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.SequenceGroup;
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39 import jalview.datamodel.SequenceI;
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40 import jalview.io.AnnotationFile;
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41 import jalview.io.AppletFormatAdapter;
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42 import jalview.io.FeaturesFile;
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43 import jalview.io.TCoffeeScoreFile;
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44 import jalview.schemes.Blosum62ColourScheme;
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45 import jalview.schemes.BuriedColourScheme;
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46 import jalview.schemes.ClustalxColourScheme;
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47 import jalview.schemes.ColourSchemeI;
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48 import jalview.schemes.HelixColourScheme;
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49 import jalview.schemes.HydrophobicColourScheme;
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50 import jalview.schemes.NucleotideColourScheme;
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51 import jalview.schemes.PIDColourScheme;
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52 import jalview.schemes.PurinePyrimidineColourScheme;
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53 import jalview.schemes.RNAHelicesColourChooser;
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54 import jalview.schemes.ResidueProperties;
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55 import jalview.schemes.StrandColourScheme;
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56 import jalview.schemes.TCoffeeColourScheme;
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57 import jalview.schemes.TaylorColourScheme;
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58 import jalview.schemes.TurnColourScheme;
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59 import jalview.schemes.ZappoColourScheme;
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60 import jalview.structure.StructureSelectionManager;
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62 import java.awt.BorderLayout;
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63 import java.awt.Canvas;
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64 import java.awt.CheckboxMenuItem;
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65 import java.awt.Color;
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66 import java.awt.Font;
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67 import java.awt.FontMetrics;
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68 import java.awt.Frame;
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69 import java.awt.Graphics;
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70 import java.awt.Label;
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71 import java.awt.Menu;
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72 import java.awt.MenuBar;
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73 import java.awt.MenuItem;
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74 import java.awt.event.ActionEvent;
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75 import java.awt.event.ActionListener;
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76 import java.awt.event.FocusEvent;
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77 import java.awt.event.FocusListener;
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78 import java.awt.event.ItemEvent;
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79 import java.awt.event.ItemListener;
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80 import java.awt.event.KeyEvent;
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81 import java.awt.event.KeyListener;
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82 import java.awt.event.WindowAdapter;
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83 import java.awt.event.WindowEvent;
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84 import java.io.IOException;
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85 import java.io.InputStreamReader;
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86 import java.net.URL;
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87 import java.net.URLEncoder;
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88 import java.util.Enumeration;
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89 import java.util.Hashtable;
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90 import java.util.StringTokenizer;
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91 import java.util.Vector;
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93 public class AlignFrame extends EmbmenuFrame implements ActionListener, ItemListener, KeyListener
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95 public AlignmentPanel alignPanel;
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97 public AlignViewport viewport;
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99 int DEFAULT_WIDTH = 700;
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101 int DEFAULT_HEIGHT = 500;
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103 String jalviewServletURL;
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106 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title, boolean embedded)
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108 if (applet != null)
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110 jalviewServletURL = applet.getParameter("APPLICATION_URL");
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116 } catch (Exception ex)
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118 ex.printStackTrace();
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121 viewport = new AlignViewport(al, applet);
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122 alignPanel = new AlignmentPanel(this, viewport);
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124 viewport.updateConservation(alignPanel);
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125 viewport.updateConsensus(alignPanel);
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127 annotationPanelMenuItem.setState(viewport.showAnnotation);
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128 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
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129 followMouseOverFlag.setState(viewport.getFollowHighlight());
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130 showGroupConsensus.setState(viewport.isShowGroupConsensus());
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131 showGroupConservation.setState(viewport.isShowGroupConservation());
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132 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
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133 showSequenceLogo.setState(viewport.isShowSequenceLogo());
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135 seqLimits.setState(viewport.showJVSuffix);
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137 if (applet != null)
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139 String param = applet.getParameter("sortBy");
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142 if (param.equalsIgnoreCase("Id"))
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144 sortIDMenuItem_actionPerformed();
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146 else if (param.equalsIgnoreCase("Pairwise Identity"))
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148 sortPairwiseMenuItem_actionPerformed();
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150 else if (param.equalsIgnoreCase("Length"))
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152 sortLengthMenuItem_actionPerformed();
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156 param = applet.getParameter("wrap");
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159 if (param.equalsIgnoreCase("true"))
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161 wrapMenuItem.setState(true);
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162 wrapMenuItem_actionPerformed();
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165 param = applet.getParameter("centrecolumnlabels");
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168 centreColumnLabelFlag.setState(true);
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169 centreColumnLabelFlag_stateChanged();
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173 param = applet.getParameter("windowWidth");
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176 int width = Integer.parseInt(param);
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177 DEFAULT_WIDTH = width;
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179 param = applet.getParameter("windowHeight");
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182 int height = Integer.parseInt(param);
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183 DEFAULT_HEIGHT = height;
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185 } catch (Exception ex)
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190 if (viewport.getAlignment().isNucleotide())
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192 viewport.updateStrucConsensus(alignPanel);
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193 if (viewport.getAlignment().hasRNAStructure())
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195 RNAHelixColour.setEnabled(true);
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198 RNAHelixColour.setEnabled(false);
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201 RNAHelixColour.setEnabled(false);
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202 purinePyrimidineColour.setEnabled(false);
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204 // Some JVMS send keyevents to Top frame or lowest panel,
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205 // Havent worked out why yet. So add to both this frame and seqCanvas for
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207 this.addKeyListener(this);
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208 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
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209 alignPanel.idPanel.idCanvas.addKeyListener(this);
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210 alignPanel.scalePanel.addKeyListener(this);
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211 alignPanel.annotationPanel.addKeyListener(this);
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212 alignPanel.annotationPanelHolder.addKeyListener(this);
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213 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
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214 alignPanel.alabels.addKeyListener(this);
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215 createAlignFrameWindow(embedded, title);
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218 alignPanel.adjustAnnotationHeight();
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219 alignPanel.paintAlignment(true);
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222 public AlignViewport getAlignViewport()
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227 public SeqCanvas getSeqcanvas()
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229 return alignPanel.seqPanel.seqCanvas;
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233 * Load a features file onto the alignment
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235 * @param file file URL, content, or other resolvable path
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236 * @param type is protocol for accessing data referred to by file
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239 public boolean parseFeaturesFile(String file, String type)
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241 return parseFeaturesFile(file, type, true);
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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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249 * @param autoenabledisplay when true, display features flag will be automatically enabled if features are loaded
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250 * @return true if data parsed as a features file
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252 public boolean parseFeaturesFile(String file, String type, boolean autoenabledisplay)
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254 // TODO: test if importing a features file onto an alignment which already has features with links overwrites the original links.
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256 Hashtable featureLinks = new Hashtable();
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257 boolean featuresFile = false;
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260 featuresFile = new jalview.io.FeaturesFile(file, type)
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261 .parse(viewport.getAlignment(),
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262 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
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263 featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));
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264 } catch (Exception ex)
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266 ex.printStackTrace();
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271 if (featureLinks.size() > 0)
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273 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
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275 if (autoenabledisplay)
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277 viewport.showSequenceFeatures = true;
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278 sequenceFeatures.setState(true);
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280 if (viewport.featureSettings != null)
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282 viewport.featureSettings.refreshTable();
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284 alignPanel.paintAlignment(true);
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285 statusBar.setText("Successfully added features to alignment.");
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287 return featuresFile;
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290 public void keyPressed(KeyEvent evt)
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292 if (viewport.cursorMode
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293 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
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294 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
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295 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
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296 && Character.isDigit(evt.getKeyChar()))
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297 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
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299 switch (evt.getKeyCode())
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301 case 27: // escape key
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302 deselectAllSequenceMenuItem_actionPerformed();
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304 alignPanel.alabels.cancelDrag();
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306 case KeyEvent.VK_X:
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307 if (evt.isControlDown() || evt.isMetaDown())
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309 cut_actionPerformed();
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312 case KeyEvent.VK_C:
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313 if (viewport.cursorMode && !evt.isControlDown())
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315 alignPanel.seqPanel.setCursorColumn();
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317 if (evt.isControlDown() || evt.isMetaDown())
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319 copy_actionPerformed();
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322 case KeyEvent.VK_V:
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323 if (evt.isControlDown())
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325 paste(evt.isShiftDown());
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328 case KeyEvent.VK_A:
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329 if (evt.isControlDown() || evt.isMetaDown())
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331 selectAllSequenceMenuItem_actionPerformed();
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334 case KeyEvent.VK_DOWN:
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335 if (viewport.cursorMode)
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337 alignPanel.seqPanel.moveCursor(0, 1);
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341 moveSelectedSequences(false);
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345 case KeyEvent.VK_UP:
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346 if (viewport.cursorMode)
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348 alignPanel.seqPanel.moveCursor(0, -1);
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352 moveSelectedSequences(true);
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356 case KeyEvent.VK_LEFT:
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357 if (evt.isAltDown() || !viewport.cursorMode)
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358 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
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360 alignPanel.seqPanel.moveCursor(-1, 0);
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363 case KeyEvent.VK_RIGHT:
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364 if (evt.isAltDown() || !viewport.cursorMode)
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365 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
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367 alignPanel.seqPanel.moveCursor(1, 0);
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370 case KeyEvent.VK_SPACE:
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371 if (viewport.cursorMode)
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373 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
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374 || evt.isShiftDown() || evt.isAltDown());
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378 case KeyEvent.VK_DELETE:
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379 case KeyEvent.VK_BACK_SPACE:
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380 if (viewport.cursorMode)
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382 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
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383 || evt.isShiftDown() || evt.isAltDown());
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387 cut_actionPerformed();
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388 alignPanel.seqPanel.seqCanvas.repaint();
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392 case KeyEvent.VK_S:
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393 if (viewport.cursorMode)
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395 alignPanel.seqPanel.setCursorRow();
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398 case KeyEvent.VK_P:
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399 if (viewport.cursorMode)
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401 alignPanel.seqPanel.setCursorPosition();
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405 case KeyEvent.VK_ENTER:
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406 case KeyEvent.VK_COMMA:
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407 if (viewport.cursorMode)
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409 alignPanel.seqPanel.setCursorRowAndColumn();
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413 case KeyEvent.VK_Q:
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414 if (viewport.cursorMode)
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416 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
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419 case KeyEvent.VK_M:
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420 if (viewport.cursorMode)
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422 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
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426 case KeyEvent.VK_F2:
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427 viewport.cursorMode = !viewport.cursorMode;
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428 statusBar.setText("Keyboard editing mode is "
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429 + (viewport.cursorMode ? "on" : "off"));
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430 if (viewport.cursorMode)
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432 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
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433 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
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437 case KeyEvent.VK_F:
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438 if (evt.isControlDown())
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440 findMenuItem_actionPerformed();
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444 case KeyEvent.VK_H:
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446 boolean toggleSeqs = !evt.isControlDown();
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447 boolean toggleCols = !evt.isShiftDown();
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448 toggleHiddenRegions(toggleSeqs, toggleCols);
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452 case KeyEvent.VK_PAGE_UP:
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453 if (viewport.wrapAlignment)
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455 alignPanel.scrollUp(true);
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459 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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460 - viewport.endSeq + viewport.startSeq);
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464 case KeyEvent.VK_PAGE_DOWN:
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465 if (viewport.wrapAlignment)
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467 alignPanel.scrollUp(false);
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471 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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472 + viewport.endSeq - viewport.startSeq);
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476 case KeyEvent.VK_Z:
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477 if (evt.isControlDown())
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479 undoMenuItem_actionPerformed();
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483 case KeyEvent.VK_Y:
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484 if (evt.isControlDown())
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486 redoMenuItem_actionPerformed();
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490 case KeyEvent.VK_L:
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491 if (evt.isControlDown())
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493 trimAlignment(true);
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497 case KeyEvent.VK_R:
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498 if (evt.isControlDown())
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500 trimAlignment(false);
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504 case KeyEvent.VK_E:
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505 if (evt.isControlDown())
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507 if (evt.isShiftDown())
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509 this.removeAllGapsMenuItem_actionPerformed();
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513 removeGappedColumnMenuItem_actionPerformed();
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517 case KeyEvent.VK_I:
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518 if (evt.isControlDown())
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520 if (evt.isAltDown())
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522 invertColSel_actionPerformed();
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526 invertSequenceMenuItem_actionPerformed();
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531 case KeyEvent.VK_U:
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532 if (evt.isControlDown())
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534 this.deleteGroups_actionPerformed();
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538 case KeyEvent.VK_T:
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539 if (evt.isControlDown())
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546 alignPanel.paintAlignment(true);
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550 * called by key handler and the hide all/show all menu items
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552 * @param toggleSeqs
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553 * @param toggleCols
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555 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
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557 boolean hide = false;
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558 SequenceGroup sg = viewport.getSelectionGroup();
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559 if (!toggleSeqs && !toggleCols)
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561 // Hide everything by the current selection - this is a hack - we do the
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562 // invert and then hide
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563 // first check that there will be visible columns after the invert.
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564 if ((viewport.getColumnSelection() != null && viewport.getColumnSelection().getSelected() != null && viewport.getColumnSelection()
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565 .getSelected().size() > 0)
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566 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
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569 // now invert the sequence set, if required - empty selection implies
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570 // that no hiding is required.
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573 invertSequenceMenuItem_actionPerformed();
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574 sg = viewport.getSelectionGroup();
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578 viewport.expandColSelection(sg, true);
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579 // finally invert the column selection and get the new sequence
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580 // selection and indicate it should be hidden.
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581 invertColSel_actionPerformed();
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588 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
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591 viewport.hideAllSelectedSeqs();
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593 else if (!(toggleCols && viewport.getColumnSelection().getSelected().size() > 0))
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595 viewport.showAllHiddenSeqs();
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601 if (viewport.getColumnSelection().getSelected().size() > 0)
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603 viewport.hideSelectedColumns();
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606 viewport.setSelectionGroup(sg);
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611 viewport.showAllHiddenColumns();
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616 public void keyReleased(KeyEvent evt)
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620 public void keyTyped(KeyEvent evt)
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624 public void itemStateChanged(ItemEvent evt)
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626 if (evt.getSource() == displayNonconservedMenuItem)
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628 displayNonconservedMenuItem_actionPerformed();
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630 else if (evt.getSource() == colourTextMenuItem)
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632 colourTextMenuItem_actionPerformed();
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634 else if (evt.getSource() == wrapMenuItem)
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636 wrapMenuItem_actionPerformed();
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638 else if (evt.getSource() == scaleAbove)
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640 viewport.setScaleAboveWrapped(scaleAbove.getState());
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642 else if (evt.getSource() == scaleLeft)
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644 viewport.setScaleLeftWrapped(scaleLeft.getState());
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646 else if (evt.getSource() == scaleRight)
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648 viewport.setScaleRightWrapped(scaleRight.getState());
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650 else if (evt.getSource() == seqLimits)
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652 seqLimits_itemStateChanged();
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654 else if (evt.getSource() == viewBoxesMenuItem)
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656 viewport.setShowBoxes(viewBoxesMenuItem.getState());
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658 else if (evt.getSource() == viewTextMenuItem)
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660 viewport.setShowText(viewTextMenuItem.getState());
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662 else if (evt.getSource() == renderGapsMenuItem)
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664 viewport.setRenderGaps(renderGapsMenuItem.getState());
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666 else if (evt.getSource() == annotationPanelMenuItem)
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668 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
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669 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
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671 else if (evt.getSource() == sequenceFeatures)
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673 viewport.showSequenceFeatures(sequenceFeatures.getState());
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674 alignPanel.seqPanel.seqCanvas.repaint();
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676 else if (evt.getSource() == conservationMenuItem)
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678 conservationMenuItem_actionPerformed();
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680 else if (evt.getSource() == abovePIDThreshold)
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682 abovePIDThreshold_actionPerformed();
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684 else if (evt.getSource() == applyToAllGroups)
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686 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
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688 else if (evt.getSource() == autoCalculate)
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690 viewport.autoCalculateConsensus = autoCalculate.getState();
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692 else if (evt.getSource() == sortByTree)
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694 viewport.sortByTree = sortByTree.getState();
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696 else if (evt.getSource() == this.centreColumnLabelFlag)
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698 centreColumnLabelFlag_stateChanged();
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700 else if (evt.getSource() == this.followMouseOverFlag)
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702 mouseOverFlag_stateChanged();
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704 else if (evt.getSource() == showGroupConsensus)
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706 showGroupConsensus_actionPerformed();
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708 else if (evt.getSource() == showGroupConservation)
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710 showGroupConservation_actionPerformed();
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712 else if (evt.getSource() == showSequenceLogo)
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714 showSequenceLogo_actionPerformed();
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716 else if (evt.getSource() == showConsensusHistogram)
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718 showConsensusHistogram_actionPerformed();
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720 else if (evt.getSource() == applyAutoAnnotationSettings)
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722 applyAutoAnnotationSettings_actionPerformed();
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724 alignPanel.paintAlignment(true);
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727 private void mouseOverFlag_stateChanged()
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729 viewport.followHighlight = followMouseOverFlag.getState();
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730 // TODO: could kick the scrollTo mechanism to reset view for current
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734 private void centreColumnLabelFlag_stateChanged()
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736 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
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737 this.alignPanel.annotationPanel.repaint();
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740 public void actionPerformed(ActionEvent evt)
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742 Object source = evt.getSource();
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744 if (source == inputText)
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746 inputText_actionPerformed();
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748 else if (source == loadTree)
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750 loadTree_actionPerformed();
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752 else if (source == loadApplication)
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754 launchFullApplication();
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756 else if (source == loadAnnotations)
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760 else if (source == outputAnnotations)
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762 outputAnnotations(true);
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764 else if (source == outputFeatures)
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766 outputFeatures(true, "Jalview");
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768 else if (source == closeMenuItem)
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770 closeMenuItem_actionPerformed();
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772 else if (source == copy)
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774 copy_actionPerformed();
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776 else if (source == undoMenuItem)
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778 undoMenuItem_actionPerformed();
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780 else if (source == redoMenuItem)
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782 redoMenuItem_actionPerformed();
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784 else if (source == inputText)
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786 inputText_actionPerformed();
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788 else if (source == closeMenuItem)
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790 closeMenuItem_actionPerformed();
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792 else if (source == undoMenuItem)
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794 undoMenuItem_actionPerformed();
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796 else if (source == redoMenuItem)
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798 redoMenuItem_actionPerformed();
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800 else if (source == copy)
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802 copy_actionPerformed();
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804 else if (source == pasteNew)
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806 pasteNew_actionPerformed();
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808 else if (source == pasteThis)
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810 pasteThis_actionPerformed();
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812 else if (source == cut)
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814 cut_actionPerformed();
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816 else if (source == delete)
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818 delete_actionPerformed();
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820 else if (source == grpsFromSelection)
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822 makeGrpsFromSelection_actionPerformed();
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824 else if (source == deleteGroups)
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826 deleteGroups_actionPerformed();
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828 else if (source == selectAllSequenceMenuItem)
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830 selectAllSequenceMenuItem_actionPerformed();
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832 else if (source == deselectAllSequenceMenuItem)
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834 deselectAllSequenceMenuItem_actionPerformed();
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836 else if (source == invertSequenceMenuItem)
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838 invertSequenceMenuItem_actionPerformed();
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840 else if (source == invertColSel)
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842 viewport.invertColumnSelection();
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843 alignPanel.paintAlignment(true);
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845 else if (source == remove2LeftMenuItem)
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847 trimAlignment(true);
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849 else if (source == remove2RightMenuItem)
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851 trimAlignment(false);
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853 else if (source == removeGappedColumnMenuItem)
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855 removeGappedColumnMenuItem_actionPerformed();
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857 else if (source == removeAllGapsMenuItem)
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859 removeAllGapsMenuItem_actionPerformed();
\r
861 else if (source == findMenuItem)
\r
863 findMenuItem_actionPerformed();
\r
865 else if (source == font)
\r
867 new FontChooser(alignPanel);
\r
869 else if (source == newView)
\r
873 else if (source == showColumns)
\r
875 viewport.showAllHiddenColumns();
\r
876 alignPanel.paintAlignment(true);
\r
878 else if (source == showSeqs)
\r
880 viewport.showAllHiddenSeqs();
\r
881 alignPanel.paintAlignment(true);
\r
883 else if (source == hideColumns)
\r
885 viewport.hideSelectedColumns();
\r
886 alignPanel.paintAlignment(true);
\r
888 else if (source == hideSequences
\r
889 && viewport.getSelectionGroup() != null)
\r
891 viewport.hideAllSelectedSeqs();
\r
892 alignPanel.paintAlignment(true);
\r
894 else if (source == hideAllButSelection)
\r
896 toggleHiddenRegions(false, false);
\r
897 alignPanel.paintAlignment(true);
\r
899 else if (source == hideAllSelection)
\r
901 SequenceGroup sg = viewport.getSelectionGroup();
\r
902 viewport.expandColSelection(sg, false);
\r
903 viewport.hideAllSelectedSeqs();
\r
904 viewport.hideSelectedColumns();
\r
905 alignPanel.paintAlignment(true);
\r
907 else if (source == showAllHidden)
\r
909 viewport.showAllHiddenColumns();
\r
910 viewport.showAllHiddenSeqs();
\r
911 alignPanel.paintAlignment(true);
\r
913 else if (source == showGroupConsensus)
\r
915 showGroupConsensus_actionPerformed();
\r
917 else if (source == showGroupConservation)
\r
919 showGroupConservation_actionPerformed();
\r
921 else if (source == showSequenceLogo)
\r
923 showSequenceLogo_actionPerformed();
\r
925 else if (source == showConsensusHistogram)
\r
927 showConsensusHistogram_actionPerformed();
\r
929 else if (source == applyAutoAnnotationSettings)
\r
931 applyAutoAnnotationSettings_actionPerformed();
\r
933 else if (source == featureSettings)
\r
935 new FeatureSettings(alignPanel);
\r
937 else if (source == alProperties)
\r
939 StringBuffer contents = new jalview.io.AlignmentProperties(
\r
940 viewport.getAlignment()).formatAsString();
\r
941 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
942 cap.setText(contents.toString());
\r
943 Frame frame = new Frame();
\r
945 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
\r
946 + getTitle(), 400, 250);
\r
948 else if (source == overviewMenuItem)
\r
950 overviewMenuItem_actionPerformed();
\r
952 else if (source == noColourmenuItem)
\r
954 changeColour(null);
\r
956 else if (source == clustalColour)
\r
958 abovePIDThreshold.setState(false);
\r
959 changeColour(new ClustalxColourScheme(
\r
960 viewport.getAlignment().getSequences(),
\r
961 viewport.getAlignment().getWidth()));
\r
963 else if (source == zappoColour)
\r
965 changeColour(new ZappoColourScheme());
\r
967 else if (source == taylorColour)
\r
969 changeColour(new TaylorColourScheme());
\r
971 else if (source == hydrophobicityColour)
\r
973 changeColour(new HydrophobicColourScheme());
\r
975 else if (source == helixColour)
\r
977 changeColour(new HelixColourScheme());
\r
979 else if (source == strandColour)
\r
981 changeColour(new StrandColourScheme());
\r
983 else if (source == turnColour)
\r
985 changeColour(new TurnColourScheme());
\r
987 else if (source == buriedColour)
\r
989 changeColour(new BuriedColourScheme());
\r
991 else if (source == nucleotideColour)
\r
993 changeColour(new NucleotideColourScheme());
\r
995 else if (source == purinePyrimidineColour)
\r
997 changeColour(new PurinePyrimidineColourScheme());
\r
999 else if (source == RNAHelixColour)
\r
1001 new RNAHelicesColourChooser(viewport, alignPanel);
\r
1003 else if (source == modifyPID)
\r
1005 modifyPID_actionPerformed();
\r
1007 else if (source == modifyConservation)
\r
1009 modifyConservation_actionPerformed();
\r
1011 else if (source == userDefinedColour)
\r
1013 new UserDefinedColours(alignPanel, null);
\r
1015 else if (source == PIDColour)
\r
1017 changeColour(new PIDColourScheme());
\r
1019 else if (source == BLOSUM62Colour)
\r
1021 changeColour(new Blosum62ColourScheme());
\r
1023 else if (source == tcoffeeColour) {
\r
1024 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
\r
1026 else if (source == annotationColour)
\r
1028 new AnnotationColourChooser(viewport, alignPanel);
\r
1030 else if (source == sortPairwiseMenuItem)
\r
1032 sortPairwiseMenuItem_actionPerformed();
\r
1034 else if (source == sortIDMenuItem)
\r
1036 sortIDMenuItem_actionPerformed();
\r
1038 else if (source == sortLengthMenuItem)
\r
1040 sortLengthMenuItem_actionPerformed();
\r
1042 else if (source == sortGroupMenuItem)
\r
1044 sortGroupMenuItem_actionPerformed();
\r
1046 else if (source == removeRedundancyMenuItem)
\r
1048 removeRedundancyMenuItem_actionPerformed();
\r
1050 else if (source == pairwiseAlignmentMenuItem)
\r
1052 pairwiseAlignmentMenuItem_actionPerformed();
\r
1054 else if (source == PCAMenuItem)
\r
1056 PCAMenuItem_actionPerformed();
\r
1058 else if (source == averageDistanceTreeMenuItem)
\r
1060 averageDistanceTreeMenuItem_actionPerformed();
\r
1062 else if (source == neighbourTreeMenuItem)
\r
1064 neighbourTreeMenuItem_actionPerformed();
\r
1066 else if (source == njTreeBlosumMenuItem)
\r
1068 njTreeBlosumMenuItem_actionPerformed();
\r
1070 else if (source == avDistanceTreeBlosumMenuItem)
\r
1072 avTreeBlosumMenuItem_actionPerformed();
\r
1074 else if (source == documentation)
\r
1076 documentation_actionPerformed();
\r
1078 else if (source == about)
\r
1080 about_actionPerformed();
\r
1085 public void inputText_actionPerformed()
\r
1087 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1088 Frame frame = new Frame();
\r
1090 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
\r
1093 protected void outputText_actionPerformed(ActionEvent e)
\r
1095 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1096 Frame frame = new Frame();
\r
1098 jalview.bin.JalviewLite.addFrame(frame,
\r
1099 "Alignment output - " + e.getActionCommand(), 600, 500);
\r
1100 cap.setText(new AppletFormatAdapter().formatSequences(
\r
1101 e.getActionCommand(), viewport.getAlignment(),
\r
1102 viewport.showJVSuffix));
\r
1105 public void loadAnnotations()
\r
1107 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1108 cap.setText("Paste your features / annotations / T-coffee score file here.");
\r
1109 cap.setAnnotationImport();
\r
1110 Frame frame = new Frame();
\r
1112 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
\r
1116 public String outputAnnotations(boolean displayTextbox)
\r
1118 String annotation = new AnnotationFile().printAnnotations(
\r
1119 viewport.showAnnotation ? viewport.getAlignment()
\r
1120 .getAlignmentAnnotation() : null, viewport.getAlignment()
\r
1122 ((Alignment) viewport.getAlignment()).alignmentProperties);
\r
1124 if (displayTextbox)
\r
1126 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
1127 Frame frame = new Frame();
\r
1129 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
\r
1130 cap.setText(annotation);
\r
1133 return annotation;
\r
1136 private Hashtable getDisplayedFeatureCols()
\r
1138 if (alignPanel.getFeatureRenderer() != null && viewport.featuresDisplayed!=null)
\r
1140 FeatureRenderer fr = alignPanel.getFeatureRenderer();
\r
1141 Hashtable fcols = new Hashtable();
\r
1142 Enumeration en = viewport.featuresDisplayed.keys();
\r
1143 while (en.hasMoreElements())
\r
1145 Object col = en.nextElement();
\r
1146 fcols.put(col, fr.featureColours.get(col));
\r
1153 public String outputFeatures(boolean displayTextbox, String format)
\r
1156 if (format.equalsIgnoreCase("Jalview"))
\r
1158 features = new FeaturesFile().printJalviewFormat(
\r
1159 viewport.getAlignment().getSequencesArray(),
\r
1160 getDisplayedFeatureCols());
\r
1164 features = new FeaturesFile().printGFFFormat(
\r
1165 viewport.getAlignment().getSequencesArray(),
\r
1166 getDisplayedFeatureCols());
\r
1169 if (displayTextbox)
\r
1171 boolean frimport=false;
\r
1172 if (features==null || features.equals("No Features Visible"))
\r
1174 features = "# No features visible - paste some and import them here.";
\r
1178 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
\r
1181 cap.setAnnotationImport();
\r
1183 Frame frame = new Frame();
\r
1185 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
\r
1186 cap.setText(features);
\r
1188 if (features==null)
\r
1195 void launchFullApplication()
\r
1197 StringBuffer url = new StringBuffer(jalviewServletURL);
\r
1199 url.append("?open="
\r
1200 + appendProtocol(viewport.applet.getParameter("file")));
\r
1202 if (viewport.applet.getParameter("features") != null)
\r
1204 url.append("&features=");
\r
1205 url.append(appendProtocol(viewport.applet.getParameter("features")));
\r
1208 if (viewport.applet.getParameter("annotations") != null)
\r
1210 url.append("&annotations=");
\r
1211 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
\r
1214 if (viewport.applet.getParameter("jnetfile") != null)
\r
1216 url.append("&annotations=");
\r
1217 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
\r
1220 if (viewport.applet.getParameter("defaultColour") != null)
\r
1222 url.append("&colour="
\r
1223 + removeWhiteSpace(viewport.applet
\r
1224 .getParameter("defaultColour")));
\r
1227 if (viewport.applet.getParameter("userDefinedColour") != null)
\r
1229 url.append("&colour="
\r
1230 + removeWhiteSpace(viewport.applet
\r
1231 .getParameter("userDefinedColour")));
\r
1233 if (viewport.applet.getParameter("tree") != null)
\r
1235 url.append("&tree="
\r
1236 + appendProtocol(viewport.applet.getParameter("tree")));
\r
1238 if (viewport.applet.getParameter("treeFile") != null)
\r
1240 url.append("&tree="
\r
1241 + appendProtocol(viewport.applet.getParameter("treeFile")));
\r
1244 showURL(url.toString(), "FULL_APP");
\r
1247 String removeWhiteSpace(String colour)
\r
1249 StringBuffer sb = new StringBuffer();
\r
1250 for (int i = 0; i < colour.length(); i++)
\r
1252 if (Character.isWhitespace(colour.charAt(i)))
\r
1258 sb.append(colour.charAt(i));
\r
1262 return sb.toString();
\r
1265 String appendProtocol(String url)
\r
1270 url = URLEncoder.encode(url);
\r
1273 * When we finally deprecate 1.1 compatibility, we can start to use
\r
1274 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
\r
1275 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
\r
1276 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
\r
1277 * ex.printStackTrace(); }
\r
1279 catch (java.net.MalformedURLException ex)
\r
1281 url = viewport.applet.getCodeBase() + url;
\r
1286 public void closeMenuItem_actionPerformed()
\r
1288 PaintRefresher.RemoveComponent(alignPanel);
\r
1289 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
\r
1290 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
\r
1292 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
\r
1298 alignPanel = null;
\r
1305 void updateEditMenuBar()
\r
1308 if (viewport.historyList.size() > 0)
\r
1310 undoMenuItem.setEnabled(true);
\r
1311 CommandI command = (CommandI) viewport.historyList.peek();
\r
1312 undoMenuItem.setLabel("Undo " + command.getDescription());
\r
1316 undoMenuItem.setEnabled(false);
\r
1317 undoMenuItem.setLabel("Undo");
\r
1320 if (viewport.redoList.size() > 0)
\r
1322 redoMenuItem.setEnabled(true);
\r
1324 CommandI command = (CommandI) viewport.redoList.peek();
\r
1325 redoMenuItem.setLabel("Redo " + command.getDescription());
\r
1329 redoMenuItem.setEnabled(false);
\r
1330 redoMenuItem.setLabel("Redo");
\r
1337 public void addHistoryItem(CommandI command)
\r
1339 if (command.getSize() > 0)
\r
1341 viewport.historyList.push(command);
\r
1342 viewport.redoList.removeAllElements();
\r
1343 updateEditMenuBar();
\r
1344 viewport.updateHiddenColumns();
\r
1355 protected void undoMenuItem_actionPerformed()
\r
1357 if (viewport.historyList.size() < 1)
\r
1362 CommandI command = (CommandI) viewport.historyList.pop();
\r
1363 viewport.redoList.push(command);
\r
1364 command.undoCommand(null);
\r
1366 AlignViewport originalSource = getOriginatingSource(command);
\r
1368 if (originalSource!=viewport) {
\r
1369 System.err.println("Warning: Viewport object mismatch whilst undoing");
\r
1371 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns = viewport.getColumnSelection().getHiddenColumns() != null;
\r
1372 updateEditMenuBar();
\r
1373 originalSource.firePropertyChange("alignment", null,
\r
1374 originalSource.getAlignment().getSequences());
\r
1384 protected void redoMenuItem_actionPerformed()
\r
1386 if (viewport.redoList.size() < 1)
\r
1391 CommandI command = (CommandI) viewport.redoList.pop();
\r
1392 viewport.historyList.push(command);
\r
1393 command.doCommand(null);
\r
1395 AlignViewport originalSource = getOriginatingSource(command);
\r
1397 if (originalSource!=viewport) {
\r
1398 System.err.println("Warning: Viewport object mismatch whilst re-doing");
\r
1400 originalSource.updateHiddenColumns(); //sethasHiddenColumns(); = viewport.getColumnSelection().getHiddenColumns() != null;
\r
1402 updateEditMenuBar();
\r
1403 originalSource.firePropertyChange("alignment", null,
\r
1404 originalSource.getAlignment().getSequences());
\r
1407 AlignViewport getOriginatingSource(CommandI command)
\r
1409 AlignViewport originalSource = null;
\r
1410 // For sequence removal and addition, we need to fire
\r
1411 // the property change event FROM the viewport where the
\r
1412 // original alignment was altered
\r
1413 AlignmentI al = null;
\r
1414 if (command instanceof EditCommand)
\r
1416 EditCommand editCommand = (EditCommand) command;
\r
1417 al = editCommand.getAlignment();
\r
1418 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
1419 .getSequenceSetId());
\r
1420 for (int i = 0; i < comps.size(); i++)
\r
1422 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
1424 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
\r
1426 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
\r
1433 if (originalSource == null)
\r
1435 // The original view is closed, we must validate
\r
1436 // the current view against the closed view first
\r
1439 PaintRefresher.validateSequences(al, viewport.getAlignment());
\r
1442 originalSource = viewport;
\r
1445 return originalSource;
\r
1448 public void moveSelectedSequences(boolean up)
\r
1450 SequenceGroup sg = viewport.getSelectionGroup();
\r
1458 for (int i = 1; i < viewport.getAlignment().getHeight(); i++)
\r
1460 SequenceI seq = viewport.getAlignment().getSequenceAt(i);
\r
1461 if (!sg.getSequences(null).contains(seq))
\r
1466 SequenceI temp = viewport.getAlignment().getSequenceAt(i - 1);
\r
1467 if (sg.getSequences(null).contains(temp))
\r
1472 viewport.getAlignment().getSequences().setElementAt(temp, i);
\r
1473 viewport.getAlignment().getSequences().setElementAt(seq, i - 1);
\r
1478 for (int i = viewport.getAlignment().getHeight() - 2; i > -1; i--)
\r
1480 SequenceI seq = viewport.getAlignment().getSequenceAt(i);
\r
1481 if (!sg.getSequences(viewport.getHiddenRepSequences()).contains(seq))
\r
1486 SequenceI temp = viewport.getAlignment().getSequenceAt(i + 1);
\r
1487 if (sg.getSequences(viewport.getHiddenRepSequences()).contains(temp))
\r
1492 viewport.getAlignment().getSequences().setElementAt(temp, i);
\r
1493 viewport.getAlignment().getSequences().setElementAt(seq, i + 1);
\r
1497 alignPanel.paintAlignment(true);
\r
1500 synchronized void slideSequences(boolean right, int size)
\r
1502 Vector sg = new Vector();
\r
1503 if (viewport.cursorMode)
\r
1505 sg.addElement(viewport.getAlignment()
\r
1506 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
\r
1508 else if (viewport.getSelectionGroup() != null
\r
1509 && viewport.getSelectionGroup().getSize() != viewport.getAlignment()
\r
1512 sg = viewport.getSelectionGroup().getSequences(
\r
1513 viewport.getHiddenRepSequences());
\r
1516 if (sg.size() < 1)
\r
1521 Vector invertGroup = new Vector();
\r
1523 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
\r
1525 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
\r
1526 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
\r
1529 SequenceI[] seqs1 = new SequenceI[sg.size()];
\r
1530 for (int i = 0; i < sg.size(); i++)
\r
1531 seqs1[i] = (SequenceI) sg.elementAt(i);
\r
1533 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
\r
1534 for (int i = 0; i < invertGroup.size(); i++)
\r
1535 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
\r
1537 SlideSequencesCommand ssc;
\r
1539 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
\r
1540 size, viewport.getGapCharacter());
\r
1542 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
\r
1543 size, viewport.getGapCharacter());
\r
1545 int groupAdjustment = 0;
\r
1546 if (ssc.getGapsInsertedBegin() && right)
\r
1548 if (viewport.cursorMode)
\r
1549 alignPanel.seqPanel.moveCursor(size, 0);
\r
1551 groupAdjustment = size;
\r
1553 else if (!ssc.getGapsInsertedBegin() && !right)
\r
1555 if (viewport.cursorMode)
\r
1556 alignPanel.seqPanel.moveCursor(-size, 0);
\r
1558 groupAdjustment = -size;
\r
1561 if (groupAdjustment != 0)
\r
1563 viewport.getSelectionGroup().setStartRes(
\r
1564 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
\r
1565 viewport.getSelectionGroup().setEndRes(
\r
1566 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
\r
1569 boolean appendHistoryItem = false;
\r
1570 if (viewport.historyList != null && viewport.historyList.size() > 0
\r
1571 && viewport.historyList.peek() instanceof SlideSequencesCommand)
\r
1573 appendHistoryItem = ssc
\r
1574 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
\r
1578 if (!appendHistoryItem)
\r
1579 addHistoryItem(ssc);
\r
1584 static StringBuffer copiedSequences;
\r
1586 static Vector copiedHiddenColumns;
\r
1588 protected void copy_actionPerformed()
\r
1590 if (viewport.getSelectionGroup() == null)
\r
1595 SequenceGroup sg = viewport.getSelectionGroup();
\r
1596 copiedSequences = new StringBuffer();
\r
1597 Hashtable orderedSeqs = new Hashtable();
\r
1598 for (int i = 0; i < sg.getSize(); i++)
\r
1600 SequenceI seq = sg.getSequenceAt(i);
\r
1601 int index = viewport.getAlignment().findIndex(seq);
\r
1602 orderedSeqs.put(index + "", seq);
\r
1605 int index = 0, startRes, endRes;
\r
1608 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
\r
1610 copiedHiddenColumns = new Vector();
\r
1611 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
\r
1612 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
\r
1615 int[] region = (int[]) viewport.getColumnSelection()
\r
1616 .getHiddenColumns().elementAt(i);
\r
1618 copiedHiddenColumns.addElement(new int[]
\r
1619 { region[0] - hiddenOffset, region[1] - hiddenOffset });
\r
1624 copiedHiddenColumns = null;
\r
1627 for (int i = 0; i < sg.getSize(); i++)
\r
1629 SequenceI seq = null;
\r
1631 while (seq == null)
\r
1633 if (orderedSeqs.containsKey(index + ""))
\r
1635 seq = (SequenceI) orderedSeqs.get(index + "");
\r
1647 // Returns residue following index if gap
\r
1648 startRes = seq.findPosition(sg.getStartRes());
\r
1651 // Need to find the residue preceeding index if gap
\r
1654 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
\r
1656 ch = seq.getCharAt(j);
\r
1657 if (!jalview.util.Comparison.isGap((ch)))
\r
1665 endRes += seq.getStart() - 1;
\r
1668 copiedSequences.append(seq.getName()
\r
1674 + seq.getSequenceAsString(sg.getStartRes(),
\r
1675 sg.getEndRes() + 1) + "\n");
\r
1680 protected void pasteNew_actionPerformed()
\r
1685 protected void pasteThis_actionPerformed()
\r
1690 void paste(boolean newAlignment)
\r
1695 if (copiedSequences == null)
\r
1700 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
1701 Vector seqs = new Vector();
\r
1702 while (st.hasMoreElements())
\r
1704 String name = st.nextToken();
\r
1705 int start = Integer.parseInt(st.nextToken());
\r
1706 int end = Integer.parseInt(st.nextToken());
\r
1707 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
\r
1709 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
1710 for (int i = 0; i < seqs.size(); i++)
\r
1712 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
1717 String newtitle = new String("Copied sequences");
\r
1718 if (getTitle().startsWith("Copied sequences"))
\r
1720 newtitle = getTitle();
\r
1724 newtitle = newtitle.concat("- from " + getTitle());
\r
1726 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
1727 viewport.applet, newtitle, false);
\r
1728 if (copiedHiddenColumns != null)
\r
1730 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
1732 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
1733 af.viewport.hideColumns(region[0], region[1]);
\r
1737 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
\r
1742 addSequences(newSeqs);
\r
1745 } catch (Exception ex)
\r
1747 } // could be anything being pasted in here
\r
1751 void addSequences(SequenceI[] seqs)
\r
1753 for (int i = 0; i < seqs.length; i++)
\r
1755 viewport.getAlignment().addSequence(seqs[i]);
\r
1759 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
\r
1760 seqs, 0, viewport.getAlignment().getWidth(), viewport.getAlignment()));
\r
1762 viewport.setEndSeq(viewport.getAlignment().getHeight());
\r
1763 viewport.getAlignment().getWidth();
\r
1764 viewport.firePropertyChange("alignment", null,
\r
1765 viewport.getAlignment().getSequences());
\r
1769 protected void cut_actionPerformed()
\r
1771 copy_actionPerformed();
\r
1772 delete_actionPerformed();
\r
1775 protected void delete_actionPerformed()
\r
1778 SequenceGroup sg = viewport.getSelectionGroup();
\r
1784 Vector seqs = new Vector();
\r
1786 for (int i = 0; i < sg.getSize(); i++)
\r
1788 seq = sg.getSequenceAt(i);
\r
1789 seqs.addElement(seq);
\r
1792 // If the cut affects all sequences, remove highlighted columns
\r
1793 if (sg.getSize() == viewport.getAlignment().getHeight())
\r
1795 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
1796 sg.getEndRes() + 1);
\r
1799 SequenceI[] cut = new SequenceI[seqs.size()];
\r
1800 for (int i = 0; i < seqs.size(); i++)
\r
1802 cut[i] = (SequenceI) seqs.elementAt(i);
\r
1806 * //ADD HISTORY ITEM
\r
1808 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
\r
1809 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
\r
1810 viewport.getAlignment()));
\r
1812 viewport.setSelectionGroup(null);
\r
1813 viewport.getAlignment().deleteGroup(sg);
\r
1815 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1818 if (viewport.getAlignment().getHeight() < 1)
\r
1820 this.setVisible(false);
\r
1822 viewport.sendSelection();
\r
1826 * group consensus toggled
\r
1829 protected void showGroupConsensus_actionPerformed()
\r
1831 viewport.setShowGroupConsensus(showGroupConsensus.getState());
\r
1832 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1837 * group conservation toggled.
\r
1839 protected void showGroupConservation_actionPerformed()
\r
1841 viewport.setShowGroupConservation(showGroupConservation.getState());
\r
1842 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1849 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
\r
1850 * .event.ActionEvent)
\r
1852 protected void showConsensusHistogram_actionPerformed()
\r
1854 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
\r
1855 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1861 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
\r
1862 * .event.ActionEvent)
\r
1864 protected void showSequenceLogo_actionPerformed()
\r
1866 viewport.setShowSequenceLogo(showSequenceLogo.getState());
\r
1867 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1870 protected void applyAutoAnnotationSettings_actionPerformed()
\r
1872 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1875 protected void makeGrpsFromSelection_actionPerformed()
\r
1877 if (viewport.getSelectionGroup() != null)
\r
1879 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
\r
1880 viewport.getSequenceSelection(),
\r
1881 viewport.getAlignmentView(true).getSequenceStrings(
\r
1882 viewport.getGapCharacter()),
\r
1883 viewport.getAlignment().getGroups());
\r
1884 viewport.getAlignment().deleteAllGroups();
\r
1885 viewport.sequenceColours = null;
\r
1886 viewport.setSelectionGroup(null);
\r
1887 // set view properties for each group
\r
1888 for (int g = 0; g < gps.length; g++)
\r
1890 // gps[g].setShowunconserved(viewport.getShowUnconserved());
\r
1891 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
\r
1892 viewport.getAlignment().addGroup(gps[g]);
\r
1893 Color col = new Color((int) (Math.random() * 255),
\r
1894 (int) (Math.random() * 255), (int) (Math.random() * 255));
\r
1895 col = col.brighter();
\r
1896 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
\r
1897 .hasMoreElements(); viewport.setSequenceColour(
\r
1898 (SequenceI) sq.nextElement(), col))
\r
1901 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
\r
1902 alignPanel.updateAnnotation();
\r
1903 alignPanel.paintAlignment(true);
\r
1907 protected void deleteGroups_actionPerformed()
\r
1909 viewport.getAlignment().deleteAllGroups();
\r
1910 viewport.sequenceColours = null;
\r
1911 viewport.setSelectionGroup(null);
\r
1913 alignPanel.paintAlignment(true);
\r
1916 public void selectAllSequenceMenuItem_actionPerformed()
\r
1918 SequenceGroup sg = new SequenceGroup();
\r
1919 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1921 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
1923 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
\r
1924 viewport.setSelectionGroup(sg);
\r
1925 alignPanel.paintAlignment(true);
\r
1926 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1927 viewport.sendSelection();
\r
1930 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1932 if (viewport.cursorMode)
\r
1934 alignPanel.seqPanel.keyboardNo1 = null;
\r
1935 alignPanel.seqPanel.keyboardNo2 = null;
\r
1937 viewport.setSelectionGroup(null);
\r
1938 viewport.getColumnSelection().clear();
\r
1939 viewport.setSelectionGroup(null);
\r
1940 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1941 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1942 alignPanel.paintAlignment(true);
\r
1943 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1944 viewport.sendSelection();
\r
1947 public void invertSequenceMenuItem_actionPerformed()
\r
1949 SequenceGroup sg = viewport.getSelectionGroup();
\r
1950 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1952 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1955 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1956 viewport.sendSelection();
\r
1959 public void invertColSel_actionPerformed()
\r
1961 viewport.invertColumnSelection();
\r
1962 alignPanel.paintAlignment(true);
\r
1963 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1964 viewport.sendSelection();
\r
1967 void trimAlignment(boolean trimLeft)
\r
1969 ColumnSelection colSel = viewport.getColumnSelection();
\r
1972 if (colSel.size() > 0)
\r
1976 column = colSel.getMin();
\r
1980 column = colSel.getMax();
\r
1984 if (viewport.getSelectionGroup() != null)
\r
1986 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
1987 viewport.getHiddenRepSequences());
\r
1991 seqs = viewport.getAlignment().getSequencesArray();
\r
1994 TrimRegionCommand trimRegion;
\r
1997 trimRegion = new TrimRegionCommand("Remove Left",
\r
1998 TrimRegionCommand.TRIM_LEFT, seqs, column,
\r
1999 viewport.getAlignment(), viewport.getColumnSelection(),
\r
2000 viewport.getSelectionGroup());
\r
2001 viewport.setStartRes(0);
\r
2005 trimRegion = new TrimRegionCommand("Remove Right",
\r
2006 TrimRegionCommand.TRIM_RIGHT, seqs, column,
\r
2007 viewport.getAlignment(), viewport.getColumnSelection(),
\r
2008 viewport.getSelectionGroup());
\r
2011 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
\r
2013 addHistoryItem(trimRegion);
\r
2015 Vector groups = viewport.getAlignment().getGroups();
\r
2017 for (int i = 0; i < groups.size(); i++)
\r
2019 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
2021 if ((trimLeft && !sg.adjustForRemoveLeft(column))
\r
2022 || (!trimLeft && !sg.adjustForRemoveRight(column)))
\r
2024 viewport.getAlignment().deleteGroup(sg);
\r
2028 viewport.firePropertyChange("alignment", null, viewport
\r
2029 .getAlignment().getSequences());
\r
2033 public void removeGappedColumnMenuItem_actionPerformed()
\r
2035 int start = 0, end = viewport.getAlignment().getWidth() - 1;
\r
2038 if (viewport.getSelectionGroup() != null)
\r
2040 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2041 viewport.getHiddenRepSequences());
\r
2042 start = viewport.getSelectionGroup().getStartRes();
\r
2043 end = viewport.getSelectionGroup().getEndRes();
\r
2047 seqs = viewport.getAlignment().getSequencesArray();
\r
2050 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
\r
2051 "Remove Gapped Columns", seqs, start, end, viewport.getAlignment());
\r
2053 addHistoryItem(removeGapCols);
\r
2055 statusBar.setText("Removed " + removeGapCols.getSize()
\r
2056 + " empty columns.");
\r
2058 // This is to maintain viewport position on first residue
\r
2059 // of first sequence
\r
2060 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
\r
2061 int startRes = seq.findPosition(viewport.startRes);
\r
2062 // ShiftList shifts;
\r
2063 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
\r
2064 // edit.alColumnChanges=shifts.getInverse();
\r
2065 // if (viewport.hasHiddenColumns)
\r
2066 // viewport.getColumnSelection().compensateForEdits(shifts);
\r
2067 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
2068 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
2073 public void removeAllGapsMenuItem_actionPerformed()
\r
2075 int start = 0, end = viewport.getAlignment().getWidth() - 1;
\r
2078 if (viewport.getSelectionGroup() != null)
\r
2080 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2081 viewport.getHiddenRepSequences());
\r
2082 start = viewport.getSelectionGroup().getStartRes();
\r
2083 end = viewport.getSelectionGroup().getEndRes();
\r
2087 seqs = viewport.getAlignment().getSequencesArray();
\r
2090 // This is to maintain viewport position on first residue
\r
2091 // of first sequence
\r
2092 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
\r
2093 int startRes = seq.findPosition(viewport.startRes);
\r
2095 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
\r
2096 viewport.getAlignment()));
\r
2098 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
2100 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
2105 public void findMenuItem_actionPerformed()
\r
2107 new Finder(alignPanel);
\r
2111 * create a new view derived from the current view
\r
2113 * @param viewtitle
\r
2114 * @return frame for the new view
\r
2116 public AlignFrame newView(String viewtitle)
\r
2119 if (viewport.hasHiddenRows())
\r
2121 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
\r
2122 .getFullAlignment().getSequencesArray());
\r
2126 newal = new Alignment(viewport.getAlignment().getSequencesArray());
\r
2129 if (viewport.getAlignment().getAlignmentAnnotation() != null)
\r
2131 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
\r
2133 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
\r
2135 newal.addAnnotation(viewport.getAlignment().getAlignmentAnnotation()[i]);
\r
2140 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
\r
2142 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
\r
2143 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
\r
2144 PaintRefresher.Register(newaf.alignPanel,
\r
2145 newaf.alignPanel.av.getSequenceSetId());
\r
2147 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
\r
2148 newaf.alignPanel.av.getSequenceSetId());
\r
2149 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
\r
2150 newaf.alignPanel.av.getSequenceSetId());
\r
2152 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
2153 .getSequenceSetId());
\r
2154 int viewSize = -1;
\r
2155 for (int i = 0; i < comps.size(); i++)
\r
2157 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
2163 String title = new String(this.getTitle());
\r
2164 if (viewtitle != null)
\r
2166 title = viewtitle + " ( " + title + ")";
\r
2170 if (title.indexOf("(View") > -1)
\r
2172 title = title.substring(0, title.indexOf("(View"));
\r
2174 title += "(View " + viewSize + ")";
\r
2177 newaf.setTitle(title.toString());
\r
2179 newaf.viewport.historyList = viewport.historyList;
\r
2180 newaf.viewport.redoList = viewport.redoList;
\r
2186 * @return list of feature groups on the view
\r
2188 public String[] getFeatureGroups()
\r
2190 FeatureRenderer fr = null;
\r
2191 if (alignPanel != null
\r
2192 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2194 return fr.getGroups();
\r
2200 * get sequence feature groups that are hidden or shown
\r
2206 public String[] getFeatureGroupsOfState(boolean visible)
\r
2208 FeatureRenderer fr = null;
\r
2209 if (alignPanel != null
\r
2210 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2212 return fr.getGroups(visible);
\r
2218 * Change the display state for the given feature groups
\r
2221 * list of group strings
\r
2223 * visible or invisible
\r
2225 public void setFeatureGroupState(String[] groups, boolean state)
\r
2227 FeatureRenderer fr = null;
\r
2228 this.sequenceFeatures.setState(true);
\r
2229 viewport.showSequenceFeatures(true);
\r
2230 if (alignPanel != null
\r
2231 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2233 fr.setGroupState(groups, state);
\r
2234 alignPanel.seqPanel.seqCanvas.repaint();
\r
2235 if (alignPanel.overviewPanel != null)
\r
2237 alignPanel.overviewPanel.updateOverviewImage();
\r
2242 public void seqLimits_itemStateChanged()
\r
2244 viewport.setShowJVSuffix(seqLimits.getState());
\r
2245 alignPanel.fontChanged();
\r
2246 alignPanel.paintAlignment(true);
\r
2249 protected void colourTextMenuItem_actionPerformed()
\r
2251 viewport.setColourText(colourTextMenuItem.getState());
\r
2252 alignPanel.paintAlignment(true);
\r
2255 protected void displayNonconservedMenuItem_actionPerformed()
\r
2257 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
\r
2258 alignPanel.paintAlignment(true);
\r
2261 protected void wrapMenuItem_actionPerformed()
\r
2263 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
2264 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
2265 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
2266 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
2267 scaleRight.setEnabled(wrapMenuItem.getState());
\r
2268 alignPanel.paintAlignment(true);
\r
2271 public void overviewMenuItem_actionPerformed()
\r
2273 if (alignPanel.overviewPanel != null)
\r
2278 Frame frame = new Frame();
\r
2279 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
2280 frame.add(overview);
\r
2281 // +50 must allow for applet frame window
\r
2282 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
2283 overview.getPreferredSize().width,
\r
2284 overview.getPreferredSize().height + 50);
\r
2287 final AlignmentPanel ap=alignPanel;
\r
2288 frame.addWindowListener(new WindowAdapter()
\r
2290 public void windowClosing(WindowEvent e)
\r
2293 ap.setOverviewPanel(null);
\r
2298 alignPanel.setOverviewPanel(overview);
\r
2302 void changeColour(ColourSchemeI cs)
\r
2304 int threshold = 0;
\r
2308 if (viewport.getAbovePIDThreshold())
\r
2310 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
2313 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2315 viewport.setGlobalColourScheme(cs);
\r
2319 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2322 if (viewport.getConservationSelected())
\r
2325 Alignment al = (Alignment) viewport.getAlignment();
\r
2326 Conservation c = new Conservation("All",
\r
2327 ResidueProperties.propHash, 3, al.getSequences(), 0,
\r
2328 al.getWidth() - 1);
\r
2331 c.verdict(false, viewport.getConsPercGaps());
\r
2333 cs.setConservation(c);
\r
2335 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
\r
2336 cs, "Background"));
\r
2341 cs.setConservation(null);
\r
2344 cs.setConsensus(viewport.getSequenceConsensusHash());
\r
2347 viewport.setGlobalColourScheme(cs);
\r
2349 if (viewport.getColourAppliesToAllGroups())
\r
2351 Vector groups = viewport.getAlignment().getGroups();
\r
2352 for (int i = 0; i < groups.size(); i++)
\r
2354 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
2361 if (cs instanceof ClustalxColourScheme)
\r
2363 sg.cs = new ClustalxColourScheme(
\r
2364 sg.getSequences(viewport.getHiddenRepSequences()),
\r
2371 sg.cs = cs.getClass().newInstance();
\r
2372 } catch (Exception ex)
\r
2374 ex.printStackTrace();
\r
2379 if (viewport.getAbovePIDThreshold()
\r
2380 || cs instanceof PIDColourScheme
\r
2381 || cs instanceof Blosum62ColourScheme)
\r
2383 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2384 sg.cs.setConsensus(AAFrequency.calculate(
\r
2385 sg.getSequences(viewport.getHiddenRepSequences()), 0,
\r
2390 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2393 if (viewport.getConservationSelected())
\r
2395 Conservation c = new Conservation("Group",
\r
2396 ResidueProperties.propHash, 3,
\r
2397 sg.getSequences(viewport.getHiddenRepSequences()), 0,
\r
2398 viewport.getAlignment().getWidth() - 1);
\r
2400 c.verdict(false, viewport.getConsPercGaps());
\r
2401 sg.cs.setConservation(c);
\r
2405 sg.cs.setConservation(null);
\r
2406 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2412 if (alignPanel.getOverviewPanel() != null)
\r
2414 alignPanel.getOverviewPanel().updateOverviewImage();
\r
2417 jalview.structure.StructureSelectionManager
\r
2418 .getStructureSelectionManager(viewport.applet).sequenceColoursChanged(
\r
2421 alignPanel.paintAlignment(true);
\r
2424 protected void modifyPID_actionPerformed()
\r
2426 if (viewport.getAbovePIDThreshold()
\r
2427 && viewport.getGlobalColourScheme() != null)
\r
2429 SliderPanel.setPIDSliderSource(alignPanel,
\r
2430 viewport.getGlobalColourScheme(), "Background");
\r
2431 SliderPanel.showPIDSlider();
\r
2435 protected void modifyConservation_actionPerformed()
\r
2437 if (viewport.getConservationSelected()
\r
2438 && viewport.getGlobalColourScheme() != null)
\r
2440 SliderPanel.setConservationSlider(alignPanel,
\r
2441 viewport.getGlobalColourScheme(), "Background");
\r
2442 SliderPanel.showConservationSlider();
\r
2446 protected void conservationMenuItem_actionPerformed()
\r
2448 viewport.setConservationSelected(conservationMenuItem.getState());
\r
2450 viewport.setAbovePIDThreshold(false);
\r
2451 abovePIDThreshold.setState(false);
\r
2453 changeColour(viewport.getGlobalColourScheme());
\r
2455 modifyConservation_actionPerformed();
\r
2458 public void abovePIDThreshold_actionPerformed()
\r
2460 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
2462 conservationMenuItem.setState(false);
\r
2463 viewport.setConservationSelected(false);
\r
2465 changeColour(viewport.getGlobalColourScheme());
\r
2467 modifyPID_actionPerformed();
\r
2470 public void sortPairwiseMenuItem_actionPerformed()
\r
2472 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2473 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
\r
2474 .getAlignment().getSequenceAt(0), null);
\r
2476 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
\r
2477 viewport.getAlignment()));
\r
2478 alignPanel.paintAlignment(true);
\r
2481 public void sortIDMenuItem_actionPerformed()
\r
2483 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2484 AlignmentSorter.sortByID(viewport.getAlignment());
\r
2485 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
\r
2486 alignPanel.paintAlignment(true);
\r
2489 public void sortLengthMenuItem_actionPerformed()
\r
2491 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2492 AlignmentSorter.sortByLength(viewport.getAlignment());
\r
2493 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
\r
2494 viewport.getAlignment()));
\r
2495 alignPanel.paintAlignment(true);
\r
2498 public void sortGroupMenuItem_actionPerformed()
\r
2500 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2501 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
2502 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
\r
2503 viewport.getAlignment()));
\r
2504 alignPanel.paintAlignment(true);
\r
2508 public void removeRedundancyMenuItem_actionPerformed()
\r
2510 new RedundancyPanel(alignPanel);
\r
2513 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
2515 if (viewport.getSelectionGroup() != null
\r
2516 && viewport.getSelectionGroup().getSize() > 1)
\r
2518 Frame frame = new Frame();
\r
2519 frame.add(new PairwiseAlignPanel(alignPanel));
\r
2520 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
\r
2525 public void PCAMenuItem_actionPerformed()
\r
2527 // are the sequences aligned?
\r
2528 if (!viewport.getAlignment().isAligned(false))
\r
2530 SequenceI current;
\r
2531 int Width = viewport.getAlignment().getWidth();
\r
2533 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2535 current = viewport.getAlignment().getSequenceAt(i);
\r
2537 if (current.getLength() < Width)
\r
2539 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2542 alignPanel.paintAlignment(true);
\r
2545 if ((viewport.getSelectionGroup() != null
\r
2546 && viewport.getSelectionGroup().getSize() < 4 && viewport
\r
2547 .getSelectionGroup().getSize() > 0)
\r
2548 || viewport.getAlignment().getHeight() < 4)
\r
2555 new PCAPanel(viewport);
\r
2556 } catch (java.lang.OutOfMemoryError ex)
\r
2562 public void averageDistanceTreeMenuItem_actionPerformed()
\r
2564 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
2567 public void neighbourTreeMenuItem_actionPerformed()
\r
2569 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
2572 protected void njTreeBlosumMenuItem_actionPerformed()
\r
2574 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2577 protected void avTreeBlosumMenuItem_actionPerformed()
\r
2579 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2582 void NewTreePanel(String type, String pwType, String title)
\r
2584 // are the sequences aligned?
\r
2585 if (!viewport.getAlignment().isAligned(false))
\r
2587 SequenceI current;
\r
2588 int Width = viewport.getAlignment().getWidth();
\r
2590 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2592 current = viewport.getAlignment().getSequenceAt(i);
\r
2594 if (current.getLength() < Width)
\r
2596 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2599 alignPanel.paintAlignment(true);
\r
2603 if ((viewport.getSelectionGroup() != null && viewport
\r
2604 .getSelectionGroup().getSize() > 1)
\r
2605 || (viewport.getSelectionGroup() == null && viewport.getAlignment()
\r
2606 .getHeight() > 1))
\r
2608 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
\r
2610 addTreeMenuItem(tp, title);
\r
2612 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
2616 void loadTree_actionPerformed()
\r
2618 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
2619 cap.setText("Paste your Newick tree file here.");
\r
2620 cap.setTreeImport();
\r
2621 Frame frame = new Frame();
\r
2623 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
2626 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
2628 TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
\r
2629 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
2630 addTreeMenuItem(tp, treeFile);
\r
2634 * sort the alignment using the given treePanel
\r
2636 * @param treePanel
\r
2637 * tree used to sort view
\r
2639 * string used for undo event name
\r
2641 public void sortByTree(TreePanel treePanel, String title)
\r
2643 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2645 .sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
2646 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2647 // HistoryItem.SORT));
\r
2648 addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
\r
2649 viewport.getAlignment()));
\r
2650 alignPanel.paintAlignment(true);
\r
2654 * Do any automatic reordering of the alignment and add the necessary bits to
\r
2655 * the menu structure for the new tree
\r
2657 * @param treePanel
\r
2660 protected void addTreeMenuItem(final TreePanel treePanel,
\r
2661 final String title)
\r
2663 final MenuItem item = new MenuItem(title);
\r
2664 sortByTreeMenu.add(item);
\r
2665 item.addActionListener(new java.awt.event.ActionListener()
\r
2667 public void actionPerformed(ActionEvent evt)
\r
2669 sortByTree(treePanel, title); // treePanel.getTitle());
\r
2673 treePanel.addWindowListener(new WindowAdapter()
\r
2675 public void windowOpened(WindowEvent e)
\r
2677 if (viewport.sortByTree)
\r
2679 sortByTree(treePanel, title);
\r
2681 super.windowOpened(e);
\r
2684 public void windowClosing(WindowEvent e)
\r
2686 sortByTreeMenu.remove(item);
\r
2690 public boolean sortBy(AlignmentOrder alorder, String undoname)
\r
2692 SequenceI[] oldOrder = viewport.getAlignment()
\r
2693 .getSequencesArray();
\r
2694 if (viewport.applet.debug)
\r
2696 System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");
\r
2698 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
\r
2699 if (undoname!=null)
\r
2701 addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.getAlignment()));
\r
2703 alignPanel.paintAlignment(true);
\r
2707 protected void documentation_actionPerformed()
\r
2709 alignPanel.av.applet.openJalviewHelpUrl();
\r
2712 protected void about_actionPerformed()
\r
2715 class AboutPanel extends Canvas
\r
2721 public AboutPanel(String version, String builddate)
\r
2723 this.version = version;
\r
2724 this.builddate = builddate;
\r
2727 public void paint(Graphics g)
\r
2729 g.setColor(Color.white);
\r
2730 g.fillRect(0, 0, getSize().width, getSize().height);
\r
2731 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2732 FontMetrics fm = g.getFontMetrics();
\r
2733 int fh = fm.getHeight();
\r
2735 g.setColor(Color.black);
\r
2736 // TODO: update this text for each release or centrally store it for
\r
2737 // lite and application
\r
2738 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
2739 g.drawString("JalviewLite - Release " + version, x, y += fh);
\r
2740 g.setFont(new Font("Helvetica", Font.BOLD, 12));
\r
2741 g.drawString("Build date: " + builddate, x, y += fh);
\r
2742 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2744 "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",
\r
2745 x, y += fh * 1.5);
\r
2746 g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
\r
2748 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
\r
2751 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
\r
2753 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
\r
2755 "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
\r
2758 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
\r
2760 g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
\r
2765 Frame frame = new Frame();
\r
2766 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
\r
2767 .getBuildDate()));
\r
2768 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
\r
2772 public void showURL(String url, String target)
\r
2774 if (viewport.applet == null)
\r
2776 System.out.println("Not running as applet - no browser available.");
\r
2780 viewport.applet.showURL(url, target);
\r
2784 // ////////////////////////////////////////////////////////////////////////////////
\r
2785 // JBuilder Graphics here
\r
2787 MenuBar alignFrameMenuBar = new MenuBar();
\r
2789 Menu fileMenu = new Menu("File");
\r
2791 MenuItem loadApplication = new MenuItem("View in Full Application");
\r
2793 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
\r
2795 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
\r
2797 MenuItem outputFeatures = new MenuItem("Export Features ...");
\r
2799 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
\r
2801 MenuItem closeMenuItem = new MenuItem("Close");
\r
2803 Menu editMenu = new Menu("Edit");
\r
2805 Menu viewMenu = new Menu("View");
\r
2807 Menu colourMenu = new Menu("Colour");
\r
2809 Menu calculateMenu = new Menu("Calculate");
\r
2811 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
2813 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
2815 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
2817 MenuItem remove2LeftMenuItem = new MenuItem();
\r
2819 MenuItem remove2RightMenuItem = new MenuItem();
\r
2821 MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
2823 MenuItem removeAllGapsMenuItem = new MenuItem();
\r
2825 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
2827 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
2829 MenuItem sortPairwiseMenuItem = new MenuItem();
\r
2831 MenuItem sortIDMenuItem = new MenuItem();
\r
2833 MenuItem sortLengthMenuItem = new MenuItem();
\r
2835 MenuItem sortGroupMenuItem = new MenuItem();
\r
2837 MenuItem removeRedundancyMenuItem = new MenuItem();
\r
2839 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
2841 MenuItem PCAMenuItem = new MenuItem();
\r
2843 MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
2845 MenuItem neighbourTreeMenuItem = new MenuItem();
\r
2847 BorderLayout borderLayout1 = new BorderLayout();
\r
2849 public Label statusBar = new Label();
\r
2851 Menu outputTextboxMenu = new Menu();
\r
2853 MenuItem clustalColour = new MenuItem();
\r
2855 MenuItem zappoColour = new MenuItem();
\r
2857 MenuItem taylorColour = new MenuItem();
\r
2859 MenuItem hydrophobicityColour = new MenuItem();
\r
2861 MenuItem helixColour = new MenuItem();
\r
2863 MenuItem strandColour = new MenuItem();
\r
2865 MenuItem turnColour = new MenuItem();
\r
2867 MenuItem buriedColour = new MenuItem();
\r
2869 MenuItem purinePyrimidineColour = new MenuItem();
\r
2870 MenuItem RNAHelixColour = new MenuItem();
\r
2872 MenuItem userDefinedColour = new MenuItem();
\r
2874 MenuItem PIDColour = new MenuItem();
\r
2876 MenuItem BLOSUM62Colour = new MenuItem();
\r
2878 MenuItem tcoffeeColour = new MenuItem();
\r
2880 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
2882 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
2884 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
2886 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
2888 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
\r
2890 MenuItem alProperties = new MenuItem("Alignment Properties...");
\r
2892 MenuItem overviewMenuItem = new MenuItem();
\r
2894 MenuItem undoMenuItem = new MenuItem();
\r
2896 MenuItem redoMenuItem = new MenuItem();
\r
2898 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
2900 MenuItem noColourmenuItem = new MenuItem();
\r
2902 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
2904 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
2906 MenuItem findMenuItem = new MenuItem();
\r
2908 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
2910 MenuItem nucleotideColour = new MenuItem();
\r
2912 MenuItem deleteGroups = new MenuItem();
\r
2914 MenuItem grpsFromSelection = new MenuItem();
\r
2916 MenuItem delete = new MenuItem();
\r
2918 MenuItem copy = new MenuItem();
\r
2920 MenuItem cut = new MenuItem();
\r
2922 Menu pasteMenu = new Menu();
\r
2924 MenuItem pasteNew = new MenuItem();
\r
2926 MenuItem pasteThis = new MenuItem();
\r
2928 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
2930 MenuItem font = new MenuItem();
\r
2932 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
2934 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
2936 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
2938 MenuItem modifyPID = new MenuItem();
\r
2940 MenuItem modifyConservation = new MenuItem();
\r
2942 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
\r
2943 "Autocalculate Consensus", true);
\r
2945 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
\r
2946 "Sort Alignment With New Tree", true);
\r
2948 Menu sortByTreeMenu = new Menu();
\r
2950 Menu sort = new Menu();
\r
2952 Menu calculate = new Menu();
\r
2954 MenuItem inputText = new MenuItem();
\r
2956 Menu helpMenu = new Menu();
\r
2958 MenuItem documentation = new MenuItem();
\r
2960 MenuItem about = new MenuItem();
\r
2962 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
2964 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
\r
2966 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
\r
2967 Menu autoAnnMenu=new Menu();
\r
2968 CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();
\r
2969 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
\r
2970 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
\r
2971 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
\r
2972 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
\r
2974 private void jbInit() throws Exception
\r
2977 setMenuBar(alignFrameMenuBar);
\r
2981 // dynamically fill save as menu with available formats
\r
2982 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
2985 item = new MenuItem(
\r
2986 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
2988 item.addActionListener(new java.awt.event.ActionListener()
\r
2990 public void actionPerformed(ActionEvent e)
\r
2992 outputText_actionPerformed(e);
\r
2996 outputTextboxMenu.add(item);
\r
2998 closeMenuItem.addActionListener(this);
\r
2999 loadApplication.addActionListener(this);
\r
3001 loadTree.addActionListener(this);
\r
3002 loadAnnotations.addActionListener(this);
\r
3003 outputFeatures.addActionListener(this);
\r
3004 outputAnnotations.addActionListener(this);
\r
3005 selectAllSequenceMenuItem.addActionListener(this);
\r
3006 deselectAllSequenceMenuItem.addActionListener(this);
\r
3007 invertSequenceMenuItem.addActionListener(this);
\r
3008 remove2LeftMenuItem.setLabel("Remove Left");
\r
3009 remove2LeftMenuItem.addActionListener(this);
\r
3010 remove2RightMenuItem.setLabel("Remove Right");
\r
3011 remove2RightMenuItem.addActionListener(this);
\r
3012 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
3013 removeGappedColumnMenuItem.addActionListener(this);
\r
3014 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
3015 removeAllGapsMenuItem.addActionListener(this);
\r
3016 viewBoxesMenuItem.setLabel("Boxes");
\r
3017 viewBoxesMenuItem.setState(true);
\r
3018 viewBoxesMenuItem.addItemListener(this);
\r
3019 viewTextMenuItem.setLabel("Text");
\r
3020 viewTextMenuItem.setState(true);
\r
3021 viewTextMenuItem.addItemListener(this);
\r
3022 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
3023 sortPairwiseMenuItem.addActionListener(this);
\r
3024 sortIDMenuItem.setLabel("by ID");
\r
3025 sortIDMenuItem.addActionListener(this);
\r
3026 sortLengthMenuItem.setLabel("by Length");
\r
3027 sortLengthMenuItem.addActionListener(this);
\r
3028 sortGroupMenuItem.setLabel("by Group");
\r
3029 sortGroupMenuItem.addActionListener(this);
\r
3030 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
3031 removeRedundancyMenuItem.addActionListener(this);
\r
3032 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
3033 pairwiseAlignmentMenuItem.addActionListener(this);
\r
3034 PCAMenuItem.setLabel("Principal Component Analysis");
\r
3035 PCAMenuItem.addActionListener(this);
\r
3036 averageDistanceTreeMenuItem
\r
3037 .setLabel("Average Distance Using % Identity");
\r
3038 averageDistanceTreeMenuItem.addActionListener(this);
\r
3039 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
3040 neighbourTreeMenuItem.addActionListener(this);
\r
3041 statusBar.setBackground(Color.white);
\r
3042 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
3043 statusBar.setText("Status bar");
\r
3044 outputTextboxMenu.setLabel("Output to Textbox");
\r
3045 clustalColour.setLabel("Clustalx");
\r
3047 clustalColour.addActionListener(this);
\r
3048 zappoColour.setLabel("Zappo");
\r
3049 zappoColour.addActionListener(this);
\r
3050 taylorColour.setLabel("Taylor");
\r
3051 taylorColour.addActionListener(this);
\r
3052 hydrophobicityColour.setLabel("Hydrophobicity");
\r
3053 hydrophobicityColour.addActionListener(this);
\r
3054 helixColour.setLabel("Helix Propensity");
\r
3055 helixColour.addActionListener(this);
\r
3056 strandColour.setLabel("Strand Propensity");
\r
3057 strandColour.addActionListener(this);
\r
3058 turnColour.setLabel("Turn Propensity");
\r
3059 turnColour.addActionListener(this);
\r
3060 buriedColour.setLabel("Buried Index");
\r
3061 buriedColour.addActionListener(this);
\r
3062 purinePyrimidineColour.setLabel("Purine/Pyrimidine");
\r
3063 purinePyrimidineColour.addActionListener(this);
\r
3064 RNAHelixColour.setLabel("by RNA Helices");
\r
3065 RNAHelixColour.addActionListener(this);
\r
3066 userDefinedColour.setLabel("User Defined...");
\r
3067 userDefinedColour.addActionListener(this);
\r
3068 PIDColour.setLabel("Percentage Identity");
\r
3069 PIDColour.addActionListener(this);
\r
3070 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
3071 BLOSUM62Colour.addActionListener(this);
\r
3072 tcoffeeColour.setLabel("T-Coffee Scores");
\r
3073 tcoffeeColour.setEnabled(false); // it will enabled only if a score file is provided
\r
3074 tcoffeeColour.addActionListener(this);
\r
3075 avDistanceTreeBlosumMenuItem .setLabel("Average Distance Using BLOSUM62");
\r
3076 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
3077 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
3078 njTreeBlosumMenuItem.addActionListener(this);
\r
3079 annotationPanelMenuItem.setLabel("Show Annotations");
\r
3080 annotationPanelMenuItem.addItemListener(this);
\r
3081 colourTextMenuItem.setLabel("Colour Text");
\r
3082 colourTextMenuItem.addItemListener(this);
\r
3083 displayNonconservedMenuItem.setLabel("Show nonconserved");
\r
3084 displayNonconservedMenuItem.addItemListener(this);
\r
3085 alProperties.addActionListener(this);
\r
3086 overviewMenuItem.setLabel("Overview Window");
\r
3087 overviewMenuItem.addActionListener(this);
\r
3088 undoMenuItem.setEnabled(false);
\r
3089 undoMenuItem.setLabel("Undo");
\r
3090 undoMenuItem.addActionListener(this);
\r
3091 redoMenuItem.setEnabled(false);
\r
3092 redoMenuItem.setLabel("Redo");
\r
3093 redoMenuItem.addActionListener(this);
\r
3094 conservationMenuItem.setLabel("by Conservation");
\r
3095 conservationMenuItem.addItemListener(this);
\r
3096 noColourmenuItem.setLabel("None");
\r
3097 noColourmenuItem.addActionListener(this);
\r
3098 wrapMenuItem.setLabel("Wrap");
\r
3099 wrapMenuItem.addItemListener(this);
\r
3100 renderGapsMenuItem.setLabel("Show Gaps");
\r
3101 renderGapsMenuItem.setState(true);
\r
3102 renderGapsMenuItem.addItemListener(this);
\r
3103 findMenuItem.setLabel("Find...");
\r
3104 findMenuItem.addActionListener(this);
\r
3105 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
3106 abovePIDThreshold.addItemListener(this);
\r
3107 nucleotideColour.setLabel("Nucleotide");
\r
3108 nucleotideColour.addActionListener(this);
\r
3109 deleteGroups.setLabel("Undefine Groups");
\r
3110 deleteGroups.addActionListener(this);
\r
3111 grpsFromSelection.setLabel("Make Groups for selection");
\r
3112 grpsFromSelection.addActionListener(this);
\r
3113 copy.setLabel("Copy");
\r
3114 copy.addActionListener(this);
\r
3115 cut.setLabel("Cut");
\r
3116 cut.addActionListener(this);
\r
3117 delete.setLabel("Delete");
\r
3118 delete.addActionListener(this);
\r
3119 pasteMenu.setLabel("Paste");
\r
3120 pasteNew.setLabel("To New Alignment");
\r
3121 pasteNew.addActionListener(this);
\r
3122 pasteThis.setLabel("Add To This Alignment");
\r
3123 pasteThis.addActionListener(this);
\r
3124 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
3125 applyToAllGroups.setState(true);
\r
3126 applyToAllGroups.addItemListener(this);
\r
3127 font.setLabel("Font...");
\r
3128 font.addActionListener(this);
\r
3129 scaleAbove.setLabel("Scale Above");
\r
3130 scaleAbove.setState(true);
\r
3131 scaleAbove.setEnabled(false);
\r
3132 scaleAbove.addItemListener(this);
\r
3133 scaleLeft.setEnabled(false);
\r
3134 scaleLeft.setState(true);
\r
3135 scaleLeft.setLabel("Scale Left");
\r
3136 scaleLeft.addItemListener(this);
\r
3137 scaleRight.setEnabled(false);
\r
3138 scaleRight.setState(true);
\r
3139 scaleRight.setLabel("Scale Right");
\r
3140 scaleRight.addItemListener(this);
\r
3141 modifyPID.setLabel("Modify Identity Threshold...");
\r
3142 modifyPID.addActionListener(this);
\r
3143 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
3144 modifyConservation.addActionListener(this);
\r
3145 sortByTreeMenu.setLabel("By Tree Order");
\r
3146 sort.setLabel("Sort");
\r
3147 calculate.setLabel("Calculate Tree");
\r
3148 autoCalculate.addItemListener(this);
\r
3149 sortByTree.addItemListener(this);
\r
3150 inputText.setLabel("Input from textbox");
\r
3151 inputText.addActionListener(this);
\r
3152 centreColumnLabelFlag.setLabel("Centre column labels");
\r
3153 centreColumnLabelFlag.addItemListener(this);
\r
3154 followMouseOverFlag.setLabel("Automatic Scrolling");
\r
3155 followMouseOverFlag.addItemListener(this);
\r
3156 helpMenu.setLabel("Help");
\r
3157 documentation.setLabel("Documentation");
\r
3158 documentation.addActionListener(this);
\r
3160 about.setLabel("About...");
\r
3161 about.addActionListener(this);
\r
3162 seqLimits.setState(true);
\r
3163 seqLimits.setLabel("Show Sequence Limits");
\r
3164 seqLimits.addItemListener(this);
\r
3165 featureSettings.setLabel("Feature Settings...");
\r
3166 featureSettings.addActionListener(this);
\r
3167 sequenceFeatures.setLabel("Sequence Features");
\r
3168 sequenceFeatures.addItemListener(this);
\r
3169 sequenceFeatures.setState(false);
\r
3170 annotationColour.setLabel("by Annotation...");
\r
3171 annotationColour.addActionListener(this);
\r
3172 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
3173 invertColSel.setLabel("Invert Column Selection");
\r
3174 menu1.setLabel("Show");
\r
3175 showColumns.setLabel("All Columns ");
\r
3176 showSeqs.setLabel("All Sequences");
\r
3177 menu2.setLabel("Hide");
\r
3178 hideColumns.setLabel("Selected Columns");
\r
3179 hideSequences.setLabel("Selected Sequences");
\r
3180 hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
\r
3181 hideAllSelection.setLabel("Selected Region");
\r
3182 showAllHidden.setLabel("All Sequences and Columns");
\r
3183 showGroupConsensus.setLabel("Group Consensus");
\r
3184 showGroupConservation.setLabel("Group Conservation");
\r
3185 showConsensusHistogram.setLabel("Show Consensus Histogram");
\r
3186 showSequenceLogo.setLabel("Show Consensus Logo");
\r
3187 applyAutoAnnotationSettings.setLabel("Apply to all groups");
\r
3188 applyAutoAnnotationSettings.setState(true);
\r
3189 autoAnnMenu.setLabel("Autocalculated Annotation");
\r
3191 invertColSel.addActionListener(this);
\r
3192 showColumns.addActionListener(this);
\r
3193 showSeqs.addActionListener(this);
\r
3194 hideColumns.addActionListener(this);
\r
3195 hideSequences.addActionListener(this);
\r
3196 hideAllButSelection.addActionListener(this);
\r
3197 hideAllSelection.addActionListener(this);
\r
3198 showAllHidden.addActionListener(this);
\r
3199 showGroupConsensus.addItemListener(this);
\r
3200 showGroupConservation.addItemListener(this);
\r
3201 showConsensusHistogram.addItemListener(this);
\r
3202 showSequenceLogo.addItemListener(this);
\r
3203 applyAutoAnnotationSettings.addItemListener(this);
\r
3204 formatMenu.setLabel("Format");
\r
3205 selectMenu.setLabel("Select");
\r
3206 newView.setLabel("New View");
\r
3207 newView.addActionListener(this);
\r
3208 alignFrameMenuBar.add(fileMenu);
\r
3209 alignFrameMenuBar.add(editMenu);
\r
3210 alignFrameMenuBar.add(selectMenu);
\r
3211 alignFrameMenuBar.add(viewMenu);
\r
3212 alignFrameMenuBar.add(formatMenu);
\r
3213 alignFrameMenuBar.add(colourMenu);
\r
3214 alignFrameMenuBar.add(calculateMenu);
\r
3215 alignFrameMenuBar.add(helpMenu);
\r
3217 fileMenu.add(inputText);
\r
3218 fileMenu.add(loadTree);
\r
3219 fileMenu.add(loadAnnotations);
\r
3221 fileMenu.addSeparator();
\r
3222 fileMenu.add(outputTextboxMenu);
\r
3223 fileMenu.add(outputFeatures);
\r
3224 fileMenu.add(outputAnnotations);
\r
3226 if (jalviewServletURL != null)
\r
3228 fileMenu.add(loadApplication);
\r
3231 fileMenu.addSeparator();
\r
3232 fileMenu.add(closeMenuItem);
\r
3234 editMenu.add(undoMenuItem);
\r
3235 editMenu.add(redoMenuItem);
\r
3236 editMenu.add(cut);
\r
3237 editMenu.add(copy);
\r
3238 editMenu.add(pasteMenu);
\r
3239 editMenu.add(delete);
\r
3240 editMenu.addSeparator();
\r
3241 editMenu.add(remove2LeftMenuItem);
\r
3242 editMenu.add(remove2RightMenuItem);
\r
3243 editMenu.add(removeGappedColumnMenuItem);
\r
3244 editMenu.add(removeAllGapsMenuItem);
\r
3245 editMenu.add(removeRedundancyMenuItem);
\r
3246 viewMenu.add(newView);
\r
3247 viewMenu.addSeparator();
\r
3248 viewMenu.add(menu1);
\r
3249 viewMenu.add(menu2);
\r
3250 viewMenu.addSeparator();
\r
3251 viewMenu.add(followMouseOverFlag);
\r
3252 viewMenu.add(annotationPanelMenuItem);
\r
3253 autoAnnMenu.add(applyAutoAnnotationSettings);
\r
3254 autoAnnMenu.add(showConsensusHistogram);
\r
3255 autoAnnMenu.add(showSequenceLogo);
\r
3256 autoAnnMenu.addSeparator();
\r
3257 autoAnnMenu.add(showGroupConservation);
\r
3258 autoAnnMenu.add(showGroupConsensus);
\r
3259 viewMenu.add(autoAnnMenu);
\r
3260 viewMenu.addSeparator();
\r
3261 viewMenu.add(sequenceFeatures);
\r
3262 viewMenu.add(featureSettings);
\r
3263 viewMenu.addSeparator();
\r
3264 viewMenu.add(alProperties);
\r
3265 viewMenu.addSeparator();
\r
3266 viewMenu.add(overviewMenuItem);
\r
3267 colourMenu.add(applyToAllGroups);
\r
3268 colourMenu.addSeparator();
\r
3269 colourMenu.add(noColourmenuItem);
\r
3270 colourMenu.add(clustalColour);
\r
3271 colourMenu.add(BLOSUM62Colour);
\r
3272 colourMenu.add(PIDColour);
\r
3273 colourMenu.add(zappoColour);
\r
3274 colourMenu.add(taylorColour);
\r
3275 colourMenu.add(hydrophobicityColour);
\r
3276 colourMenu.add(helixColour);
\r
3277 colourMenu.add(strandColour);
\r
3278 colourMenu.add(turnColour);
\r
3279 colourMenu.add(buriedColour);
\r
3280 colourMenu.add(nucleotideColour);
\r
3281 colourMenu.add(purinePyrimidineColour);
\r
3282 colourMenu.add(tcoffeeColour);
\r
3283 colourMenu.add(userDefinedColour);
\r
3284 colourMenu.addSeparator();
\r
3285 colourMenu.add(conservationMenuItem);
\r
3286 colourMenu.add(modifyConservation);
\r
3287 colourMenu.add(abovePIDThreshold);
\r
3288 colourMenu.add(modifyPID);
\r
3289 colourMenu.add(annotationColour);
\r
3290 colourMenu.add(RNAHelixColour);
\r
3291 calculateMenu.add(sort);
\r
3292 calculateMenu.add(calculate);
\r
3293 calculateMenu.addSeparator();
\r
3294 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
3295 calculateMenu.add(PCAMenuItem);
\r
3296 calculateMenu.add(autoCalculate);
\r
3297 calculateMenu.add(sortByTree);
\r
3298 this.add(statusBar, BorderLayout.SOUTH);
\r
3299 pasteMenu.add(pasteNew);
\r
3300 pasteMenu.add(pasteThis);
\r
3301 sort.add(sortIDMenuItem);
\r
3302 sort.add(sortLengthMenuItem);
\r
3303 sort.add(sortByTreeMenu);
\r
3304 sort.add(sortGroupMenuItem);
\r
3305 sort.add(sortPairwiseMenuItem);
\r
3306 calculate.add(averageDistanceTreeMenuItem);
\r
3307 calculate.add(neighbourTreeMenuItem);
\r
3308 calculate.add(avDistanceTreeBlosumMenuItem);
\r
3309 calculate.add(njTreeBlosumMenuItem);
\r
3310 helpMenu.add(documentation);
\r
3311 helpMenu.add(about);
\r
3312 menu1.add(showColumns);
\r
3313 menu1.add(showSeqs);
\r
3314 menu1.add(showAllHidden);
\r
3315 menu2.add(hideColumns);
\r
3316 menu2.add(hideSequences);
\r
3317 menu2.add(hideAllSelection);
\r
3318 menu2.add(hideAllButSelection);
\r
3319 formatMenu.add(font);
\r
3320 formatMenu.add(seqLimits);
\r
3321 formatMenu.add(wrapMenuItem);
\r
3322 formatMenu.add(scaleAbove);
\r
3323 formatMenu.add(scaleLeft);
\r
3324 formatMenu.add(scaleRight);
\r
3325 formatMenu.add(viewBoxesMenuItem);
\r
3326 formatMenu.add(viewTextMenuItem);
\r
3327 formatMenu.add(colourTextMenuItem);
\r
3328 formatMenu.add(displayNonconservedMenuItem);
\r
3329 formatMenu.add(renderGapsMenuItem);
\r
3330 formatMenu.add(centreColumnLabelFlag);
\r
3331 selectMenu.add(findMenuItem);
\r
3332 selectMenu.addSeparator();
\r
3333 selectMenu.add(selectAllSequenceMenuItem);
\r
3334 selectMenu.add(deselectAllSequenceMenuItem);
\r
3335 selectMenu.add(invertSequenceMenuItem);
\r
3336 selectMenu.add(invertColSel);
\r
3337 selectMenu.add(grpsFromSelection);
\r
3338 selectMenu.add(deleteGroups);
\r
3342 MenuItem featureSettings = new MenuItem();
\r
3344 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
3346 MenuItem annotationColour = new MenuItem();
\r
3348 MenuItem invertColSel = new MenuItem();
\r
3350 Menu menu1 = new Menu();
\r
3352 MenuItem showColumns = new MenuItem();
\r
3354 MenuItem showSeqs = new MenuItem();
\r
3356 Menu menu2 = new Menu();
\r
3358 MenuItem hideColumns = new MenuItem();
\r
3360 MenuItem hideSequences = new MenuItem();
\r
3362 MenuItem hideAllButSelection = new MenuItem();
\r
3364 MenuItem hideAllSelection = new MenuItem();
\r
3366 MenuItem showAllHidden = new MenuItem();
\r
3368 Menu formatMenu = new Menu();
\r
3370 Menu selectMenu = new Menu();
\r
3372 MenuItem newView = new MenuItem();
\r
3375 * Attach the alignFrame panels after embedding menus, if necessary. This used
\r
3376 * to be called setEmbedded, but is now creates the dropdown menus in a
\r
3377 * platform independent manner to avoid OSX/Mac menu appendage daftness.
\r
3379 * @param reallyEmbedded
\r
3380 * true to attach the view to the applet area on the page rather than
\r
3383 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
\r
3385 if (reallyEmbedded)
\r
3388 // Explicly build the embedded menu panel for the on-page applet
\r
3390 // view cannot be closed if its actually on the page
\r
3391 fileMenu.remove(closeMenuItem);
\r
3392 fileMenu.remove(3); // Remove Seperator
\r
3393 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
\r
3394 Font.PLAIN, 10, false); // use our own fonts.
\r
3395 // and actually add the components to the applet area
\r
3396 viewport.applet.setLayout(new BorderLayout());
\r
3397 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
\r
3398 viewport.applet.add(statusBar, BorderLayout.SOUTH);
\r
3399 alignPanel.setSize(viewport.applet.getSize().width,
\r
3400 viewport.applet.getSize().height - embeddedMenu.HEIGHT
\r
3401 - statusBar.HEIGHT);
\r
3402 viewport.applet.add(alignPanel, BorderLayout.CENTER);
\r
3403 final AlignFrame me = this;
\r
3404 viewport.applet.addFocusListener(new FocusListener()
\r
3408 public void focusLost(FocusEvent e)
\r
3410 if (me.viewport.applet.currentAlignFrame==me) {
\r
3411 me.viewport.applet.currentAlignFrame = null;
\r
3415 public void focusGained(FocusEvent e)
\r
3417 me.viewport.applet.currentAlignFrame = me;
\r
3420 viewport.applet.validate();
\r
3425 // test and embed menu bar if necessary.
\r
3427 if (embedMenuIfNeeded(alignPanel))
\r
3429 // adjust for status bar height too
\r
3430 alignPanel.setSize(getSize().width, getSize().height
\r
3431 - statusBar.HEIGHT);
\r
3433 add(statusBar, BorderLayout.SOUTH);
\r
3434 add(alignPanel, BorderLayout.CENTER);
\r
3435 // and register with the applet so it can pass external API calls to us
\r
3436 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
\r
3442 * create a new binding between structures in an existing jmol viewer instance
\r
3443 * and an alignpanel with sequences that have existing PDBFile entries. Note,
\r
3444 * this does not open a new Jmol window, or modify the display of the
\r
3445 * structures in the original jmol window. Note This method doesn't work
\r
3446 * without an additional javascript library to exchange messages between the
\r
3447 * distinct applets. See http://issues.jalview.org/browse/JAL-621
\r
3450 * JmolViewer instance
\r
3451 * @param sequenceIds
\r
3452 * - sequence Ids to search for associations
\r
3454 public SequenceStructureBinding addStructureViewInstance(
\r
3455 Object jmolviewer, String[] sequenceIds)
\r
3457 org.jmol.api.JmolViewer viewer = null;
\r
3460 viewer = (org.jmol.api.JmolViewer) jmolviewer;
\r
3461 } catch (ClassCastException ex)
\r
3463 System.err.println("Unsupported viewer object :"
\r
3464 + jmolviewer.getClass());
\r
3466 if (viewer == null)
\r
3468 System.err.println("Can't use this object as a structure viewer:"
\r
3469 + jmolviewer.getClass());
\r
3472 SequenceI[] seqs = null;
\r
3473 if (sequenceIds == null || sequenceIds.length == 0)
\r
3475 seqs = viewport.getAlignment().getSequencesArray();
\r
3479 Vector sqi = new Vector();
\r
3480 AlignmentI al = viewport.getAlignment();
\r
3481 for (int sid = 0; sid < sequenceIds.length; sid++)
\r
3483 SequenceI sq = al.findName(sequenceIds[sid]);
\r
3486 sqi.addElement(sq);
\r
3489 if (sqi.size() > 0)
\r
3491 seqs = new SequenceI[sqi.size()];
\r
3492 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
\r
3494 seqs[sid] = (SequenceI) sqi.elementAt(sid);
\r
3502 ExtJmol jmv = null;
\r
3503 // TODO: search for a jmv that involves viewer
\r
3505 { // create a new viewer/jalview binding.
\r
3506 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs});
\r
3512 * bind a pdb file to a sequence in the current view
\r
3514 * @param sequenceId
\r
3515 * - sequenceId within the dataset.
\r
3516 * @param pdbEntryString
\r
3517 * - the short name for the PDB file
\r
3519 * - pdb file - either a URL or a valid PDB file.
\r
3520 * @return true if binding was as success TODO: consider making an exception
\r
3521 * structure for indicating when PDB parsing or sequenceId location
\r
3524 public boolean addPdbFile(String sequenceId, String pdbEntryString,
\r
3527 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
\r
3528 boolean needtoadd = false;
\r
3529 if (toaddpdb != null)
\r
3531 Vector pdbe = toaddpdb.getPDBId();
\r
3532 PDBEntry pdbentry = null;
\r
3533 if (pdbe != null && pdbe.size() > 0)
\r
3535 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
\r
3537 pdbentry = (PDBEntry) pdbe.elementAt(pe);
\r
3538 if (!pdbentry.getId().equals(pdbEntryString)
\r
3539 && !pdbentry.getFile().equals(pdbFile))
\r
3549 if (pdbentry == null)
\r
3551 pdbentry = new PDBEntry();
\r
3552 pdbentry.setId(pdbEntryString);
\r
3553 pdbentry.setFile(pdbFile);
\r
3554 needtoadd = true; // add this new entry to sequence.
\r
3556 // resolve data source
\r
3557 // TODO: this code should be a refactored to an io package
\r
3558 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
\r
3559 if (protocol == null)
\r
3565 // make a note of the access mode and add
\r
3566 if (pdbentry.getProperty() == null)
\r
3568 pdbentry.setProperty(new Hashtable());
\r
3570 pdbentry.getProperty().put("protocol", protocol);
\r
3571 toaddpdb.addPDBId(pdbentry);
\r
3577 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
\r
3581 Vector sequences = new Vector();
\r
3582 for (int i = 0; i < seqs.length; i++)
\r
3584 if (seqs[i] != null)
\r
3586 sequences.addElement(new Object[]
\r
3587 { seqs[i], (chains != null) ? chains[i] : null });
\r
3590 seqs = new SequenceI[sequences.size()];
\r
3591 chains = new String[sequences.size()];
\r
3592 for (int i = 0, isize = sequences.size(); i < isize; i++)
\r
3594 Object[] oj = (Object[]) sequences.elementAt(i);
\r
3596 seqs[i] = (SequenceI) oj[0];
\r
3597 chains[i] = (String) oj[1];
\r
3600 return new Object[]
\r
3605 public void newStructureView(JalviewLite applet, PDBEntry pdb,
\r
3606 SequenceI[] seqs, String[] chains, String protocol)
\r
3608 // Scrub any null sequences from the array
\r
3609 Object[] sqch = cleanSeqChainArrays(seqs, chains);
\r
3610 seqs = (SequenceI[]) sqch[0];
\r
3611 chains = (String[]) sqch[1];
\r
3612 if (seqs == null || seqs.length == 0)
\r
3615 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
\r
3617 if (protocol == null || protocol.trim().length() == 0
\r
3618 || protocol.equals("null"))
\r
3620 protocol = (String) pdb.getProperty().get("protocol");
\r
3621 if (protocol == null)
\r
3623 System.err.println("Couldn't work out protocol to open structure: "
\r
3628 if (applet.useXtrnalSviewer)
\r
3630 // register the association(s) and quit, don't create any windows.
\r
3631 if (StructureSelectionManager.getStructureSelectionManager(applet).setMapping(seqs, chains, pdb.getFile(), protocol)==null) {
\r
3632 System.err.println("Failed to map "+pdb.getFile()+" ("+protocol+") to any sequences");
\r
3636 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
\r
3638 // can only do alignments with Jmol
\r
3639 // find the last jmol window assigned to this alignment
\r
3640 jalview.appletgui.AppletJmol ajm = null, tajm;
\r
3641 Vector jmols = applet
\r
3642 .getAppletWindow(jalview.appletgui.AppletJmol.class);
\r
3643 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
\r
3645 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
\r
3646 if (tajm.ap.alignFrame == this)
\r
3655 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
\r
3656 // try and add the pdb structure
\r
3661 // otherwise, create a new window
\r
3662 if (applet.jmolAvailable)
\r
3664 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
\r
3666 applet.lastFrameX += 40;
\r
3667 applet.lastFrameY += 40;
\r
3671 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
\r
3676 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
\r
3677 SequenceI[][] seqs, String[][] chains, String[] protocols)
\r
3679 // TODO Auto-generated method stub
\r
3680 System.err.println("Aligned Structure View: Not yet implemented.");
\r
3684 * modify the current selection, providing the user has not made a selection already.
\r
3685 * @param sel - sequences from this alignment
\r
3686 * @param csel - columns to be selected on the alignment
\r
3688 public void select(SequenceGroup sel, ColumnSelection csel)
\r
3690 alignPanel.seqPanel.selection(sel, csel, null);
\r
3693 public void scrollTo(int row, int column)
\r
3695 alignPanel.seqPanel.scrollTo(row, column);
\r
3697 public void scrollToRow(int row)
\r
3699 alignPanel.seqPanel.scrollToRow(row);
\r
3701 public void scrollToColumn(int column)
\r
3703 alignPanel.seqPanel.scrollToColumn(column);
\r
3706 * @return the alignments unique ID.
\r
3708 public String getSequenceSetId() {
\r
3709 return viewport.getSequenceSetId();
\r
3714 * Load the (T-Coffee) score file from the specified url
\r
3716 * @param source File/URL/T-COFFEE score file contents
\r
3717 * @throws IOException
\r
3718 * @return true if alignment was annotated with data from source
\r
3720 public boolean loadScoreFile( String source ) throws IOException {
\r
3722 TCoffeeScoreFile file = new TCoffeeScoreFile(source, AppletFormatAdapter.checkProtocol(source));
\r
3723 if( !file.isValid()) {
\r
3724 // TODO: raise dialog for gui
\r
3725 System.err.println("Problems parsing T-Coffee scores: "+file.getWarningMessage());
\r
3726 System.err.println("Origin was:\n"+source);
\r
3731 * check that the score matrix matches the alignment dimensions
\r
3734 if( (aln=viewport.getAlignment()) != null && (aln.getHeight() != file.getHeight() || aln.getWidth() != file.getWidth()) ) {
\r
3735 // TODO: raise a dialog box here rather than bomb out.
\r
3736 System.err.println("The scores matrix does not match the alignment dimensions");
\r
3740 // TODO add parameter to indicate if matching should be done
\r
3741 if (file.annotateAlignment(alignPanel.getAlignment(), false))
\r
3743 alignPanel.fontChanged();
\r
3744 tcoffeeColour.setEnabled(true);
\r
3745 // switch to this color
\r
3746 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
\r
3749 System.err.println("Problems resolving T-Coffee scores:");
\r
3750 if (file.getWarningMessage()!=null) {
\r
3751 System.err.println(file.getWarningMessage());
\r