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 void parseFeaturesFile(String file, String type)
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241 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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251 public void parseFeaturesFile(String file, String type, boolean autoenabledisplay)
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253 Hashtable featureLinks = new Hashtable();
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254 boolean featuresFile = false;
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257 featuresFile = new jalview.io.FeaturesFile(file, type)
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258 .parse(viewport.getAlignment(),
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259 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
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260 featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));
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261 } catch (Exception ex)
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263 ex.printStackTrace();
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268 if (featureLinks.size() > 0)
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270 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
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272 if (autoenabledisplay)
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274 viewport.showSequenceFeatures = true;
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275 sequenceFeatures.setState(true);
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277 if (viewport.featureSettings != null)
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279 viewport.featureSettings.refreshTable();
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281 alignPanel.paintAlignment(true);
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286 public void keyPressed(KeyEvent evt)
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288 if (viewport.cursorMode
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289 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
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290 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
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291 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
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292 && Character.isDigit(evt.getKeyChar()))
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293 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
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295 switch (evt.getKeyCode())
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297 case 27: // escape key
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298 deselectAllSequenceMenuItem_actionPerformed();
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300 alignPanel.alabels.cancelDrag();
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302 case KeyEvent.VK_X:
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303 if (evt.isControlDown() || evt.isMetaDown())
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305 cut_actionPerformed();
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308 case KeyEvent.VK_C:
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309 if (viewport.cursorMode && !evt.isControlDown())
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311 alignPanel.seqPanel.setCursorColumn();
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313 if (evt.isControlDown() || evt.isMetaDown())
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315 copy_actionPerformed();
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318 case KeyEvent.VK_V:
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319 if (evt.isControlDown())
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321 paste(evt.isShiftDown());
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324 case KeyEvent.VK_A:
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325 if (evt.isControlDown() || evt.isMetaDown())
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327 selectAllSequenceMenuItem_actionPerformed();
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330 case KeyEvent.VK_DOWN:
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331 if (viewport.cursorMode)
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333 alignPanel.seqPanel.moveCursor(0, 1);
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337 moveSelectedSequences(false);
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341 case KeyEvent.VK_UP:
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342 if (viewport.cursorMode)
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344 alignPanel.seqPanel.moveCursor(0, -1);
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348 moveSelectedSequences(true);
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352 case KeyEvent.VK_LEFT:
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353 if (evt.isAltDown() || !viewport.cursorMode)
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354 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
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356 alignPanel.seqPanel.moveCursor(-1, 0);
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359 case KeyEvent.VK_RIGHT:
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360 if (evt.isAltDown() || !viewport.cursorMode)
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361 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
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363 alignPanel.seqPanel.moveCursor(1, 0);
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366 case KeyEvent.VK_SPACE:
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367 if (viewport.cursorMode)
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369 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
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370 || evt.isShiftDown() || evt.isAltDown());
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374 case KeyEvent.VK_DELETE:
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375 case KeyEvent.VK_BACK_SPACE:
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376 if (viewport.cursorMode)
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378 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
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379 || evt.isShiftDown() || evt.isAltDown());
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383 cut_actionPerformed();
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384 alignPanel.seqPanel.seqCanvas.repaint();
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388 case KeyEvent.VK_S:
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389 if (viewport.cursorMode)
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391 alignPanel.seqPanel.setCursorRow();
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394 case KeyEvent.VK_P:
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395 if (viewport.cursorMode)
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397 alignPanel.seqPanel.setCursorPosition();
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401 case KeyEvent.VK_ENTER:
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402 case KeyEvent.VK_COMMA:
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403 if (viewport.cursorMode)
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405 alignPanel.seqPanel.setCursorRowAndColumn();
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409 case KeyEvent.VK_Q:
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410 if (viewport.cursorMode)
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412 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
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415 case KeyEvent.VK_M:
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416 if (viewport.cursorMode)
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418 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
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422 case KeyEvent.VK_F2:
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423 viewport.cursorMode = !viewport.cursorMode;
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424 statusBar.setText("Keyboard editing mode is "
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425 + (viewport.cursorMode ? "on" : "off"));
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426 if (viewport.cursorMode)
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428 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
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429 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
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433 case KeyEvent.VK_F:
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434 if (evt.isControlDown())
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436 findMenuItem_actionPerformed();
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440 case KeyEvent.VK_H:
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442 boolean toggleSeqs = !evt.isControlDown();
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443 boolean toggleCols = !evt.isShiftDown();
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444 toggleHiddenRegions(toggleSeqs, toggleCols);
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448 case KeyEvent.VK_PAGE_UP:
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449 if (viewport.wrapAlignment)
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451 alignPanel.scrollUp(true);
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455 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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456 - viewport.endSeq + viewport.startSeq);
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460 case KeyEvent.VK_PAGE_DOWN:
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461 if (viewport.wrapAlignment)
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463 alignPanel.scrollUp(false);
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467 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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468 + viewport.endSeq - viewport.startSeq);
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472 case KeyEvent.VK_Z:
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473 if (evt.isControlDown())
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475 undoMenuItem_actionPerformed();
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479 case KeyEvent.VK_Y:
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480 if (evt.isControlDown())
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482 redoMenuItem_actionPerformed();
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486 case KeyEvent.VK_L:
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487 if (evt.isControlDown())
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489 trimAlignment(true);
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493 case KeyEvent.VK_R:
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494 if (evt.isControlDown())
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496 trimAlignment(false);
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500 case KeyEvent.VK_E:
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501 if (evt.isControlDown())
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503 if (evt.isShiftDown())
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505 this.removeAllGapsMenuItem_actionPerformed();
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509 removeGappedColumnMenuItem_actionPerformed();
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513 case KeyEvent.VK_I:
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514 if (evt.isControlDown())
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516 if (evt.isAltDown())
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518 invertColSel_actionPerformed();
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522 invertSequenceMenuItem_actionPerformed();
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527 case KeyEvent.VK_U:
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528 if (evt.isControlDown())
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530 this.deleteGroups_actionPerformed();
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534 case KeyEvent.VK_T:
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535 if (evt.isControlDown())
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542 alignPanel.paintAlignment(true);
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546 * called by key handler and the hide all/show all menu items
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548 * @param toggleSeqs
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549 * @param toggleCols
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551 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
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553 boolean hide = false;
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554 SequenceGroup sg = viewport.getSelectionGroup();
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555 if (!toggleSeqs && !toggleCols)
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557 // Hide everything by the current selection - this is a hack - we do the
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558 // invert and then hide
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559 // first check that there will be visible columns after the invert.
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560 if ((viewport.getColumnSelection() != null && viewport.getColumnSelection().getSelected() != null && viewport.getColumnSelection()
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561 .getSelected().size() > 0)
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562 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
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565 // now invert the sequence set, if required - empty selection implies
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566 // that no hiding is required.
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569 invertSequenceMenuItem_actionPerformed();
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570 sg = viewport.getSelectionGroup();
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574 viewport.expandColSelection(sg, true);
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575 // finally invert the column selection and get the new sequence
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576 // selection and indicate it should be hidden.
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577 invertColSel_actionPerformed();
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584 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
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587 viewport.hideAllSelectedSeqs();
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589 else if (!(toggleCols && viewport.getColumnSelection().getSelected().size() > 0))
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591 viewport.showAllHiddenSeqs();
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597 if (viewport.getColumnSelection().getSelected().size() > 0)
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599 viewport.hideSelectedColumns();
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602 viewport.setSelectionGroup(sg);
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607 viewport.showAllHiddenColumns();
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612 public void keyReleased(KeyEvent evt)
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616 public void keyTyped(KeyEvent evt)
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620 public void itemStateChanged(ItemEvent evt)
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622 if (evt.getSource() == displayNonconservedMenuItem)
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624 displayNonconservedMenuItem_actionPerformed();
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626 else if (evt.getSource() == colourTextMenuItem)
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628 colourTextMenuItem_actionPerformed();
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630 else if (evt.getSource() == wrapMenuItem)
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632 wrapMenuItem_actionPerformed();
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634 else if (evt.getSource() == scaleAbove)
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636 viewport.setScaleAboveWrapped(scaleAbove.getState());
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638 else if (evt.getSource() == scaleLeft)
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640 viewport.setScaleLeftWrapped(scaleLeft.getState());
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642 else if (evt.getSource() == scaleRight)
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644 viewport.setScaleRightWrapped(scaleRight.getState());
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646 else if (evt.getSource() == seqLimits)
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648 seqLimits_itemStateChanged();
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650 else if (evt.getSource() == viewBoxesMenuItem)
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652 viewport.setShowBoxes(viewBoxesMenuItem.getState());
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654 else if (evt.getSource() == viewTextMenuItem)
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656 viewport.setShowText(viewTextMenuItem.getState());
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658 else if (evt.getSource() == renderGapsMenuItem)
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660 viewport.setRenderGaps(renderGapsMenuItem.getState());
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662 else if (evt.getSource() == annotationPanelMenuItem)
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664 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
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665 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
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667 else if (evt.getSource() == sequenceFeatures)
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669 viewport.showSequenceFeatures(sequenceFeatures.getState());
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670 alignPanel.seqPanel.seqCanvas.repaint();
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672 else if (evt.getSource() == conservationMenuItem)
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674 conservationMenuItem_actionPerformed();
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676 else if (evt.getSource() == abovePIDThreshold)
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678 abovePIDThreshold_actionPerformed();
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680 else if (evt.getSource() == applyToAllGroups)
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682 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
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684 else if (evt.getSource() == autoCalculate)
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686 viewport.autoCalculateConsensus = autoCalculate.getState();
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688 else if (evt.getSource() == sortByTree)
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690 viewport.sortByTree = sortByTree.getState();
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692 else if (evt.getSource() == this.centreColumnLabelFlag)
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694 centreColumnLabelFlag_stateChanged();
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696 else if (evt.getSource() == this.followMouseOverFlag)
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698 mouseOverFlag_stateChanged();
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700 else if (evt.getSource() == showGroupConsensus)
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702 showGroupConsensus_actionPerformed();
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704 else if (evt.getSource() == showGroupConservation)
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706 showGroupConservation_actionPerformed();
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708 else if (evt.getSource() == showSequenceLogo)
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710 showSequenceLogo_actionPerformed();
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712 else if (evt.getSource() == showConsensusHistogram)
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714 showConsensusHistogram_actionPerformed();
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716 else if (evt.getSource() == applyAutoAnnotationSettings)
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718 applyAutoAnnotationSettings_actionPerformed();
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720 alignPanel.paintAlignment(true);
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723 private void mouseOverFlag_stateChanged()
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725 viewport.followHighlight = followMouseOverFlag.getState();
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726 // TODO: could kick the scrollTo mechanism to reset view for current
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730 private void centreColumnLabelFlag_stateChanged()
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732 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
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733 this.alignPanel.annotationPanel.repaint();
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736 public void actionPerformed(ActionEvent evt)
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738 Object source = evt.getSource();
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740 if (source == inputText)
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742 inputText_actionPerformed();
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744 else if (source == loadTree)
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746 loadTree_actionPerformed();
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748 else if (source == loadApplication)
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750 launchFullApplication();
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752 else if (source == loadAnnotations)
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756 else if( source == loadScores ) {
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759 else if (source == outputAnnotations)
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761 outputAnnotations(true);
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763 else if (source == outputFeatures)
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765 outputFeatures(true, "Jalview");
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767 else if (source == closeMenuItem)
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769 closeMenuItem_actionPerformed();
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771 else if (source == copy)
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773 copy_actionPerformed();
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775 else if (source == undoMenuItem)
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777 undoMenuItem_actionPerformed();
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779 else if (source == redoMenuItem)
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781 redoMenuItem_actionPerformed();
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783 else if (source == inputText)
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785 inputText_actionPerformed();
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787 else if (source == closeMenuItem)
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789 closeMenuItem_actionPerformed();
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791 else if (source == undoMenuItem)
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793 undoMenuItem_actionPerformed();
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795 else if (source == redoMenuItem)
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797 redoMenuItem_actionPerformed();
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799 else if (source == copy)
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801 copy_actionPerformed();
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803 else if (source == pasteNew)
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805 pasteNew_actionPerformed();
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807 else if (source == pasteThis)
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809 pasteThis_actionPerformed();
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811 else if (source == cut)
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813 cut_actionPerformed();
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815 else if (source == delete)
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817 delete_actionPerformed();
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819 else if (source == grpsFromSelection)
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821 makeGrpsFromSelection_actionPerformed();
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823 else if (source == deleteGroups)
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825 deleteGroups_actionPerformed();
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827 else if (source == selectAllSequenceMenuItem)
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829 selectAllSequenceMenuItem_actionPerformed();
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831 else if (source == deselectAllSequenceMenuItem)
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833 deselectAllSequenceMenuItem_actionPerformed();
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835 else if (source == invertSequenceMenuItem)
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837 invertSequenceMenuItem_actionPerformed();
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839 else if (source == invertColSel)
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841 viewport.invertColumnSelection();
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842 alignPanel.paintAlignment(true);
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844 else if (source == remove2LeftMenuItem)
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846 trimAlignment(true);
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848 else if (source == remove2RightMenuItem)
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850 trimAlignment(false);
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852 else if (source == removeGappedColumnMenuItem)
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854 removeGappedColumnMenuItem_actionPerformed();
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856 else if (source == removeAllGapsMenuItem)
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858 removeAllGapsMenuItem_actionPerformed();
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860 else if (source == findMenuItem)
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862 findMenuItem_actionPerformed();
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864 else if (source == font)
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866 new FontChooser(alignPanel);
\r
868 else if (source == newView)
\r
872 else if (source == showColumns)
\r
874 viewport.showAllHiddenColumns();
\r
875 alignPanel.paintAlignment(true);
\r
877 else if (source == showSeqs)
\r
879 viewport.showAllHiddenSeqs();
\r
880 alignPanel.paintAlignment(true);
\r
882 else if (source == hideColumns)
\r
884 viewport.hideSelectedColumns();
\r
885 alignPanel.paintAlignment(true);
\r
887 else if (source == hideSequences
\r
888 && viewport.getSelectionGroup() != null)
\r
890 viewport.hideAllSelectedSeqs();
\r
891 alignPanel.paintAlignment(true);
\r
893 else if (source == hideAllButSelection)
\r
895 toggleHiddenRegions(false, false);
\r
896 alignPanel.paintAlignment(true);
\r
898 else if (source == hideAllSelection)
\r
900 SequenceGroup sg = viewport.getSelectionGroup();
\r
901 viewport.expandColSelection(sg, false);
\r
902 viewport.hideAllSelectedSeqs();
\r
903 viewport.hideSelectedColumns();
\r
904 alignPanel.paintAlignment(true);
\r
906 else if (source == showAllHidden)
\r
908 viewport.showAllHiddenColumns();
\r
909 viewport.showAllHiddenSeqs();
\r
910 alignPanel.paintAlignment(true);
\r
912 else if (source == showGroupConsensus)
\r
914 showGroupConsensus_actionPerformed();
\r
916 else if (source == showGroupConservation)
\r
918 showGroupConservation_actionPerformed();
\r
920 else if (source == showSequenceLogo)
\r
922 showSequenceLogo_actionPerformed();
\r
924 else if (source == showConsensusHistogram)
\r
926 showConsensusHistogram_actionPerformed();
\r
928 else if (source == applyAutoAnnotationSettings)
\r
930 applyAutoAnnotationSettings_actionPerformed();
\r
932 else if (source == featureSettings)
\r
934 new FeatureSettings(alignPanel);
\r
936 else if (source == alProperties)
\r
938 StringBuffer contents = new jalview.io.AlignmentProperties(
\r
939 viewport.getAlignment()).formatAsString();
\r
940 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
941 cap.setText(contents.toString());
\r
942 Frame frame = new Frame();
\r
944 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
\r
945 + getTitle(), 400, 250);
\r
947 else if (source == overviewMenuItem)
\r
949 overviewMenuItem_actionPerformed();
\r
951 else if (source == noColourmenuItem)
\r
953 changeColour(null);
\r
955 else if (source == clustalColour)
\r
957 abovePIDThreshold.setState(false);
\r
958 changeColour(new ClustalxColourScheme(
\r
959 viewport.getAlignment().getSequences(),
\r
960 viewport.getAlignment().getWidth()));
\r
962 else if (source == zappoColour)
\r
964 changeColour(new ZappoColourScheme());
\r
966 else if (source == taylorColour)
\r
968 changeColour(new TaylorColourScheme());
\r
970 else if (source == hydrophobicityColour)
\r
972 changeColour(new HydrophobicColourScheme());
\r
974 else if (source == helixColour)
\r
976 changeColour(new HelixColourScheme());
\r
978 else if (source == strandColour)
\r
980 changeColour(new StrandColourScheme());
\r
982 else if (source == turnColour)
\r
984 changeColour(new TurnColourScheme());
\r
986 else if (source == buriedColour)
\r
988 changeColour(new BuriedColourScheme());
\r
990 else if (source == nucleotideColour)
\r
992 changeColour(new NucleotideColourScheme());
\r
994 else if (source == purinePyrimidineColour)
\r
996 changeColour(new PurinePyrimidineColourScheme());
\r
998 else if (source == RNAHelixColour)
\r
1000 new RNAHelicesColourChooser(viewport, alignPanel);
\r
1002 else if (source == modifyPID)
\r
1004 modifyPID_actionPerformed();
\r
1006 else if (source == modifyConservation)
\r
1008 modifyConservation_actionPerformed();
\r
1010 else if (source == userDefinedColour)
\r
1012 new UserDefinedColours(alignPanel, null);
\r
1014 else if (source == PIDColour)
\r
1016 changeColour(new PIDColourScheme());
\r
1018 else if (source == BLOSUM62Colour)
\r
1020 changeColour(new Blosum62ColourScheme());
\r
1022 else if (source == tcoffeeColour) {
\r
1023 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
\r
1025 else if (source == annotationColour)
\r
1027 new AnnotationColourChooser(viewport, alignPanel);
\r
1029 else if (source == sortPairwiseMenuItem)
\r
1031 sortPairwiseMenuItem_actionPerformed();
\r
1033 else if (source == sortIDMenuItem)
\r
1035 sortIDMenuItem_actionPerformed();
\r
1037 else if (source == sortLengthMenuItem)
\r
1039 sortLengthMenuItem_actionPerformed();
\r
1041 else if (source == sortGroupMenuItem)
\r
1043 sortGroupMenuItem_actionPerformed();
\r
1045 else if (source == removeRedundancyMenuItem)
\r
1047 removeRedundancyMenuItem_actionPerformed();
\r
1049 else if (source == pairwiseAlignmentMenuItem)
\r
1051 pairwiseAlignmentMenuItem_actionPerformed();
\r
1053 else if (source == PCAMenuItem)
\r
1055 PCAMenuItem_actionPerformed();
\r
1057 else if (source == averageDistanceTreeMenuItem)
\r
1059 averageDistanceTreeMenuItem_actionPerformed();
\r
1061 else if (source == neighbourTreeMenuItem)
\r
1063 neighbourTreeMenuItem_actionPerformed();
\r
1065 else if (source == njTreeBlosumMenuItem)
\r
1067 njTreeBlosumMenuItem_actionPerformed();
\r
1069 else if (source == avDistanceTreeBlosumMenuItem)
\r
1071 avTreeBlosumMenuItem_actionPerformed();
\r
1073 else if (source == documentation)
\r
1075 documentation_actionPerformed();
\r
1077 else if (source == about)
\r
1079 about_actionPerformed();
\r
1084 public void inputText_actionPerformed()
\r
1086 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1087 Frame frame = new Frame();
\r
1089 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
\r
1092 protected void outputText_actionPerformed(ActionEvent e)
\r
1094 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1095 Frame frame = new Frame();
\r
1097 jalview.bin.JalviewLite.addFrame(frame,
\r
1098 "Alignment output - " + e.getActionCommand(), 600, 500);
\r
1099 cap.setText(new AppletFormatAdapter().formatSequences(
\r
1100 e.getActionCommand(), viewport.getAlignment(),
\r
1101 viewport.showJVSuffix));
\r
1104 public void loadAnnotations()
\r
1106 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1107 cap.setText("Paste your features / annotations file here.");
\r
1108 cap.setAnnotationImport();
\r
1109 Frame frame = new Frame();
\r
1111 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
\r
1115 public void loadScores() {
\r
1120 public String outputAnnotations(boolean displayTextbox)
\r
1122 String annotation = new AnnotationFile().printAnnotations(
\r
1123 viewport.showAnnotation ? viewport.getAlignment()
\r
1124 .getAlignmentAnnotation() : null, viewport.getAlignment()
\r
1126 ((Alignment) viewport.getAlignment()).alignmentProperties);
\r
1128 if (displayTextbox)
\r
1130 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
1131 Frame frame = new Frame();
\r
1133 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
\r
1134 cap.setText(annotation);
\r
1137 return annotation;
\r
1140 private Hashtable getDisplayedFeatureCols()
\r
1142 if (alignPanel.getFeatureRenderer() != null && viewport.featuresDisplayed!=null)
\r
1144 FeatureRenderer fr = alignPanel.getFeatureRenderer();
\r
1145 Hashtable fcols = new Hashtable();
\r
1146 Enumeration en = viewport.featuresDisplayed.keys();
\r
1147 while (en.hasMoreElements())
\r
1149 Object col = en.nextElement();
\r
1150 fcols.put(col, fr.featureColours.get(col));
\r
1157 public String outputFeatures(boolean displayTextbox, String format)
\r
1160 if (format.equalsIgnoreCase("Jalview"))
\r
1162 features = new FeaturesFile().printJalviewFormat(
\r
1163 viewport.getAlignment().getSequencesArray(),
\r
1164 getDisplayedFeatureCols());
\r
1168 features = new FeaturesFile().printGFFFormat(
\r
1169 viewport.getAlignment().getSequencesArray(),
\r
1170 getDisplayedFeatureCols());
\r
1173 if (displayTextbox)
\r
1175 boolean frimport=false;
\r
1176 if (features==null || features.equals("No Features Visible"))
\r
1178 features = "# No features visible - paste some and import them here.";
\r
1182 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
\r
1185 cap.setAnnotationImport();
\r
1187 Frame frame = new Frame();
\r
1189 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
\r
1190 cap.setText(features);
\r
1192 if (features==null)
\r
1199 void launchFullApplication()
\r
1201 StringBuffer url = new StringBuffer(jalviewServletURL);
\r
1203 url.append("?open="
\r
1204 + appendProtocol(viewport.applet.getParameter("file")));
\r
1206 if (viewport.applet.getParameter("features") != null)
\r
1208 url.append("&features=");
\r
1209 url.append(appendProtocol(viewport.applet.getParameter("features")));
\r
1212 if (viewport.applet.getParameter("annotations") != null)
\r
1214 url.append("&annotations=");
\r
1215 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
\r
1218 if (viewport.applet.getParameter("jnetfile") != null)
\r
1220 url.append("&annotations=");
\r
1221 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
\r
1224 if (viewport.applet.getParameter("defaultColour") != null)
\r
1226 url.append("&colour="
\r
1227 + removeWhiteSpace(viewport.applet
\r
1228 .getParameter("defaultColour")));
\r
1231 if (viewport.applet.getParameter("userDefinedColour") != null)
\r
1233 url.append("&colour="
\r
1234 + removeWhiteSpace(viewport.applet
\r
1235 .getParameter("userDefinedColour")));
\r
1237 if (viewport.applet.getParameter("tree") != null)
\r
1239 url.append("&tree="
\r
1240 + appendProtocol(viewport.applet.getParameter("tree")));
\r
1242 if (viewport.applet.getParameter("treeFile") != null)
\r
1244 url.append("&tree="
\r
1245 + appendProtocol(viewport.applet.getParameter("treeFile")));
\r
1248 showURL(url.toString(), "FULL_APP");
\r
1251 String removeWhiteSpace(String colour)
\r
1253 StringBuffer sb = new StringBuffer();
\r
1254 for (int i = 0; i < colour.length(); i++)
\r
1256 if (Character.isWhitespace(colour.charAt(i)))
\r
1262 sb.append(colour.charAt(i));
\r
1266 return sb.toString();
\r
1269 String appendProtocol(String url)
\r
1274 url = URLEncoder.encode(url);
\r
1277 * When we finally deprecate 1.1 compatibility, we can start to use
\r
1278 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
\r
1279 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
\r
1280 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
\r
1281 * ex.printStackTrace(); }
\r
1283 catch (java.net.MalformedURLException ex)
\r
1285 url = viewport.applet.getCodeBase() + url;
\r
1290 public void closeMenuItem_actionPerformed()
\r
1292 PaintRefresher.RemoveComponent(alignPanel);
\r
1293 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
\r
1294 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
\r
1296 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
\r
1302 alignPanel = null;
\r
1309 void updateEditMenuBar()
\r
1312 if (viewport.historyList.size() > 0)
\r
1314 undoMenuItem.setEnabled(true);
\r
1315 CommandI command = (CommandI) viewport.historyList.peek();
\r
1316 undoMenuItem.setLabel("Undo " + command.getDescription());
\r
1320 undoMenuItem.setEnabled(false);
\r
1321 undoMenuItem.setLabel("Undo");
\r
1324 if (viewport.redoList.size() > 0)
\r
1326 redoMenuItem.setEnabled(true);
\r
1328 CommandI command = (CommandI) viewport.redoList.peek();
\r
1329 redoMenuItem.setLabel("Redo " + command.getDescription());
\r
1333 redoMenuItem.setEnabled(false);
\r
1334 redoMenuItem.setLabel("Redo");
\r
1338 public void addHistoryItem(CommandI command)
\r
1340 if (command.getSize() > 0)
\r
1342 viewport.historyList.push(command);
\r
1343 viewport.redoList.removeAllElements();
\r
1344 updateEditMenuBar();
\r
1345 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
1383 protected void redoMenuItem_actionPerformed()
\r
1385 if (viewport.redoList.size() < 1)
\r
1390 CommandI command = (CommandI) viewport.redoList.pop();
\r
1391 viewport.historyList.push(command);
\r
1392 command.doCommand(null);
\r
1394 AlignViewport originalSource = getOriginatingSource(command);
\r
1396 if (originalSource!=viewport) {
\r
1397 System.err.println("Warning: Viewport object mismatch whilst re-doing");
\r
1399 originalSource.updateHiddenColumns(); //sethasHiddenColumns(); = viewport.getColumnSelection().getHiddenColumns() != null;
\r
1401 updateEditMenuBar();
\r
1402 originalSource.firePropertyChange("alignment", null,
\r
1403 originalSource.getAlignment().getSequences());
\r
1406 AlignViewport getOriginatingSource(CommandI command)
\r
1408 AlignViewport originalSource = null;
\r
1409 // For sequence removal and addition, we need to fire
\r
1410 // the property change event FROM the viewport where the
\r
1411 // original alignment was altered
\r
1412 AlignmentI al = null;
\r
1413 if (command instanceof EditCommand)
\r
1415 EditCommand editCommand = (EditCommand) command;
\r
1416 al = editCommand.getAlignment();
\r
1417 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
1418 .getSequenceSetId());
\r
1419 for (int i = 0; i < comps.size(); i++)
\r
1421 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
1423 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
\r
1425 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
\r
1432 if (originalSource == null)
\r
1434 // The original view is closed, we must validate
\r
1435 // the current view against the closed view first
\r
1438 PaintRefresher.validateSequences(al, viewport.getAlignment());
\r
1441 originalSource = viewport;
\r
1444 return originalSource;
\r
1447 public void moveSelectedSequences(boolean up)
\r
1449 SequenceGroup sg = viewport.getSelectionGroup();
\r
1457 for (int i = 1; i < viewport.getAlignment().getHeight(); i++)
\r
1459 SequenceI seq = viewport.getAlignment().getSequenceAt(i);
\r
1460 if (!sg.getSequences(null).contains(seq))
\r
1465 SequenceI temp = viewport.getAlignment().getSequenceAt(i - 1);
\r
1466 if (sg.getSequences(null).contains(temp))
\r
1471 viewport.getAlignment().getSequences().setElementAt(temp, i);
\r
1472 viewport.getAlignment().getSequences().setElementAt(seq, i - 1);
\r
1477 for (int i = viewport.getAlignment().getHeight() - 2; i > -1; i--)
\r
1479 SequenceI seq = viewport.getAlignment().getSequenceAt(i);
\r
1480 if (!sg.getSequences(viewport.getHiddenRepSequences()).contains(seq))
\r
1485 SequenceI temp = viewport.getAlignment().getSequenceAt(i + 1);
\r
1486 if (sg.getSequences(viewport.getHiddenRepSequences()).contains(temp))
\r
1491 viewport.getAlignment().getSequences().setElementAt(temp, i);
\r
1492 viewport.getAlignment().getSequences().setElementAt(seq, i + 1);
\r
1496 alignPanel.paintAlignment(true);
\r
1499 synchronized void slideSequences(boolean right, int size)
\r
1501 Vector sg = new Vector();
\r
1502 if (viewport.cursorMode)
\r
1504 sg.addElement(viewport.getAlignment()
\r
1505 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
\r
1507 else if (viewport.getSelectionGroup() != null
\r
1508 && viewport.getSelectionGroup().getSize() != viewport.getAlignment()
\r
1511 sg = viewport.getSelectionGroup().getSequences(
\r
1512 viewport.getHiddenRepSequences());
\r
1515 if (sg.size() < 1)
\r
1520 Vector invertGroup = new Vector();
\r
1522 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
\r
1524 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
\r
1525 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
\r
1528 SequenceI[] seqs1 = new SequenceI[sg.size()];
\r
1529 for (int i = 0; i < sg.size(); i++)
\r
1530 seqs1[i] = (SequenceI) sg.elementAt(i);
\r
1532 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
\r
1533 for (int i = 0; i < invertGroup.size(); i++)
\r
1534 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
\r
1536 SlideSequencesCommand ssc;
\r
1538 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
\r
1539 size, viewport.getGapCharacter());
\r
1541 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
\r
1542 size, viewport.getGapCharacter());
\r
1544 int groupAdjustment = 0;
\r
1545 if (ssc.getGapsInsertedBegin() && right)
\r
1547 if (viewport.cursorMode)
\r
1548 alignPanel.seqPanel.moveCursor(size, 0);
\r
1550 groupAdjustment = size;
\r
1552 else if (!ssc.getGapsInsertedBegin() && !right)
\r
1554 if (viewport.cursorMode)
\r
1555 alignPanel.seqPanel.moveCursor(-size, 0);
\r
1557 groupAdjustment = -size;
\r
1560 if (groupAdjustment != 0)
\r
1562 viewport.getSelectionGroup().setStartRes(
\r
1563 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
\r
1564 viewport.getSelectionGroup().setEndRes(
\r
1565 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
\r
1568 boolean appendHistoryItem = false;
\r
1569 if (viewport.historyList != null && viewport.historyList.size() > 0
\r
1570 && viewport.historyList.peek() instanceof SlideSequencesCommand)
\r
1572 appendHistoryItem = ssc
\r
1573 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
\r
1577 if (!appendHistoryItem)
\r
1578 addHistoryItem(ssc);
\r
1583 static StringBuffer copiedSequences;
\r
1585 static Vector copiedHiddenColumns;
\r
1587 protected void copy_actionPerformed()
\r
1589 if (viewport.getSelectionGroup() == null)
\r
1594 SequenceGroup sg = viewport.getSelectionGroup();
\r
1595 copiedSequences = new StringBuffer();
\r
1596 Hashtable orderedSeqs = new Hashtable();
\r
1597 for (int i = 0; i < sg.getSize(); i++)
\r
1599 SequenceI seq = sg.getSequenceAt(i);
\r
1600 int index = viewport.getAlignment().findIndex(seq);
\r
1601 orderedSeqs.put(index + "", seq);
\r
1604 int index = 0, startRes, endRes;
\r
1607 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
\r
1609 copiedHiddenColumns = new Vector();
\r
1610 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
\r
1611 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
\r
1614 int[] region = (int[]) viewport.getColumnSelection()
\r
1615 .getHiddenColumns().elementAt(i);
\r
1617 copiedHiddenColumns.addElement(new int[]
\r
1618 { region[0] - hiddenOffset, region[1] - hiddenOffset });
\r
1623 copiedHiddenColumns = null;
\r
1626 for (int i = 0; i < sg.getSize(); i++)
\r
1628 SequenceI seq = null;
\r
1630 while (seq == null)
\r
1632 if (orderedSeqs.containsKey(index + ""))
\r
1634 seq = (SequenceI) orderedSeqs.get(index + "");
\r
1646 // Returns residue following index if gap
\r
1647 startRes = seq.findPosition(sg.getStartRes());
\r
1650 // Need to find the residue preceeding index if gap
\r
1653 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
\r
1655 ch = seq.getCharAt(j);
\r
1656 if (!jalview.util.Comparison.isGap((ch)))
\r
1664 endRes += seq.getStart() - 1;
\r
1667 copiedSequences.append(seq.getName()
\r
1673 + seq.getSequenceAsString(sg.getStartRes(),
\r
1674 sg.getEndRes() + 1) + "\n");
\r
1679 protected void pasteNew_actionPerformed()
\r
1684 protected void pasteThis_actionPerformed()
\r
1689 void paste(boolean newAlignment)
\r
1694 if (copiedSequences == null)
\r
1699 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
1700 Vector seqs = new Vector();
\r
1701 while (st.hasMoreElements())
\r
1703 String name = st.nextToken();
\r
1704 int start = Integer.parseInt(st.nextToken());
\r
1705 int end = Integer.parseInt(st.nextToken());
\r
1706 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
\r
1708 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
1709 for (int i = 0; i < seqs.size(); i++)
\r
1711 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
1716 String newtitle = new String("Copied sequences");
\r
1717 if (getTitle().startsWith("Copied sequences"))
\r
1719 newtitle = getTitle();
\r
1723 newtitle = newtitle.concat("- from " + getTitle());
\r
1725 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
1726 viewport.applet, newtitle, false);
\r
1727 if (copiedHiddenColumns != null)
\r
1729 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
1731 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
1732 af.viewport.hideColumns(region[0], region[1]);
\r
1736 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
\r
1741 addSequences(newSeqs);
\r
1744 } catch (Exception ex)
\r
1746 } // could be anything being pasted in here
\r
1750 void addSequences(SequenceI[] seqs)
\r
1752 for (int i = 0; i < seqs.length; i++)
\r
1754 viewport.getAlignment().addSequence(seqs[i]);
\r
1758 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
\r
1759 seqs, 0, viewport.getAlignment().getWidth(), viewport.getAlignment()));
\r
1761 viewport.setEndSeq(viewport.getAlignment().getHeight());
\r
1762 viewport.getAlignment().getWidth();
\r
1763 viewport.firePropertyChange("alignment", null,
\r
1764 viewport.getAlignment().getSequences());
\r
1768 protected void cut_actionPerformed()
\r
1770 copy_actionPerformed();
\r
1771 delete_actionPerformed();
\r
1774 protected void delete_actionPerformed()
\r
1777 SequenceGroup sg = viewport.getSelectionGroup();
\r
1783 Vector seqs = new Vector();
\r
1785 for (int i = 0; i < sg.getSize(); i++)
\r
1787 seq = sg.getSequenceAt(i);
\r
1788 seqs.addElement(seq);
\r
1791 // If the cut affects all sequences, remove highlighted columns
\r
1792 if (sg.getSize() == viewport.getAlignment().getHeight())
\r
1794 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
1795 sg.getEndRes() + 1);
\r
1798 SequenceI[] cut = new SequenceI[seqs.size()];
\r
1799 for (int i = 0; i < seqs.size(); i++)
\r
1801 cut[i] = (SequenceI) seqs.elementAt(i);
\r
1805 * //ADD HISTORY ITEM
\r
1807 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
\r
1808 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
\r
1809 viewport.getAlignment()));
\r
1811 viewport.setSelectionGroup(null);
\r
1812 viewport.getAlignment().deleteGroup(sg);
\r
1814 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1817 if (viewport.getAlignment().getHeight() < 1)
\r
1819 this.setVisible(false);
\r
1821 viewport.sendSelection();
\r
1825 * group consensus toggled
\r
1828 protected void showGroupConsensus_actionPerformed()
\r
1830 viewport.setShowGroupConsensus(showGroupConsensus.getState());
\r
1831 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1836 * group conservation toggled.
\r
1838 protected void showGroupConservation_actionPerformed()
\r
1840 viewport.setShowGroupConservation(showGroupConservation.getState());
\r
1841 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1848 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
\r
1849 * .event.ActionEvent)
\r
1851 protected void showConsensusHistogram_actionPerformed()
\r
1853 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
\r
1854 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1860 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
\r
1861 * .event.ActionEvent)
\r
1863 protected void showSequenceLogo_actionPerformed()
\r
1865 viewport.setShowSequenceLogo(showSequenceLogo.getState());
\r
1866 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1869 protected void applyAutoAnnotationSettings_actionPerformed()
\r
1871 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1874 protected void makeGrpsFromSelection_actionPerformed()
\r
1876 if (viewport.getSelectionGroup() != null)
\r
1878 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
\r
1879 viewport.getSequenceSelection(),
\r
1880 viewport.getAlignmentView(true).getSequenceStrings(
\r
1881 viewport.getGapCharacter()),
\r
1882 viewport.getAlignment().getGroups());
\r
1883 viewport.getAlignment().deleteAllGroups();
\r
1884 viewport.sequenceColours = null;
\r
1885 viewport.setSelectionGroup(null);
\r
1886 // set view properties for each group
\r
1887 for (int g = 0; g < gps.length; g++)
\r
1889 // gps[g].setShowunconserved(viewport.getShowUnconserved());
\r
1890 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
\r
1891 viewport.getAlignment().addGroup(gps[g]);
\r
1892 Color col = new Color((int) (Math.random() * 255),
\r
1893 (int) (Math.random() * 255), (int) (Math.random() * 255));
\r
1894 col = col.brighter();
\r
1895 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
\r
1896 .hasMoreElements(); viewport.setSequenceColour(
\r
1897 (SequenceI) sq.nextElement(), col))
\r
1900 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
\r
1901 alignPanel.updateAnnotation();
\r
1902 alignPanel.paintAlignment(true);
\r
1906 protected void deleteGroups_actionPerformed()
\r
1908 viewport.getAlignment().deleteAllGroups();
\r
1909 viewport.sequenceColours = null;
\r
1910 viewport.setSelectionGroup(null);
\r
1912 alignPanel.paintAlignment(true);
\r
1915 public void selectAllSequenceMenuItem_actionPerformed()
\r
1917 SequenceGroup sg = new SequenceGroup();
\r
1918 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1920 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
1922 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
\r
1923 viewport.setSelectionGroup(sg);
\r
1924 alignPanel.paintAlignment(true);
\r
1925 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1926 viewport.sendSelection();
\r
1929 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1931 if (viewport.cursorMode)
\r
1933 alignPanel.seqPanel.keyboardNo1 = null;
\r
1934 alignPanel.seqPanel.keyboardNo2 = null;
\r
1936 viewport.setSelectionGroup(null);
\r
1937 viewport.getColumnSelection().clear();
\r
1938 viewport.setSelectionGroup(null);
\r
1939 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1940 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1941 alignPanel.paintAlignment(true);
\r
1942 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1943 viewport.sendSelection();
\r
1946 public void invertSequenceMenuItem_actionPerformed()
\r
1948 SequenceGroup sg = viewport.getSelectionGroup();
\r
1949 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1951 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1954 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1955 viewport.sendSelection();
\r
1958 public void invertColSel_actionPerformed()
\r
1960 viewport.invertColumnSelection();
\r
1961 alignPanel.paintAlignment(true);
\r
1962 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1963 viewport.sendSelection();
\r
1966 void trimAlignment(boolean trimLeft)
\r
1968 ColumnSelection colSel = viewport.getColumnSelection();
\r
1971 if (colSel.size() > 0)
\r
1975 column = colSel.getMin();
\r
1979 column = colSel.getMax();
\r
1983 if (viewport.getSelectionGroup() != null)
\r
1985 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
1986 viewport.getHiddenRepSequences());
\r
1990 seqs = viewport.getAlignment().getSequencesArray();
\r
1993 TrimRegionCommand trimRegion;
\r
1996 trimRegion = new TrimRegionCommand("Remove Left",
\r
1997 TrimRegionCommand.TRIM_LEFT, seqs, column,
\r
1998 viewport.getAlignment(), viewport.getColumnSelection(),
\r
1999 viewport.getSelectionGroup());
\r
2000 viewport.setStartRes(0);
\r
2004 trimRegion = new TrimRegionCommand("Remove Right",
\r
2005 TrimRegionCommand.TRIM_RIGHT, seqs, column,
\r
2006 viewport.getAlignment(), viewport.getColumnSelection(),
\r
2007 viewport.getSelectionGroup());
\r
2010 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
\r
2012 addHistoryItem(trimRegion);
\r
2014 Vector groups = viewport.getAlignment().getGroups();
\r
2016 for (int i = 0; i < groups.size(); i++)
\r
2018 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
2020 if ((trimLeft && !sg.adjustForRemoveLeft(column))
\r
2021 || (!trimLeft && !sg.adjustForRemoveRight(column)))
\r
2023 viewport.getAlignment().deleteGroup(sg);
\r
2027 viewport.firePropertyChange("alignment", null, viewport
\r
2028 .getAlignment().getSequences());
\r
2032 public void removeGappedColumnMenuItem_actionPerformed()
\r
2034 int start = 0, end = viewport.getAlignment().getWidth() - 1;
\r
2037 if (viewport.getSelectionGroup() != null)
\r
2039 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2040 viewport.getHiddenRepSequences());
\r
2041 start = viewport.getSelectionGroup().getStartRes();
\r
2042 end = viewport.getSelectionGroup().getEndRes();
\r
2046 seqs = viewport.getAlignment().getSequencesArray();
\r
2049 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
\r
2050 "Remove Gapped Columns", seqs, start, end, viewport.getAlignment());
\r
2052 addHistoryItem(removeGapCols);
\r
2054 statusBar.setText("Removed " + removeGapCols.getSize()
\r
2055 + " empty columns.");
\r
2057 // This is to maintain viewport position on first residue
\r
2058 // of first sequence
\r
2059 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
\r
2060 int startRes = seq.findPosition(viewport.startRes);
\r
2061 // ShiftList shifts;
\r
2062 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
\r
2063 // edit.alColumnChanges=shifts.getInverse();
\r
2064 // if (viewport.hasHiddenColumns)
\r
2065 // viewport.getColumnSelection().compensateForEdits(shifts);
\r
2066 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
2067 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
2072 public void removeAllGapsMenuItem_actionPerformed()
\r
2074 int start = 0, end = viewport.getAlignment().getWidth() - 1;
\r
2077 if (viewport.getSelectionGroup() != null)
\r
2079 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2080 viewport.getHiddenRepSequences());
\r
2081 start = viewport.getSelectionGroup().getStartRes();
\r
2082 end = viewport.getSelectionGroup().getEndRes();
\r
2086 seqs = viewport.getAlignment().getSequencesArray();
\r
2089 // This is to maintain viewport position on first residue
\r
2090 // of first sequence
\r
2091 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
\r
2092 int startRes = seq.findPosition(viewport.startRes);
\r
2094 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
\r
2095 viewport.getAlignment()));
\r
2097 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
2099 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
2104 public void findMenuItem_actionPerformed()
\r
2106 new Finder(alignPanel);
\r
2110 * create a new view derived from the current view
\r
2112 * @param viewtitle
\r
2113 * @return frame for the new view
\r
2115 public AlignFrame newView(String viewtitle)
\r
2118 if (viewport.hasHiddenRows())
\r
2120 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
\r
2121 .getFullAlignment().getSequencesArray());
\r
2125 newal = new Alignment(viewport.getAlignment().getSequencesArray());
\r
2128 if (viewport.getAlignment().getAlignmentAnnotation() != null)
\r
2130 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
\r
2132 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
\r
2134 newal.addAnnotation(viewport.getAlignment().getAlignmentAnnotation()[i]);
\r
2139 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
\r
2141 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
\r
2142 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
\r
2143 PaintRefresher.Register(newaf.alignPanel,
\r
2144 newaf.alignPanel.av.getSequenceSetId());
\r
2146 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
\r
2147 newaf.alignPanel.av.getSequenceSetId());
\r
2148 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
\r
2149 newaf.alignPanel.av.getSequenceSetId());
\r
2151 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
2152 .getSequenceSetId());
\r
2153 int viewSize = -1;
\r
2154 for (int i = 0; i < comps.size(); i++)
\r
2156 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
2162 String title = new String(this.getTitle());
\r
2163 if (viewtitle != null)
\r
2165 title = viewtitle + " ( " + title + ")";
\r
2169 if (title.indexOf("(View") > -1)
\r
2171 title = title.substring(0, title.indexOf("(View"));
\r
2173 title += "(View " + viewSize + ")";
\r
2176 newaf.setTitle(title.toString());
\r
2178 newaf.viewport.historyList = viewport.historyList;
\r
2179 newaf.viewport.redoList = viewport.redoList;
\r
2185 * @return list of feature groups on the view
\r
2187 public String[] getFeatureGroups()
\r
2189 FeatureRenderer fr = null;
\r
2190 if (alignPanel != null
\r
2191 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2193 return fr.getGroups();
\r
2199 * get sequence feature groups that are hidden or shown
\r
2205 public String[] getFeatureGroupsOfState(boolean visible)
\r
2207 FeatureRenderer fr = null;
\r
2208 if (alignPanel != null
\r
2209 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2211 return fr.getGroups(visible);
\r
2217 * Change the display state for the given feature groups
\r
2220 * list of group strings
\r
2222 * visible or invisible
\r
2224 public void setFeatureGroupState(String[] groups, boolean state)
\r
2226 FeatureRenderer fr = null;
\r
2227 this.sequenceFeatures.setState(true);
\r
2228 viewport.showSequenceFeatures(true);
\r
2229 if (alignPanel != null
\r
2230 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2232 fr.setGroupState(groups, state);
\r
2233 alignPanel.seqPanel.seqCanvas.repaint();
\r
2234 if (alignPanel.overviewPanel != null)
\r
2236 alignPanel.overviewPanel.updateOverviewImage();
\r
2241 public void seqLimits_itemStateChanged()
\r
2243 viewport.setShowJVSuffix(seqLimits.getState());
\r
2244 alignPanel.fontChanged();
\r
2245 alignPanel.paintAlignment(true);
\r
2248 protected void colourTextMenuItem_actionPerformed()
\r
2250 viewport.setColourText(colourTextMenuItem.getState());
\r
2251 alignPanel.paintAlignment(true);
\r
2254 protected void displayNonconservedMenuItem_actionPerformed()
\r
2256 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
\r
2257 alignPanel.paintAlignment(true);
\r
2260 protected void wrapMenuItem_actionPerformed()
\r
2262 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
2263 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
2264 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
2265 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
2266 scaleRight.setEnabled(wrapMenuItem.getState());
\r
2267 alignPanel.paintAlignment(true);
\r
2270 public void overviewMenuItem_actionPerformed()
\r
2272 if (alignPanel.overviewPanel != null)
\r
2277 Frame frame = new Frame();
\r
2278 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
2279 frame.add(overview);
\r
2280 // +50 must allow for applet frame window
\r
2281 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
2282 overview.getPreferredSize().width,
\r
2283 overview.getPreferredSize().height + 50);
\r
2286 frame.addWindowListener(new WindowAdapter()
\r
2288 public void windowClosing(WindowEvent e)
\r
2290 alignPanel.setOverviewPanel(null);
\r
2294 alignPanel.setOverviewPanel(overview);
\r
2298 void changeColour(ColourSchemeI cs)
\r
2300 int threshold = 0;
\r
2304 if (viewport.getAbovePIDThreshold())
\r
2306 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
2309 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2311 viewport.setGlobalColourScheme(cs);
\r
2315 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2318 if (viewport.getConservationSelected())
\r
2321 Alignment al = (Alignment) viewport.getAlignment();
\r
2322 Conservation c = new Conservation("All",
\r
2323 ResidueProperties.propHash, 3, al.getSequences(), 0,
\r
2324 al.getWidth() - 1);
\r
2327 c.verdict(false, viewport.getConsPercGaps());
\r
2329 cs.setConservation(c);
\r
2331 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
\r
2332 cs, "Background"));
\r
2337 cs.setConservation(null);
\r
2340 cs.setConsensus(viewport.getSequenceConsensusHash());
\r
2343 viewport.setGlobalColourScheme(cs);
\r
2345 if (viewport.getColourAppliesToAllGroups())
\r
2347 Vector groups = viewport.getAlignment().getGroups();
\r
2348 for (int i = 0; i < groups.size(); i++)
\r
2350 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
2357 if (cs instanceof ClustalxColourScheme)
\r
2359 sg.cs = new ClustalxColourScheme(
\r
2360 sg.getSequences(viewport.getHiddenRepSequences()),
\r
2367 sg.cs = cs.getClass().newInstance();
\r
2368 } catch (Exception ex)
\r
2370 ex.printStackTrace();
\r
2375 if (viewport.getAbovePIDThreshold()
\r
2376 || cs instanceof PIDColourScheme
\r
2377 || cs instanceof Blosum62ColourScheme)
\r
2379 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2380 sg.cs.setConsensus(AAFrequency.calculate(
\r
2381 sg.getSequences(viewport.getHiddenRepSequences()), 0,
\r
2386 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2389 if (viewport.getConservationSelected())
\r
2391 Conservation c = new Conservation("Group",
\r
2392 ResidueProperties.propHash, 3,
\r
2393 sg.getSequences(viewport.getHiddenRepSequences()), 0,
\r
2394 viewport.getAlignment().getWidth() - 1);
\r
2396 c.verdict(false, viewport.getConsPercGaps());
\r
2397 sg.cs.setConservation(c);
\r
2401 sg.cs.setConservation(null);
\r
2402 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2408 if (alignPanel.getOverviewPanel() != null)
\r
2410 alignPanel.getOverviewPanel().updateOverviewImage();
\r
2413 jalview.structure.StructureSelectionManager
\r
2414 .getStructureSelectionManager(viewport.applet).sequenceColoursChanged(
\r
2417 alignPanel.paintAlignment(true);
\r
2420 protected void modifyPID_actionPerformed()
\r
2422 if (viewport.getAbovePIDThreshold()
\r
2423 && viewport.getGlobalColourScheme() != null)
\r
2425 SliderPanel.setPIDSliderSource(alignPanel,
\r
2426 viewport.getGlobalColourScheme(), "Background");
\r
2427 SliderPanel.showPIDSlider();
\r
2431 protected void modifyConservation_actionPerformed()
\r
2433 if (viewport.getConservationSelected()
\r
2434 && viewport.getGlobalColourScheme() != null)
\r
2436 SliderPanel.setConservationSlider(alignPanel,
\r
2437 viewport.getGlobalColourScheme(), "Background");
\r
2438 SliderPanel.showConservationSlider();
\r
2442 protected void conservationMenuItem_actionPerformed()
\r
2444 viewport.setConservationSelected(conservationMenuItem.getState());
\r
2446 viewport.setAbovePIDThreshold(false);
\r
2447 abovePIDThreshold.setState(false);
\r
2449 changeColour(viewport.getGlobalColourScheme());
\r
2451 modifyConservation_actionPerformed();
\r
2454 public void abovePIDThreshold_actionPerformed()
\r
2456 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
2458 conservationMenuItem.setState(false);
\r
2459 viewport.setConservationSelected(false);
\r
2461 changeColour(viewport.getGlobalColourScheme());
\r
2463 modifyPID_actionPerformed();
\r
2466 public void sortPairwiseMenuItem_actionPerformed()
\r
2468 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2469 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
\r
2470 .getAlignment().getSequenceAt(0), null);
\r
2472 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
\r
2473 viewport.getAlignment()));
\r
2474 alignPanel.paintAlignment(true);
\r
2477 public void sortIDMenuItem_actionPerformed()
\r
2479 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2480 AlignmentSorter.sortByID(viewport.getAlignment());
\r
2481 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
\r
2482 alignPanel.paintAlignment(true);
\r
2485 public void sortLengthMenuItem_actionPerformed()
\r
2487 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2488 AlignmentSorter.sortByLength(viewport.getAlignment());
\r
2489 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
\r
2490 viewport.getAlignment()));
\r
2491 alignPanel.paintAlignment(true);
\r
2494 public void sortGroupMenuItem_actionPerformed()
\r
2496 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2497 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
2498 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
\r
2499 viewport.getAlignment()));
\r
2500 alignPanel.paintAlignment(true);
\r
2504 public void removeRedundancyMenuItem_actionPerformed()
\r
2506 new RedundancyPanel(alignPanel);
\r
2509 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
2511 if (viewport.getSelectionGroup() != null
\r
2512 && viewport.getSelectionGroup().getSize() > 1)
\r
2514 Frame frame = new Frame();
\r
2515 frame.add(new PairwiseAlignPanel(alignPanel));
\r
2516 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
\r
2521 public void PCAMenuItem_actionPerformed()
\r
2523 // are the sequences aligned?
\r
2524 if (!viewport.getAlignment().isAligned(false))
\r
2526 SequenceI current;
\r
2527 int Width = viewport.getAlignment().getWidth();
\r
2529 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2531 current = viewport.getAlignment().getSequenceAt(i);
\r
2533 if (current.getLength() < Width)
\r
2535 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2538 alignPanel.paintAlignment(true);
\r
2541 if ((viewport.getSelectionGroup() != null
\r
2542 && viewport.getSelectionGroup().getSize() < 4 && viewport
\r
2543 .getSelectionGroup().getSize() > 0)
\r
2544 || viewport.getAlignment().getHeight() < 4)
\r
2551 new PCAPanel(viewport);
\r
2552 } catch (java.lang.OutOfMemoryError ex)
\r
2558 public void averageDistanceTreeMenuItem_actionPerformed()
\r
2560 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
2563 public void neighbourTreeMenuItem_actionPerformed()
\r
2565 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
2568 protected void njTreeBlosumMenuItem_actionPerformed()
\r
2570 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2573 protected void avTreeBlosumMenuItem_actionPerformed()
\r
2575 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2578 void NewTreePanel(String type, String pwType, String title)
\r
2580 // are the sequences aligned?
\r
2581 if (!viewport.getAlignment().isAligned(false))
\r
2583 SequenceI current;
\r
2584 int Width = viewport.getAlignment().getWidth();
\r
2586 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2588 current = viewport.getAlignment().getSequenceAt(i);
\r
2590 if (current.getLength() < Width)
\r
2592 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2595 alignPanel.paintAlignment(true);
\r
2599 if ((viewport.getSelectionGroup() != null && viewport
\r
2600 .getSelectionGroup().getSize() > 1)
\r
2601 || (viewport.getSelectionGroup() == null && viewport.getAlignment()
\r
2602 .getHeight() > 1))
\r
2604 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
\r
2606 addTreeMenuItem(tp, title);
\r
2608 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
2612 void loadTree_actionPerformed()
\r
2614 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
2615 cap.setText("Paste your Newick tree file here.");
\r
2616 cap.setTreeImport();
\r
2617 Frame frame = new Frame();
\r
2619 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
2622 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
2624 TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
\r
2625 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
2626 addTreeMenuItem(tp, treeFile);
\r
2630 * sort the alignment using the given treePanel
\r
2632 * @param treePanel
\r
2633 * tree used to sort view
\r
2635 * string used for undo event name
\r
2637 public void sortByTree(TreePanel treePanel, String title)
\r
2639 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2641 .sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
2642 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2643 // HistoryItem.SORT));
\r
2644 addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
\r
2645 viewport.getAlignment()));
\r
2646 alignPanel.paintAlignment(true);
\r
2650 * Do any automatic reordering of the alignment and add the necessary bits to
\r
2651 * the menu structure for the new tree
\r
2653 * @param treePanel
\r
2656 protected void addTreeMenuItem(final TreePanel treePanel,
\r
2657 final String title)
\r
2659 final MenuItem item = new MenuItem(title);
\r
2660 sortByTreeMenu.add(item);
\r
2661 item.addActionListener(new java.awt.event.ActionListener()
\r
2663 public void actionPerformed(ActionEvent evt)
\r
2665 sortByTree(treePanel, title); // treePanel.getTitle());
\r
2669 treePanel.addWindowListener(new WindowAdapter()
\r
2671 public void windowOpened(WindowEvent e)
\r
2673 if (viewport.sortByTree)
\r
2675 sortByTree(treePanel, title);
\r
2677 super.windowOpened(e);
\r
2680 public void windowClosing(WindowEvent e)
\r
2682 sortByTreeMenu.remove(item);
\r
2686 public boolean sortBy(AlignmentOrder alorder, String undoname)
\r
2688 SequenceI[] oldOrder = viewport.getAlignment()
\r
2689 .getSequencesArray();
\r
2690 if (viewport.applet.debug)
\r
2692 System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");
\r
2694 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
\r
2695 if (undoname!=null)
\r
2697 addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.getAlignment()));
\r
2699 alignPanel.paintAlignment(true);
\r
2703 protected void documentation_actionPerformed()
\r
2705 alignPanel.av.applet.openJalviewHelpUrl();
\r
2708 protected void about_actionPerformed()
\r
2711 class AboutPanel extends Canvas
\r
2717 public AboutPanel(String version, String builddate)
\r
2719 this.version = version;
\r
2720 this.builddate = builddate;
\r
2723 public void paint(Graphics g)
\r
2725 g.setColor(Color.white);
\r
2726 g.fillRect(0, 0, getSize().width, getSize().height);
\r
2727 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2728 FontMetrics fm = g.getFontMetrics();
\r
2729 int fh = fm.getHeight();
\r
2731 g.setColor(Color.black);
\r
2732 // TODO: update this text for each release or centrally store it for
\r
2733 // lite and application
\r
2734 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
2735 g.drawString("JalviewLite - Release " + version, x, y += fh);
\r
2736 g.setFont(new Font("Helvetica", Font.BOLD, 12));
\r
2737 g.drawString("Build date: " + builddate, x, y += fh);
\r
2738 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2740 "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",
\r
2741 x, y += fh * 1.5);
\r
2742 g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
\r
2744 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
\r
2747 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
\r
2749 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
\r
2751 "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
\r
2754 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
\r
2756 g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
\r
2761 Frame frame = new Frame();
\r
2762 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
\r
2763 .getBuildDate()));
\r
2764 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
\r
2768 public void showURL(String url, String target)
\r
2770 if (viewport.applet == null)
\r
2772 System.out.println("Not running as applet - no browser available.");
\r
2776 viewport.applet.showURL(url, target);
\r
2780 // ////////////////////////////////////////////////////////////////////////////////
\r
2781 // JBuilder Graphics here
\r
2783 MenuBar alignFrameMenuBar = new MenuBar();
\r
2785 Menu fileMenu = new Menu("File");
\r
2787 MenuItem loadApplication = new MenuItem("View in Full Application");
\r
2789 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
\r
2791 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
\r
2793 MenuItem loadScores = new MenuItem("Load Associated T-Coffee scores ...");
\r
2795 MenuItem outputFeatures = new MenuItem("Export Features ...");
\r
2797 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
\r
2799 MenuItem closeMenuItem = new MenuItem("Close");
\r
2801 Menu editMenu = new Menu("Edit");
\r
2803 Menu viewMenu = new Menu("View");
\r
2805 Menu colourMenu = new Menu("Colour");
\r
2807 Menu calculateMenu = new Menu("Calculate");
\r
2809 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
2811 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
2813 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
2815 MenuItem remove2LeftMenuItem = new MenuItem();
\r
2817 MenuItem remove2RightMenuItem = new MenuItem();
\r
2819 MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
2821 MenuItem removeAllGapsMenuItem = new MenuItem();
\r
2823 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
2825 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
2827 MenuItem sortPairwiseMenuItem = new MenuItem();
\r
2829 MenuItem sortIDMenuItem = new MenuItem();
\r
2831 MenuItem sortLengthMenuItem = new MenuItem();
\r
2833 MenuItem sortGroupMenuItem = new MenuItem();
\r
2835 MenuItem removeRedundancyMenuItem = new MenuItem();
\r
2837 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
2839 MenuItem PCAMenuItem = new MenuItem();
\r
2841 MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
2843 MenuItem neighbourTreeMenuItem = new MenuItem();
\r
2845 BorderLayout borderLayout1 = new BorderLayout();
\r
2847 public Label statusBar = new Label();
\r
2849 Menu outputTextboxMenu = new Menu();
\r
2851 MenuItem clustalColour = new MenuItem();
\r
2853 MenuItem zappoColour = new MenuItem();
\r
2855 MenuItem taylorColour = new MenuItem();
\r
2857 MenuItem hydrophobicityColour = new MenuItem();
\r
2859 MenuItem helixColour = new MenuItem();
\r
2861 MenuItem strandColour = new MenuItem();
\r
2863 MenuItem turnColour = new MenuItem();
\r
2865 MenuItem buriedColour = new MenuItem();
\r
2867 MenuItem purinePyrimidineColour = new MenuItem();
\r
2868 MenuItem RNAHelixColour = new MenuItem();
\r
2870 MenuItem userDefinedColour = new MenuItem();
\r
2872 MenuItem PIDColour = new MenuItem();
\r
2874 MenuItem BLOSUM62Colour = new MenuItem();
\r
2876 MenuItem tcoffeeColour = new MenuItem();
\r
2878 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
2880 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
2882 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
2884 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
2886 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
\r
2888 MenuItem alProperties = new MenuItem("Alignment Properties...");
\r
2890 MenuItem overviewMenuItem = new MenuItem();
\r
2892 MenuItem undoMenuItem = new MenuItem();
\r
2894 MenuItem redoMenuItem = new MenuItem();
\r
2896 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
2898 MenuItem noColourmenuItem = new MenuItem();
\r
2900 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
2902 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
2904 MenuItem findMenuItem = new MenuItem();
\r
2906 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
2908 MenuItem nucleotideColour = new MenuItem();
\r
2910 MenuItem deleteGroups = new MenuItem();
\r
2912 MenuItem grpsFromSelection = new MenuItem();
\r
2914 MenuItem delete = new MenuItem();
\r
2916 MenuItem copy = new MenuItem();
\r
2918 MenuItem cut = new MenuItem();
\r
2920 Menu pasteMenu = new Menu();
\r
2922 MenuItem pasteNew = new MenuItem();
\r
2924 MenuItem pasteThis = new MenuItem();
\r
2926 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
2928 MenuItem font = new MenuItem();
\r
2930 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
2932 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
2934 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
2936 MenuItem modifyPID = new MenuItem();
\r
2938 MenuItem modifyConservation = new MenuItem();
\r
2940 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
\r
2941 "Autocalculate Consensus", true);
\r
2943 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
\r
2944 "Sort Alignment With New Tree", true);
\r
2946 Menu sortByTreeMenu = new Menu();
\r
2948 Menu sort = new Menu();
\r
2950 Menu calculate = new Menu();
\r
2952 MenuItem inputText = new MenuItem();
\r
2954 Menu helpMenu = new Menu();
\r
2956 MenuItem documentation = new MenuItem();
\r
2958 MenuItem about = new MenuItem();
\r
2960 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
2962 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
\r
2964 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
\r
2965 Menu autoAnnMenu=new Menu();
\r
2966 CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();
\r
2967 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
\r
2968 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
\r
2969 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
\r
2970 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
\r
2972 private void jbInit() throws Exception
\r
2975 setMenuBar(alignFrameMenuBar);
\r
2979 // dynamically fill save as menu with available formats
\r
2980 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
2983 item = new MenuItem(
\r
2984 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
2986 item.addActionListener(new java.awt.event.ActionListener()
\r
2988 public void actionPerformed(ActionEvent e)
\r
2990 outputText_actionPerformed(e);
\r
2994 outputTextboxMenu.add(item);
\r
2996 closeMenuItem.addActionListener(this);
\r
2997 loadApplication.addActionListener(this);
\r
2999 loadTree.addActionListener(this);
\r
3000 loadAnnotations.addActionListener(this);
\r
3001 loadScores.addActionListener(this);
\r
3002 outputFeatures.addActionListener(this);
\r
3003 outputAnnotations.addActionListener(this);
\r
3004 selectAllSequenceMenuItem.addActionListener(this);
\r
3005 deselectAllSequenceMenuItem.addActionListener(this);
\r
3006 invertSequenceMenuItem.addActionListener(this);
\r
3007 remove2LeftMenuItem.setLabel("Remove Left");
\r
3008 remove2LeftMenuItem.addActionListener(this);
\r
3009 remove2RightMenuItem.setLabel("Remove Right");
\r
3010 remove2RightMenuItem.addActionListener(this);
\r
3011 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
3012 removeGappedColumnMenuItem.addActionListener(this);
\r
3013 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
3014 removeAllGapsMenuItem.addActionListener(this);
\r
3015 viewBoxesMenuItem.setLabel("Boxes");
\r
3016 viewBoxesMenuItem.setState(true);
\r
3017 viewBoxesMenuItem.addItemListener(this);
\r
3018 viewTextMenuItem.setLabel("Text");
\r
3019 viewTextMenuItem.setState(true);
\r
3020 viewTextMenuItem.addItemListener(this);
\r
3021 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
3022 sortPairwiseMenuItem.addActionListener(this);
\r
3023 sortIDMenuItem.setLabel("by ID");
\r
3024 sortIDMenuItem.addActionListener(this);
\r
3025 sortLengthMenuItem.setLabel("by Length");
\r
3026 sortLengthMenuItem.addActionListener(this);
\r
3027 sortGroupMenuItem.setLabel("by Group");
\r
3028 sortGroupMenuItem.addActionListener(this);
\r
3029 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
3030 removeRedundancyMenuItem.addActionListener(this);
\r
3031 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
3032 pairwiseAlignmentMenuItem.addActionListener(this);
\r
3033 PCAMenuItem.setLabel("Principal Component Analysis");
\r
3034 PCAMenuItem.addActionListener(this);
\r
3035 averageDistanceTreeMenuItem
\r
3036 .setLabel("Average Distance Using % Identity");
\r
3037 averageDistanceTreeMenuItem.addActionListener(this);
\r
3038 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
3039 neighbourTreeMenuItem.addActionListener(this);
\r
3040 statusBar.setBackground(Color.white);
\r
3041 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
3042 statusBar.setText("Status bar");
\r
3043 outputTextboxMenu.setLabel("Output to Textbox");
\r
3044 clustalColour.setLabel("Clustalx");
\r
3046 clustalColour.addActionListener(this);
\r
3047 zappoColour.setLabel("Zappo");
\r
3048 zappoColour.addActionListener(this);
\r
3049 taylorColour.setLabel("Taylor");
\r
3050 taylorColour.addActionListener(this);
\r
3051 hydrophobicityColour.setLabel("Hydrophobicity");
\r
3052 hydrophobicityColour.addActionListener(this);
\r
3053 helixColour.setLabel("Helix Propensity");
\r
3054 helixColour.addActionListener(this);
\r
3055 strandColour.setLabel("Strand Propensity");
\r
3056 strandColour.addActionListener(this);
\r
3057 turnColour.setLabel("Turn Propensity");
\r
3058 turnColour.addActionListener(this);
\r
3059 buriedColour.setLabel("Buried Index");
\r
3060 buriedColour.addActionListener(this);
\r
3061 purinePyrimidineColour.setLabel("Purine/Pyrimidine");
\r
3062 purinePyrimidineColour.addActionListener(this);
\r
3063 RNAHelixColour.setLabel("by RNA Helices");
\r
3064 RNAHelixColour.addActionListener(this);
\r
3065 userDefinedColour.setLabel("User Defined...");
\r
3066 userDefinedColour.addActionListener(this);
\r
3067 PIDColour.setLabel("Percentage Identity");
\r
3068 PIDColour.addActionListener(this);
\r
3069 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
3070 BLOSUM62Colour.addActionListener(this);
\r
3071 tcoffeeColour.setLabel("T-Coffee Scores");
\r
3072 tcoffeeColour.setEnabled(false); // it will enabled only if a score file is provided
\r
3073 tcoffeeColour.addActionListener(this);
\r
3074 avDistanceTreeBlosumMenuItem .setLabel("Average Distance Using BLOSUM62");
\r
3075 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
3076 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
3077 njTreeBlosumMenuItem.addActionListener(this);
\r
3078 annotationPanelMenuItem.setLabel("Show Annotations");
\r
3079 annotationPanelMenuItem.addItemListener(this);
\r
3080 colourTextMenuItem.setLabel("Colour Text");
\r
3081 colourTextMenuItem.addItemListener(this);
\r
3082 displayNonconservedMenuItem.setLabel("Show nonconserved");
\r
3083 displayNonconservedMenuItem.addItemListener(this);
\r
3084 alProperties.addActionListener(this);
\r
3085 overviewMenuItem.setLabel("Overview Window");
\r
3086 overviewMenuItem.addActionListener(this);
\r
3087 undoMenuItem.setEnabled(false);
\r
3088 undoMenuItem.setLabel("Undo");
\r
3089 undoMenuItem.addActionListener(this);
\r
3090 redoMenuItem.setEnabled(false);
\r
3091 redoMenuItem.setLabel("Redo");
\r
3092 redoMenuItem.addActionListener(this);
\r
3093 conservationMenuItem.setLabel("by Conservation");
\r
3094 conservationMenuItem.addItemListener(this);
\r
3095 noColourmenuItem.setLabel("None");
\r
3096 noColourmenuItem.addActionListener(this);
\r
3097 wrapMenuItem.setLabel("Wrap");
\r
3098 wrapMenuItem.addItemListener(this);
\r
3099 renderGapsMenuItem.setLabel("Show Gaps");
\r
3100 renderGapsMenuItem.setState(true);
\r
3101 renderGapsMenuItem.addItemListener(this);
\r
3102 findMenuItem.setLabel("Find...");
\r
3103 findMenuItem.addActionListener(this);
\r
3104 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
3105 abovePIDThreshold.addItemListener(this);
\r
3106 nucleotideColour.setLabel("Nucleotide");
\r
3107 nucleotideColour.addActionListener(this);
\r
3108 deleteGroups.setLabel("Undefine Groups");
\r
3109 deleteGroups.addActionListener(this);
\r
3110 grpsFromSelection.setLabel("Make Groups for selection");
\r
3111 grpsFromSelection.addActionListener(this);
\r
3112 copy.setLabel("Copy");
\r
3113 copy.addActionListener(this);
\r
3114 cut.setLabel("Cut");
\r
3115 cut.addActionListener(this);
\r
3116 delete.setLabel("Delete");
\r
3117 delete.addActionListener(this);
\r
3118 pasteMenu.setLabel("Paste");
\r
3119 pasteNew.setLabel("To New Alignment");
\r
3120 pasteNew.addActionListener(this);
\r
3121 pasteThis.setLabel("Add To This Alignment");
\r
3122 pasteThis.addActionListener(this);
\r
3123 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
3124 applyToAllGroups.setState(true);
\r
3125 applyToAllGroups.addItemListener(this);
\r
3126 font.setLabel("Font...");
\r
3127 font.addActionListener(this);
\r
3128 scaleAbove.setLabel("Scale Above");
\r
3129 scaleAbove.setState(true);
\r
3130 scaleAbove.setEnabled(false);
\r
3131 scaleAbove.addItemListener(this);
\r
3132 scaleLeft.setEnabled(false);
\r
3133 scaleLeft.setState(true);
\r
3134 scaleLeft.setLabel("Scale Left");
\r
3135 scaleLeft.addItemListener(this);
\r
3136 scaleRight.setEnabled(false);
\r
3137 scaleRight.setState(true);
\r
3138 scaleRight.setLabel("Scale Right");
\r
3139 scaleRight.addItemListener(this);
\r
3140 modifyPID.setLabel("Modify Identity Threshold...");
\r
3141 modifyPID.addActionListener(this);
\r
3142 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
3143 modifyConservation.addActionListener(this);
\r
3144 sortByTreeMenu.setLabel("By Tree Order");
\r
3145 sort.setLabel("Sort");
\r
3146 calculate.setLabel("Calculate Tree");
\r
3147 autoCalculate.addItemListener(this);
\r
3148 sortByTree.addItemListener(this);
\r
3149 inputText.setLabel("Input from textbox");
\r
3150 inputText.addActionListener(this);
\r
3151 centreColumnLabelFlag.setLabel("Centre column labels");
\r
3152 centreColumnLabelFlag.addItemListener(this);
\r
3153 followMouseOverFlag.setLabel("Automatic Scrolling");
\r
3154 followMouseOverFlag.addItemListener(this);
\r
3155 helpMenu.setLabel("Help");
\r
3156 documentation.setLabel("Documentation");
\r
3157 documentation.addActionListener(this);
\r
3159 about.setLabel("About...");
\r
3160 about.addActionListener(this);
\r
3161 seqLimits.setState(true);
\r
3162 seqLimits.setLabel("Show Sequence Limits");
\r
3163 seqLimits.addItemListener(this);
\r
3164 featureSettings.setLabel("Feature Settings...");
\r
3165 featureSettings.addActionListener(this);
\r
3166 sequenceFeatures.setLabel("Sequence Features");
\r
3167 sequenceFeatures.addItemListener(this);
\r
3168 sequenceFeatures.setState(false);
\r
3169 annotationColour.setLabel("by Annotation...");
\r
3170 annotationColour.addActionListener(this);
\r
3171 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
3172 invertColSel.setLabel("Invert Column Selection");
\r
3173 menu1.setLabel("Show");
\r
3174 showColumns.setLabel("All Columns ");
\r
3175 showSeqs.setLabel("All Sequences");
\r
3176 menu2.setLabel("Hide");
\r
3177 hideColumns.setLabel("Selected Columns");
\r
3178 hideSequences.setLabel("Selected Sequences");
\r
3179 hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
\r
3180 hideAllSelection.setLabel("Selected Region");
\r
3181 showAllHidden.setLabel("All Sequences and Columns");
\r
3182 showGroupConsensus.setLabel("Group Consensus");
\r
3183 showGroupConservation.setLabel("Group Conservation");
\r
3184 showConsensusHistogram.setLabel("Show Consensus Histogram");
\r
3185 showSequenceLogo.setLabel("Show Consensus Logo");
\r
3186 applyAutoAnnotationSettings.setLabel("Apply to all groups");
\r
3187 applyAutoAnnotationSettings.setState(true);
\r
3188 autoAnnMenu.setLabel("Autocalculated Annotation");
\r
3190 invertColSel.addActionListener(this);
\r
3191 showColumns.addActionListener(this);
\r
3192 showSeqs.addActionListener(this);
\r
3193 hideColumns.addActionListener(this);
\r
3194 hideSequences.addActionListener(this);
\r
3195 hideAllButSelection.addActionListener(this);
\r
3196 hideAllSelection.addActionListener(this);
\r
3197 showAllHidden.addActionListener(this);
\r
3198 showGroupConsensus.addItemListener(this);
\r
3199 showGroupConservation.addItemListener(this);
\r
3200 showConsensusHistogram.addItemListener(this);
\r
3201 showSequenceLogo.addItemListener(this);
\r
3202 applyAutoAnnotationSettings.addItemListener(this);
\r
3203 formatMenu.setLabel("Format");
\r
3204 selectMenu.setLabel("Select");
\r
3205 newView.setLabel("New View");
\r
3206 newView.addActionListener(this);
\r
3207 alignFrameMenuBar.add(fileMenu);
\r
3208 alignFrameMenuBar.add(editMenu);
\r
3209 alignFrameMenuBar.add(selectMenu);
\r
3210 alignFrameMenuBar.add(viewMenu);
\r
3211 alignFrameMenuBar.add(formatMenu);
\r
3212 alignFrameMenuBar.add(colourMenu);
\r
3213 alignFrameMenuBar.add(calculateMenu);
\r
3214 alignFrameMenuBar.add(helpMenu);
\r
3216 fileMenu.add(inputText);
\r
3217 fileMenu.add(loadTree);
\r
3218 fileMenu.add(loadAnnotations);
\r
3219 fileMenu.add(loadScores);
\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 url The absolute path from where download and read the score file
\r
3717 * @throws IOException
\r
3719 public void loadScoreFile( URL url ) throws IOException {
\r
3720 // TODO: refactor to string/standard jalview data importer
\r
3721 TCoffeeScoreFile file = TCoffeeScoreFile.load( new InputStreamReader( url.openStream() ) );
\r
3722 if( file == null ) {
\r
3723 // TODO: raise a dialog box here rather than bomb out.
\r
3725 throw new RuntimeException("The file provided does not match the T-Coffee scores file format");
\r
3729 * check that the score matrix matches the alignment dimensions
\r
3732 if( (aln=viewport.getAlignment()) != null && (aln.getHeight() != file.getHeight() || aln.getWidth() != file.getWidth()) ) {
\r
3733 // TODO: raise a dialog box here rather than bomb out.
\r
3734 throw new RuntimeException("The scores matrix does not match the alignment dimensions");
\r
3738 // TODO add parameter to indicate if matching should be done
\r
3739 if (file.annotateAlignment(alignPanel.getAlignment(), false))
\r
3741 tcoffeeColour.setEnabled(true);
\r
3742 // switch to this color
\r
3743 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
\r