet.getParameter("centrecolumnlabels");
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182 centreColumnLabelFlag.setState(true);
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183 centreColumnLabelFlag_stateChanged();
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187 param = applet.getParameter("windowWidth");
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190 int width = Integer.parseInt(param);
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191 DEFAULT_WIDTH = width;
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193 param = applet.getParameter("windowHeight");
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196 int height = Integer.parseInt(param);
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197 DEFAULT_HEIGHT = height;
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199 } catch (Exception ex)
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204 if (viewport.getAlignment().isNucleotide())
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206 viewport.updateStrucConsensus(alignPanel);
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207 if (viewport.getAlignment().hasRNAStructure())
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209 RNAHelixColour.setEnabled(true);
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213 RNAHelixColour.setEnabled(false);
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218 RNAHelixColour.setEnabled(false);
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219 purinePyrimidineColour.setEnabled(false);
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222 // Some JVMS send keyevents to Top frame or lowest panel,
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223 // Havent worked out why yet. So add to both this frame and seqCanvas for
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225 this.addKeyListener(this);
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226 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
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227 alignPanel.idPanel.idCanvas.addKeyListener(this);
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228 alignPanel.scalePanel.addKeyListener(this);
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229 alignPanel.annotationPanel.addKeyListener(this);
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230 alignPanel.annotationPanelHolder.addKeyListener(this);
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231 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
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232 alignPanel.alabels.addKeyListener(this);
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233 createAlignFrameWindow(embedded, title);
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236 alignPanel.adjustAnnotationHeight();
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237 alignPanel.paintAlignment(true);
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240 public AlignViewport getAlignViewport()
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245 public SeqCanvas getSeqcanvas()
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247 return alignPanel.seqPanel.seqCanvas;
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251 * Load a features file onto the alignment
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254 * file URL, content, or other resolvable path
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256 * is protocol for accessing data referred to by file
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259 public boolean parseFeaturesFile(String file, String type)
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261 return parseFeaturesFile(file, type, true);
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265 * Load a features file onto the alignment
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268 * file URL, content, or other resolvable path
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270 * is protocol for accessing data referred to by file
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271 * @param autoenabledisplay
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272 * when true, display features flag will be automatically enabled if
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273 * features are loaded
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274 * @return true if data parsed as a features file
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276 public boolean parseFeaturesFile(String file, String type,
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277 boolean autoenabledisplay)
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279 // TODO: test if importing a features file onto an alignment which already
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280 // has features with links overwrites the original links.
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282 Hashtable featureLinks = new Hashtable();
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283 boolean featuresFile = false;
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286 featuresFile = new jalview.io.FeaturesFile(file, type)
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287 .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
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288 .getFeatureRenderer().featureColours, featureLinks,
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289 true, viewport.applet.getDefaultParameter(
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290 "relaxedidmatch", false));
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291 } catch (Exception ex)
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293 ex.printStackTrace();
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298 if (featureLinks.size() > 0)
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300 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
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302 if (autoenabledisplay)
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304 viewport.showSequenceFeatures = true;
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305 sequenceFeatures.setState(true);
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307 if (viewport.featureSettings != null)
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309 viewport.featureSettings.refreshTable();
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311 alignPanel.paintAlignment(true);
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312 statusBar.setText("Successfully added features to alignment.");
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314 return featuresFile;
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318 public void keyPressed(KeyEvent evt)
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320 if (viewport.cursorMode
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321 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
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322 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
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323 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
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324 && Character.isDigit(evt.getKeyChar()))
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325 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
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327 switch (evt.getKeyCode())
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329 case 27: // escape key
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330 deselectAllSequenceMenuItem_actionPerformed();
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332 alignPanel.alabels.cancelDrag();
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334 case KeyEvent.VK_X:
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335 if (evt.isControlDown() || evt.isMetaDown())
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337 cut_actionPerformed();
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340 case KeyEvent.VK_C:
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341 if (viewport.cursorMode && !evt.isControlDown())
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343 alignPanel.seqPanel.setCursorColumn();
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345 if (evt.isControlDown() || evt.isMetaDown())
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347 copy_actionPerformed();
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350 case KeyEvent.VK_V:
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351 if (evt.isControlDown())
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353 paste(evt.isShiftDown());
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356 case KeyEvent.VK_A:
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357 if (evt.isControlDown() || evt.isMetaDown())
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359 selectAllSequenceMenuItem_actionPerformed();
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362 case KeyEvent.VK_DOWN:
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363 if (viewport.cursorMode)
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365 alignPanel.seqPanel.moveCursor(0, 1);
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369 moveSelectedSequences(false);
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373 case KeyEvent.VK_UP:
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374 if (viewport.cursorMode)
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376 alignPanel.seqPanel.moveCursor(0, -1);
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380 moveSelectedSequences(true);
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384 case KeyEvent.VK_LEFT:
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385 if (evt.isAltDown() || !viewport.cursorMode)
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386 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
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388 alignPanel.seqPanel.moveCursor(-1, 0);
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391 case KeyEvent.VK_RIGHT:
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392 if (evt.isAltDown() || !viewport.cursorMode)
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393 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
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395 alignPanel.seqPanel.moveCursor(1, 0);
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398 case KeyEvent.VK_SPACE:
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399 if (viewport.cursorMode)
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401 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
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402 || evt.isShiftDown() || evt.isAltDown());
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406 case KeyEvent.VK_DELETE:
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407 case KeyEvent.VK_BACK_SPACE:
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408 if (viewport.cursorMode)
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410 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
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411 || evt.isShiftDown() || evt.isAltDown());
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415 cut_actionPerformed();
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416 alignPanel.seqPanel.seqCanvas.repaint();
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420 case KeyEvent.VK_S:
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421 if (viewport.cursorMode)
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423 alignPanel.seqPanel.setCursorRow();
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426 case KeyEvent.VK_P:
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427 if (viewport.cursorMode)
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429 alignPanel.seqPanel.setCursorPosition();
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433 case KeyEvent.VK_ENTER:
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434 case KeyEvent.VK_COMMA:
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435 if (viewport.cursorMode)
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437 alignPanel.seqPanel.setCursorRowAndColumn();
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441 case KeyEvent.VK_Q:
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442 if (viewport.cursorMode)
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444 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
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447 case KeyEvent.VK_M:
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448 if (viewport.cursorMode)
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450 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
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454 case KeyEvent.VK_F2:
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455 viewport.cursorMode = !viewport.cursorMode;
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456 statusBar.setText("Keyboard editing mode is "
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457 + (viewport.cursorMode ? "on" : "off"));
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458 if (viewport.cursorMode)
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460 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
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461 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
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465 case KeyEvent.VK_F:
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466 if (evt.isControlDown())
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468 findMenuItem_actionPerformed();
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472 case KeyEvent.VK_H:
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474 boolean toggleSeqs = !evt.isControlDown();
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475 boolean toggleCols = !evt.isShiftDown();
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476 toggleHiddenRegions(toggleSeqs, toggleCols);
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480 case KeyEvent.VK_PAGE_UP:
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481 if (viewport.wrapAlignment)
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483 alignPanel.scrollUp(true);
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487 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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488 - viewport.endSeq + viewport.startSeq);
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492 case KeyEvent.VK_PAGE_DOWN:
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493 if (viewport.wrapAlignment)
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495 alignPanel.scrollUp(false);
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499 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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500 + viewport.endSeq - viewport.startSeq);
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504 case KeyEvent.VK_Z:
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505 if (evt.isControlDown())
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507 undoMenuItem_actionPerformed();
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511 case KeyEvent.VK_Y:
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512 if (evt.isControlDown())
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514 redoMenuItem_actionPerformed();
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518 case KeyEvent.VK_L:
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519 if (evt.isControlDown())
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521 trimAlignment(true);
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525 case KeyEvent.VK_R:
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526 if (evt.isControlDown())
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528 trimAlignment(false);
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532 case KeyEvent.VK_E:
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533 if (evt.isControlDown())
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535 if (evt.isShiftDown())
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537 this.removeAllGapsMenuItem_actionPerformed();
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541 removeGappedColumnMenuItem_actionPerformed();
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545 case KeyEvent.VK_I:
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546 if (evt.isControlDown())
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548 if (evt.isAltDown())
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550 invertColSel_actionPerformed();
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554 invertSequenceMenuItem_actionPerformed();
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559 case KeyEvent.VK_U:
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560 if (evt.isControlDown())
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562 this.deleteGroups_actionPerformed();
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566 case KeyEvent.VK_T:
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567 if (evt.isControlDown())
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574 alignPanel.paintAlignment(true);
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578 * called by key handler and the hide all/show all menu items
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580 * @param toggleSeqs
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581 * @param toggleCols
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583 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
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585 boolean hide = false;
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586 SequenceGroup sg = viewport.getSelectionGroup();
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587 if (!toggleSeqs && !toggleCols)
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589 // Hide everything by the current selection - this is a hack - we do the
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590 // invert and then hide
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591 // first check that there will be visible columns after the invert.
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592 if ((viewport.getColumnSelection() != null
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593 && viewport.getColumnSelection().getSelected() != null && viewport
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594 .getColumnSelection().getSelected().size() > 0)
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595 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
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598 // now invert the sequence set, if required - empty selection implies
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599 // that no hiding is required.
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602 invertSequenceMenuItem_actionPerformed();
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603 sg = viewport.getSelectionGroup();
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607 viewport.expandColSelection(sg, true);
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608 // finally invert the column selection and get the new sequence
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609 // selection and indicate it should be hidden.
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610 invertColSel_actionPerformed();
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617 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
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620 viewport.hideAllSelectedSeqs();
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622 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
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625 viewport.showAllHiddenSeqs();
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631 if (viewport.getColumnSelection().getSelected().size() > 0)
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633 viewport.hideSelectedColumns();
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636 viewport.setSelectionGroup(sg);
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641 viewport.showAllHiddenColumns();
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647 public void keyReleased(KeyEvent evt)
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652 public void keyTyped(KeyEvent evt)
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657 public void itemStateChanged(ItemEvent evt)
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659 if (evt.getSource() == displayNonconservedMenuItem)
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661 displayNonconservedMenuItem_actionPerformed();
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663 else if (evt.getSource() == colourTextMenuItem)
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665 colourTextMenuItem_actionPerformed();
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667 else if (evt.getSource() == wrapMenuItem)
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669 wrapMenuItem_actionPerformed();
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671 else if (evt.getSource() == scaleAbove)
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673 viewport.setScaleAboveWrapped(scaleAbove.getState());
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675 else if (evt.getSource() == scaleLeft)
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677 viewport.setScaleLeftWrapped(scaleLeft.getState());
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679 else if (evt.getSource() == scaleRight)
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681 viewport.setScaleRightWrapped(scaleRight.getState());
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683 else if (evt.getSource() == seqLimits)
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685 seqLimits_itemStateChanged();
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687 else if (evt.getSource() == viewBoxesMenuItem)
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689 viewport.setShowBoxes(viewBoxesMenuItem.getState());
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691 else if (evt.getSource() == viewTextMenuItem)
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693 viewport.setShowText(viewTextMenuItem.getState());
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695 else if (evt.getSource() == renderGapsMenuItem)
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697 viewport.setRenderGaps(renderGapsMenuItem.getState());
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699 else if (evt.getSource() == annotationPanelMenuItem)
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701 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
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702 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
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704 else if (evt.getSource() == sequenceFeatures)
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706 viewport.showSequenceFeatures(sequenceFeatures.getState());
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707 alignPanel.seqPanel.seqCanvas.repaint();
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709 else if (evt.getSource() == conservationMenuItem)
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711 conservationMenuItem_actionPerformed();
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713 else if (evt.getSource() == abovePIDThreshold)
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715 abovePIDThreshold_actionPerformed();
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717 else if (evt.getSource() == applyToAllGroups)
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719 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
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721 else if (evt.getSource() == autoCalculate)
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723 viewport.autoCalculateConsensus = autoCalculate.getState();
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725 else if (evt.getSource() == sortByTree)
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727 viewport.sortByTree = sortByTree.getState();
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729 else if (evt.getSource() == this.centreColumnLabelFlag)
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731 centreColumnLabelFlag_stateChanged();
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733 else if (evt.getSource() == this.followMouseOverFlag)
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735 mouseOverFlag_stateChanged();
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737 else if (evt.getSource() == showGroupConsensus)
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739 showGroupConsensus_actionPerformed();
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741 else if (evt.getSource() == showGroupConservation)
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743 showGroupConservation_actionPerformed();
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745 else if (evt.getSource() == showSequenceLogo)
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747 showSequenceLogo_actionPerformed();
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749 else if (evt.getSource() == normSequenceLogo)
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751 normSequenceLogo_actionPerformed();
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753 else if (evt.getSource() == showConsensusHistogram)
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755 showConsensusHistogram_actionPerformed();
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757 else if (evt.getSource() == applyAutoAnnotationSettings)
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759 applyAutoAnnotationSettings_actionPerformed();
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761 alignPanel.paintAlignment(true);
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764 private void mouseOverFlag_stateChanged()
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766 viewport.followHighlight = followMouseOverFlag.getState();
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767 // TODO: could kick the scrollTo mechanism to reset view for current
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771 private void centreColumnLabelFlag_stateChanged()
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773 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
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774 this.alignPanel.annotationPanel.repaint();
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778 public void actionPerformed(ActionEvent evt)
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780 Object source = evt.getSource();
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782 if (source == inputText)
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784 inputText_actionPerformed();
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786 else if (source == loadTree)
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788 loadTree_actionPerformed();
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790 else if (source == loadApplication)
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792 launchFullApplication();
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794 else if (source == loadAnnotations)
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798 else if (source == outputAnnotations)
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800 outputAnnotations(true);
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802 else if (source == outputFeatures)
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804 outputFeatures(true, "Jalview");
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806 else if (source == closeMenuItem)
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808 closeMenuItem_actionPerformed();
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810 else if (source == copy)
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812 copy_actionPerformed();
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814 else if (source == undoMenuItem)
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816 undoMenuItem_actionPerformed();
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818 else if (source == redoMenuItem)
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820 redoMenuItem_actionPerformed();
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822 else if (source == inputText)
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824 inputText_actionPerformed();
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826 else if (source == closeMenuItem)
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828 closeMenuItem_actionPerformed();
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830 else if (source == undoMenuItem)
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832 undoMenuItem_actionPerformed();
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834 else if (source == redoMenuItem)
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836 redoMenuItem_actionPerformed();
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838 else if (source == copy)
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840 copy_actionPerformed();
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842 else if (source == pasteNew)
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844 pasteNew_actionPerformed();
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846 else if (source == pasteThis)
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848 pasteThis_actionPerformed();
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850 else if (source == cut)
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852 cut_actionPerformed();
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854 else if (source == delete)
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856 delete_actionPerformed();
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858 else if (source == grpsFromSelection)
\r
860 makeGrpsFromSelection_actionPerformed();
\r
862 else if (source == deleteGroups)
\r
864 deleteGroups_actionPerformed();
\r
866 else if (source == selectAllSequenceMenuItem)
\r
868 selectAllSequenceMenuItem_actionPerformed();
\r
870 else if (source == deselectAllSequenceMenuItem)
\r
872 deselectAllSequenceMenuItem_actionPerformed();
\r
874 else if (source == invertSequenceMenuItem)
\r
876 invertSequenceMenuItem_actionPerformed();
\r
878 else if (source == invertColSel)
\r
880 viewport.invertColumnSelection();
\r
881 alignPanel.paintAlignment(true);
\r
883 else if (source == remove2LeftMenuItem)
\r
885 trimAlignment(true);
\r
887 else if (source == remove2RightMenuItem)
\r
889 trimAlignment(false);
\r
891 else if (source == removeGappedColumnMenuItem)
\r
893 removeGappedColumnMenuItem_actionPerformed();
\r
895 else if (source == removeAllGapsMenuItem)
\r
897 removeAllGapsMenuItem_actionPerformed();
\r
899 else if (source == findMenuItem)
\r
901 findMenuItem_actionPerformed();
\r
903 else if (source == font)
\r
905 new FontChooser(alignPanel);
\r
907 else if (source == newView)
\r
911 else if (source == showColumns)
\r
913 viewport.showAllHiddenColumns();
\r
914 alignPanel.paintAlignment(true);
\r
916 else if (source == showSeqs)
\r
918 viewport.showAllHiddenSeqs();
\r
919 alignPanel.paintAlignment(true);
\r
921 else if (source == hideColumns)
\r
923 viewport.hideSelectedColumns();
\r
924 alignPanel.paintAlignment(true);
\r
926 else if (source == hideSequences
\r
927 && viewport.getSelectionGroup() != null)
\r
929 viewport.hideAllSelectedSeqs();
\r
930 alignPanel.paintAlignment(true);
\r
932 else if (source == hideAllButSelection)
\r
934 toggleHiddenRegions(false, false);
\r
935 alignPanel.paintAlignment(true);
\r
937 else if (source == hideAllSelection)
\r
939 SequenceGroup sg = viewport.getSelectionGroup();
\r
940 viewport.expandColSelection(sg, false);
\r
941 viewport.hideAllSelectedSeqs();
\r
942 viewport.hideSelectedColumns();
\r
943 alignPanel.paintAlignment(true);
\r
945 else if (source == showAllHidden)
\r
947 viewport.showAllHiddenColumns();
\r
948 viewport.showAllHiddenSeqs();
\r
949 alignPanel.paintAlignment(true);
\r
951 else if (source == showGroupConsensus)
\r
953 showGroupConsensus_actionPerformed();
\r
955 else if (source == showGroupConservation)
\r
957 showGroupConservation_actionPerformed();
\r
959 else if (source == showSequenceLogo)
\r
961 showSequenceLogo_actionPerformed();
\r
963 else if (source == normSequenceLogo)
\r
965 normSequenceLogo_actionPerformed();
\r
967 else if (source == showConsensusHistogram)
\r
969 showConsensusHistogram_actionPerformed();
\r
971 else if (source == applyAutoAnnotationSettings)
\r
973 applyAutoAnnotationSettings_actionPerformed();
\r
975 else if (source == featureSettings)
\r
977 new FeatureSettings(alignPanel);
\r
979 else if (source == alProperties)
\r
981 StringBuffer contents = new jalview.io.AlignmentProperties(
\r
982 viewport.getAlignment()).formatAsString();
\r
983 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
984 cap.setText(contents.toString());
\r
985 Frame frame = new Frame();
\r
987 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
\r
988 + getTitle(), 400, 250);
\r
990 else if (source == overviewMenuItem)
\r
992 overviewMenuItem_actionPerformed();
\r
994 else if (source == noColourmenuItem)
\r
996 changeColour(null);
\r
998 else if (source == clustalColour)
\r
1000 abovePIDThreshold.setState(false);
\r
1001 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
\r
1003 else if (source == zappoColour)
\r
1005 changeColour(new ZappoColourScheme());
\r
1007 else if (source == taylorColour)
\r
1009 changeColour(new TaylorColourScheme());
\r
1011 else if (source == hydrophobicityColour)
\r
1013 changeColour(new HydrophobicColourScheme());
\r
1015 else if (source == helixColour)
\r
1017 changeColour(new HelixColourScheme());
\r
1019 else if (source == strandColour)
\r
1021 changeColour(new StrandColourScheme());
\r
1023 else if (source == turnColour)
\r
1025 changeColour(new TurnColourScheme());
\r
1027 else if (source == buriedColour)
\r
1029 changeColour(new BuriedColourScheme());
\r
1031 else if (source == nucleotideColour)
\r
1033 changeColour(new NucleotideColourScheme());
\r
1035 else if (source == purinePyrimidineColour)
\r
1037 changeColour(new PurinePyrimidineColourScheme());
\r
1039 else if (source == RNAInteractionColour)
\r
1041 changeColour(new RNAInteractionColourScheme());
\r
1043 else if (source == RNAHelixColour)
\r
1045 new RNAHelicesColourChooser(viewport, alignPanel);
\r
1047 else if (source == modifyPID)
\r
1049 modifyPID_actionPerformed();
\r
1051 else if (source == modifyConservation)
\r
1053 modifyConservation_actionPerformed();
\r
1055 else if (source == userDefinedColour)
\r
1057 new UserDefinedColours(alignPanel, null);
\r
1059 else if (source == PIDColour)
\r
1061 changeColour(new PIDColourScheme());
\r
1063 else if (source == BLOSUM62Colour)
\r
1065 changeColour(new Blosum62ColourScheme());
\r
1067 else if (source == tcoffeeColour)
\r
1069 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
\r
1071 else if (source == annotationColour)
\r
1073 new AnnotationColourChooser(viewport, alignPanel);
\r
1075 else if (source == sortPairwiseMenuItem)
\r
1077 sortPairwiseMenuItem_actionPerformed();
\r
1079 else if (source == sortIDMenuItem)
\r
1081 sortIDMenuItem_actionPerformed();
\r
1083 else if (source == sortLengthMenuItem)
\r
1085 sortLengthMenuItem_actionPerformed();
\r
1087 else if (source == sortGroupMenuItem)
\r
1089 sortGroupMenuItem_actionPerformed();
\r
1091 else if (source == removeRedundancyMenuItem)
\r
1093 removeRedundancyMenuItem_actionPerformed();
\r
1095 else if (source == pairwiseAlignmentMenuItem)
\r
1097 pairwiseAlignmentMenuItem_actionPerformed();
\r
1099 else if (source == PCAMenuItem)
\r
1101 PCAMenuItem_actionPerformed();
\r
1103 else if (source == averageDistanceTreeMenuItem)
\r
1105 averageDistanceTreeMenuItem_actionPerformed();
\r
1107 else if (source == neighbourTreeMenuItem)
\r
1109 neighbourTreeMenuItem_actionPerformed();
\r
1111 else if (source == njTreeBlosumMenuItem)
\r
1113 njTreeBlosumMenuItem_actionPerformed();
\r
1115 else if (source == avDistanceTreeBlosumMenuItem)
\r
1117 avTreeBlosumMenuItem_actionPerformed();
\r
1119 else if (source == documentation)
\r
1121 documentation_actionPerformed();
\r
1123 else if (source == about)
\r
1125 about_actionPerformed();
\r
1130 public void inputText_actionPerformed()
\r
1132 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1133 Frame frame = new Frame();
\r
1135 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
\r
1138 protected void outputText_actionPerformed(ActionEvent e)
\r
1140 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1141 Frame frame = new Frame();
\r
1143 jalview.bin.JalviewLite.addFrame(frame,
\r
1144 "Alignment output - " + e.getActionCommand(), 600, 500);
\r
1145 cap.setText(new AppletFormatAdapter().formatSequences(
\r
1146 e.getActionCommand(), viewport.getAlignment(),
\r
1147 viewport.showJVSuffix));
\r
1150 public void loadAnnotations()
\r
1152 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1153 cap.setText("Paste your features / annotations / T-coffee score file here.");
\r
1154 cap.setAnnotationImport();
\r
1155 Frame frame = new Frame();
\r
1157 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
\r
1161 public String outputAnnotations(boolean displayTextbox)
\r
1163 String annotation = new AnnotationFile().printAnnotations(
\r
1164 viewport.showAnnotation ? viewport.getAlignment()
\r
1165 .getAlignmentAnnotation() : null, viewport
\r
1166 .getAlignment().getGroups(), ((Alignment) viewport
\r
1167 .getAlignment()).alignmentProperties);
\r
1169 if (displayTextbox)
\r
1171 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
1172 Frame frame = new Frame();
\r
1174 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
\r
1175 cap.setText(annotation);
\r
1178 return annotation;
\r
1181 private Hashtable getDisplayedFeatureCols()
\r
1183 if (alignPanel.getFeatureRenderer() != null
\r
1184 && viewport.featuresDisplayed != null)
\r
1186 FeatureRenderer fr = alignPanel.getFeatureRenderer();
\r
1187 Hashtable fcols = new Hashtable();
\r
1188 Enumeration en = viewport.featuresDisplayed.keys();
\r
1189 while (en.hasMoreElements())
\r
1191 Object col = en.nextElement();
\r
1192 fcols.put(col, fr.featureColours.get(col));
\r
1199 public String outputFeatures(boolean displayTextbox, String format)
\r
1202 if (format.equalsIgnoreCase("Jalview"))
\r
1204 features = new FeaturesFile().printJalviewFormat(viewport
\r
1205 .getAlignment().getSequencesArray(),
\r
1206 getDisplayedFeatureCols());
\r
1210 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
\r
1211 .getSequencesArray(), getDisplayedFeatureCols());
\r
1214 if (displayTextbox)
\r
1216 boolean frimport = false;
\r
1217 if (features == null || features.equals("No Features Visible"))
\r
1219 features = "# No features visible - paste some and import them here.";
\r
1223 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
\r
1226 cap.setAnnotationImport();
\r
1228 Frame frame = new Frame();
\r
1230 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
\r
1231 cap.setText(features);
\r
1235 if (features == null)
\r
1242 void launchFullApplication()
\r
1244 StringBuffer url = new StringBuffer(jalviewServletURL);
\r
1246 url.append("?open="
\r
1247 + appendProtocol(viewport.applet.getParameter("file")));
\r
1249 if (viewport.applet.getParameter("features") != null)
\r
1251 url.append("&features=");
\r
1252 url.append(appendProtocol(viewport.applet.getParameter("features")));
\r
1255 if (viewport.applet.getParameter("annotations") != null)
\r
1257 url.append("&annotations=");
\r
1258 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
\r
1261 if (viewport.applet.getParameter("jnetfile") != null)
\r
1263 url.append("&annotations=");
\r
1264 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
\r
1267 if (viewport.applet.getParameter("defaultColour") != null)
\r
1269 url.append("&colour="
\r
1270 + removeWhiteSpace(viewport.applet
\r
1271 .getParameter("defaultColour")));
\r
1274 if (viewport.applet.getParameter("userDefinedColour") != null)
\r
1276 url.append("&colour="
\r
1277 + removeWhiteSpace(viewport.applet
\r
1278 .getParameter("userDefinedColour")));
\r
1280 if (viewport.applet.getParameter("tree") != null)
\r
1282 url.append("&tree="
\r
1283 + appendProtocol(viewport.applet.getParameter("tree")));
\r
1285 if (viewport.applet.getParameter("treeFile") != null)
\r
1287 url.append("&tree="
\r
1288 + appendProtocol(viewport.applet.getParameter("treeFile")));
\r
1291 showURL(url.toString(), "FULL_APP");
\r
1294 String removeWhiteSpace(String colour)
\r
1296 StringBuffer sb = new StringBuffer();
\r
1297 for (int i = 0; i < colour.length(); i++)
\r
1299 if (Character.isWhitespace(colour.charAt(i)))
\r
1305 sb.append(colour.charAt(i));
\r
1309 return sb.toString();
\r
1312 String appendProtocol(String url)
\r
1317 url = URLEncoder.encode(url);
\r
1320 * When we finally deprecate 1.1 compatibility, we can start to use
\r
1321 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
\r
1322 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
\r
1323 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
\r
1324 * ex.printStackTrace(); }
\r
1326 catch (java.net.MalformedURLException ex)
\r
1328 url = viewport.applet.getCodeBase() + url;
\r
1333 public void closeMenuItem_actionPerformed()
\r
1335 PaintRefresher.RemoveComponent(alignPanel);
\r
1336 if (alignPanel.seqPanel != null
\r
1337 && alignPanel.seqPanel.seqCanvas != null)
\r
1339 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
\r
1341 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
\r
1343 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
\r
1346 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
\r
1354 alignPanel = null;
\r
1361 void updateEditMenuBar()
\r
1364 if (viewport.historyList.size() > 0)
\r
1366 undoMenuItem.setEnabled(true);
\r
1367 CommandI command = (CommandI) viewport.historyList.peek();
\r
1368 undoMenuItem.setLabel("Undo " + command.getDescription());
\r
1372 undoMenuItem.setEnabled(false);
\r
1373 undoMenuItem.setLabel("Undo");
\r
1376 if (viewport.redoList.size() > 0)
\r
1378 redoMenuItem.setEnabled(true);
\r
1380 CommandI command = (CommandI) viewport.redoList.peek();
\r
1381 redoMenuItem.setLabel("Redo " + command.getDescription());
\r
1385 redoMenuItem.setEnabled(false);
\r
1386 redoMenuItem.setLabel("Redo");
\r
1393 public void addHistoryItem(CommandI command)
\r
1395 if (command.getSize() > 0)
\r
1397 viewport.historyList.push(command);
\r
1398 viewport.redoList.removeAllElements();
\r
1399 updateEditMenuBar();
\r
1400 viewport.updateHiddenColumns();
\r
1405 * TODO: JAL-1104 DOCUMENT ME!
\r
1410 protected void undoMenuItem_actionPerformed()
\r
1412 if (viewport.historyList.size() < 1)
\r
1417 CommandI command = (CommandI) viewport.historyList.pop();
\r
1418 viewport.redoList.push(command);
\r
1419 command.undoCommand(null);
\r
1421 AlignViewport originalSource = getOriginatingSource(command);
\r
1423 if (originalSource != viewport)
\r
1426 .println("Warning: Viewport object mismatch whilst undoing");
\r
1428 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
\r
1429 // viewport.getColumnSelection().getHiddenColumns()
\r
1431 updateEditMenuBar();
\r
1432 originalSource.firePropertyChange("alignment", null, originalSource
\r
1433 .getAlignment().getSequences());
\r
1437 * TODO: JAL-1104 DOCUMENT ME!
\r
1442 protected void redoMenuItem_actionPerformed()
\r
1444 if (viewport.redoList.size() < 1)
\r
1449 CommandI command = (CommandI) viewport.redoList.pop();
\r
1450 viewport.historyList.push(command);
\r
1451 command.doCommand(null);
\r
1453 AlignViewport originalSource = getOriginatingSource(command);
\r
1455 if (originalSource != viewport)
\r
1458 .println("Warning: Viewport object mismatch whilst re-doing");
\r
1460 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
\r
1461 // viewport.getColumnSelection().getHiddenColumns()
\r
1464 updateEditMenuBar();
\r
1465 originalSource.firePropertyChange("alignment", null, originalSource
\r
1466 .getAlignment().getSequences());
\r
1469 AlignViewport getOriginatingSource(CommandI command)
\r
1471 AlignViewport originalSource = null;
\r
1472 // For sequence removal and addition, we need to fire
\r
1473 // the property change event FROM the viewport where the
\r
1474 // original alignment was altered
\r
1475 AlignmentI al = null;
\r
1476 if (command instanceof EditCommand)
\r
1478 EditCommand editCommand = (EditCommand) command;
\r
1479 al = editCommand.getAlignment();
\r
1480 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
1481 .getSequenceSetId());
\r
1482 for (int i = 0; i < comps.size(); i++)
\r
1484 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
1486 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
\r
1488 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
\r
1495 if (originalSource == null)
\r
1497 // The original view is closed, we must validate
\r
1498 // the current view against the closed view first
\r
1501 PaintRefresher.validateSequences(al, viewport.getAlignment());
\r
1504 originalSource = viewport;
\r
1507 return originalSource;
\r
1510 public void moveSelectedSequences(boolean up)
\r
1512 SequenceGroup sg = viewport.getSelectionGroup();
\r
1517 viewport.getAlignment().moveSelectedSequencesByOne(sg,
\r
1518 up ? null : viewport.getHiddenRepSequences(), up);
\r
1519 alignPanel.paintAlignment(true);
\r
1522 synchronized void slideSequences(boolean right, int size)
\r
1524 List<SequenceI> sg = new Vector<SequenceI>();
\r
1525 if (viewport.cursorMode)
\r
1527 sg.add(viewport.getAlignment().getSequenceAt(
\r
1528 alignPanel.seqPanel.seqCanvas.cursorY));
\r
1530 else if (viewport.getSelectionGroup() != null
\r
1531 && viewport.getSelectionGroup().getSize() != viewport
\r
1532 .getAlignment().getHeight())
\r
1534 sg = viewport.getSelectionGroup().getSequences(
\r
1535 viewport.getHiddenRepSequences());
\r
1538 if (sg.size() < 1)
\r
1543 Vector<SequenceI> invertGroup = new Vector();
\r
1545 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
\r
1547 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
\r
1548 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
\r
1551 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
\r
1553 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
\r
1555 for (int i = 0; i < invertGroup.size(); i++)
\r
1556 seqs2[i] = invertGroup.elementAt(i);
\r
1558 SlideSequencesCommand ssc;
\r
1560 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
\r
1561 size, viewport.getGapCharacter());
\r
1563 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
\r
1564 size, viewport.getGapCharacter());
\r
1566 int groupAdjustment = 0;
\r
1567 if (ssc.getGapsInsertedBegin() && right)
\r
1569 if (viewport.cursorMode)
\r
1570 alignPanel.seqPanel.moveCursor(size, 0);
\r
1572 groupAdjustment = size;
\r
1574 else if (!ssc.getGapsInsertedBegin() && !right)
\r
1576 if (viewport.cursorMode)
\r
1577 alignPanel.seqPanel.moveCursor(-size, 0);
\r
1579 groupAdjustment = -size;
\r
1582 if (groupAdjustment != 0)
\r
1584 viewport.getSelectionGroup().setStartRes(
\r
1585 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
\r
1586 viewport.getSelectionGroup().setEndRes(
\r
1587 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
\r
1590 boolean appendHistoryItem = false;
\r
1591 if (viewport.historyList != null && viewport.historyList.size() > 0
\r
1592 && viewport.historyList.peek() instanceof SlideSequencesCommand)
\r
1594 appendHistoryItem = ssc
\r
1595 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
\r
1599 if (!appendHistoryItem)
\r
1600 addHistoryItem(ssc);
\r
1605 static StringBuffer copiedSequences;
\r
1607 static Vector copiedHiddenColumns;
\r
1609 protected void copy_actionPerformed()
\r
1611 if (viewport.getSelectionGroup() == null)
\r
1616 SequenceGroup sg = viewport.getSelectionGroup();
\r
1617 copiedSequences = new StringBuffer();
\r
1618 Hashtable orderedSeqs = new Hashtable();
\r
1619 for (int i = 0; i < sg.getSize(); i++)
\r
1621 SequenceI seq = sg.getSequenceAt(i);
\r
1622 int index = viewport.getAlignment().findIndex(seq);
\r
1623 orderedSeqs.put(index + "", seq);
\r
1626 int index = 0, startRes, endRes;
\r
1629 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
\r
1631 copiedHiddenColumns = new Vector();
\r
1632 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
\r
1633 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
\r
1636 int[] region = (int[]) viewport.getColumnSelection()
\r
1637 .getHiddenColumns().elementAt(i);
\r
1639 copiedHiddenColumns.addElement(new int[]
\r
1640 { region[0] - hiddenOffset, region[1] - hiddenOffset });
\r
1645 copiedHiddenColumns = null;
\r
1648 for (int i = 0; i < sg.getSize(); i++)
\r
1650 SequenceI seq = null;
\r
1652 while (seq == null)
\r
1654 if (orderedSeqs.containsKey(index + ""))
\r
1656 seq = (SequenceI) orderedSeqs.get(index + "");
\r
1668 // Returns residue following index if gap
\r
1669 startRes = seq.findPosition(sg.getStartRes());
\r
1672 // Need to find the residue preceeding index if gap
\r
1675 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
\r
1677 ch = seq.getCharAt(j);
\r
1678 if (!jalview.util.Comparison.isGap((ch)))
\r
1686 endRes += seq.getStart() - 1;
\r
1689 copiedSequences.append(seq.getName()
\r
1695 + seq.getSequenceAsString(sg.getStartRes(),
\r
1696 sg.getEndRes() + 1) + "\n");
\r
1701 protected void pasteNew_actionPerformed()
\r
1706 protected void pasteThis_actionPerformed()
\r
1711 void paste(boolean newAlignment)
\r
1716 if (copiedSequences == null)
\r
1721 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
1722 Vector seqs = new Vector();
\r
1723 while (st.hasMoreElements())
\r
1725 String name = st.nextToken();
\r
1726 int start = Integer.parseInt(st.nextToken());
\r
1727 int end = Integer.parseInt(st.nextToken());
\r
1728 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
\r
1730 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
1731 for (int i = 0; i < seqs.size(); i++)
\r
1733 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
1738 String newtitle = new String("Copied sequences");
\r
1739 if (getTitle().startsWith("Copied sequences"))
\r
1741 newtitle = getTitle();
\r
1745 newtitle = newtitle.concat("- from " + getTitle());
\r
1747 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
1748 viewport.applet, newtitle, false);
\r
1749 if (copiedHiddenColumns != null)
\r
1751 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
1753 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
1754 af.viewport.hideColumns(region[0], region[1]);
\r
1758 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
\r
1763 addSequences(newSeqs);
\r
1766 } catch (Exception ex)
\r
1768 } // could be anything being pasted in here
\r
1772 void addSequences(SequenceI[] seqs)
\r
1774 for (int i = 0; i < seqs.length; i++)
\r
1776 viewport.getAlignment().addSequence(seqs[i]);
\r
1780 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
\r
1781 seqs, 0, viewport.getAlignment().getWidth(),
\r
1782 viewport.getAlignment()));
\r
1784 viewport.setEndSeq(viewport.getAlignment().getHeight());
\r
1785 viewport.getAlignment().getWidth();
\r
1786 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1791 protected void cut_actionPerformed()
\r
1793 copy_actionPerformed();
\r
1794 delete_actionPerformed();
\r
1797 protected void delete_actionPerformed()
\r
1800 SequenceGroup sg = viewport.getSelectionGroup();
\r
1806 Vector seqs = new Vector();
\r
1808 for (int i = 0; i < sg.getSize(); i++)
\r
1810 seq = sg.getSequenceAt(i);
\r
1811 seqs.addElement(seq);
\r
1814 // If the cut affects all sequences, remove highlighted columns
\r
1815 if (sg.getSize() == viewport.getAlignment().getHeight())
\r
1817 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
1818 sg.getEndRes() + 1);
\r
1821 SequenceI[] cut = new SequenceI[seqs.size()];
\r
1822 for (int i = 0; i < seqs.size(); i++)
\r
1824 cut[i] = (SequenceI) seqs.elementAt(i);
\r
1828 * //ADD HISTORY ITEM
\r
1830 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
\r
1831 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
\r
1832 viewport.getAlignment()));
\r
1834 viewport.setSelectionGroup(null);
\r
1835 viewport.getAlignment().deleteGroup(sg);
\r
1837 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1840 if (viewport.getAlignment().getHeight() < 1)
\r
1842 this.setVisible(false);
\r
1844 viewport.sendSelection();
\r
1848 * group consensus toggled
\r
1851 protected void showGroupConsensus_actionPerformed()
\r
1853 viewport.setShowGroupConsensus(showGroupConsensus.getState());
\r
1854 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1859 * group conservation toggled.
\r
1861 protected void showGroupConservation_actionPerformed()
\r
1863 viewport.setShowGroupConservation(showGroupConservation.getState());
\r
1864 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1871 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
\r
1872 * .event.ActionEvent)
\r
1874 protected void showConsensusHistogram_actionPerformed()
\r
1876 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
\r
1877 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1884 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
\r
1885 * .event.ActionEvent)
\r
1887 protected void showSequenceLogo_actionPerformed()
\r
1889 viewport.setShowSequenceLogo(showSequenceLogo.getState());
\r
1890 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1893 protected void normSequenceLogo_actionPerformed()
\r
1895 showSequenceLogo.setState(true);
\r
1896 viewport.setShowSequenceLogo(true);
\r
1897 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
\r
1898 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1901 protected void applyAutoAnnotationSettings_actionPerformed()
\r
1903 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1906 protected void makeGrpsFromSelection_actionPerformed()
\r
1908 if (viewport.getSelectionGroup() != null)
\r
1910 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
\r
1911 viewport.getSequenceSelection(),
\r
1912 viewport.getAlignmentView(true).getSequenceStrings(
\r
1913 viewport.getGapCharacter()), viewport.getAlignment()
\r
1915 viewport.getAlignment().deleteAllGroups();
\r
1916 viewport.sequenceColours = null;
\r
1917 viewport.setSelectionGroup(null);
\r
1918 // set view properties for each group
\r
1919 for (int g = 0; g < gps.length; g++)
\r
1921 // gps[g].setShowunconserved(viewport.getShowUnconserved());
\r
1922 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
\r
1923 viewport.getAlignment().addGroup(gps[g]);
\r
1924 Color col = new Color((int) (Math.random() * 255),
\r
1925 (int) (Math.random() * 255), (int) (Math.random() * 255));
\r
1926 col = col.brighter();
\r
1927 for (SequenceI sq : gps[g].getSequences(null))
\r
1928 viewport.setSequenceColour(sq, col);
\r
1930 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
\r
1931 alignPanel.updateAnnotation();
\r
1932 alignPanel.paintAlignment(true);
\r
1936 protected void deleteGroups_actionPerformed()
\r
1938 viewport.getAlignment().deleteAllGroups();
\r
1939 viewport.sequenceColours = null;
\r
1940 viewport.setSelectionGroup(null);
\r
1942 alignPanel.paintAlignment(true);
\r
1945 public void selectAllSequenceMenuItem_actionPerformed()
\r
1947 SequenceGroup sg = new SequenceGroup();
\r
1948 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1950 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
1952 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
\r
1953 viewport.setSelectionGroup(sg);
\r
1954 alignPanel.paintAlignment(true);
\r
1955 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1956 viewport.sendSelection();
\r
1959 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1961 if (viewport.cursorMode)
\r
1963 alignPanel.seqPanel.keyboardNo1 = null;
\r
1964 alignPanel.seqPanel.keyboardNo2 = null;
\r
1966 viewport.setSelectionGroup(null);
\r
1967 viewport.getColumnSelection().clear();
\r
1968 viewport.setSelectionGroup(null);
\r
1969 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1970 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1971 alignPanel.paintAlignment(true);
\r
1972 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1973 viewport.sendSelection();
\r
1976 public void invertSequenceMenuItem_actionPerformed()
\r
1978 SequenceGroup sg = viewport.getSelectionGroup();
\r
1979 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1981 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1984 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1985 viewport.sendSelection();
\r
1988 public void invertColSel_actionPerformed()
\r
1990 viewport.invertColumnSelection();
\r
1991 alignPanel.paintAlignment(true);
\r
1992 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1993 viewport.sendSelection();
\r
1996 void trimAlignment(boolean trimLeft)
\r
1998 ColumnSelection colSel = viewport.getColumnSelection();
\r
2001 if (colSel.size() > 0)
\r
2005 column = colSel.getMin();
\r
2009 column = colSel.getMax();
\r
2013 if (viewport.getSelectionGroup() != null)
\r
2015 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2016 viewport.getHiddenRepSequences());
\r
2020 seqs = viewport.getAlignment().getSequencesArray();
\r
2023 TrimRegionCommand trimRegion;
\r
2026 trimRegion = new TrimRegionCommand("Remove Left",
\r
2027 TrimRegionCommand.TRIM_LEFT, seqs, column,
\r
2028 viewport.getAlignment(), viewport.getColumnSelection(),
\r
2029 viewport.getSelectionGroup());
\r
2030 viewport.setStartRes(0);
\r
2034 trimRegion = new TrimRegionCommand("Remove Right",
\r
2035 TrimRegionCommand.TRIM_RIGHT, seqs, column,
\r
2036 viewport.getAlignment(), viewport.getColumnSelection(),
\r
2037 viewport.getSelectionGroup());
\r
2040 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
\r
2042 addHistoryItem(trimRegion);
\r
2044 for (SequenceGroup sg : viewport.getAlignment().getGroups())
\r
2046 if ((trimLeft && !sg.adjustForRemoveLeft(column))
\r
2047 || (!trimLeft && !sg.adjustForRemoveRight(column)))
\r
2049 viewport.getAlignment().deleteGroup(sg);
\r
2053 viewport.firePropertyChange("alignment", null, viewport
\r
2054 .getAlignment().getSequences());
\r
2058 public void removeGappedColumnMenuItem_actionPerformed()
\r
2060 int start = 0, end = viewport.getAlignment().getWidth() - 1;
\r
2063 if (viewport.getSelectionGroup() != null)
\r
2065 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2066 viewport.getHiddenRepSequences());
\r
2067 start = viewport.getSelectionGroup().getStartRes();
\r
2068 end = viewport.getSelectionGroup().getEndRes();
\r
2072 seqs = viewport.getAlignment().getSequencesArray();
\r
2075 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
\r
2076 "Remove Gapped Columns", seqs, start, end,
\r
2077 viewport.getAlignment());
\r
2079 addHistoryItem(removeGapCols);
\r
2081 statusBar.setText("Removed " + removeGapCols.getSize()
\r
2082 + " empty columns.");
\r
2084 // This is to maintain viewport position on first residue
\r
2085 // of first sequence
\r
2086 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
\r
2087 int startRes = seq.findPosition(viewport.startRes);
\r
2088 // ShiftList shifts;
\r
2089 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
\r
2090 // edit.alColumnChanges=shifts.getInverse();
\r
2091 // if (viewport.hasHiddenColumns)
\r
2092 // viewport.getColumnSelection().compensateForEdits(shifts);
\r
2093 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
2094 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
2099 public void removeAllGapsMenuItem_actionPerformed()
\r
2101 int start = 0, end = viewport.getAlignment().getWidth() - 1;
\r
2104 if (viewport.getSelectionGroup() != null)
\r
2106 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2107 viewport.getHiddenRepSequences());
\r
2108 start = viewport.getSelectionGroup().getStartRes();
\r
2109 end = viewport.getSelectionGroup().getEndRes();
\r
2113 seqs = viewport.getAlignment().getSequencesArray();
\r
2116 // This is to maintain viewport position on first residue
\r
2117 // of first sequence
\r
2118 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
\r
2119 int startRes = seq.findPosition(viewport.startRes);
\r
2121 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
\r
2122 viewport.getAlignment()));
\r
2124 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
2126 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
2131 public void findMenuItem_actionPerformed()
\r
2133 new Finder(alignPanel);
\r
2137 * create a new view derived from the current view
\r
2139 * @param viewtitle
\r
2140 * @return frame for the new view
\r
2142 public AlignFrame newView(String viewtitle)
\r
2145 if (viewport.hasHiddenRows())
\r
2147 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
\r
2148 .getFullAlignment().getSequencesArray());
\r
2152 newal = new Alignment(viewport.getAlignment().getSequencesArray());
\r
2155 if (viewport.getAlignment().getAlignmentAnnotation() != null)
\r
2157 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
\r
2159 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
\r
2161 newal.addAnnotation(viewport.getAlignment()
\r
2162 .getAlignmentAnnotation()[i]);
\r
2167 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
\r
2169 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
\r
2170 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
\r
2171 PaintRefresher.Register(newaf.alignPanel,
\r
2172 newaf.alignPanel.av.getSequenceSetId());
\r
2174 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
\r
2175 newaf.alignPanel.av.getSequenceSetId());
\r
2176 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
\r
2177 newaf.alignPanel.av.getSequenceSetId());
\r
2179 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
2180 .getSequenceSetId());
\r
2181 int viewSize = -1;
\r
2182 for (int i = 0; i < comps.size(); i++)
\r
2184 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
2190 String title = new String(this.getTitle());
\r
2191 if (viewtitle != null)
\r
2193 title = viewtitle + " ( " + title + ")";
\r
2197 if (title.indexOf("(View") > -1)
\r
2199 title = title.substring(0, title.indexOf("(View"));
\r
2201 title += "(View " + viewSize + ")";
\r
2204 newaf.setTitle(title.toString());
\r
2206 newaf.viewport.historyList = viewport.historyList;
\r
2207 newaf.viewport.redoList = viewport.redoList;
\r
2213 * @return list of feature groups on the view
\r
2215 public String[] getFeatureGroups()
\r
2217 FeatureRenderer fr = null;
\r
2218 if (alignPanel != null
\r
2219 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2221 return fr.getGroups();
\r
2227 * get sequence feature groups that are hidden or shown
\r
2233 public String[] getFeatureGroupsOfState(boolean visible)
\r
2235 FeatureRenderer fr = null;
\r
2236 if (alignPanel != null
\r
2237 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2239 return fr.getGroups(visible);
\r
2245 * Change the display state for the given feature groups
\r
2248 * list of group strings
\r
2250 * visible or invisible
\r
2252 public void setFeatureGroupState(String[] groups, boolean state)
\r
2254 FeatureRenderer fr = null;
\r
2255 this.sequenceFeatures.setState(true);
\r
2256 viewport.showSequenceFeatures(true);
\r
2257 if (alignPanel != null
\r
2258 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2260 fr.setGroupState(groups, state);
\r
2261 alignPanel.seqPanel.seqCanvas.repaint();
\r
2262 if (alignPanel.overviewPanel != null)
\r
2264 alignPanel.overviewPanel.updateOverviewImage();
\r
2269 public void seqLimits_itemStateChanged()
\r
2271 viewport.setShowJVSuffix(seqLimits.getState());
\r
2272 alignPanel.fontChanged();
\r
2273 alignPanel.paintAlignment(true);
\r
2276 protected void colourTextMenuItem_actionPerformed()
\r
2278 viewport.setColourText(colourTextMenuItem.getState());
\r
2279 alignPanel.paintAlignment(true);
\r
2282 protected void displayNonconservedMenuItem_actionPerformed()
\r
2284 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
\r
2285 alignPanel.paintAlignment(true);
\r
2288 protected void wrapMenuItem_actionPerformed()
\r
2290 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
2291 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
2292 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
2293 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
2294 scaleRight.setEnabled(wrapMenuItem.getState());
\r
2295 alignPanel.paintAlignment(true);
\r
2298 public void overviewMenuItem_actionPerformed()
\r
2300 if (alignPanel.overviewPanel != null)
\r
2305 Frame frame = new Frame();
\r
2306 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
2307 frame.add(overview);
\r
2308 // +50 must allow for applet frame window
\r
2309 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
2310 overview.getPreferredSize().width,
\r
2311 overview.getPreferredSize().height + 50);
\r
2314 final AlignmentPanel ap = alignPanel;
\r
2315 frame.addWindowListener(new WindowAdapter()
\r
2318 public void windowClosing(WindowEvent e)
\r
2322 ap.setOverviewPanel(null);
\r
2327 alignPanel.setOverviewPanel(overview);
\r
2331 void changeColour(ColourSchemeI cs)
\r
2333 int threshold = 0;
\r
2337 if (viewport.getAbovePIDThreshold())
\r
2339 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
2342 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2344 viewport.setGlobalColourScheme(cs);
\r
2348 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2351 if (viewport.getConservationSelected())
\r
2354 Alignment al = (Alignment) viewport.getAlignment();
\r
2355 Conservation c = new Conservation("All",
\r
2356 ResidueProperties.propHash, 3, al.getSequences(), 0,
\r
2357 al.getWidth() - 1);
\r
2360 c.verdict(false, viewport.getConsPercGaps());
\r
2362 cs.setConservation(c);
\r
2364 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
\r
2365 cs, "Background"));
\r
2370 cs.setConservation(null);
\r
2373 cs.setConsensus(viewport.getSequenceConsensusHash());
\r
2376 viewport.setGlobalColourScheme(cs);
\r
2378 if (alignPanel.getOverviewPanel() != null)
\r
2380 alignPanel.getOverviewPanel().updateOverviewImage();
\r
2383 jalview.structure.StructureSelectionManager
\r
2384 .getStructureSelectionManager(viewport.applet)
\r
2385 .sequenceColoursChanged(alignPanel);
\r
2387 alignPanel.paintAlignment(true);
\r
2390 protected void modifyPID_actionPerformed()
\r
2392 if (viewport.getAbovePIDThreshold()
\r
2393 && viewport.getGlobalColourScheme() != null)
\r
2395 SliderPanel.setPIDSliderSource(alignPanel,
\r
2396 viewport.getGlobalColourScheme(), "Background");
\r
2397 SliderPanel.showPIDSlider();
\r
2401 protected void modifyConservation_actionPerformed()
\r
2403 if (viewport.getConservationSelected()
\r
2404 && viewport.getGlobalColourScheme() != null)
\r
2406 SliderPanel.setConservationSlider(alignPanel,
\r
2407 viewport.getGlobalColourScheme(), "Background");
\r
2408 SliderPanel.showConservationSlider();
\r
2412 protected void conservationMenuItem_actionPerformed()
\r
2414 viewport.setConservationSelected(conservationMenuItem.getState());
\r
2416 viewport.setAbovePIDThreshold(false);
\r
2417 abovePIDThreshold.setState(false);
\r
2419 changeColour(viewport.getGlobalColourScheme());
\r
2421 modifyConservation_actionPerformed();
\r
2424 public void abovePIDThreshold_actionPerformed()
\r
2426 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
2428 conservationMenuItem.setState(false);
\r
2429 viewport.setConservationSelected(false);
\r
2431 changeColour(viewport.getGlobalColourScheme());
\r
2433 modifyPID_actionPerformed();
\r
2436 public void sortPairwiseMenuItem_actionPerformed()
\r
2438 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2439 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
\r
2440 .getAlignment().getSequenceAt(0), null);
\r
2442 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
\r
2443 viewport.getAlignment()));
\r
2444 alignPanel.paintAlignment(true);
\r
2447 public void sortIDMenuItem_actionPerformed()
\r
2449 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2450 AlignmentSorter.sortByID(viewport.getAlignment());
\r
2451 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
\r
2452 viewport.getAlignment()));
\r
2453 alignPanel.paintAlignment(true);
\r
2456 public void sortLengthMenuItem_actionPerformed()
\r
2458 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2459 AlignmentSorter.sortByLength(viewport.getAlignment());
\r
2460 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
\r
2461 viewport.getAlignment()));
\r
2462 alignPanel.paintAlignment(true);
\r
2465 public void sortGroupMenuItem_actionPerformed()
\r
2467 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2468 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
2469 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
\r
2470 viewport.getAlignment()));
\r
2471 alignPanel.paintAlignment(true);
\r
2475 public void removeRedundancyMenuItem_actionPerformed()
\r
2477 new RedundancyPanel(alignPanel);
\r
2480 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
2482 if (viewport.getSelectionGroup() != null
\r
2483 && viewport.getSelectionGroup().getSize() > 1)
\r
2485 Frame frame = new Frame();
\r
2486 frame.add(new PairwiseAlignPanel(alignPanel));
\r
2487 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
\r
2492 public void PCAMenuItem_actionPerformed()
\r
2494 // are the sequences aligned?
\r
2495 if (!viewport.getAlignment().isAligned(false))
\r
2497 SequenceI current;
\r
2498 int Width = viewport.getAlignment().getWidth();
\r
2500 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2502 current = viewport.getAlignment().getSequenceAt(i);
\r
2504 if (current.getLength() < Width)
\r
2506 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2509 alignPanel.paintAlignment(true);
\r
2512 if ((viewport.getSelectionGroup() != null
\r
2513 && viewport.getSelectionGroup().getSize() < 4 && viewport
\r
2514 .getSelectionGroup().getSize() > 0)
\r
2515 || viewport.getAlignment().getHeight() < 4)
\r
2522 new PCAPanel(viewport);
\r
2523 } catch (java.lang.OutOfMemoryError ex)
\r
2529 public void averageDistanceTreeMenuItem_actionPerformed()
\r
2531 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
2534 public void neighbourTreeMenuItem_actionPerformed()
\r
2536 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
2539 protected void njTreeBlosumMenuItem_actionPerformed()
\r
2541 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2544 protected void avTreeBlosumMenuItem_actionPerformed()
\r
2546 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2549 void NewTreePanel(String type, String pwType, String title)
\r
2551 // are the sequences aligned?
\r
2552 if (!viewport.getAlignment().isAligned(false))
\r
2554 SequenceI current;
\r
2555 int Width = viewport.getAlignment().getWidth();
\r
2557 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2559 current = viewport.getAlignment().getSequenceAt(i);
\r
2561 if (current.getLength() < Width)
\r
2563 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2566 alignPanel.paintAlignment(true);
\r
2570 if ((viewport.getSelectionGroup() != null && viewport
\r
2571 .getSelectionGroup().getSize() > 1)
\r
2572 || (viewport.getAlignment().getHeight() > 1))
\r
2574 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
\r
2576 addTreeMenuItem(tp, title);
\r
2578 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
2582 void loadTree_actionPerformed()
\r
2584 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
2585 cap.setText("Paste your Newick tree file here.");
\r
2586 cap.setTreeImport();
\r
2587 Frame frame = new Frame();
\r
2589 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
2592 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
2594 TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
\r
2595 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
2596 addTreeMenuItem(tp, treeFile);
\r
2600 * sort the alignment using the given treePanel
\r
2602 * @param treePanel
\r
2603 * tree used to sort view
\r
2605 * string used for undo event name
\r
2607 public void sortByTree(TreePanel treePanel, String title)
\r
2609 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2611 .sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
2612 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2613 // HistoryItem.SORT));
\r
2614 addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
\r
2615 viewport.getAlignment()));
\r
2616 alignPanel.paintAlignment(true);
\r
2620 * Do any automatic reordering of the alignment and add the necessary bits to
\r
2621 * the menu structure for the new tree
\r
2623 * @param treePanel
\r
2626 protected void addTreeMenuItem(final TreePanel treePanel,
\r
2627 final String title)
\r
2629 final MenuItem item = new MenuItem(title);
\r
2630 sortByTreeMenu.add(item);
\r
2631 item.addActionListener(new java.awt.event.ActionListener()
\r
2634 public void actionPerformed(ActionEvent evt)
\r
2636 sortByTree(treePanel, title); // treePanel.getTitle());
\r
2640 treePanel.addWindowListener(new WindowAdapter()
\r
2643 public void windowOpened(WindowEvent e)
\r
2645 if (viewport.sortByTree)
\r
2647 sortByTree(treePanel, title);
\r
2649 super.windowOpened(e);
\r
2653 public void windowClosing(WindowEvent e)
\r
2655 sortByTreeMenu.remove(item);
\r
2660 public boolean sortBy(AlignmentOrder alorder, String undoname)
\r
2662 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2663 if (viewport.applet.debug)
\r
2665 System.err.println("Sorting " + alorder.getOrder().size()
\r
2666 + " in alignment '" + getTitle() + "'");
\r
2668 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
\r
2669 if (undoname != null)
\r
2671 addHistoryItem(new OrderCommand(undoname, oldOrder,
\r
2672 viewport.getAlignment()));
\r
2674 alignPanel.paintAlignment(true);
\r
2678 protected void documentation_actionPerformed()
\r
2680 alignPanel.av.applet.openJalviewHelpUrl();
\r
2683 protected void about_actionPerformed()
\r
2686 class AboutPanel extends Canvas
\r
2692 public AboutPanel(String version, String builddate)
\r
2694 this.version = version;
\r
2695 this.builddate = builddate;
\r
2699 public void paint(Graphics g)
\r
2701 g.setColor(Color.white);
\r
2702 g.fillRect(0, 0, getSize().width, getSize().height);
\r
2703 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2704 FontMetrics fm = g.getFontMetrics();
\r
2705 int fh = fm.getHeight();
\r
2707 g.setColor(Color.black);
\r
2708 // TODO: update this text for each release or centrally store it for
\r
2709 // lite and application
\r
2710 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
2711 g.drawString("JalviewLite - Release " + version, x, y += fh);
\r
2712 g.setFont(new Font("Helvetica", Font.BOLD, 12));
\r
2713 g.drawString("Build date: " + builddate, x, y += fh);
\r
2714 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2716 "Authors: Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui,",
\r
2717 x, y += fh * 1.5);
\r
2719 "Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.",
\r
2720 x + 50, y += fh + 8);
\r
2722 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
\r
2725 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
\r
2727 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
\r
2729 "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
\r
2732 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
\r
2734 g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
\r
2739 Frame frame = new Frame();
\r
2740 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
\r
2741 .getBuildDate()));
\r
2742 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
\r
2746 public void showURL(String url, String target)
\r
2748 if (viewport.applet == null)
\r
2750 System.out.println("Not running as applet - no browser available.");
\r
2754 viewport.applet.showURL(url, target);
\r
2758 // ////////////////////////////////////////////////////////////////////////////////
\r
2759 // JBuilder Graphics here
\r
2761 MenuBar alignFrameMenuBar = new MenuBar();
\r
2763 Menu fileMenu = new Menu("File");
\r
2765 MenuItem loadApplication = new MenuItem("View in Full Application");
\r
2767 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
\r
2769 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
\r
2771 MenuItem outputFeatures = new MenuItem("Export Features ...");
\r
2773 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
\r
2775 MenuItem closeMenuItem = new MenuItem("Close");
\r
2777 Menu editMenu = new Menu("Edit");
\r
2779 Menu viewMenu = new Menu("View");
\r
2781 Menu colourMenu = new Menu("Colour");
\r
2783 Menu calculateMenu = new Menu("Calculate");
\r
2785 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
2787 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
2789 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
2791 MenuItem remove2LeftMenuItem = new MenuItem();
\r
2793 MenuItem remove2RightMenuItem = new MenuItem();
\r
2795 MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
2797 MenuItem removeAllGapsMenuItem = new MenuItem();
\r
2799 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
2801 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
2803 MenuItem sortPairwiseMenuItem = new MenuItem();
\r
2805 MenuItem sortIDMenuItem = new MenuItem();
\r
2807 MenuItem sortLengthMenuItem = new MenuItem();
\r
2809 MenuItem sortGroupMenuItem = new MenuItem();
\r
2811 MenuItem removeRedundancyMenuItem = new MenuItem();
\r
2813 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
2815 MenuItem PCAMenuItem = new MenuItem();
\r
2817 MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
2819 MenuItem neighbourTreeMenuItem = new MenuItem();
\r
2821 BorderLayout borderLayout1 = new BorderLayout();
\r
2823 public Label statusBar = new Label();
\r
2825 Menu outputTextboxMenu = new Menu();
\r
2827 MenuItem clustalColour = new MenuItem();
\r
2829 MenuItem zappoColour = new MenuItem();
\r
2831 MenuItem taylorColour = new MenuItem();
\r
2833 MenuItem hydrophobicityColour = new MenuItem();
\r
2835 MenuItem helixColour = new MenuItem();
\r
2837 MenuItem strandColour = new MenuItem();
\r
2839 MenuItem turnColour = new MenuItem();
\r
2841 MenuItem buriedColour = new MenuItem();
\r
2843 MenuItem purinePyrimidineColour = new MenuItem();
\r
2845 MenuItem RNAInteractionColour = new MenuItem();
\r
2847 MenuItem RNAHelixColour = new MenuItem();
\r
2849 MenuItem userDefinedColour = new MenuItem();
\r
2851 MenuItem PIDColour = new MenuItem();
\r
2853 MenuItem BLOSUM62Colour = new MenuItem();
\r
2855 MenuItem tcoffeeColour = new MenuItem();
\r
2857 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
2859 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
2861 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
2863 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
2865 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
\r
2867 MenuItem alProperties = new MenuItem("Alignment Properties...");
\r
2869 MenuItem overviewMenuItem = new MenuItem();
\r
2871 MenuItem undoMenuItem = new MenuItem();
\r
2873 MenuItem redoMenuItem = new MenuItem();
\r
2875 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
2877 MenuItem noColourmenuItem = new MenuItem();
\r
2879 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
2881 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
2883 MenuItem findMenuItem = new MenuItem();
\r
2885 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
2887 MenuItem nucleotideColour = new MenuItem();
\r
2889 MenuItem deleteGroups = new MenuItem();
\r
2891 MenuItem grpsFromSelection = new MenuItem();
\r
2893 MenuItem delete = new MenuItem();
\r
2895 MenuItem copy = new MenuItem();
\r
2897 MenuItem cut = new MenuItem();
\r
2899 Menu pasteMenu = new Menu();
\r
2901 MenuItem pasteNew = new MenuItem();
\r
2903 MenuItem pasteThis = new MenuItem();
\r
2905 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
2907 MenuItem font = new MenuItem();
\r
2909 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
2911 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
2913 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
2915 MenuItem modifyPID = new MenuItem();
\r
2917 MenuItem modifyConservation = new MenuItem();
\r
2919 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
\r
2920 "Autocalculate Consensus", true);
\r
2922 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
\r
2923 "Sort Alignment With New Tree", true);
\r
2925 Menu sortByTreeMenu = new Menu();
\r
2927 Menu sort = new Menu();
\r
2929 Menu calculate = new Menu();
\r
2931 MenuItem inputText = new MenuItem();
\r
2933 Menu helpMenu = new Menu();
\r
2935 MenuItem documentation = new MenuItem();
\r
2937 MenuItem about = new MenuItem();
\r
2939 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
2941 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
\r
2943 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
\r
2945 Menu autoAnnMenu = new Menu();
\r
2947 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
\r
2949 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
\r
2951 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
\r
2953 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
\r
2955 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
\r
2957 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
\r
2959 private void jbInit() throws Exception
\r
2962 setMenuBar(alignFrameMenuBar);
\r
2966 // dynamically fill save as menu with available formats
\r
2967 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
2970 item = new MenuItem(
\r
2971 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
2973 item.addActionListener(new java.awt.event.ActionListener()
\r
2976 public void actionPerformed(ActionEvent e)
\r
2978 outputText_actionPerformed(e);
\r
2982 outputTextboxMenu.add(item);
\r
2984 closeMenuItem.addActionListener(this);
\r
2985 loadApplication.addActionListener(this);
\r
2987 loadTree.addActionListener(this);
\r
2988 loadAnnotations.addActionListener(this);
\r
2989 outputFeatures.addActionListener(this);
\r
2990 outputAnnotations.addActionListener(this);
\r
2991 selectAllSequenceMenuItem.addActionListener(this);
\r
2992 deselectAllSequenceMenuItem.addActionListener(this);
\r
2993 invertSequenceMenuItem.addActionListener(this);
\r
2994 remove2LeftMenuItem.setLabel("Remove Left");
\r
2995 remove2LeftMenuItem.addActionListener(this);
\r
2996 remove2RightMenuItem.setLabel("Remove Right");
\r
2997 remove2RightMenuItem.addActionListener(this);
\r
2998 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
2999 removeGappedColumnMenuItem.addActionListener(this);
\r
3000 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
3001 removeAllGapsMenuItem.addActionListener(this);
\r
3002 viewBoxesMenuItem.setLabel("Boxes");
\r
3003 viewBoxesMenuItem.setState(true);
\r
3004 viewBoxesMenuItem.addItemListener(this);
\r
3005 viewTextMenuItem.setLabel("Text");
\r
3006 viewTextMenuItem.setState(true);
\r
3007 viewTextMenuItem.addItemListener(this);
\r
3008 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
3009 sortPairwiseMenuItem.addActionListener(this);
\r
3010 sortIDMenuItem.setLabel("by ID");
\r
3011 sortIDMenuItem.addActionListener(this);
\r
3012 sortLengthMenuItem.setLabel("by Length");
\r
3013 sortLengthMenuItem.addActionListener(this);
\r
3014 sortGroupMenuItem.setLabel("by Group");
\r
3015 sortGroupMenuItem.addActionListener(this);
\r
3016 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
3017 removeRedundancyMenuItem.addActionListener(this);
\r
3018 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
3019 pairwiseAlignmentMenuItem.addActionListener(this);
\r
3020 PCAMenuItem.setLabel("Principal Component Analysis");
\r
3021 PCAMenuItem.addActionListener(this);
\r
3022 averageDistanceTreeMenuItem
\r
3023 .setLabel("Average Distance Using % Identity");
\r
3024 averageDistanceTreeMenuItem.addActionListener(this);
\r
3025 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
3026 neighbourTreeMenuItem.addActionListener(this);
\r
3027 statusBar.setBackground(Color.white);
\r
3028 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
3029 statusBar.setText("Status bar");
\r
3030 outputTextboxMenu.setLabel("Output to Textbox");
\r
3031 clustalColour.setLabel("Clustalx");
\r
3033 clustalColour.addActionListener(this);
\r
3034 zappoColour.setLabel("Zappo");
\r
3035 zappoColour.addActionListener(this);
\r
3036 taylorColour.setLabel("Taylor");
\r
3037 taylorColour.addActionListener(this);
\r
3038 hydrophobicityColour.setLabel("Hydrophobicity");
\r
3039 hydrophobicityColour.addActionListener(this);
\r
3040 helixColour.setLabel("Helix Propensity");
\r
3041 helixColour.addActionListener(this);
\r
3042 strandColour.setLabel("Strand Propensity");
\r
3043 strandColour.addActionListener(this);
\r
3044 turnColour.setLabel("Turn Propensity");
\r
3045 turnColour.addActionListener(this);
\r
3046 buriedColour.setLabel("Buried Index");
\r
3047 buriedColour.addActionListener(this);
\r
3048 purinePyrimidineColour.setLabel("Purine/Pyrimidine");
\r
3049 purinePyrimidineColour.addActionListener(this);
\r
3050 RNAInteractionColour.setLabel("Purine/Pyrimidine");
\r
3051 RNAInteractionColour.addActionListener(this);
\r
3052 RNAHelixColour.setLabel("by RNA Helices");
\r
3053 RNAHelixColour.addActionListener(this);
\r
3054 userDefinedColour.setLabel("User Defined...");
\r
3055 userDefinedColour.addActionListener(this);
\r
3056 PIDColour.setLabel("Percentage Identity");
\r
3057 PIDColour.addActionListener(this);
\r
3058 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
3059 BLOSUM62Colour.addActionListener(this);
\r
3060 tcoffeeColour.setLabel("T-Coffee Scores");
\r
3061 tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
\r
3063 tcoffeeColour.addActionListener(this);
\r
3064 avDistanceTreeBlosumMenuItem
\r
3065 .setLabel("Average Distance Using BLOSUM62");
\r
3066 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
3067 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
3068 njTreeBlosumMenuItem.addActionListener(this);
\r
3069 annotationPanelMenuItem.setLabel("Show Annotations");
\r
3070 annotationPanelMenuItem.addItemListener(this);
\r
3071 colourTextMenuItem.setLabel("Colour Text");
\r
3072 colourTextMenuItem.addItemListener(this);
\r
3073 displayNonconservedMenuItem.setLabel("Show nonconserved");
\r
3074 displayNonconservedMenuItem.addItemListener(this);
\r
3075 alProperties.addActionListener(this);
\r
3076 overviewMenuItem.setLabel("Overview Window");
\r
3077 overviewMenuItem.addActionListener(this);
\r
3078 undoMenuItem.setEnabled(false);
\r
3079 undoMenuItem.setLabel("Undo");
\r
3080 undoMenuItem.addActionListener(this);
\r
3081 redoMenuItem.setEnabled(false);
\r
3082 redoMenuItem.setLabel("Redo");
\r
3083 redoMenuItem.addActionListener(this);
\r
3084 conservationMenuItem.setLabel("by Conservation");
\r
3085 conservationMenuItem.addItemListener(this);
\r
3086 noColourmenuItem.setLabel("None");
\r
3087 noColourmenuItem.addActionListener(this);
\r
3088 wrapMenuItem.setLabel("Wrap");
\r
3089 wrapMenuItem.addItemListener(this);
\r
3090 renderGapsMenuItem.setLabel("Show Gaps");
\r
3091 renderGapsMenuItem.setState(true);
\r
3092 renderGapsMenuItem.addItemListener(this);
\r
3093 findMenuItem.setLabel("Find...");
\r
3094 findMenuItem.addActionListener(this);
\r
3095 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
3096 abovePIDThreshold.addItemListener(this);
\r
3097 nucleotideColour.setLabel("Nucleotide");
\r
3098 nucleotideColour.addActionListener(this);
\r
3099 deleteGroups.setLabel("Undefine Groups");
\r
3100 deleteGroups.addActionListener(this);
\r
3101 grpsFromSelection.setLabel("Make Groups for selection");
\r
3102 grpsFromSelection.addActionListener(this);
\r
3103 copy.setLabel("Copy");
\r
3104 copy.addActionListener(this);
\r
3105 cut.setLabel("Cut");
\r
3106 cut.addActionListener(this);
\r
3107 delete.setLabel("Delete");
\r
3108 delete.addActionListener(this);
\r
3109 pasteMenu.setLabel("Paste");
\r
3110 pasteNew.setLabel("To New Alignment");
\r
3111 pasteNew.addActionListener(this);
\r
3112 pasteThis.setLabel("Add To This Alignment");
\r
3113 pasteThis.addActionListener(this);
\r
3114 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
3115 applyToAllGroups.setState(true);
\r
3116 applyToAllGroups.addItemListener(this);
\r
3117 font.setLabel("Font...");
\r
3118 font.addActionListener(this);
\r
3119 scaleAbove.setLabel("Scale Above");
\r
3120 scaleAbove.setState(true);
\r
3121 scaleAbove.setEnabled(false);
\r
3122 scaleAbove.addItemListener(this);
\r
3123 scaleLeft.setEnabled(false);
\r
3124 scaleLeft.setState(true);
\r
3125 scaleLeft.setLabel("Scale Left");
\r
3126 scaleLeft.addItemListener(this);
\r
3127 scaleRight.setEnabled(false);
\r
3128 scaleRight.setState(true);
\r
3129 scaleRight.setLabel("Scale Right");
\r
3130 scaleRight.addItemListener(this);
\r
3131 modifyPID.setLabel("Modify Identity Threshold...");
\r
3132 modifyPID.addActionListener(this);
\r
3133 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
3134 modifyConservation.addActionListener(this);
\r
3135 sortByTreeMenu.setLabel("By Tree Order");
\r
3136 sort.setLabel("Sort");
\r
3137 calculate.setLabel("Calculate Tree");
\r
3138 autoCalculate.addItemListener(this);
\r
3139 sortByTree.addItemListener(this);
\r
3140 inputText.setLabel("Input from textbox");
\r
3141 inputText.addActionListener(this);
\r
3142 centreColumnLabelFlag.setLabel("Centre column labels");
\r
3143 centreColumnLabelFlag.addItemListener(this);
\r
3144 followMouseOverFlag.setLabel("Automatic Scrolling");
\r
3145 followMouseOverFlag.addItemListener(this);
\r
3146 helpMenu.setLabel("Help");
\r
3147 documentation.setLabel("Documentation");
\r
3148 documentation.addActionListener(this);
\r
3150 about.setLabel("About...");
\r
3151 about.addActionListener(this);
\r
3152 seqLimits.setState(true);
\r
3153 seqLimits.setLabel("Show Sequence Limits");
\r
3154 seqLimits.addItemListener(this);
\r
3155 featureSettings.setLabel("Feature Settings...");
\r
3156 featureSettings.addActionListener(this);
\r
3157 sequenceFeatures.setLabel("Sequence Features");
\r
3158 sequenceFeatures.addItemListener(this);
\r
3159 sequenceFeatures.setState(false);
\r
3160 annotationColour.setLabel("by Annotation...");
\r
3161 annotationColour.addActionListener(this);
\r
3162 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
3163 invertColSel.setLabel("Invert Column Selection");
\r
3164 menu1.setLabel("Show");
\r
3165 showColumns.setLabel("All Columns ");
\r
3166 showSeqs.setLabel("All Sequences");
\r
3167 menu2.setLabel("Hide");
\r
3168 hideColumns.setLabel("Selected Columns");
\r
3169 hideSequences.setLabel("Selected Sequences");
\r
3170 hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
\r
3171 hideAllSelection.setLabel("Selected Region");
\r
3172 showAllHidden.setLabel("All Sequences and Columns");
\r
3173 showGroupConsensus.setLabel("Group Consensus");
\r
3174 showGroupConservation.setLabel("Group Conservation");
\r
3175 showConsensusHistogram.setLabel("Show Consensus Histogram");
\r
3176 showSequenceLogo.setLabel("Show Consensus Logo");
\r
3177 normSequenceLogo.setLabel("Normalise Consensus Logo");
\r
3178 applyAutoAnnotationSettings.setLabel("Apply to all groups");
\r
3179 applyAutoAnnotationSettings.setState(true);
\r
3180 autoAnnMenu.setLabel("Autocalculated Annotation");
\r
3182 invertColSel.addActionListener(this);
\r
3183 showColumns.addActionListener(this);
\r
3184 showSeqs.addActionListener(this);
\r
3185 hideColumns.addActionListener(this);
\r
3186 hideSequences.addActionListener(this);
\r
3187 hideAllButSelection.addActionListener(this);
\r
3188 hideAllSelection.addActionListener(this);
\r
3189 showAllHidden.addActionListener(this);
\r
3190 showGroupConsensus.addItemListener(this);
\r
3191 showGroupConservation.addItemListener(this);
\r
3192 showConsensusHistogram.addItemListener(this);
\r
3193 showSequenceLogo.addItemListener(this);
\r
3194 applyAutoAnnotationSettings.addItemListener(this);
\r
3195 formatMenu.setLabel("Format");
\r
3196 selectMenu.setLabel("Select");
\r
3197 newView.setLabel("New View");
\r
3198 newView.addActionListener(this);
\r
3199 alignFrameMenuBar.add(fileMenu);
\r
3200 alignFrameMenuBar.add(editMenu);
\r
3201 alignFrameMenuBar.add(selectMenu);
\r
3202 alignFrameMenuBar.add(viewMenu);
\r
3203 alignFrameMenuBar.add(formatMenu);
\r
3204 alignFrameMenuBar.add(colourMenu);
\r
3205 alignFrameMenuBar.add(calculateMenu);
\r
3206 alignFrameMenuBar.add(helpMenu);
\r
3208 fileMenu.add(inputText);
\r
3209 fileMenu.add(loadTree);
\r
3210 fileMenu.add(loadAnnotations);
\r
3212 fileMenu.addSeparator();
\r
3213 fileMenu.add(outputTextboxMenu);
\r
3214 fileMenu.add(outputFeatures);
\r
3215 fileMenu.add(outputAnnotations);
\r
3217 if (jalviewServletURL != null)
\r
3219 fileMenu.add(loadApplication);
\r
3222 fileMenu.addSeparator();
\r
3223 fileMenu.add(closeMenuItem);
\r
3225 editMenu.add(undoMenuItem);
\r
3226 editMenu.add(redoMenuItem);
\r
3227 editMenu.add(cut);
\r
3228 editMenu.add(copy);
\r
3229 editMenu.add(pasteMenu);
\r
3230 editMenu.add(delete);
\r
3231 editMenu.addSeparator();
\r
3232 editMenu.add(remove2LeftMenuItem);
\r
3233 editMenu.add(remove2RightMenuItem);
\r
3234 editMenu.add(removeGappedColumnMenuItem);
\r
3235 editMenu.add(removeAllGapsMenuItem);
\r
3236 editMenu.add(removeRedundancyMenuItem);
\r
3237 viewMenu.add(newView);
\r
3238 viewMenu.addSeparator();
\r
3239 viewMenu.add(menu1);
\r
3240 viewMenu.add(menu2);
\r
3241 viewMenu.addSeparator();
\r
3242 viewMenu.add(followMouseOverFlag);
\r
3243 viewMenu.add(annotationPanelMenuItem);
\r
3244 autoAnnMenu.add(applyAutoAnnotationSettings);
\r
3245 autoAnnMenu.add(showConsensusHistogram);
\r
3246 autoAnnMenu.add(showSequenceLogo);
\r
3247 autoAnnMenu.add(normSequenceLogo);
\r
3248 autoAnnMenu.addSeparator();
\r
3249 autoAnnMenu.add(showGroupConservation);
\r
3250 autoAnnMenu.add(showGroupConsensus);
\r
3251 viewMenu.add(autoAnnMenu);
\r
3252 viewMenu.addSeparator();
\r
3253 viewMenu.add(sequenceFeatures);
\r
3254 viewMenu.add(featureSettings);
\r
3255 viewMenu.addSeparator();
\r
3256 viewMenu.add(alProperties);
\r
3257 viewMenu.addSeparator();
\r
3258 viewMenu.add(overviewMenuItem);
\r
3259 colourMenu.add(applyToAllGroups);
\r
3260 colourMenu.addSeparator();
\r
3261 colourMenu.add(noColourmenuItem);
\r
3262 colourMenu.add(clustalColour);
\r
3263 colourMenu.add(BLOSUM62Colour);
\r
3264 colourMenu.add(PIDColour);
\r
3265 colourMenu.add(zappoColour);
\r
3266 colourMenu.add(taylorColour);
\r
3267 colourMenu.add(hydrophobicityColour);
\r
3268 colourMenu.add(helixColour);
\r
3269 colourMenu.add(strandColour);
\r
3270 colourMenu.add(turnColour);
\r
3271 colourMenu.add(buriedColour);
\r
3272 colourMenu.add(nucleotideColour);
\r
3273 colourMenu.add(purinePyrimidineColour);
\r
3274 colourMenu.add(RNAInteractionColour);
\r
3275 colourMenu.add(tcoffeeColour);
\r
3276 colourMenu.add(userDefinedColour);
\r
3277 colourMenu.addSeparator();
\r
3278 colourMenu.add(conservationMenuItem);
\r
3279 colourMenu.add(modifyConservation);
\r
3280 colourMenu.add(abovePIDThreshold);
\r
3281 colourMenu.add(modifyPID);
\r
3282 colourMenu.add(annotationColour);
\r
3283 colourMenu.add(RNAHelixColour);
\r
3284 calculateMenu.add(sort);
\r
3285 calculateMenu.add(calculate);
\r
3286 calculateMenu.addSeparator();
\r
3287 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
3288 calculateMenu.add(PCAMenuItem);
\r
3289 calculateMenu.add(autoCalculate);
\r
3290 calculateMenu.add(sortByTree);
\r
3291 this.add(statusBar, BorderLayout.SOUTH);
\r
3292 pasteMenu.add(pasteNew);
\r
3293 pasteMenu.add(pasteThis);
\r
3294 sort.add(sortIDMenuItem);
\r
3295 sort.add(sortLengthMenuItem);
\r
3296 sort.add(sortByTreeMenu);
\r
3297 sort.add(sortGroupMenuItem);
\r
3298 sort.add(sortPairwiseMenuItem);
\r
3299 calculate.add(averageDistanceTreeMenuItem);
\r
3300 calculate.add(neighbourTreeMenuItem);
\r
3301 calculate.add(avDistanceTreeBlosumMenuItem);
\r
3302 calculate.add(njTreeBlosumMenuItem);
\r
3303 helpMenu.add(documentation);
\r
3304 helpMenu.add(about);
\r
3305 menu1.add(showColumns);
\r
3306 menu1.add(showSeqs);
\r
3307 menu1.add(showAllHidden);
\r
3308 menu2.add(hideColumns);
\r
3309 menu2.add(hideSequences);
\r
3310 menu2.add(hideAllSelection);
\r
3311 menu2.add(hideAllButSelection);
\r
3312 formatMenu.add(font);
\r
3313 formatMenu.add(seqLimits);
\r
3314 formatMenu.add(wrapMenuItem);
\r
3315 formatMenu.add(scaleAbove);
\r
3316 formatMenu.add(scaleLeft);
\r
3317 formatMenu.add(scaleRight);
\r
3318 formatMenu.add(viewBoxesMenuItem);
\r
3319 formatMenu.add(viewTextMenuItem);
\r
3320 formatMenu.add(colourTextMenuItem);
\r
3321 formatMenu.add(displayNonconservedMenuItem);
\r
3322 formatMenu.add(renderGapsMenuItem);
\r
3323 formatMenu.add(centreColumnLabelFlag);
\r
3324 selectMenu.add(findMenuItem);
\r
3325 selectMenu.addSeparator();
\r
3326 selectMenu.add(selectAllSequenceMenuItem);
\r
3327 selectMenu.add(deselectAllSequenceMenuItem);
\r
3328 selectMenu.add(invertSequenceMenuItem);
\r
3329 selectMenu.add(invertColSel);
\r
3330 selectMenu.add(grpsFromSelection);
\r
3331 selectMenu.add(deleteGroups);
\r
3335 MenuItem featureSettings = new MenuItem();
\r
3337 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
3339 MenuItem annotationColour = new MenuItem();
\r
3341 MenuItem invertColSel = new MenuItem();
\r
3343 Menu menu1 = new Menu();
\r
3345 MenuItem showColumns = new MenuItem();
\r
3347 MenuItem showSeqs = new MenuItem();
\r
3349 Menu menu2 = new Menu();
\r
3351 MenuItem hideColumns = new MenuItem();
\r
3353 MenuItem hideSequences = new MenuItem();
\r
3355 MenuItem hideAllButSelection = new MenuItem();
\r
3357 MenuItem hideAllSelection = new MenuItem();
\r
3359 MenuItem showAllHidden = new MenuItem();
\r
3361 Menu formatMenu = new Menu();
\r
3363 Menu selectMenu = new Menu();
\r
3365 MenuItem newView = new MenuItem();
\r
3368 * Attach the alignFrame panels after embedding menus, if necessary. This used
\r
3369 * to be called setEmbedded, but is now creates the dropdown menus in a
\r
3370 * platform independent manner to avoid OSX/Mac menu appendage daftness.
\r
3372 * @param reallyEmbedded
\r
3373 * true to attach the view to the applet area on the page rather than
\r
3376 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
\r
3378 if (reallyEmbedded)
\r
3381 // Explicly build the embedded menu panel for the on-page applet
\r
3383 // view cannot be closed if its actually on the page
\r
3384 fileMenu.remove(closeMenuItem);
\r
3385 fileMenu.remove(3); // Remove Seperator
\r
3386 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
\r
3387 Font.PLAIN, 10, false); // use our own fonts.
\r
3388 // and actually add the components to the applet area
\r
3389 viewport.applet.setLayout(new BorderLayout());
\r
3390 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
\r
3391 viewport.applet.add(statusBar, BorderLayout.SOUTH);
\r
3392 alignPanel.setSize(viewport.applet.getSize().width,
\r
3393 viewport.applet.getSize().height - embeddedMenu.HEIGHT
\r
3394 - statusBar.HEIGHT);
\r
3395 viewport.applet.add(alignPanel, BorderLayout.CENTER);
\r
3396 final AlignFrame me = this;
\r
3397 viewport.applet.addFocusListener(new FocusListener()
\r
3401 public void focusLost(FocusEvent e)
\r
3403 if (me.viewport.applet.currentAlignFrame == me)
\r
3405 me.viewport.applet.currentAlignFrame = null;
\r
3410 public void focusGained(FocusEvent e)
\r
3412 me.viewport.applet.currentAlignFrame = me;
\r
3415 viewport.applet.validate();
\r
3420 // test and embed menu bar if necessary.
\r
3422 if (embedMenuIfNeeded(alignPanel))
\r
3424 // adjust for status bar height too
\r
3425 alignPanel.setSize(getSize().width, getSize().height
\r
3426 - statusBar.HEIGHT);
\r
3428 add(statusBar, BorderLayout.SOUTH);
\r
3429 add(alignPanel, BorderLayout.CENTER);
\r
3430 // and register with the applet so it can pass external API calls to us
\r
3431 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
\r
3437 * create a new binding between structures in an existing jmol viewer instance
\r
3438 * and an alignpanel with sequences that have existing PDBFile entries. Note,
\r
3439 * this does not open a new Jmol window, or modify the display of the
\r
3440 * structures in the original jmol window. Note This method doesn't work
\r
3441 * without an additional javascript library to exchange messages between the
\r
3442 * distinct applets. See http://issues.jalview.org/browse/JAL-621
\r
3445 * JmolViewer instance
\r
3446 * @param sequenceIds
\r
3447 * - sequence Ids to search for associations
\r
3449 public SequenceStructureBinding addStructureViewInstance(
\r
3450 Object jmolviewer, String[] sequenceIds)
\r
3452 org.jmol.api.JmolViewer viewer = null;
\r
3455 viewer = (org.jmol.api.JmolViewer) jmolviewer;
\r
3456 } catch (ClassCastException ex)
\r
3458 System.err.println("Unsupported viewer object :"
\r
3459 + jmolviewer.getClass());
\r
3461 if (viewer == null)
\r
3463 System.err.println("Can't use this object as a structure viewer:"
\r
3464 + jmolviewer.getClass());
\r
3467 SequenceI[] seqs = null;
\r
3468 if (sequenceIds == null || sequenceIds.length == 0)
\r
3470 seqs = viewport.getAlignment().getSequencesArray();
\r
3474 Vector sqi = new Vector();
\r
3475 AlignmentI al = viewport.getAlignment();
\r
3476 for (int sid = 0; sid < sequenceIds.length; sid++)
\r
3478 SequenceI sq = al.findName(sequenceIds[sid]);
\r
3481 sqi.addElement(sq);
\r
3484 if (sqi.size() > 0)
\r
3486 seqs = new SequenceI[sqi.size()];
\r
3487 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
\r
3489 seqs[sid] = (SequenceI) sqi.elementAt(sid);
\r
3497 ExtJmol jmv = null;
\r
3498 // TODO: search for a jmv that involves viewer
\r
3500 { // create a new viewer/jalview binding.
\r
3501 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
\r
3509 * bind a pdb file to a sequence in the current view
\r
3511 * @param sequenceId
\r
3512 * - sequenceId within the dataset.
\r
3513 * @param pdbEntryString
\r
3514 * - the short name for the PDB file
\r
3516 * - pdb file - either a URL or a valid PDB file.
\r
3517 * @return true if binding was as success TODO: consider making an exception
\r
3518 * structure for indicating when PDB parsing or sequenceId location
\r
3521 public boolean addPdbFile(String sequenceId, String pdbEntryString,
\r
3524 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
\r
3525 boolean needtoadd = false;
\r
3526 if (toaddpdb != null)
\r
3528 Vector pdbe = toaddpdb.getPDBId();
\r
3529 PDBEntry pdbentry = null;
\r
3530 if (pdbe != null && pdbe.size() > 0)
\r
3532 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
\r
3534 pdbentry = (PDBEntry) pdbe.elementAt(pe);
\r
3535 if (!pdbentry.getId().equals(pdbEntryString)
\r
3536 && !pdbentry.getFile().equals(pdbFile))
\r
3546 if (pdbentry == null)
\r
3548 pdbentry = new PDBEntry();
\r
3549 pdbentry.setId(pdbEntryString);
\r
3550 pdbentry.setFile(pdbFile);
\r
3551 needtoadd = true; // add this new entry to sequence.
\r
3553 // resolve data source
\r
3554 // TODO: this code should be a refactored to an io package
\r
3555 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
\r
3556 if (protocol == null)
\r
3562 // make a note of the access mode and add
\r
3563 if (pdbentry.getProperty() == null)
\r
3565 pdbentry.setProperty(new Hashtable());
\r
3567 pdbentry.getProperty().put("protocol", protocol);
\r
3568 toaddpdb.addPDBId(pdbentry);
\r
3574 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
\r
3578 Vector sequences = new Vector();
\r
3579 for (int i = 0; i < seqs.length; i++)
\r
3581 if (seqs[i] != null)
\r
3583 sequences.addElement(new Object[]
\r
3584 { seqs[i], (chains != null) ? chains[i] : null });
\r
3587 seqs = new SequenceI[sequences.size()];
\r
3588 chains = new String[sequences.size()];
\r
3589 for (int i = 0, isize = sequences.size(); i < isize; i++)
\r
3591 Object[] oj = (Object[]) sequences.elementAt(i);
\r
3593 seqs[i] = (SequenceI) oj[0];
\r
3594 chains[i] = (String) oj[1];
\r
3597 return new Object[]
\r
3602 public void newStructureView(JalviewLite applet, PDBEntry pdb,
\r
3603 SequenceI[] seqs, String[] chains, String protocol)
\r
3605 // Scrub any null sequences from the array
\r
3606 Object[] sqch = cleanSeqChainArrays(seqs, chains);
\r
3607 seqs = (SequenceI[]) sqch[0];
\r
3608 chains = (String[]) sqch[1];
\r
3609 if (seqs == null || seqs.length == 0)
\r
3612 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
\r
3614 if (protocol == null || protocol.trim().length() == 0
\r
3615 || protocol.equals("null"))
\r
3617 protocol = (String) pdb.getProperty().get("protocol");
\r
3618 if (protocol == null)
\r
3620 System.err.println("Couldn't work out protocol to open structure: "
\r
3625 if (applet.useXtrnalSviewer)
\r
3627 // register the association(s) and quit, don't create any windows.
\r
3628 if (StructureSelectionManager.getStructureSelectionManager(applet)
\r
3629 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
\r
3631 System.err.println("Failed to map " + pdb.getFile() + " ("
\r
3632 + protocol + ") to any sequences");
\r
3636 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
\r
3638 // can only do alignments with Jmol
\r
3639 // find the last jmol window assigned to this alignment
\r
3640 jalview.appletgui.AppletJmol ajm = null, tajm;
\r
3641 Vector jmols = applet
\r
3642 .getAppletWindow(jalview.appletgui.AppletJmol.class);
\r
3643 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
\r
3645 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
\r
3646 if (tajm.ap.alignFrame == this)
\r
3655 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
\r
3656 // try and add the pdb structure
\r
3661 // otherwise, create a new window
\r
3662 if (applet.jmolAvailable)
\r
3664 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
\r
3666 applet.lastFrameX += 40;
\r
3667 applet.lastFrameY += 40;
\r
3671 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
\r
3676 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
\r
3677 SequenceI[][] seqs, String[][] chains, String[] protocols)
\r
3679 // TODO Auto-generated method stub
\r
3680 System.err.println("Aligned Structure View: Not yet implemented.");
\r
3684 * modify the current selection, providing the user has not made a selection
\r
3688 * - sequences from this alignment
\r
3690 * - columns to be selected on the alignment
\r
3692 public void select(SequenceGroup sel, ColumnSelection csel)
\r
3694 alignPanel.seqPanel.selection(sel, csel, null);
\r
3697 public void scrollTo(int row, int column)
\r
3699 alignPanel.seqPanel.scrollTo(row, column);
\r
3702 public void scrollToRow(int row)
\r
3704 alignPanel.seqPanel.scrollToRow(row);
\r
3707 public void scrollToColumn(int column)
\r
3709 alignPanel.seqPanel.scrollToColumn(column);
\r
3713 * @return the alignments unique ID.
\r
3715 public String getSequenceSetId()
\r
3717 return viewport.getSequenceSetId();
\r
3721 * Load the (T-Coffee) score file from the specified url
\r
3724 * File/URL/T-COFFEE score file contents
\r
3725 * @throws IOException
\r
3726 * @return true if alignment was annotated with data from source
\r
3727 * @throws SAXException
\r
3728 * @throws ParserConfigurationException
\r
3729 * @throws ExceptionFileFormatOrSyntax
\r
3730 * @throws ExceptionLoadingFailed
\r
3731 * @throws ExceptionPermissionDenied
\r
3732 * @throws InterruptedException
\r
3733 * @throws ExceptionUnmatchedClosingParentheses
\r
3735 public boolean loadScoreFile(String source) throws Exception
\r
3738 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
\r
3739 AppletFormatAdapter.checkProtocol(source));
\r
3740 if (!file.isValid())
\r
3742 // TODO: raise dialog for gui
\r
3743 System.err.println("Problems parsing T-Coffee scores: "
\r
3744 + file.getWarningMessage());
\r
3745 System.err.println("Origin was:\n" + source);
\r
3750 * check that the score matrix matches the alignment dimensions
\r
3753 if ((aln = viewport.getAlignment()) != null
\r
3754 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
\r
3757 // TODO: raise a dialog box here rather than bomb out.
\r
3759 .println("The scores matrix does not match the alignment dimensions");
\r
3763 // TODO add parameter to indicate if matching should be done
\r
3764 if (file.annotateAlignment(alignPanel.getAlignment(), false))
\r
3766 alignPanel.fontChanged();
\r
3767 tcoffeeColour.setEnabled(true);
\r
3768 // switch to this color
\r
3769 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
\r
3774 System.err.println("Problems resolving T-Coffee scores:");
\r
3775 if (file.getWarningMessage() != null)
\r
3777 System.err.println(file.getWarningMessage());
\r