2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
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3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
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5 * This file is part of Jalview.
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7 * Jalview is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License
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9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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11 * Jalview is distributed in the hope that it will be useful, but
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12 * WITHOUT ANY WARRANTY; without even the implied warranty
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13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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14 * PURPOSE. See the GNU General Public License for more details.
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16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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18 package jalview.appletgui;
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20 import jalview.analysis.AAFrequency;
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21 import jalview.analysis.AlignmentSorter;
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22 import jalview.analysis.Conservation;
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23 import jalview.api.SequenceStructureBinding;
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24 import jalview.bin.JalviewLite;
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25 import jalview.commands.CommandI;
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26 import jalview.commands.EditCommand;
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27 import jalview.commands.OrderCommand;
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28 import jalview.commands.RemoveGapColCommand;
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29 import jalview.commands.RemoveGapsCommand;
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30 import jalview.commands.SlideSequencesCommand;
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31 import jalview.commands.TrimRegionCommand;
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32 import jalview.datamodel.Alignment;
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33 import jalview.datamodel.AlignmentI;
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34 import jalview.datamodel.AlignmentOrder;
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35 import jalview.datamodel.ColumnSelection;
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36 import jalview.datamodel.PDBEntry;
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37 import jalview.datamodel.Sequence;
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38 import jalview.datamodel.SequenceCollectionI;
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39 import jalview.datamodel.SequenceGroup;
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40 import jalview.datamodel.SequenceI;
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41 import jalview.io.AnnotationFile;
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42 import jalview.io.AppletFormatAdapter;
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43 import jalview.io.FeaturesFile;
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44 import jalview.io.TCoffeeScoreFile;
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45 import jalview.schemes.Blosum62ColourScheme;
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46 import jalview.schemes.BuriedColourScheme;
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47 import jalview.schemes.ClustalxColourScheme;
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48 import jalview.schemes.ColourSchemeI;
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49 import jalview.schemes.HelixColourScheme;
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50 import jalview.schemes.HydrophobicColourScheme;
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51 import jalview.schemes.NucleotideColourScheme;
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52 import jalview.schemes.PIDColourScheme;
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53 import jalview.schemes.PurinePyrimidineColourScheme;
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54 import jalview.schemes.RNAHelicesColourChooser;
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55 import jalview.schemes.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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104 public class AlignFrame extends EmbmenuFrame implements ActionListener, ItemListener, KeyListener
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106 public AlignmentPanel alignPanel;
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108 public AlignViewport viewport;
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110 int DEFAULT_WIDTH = 700;
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112 int DEFAULT_HEIGHT = 500;
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114 String jalviewServletURL;
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117 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title, boolean embedded)
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119 if (applet != null)
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121 jalviewServletURL = applet.getParameter("APPLICATION_URL");
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127 } catch (Exception ex)
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129 ex.printStackTrace();
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132 viewport = new AlignViewport(al, applet);
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133 alignPanel = new AlignmentPanel(this, viewport);
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135 viewport.updateConservation(alignPanel);
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136 viewport.updateConsensus(alignPanel);
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138 annotationPanelMenuItem.setState(viewport.showAnnotation);
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139 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
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140 followMouseOverFlag.setState(viewport.getFollowHighlight());
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141 showGroupConsensus.setState(viewport.isShowGroupConsensus());
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142 showGroupConservation.setState(viewport.isShowGroupConservation());
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143 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
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144 showSequenceLogo.setState(viewport.isShowSequenceLogo());
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146 seqLimits.setState(viewport.showJVSuffix);
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148 if (applet != null)
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150 String param = applet.getParameter("sortBy");
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153 if (param.equalsIgnoreCase("Id"))
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155 sortIDMenuItem_actionPerformed();
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157 else if (param.equalsIgnoreCase("Pairwise Identity"))
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159 sortPairwiseMenuItem_actionPerformed();
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161 else if (param.equalsIgnoreCase("Length"))
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163 sortLengthMenuItem_actionPerformed();
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167 param = applet.getParameter("wrap");
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170 if (param.equalsIgnoreCase("true"))
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172 wrapMenuItem.setState(true);
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173 wrapMenuItem_actionPerformed();
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176 param = applet.getParameter("centrecolumnlabels");
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179 centreColumnLabelFlag.setState(true);
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180 centreColumnLabelFlag_stateChanged();
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184 param = applet.getParameter("windowWidth");
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187 int width = Integer.parseInt(param);
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188 DEFAULT_WIDTH = width;
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190 param = applet.getParameter("windowHeight");
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193 int height = Integer.parseInt(param);
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194 DEFAULT_HEIGHT = height;
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196 } catch (Exception ex)
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201 if (viewport.getAlignment().isNucleotide())
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203 viewport.updateStrucConsensus(alignPanel);
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204 if (viewport.getAlignment().hasRNAStructure())
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206 RNAHelixColour.setEnabled(true);
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209 RNAHelixColour.setEnabled(false);
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212 RNAHelixColour.setEnabled(false);
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213 purinePyrimidineColour.setEnabled(false);
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216 // Some JVMS send keyevents to Top frame or lowest panel,
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217 // Havent worked out why yet. So add to both this frame and seqCanvas for
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219 this.addKeyListener(this);
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220 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
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221 alignPanel.idPanel.idCanvas.addKeyListener(this);
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222 alignPanel.scalePanel.addKeyListener(this);
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223 alignPanel.annotationPanel.addKeyListener(this);
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224 alignPanel.annotationPanelHolder.addKeyListener(this);
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225 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
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226 alignPanel.alabels.addKeyListener(this);
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227 createAlignFrameWindow(embedded, title);
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230 alignPanel.adjustAnnotationHeight();
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231 alignPanel.paintAlignment(true);
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234 public AlignViewport getAlignViewport()
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239 public SeqCanvas getSeqcanvas()
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241 return alignPanel.seqPanel.seqCanvas;
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245 * Load a features file onto the alignment
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247 * @param file file URL, content, or other resolvable path
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248 * @param type is protocol for accessing data referred to by file
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251 public boolean parseFeaturesFile(String file, String type)
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253 return parseFeaturesFile(file, type, true);
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257 * Load a features file onto the alignment
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259 * @param file file URL, content, or other resolvable path
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260 * @param type is protocol for accessing data referred to by file
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261 * @param autoenabledisplay when true, display features flag will be automatically enabled if features are loaded
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262 * @return true if data parsed as a features file
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264 public boolean parseFeaturesFile(String file, String type, boolean autoenabledisplay)
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266 // TODO: test if importing a features file onto an alignment which already has features with links overwrites the original links.
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268 Hashtable featureLinks = new Hashtable();
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269 boolean featuresFile = false;
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272 featuresFile = new jalview.io.FeaturesFile(file, type)
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273 .parse(viewport.getAlignment(),
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274 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
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275 featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));
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276 } catch (Exception ex)
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278 ex.printStackTrace();
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283 if (featureLinks.size() > 0)
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285 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
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287 if (autoenabledisplay)
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289 viewport.showSequenceFeatures = true;
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290 sequenceFeatures.setState(true);
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292 if (viewport.featureSettings != null)
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294 viewport.featureSettings.refreshTable();
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296 alignPanel.paintAlignment(true);
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297 statusBar.setText("Successfully added features to alignment.");
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299 return featuresFile;
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303 public void keyPressed(KeyEvent evt)
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305 if (viewport.cursorMode
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306 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
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307 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
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308 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
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309 && Character.isDigit(evt.getKeyChar()))
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310 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
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312 switch (evt.getKeyCode())
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314 case 27: // escape key
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315 deselectAllSequenceMenuItem_actionPerformed();
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317 alignPanel.alabels.cancelDrag();
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319 case KeyEvent.VK_X:
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320 if (evt.isControlDown() || evt.isMetaDown())
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322 cut_actionPerformed();
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325 case KeyEvent.VK_C:
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326 if (viewport.cursorMode && !evt.isControlDown())
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328 alignPanel.seqPanel.setCursorColumn();
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330 if (evt.isControlDown() || evt.isMetaDown())
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332 copy_actionPerformed();
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335 case KeyEvent.VK_V:
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336 if (evt.isControlDown())
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338 paste(evt.isShiftDown());
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341 case KeyEvent.VK_A:
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342 if (evt.isControlDown() || evt.isMetaDown())
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344 selectAllSequenceMenuItem_actionPerformed();
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347 case KeyEvent.VK_DOWN:
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348 if (viewport.cursorMode)
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350 alignPanel.seqPanel.moveCursor(0, 1);
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354 moveSelectedSequences(false);
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358 case KeyEvent.VK_UP:
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359 if (viewport.cursorMode)
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361 alignPanel.seqPanel.moveCursor(0, -1);
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365 moveSelectedSequences(true);
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369 case KeyEvent.VK_LEFT:
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370 if (evt.isAltDown() || !viewport.cursorMode)
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371 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
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373 alignPanel.seqPanel.moveCursor(-1, 0);
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376 case KeyEvent.VK_RIGHT:
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377 if (evt.isAltDown() || !viewport.cursorMode)
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378 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
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380 alignPanel.seqPanel.moveCursor(1, 0);
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383 case KeyEvent.VK_SPACE:
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384 if (viewport.cursorMode)
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386 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
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387 || evt.isShiftDown() || evt.isAltDown());
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391 case KeyEvent.VK_DELETE:
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392 case KeyEvent.VK_BACK_SPACE:
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393 if (viewport.cursorMode)
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395 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
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396 || evt.isShiftDown() || evt.isAltDown());
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400 cut_actionPerformed();
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401 alignPanel.seqPanel.seqCanvas.repaint();
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405 case KeyEvent.VK_S:
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406 if (viewport.cursorMode)
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408 alignPanel.seqPanel.setCursorRow();
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411 case KeyEvent.VK_P:
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412 if (viewport.cursorMode)
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414 alignPanel.seqPanel.setCursorPosition();
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418 case KeyEvent.VK_ENTER:
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419 case KeyEvent.VK_COMMA:
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420 if (viewport.cursorMode)
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422 alignPanel.seqPanel.setCursorRowAndColumn();
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426 case KeyEvent.VK_Q:
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427 if (viewport.cursorMode)
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429 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
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432 case KeyEvent.VK_M:
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433 if (viewport.cursorMode)
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435 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
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439 case KeyEvent.VK_F2:
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440 viewport.cursorMode = !viewport.cursorMode;
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441 statusBar.setText("Keyboard editing mode is "
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442 + (viewport.cursorMode ? "on" : "off"));
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443 if (viewport.cursorMode)
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445 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
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446 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
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450 case KeyEvent.VK_F:
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451 if (evt.isControlDown())
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453 findMenuItem_actionPerformed();
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457 case KeyEvent.VK_H:
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459 boolean toggleSeqs = !evt.isControlDown();
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460 boolean toggleCols = !evt.isShiftDown();
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461 toggleHiddenRegions(toggleSeqs, toggleCols);
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465 case KeyEvent.VK_PAGE_UP:
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466 if (viewport.wrapAlignment)
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468 alignPanel.scrollUp(true);
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472 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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473 - viewport.endSeq + viewport.startSeq);
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477 case KeyEvent.VK_PAGE_DOWN:
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478 if (viewport.wrapAlignment)
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480 alignPanel.scrollUp(false);
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484 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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485 + viewport.endSeq - viewport.startSeq);
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489 case KeyEvent.VK_Z:
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490 if (evt.isControlDown())
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492 undoMenuItem_actionPerformed();
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496 case KeyEvent.VK_Y:
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497 if (evt.isControlDown())
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499 redoMenuItem_actionPerformed();
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503 case KeyEvent.VK_L:
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504 if (evt.isControlDown())
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506 trimAlignment(true);
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510 case KeyEvent.VK_R:
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511 if (evt.isControlDown())
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513 trimAlignment(false);
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517 case KeyEvent.VK_E:
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518 if (evt.isControlDown())
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520 if (evt.isShiftDown())
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522 this.removeAllGapsMenuItem_actionPerformed();
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526 removeGappedColumnMenuItem_actionPerformed();
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530 case KeyEvent.VK_I:
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531 if (evt.isControlDown())
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533 if (evt.isAltDown())
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535 invertColSel_actionPerformed();
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539 invertSequenceMenuItem_actionPerformed();
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544 case KeyEvent.VK_U:
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545 if (evt.isControlDown())
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547 this.deleteGroups_actionPerformed();
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551 case KeyEvent.VK_T:
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552 if (evt.isControlDown())
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559 alignPanel.paintAlignment(true);
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563 * called by key handler and the hide all/show all menu items
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565 * @param toggleSeqs
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566 * @param toggleCols
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568 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
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570 boolean hide = false;
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571 SequenceGroup sg = viewport.getSelectionGroup();
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572 if (!toggleSeqs && !toggleCols)
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574 // Hide everything by the current selection - this is a hack - we do the
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575 // invert and then hide
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576 // first check that there will be visible columns after the invert.
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577 if ((viewport.getColumnSelection() != null && viewport.getColumnSelection().getSelected() != null && viewport.getColumnSelection()
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578 .getSelected().size() > 0)
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579 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
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582 // now invert the sequence set, if required - empty selection implies
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583 // that no hiding is required.
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586 invertSequenceMenuItem_actionPerformed();
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587 sg = viewport.getSelectionGroup();
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591 viewport.expandColSelection(sg, true);
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592 // finally invert the column selection and get the new sequence
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593 // selection and indicate it should be hidden.
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594 invertColSel_actionPerformed();
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601 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
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604 viewport.hideAllSelectedSeqs();
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606 else if (!(toggleCols && viewport.getColumnSelection().getSelected().size() > 0))
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608 viewport.showAllHiddenSeqs();
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614 if (viewport.getColumnSelection().getSelected().size() > 0)
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616 viewport.hideSelectedColumns();
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619 viewport.setSelectionGroup(sg);
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624 viewport.showAllHiddenColumns();
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630 public void keyReleased(KeyEvent evt)
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635 public void keyTyped(KeyEvent evt)
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640 public void itemStateChanged(ItemEvent evt)
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642 if (evt.getSource() == displayNonconservedMenuItem)
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644 displayNonconservedMenuItem_actionPerformed();
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646 else if (evt.getSource() == colourTextMenuItem)
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648 colourTextMenuItem_actionPerformed();
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650 else if (evt.getSource() == wrapMenuItem)
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652 wrapMenuItem_actionPerformed();
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654 else if (evt.getSource() == scaleAbove)
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656 viewport.setScaleAboveWrapped(scaleAbove.getState());
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658 else if (evt.getSource() == scaleLeft)
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660 viewport.setScaleLeftWrapped(scaleLeft.getState());
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662 else if (evt.getSource() == scaleRight)
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664 viewport.setScaleRightWrapped(scaleRight.getState());
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666 else if (evt.getSource() == seqLimits)
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668 seqLimits_itemStateChanged();
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670 else if (evt.getSource() == viewBoxesMenuItem)
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672 viewport.setShowBoxes(viewBoxesMenuItem.getState());
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674 else if (evt.getSource() == viewTextMenuItem)
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676 viewport.setShowText(viewTextMenuItem.getState());
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678 else if (evt.getSource() == renderGapsMenuItem)
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680 viewport.setRenderGaps(renderGapsMenuItem.getState());
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682 else if (evt.getSource() == annotationPanelMenuItem)
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684 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
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685 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
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687 else if (evt.getSource() == sequenceFeatures)
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689 viewport.showSequenceFeatures(sequenceFeatures.getState());
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690 alignPanel.seqPanel.seqCanvas.repaint();
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692 else if (evt.getSource() == conservationMenuItem)
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694 conservationMenuItem_actionPerformed();
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696 else if (evt.getSource() == abovePIDThreshold)
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698 abovePIDThreshold_actionPerformed();
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700 else if (evt.getSource() == applyToAllGroups)
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702 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
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704 else if (evt.getSource() == autoCalculate)
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706 viewport.autoCalculateConsensus = autoCalculate.getState();
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708 else if (evt.getSource() == sortByTree)
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710 viewport.sortByTree = sortByTree.getState();
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712 else if (evt.getSource() == this.centreColumnLabelFlag)
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714 centreColumnLabelFlag_stateChanged();
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716 else if (evt.getSource() == this.followMouseOverFlag)
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718 mouseOverFlag_stateChanged();
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720 else if (evt.getSource() == showGroupConsensus)
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722 showGroupConsensus_actionPerformed();
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724 else if (evt.getSource() == showGroupConservation)
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726 showGroupConservation_actionPerformed();
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728 else if (evt.getSource() == showSequenceLogo)
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730 showSequenceLogo_actionPerformed();
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732 else if (evt.getSource() == showConsensusHistogram)
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734 showConsensusHistogram_actionPerformed();
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736 else if (evt.getSource() == applyAutoAnnotationSettings)
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738 applyAutoAnnotationSettings_actionPerformed();
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740 alignPanel.paintAlignment(true);
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743 private void mouseOverFlag_stateChanged()
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745 viewport.followHighlight = followMouseOverFlag.getState();
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746 // TODO: could kick the scrollTo mechanism to reset view for current
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750 private void centreColumnLabelFlag_stateChanged()
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752 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
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753 this.alignPanel.annotationPanel.repaint();
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757 public void actionPerformed(ActionEvent evt)
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759 Object source = evt.getSource();
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761 if (source == inputText)
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763 inputText_actionPerformed();
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765 else if (source == loadTree)
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767 loadTree_actionPerformed();
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769 else if (source == loadApplication)
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771 launchFullApplication();
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773 else if (source == loadAnnotations)
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777 else if (source == outputAnnotations)
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779 outputAnnotations(true);
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781 else if (source == outputFeatures)
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783 outputFeatures(true, "Jalview");
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785 else if (source == closeMenuItem)
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787 closeMenuItem_actionPerformed();
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789 else if (source == copy)
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791 copy_actionPerformed();
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793 else if (source == undoMenuItem)
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795 undoMenuItem_actionPerformed();
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797 else if (source == redoMenuItem)
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799 redoMenuItem_actionPerformed();
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801 else if (source == inputText)
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803 inputText_actionPerformed();
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805 else if (source == closeMenuItem)
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807 closeMenuItem_actionPerformed();
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809 else if (source == undoMenuItem)
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811 undoMenuItem_actionPerformed();
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813 else if (source == redoMenuItem)
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815 redoMenuItem_actionPerformed();
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817 else if (source == copy)
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819 copy_actionPerformed();
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821 else if (source == pasteNew)
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823 pasteNew_actionPerformed();
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825 else if (source == pasteThis)
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827 pasteThis_actionPerformed();
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829 else if (source == cut)
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831 cut_actionPerformed();
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833 else if (source == delete)
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835 delete_actionPerformed();
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837 else if (source == grpsFromSelection)
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839 makeGrpsFromSelection_actionPerformed();
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841 else if (source == deleteGroups)
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843 deleteGroups_actionPerformed();
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845 else if (source == selectAllSequenceMenuItem)
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847 selectAllSequenceMenuItem_actionPerformed();
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849 else if (source == deselectAllSequenceMenuItem)
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851 deselectAllSequenceMenuItem_actionPerformed();
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853 else if (source == invertSequenceMenuItem)
\r
855 invertSequenceMenuItem_actionPerformed();
\r
857 else if (source == invertColSel)
\r
859 viewport.invertColumnSelection();
\r
860 alignPanel.paintAlignment(true);
\r
862 else if (source == remove2LeftMenuItem)
\r
864 trimAlignment(true);
\r
866 else if (source == remove2RightMenuItem)
\r
868 trimAlignment(false);
\r
870 else if (source == removeGappedColumnMenuItem)
\r
872 removeGappedColumnMenuItem_actionPerformed();
\r
874 else if (source == removeAllGapsMenuItem)
\r
876 removeAllGapsMenuItem_actionPerformed();
\r
878 else if (source == findMenuItem)
\r
880 findMenuItem_actionPerformed();
\r
882 else if (source == font)
\r
884 new FontChooser(alignPanel);
\r
886 else if (source == newView)
\r
890 else if (source == showColumns)
\r
892 viewport.showAllHiddenColumns();
\r
893 alignPanel.paintAlignment(true);
\r
895 else if (source == showSeqs)
\r
897 viewport.showAllHiddenSeqs();
\r
898 alignPanel.paintAlignment(true);
\r
900 else if (source == hideColumns)
\r
902 viewport.hideSelectedColumns();
\r
903 alignPanel.paintAlignment(true);
\r
905 else if (source == hideSequences
\r
906 && viewport.getSelectionGroup() != null)
\r
908 viewport.hideAllSelectedSeqs();
\r
909 alignPanel.paintAlignment(true);
\r
911 else if (source == hideAllButSelection)
\r
913 toggleHiddenRegions(false, false);
\r
914 alignPanel.paintAlignment(true);
\r
916 else if (source == hideAllSelection)
\r
918 SequenceGroup sg = viewport.getSelectionGroup();
\r
919 viewport.expandColSelection(sg, false);
\r
920 viewport.hideAllSelectedSeqs();
\r
921 viewport.hideSelectedColumns();
\r
922 alignPanel.paintAlignment(true);
\r
924 else if (source == showAllHidden)
\r
926 viewport.showAllHiddenColumns();
\r
927 viewport.showAllHiddenSeqs();
\r
928 alignPanel.paintAlignment(true);
\r
930 else if (source == showGroupConsensus)
\r
932 showGroupConsensus_actionPerformed();
\r
934 else if (source == showGroupConservation)
\r
936 showGroupConservation_actionPerformed();
\r
938 else if (source == showSequenceLogo)
\r
940 showSequenceLogo_actionPerformed();
\r
942 else if (source == showConsensusHistogram)
\r
944 showConsensusHistogram_actionPerformed();
\r
946 else if (source == applyAutoAnnotationSettings)
\r
948 applyAutoAnnotationSettings_actionPerformed();
\r
950 else if (source == featureSettings)
\r
952 new FeatureSettings(alignPanel);
\r
954 else if (source == alProperties)
\r
956 StringBuffer contents = new jalview.io.AlignmentProperties(
\r
957 viewport.getAlignment()).formatAsString();
\r
958 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
959 cap.setText(contents.toString());
\r
960 Frame frame = new Frame();
\r
962 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
\r
963 + getTitle(), 400, 250);
\r
965 else if (source == overviewMenuItem)
\r
967 overviewMenuItem_actionPerformed();
\r
969 else if (source == noColourmenuItem)
\r
971 changeColour(null);
\r
973 else if (source == clustalColour)
\r
975 abovePIDThreshold.setState(false);
\r
976 changeColour(new ClustalxColourScheme(viewport.getAlignment(),null));
\r
978 else if (source == zappoColour)
\r
980 changeColour(new ZappoColourScheme());
\r
982 else if (source == taylorColour)
\r
984 changeColour(new TaylorColourScheme());
\r
986 else if (source == hydrophobicityColour)
\r
988 changeColour(new HydrophobicColourScheme());
\r
990 else if (source == helixColour)
\r
992 changeColour(new HelixColourScheme());
\r
994 else if (source == strandColour)
\r
996 changeColour(new StrandColourScheme());
\r
998 else if (source == turnColour)
\r
1000 changeColour(new TurnColourScheme());
\r
1002 else if (source == buriedColour)
\r
1004 changeColour(new BuriedColourScheme());
\r
1006 else if (source == nucleotideColour)
\r
1008 changeColour(new NucleotideColourScheme());
\r
1010 else if (source == purinePyrimidineColour)
\r
1012 changeColour(new PurinePyrimidineColourScheme());
\r
1014 else if (source == RNAInteractionColour)
\r
1016 changeColour(new RNAInteractionColourScheme());
\r
1018 else if (source == RNAHelixColour)
\r
1020 new RNAHelicesColourChooser(viewport, alignPanel);
\r
1022 else if (source == modifyPID)
\r
1024 modifyPID_actionPerformed();
\r
1026 else if (source == modifyConservation)
\r
1028 modifyConservation_actionPerformed();
\r
1030 else if (source == userDefinedColour)
\r
1032 new UserDefinedColours(alignPanel, null);
\r
1034 else if (source == PIDColour)
\r
1036 changeColour(new PIDColourScheme());
\r
1038 else if (source == BLOSUM62Colour)
\r
1040 changeColour(new Blosum62ColourScheme());
\r
1042 else if (source == tcoffeeColour) {
\r
1043 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
\r
1045 else if (source == annotationColour)
\r
1047 new AnnotationColourChooser(viewport, alignPanel);
\r
1049 else if (source == sortPairwiseMenuItem)
\r
1051 sortPairwiseMenuItem_actionPerformed();
\r
1053 else if (source == sortIDMenuItem)
\r
1055 sortIDMenuItem_actionPerformed();
\r
1057 else if (source == sortLengthMenuItem)
\r
1059 sortLengthMenuItem_actionPerformed();
\r
1061 else if (source == sortGroupMenuItem)
\r
1063 sortGroupMenuItem_actionPerformed();
\r
1065 else if (source == removeRedundancyMenuItem)
\r
1067 removeRedundancyMenuItem_actionPerformed();
\r
1069 else if (source == pairwiseAlignmentMenuItem)
\r
1071 pairwiseAlignmentMenuItem_actionPerformed();
\r
1073 else if (source == PCAMenuItem)
\r
1075 PCAMenuItem_actionPerformed();
\r
1077 else if (source == averageDistanceTreeMenuItem)
\r
1079 averageDistanceTreeMenuItem_actionPerformed();
\r
1081 else if (source == neighbourTreeMenuItem)
\r
1083 neighbourTreeMenuItem_actionPerformed();
\r
1085 else if (source == njTreeBlosumMenuItem)
\r
1087 njTreeBlosumMenuItem_actionPerformed();
\r
1089 else if (source == avDistanceTreeBlosumMenuItem)
\r
1091 avTreeBlosumMenuItem_actionPerformed();
\r
1093 else if (source == documentation)
\r
1095 documentation_actionPerformed();
\r
1097 else if (source == about)
\r
1099 about_actionPerformed();
\r
1104 public void inputText_actionPerformed()
\r
1106 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1107 Frame frame = new Frame();
\r
1109 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
\r
1112 protected void outputText_actionPerformed(ActionEvent e)
\r
1114 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1115 Frame frame = new Frame();
\r
1117 jalview.bin.JalviewLite.addFrame(frame,
\r
1118 "Alignment output - " + e.getActionCommand(), 600, 500);
\r
1119 cap.setText(new AppletFormatAdapter().formatSequences(
\r
1120 e.getActionCommand(), viewport.getAlignment(),
\r
1121 viewport.showJVSuffix));
\r
1124 public void loadAnnotations()
\r
1126 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1127 cap.setText("Paste your features / annotations / T-coffee score file here.");
\r
1128 cap.setAnnotationImport();
\r
1129 Frame frame = new Frame();
\r
1131 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
\r
1135 public String outputAnnotations(boolean displayTextbox)
\r
1137 String annotation = new AnnotationFile().printAnnotations(
\r
1138 viewport.showAnnotation ? viewport.getAlignment()
\r
1139 .getAlignmentAnnotation() : null, viewport.getAlignment()
\r
1141 ((Alignment) viewport.getAlignment()).alignmentProperties);
\r
1143 if (displayTextbox)
\r
1145 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
1146 Frame frame = new Frame();
\r
1148 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
\r
1149 cap.setText(annotation);
\r
1152 return annotation;
\r
1155 private Hashtable getDisplayedFeatureCols()
\r
1157 if (alignPanel.getFeatureRenderer() != null && viewport.featuresDisplayed!=null)
\r
1159 FeatureRenderer fr = alignPanel.getFeatureRenderer();
\r
1160 Hashtable fcols = new Hashtable();
\r
1161 Enumeration en = viewport.featuresDisplayed.keys();
\r
1162 while (en.hasMoreElements())
\r
1164 Object col = en.nextElement();
\r
1165 fcols.put(col, fr.featureColours.get(col));
\r
1172 public String outputFeatures(boolean displayTextbox, String format)
\r
1175 if (format.equalsIgnoreCase("Jalview"))
\r
1177 features = new FeaturesFile().printJalviewFormat(
\r
1178 viewport.getAlignment().getSequencesArray(),
\r
1179 getDisplayedFeatureCols());
\r
1183 features = new FeaturesFile().printGFFFormat(
\r
1184 viewport.getAlignment().getSequencesArray(),
\r
1185 getDisplayedFeatureCols());
\r
1188 if (displayTextbox)
\r
1190 boolean frimport=false;
\r
1191 if (features==null || features.equals("No Features Visible"))
\r
1193 features = "# No features visible - paste some and import them here.";
\r
1197 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
\r
1200 cap.setAnnotationImport();
\r
1202 Frame frame = new Frame();
\r
1204 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
\r
1205 cap.setText(features);
\r
1207 if (features==null)
\r
1214 void launchFullApplication()
\r
1216 StringBuffer url = new StringBuffer(jalviewServletURL);
\r
1218 url.append("?open="
\r
1219 + appendProtocol(viewport.applet.getParameter("file")));
\r
1221 if (viewport.applet.getParameter("features") != null)
\r
1223 url.append("&features=");
\r
1224 url.append(appendProtocol(viewport.applet.getParameter("features")));
\r
1227 if (viewport.applet.getParameter("annotations") != null)
\r
1229 url.append("&annotations=");
\r
1230 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
\r
1233 if (viewport.applet.getParameter("jnetfile") != null)
\r
1235 url.append("&annotations=");
\r
1236 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
\r
1239 if (viewport.applet.getParameter("defaultColour") != null)
\r
1241 url.append("&colour="
\r
1242 + removeWhiteSpace(viewport.applet
\r
1243 .getParameter("defaultColour")));
\r
1246 if (viewport.applet.getParameter("userDefinedColour") != null)
\r
1248 url.append("&colour="
\r
1249 + removeWhiteSpace(viewport.applet
\r
1250 .getParameter("userDefinedColour")));
\r
1252 if (viewport.applet.getParameter("tree") != null)
\r
1254 url.append("&tree="
\r
1255 + appendProtocol(viewport.applet.getParameter("tree")));
\r
1257 if (viewport.applet.getParameter("treeFile") != null)
\r
1259 url.append("&tree="
\r
1260 + appendProtocol(viewport.applet.getParameter("treeFile")));
\r
1263 showURL(url.toString(), "FULL_APP");
\r
1266 String removeWhiteSpace(String colour)
\r
1268 StringBuffer sb = new StringBuffer();
\r
1269 for (int i = 0; i < colour.length(); i++)
\r
1271 if (Character.isWhitespace(colour.charAt(i)))
\r
1277 sb.append(colour.charAt(i));
\r
1281 return sb.toString();
\r
1284 String appendProtocol(String url)
\r
1289 url = URLEncoder.encode(url);
\r
1292 * When we finally deprecate 1.1 compatibility, we can start to use
\r
1293 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
\r
1294 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
\r
1295 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
\r
1296 * ex.printStackTrace(); }
\r
1298 catch (java.net.MalformedURLException ex)
\r
1300 url = viewport.applet.getCodeBase() + url;
\r
1305 public void closeMenuItem_actionPerformed()
\r
1307 PaintRefresher.RemoveComponent(alignPanel);
\r
1308 if (alignPanel.seqPanel!=null && alignPanel.seqPanel.seqCanvas!=null)
\r
1310 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
\r
1312 if (alignPanel.idPanel!=null && alignPanel.idPanel.idCanvas!=null) {
\r
1313 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
\r
1316 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
\r
1322 alignPanel = null;
\r
1329 void updateEditMenuBar()
\r
1332 if (viewport.historyList.size() > 0)
\r
1334 undoMenuItem.setEnabled(true);
\r
1335 CommandI command = (CommandI) viewport.historyList.peek();
\r
1336 undoMenuItem.setLabel("Undo " + command.getDescription());
\r
1340 undoMenuItem.setEnabled(false);
\r
1341 undoMenuItem.setLabel("Undo");
\r
1344 if (viewport.redoList.size() > 0)
\r
1346 redoMenuItem.setEnabled(true);
\r
1348 CommandI command = (CommandI) viewport.redoList.peek();
\r
1349 redoMenuItem.setLabel("Redo " + command.getDescription());
\r
1353 redoMenuItem.setEnabled(false);
\r
1354 redoMenuItem.setLabel("Redo");
\r
1361 public void addHistoryItem(CommandI command)
\r
1363 if (command.getSize() > 0)
\r
1365 viewport.historyList.push(command);
\r
1366 viewport.redoList.removeAllElements();
\r
1367 updateEditMenuBar();
\r
1368 viewport.updateHiddenColumns();
\r
1379 protected void undoMenuItem_actionPerformed()
\r
1381 if (viewport.historyList.size() < 1)
\r
1386 CommandI command = (CommandI) viewport.historyList.pop();
\r
1387 viewport.redoList.push(command);
\r
1388 command.undoCommand(null);
\r
1390 AlignViewport originalSource = getOriginatingSource(command);
\r
1392 if (originalSource!=viewport) {
\r
1393 System.err.println("Warning: Viewport object mismatch whilst undoing");
\r
1395 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns = viewport.getColumnSelection().getHiddenColumns() != null;
\r
1396 updateEditMenuBar();
\r
1397 originalSource.firePropertyChange("alignment", null,
\r
1398 originalSource.getAlignment().getSequences());
\r
1408 protected void redoMenuItem_actionPerformed()
\r
1410 if (viewport.redoList.size() < 1)
\r
1415 CommandI command = (CommandI) viewport.redoList.pop();
\r
1416 viewport.historyList.push(command);
\r
1417 command.doCommand(null);
\r
1419 AlignViewport originalSource = getOriginatingSource(command);
\r
1421 if (originalSource!=viewport) {
\r
1422 System.err.println("Warning: Viewport object mismatch whilst re-doing");
\r
1424 originalSource.updateHiddenColumns(); //sethasHiddenColumns(); = viewport.getColumnSelection().getHiddenColumns() != null;
\r
1426 updateEditMenuBar();
\r
1427 originalSource.firePropertyChange("alignment", null,
\r
1428 originalSource.getAlignment().getSequences());
\r
1431 AlignViewport getOriginatingSource(CommandI command)
\r
1433 AlignViewport originalSource = null;
\r
1434 // For sequence removal and addition, we need to fire
\r
1435 // the property change event FROM the viewport where the
\r
1436 // original alignment was altered
\r
1437 AlignmentI al = null;
\r
1438 if (command instanceof EditCommand)
\r
1440 EditCommand editCommand = (EditCommand) command;
\r
1441 al = editCommand.getAlignment();
\r
1442 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
1443 .getSequenceSetId());
\r
1444 for (int i = 0; i < comps.size(); i++)
\r
1446 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
1448 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
\r
1450 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
\r
1457 if (originalSource == null)
\r
1459 // The original view is closed, we must validate
\r
1460 // the current view against the closed view first
\r
1463 PaintRefresher.validateSequences(al, viewport.getAlignment());
\r
1466 originalSource = viewport;
\r
1469 return originalSource;
\r
1472 public void moveSelectedSequences(boolean up)
\r
1474 SequenceGroup sg = viewport.getSelectionGroup();
\r
1479 viewport.getAlignment().moveSelectedSequencesByOne(sg, up ? null : viewport.getHiddenRepSequences(), up);
\r
1480 alignPanel.paintAlignment(true);
\r
1483 synchronized void slideSequences(boolean right, int size)
\r
1485 List<SequenceI>sg = new Vector<SequenceI>();
\r
1486 if (viewport.cursorMode)
\r
1488 sg.add(viewport.getAlignment()
\r
1489 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
\r
1491 else if (viewport.getSelectionGroup() != null
\r
1492 && viewport.getSelectionGroup().getSize() != viewport.getAlignment()
\r
1495 sg = viewport.getSelectionGroup().getSequences(
\r
1496 viewport.getHiddenRepSequences());
\r
1499 if (sg.size() < 1)
\r
1504 Vector<SequenceI> invertGroup = new Vector();
\r
1506 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
\r
1508 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
\r
1509 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
\r
1512 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
\r
1514 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup.size()]);
\r
1515 for (int i = 0; i < invertGroup.size(); i++)
\r
1516 seqs2[i] = invertGroup.elementAt(i);
\r
1518 SlideSequencesCommand ssc;
\r
1520 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
\r
1521 size, viewport.getGapCharacter());
\r
1523 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
\r
1524 size, viewport.getGapCharacter());
\r
1526 int groupAdjustment = 0;
\r
1527 if (ssc.getGapsInsertedBegin() && right)
\r
1529 if (viewport.cursorMode)
\r
1530 alignPanel.seqPanel.moveCursor(size, 0);
\r
1532 groupAdjustment = size;
\r
1534 else if (!ssc.getGapsInsertedBegin() && !right)
\r
1536 if (viewport.cursorMode)
\r
1537 alignPanel.seqPanel.moveCursor(-size, 0);
\r
1539 groupAdjustment = -size;
\r
1542 if (groupAdjustment != 0)
\r
1544 viewport.getSelectionGroup().setStartRes(
\r
1545 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
\r
1546 viewport.getSelectionGroup().setEndRes(
\r
1547 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
\r
1550 boolean appendHistoryItem = false;
\r
1551 if (viewport.historyList != null && viewport.historyList.size() > 0
\r
1552 && viewport.historyList.peek() instanceof SlideSequencesCommand)
\r
1554 appendHistoryItem = ssc
\r
1555 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
\r
1559 if (!appendHistoryItem)
\r
1560 addHistoryItem(ssc);
\r
1565 static StringBuffer copiedSequences;
\r
1567 static Vector copiedHiddenColumns;
\r
1569 protected void copy_actionPerformed()
\r
1571 if (viewport.getSelectionGroup() == null)
\r
1576 SequenceGroup sg = viewport.getSelectionGroup();
\r
1577 copiedSequences = new StringBuffer();
\r
1578 Hashtable orderedSeqs = new Hashtable();
\r
1579 for (int i = 0; i < sg.getSize(); i++)
\r
1581 SequenceI seq = sg.getSequenceAt(i);
\r
1582 int index = viewport.getAlignment().findIndex(seq);
\r
1583 orderedSeqs.put(index + "", seq);
\r
1586 int index = 0, startRes, endRes;
\r
1589 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
\r
1591 copiedHiddenColumns = new Vector();
\r
1592 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
\r
1593 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
\r
1596 int[] region = (int[]) viewport.getColumnSelection()
\r
1597 .getHiddenColumns().elementAt(i);
\r
1599 copiedHiddenColumns.addElement(new int[]
\r
1600 { region[0] - hiddenOffset, region[1] - hiddenOffset });
\r
1605 copiedHiddenColumns = null;
\r
1608 for (int i = 0; i < sg.getSize(); i++)
\r
1610 SequenceI seq = null;
\r
1612 while (seq == null)
\r
1614 if (orderedSeqs.containsKey(index + ""))
\r
1616 seq = (SequenceI) orderedSeqs.get(index + "");
\r
1628 // Returns residue following index if gap
\r
1629 startRes = seq.findPosition(sg.getStartRes());
\r
1632 // Need to find the residue preceeding index if gap
\r
1635 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
\r
1637 ch = seq.getCharAt(j);
\r
1638 if (!jalview.util.Comparison.isGap((ch)))
\r
1646 endRes += seq.getStart() - 1;
\r
1649 copiedSequences.append(seq.getName()
\r
1655 + seq.getSequenceAsString(sg.getStartRes(),
\r
1656 sg.getEndRes() + 1) + "\n");
\r
1661 protected void pasteNew_actionPerformed()
\r
1666 protected void pasteThis_actionPerformed()
\r
1671 void paste(boolean newAlignment)
\r
1676 if (copiedSequences == null)
\r
1681 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
1682 Vector seqs = new Vector();
\r
1683 while (st.hasMoreElements())
\r
1685 String name = st.nextToken();
\r
1686 int start = Integer.parseInt(st.nextToken());
\r
1687 int end = Integer.parseInt(st.nextToken());
\r
1688 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
\r
1690 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
1691 for (int i = 0; i < seqs.size(); i++)
\r
1693 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
1698 String newtitle = new String("Copied sequences");
\r
1699 if (getTitle().startsWith("Copied sequences"))
\r
1701 newtitle = getTitle();
\r
1705 newtitle = newtitle.concat("- from " + getTitle());
\r
1707 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
1708 viewport.applet, newtitle, false);
\r
1709 if (copiedHiddenColumns != null)
\r
1711 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
1713 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
1714 af.viewport.hideColumns(region[0], region[1]);
\r
1718 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
\r
1723 addSequences(newSeqs);
\r
1726 } catch (Exception ex)
\r
1728 } // could be anything being pasted in here
\r
1732 void addSequences(SequenceI[] seqs)
\r
1734 for (int i = 0; i < seqs.length; i++)
\r
1736 viewport.getAlignment().addSequence(seqs[i]);
\r
1740 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
\r
1741 seqs, 0, viewport.getAlignment().getWidth(), viewport.getAlignment()));
\r
1743 viewport.setEndSeq(viewport.getAlignment().getHeight());
\r
1744 viewport.getAlignment().getWidth();
\r
1745 viewport.firePropertyChange("alignment", null,
\r
1746 viewport.getAlignment().getSequences());
\r
1750 protected void cut_actionPerformed()
\r
1752 copy_actionPerformed();
\r
1753 delete_actionPerformed();
\r
1756 protected void delete_actionPerformed()
\r
1759 SequenceGroup sg = viewport.getSelectionGroup();
\r
1765 Vector seqs = new Vector();
\r
1767 for (int i = 0; i < sg.getSize(); i++)
\r
1769 seq = sg.getSequenceAt(i);
\r
1770 seqs.addElement(seq);
\r
1773 // If the cut affects all sequences, remove highlighted columns
\r
1774 if (sg.getSize() == viewport.getAlignment().getHeight())
\r
1776 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
1777 sg.getEndRes() + 1);
\r
1780 SequenceI[] cut = new SequenceI[seqs.size()];
\r
1781 for (int i = 0; i < seqs.size(); i++)
\r
1783 cut[i] = (SequenceI) seqs.elementAt(i);
\r
1787 * //ADD HISTORY ITEM
\r
1789 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
\r
1790 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
\r
1791 viewport.getAlignment()));
\r
1793 viewport.setSelectionGroup(null);
\r
1794 viewport.getAlignment().deleteGroup(sg);
\r
1796 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1799 if (viewport.getAlignment().getHeight() < 1)
\r
1801 this.setVisible(false);
\r
1803 viewport.sendSelection();
\r
1807 * group consensus toggled
\r
1810 protected void showGroupConsensus_actionPerformed()
\r
1812 viewport.setShowGroupConsensus(showGroupConsensus.getState());
\r
1813 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1818 * group conservation toggled.
\r
1820 protected void showGroupConservation_actionPerformed()
\r
1822 viewport.setShowGroupConservation(showGroupConservation.getState());
\r
1823 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1830 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
\r
1831 * .event.ActionEvent)
\r
1833 protected void showConsensusHistogram_actionPerformed()
\r
1835 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
\r
1836 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1842 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
\r
1843 * .event.ActionEvent)
\r
1845 protected void showSequenceLogo_actionPerformed()
\r
1847 viewport.setShowSequenceLogo(showSequenceLogo.getState());
\r
1848 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1851 protected void applyAutoAnnotationSettings_actionPerformed()
\r
1853 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1856 protected void makeGrpsFromSelection_actionPerformed()
\r
1858 if (viewport.getSelectionGroup() != null)
\r
1860 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
\r
1861 viewport.getSequenceSelection(),
\r
1862 viewport.getAlignmentView(true).getSequenceStrings(
\r
1863 viewport.getGapCharacter()),
\r
1864 viewport.getAlignment().getGroups());
\r
1865 viewport.getAlignment().deleteAllGroups();
\r
1866 viewport.sequenceColours = null;
\r
1867 viewport.setSelectionGroup(null);
\r
1868 // set view properties for each group
\r
1869 for (int g = 0; g < gps.length; g++)
\r
1871 // gps[g].setShowunconserved(viewport.getShowUnconserved());
\r
1872 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
\r
1873 viewport.getAlignment().addGroup(gps[g]);
\r
1874 Color col = new Color((int) (Math.random() * 255),
\r
1875 (int) (Math.random() * 255), (int) (Math.random() * 255));
\r
1876 col = col.brighter();
\r
1877 for (SequenceI sq : gps[g].getSequences(null))
\r
1878 viewport.setSequenceColour(
\r
1882 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
\r
1883 alignPanel.updateAnnotation();
\r
1884 alignPanel.paintAlignment(true);
\r
1888 protected void deleteGroups_actionPerformed()
\r
1890 viewport.getAlignment().deleteAllGroups();
\r
1891 viewport.sequenceColours = null;
\r
1892 viewport.setSelectionGroup(null);
\r
1894 alignPanel.paintAlignment(true);
\r
1897 public void selectAllSequenceMenuItem_actionPerformed()
\r
1899 SequenceGroup sg = new SequenceGroup();
\r
1900 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1902 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
1904 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
\r
1905 viewport.setSelectionGroup(sg);
\r
1906 alignPanel.paintAlignment(true);
\r
1907 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1908 viewport.sendSelection();
\r
1911 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1913 if (viewport.cursorMode)
\r
1915 alignPanel.seqPanel.keyboardNo1 = null;
\r
1916 alignPanel.seqPanel.keyboardNo2 = null;
\r
1918 viewport.setSelectionGroup(null);
\r
1919 viewport.getColumnSelection().clear();
\r
1920 viewport.setSelectionGroup(null);
\r
1921 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1922 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1923 alignPanel.paintAlignment(true);
\r
1924 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1925 viewport.sendSelection();
\r
1928 public void invertSequenceMenuItem_actionPerformed()
\r
1930 SequenceGroup sg = viewport.getSelectionGroup();
\r
1931 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1933 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1936 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1937 viewport.sendSelection();
\r
1940 public void invertColSel_actionPerformed()
\r
1942 viewport.invertColumnSelection();
\r
1943 alignPanel.paintAlignment(true);
\r
1944 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1945 viewport.sendSelection();
\r
1948 void trimAlignment(boolean trimLeft)
\r
1950 ColumnSelection colSel = viewport.getColumnSelection();
\r
1953 if (colSel.size() > 0)
\r
1957 column = colSel.getMin();
\r
1961 column = colSel.getMax();
\r
1965 if (viewport.getSelectionGroup() != null)
\r
1967 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
1968 viewport.getHiddenRepSequences());
\r
1972 seqs = viewport.getAlignment().getSequencesArray();
\r
1975 TrimRegionCommand trimRegion;
\r
1978 trimRegion = new TrimRegionCommand("Remove Left",
\r
1979 TrimRegionCommand.TRIM_LEFT, seqs, column,
\r
1980 viewport.getAlignment(), viewport.getColumnSelection(),
\r
1981 viewport.getSelectionGroup());
\r
1982 viewport.setStartRes(0);
\r
1986 trimRegion = new TrimRegionCommand("Remove Right",
\r
1987 TrimRegionCommand.TRIM_RIGHT, seqs, column,
\r
1988 viewport.getAlignment(), viewport.getColumnSelection(),
\r
1989 viewport.getSelectionGroup());
\r
1992 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
\r
1994 addHistoryItem(trimRegion);
\r
1998 for (SequenceGroup sg:viewport.getAlignment().getGroups())
\r
2000 if ((trimLeft && !sg.adjustForRemoveLeft(column))
\r
2001 || (!trimLeft && !sg.adjustForRemoveRight(column)))
\r
2003 viewport.getAlignment().deleteGroup(sg);
\r
2007 viewport.firePropertyChange("alignment", null, viewport
\r
2008 .getAlignment().getSequences());
\r
2012 public void removeGappedColumnMenuItem_actionPerformed()
\r
2014 int start = 0, end = viewport.getAlignment().getWidth() - 1;
\r
2017 if (viewport.getSelectionGroup() != null)
\r
2019 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2020 viewport.getHiddenRepSequences());
\r
2021 start = viewport.getSelectionGroup().getStartRes();
\r
2022 end = viewport.getSelectionGroup().getEndRes();
\r
2026 seqs = viewport.getAlignment().getSequencesArray();
\r
2029 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
\r
2030 "Remove Gapped Columns", seqs, start, end, viewport.getAlignment());
\r
2032 addHistoryItem(removeGapCols);
\r
2034 statusBar.setText("Removed " + removeGapCols.getSize()
\r
2035 + " empty columns.");
\r
2037 // This is to maintain viewport position on first residue
\r
2038 // of first sequence
\r
2039 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
\r
2040 int startRes = seq.findPosition(viewport.startRes);
\r
2041 // ShiftList shifts;
\r
2042 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
\r
2043 // edit.alColumnChanges=shifts.getInverse();
\r
2044 // if (viewport.hasHiddenColumns)
\r
2045 // viewport.getColumnSelection().compensateForEdits(shifts);
\r
2046 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
2047 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
2052 public void removeAllGapsMenuItem_actionPerformed()
\r
2054 int start = 0, end = viewport.getAlignment().getWidth() - 1;
\r
2057 if (viewport.getSelectionGroup() != null)
\r
2059 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2060 viewport.getHiddenRepSequences());
\r
2061 start = viewport.getSelectionGroup().getStartRes();
\r
2062 end = viewport.getSelectionGroup().getEndRes();
\r
2066 seqs = viewport.getAlignment().getSequencesArray();
\r
2069 // This is to maintain viewport position on first residue
\r
2070 // of first sequence
\r
2071 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
\r
2072 int startRes = seq.findPosition(viewport.startRes);
\r
2074 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
\r
2075 viewport.getAlignment()));
\r
2077 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
2079 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
2084 public void findMenuItem_actionPerformed()
\r
2086 new Finder(alignPanel);
\r
2090 * create a new view derived from the current view
\r
2092 * @param viewtitle
\r
2093 * @return frame for the new view
\r
2095 public AlignFrame newView(String viewtitle)
\r
2098 if (viewport.hasHiddenRows())
\r
2100 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
\r
2101 .getFullAlignment().getSequencesArray());
\r
2105 newal = new Alignment(viewport.getAlignment().getSequencesArray());
\r
2108 if (viewport.getAlignment().getAlignmentAnnotation() != null)
\r
2110 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
\r
2112 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
\r
2114 newal.addAnnotation(viewport.getAlignment().getAlignmentAnnotation()[i]);
\r
2119 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
\r
2121 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
\r
2122 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
\r
2123 PaintRefresher.Register(newaf.alignPanel,
\r
2124 newaf.alignPanel.av.getSequenceSetId());
\r
2126 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
\r
2127 newaf.alignPanel.av.getSequenceSetId());
\r
2128 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
\r
2129 newaf.alignPanel.av.getSequenceSetId());
\r
2131 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
2132 .getSequenceSetId());
\r
2133 int viewSize = -1;
\r
2134 for (int i = 0; i < comps.size(); i++)
\r
2136 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
2142 String title = new String(this.getTitle());
\r
2143 if (viewtitle != null)
\r
2145 title = viewtitle + " ( " + title + ")";
\r
2149 if (title.indexOf("(View") > -1)
\r
2151 title = title.substring(0, title.indexOf("(View"));
\r
2153 title += "(View " + viewSize + ")";
\r
2156 newaf.setTitle(title.toString());
\r
2158 newaf.viewport.historyList = viewport.historyList;
\r
2159 newaf.viewport.redoList = viewport.redoList;
\r
2165 * @return list of feature groups on the view
\r
2167 public String[] getFeatureGroups()
\r
2169 FeatureRenderer fr = null;
\r
2170 if (alignPanel != null
\r
2171 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2173 return fr.getGroups();
\r
2179 * get sequence feature groups that are hidden or shown
\r
2185 public String[] getFeatureGroupsOfState(boolean visible)
\r
2187 FeatureRenderer fr = null;
\r
2188 if (alignPanel != null
\r
2189 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2191 return fr.getGroups(visible);
\r
2197 * Change the display state for the given feature groups
\r
2200 * list of group strings
\r
2202 * visible or invisible
\r
2204 public void setFeatureGroupState(String[] groups, boolean state)
\r
2206 FeatureRenderer fr = null;
\r
2207 this.sequenceFeatures.setState(true);
\r
2208 viewport.showSequenceFeatures(true);
\r
2209 if (alignPanel != null
\r
2210 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2212 fr.setGroupState(groups, state);
\r
2213 alignPanel.seqPanel.seqCanvas.repaint();
\r
2214 if (alignPanel.overviewPanel != null)
\r
2216 alignPanel.overviewPanel.updateOverviewImage();
\r
2221 public void seqLimits_itemStateChanged()
\r
2223 viewport.setShowJVSuffix(seqLimits.getState());
\r
2224 alignPanel.fontChanged();
\r
2225 alignPanel.paintAlignment(true);
\r
2228 protected void colourTextMenuItem_actionPerformed()
\r
2230 viewport.setColourText(colourTextMenuItem.getState());
\r
2231 alignPanel.paintAlignment(true);
\r
2234 protected void displayNonconservedMenuItem_actionPerformed()
\r
2236 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
\r
2237 alignPanel.paintAlignment(true);
\r
2240 protected void wrapMenuItem_actionPerformed()
\r
2242 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
2243 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
2244 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
2245 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
2246 scaleRight.setEnabled(wrapMenuItem.getState());
\r
2247 alignPanel.paintAlignment(true);
\r
2250 public void overviewMenuItem_actionPerformed()
\r
2252 if (alignPanel.overviewPanel != null)
\r
2257 Frame frame = new Frame();
\r
2258 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
2259 frame.add(overview);
\r
2260 // +50 must allow for applet frame window
\r
2261 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
2262 overview.getPreferredSize().width,
\r
2263 overview.getPreferredSize().height + 50);
\r
2266 final AlignmentPanel ap=alignPanel;
\r
2267 frame.addWindowListener(new WindowAdapter()
\r
2270 public void windowClosing(WindowEvent e)
\r
2273 ap.setOverviewPanel(null);
\r
2278 alignPanel.setOverviewPanel(overview);
\r
2282 void changeColour(ColourSchemeI cs)
\r
2284 int threshold = 0;
\r
2288 if (viewport.getAbovePIDThreshold())
\r
2290 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
2293 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2295 viewport.setGlobalColourScheme(cs);
\r
2299 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2302 if (viewport.getConservationSelected())
\r
2305 Alignment al = (Alignment) viewport.getAlignment();
\r
2306 Conservation c = new Conservation("All",
\r
2307 ResidueProperties.propHash, 3, al.getSequences(), 0,
\r
2308 al.getWidth() - 1);
\r
2311 c.verdict(false, viewport.getConsPercGaps());
\r
2313 cs.setConservation(c);
\r
2315 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
\r
2316 cs, "Background"));
\r
2321 cs.setConservation(null);
\r
2324 cs.setConsensus(viewport.getSequenceConsensusHash());
\r
2327 viewport.setGlobalColourScheme(cs);
\r
2330 if (alignPanel.getOverviewPanel() != null)
\r
2332 alignPanel.getOverviewPanel().updateOverviewImage();
\r
2335 jalview.structure.StructureSelectionManager
\r
2336 .getStructureSelectionManager(viewport.applet).sequenceColoursChanged(
\r
2339 alignPanel.paintAlignment(true);
\r
2342 protected void modifyPID_actionPerformed()
\r
2344 if (viewport.getAbovePIDThreshold()
\r
2345 && viewport.getGlobalColourScheme() != null)
\r
2347 SliderPanel.setPIDSliderSource(alignPanel,
\r
2348 viewport.getGlobalColourScheme(), "Background");
\r
2349 SliderPanel.showPIDSlider();
\r
2353 protected void modifyConservation_actionPerformed()
\r
2355 if (viewport.getConservationSelected()
\r
2356 && viewport.getGlobalColourScheme() != null)
\r
2358 SliderPanel.setConservationSlider(alignPanel,
\r
2359 viewport.getGlobalColourScheme(), "Background");
\r
2360 SliderPanel.showConservationSlider();
\r
2364 protected void conservationMenuItem_actionPerformed()
\r
2366 viewport.setConservationSelected(conservationMenuItem.getState());
\r
2368 viewport.setAbovePIDThreshold(false);
\r
2369 abovePIDThreshold.setState(false);
\r
2371 changeColour(viewport.getGlobalColourScheme());
\r
2373 modifyConservation_actionPerformed();
\r
2376 public void abovePIDThreshold_actionPerformed()
\r
2378 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
2380 conservationMenuItem.setState(false);
\r
2381 viewport.setConservationSelected(false);
\r
2383 changeColour(viewport.getGlobalColourScheme());
\r
2385 modifyPID_actionPerformed();
\r
2388 public void sortPairwiseMenuItem_actionPerformed()
\r
2390 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2391 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
\r
2392 .getAlignment().getSequenceAt(0), null);
\r
2394 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
\r
2395 viewport.getAlignment()));
\r
2396 alignPanel.paintAlignment(true);
\r
2399 public void sortIDMenuItem_actionPerformed()
\r
2401 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2402 AlignmentSorter.sortByID(viewport.getAlignment());
\r
2403 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
\r
2404 alignPanel.paintAlignment(true);
\r
2407 public void sortLengthMenuItem_actionPerformed()
\r
2409 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2410 AlignmentSorter.sortByLength(viewport.getAlignment());
\r
2411 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
\r
2412 viewport.getAlignment()));
\r
2413 alignPanel.paintAlignment(true);
\r
2416 public void sortGroupMenuItem_actionPerformed()
\r
2418 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2419 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
2420 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
\r
2421 viewport.getAlignment()));
\r
2422 alignPanel.paintAlignment(true);
\r
2426 public void removeRedundancyMenuItem_actionPerformed()
\r
2428 new RedundancyPanel(alignPanel);
\r
2431 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
2433 if (viewport.getSelectionGroup() != null
\r
2434 && viewport.getSelectionGroup().getSize() > 1)
\r
2436 Frame frame = new Frame();
\r
2437 frame.add(new PairwiseAlignPanel(alignPanel));
\r
2438 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
\r
2443 public void PCAMenuItem_actionPerformed()
\r
2445 // are the sequences aligned?
\r
2446 if (!viewport.getAlignment().isAligned(false))
\r
2448 SequenceI current;
\r
2449 int Width = viewport.getAlignment().getWidth();
\r
2451 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2453 current = viewport.getAlignment().getSequenceAt(i);
\r
2455 if (current.getLength() < Width)
\r
2457 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2460 alignPanel.paintAlignment(true);
\r
2463 if ((viewport.getSelectionGroup() != null
\r
2464 && viewport.getSelectionGroup().getSize() < 4 && viewport
\r
2465 .getSelectionGroup().getSize() > 0)
\r
2466 || viewport.getAlignment().getHeight() < 4)
\r
2473 new PCAPanel(viewport);
\r
2474 } catch (java.lang.OutOfMemoryError ex)
\r
2480 public void averageDistanceTreeMenuItem_actionPerformed()
\r
2482 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
2485 public void neighbourTreeMenuItem_actionPerformed()
\r
2487 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
2490 protected void njTreeBlosumMenuItem_actionPerformed()
\r
2492 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2495 protected void avTreeBlosumMenuItem_actionPerformed()
\r
2497 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2500 void NewTreePanel(String type, String pwType, String title)
\r
2502 // are the sequences aligned?
\r
2503 if (!viewport.getAlignment().isAligned(false))
\r
2505 SequenceI current;
\r
2506 int Width = viewport.getAlignment().getWidth();
\r
2508 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2510 current = viewport.getAlignment().getSequenceAt(i);
\r
2512 if (current.getLength() < Width)
\r
2514 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2517 alignPanel.paintAlignment(true);
\r
2521 if ((viewport.getSelectionGroup() != null && viewport
\r
2522 .getSelectionGroup().getSize() > 1)
\r
2523 || (viewport.getSelectionGroup() == null && viewport.getAlignment()
\r
2524 .getHeight() > 1))
\r
2526 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
\r
2528 addTreeMenuItem(tp, title);
\r
2530 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
2534 void loadTree_actionPerformed()
\r
2536 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
2537 cap.setText("Paste your Newick tree file here.");
\r
2538 cap.setTreeImport();
\r
2539 Frame frame = new Frame();
\r
2541 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
2544 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
2546 TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
\r
2547 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
2548 addTreeMenuItem(tp, treeFile);
\r
2552 * sort the alignment using the given treePanel
\r
2554 * @param treePanel
\r
2555 * tree used to sort view
\r
2557 * string used for undo event name
\r
2559 public void sortByTree(TreePanel treePanel, String title)
\r
2561 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2563 .sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
2564 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2565 // HistoryItem.SORT));
\r
2566 addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
\r
2567 viewport.getAlignment()));
\r
2568 alignPanel.paintAlignment(true);
\r
2572 * Do any automatic reordering of the alignment and add the necessary bits to
\r
2573 * the menu structure for the new tree
\r
2575 * @param treePanel
\r
2578 protected void addTreeMenuItem(final TreePanel treePanel,
\r
2579 final String title)
\r
2581 final MenuItem item = new MenuItem(title);
\r
2582 sortByTreeMenu.add(item);
\r
2583 item.addActionListener(new java.awt.event.ActionListener()
\r
2586 public void actionPerformed(ActionEvent evt)
\r
2588 sortByTree(treePanel, title); // treePanel.getTitle());
\r
2592 treePanel.addWindowListener(new WindowAdapter()
\r
2595 public void windowOpened(WindowEvent e)
\r
2597 if (viewport.sortByTree)
\r
2599 sortByTree(treePanel, title);
\r
2601 super.windowOpened(e);
\r
2605 public void windowClosing(WindowEvent e)
\r
2607 sortByTreeMenu.remove(item);
\r
2611 public boolean sortBy(AlignmentOrder alorder, String undoname)
\r
2613 SequenceI[] oldOrder = viewport.getAlignment()
\r
2614 .getSequencesArray();
\r
2615 if (viewport.applet.debug)
\r
2617 System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");
\r
2619 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
\r
2620 if (undoname!=null)
\r
2622 addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.getAlignment()));
\r
2624 alignPanel.paintAlignment(true);
\r
2628 protected void documentation_actionPerformed()
\r
2630 alignPanel.av.applet.openJalviewHelpUrl();
\r
2633 protected void about_actionPerformed()
\r
2636 class AboutPanel extends Canvas
\r
2642 public AboutPanel(String version, String builddate)
\r
2644 this.version = version;
\r
2645 this.builddate = builddate;
\r
2649 public void paint(Graphics g)
\r
2651 g.setColor(Color.white);
\r
2652 g.fillRect(0, 0, getSize().width, getSize().height);
\r
2653 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2654 FontMetrics fm = g.getFontMetrics();
\r
2655 int fh = fm.getHeight();
\r
2657 g.setColor(Color.black);
\r
2658 // TODO: update this text for each release or centrally store it for
\r
2659 // lite and application
\r
2660 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
2661 g.drawString("JalviewLite - Release " + version, x, y += fh);
\r
2662 g.setFont(new Font("Helvetica", Font.BOLD, 12));
\r
2663 g.drawString("Build date: " + builddate, x, y += fh);
\r
2664 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2666 "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",
\r
2667 x, y += fh * 1.5);
\r
2668 g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
\r
2670 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
\r
2673 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
\r
2675 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
\r
2677 "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
\r
2680 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
\r
2682 g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
\r
2687 Frame frame = new Frame();
\r
2688 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
\r
2689 .getBuildDate()));
\r
2690 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
\r
2694 public void showURL(String url, String target)
\r
2696 if (viewport.applet == null)
\r
2698 System.out.println("Not running as applet - no browser available.");
\r
2702 viewport.applet.showURL(url, target);
\r
2706 // ////////////////////////////////////////////////////////////////////////////////
\r
2707 // JBuilder Graphics here
\r
2709 MenuBar alignFrameMenuBar = new MenuBar();
\r
2711 Menu fileMenu = new Menu("File");
\r
2713 MenuItem loadApplication = new MenuItem("View in Full Application");
\r
2715 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
\r
2717 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
\r
2719 MenuItem outputFeatures = new MenuItem("Export Features ...");
\r
2721 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
\r
2723 MenuItem closeMenuItem = new MenuItem("Close");
\r
2725 Menu editMenu = new Menu("Edit");
\r
2727 Menu viewMenu = new Menu("View");
\r
2729 Menu colourMenu = new Menu("Colour");
\r
2731 Menu calculateMenu = new Menu("Calculate");
\r
2733 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
2735 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
2737 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
2739 MenuItem remove2LeftMenuItem = new MenuItem();
\r
2741 MenuItem remove2RightMenuItem = new MenuItem();
\r
2743 MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
2745 MenuItem removeAllGapsMenuItem = new MenuItem();
\r
2747 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
2749 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
2751 MenuItem sortPairwiseMenuItem = new MenuItem();
\r
2753 MenuItem sortIDMenuItem = new MenuItem();
\r
2755 MenuItem sortLengthMenuItem = new MenuItem();
\r
2757 MenuItem sortGroupMenuItem = new MenuItem();
\r
2759 MenuItem removeRedundancyMenuItem = new MenuItem();
\r
2761 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
2763 MenuItem PCAMenuItem = new MenuItem();
\r
2765 MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
2767 MenuItem neighbourTreeMenuItem = new MenuItem();
\r
2769 BorderLayout borderLayout1 = new BorderLayout();
\r
2771 public Label statusBar = new Label();
\r
2773 Menu outputTextboxMenu = new Menu();
\r
2775 MenuItem clustalColour = new MenuItem();
\r
2777 MenuItem zappoColour = new MenuItem();
\r
2779 MenuItem taylorColour = new MenuItem();
\r
2781 MenuItem hydrophobicityColour = new MenuItem();
\r
2783 MenuItem helixColour = new MenuItem();
\r
2785 MenuItem strandColour = new MenuItem();
\r
2787 MenuItem turnColour = new MenuItem();
\r
2789 MenuItem buriedColour = new MenuItem();
\r
2791 MenuItem purinePyrimidineColour = new MenuItem();
\r
2792 MenuItem RNAInteractionColour = new MenuItem();
\r
2793 MenuItem RNAHelixColour = new MenuItem();
\r
2795 MenuItem userDefinedColour = new MenuItem();
\r
2797 MenuItem PIDColour = new MenuItem();
\r
2799 MenuItem BLOSUM62Colour = new MenuItem();
\r
2801 MenuItem tcoffeeColour = new MenuItem();
\r
2803 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
2805 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
2807 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
2809 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
2811 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
\r
2813 MenuItem alProperties = new MenuItem("Alignment Properties...");
\r
2815 MenuItem overviewMenuItem = new MenuItem();
\r
2817 MenuItem undoMenuItem = new MenuItem();
\r
2819 MenuItem redoMenuItem = new MenuItem();
\r
2821 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
2823 MenuItem noColourmenuItem = new MenuItem();
\r
2825 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
2827 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
2829 MenuItem findMenuItem = new MenuItem();
\r
2831 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
2833 MenuItem nucleotideColour = new MenuItem();
\r
2835 MenuItem deleteGroups = new MenuItem();
\r
2837 MenuItem grpsFromSelection = new MenuItem();
\r
2839 MenuItem delete = new MenuItem();
\r
2841 MenuItem copy = new MenuItem();
\r
2843 MenuItem cut = new MenuItem();
\r
2845 Menu pasteMenu = new Menu();
\r
2847 MenuItem pasteNew = new MenuItem();
\r
2849 MenuItem pasteThis = new MenuItem();
\r
2851 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
2853 MenuItem font = new MenuItem();
\r
2855 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
2857 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
2859 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
2861 MenuItem modifyPID = new MenuItem();
\r
2863 MenuItem modifyConservation = new MenuItem();
\r
2865 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
\r
2866 "Autocalculate Consensus", true);
\r
2868 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
\r
2869 "Sort Alignment With New Tree", true);
\r
2871 Menu sortByTreeMenu = new Menu();
\r
2873 Menu sort = new Menu();
\r
2875 Menu calculate = new Menu();
\r
2877 MenuItem inputText = new MenuItem();
\r
2879 Menu helpMenu = new Menu();
\r
2881 MenuItem documentation = new MenuItem();
\r
2883 MenuItem about = new MenuItem();
\r
2885 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
2887 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
\r
2889 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
\r
2890 Menu autoAnnMenu=new Menu();
\r
2891 CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();
\r
2892 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
\r
2893 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
\r
2894 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
\r
2895 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
\r
2897 private void jbInit() throws Exception
\r
2900 setMenuBar(alignFrameMenuBar);
\r
2904 // dynamically fill save as menu with available formats
\r
2905 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
2908 item = new MenuItem(
\r
2909 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
2911 item.addActionListener(new java.awt.event.ActionListener()
\r
2914 public void actionPerformed(ActionEvent e)
\r
2916 outputText_actionPerformed(e);
\r
2920 outputTextboxMenu.add(item);
\r
2922 closeMenuItem.addActionListener(this);
\r
2923 loadApplication.addActionListener(this);
\r
2925 loadTree.addActionListener(this);
\r
2926 loadAnnotations.addActionListener(this);
\r
2927 outputFeatures.addActionListener(this);
\r
2928 outputAnnotations.addActionListener(this);
\r
2929 selectAllSequenceMenuItem.addActionListener(this);
\r
2930 deselectAllSequenceMenuItem.addActionListener(this);
\r
2931 invertSequenceMenuItem.addActionListener(this);
\r
2932 remove2LeftMenuItem.setLabel("Remove Left");
\r
2933 remove2LeftMenuItem.addActionListener(this);
\r
2934 remove2RightMenuItem.setLabel("Remove Right");
\r
2935 remove2RightMenuItem.addActionListener(this);
\r
2936 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
2937 removeGappedColumnMenuItem.addActionListener(this);
\r
2938 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
2939 removeAllGapsMenuItem.addActionListener(this);
\r
2940 viewBoxesMenuItem.setLabel("Boxes");
\r
2941 viewBoxesMenuItem.setState(true);
\r
2942 viewBoxesMenuItem.addItemListener(this);
\r
2943 viewTextMenuItem.setLabel("Text");
\r
2944 viewTextMenuItem.setState(true);
\r
2945 viewTextMenuItem.addItemListener(this);
\r
2946 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
2947 sortPairwiseMenuItem.addActionListener(this);
\r
2948 sortIDMenuItem.setLabel("by ID");
\r
2949 sortIDMenuItem.addActionListener(this);
\r
2950 sortLengthMenuItem.setLabel("by Length");
\r
2951 sortLengthMenuItem.addActionListener(this);
\r
2952 sortGroupMenuItem.setLabel("by Group");
\r
2953 sortGroupMenuItem.addActionListener(this);
\r
2954 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
2955 removeRedundancyMenuItem.addActionListener(this);
\r
2956 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
2957 pairwiseAlignmentMenuItem.addActionListener(this);
\r
2958 PCAMenuItem.setLabel("Principal Component Analysis");
\r
2959 PCAMenuItem.addActionListener(this);
\r
2960 averageDistanceTreeMenuItem
\r
2961 .setLabel("Average Distance Using % Identity");
\r
2962 averageDistanceTreeMenuItem.addActionListener(this);
\r
2963 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
2964 neighbourTreeMenuItem.addActionListener(this);
\r
2965 statusBar.setBackground(Color.white);
\r
2966 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
2967 statusBar.setText("Status bar");
\r
2968 outputTextboxMenu.setLabel("Output to Textbox");
\r
2969 clustalColour.setLabel("Clustalx");
\r
2971 clustalColour.addActionListener(this);
\r
2972 zappoColour.setLabel("Zappo");
\r
2973 zappoColour.addActionListener(this);
\r
2974 taylorColour.setLabel("Taylor");
\r
2975 taylorColour.addActionListener(this);
\r
2976 hydrophobicityColour.setLabel("Hydrophobicity");
\r
2977 hydrophobicityColour.addActionListener(this);
\r
2978 helixColour.setLabel("Helix Propensity");
\r
2979 helixColour.addActionListener(this);
\r
2980 strandColour.setLabel("Strand Propensity");
\r
2981 strandColour.addActionListener(this);
\r
2982 turnColour.setLabel("Turn Propensity");
\r
2983 turnColour.addActionListener(this);
\r
2984 buriedColour.setLabel("Buried Index");
\r
2985 buriedColour.addActionListener(this);
\r
2986 purinePyrimidineColour.setLabel("Purine/Pyrimidine");
\r
2987 purinePyrimidineColour.addActionListener(this);
\r
2988 RNAInteractionColour.setLabel("Purine/Pyrimidine");
\r
2989 RNAInteractionColour.addActionListener(this);
\r
2990 RNAHelixColour.setLabel("by RNA Helices");
\r
2991 RNAHelixColour.addActionListener(this);
\r
2992 userDefinedColour.setLabel("User Defined...");
\r
2993 userDefinedColour.addActionListener(this);
\r
2994 PIDColour.setLabel("Percentage Identity");
\r
2995 PIDColour.addActionListener(this);
\r
2996 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
2997 BLOSUM62Colour.addActionListener(this);
\r
2998 tcoffeeColour.setLabel("T-Coffee Scores");
\r
2999 tcoffeeColour.setEnabled(false); // it will enabled only if a score file is provided
\r
3000 tcoffeeColour.addActionListener(this);
\r
3001 avDistanceTreeBlosumMenuItem .setLabel("Average Distance Using BLOSUM62");
\r
3002 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
3003 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
3004 njTreeBlosumMenuItem.addActionListener(this);
\r
3005 annotationPanelMenuItem.setLabel("Show Annotations");
\r
3006 annotationPanelMenuItem.addItemListener(this);
\r
3007 colourTextMenuItem.setLabel("Colour Text");
\r
3008 colourTextMenuItem.addItemListener(this);
\r
3009 displayNonconservedMenuItem.setLabel("Show nonconserved");
\r
3010 displayNonconservedMenuItem.addItemListener(this);
\r
3011 alProperties.addActionListener(this);
\r
3012 overviewMenuItem.setLabel("Overview Window");
\r
3013 overviewMenuItem.addActionListener(this);
\r
3014 undoMenuItem.setEnabled(false);
\r
3015 undoMenuItem.setLabel("Undo");
\r
3016 undoMenuItem.addActionListener(this);
\r
3017 redoMenuItem.setEnabled(false);
\r
3018 redoMenuItem.setLabel("Redo");
\r
3019 redoMenuItem.addActionListener(this);
\r
3020 conservationMenuItem.setLabel("by Conservation");
\r
3021 conservationMenuItem.addItemListener(this);
\r
3022 noColourmenuItem.setLabel("None");
\r
3023 noColourmenuItem.addActionListener(this);
\r
3024 wrapMenuItem.setLabel("Wrap");
\r
3025 wrapMenuItem.addItemListener(this);
\r
3026 renderGapsMenuItem.setLabel("Show Gaps");
\r
3027 renderGapsMenuItem.setState(true);
\r
3028 renderGapsMenuItem.addItemListener(this);
\r
3029 findMenuItem.setLabel("Find...");
\r
3030 findMenuItem.addActionListener(this);
\r
3031 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
3032 abovePIDThreshold.addItemListener(this);
\r
3033 nucleotideColour.setLabel("Nucleotide");
\r
3034 nucleotideColour.addActionListener(this);
\r
3035 deleteGroups.setLabel("Undefine Groups");
\r
3036 deleteGroups.addActionListener(this);
\r
3037 grpsFromSelection.setLabel("Make Groups for selection");
\r
3038 grpsFromSelection.addActionListener(this);
\r
3039 copy.setLabel("Copy");
\r
3040 copy.addActionListener(this);
\r
3041 cut.setLabel("Cut");
\r
3042 cut.addActionListener(this);
\r
3043 delete.setLabel("Delete");
\r
3044 delete.addActionListener(this);
\r
3045 pasteMenu.setLabel("Paste");
\r
3046 pasteNew.setLabel("To New Alignment");
\r
3047 pasteNew.addActionListener(this);
\r
3048 pasteThis.setLabel("Add To This Alignment");
\r
3049 pasteThis.addActionListener(this);
\r
3050 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
3051 applyToAllGroups.setState(true);
\r
3052 applyToAllGroups.addItemListener(this);
\r
3053 font.setLabel("Font...");
\r
3054 font.addActionListener(this);
\r
3055 scaleAbove.setLabel("Scale Above");
\r
3056 scaleAbove.setState(true);
\r
3057 scaleAbove.setEnabled(false);
\r
3058 scaleAbove.addItemListener(this);
\r
3059 scaleLeft.setEnabled(false);
\r
3060 scaleLeft.setState(true);
\r
3061 scaleLeft.setLabel("Scale Left");
\r
3062 scaleLeft.addItemListener(this);
\r
3063 scaleRight.setEnabled(false);
\r
3064 scaleRight.setState(true);
\r
3065 scaleRight.setLabel("Scale Right");
\r
3066 scaleRight.addItemListener(this);
\r
3067 modifyPID.setLabel("Modify Identity Threshold...");
\r
3068 modifyPID.addActionListener(this);
\r
3069 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
3070 modifyConservation.addActionListener(this);
\r
3071 sortByTreeMenu.setLabel("By Tree Order");
\r
3072 sort.setLabel("Sort");
\r
3073 calculate.setLabel("Calculate Tree");
\r
3074 autoCalculate.addItemListener(this);
\r
3075 sortByTree.addItemListener(this);
\r
3076 inputText.setLabel("Input from textbox");
\r
3077 inputText.addActionListener(this);
\r
3078 centreColumnLabelFlag.setLabel("Centre column labels");
\r
3079 centreColumnLabelFlag.addItemListener(this);
\r
3080 followMouseOverFlag.setLabel("Automatic Scrolling");
\r
3081 followMouseOverFlag.addItemListener(this);
\r
3082 helpMenu.setLabel("Help");
\r
3083 documentation.setLabel("Documentation");
\r
3084 documentation.addActionListener(this);
\r
3086 about.setLabel("About...");
\r
3087 about.addActionListener(this);
\r
3088 seqLimits.setState(true);
\r
3089 seqLimits.setLabel("Show Sequence Limits");
\r
3090 seqLimits.addItemListener(this);
\r
3091 featureSettings.setLabel("Feature Settings...");
\r
3092 featureSettings.addActionListener(this);
\r
3093 sequenceFeatures.setLabel("Sequence Features");
\r
3094 sequenceFeatures.addItemListener(this);
\r
3095 sequenceFeatures.setState(false);
\r
3096 annotationColour.setLabel("by Annotation...");
\r
3097 annotationColour.addActionListener(this);
\r
3098 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
3099 invertColSel.setLabel("Invert Column Selection");
\r
3100 menu1.setLabel("Show");
\r
3101 showColumns.setLabel("All Columns ");
\r
3102 showSeqs.setLabel("All Sequences");
\r
3103 menu2.setLabel("Hide");
\r
3104 hideColumns.setLabel("Selected Columns");
\r
3105 hideSequences.setLabel("Selected Sequences");
\r
3106 hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
\r
3107 hideAllSelection.setLabel("Selected Region");
\r
3108 showAllHidden.setLabel("All Sequences and Columns");
\r
3109 showGroupConsensus.setLabel("Group Consensus");
\r
3110 showGroupConservation.setLabel("Group Conservation");
\r
3111 showConsensusHistogram.setLabel("Show Consensus Histogram");
\r
3112 showSequenceLogo.setLabel("Show Consensus Logo");
\r
3113 applyAutoAnnotationSettings.setLabel("Apply to all groups");
\r
3114 applyAutoAnnotationSettings.setState(true);
\r
3115 autoAnnMenu.setLabel("Autocalculated Annotation");
\r
3117 invertColSel.addActionListener(this);
\r
3118 showColumns.addActionListener(this);
\r
3119 showSeqs.addActionListener(this);
\r
3120 hideColumns.addActionListener(this);
\r
3121 hideSequences.addActionListener(this);
\r
3122 hideAllButSelection.addActionListener(this);
\r
3123 hideAllSelection.addActionListener(this);
\r
3124 showAllHidden.addActionListener(this);
\r
3125 showGroupConsensus.addItemListener(this);
\r
3126 showGroupConservation.addItemListener(this);
\r
3127 showConsensusHistogram.addItemListener(this);
\r
3128 showSequenceLogo.addItemListener(this);
\r
3129 applyAutoAnnotationSettings.addItemListener(this);
\r
3130 formatMenu.setLabel("Format");
\r
3131 selectMenu.setLabel("Select");
\r
3132 newView.setLabel("New View");
\r
3133 newView.addActionListener(this);
\r
3134 alignFrameMenuBar.add(fileMenu);
\r
3135 alignFrameMenuBar.add(editMenu);
\r
3136 alignFrameMenuBar.add(selectMenu);
\r
3137 alignFrameMenuBar.add(viewMenu);
\r
3138 alignFrameMenuBar.add(formatMenu);
\r
3139 alignFrameMenuBar.add(colourMenu);
\r
3140 alignFrameMenuBar.add(calculateMenu);
\r
3141 alignFrameMenuBar.add(helpMenu);
\r
3143 fileMenu.add(inputText);
\r
3144 fileMenu.add(loadTree);
\r
3145 fileMenu.add(loadAnnotations);
\r
3147 fileMenu.addSeparator();
\r
3148 fileMenu.add(outputTextboxMenu);
\r
3149 fileMenu.add(outputFeatures);
\r
3150 fileMenu.add(outputAnnotations);
\r
3152 if (jalviewServletURL != null)
\r
3154 fileMenu.add(loadApplication);
\r
3157 fileMenu.addSeparator();
\r
3158 fileMenu.add(closeMenuItem);
\r
3160 editMenu.add(undoMenuItem);
\r
3161 editMenu.add(redoMenuItem);
\r
3162 editMenu.add(cut);
\r
3163 editMenu.add(copy);
\r
3164 editMenu.add(pasteMenu);
\r
3165 editMenu.add(delete);
\r
3166 editMenu.addSeparator();
\r
3167 editMenu.add(remove2LeftMenuItem);
\r
3168 editMenu.add(remove2RightMenuItem);
\r
3169 editMenu.add(removeGappedColumnMenuItem);
\r
3170 editMenu.add(removeAllGapsMenuItem);
\r
3171 editMenu.add(removeRedundancyMenuItem);
\r
3172 viewMenu.add(newView);
\r
3173 viewMenu.addSeparator();
\r
3174 viewMenu.add(menu1);
\r
3175 viewMenu.add(menu2);
\r
3176 viewMenu.addSeparator();
\r
3177 viewMenu.add(followMouseOverFlag);
\r
3178 viewMenu.add(annotationPanelMenuItem);
\r
3179 autoAnnMenu.add(applyAutoAnnotationSettings);
\r
3180 autoAnnMenu.add(showConsensusHistogram);
\r
3181 autoAnnMenu.add(showSequenceLogo);
\r
3182 autoAnnMenu.addSeparator();
\r
3183 autoAnnMenu.add(showGroupConservation);
\r
3184 autoAnnMenu.add(showGroupConsensus);
\r
3185 viewMenu.add(autoAnnMenu);
\r
3186 viewMenu.addSeparator();
\r
3187 viewMenu.add(sequenceFeatures);
\r
3188 viewMenu.add(featureSettings);
\r
3189 viewMenu.addSeparator();
\r
3190 viewMenu.add(alProperties);
\r
3191 viewMenu.addSeparator();
\r
3192 viewMenu.add(overviewMenuItem);
\r
3193 colourMenu.add(applyToAllGroups);
\r
3194 colourMenu.addSeparator();
\r
3195 colourMenu.add(noColourmenuItem);
\r
3196 colourMenu.add(clustalColour);
\r
3197 colourMenu.add(BLOSUM62Colour);
\r
3198 colourMenu.add(PIDColour);
\r
3199 colourMenu.add(zappoColour);
\r
3200 colourMenu.add(taylorColour);
\r
3201 colourMenu.add(hydrophobicityColour);
\r
3202 colourMenu.add(helixColour);
\r
3203 colourMenu.add(strandColour);
\r
3204 colourMenu.add(turnColour);
\r
3205 colourMenu.add(buriedColour);
\r
3206 colourMenu.add(nucleotideColour);
\r
3207 colourMenu.add(purinePyrimidineColour);
\r
3208 colourMenu.add(RNAInteractionColour);
\r
3209 colourMenu.add(tcoffeeColour);
\r
3210 colourMenu.add(userDefinedColour);
\r
3211 colourMenu.addSeparator();
\r
3212 colourMenu.add(conservationMenuItem);
\r
3213 colourMenu.add(modifyConservation);
\r
3214 colourMenu.add(abovePIDThreshold);
\r
3215 colourMenu.add(modifyPID);
\r
3216 colourMenu.add(annotationColour);
\r
3217 colourMenu.add(RNAHelixColour);
\r
3218 calculateMenu.add(sort);
\r
3219 calculateMenu.add(calculate);
\r
3220 calculateMenu.addSeparator();
\r
3221 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
3222 calculateMenu.add(PCAMenuItem);
\r
3223 calculateMenu.add(autoCalculate);
\r
3224 calculateMenu.add(sortByTree);
\r
3225 this.add(statusBar, BorderLayout.SOUTH);
\r
3226 pasteMenu.add(pasteNew);
\r
3227 pasteMenu.add(pasteThis);
\r
3228 sort.add(sortIDMenuItem);
\r
3229 sort.add(sortLengthMenuItem);
\r
3230 sort.add(sortByTreeMenu);
\r
3231 sort.add(sortGroupMenuItem);
\r
3232 sort.add(sortPairwiseMenuItem);
\r
3233 calculate.add(averageDistanceTreeMenuItem);
\r
3234 calculate.add(neighbourTreeMenuItem);
\r
3235 calculate.add(avDistanceTreeBlosumMenuItem);
\r
3236 calculate.add(njTreeBlosumMenuItem);
\r
3237 helpMenu.add(documentation);
\r
3238 helpMenu.add(about);
\r
3239 menu1.add(showColumns);
\r
3240 menu1.add(showSeqs);
\r
3241 menu1.add(showAllHidden);
\r
3242 menu2.add(hideColumns);
\r
3243 menu2.add(hideSequences);
\r
3244 menu2.add(hideAllSelection);
\r
3245 menu2.add(hideAllButSelection);
\r
3246 formatMenu.add(font);
\r
3247 formatMenu.add(seqLimits);
\r
3248 formatMenu.add(wrapMenuItem);
\r
3249 formatMenu.add(scaleAbove);
\r
3250 formatMenu.add(scaleLeft);
\r
3251 formatMenu.add(scaleRight);
\r
3252 formatMenu.add(viewBoxesMenuItem);
\r
3253 formatMenu.add(viewTextMenuItem);
\r
3254 formatMenu.add(colourTextMenuItem);
\r
3255 formatMenu.add(displayNonconservedMenuItem);
\r
3256 formatMenu.add(renderGapsMenuItem);
\r
3257 formatMenu.add(centreColumnLabelFlag);
\r
3258 selectMenu.add(findMenuItem);
\r
3259 selectMenu.addSeparator();
\r
3260 selectMenu.add(selectAllSequenceMenuItem);
\r
3261 selectMenu.add(deselectAllSequenceMenuItem);
\r
3262 selectMenu.add(invertSequenceMenuItem);
\r
3263 selectMenu.add(invertColSel);
\r
3264 selectMenu.add(grpsFromSelection);
\r
3265 selectMenu.add(deleteGroups);
\r
3269 MenuItem featureSettings = new MenuItem();
\r
3271 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
3273 MenuItem annotationColour = new MenuItem();
\r
3275 MenuItem invertColSel = new MenuItem();
\r
3277 Menu menu1 = new Menu();
\r
3279 MenuItem showColumns = new MenuItem();
\r
3281 MenuItem showSeqs = new MenuItem();
\r
3283 Menu menu2 = new Menu();
\r
3285 MenuItem hideColumns = new MenuItem();
\r
3287 MenuItem hideSequences = new MenuItem();
\r
3289 MenuItem hideAllButSelection = new MenuItem();
\r
3291 MenuItem hideAllSelection = new MenuItem();
\r
3293 MenuItem showAllHidden = new MenuItem();
\r
3295 Menu formatMenu = new Menu();
\r
3297 Menu selectMenu = new Menu();
\r
3299 MenuItem newView = new MenuItem();
\r
3302 * Attach the alignFrame panels after embedding menus, if necessary. This used
\r
3303 * to be called setEmbedded, but is now creates the dropdown menus in a
\r
3304 * platform independent manner to avoid OSX/Mac menu appendage daftness.
\r
3306 * @param reallyEmbedded
\r
3307 * true to attach the view to the applet area on the page rather than
\r
3310 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
\r
3312 if (reallyEmbedded)
\r
3315 // Explicly build the embedded menu panel for the on-page applet
\r
3317 // view cannot be closed if its actually on the page
\r
3318 fileMenu.remove(closeMenuItem);
\r
3319 fileMenu.remove(3); // Remove Seperator
\r
3320 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
\r
3321 Font.PLAIN, 10, false); // use our own fonts.
\r
3322 // and actually add the components to the applet area
\r
3323 viewport.applet.setLayout(new BorderLayout());
\r
3324 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
\r
3325 viewport.applet.add(statusBar, BorderLayout.SOUTH);
\r
3326 alignPanel.setSize(viewport.applet.getSize().width,
\r
3327 viewport.applet.getSize().height - embeddedMenu.HEIGHT
\r
3328 - statusBar.HEIGHT);
\r
3329 viewport.applet.add(alignPanel, BorderLayout.CENTER);
\r
3330 final AlignFrame me = this;
\r
3331 viewport.applet.addFocusListener(new FocusListener()
\r
3335 public void focusLost(FocusEvent e)
\r
3337 if (me.viewport.applet.currentAlignFrame==me) {
\r
3338 me.viewport.applet.currentAlignFrame = null;
\r
3342 public void focusGained(FocusEvent e)
\r
3344 me.viewport.applet.currentAlignFrame = me;
\r
3347 viewport.applet.validate();
\r
3352 // test and embed menu bar if necessary.
\r
3354 if (embedMenuIfNeeded(alignPanel))
\r
3356 // adjust for status bar height too
\r
3357 alignPanel.setSize(getSize().width, getSize().height
\r
3358 - statusBar.HEIGHT);
\r
3360 add(statusBar, BorderLayout.SOUTH);
\r
3361 add(alignPanel, BorderLayout.CENTER);
\r
3362 // and register with the applet so it can pass external API calls to us
\r
3363 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
\r
3369 * create a new binding between structures in an existing jmol viewer instance
\r
3370 * and an alignpanel with sequences that have existing PDBFile entries. Note,
\r
3371 * this does not open a new Jmol window, or modify the display of the
\r
3372 * structures in the original jmol window. Note This method doesn't work
\r
3373 * without an additional javascript library to exchange messages between the
\r
3374 * distinct applets. See http://issues.jalview.org/browse/JAL-621
\r
3377 * JmolViewer instance
\r
3378 * @param sequenceIds
\r
3379 * - sequence Ids to search for associations
\r
3381 public SequenceStructureBinding addStructureViewInstance(
\r
3382 Object jmolviewer, String[] sequenceIds)
\r
3384 org.jmol.api.JmolViewer viewer = null;
\r
3387 viewer = (org.jmol.api.JmolViewer) jmolviewer;
\r
3388 } catch (ClassCastException ex)
\r
3390 System.err.println("Unsupported viewer object :"
\r
3391 + jmolviewer.getClass());
\r
3393 if (viewer == null)
\r
3395 System.err.println("Can't use this object as a structure viewer:"
\r
3396 + jmolviewer.getClass());
\r
3399 SequenceI[] seqs = null;
\r
3400 if (sequenceIds == null || sequenceIds.length == 0)
\r
3402 seqs = viewport.getAlignment().getSequencesArray();
\r
3406 Vector sqi = new Vector();
\r
3407 AlignmentI al = viewport.getAlignment();
\r
3408 for (int sid = 0; sid < sequenceIds.length; sid++)
\r
3410 SequenceI sq = al.findName(sequenceIds[sid]);
\r
3413 sqi.addElement(sq);
\r
3416 if (sqi.size() > 0)
\r
3418 seqs = new SequenceI[sqi.size()];
\r
3419 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
\r
3421 seqs[sid] = (SequenceI) sqi.elementAt(sid);
\r
3429 ExtJmol jmv = null;
\r
3430 // TODO: search for a jmv that involves viewer
\r
3432 { // create a new viewer/jalview binding.
\r
3433 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs});
\r
3439 * bind a pdb file to a sequence in the current view
\r
3441 * @param sequenceId
\r
3442 * - sequenceId within the dataset.
\r
3443 * @param pdbEntryString
\r
3444 * - the short name for the PDB file
\r
3446 * - pdb file - either a URL or a valid PDB file.
\r
3447 * @return true if binding was as success TODO: consider making an exception
\r
3448 * structure for indicating when PDB parsing or sequenceId location
\r
3451 public boolean addPdbFile(String sequenceId, String pdbEntryString,
\r
3454 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
\r
3455 boolean needtoadd = false;
\r
3456 if (toaddpdb != null)
\r
3458 Vector pdbe = toaddpdb.getPDBId();
\r
3459 PDBEntry pdbentry = null;
\r
3460 if (pdbe != null && pdbe.size() > 0)
\r
3462 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
\r
3464 pdbentry = (PDBEntry) pdbe.elementAt(pe);
\r
3465 if (!pdbentry.getId().equals(pdbEntryString)
\r
3466 && !pdbentry.getFile().equals(pdbFile))
\r
3476 if (pdbentry == null)
\r
3478 pdbentry = new PDBEntry();
\r
3479 pdbentry.setId(pdbEntryString);
\r
3480 pdbentry.setFile(pdbFile);
\r
3481 needtoadd = true; // add this new entry to sequence.
\r
3483 // resolve data source
\r
3484 // TODO: this code should be a refactored to an io package
\r
3485 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
\r
3486 if (protocol == null)
\r
3492 // make a note of the access mode and add
\r
3493 if (pdbentry.getProperty() == null)
\r
3495 pdbentry.setProperty(new Hashtable());
\r
3497 pdbentry.getProperty().put("protocol", protocol);
\r
3498 toaddpdb.addPDBId(pdbentry);
\r
3504 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
\r
3508 Vector sequences = new Vector();
\r
3509 for (int i = 0; i < seqs.length; i++)
\r
3511 if (seqs[i] != null)
\r
3513 sequences.addElement(new Object[]
\r
3514 { seqs[i], (chains != null) ? chains[i] : null });
\r
3517 seqs = new SequenceI[sequences.size()];
\r
3518 chains = new String[sequences.size()];
\r
3519 for (int i = 0, isize = sequences.size(); i < isize; i++)
\r
3521 Object[] oj = (Object[]) sequences.elementAt(i);
\r
3523 seqs[i] = (SequenceI) oj[0];
\r
3524 chains[i] = (String) oj[1];
\r
3527 return new Object[]
\r
3532 public void newStructureView(JalviewLite applet, PDBEntry pdb,
\r
3533 SequenceI[] seqs, String[] chains, String protocol)
\r
3535 // Scrub any null sequences from the array
\r
3536 Object[] sqch = cleanSeqChainArrays(seqs, chains);
\r
3537 seqs = (SequenceI[]) sqch[0];
\r
3538 chains = (String[]) sqch[1];
\r
3539 if (seqs == null || seqs.length == 0)
\r
3542 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
\r
3544 if (protocol == null || protocol.trim().length() == 0
\r
3545 || protocol.equals("null"))
\r
3547 protocol = (String) pdb.getProperty().get("protocol");
\r
3548 if (protocol == null)
\r
3550 System.err.println("Couldn't work out protocol to open structure: "
\r
3555 if (applet.useXtrnalSviewer)
\r
3557 // register the association(s) and quit, don't create any windows.
\r
3558 if (StructureSelectionManager.getStructureSelectionManager(applet).setMapping(seqs, chains, pdb.getFile(), protocol)==null) {
\r
3559 System.err.println("Failed to map "+pdb.getFile()+" ("+protocol+") to any sequences");
\r
3563 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
\r
3565 // can only do alignments with Jmol
\r
3566 // find the last jmol window assigned to this alignment
\r
3567 jalview.appletgui.AppletJmol ajm = null, tajm;
\r
3568 Vector jmols = applet
\r
3569 .getAppletWindow(jalview.appletgui.AppletJmol.class);
\r
3570 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
\r
3572 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
\r
3573 if (tajm.ap.alignFrame == this)
\r
3582 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
\r
3583 // try and add the pdb structure
\r
3588 // otherwise, create a new window
\r
3589 if (applet.jmolAvailable)
\r
3591 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
\r
3593 applet.lastFrameX += 40;
\r
3594 applet.lastFrameY += 40;
\r
3598 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
\r
3603 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
\r
3604 SequenceI[][] seqs, String[][] chains, String[] protocols)
\r
3606 // TODO Auto-generated method stub
\r
3607 System.err.println("Aligned Structure View: Not yet implemented.");
\r
3611 * modify the current selection, providing the user has not made a selection already.
\r
3612 * @param sel - sequences from this alignment
\r
3613 * @param csel - columns to be selected on the alignment
\r
3615 public void select(SequenceGroup sel, ColumnSelection csel)
\r
3617 alignPanel.seqPanel.selection(sel, csel, null);
\r
3620 public void scrollTo(int row, int column)
\r
3622 alignPanel.seqPanel.scrollTo(row, column);
\r
3624 public void scrollToRow(int row)
\r
3626 alignPanel.seqPanel.scrollToRow(row);
\r
3628 public void scrollToColumn(int column)
\r
3630 alignPanel.seqPanel.scrollToColumn(column);
\r
3633 * @return the alignments unique ID.
\r
3635 public String getSequenceSetId() {
\r
3636 return viewport.getSequenceSetId();
\r
3641 * Load the (T-Coffee) score file from the specified url
\r
3643 * @param source File/URL/T-COFFEE score file contents
\r
3644 * @throws IOException
\r
3645 * @return true if alignment was annotated with data from source
\r
3646 * @throws SAXException
\r
3647 * @throws ParserConfigurationException
\r
3648 * @throws ExceptionFileFormatOrSyntax
\r
3649 * @throws ExceptionLoadingFailed
\r
3650 * @throws ExceptionPermissionDenied
\r
3651 * @throws InterruptedException
\r
3653 public boolean loadScoreFile( String source ) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException {
\r
3655 TCoffeeScoreFile file = new TCoffeeScoreFile(source, AppletFormatAdapter.checkProtocol(source));
\r
3656 if( !file.isValid()) {
\r
3657 // TODO: raise dialog for gui
\r
3658 System.err.println("Problems parsing T-Coffee scores: "+file.getWarningMessage());
\r
3659 System.err.println("Origin was:\n"+source);
\r
3664 * check that the score matrix matches the alignment dimensions
\r
3667 if( (aln=viewport.getAlignment()) != null && (aln.getHeight() != file.getHeight() || aln.getWidth() != file.getWidth()) ) {
\r
3668 // TODO: raise a dialog box here rather than bomb out.
\r
3669 System.err.println("The scores matrix does not match the alignment dimensions");
\r
3673 // TODO add parameter to indicate if matching should be done
\r
3674 if (file.annotateAlignment(alignPanel.getAlignment(), false))
\r
3676 alignPanel.fontChanged();
\r
3677 tcoffeeColour.setEnabled(true);
\r
3678 // switch to this color
\r
3679 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
\r
3682 System.err.println("Problems resolving T-Coffee scores:");
\r
3683 if (file.getWarningMessage()!=null) {
\r
3684 System.err.println(file.getWarningMessage());
\r