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.List;
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91 import java.util.StringTokenizer;
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92 import java.util.Vector;
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94 public class AlignFrame extends EmbmenuFrame implements ActionListener, ItemListener, KeyListener
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96 public AlignmentPanel alignPanel;
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98 public AlignViewport viewport;
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100 int DEFAULT_WIDTH = 700;
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102 int DEFAULT_HEIGHT = 500;
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104 String jalviewServletURL;
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107 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title, boolean embedded)
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109 if (applet != null)
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111 jalviewServletURL = applet.getParameter("APPLICATION_URL");
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117 } catch (Exception ex)
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119 ex.printStackTrace();
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122 viewport = new AlignViewport(al, applet);
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123 alignPanel = new AlignmentPanel(this, viewport);
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125 viewport.updateConservation(alignPanel);
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126 viewport.updateConsensus(alignPanel);
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128 annotationPanelMenuItem.setState(viewport.showAnnotation);
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129 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
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130 followMouseOverFlag.setState(viewport.getFollowHighlight());
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131 showGroupConsensus.setState(viewport.isShowGroupConsensus());
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132 showGroupConservation.setState(viewport.isShowGroupConservation());
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133 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
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134 showSequenceLogo.setState(viewport.isShowSequenceLogo());
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136 seqLimits.setState(viewport.showJVSuffix);
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138 if (applet != null)
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140 String param = applet.getParameter("sortBy");
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143 if (param.equalsIgnoreCase("Id"))
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145 sortIDMenuItem_actionPerformed();
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147 else if (param.equalsIgnoreCase("Pairwise Identity"))
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149 sortPairwiseMenuItem_actionPerformed();
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151 else if (param.equalsIgnoreCase("Length"))
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153 sortLengthMenuItem_actionPerformed();
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157 param = applet.getParameter("wrap");
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160 if (param.equalsIgnoreCase("true"))
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162 wrapMenuItem.setState(true);
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163 wrapMenuItem_actionPerformed();
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166 param = applet.getParameter("centrecolumnlabels");
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169 centreColumnLabelFlag.setState(true);
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170 centreColumnLabelFlag_stateChanged();
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174 param = applet.getParameter("windowWidth");
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177 int width = Integer.parseInt(param);
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178 DEFAULT_WIDTH = width;
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180 param = applet.getParameter("windowHeight");
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183 int height = Integer.parseInt(param);
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184 DEFAULT_HEIGHT = height;
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186 } catch (Exception ex)
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191 if (viewport.getAlignment().isNucleotide())
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193 viewport.updateStrucConsensus(alignPanel);
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194 if (viewport.getAlignment().hasRNAStructure())
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196 RNAHelixColour.setEnabled(true);
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199 RNAHelixColour.setEnabled(false);
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202 RNAHelixColour.setEnabled(false);
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203 purinePyrimidineColour.setEnabled(false);
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205 // Some JVMS send keyevents to Top frame or lowest panel,
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206 // Havent worked out why yet. So add to both this frame and seqCanvas for
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208 this.addKeyListener(this);
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209 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
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210 alignPanel.idPanel.idCanvas.addKeyListener(this);
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211 alignPanel.scalePanel.addKeyListener(this);
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212 alignPanel.annotationPanel.addKeyListener(this);
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213 alignPanel.annotationPanelHolder.addKeyListener(this);
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214 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
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215 alignPanel.alabels.addKeyListener(this);
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216 createAlignFrameWindow(embedded, title);
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219 alignPanel.adjustAnnotationHeight();
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220 alignPanel.paintAlignment(true);
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223 public AlignViewport getAlignViewport()
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228 public SeqCanvas getSeqcanvas()
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230 return alignPanel.seqPanel.seqCanvas;
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234 * Load a features file onto the alignment
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236 * @param file file URL, content, or other resolvable path
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237 * @param type is protocol for accessing data referred to by file
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240 public boolean parseFeaturesFile(String file, String type)
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242 return parseFeaturesFile(file, type, true);
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246 * Load a features file onto the alignment
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248 * @param file file URL, content, or other resolvable path
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249 * @param type is protocol for accessing data referred to by file
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250 * @param autoenabledisplay when true, display features flag will be automatically enabled if features are loaded
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251 * @return true if data parsed as a features file
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253 public boolean parseFeaturesFile(String file, String type, boolean autoenabledisplay)
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255 // TODO: test if importing a features file onto an alignment which already has features with links overwrites the original links.
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257 Hashtable featureLinks = new Hashtable();
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258 boolean featuresFile = false;
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261 featuresFile = new jalview.io.FeaturesFile(file, type)
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262 .parse(viewport.getAlignment(),
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263 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
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264 featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));
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265 } catch (Exception ex)
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267 ex.printStackTrace();
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272 if (featureLinks.size() > 0)
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274 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
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276 if (autoenabledisplay)
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278 viewport.showSequenceFeatures = true;
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279 sequenceFeatures.setState(true);
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281 if (viewport.featureSettings != null)
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283 viewport.featureSettings.refreshTable();
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285 alignPanel.paintAlignment(true);
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286 statusBar.setText("Successfully added features to alignment.");
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288 return featuresFile;
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291 public void keyPressed(KeyEvent evt)
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293 if (viewport.cursorMode
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294 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
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295 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
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296 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
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297 && Character.isDigit(evt.getKeyChar()))
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298 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
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300 switch (evt.getKeyCode())
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302 case 27: // escape key
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303 deselectAllSequenceMenuItem_actionPerformed();
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305 alignPanel.alabels.cancelDrag();
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307 case KeyEvent.VK_X:
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308 if (evt.isControlDown() || evt.isMetaDown())
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310 cut_actionPerformed();
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313 case KeyEvent.VK_C:
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314 if (viewport.cursorMode && !evt.isControlDown())
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316 alignPanel.seqPanel.setCursorColumn();
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318 if (evt.isControlDown() || evt.isMetaDown())
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320 copy_actionPerformed();
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323 case KeyEvent.VK_V:
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324 if (evt.isControlDown())
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326 paste(evt.isShiftDown());
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329 case KeyEvent.VK_A:
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330 if (evt.isControlDown() || evt.isMetaDown())
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332 selectAllSequenceMenuItem_actionPerformed();
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335 case KeyEvent.VK_DOWN:
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336 if (viewport.cursorMode)
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338 alignPanel.seqPanel.moveCursor(0, 1);
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342 moveSelectedSequences(false);
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346 case KeyEvent.VK_UP:
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347 if (viewport.cursorMode)
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349 alignPanel.seqPanel.moveCursor(0, -1);
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353 moveSelectedSequences(true);
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357 case KeyEvent.VK_LEFT:
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358 if (evt.isAltDown() || !viewport.cursorMode)
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359 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
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361 alignPanel.seqPanel.moveCursor(-1, 0);
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364 case KeyEvent.VK_RIGHT:
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365 if (evt.isAltDown() || !viewport.cursorMode)
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366 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
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368 alignPanel.seqPanel.moveCursor(1, 0);
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371 case KeyEvent.VK_SPACE:
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372 if (viewport.cursorMode)
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374 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
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375 || evt.isShiftDown() || evt.isAltDown());
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379 case KeyEvent.VK_DELETE:
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380 case KeyEvent.VK_BACK_SPACE:
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381 if (viewport.cursorMode)
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383 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
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384 || evt.isShiftDown() || evt.isAltDown());
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388 cut_actionPerformed();
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389 alignPanel.seqPanel.seqCanvas.repaint();
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393 case KeyEvent.VK_S:
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394 if (viewport.cursorMode)
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396 alignPanel.seqPanel.setCursorRow();
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399 case KeyEvent.VK_P:
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400 if (viewport.cursorMode)
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402 alignPanel.seqPanel.setCursorPosition();
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406 case KeyEvent.VK_ENTER:
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407 case KeyEvent.VK_COMMA:
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408 if (viewport.cursorMode)
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410 alignPanel.seqPanel.setCursorRowAndColumn();
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414 case KeyEvent.VK_Q:
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415 if (viewport.cursorMode)
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417 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
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420 case KeyEvent.VK_M:
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421 if (viewport.cursorMode)
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423 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
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427 case KeyEvent.VK_F2:
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428 viewport.cursorMode = !viewport.cursorMode;
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429 statusBar.setText("Keyboard editing mode is "
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430 + (viewport.cursorMode ? "on" : "off"));
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431 if (viewport.cursorMode)
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433 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
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434 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
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438 case KeyEvent.VK_F:
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439 if (evt.isControlDown())
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441 findMenuItem_actionPerformed();
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445 case KeyEvent.VK_H:
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447 boolean toggleSeqs = !evt.isControlDown();
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448 boolean toggleCols = !evt.isShiftDown();
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449 toggleHiddenRegions(toggleSeqs, toggleCols);
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453 case KeyEvent.VK_PAGE_UP:
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454 if (viewport.wrapAlignment)
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456 alignPanel.scrollUp(true);
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460 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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461 - viewport.endSeq + viewport.startSeq);
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465 case KeyEvent.VK_PAGE_DOWN:
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466 if (viewport.wrapAlignment)
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468 alignPanel.scrollUp(false);
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472 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
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473 + viewport.endSeq - viewport.startSeq);
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477 case KeyEvent.VK_Z:
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478 if (evt.isControlDown())
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480 undoMenuItem_actionPerformed();
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484 case KeyEvent.VK_Y:
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485 if (evt.isControlDown())
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487 redoMenuItem_actionPerformed();
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491 case KeyEvent.VK_L:
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492 if (evt.isControlDown())
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494 trimAlignment(true);
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498 case KeyEvent.VK_R:
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499 if (evt.isControlDown())
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501 trimAlignment(false);
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505 case KeyEvent.VK_E:
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506 if (evt.isControlDown())
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508 if (evt.isShiftDown())
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510 this.removeAllGapsMenuItem_actionPerformed();
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514 removeGappedColumnMenuItem_actionPerformed();
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518 case KeyEvent.VK_I:
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519 if (evt.isControlDown())
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521 if (evt.isAltDown())
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523 invertColSel_actionPerformed();
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527 invertSequenceMenuItem_actionPerformed();
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532 case KeyEvent.VK_U:
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533 if (evt.isControlDown())
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535 this.deleteGroups_actionPerformed();
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539 case KeyEvent.VK_T:
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540 if (evt.isControlDown())
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547 alignPanel.paintAlignment(true);
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551 * called by key handler and the hide all/show all menu items
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553 * @param toggleSeqs
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554 * @param toggleCols
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556 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
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558 boolean hide = false;
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559 SequenceGroup sg = viewport.getSelectionGroup();
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560 if (!toggleSeqs && !toggleCols)
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562 // Hide everything by the current selection - this is a hack - we do the
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563 // invert and then hide
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564 // first check that there will be visible columns after the invert.
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565 if ((viewport.getColumnSelection() != null && viewport.getColumnSelection().getSelected() != null && viewport.getColumnSelection()
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566 .getSelected().size() > 0)
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567 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
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570 // now invert the sequence set, if required - empty selection implies
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571 // that no hiding is required.
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574 invertSequenceMenuItem_actionPerformed();
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575 sg = viewport.getSelectionGroup();
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579 viewport.expandColSelection(sg, true);
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580 // finally invert the column selection and get the new sequence
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581 // selection and indicate it should be hidden.
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582 invertColSel_actionPerformed();
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589 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
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592 viewport.hideAllSelectedSeqs();
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594 else if (!(toggleCols && viewport.getColumnSelection().getSelected().size() > 0))
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596 viewport.showAllHiddenSeqs();
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602 if (viewport.getColumnSelection().getSelected().size() > 0)
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604 viewport.hideSelectedColumns();
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607 viewport.setSelectionGroup(sg);
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612 viewport.showAllHiddenColumns();
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617 public void keyReleased(KeyEvent evt)
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621 public void keyTyped(KeyEvent evt)
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625 public void itemStateChanged(ItemEvent evt)
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627 if (evt.getSource() == displayNonconservedMenuItem)
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629 displayNonconservedMenuItem_actionPerformed();
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631 else if (evt.getSource() == colourTextMenuItem)
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633 colourTextMenuItem_actionPerformed();
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635 else if (evt.getSource() == wrapMenuItem)
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637 wrapMenuItem_actionPerformed();
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639 else if (evt.getSource() == scaleAbove)
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641 viewport.setScaleAboveWrapped(scaleAbove.getState());
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643 else if (evt.getSource() == scaleLeft)
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645 viewport.setScaleLeftWrapped(scaleLeft.getState());
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647 else if (evt.getSource() == scaleRight)
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649 viewport.setScaleRightWrapped(scaleRight.getState());
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651 else if (evt.getSource() == seqLimits)
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653 seqLimits_itemStateChanged();
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655 else if (evt.getSource() == viewBoxesMenuItem)
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657 viewport.setShowBoxes(viewBoxesMenuItem.getState());
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659 else if (evt.getSource() == viewTextMenuItem)
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661 viewport.setShowText(viewTextMenuItem.getState());
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663 else if (evt.getSource() == renderGapsMenuItem)
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665 viewport.setRenderGaps(renderGapsMenuItem.getState());
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667 else if (evt.getSource() == annotationPanelMenuItem)
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669 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
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670 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
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672 else if (evt.getSource() == sequenceFeatures)
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674 viewport.showSequenceFeatures(sequenceFeatures.getState());
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675 alignPanel.seqPanel.seqCanvas.repaint();
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677 else if (evt.getSource() == conservationMenuItem)
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679 conservationMenuItem_actionPerformed();
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681 else if (evt.getSource() == abovePIDThreshold)
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683 abovePIDThreshold_actionPerformed();
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685 else if (evt.getSource() == applyToAllGroups)
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687 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
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689 else if (evt.getSource() == autoCalculate)
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691 viewport.autoCalculateConsensus = autoCalculate.getState();
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693 else if (evt.getSource() == sortByTree)
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695 viewport.sortByTree = sortByTree.getState();
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697 else if (evt.getSource() == this.centreColumnLabelFlag)
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699 centreColumnLabelFlag_stateChanged();
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701 else if (evt.getSource() == this.followMouseOverFlag)
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703 mouseOverFlag_stateChanged();
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705 else if (evt.getSource() == showGroupConsensus)
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707 showGroupConsensus_actionPerformed();
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709 else if (evt.getSource() == showGroupConservation)
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711 showGroupConservation_actionPerformed();
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713 else if (evt.getSource() == showSequenceLogo)
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715 showSequenceLogo_actionPerformed();
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717 else if (evt.getSource() == showConsensusHistogram)
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719 showConsensusHistogram_actionPerformed();
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721 else if (evt.getSource() == applyAutoAnnotationSettings)
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723 applyAutoAnnotationSettings_actionPerformed();
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725 alignPanel.paintAlignment(true);
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728 private void mouseOverFlag_stateChanged()
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730 viewport.followHighlight = followMouseOverFlag.getState();
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731 // TODO: could kick the scrollTo mechanism to reset view for current
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735 private void centreColumnLabelFlag_stateChanged()
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737 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
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738 this.alignPanel.annotationPanel.repaint();
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741 public void actionPerformed(ActionEvent evt)
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743 Object source = evt.getSource();
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745 if (source == inputText)
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747 inputText_actionPerformed();
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749 else if (source == loadTree)
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751 loadTree_actionPerformed();
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753 else if (source == loadApplication)
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755 launchFullApplication();
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757 else if (source == loadAnnotations)
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761 else if (source == outputAnnotations)
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763 outputAnnotations(true);
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765 else if (source == outputFeatures)
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767 outputFeatures(true, "Jalview");
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769 else if (source == closeMenuItem)
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771 closeMenuItem_actionPerformed();
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773 else if (source == copy)
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775 copy_actionPerformed();
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777 else if (source == undoMenuItem)
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779 undoMenuItem_actionPerformed();
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781 else if (source == redoMenuItem)
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783 redoMenuItem_actionPerformed();
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785 else if (source == inputText)
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787 inputText_actionPerformed();
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789 else if (source == closeMenuItem)
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791 closeMenuItem_actionPerformed();
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793 else if (source == undoMenuItem)
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795 undoMenuItem_actionPerformed();
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797 else if (source == redoMenuItem)
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799 redoMenuItem_actionPerformed();
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801 else if (source == copy)
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803 copy_actionPerformed();
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805 else if (source == pasteNew)
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807 pasteNew_actionPerformed();
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809 else if (source == pasteThis)
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811 pasteThis_actionPerformed();
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813 else if (source == cut)
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815 cut_actionPerformed();
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817 else if (source == delete)
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819 delete_actionPerformed();
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821 else if (source == grpsFromSelection)
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823 makeGrpsFromSelection_actionPerformed();
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825 else if (source == deleteGroups)
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827 deleteGroups_actionPerformed();
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829 else if (source == selectAllSequenceMenuItem)
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831 selectAllSequenceMenuItem_actionPerformed();
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833 else if (source == deselectAllSequenceMenuItem)
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835 deselectAllSequenceMenuItem_actionPerformed();
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837 else if (source == invertSequenceMenuItem)
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839 invertSequenceMenuItem_actionPerformed();
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841 else if (source == invertColSel)
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843 viewport.invertColumnSelection();
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844 alignPanel.paintAlignment(true);
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846 else if (source == remove2LeftMenuItem)
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848 trimAlignment(true);
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850 else if (source == remove2RightMenuItem)
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852 trimAlignment(false);
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854 else if (source == removeGappedColumnMenuItem)
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856 removeGappedColumnMenuItem_actionPerformed();
\r
858 else if (source == removeAllGapsMenuItem)
\r
860 removeAllGapsMenuItem_actionPerformed();
\r
862 else if (source == findMenuItem)
\r
864 findMenuItem_actionPerformed();
\r
866 else if (source == font)
\r
868 new FontChooser(alignPanel);
\r
870 else if (source == newView)
\r
874 else if (source == showColumns)
\r
876 viewport.showAllHiddenColumns();
\r
877 alignPanel.paintAlignment(true);
\r
879 else if (source == showSeqs)
\r
881 viewport.showAllHiddenSeqs();
\r
882 alignPanel.paintAlignment(true);
\r
884 else if (source == hideColumns)
\r
886 viewport.hideSelectedColumns();
\r
887 alignPanel.paintAlignment(true);
\r
889 else if (source == hideSequences
\r
890 && viewport.getSelectionGroup() != null)
\r
892 viewport.hideAllSelectedSeqs();
\r
893 alignPanel.paintAlignment(true);
\r
895 else if (source == hideAllButSelection)
\r
897 toggleHiddenRegions(false, false);
\r
898 alignPanel.paintAlignment(true);
\r
900 else if (source == hideAllSelection)
\r
902 SequenceGroup sg = viewport.getSelectionGroup();
\r
903 viewport.expandColSelection(sg, false);
\r
904 viewport.hideAllSelectedSeqs();
\r
905 viewport.hideSelectedColumns();
\r
906 alignPanel.paintAlignment(true);
\r
908 else if (source == showAllHidden)
\r
910 viewport.showAllHiddenColumns();
\r
911 viewport.showAllHiddenSeqs();
\r
912 alignPanel.paintAlignment(true);
\r
914 else if (source == showGroupConsensus)
\r
916 showGroupConsensus_actionPerformed();
\r
918 else if (source == showGroupConservation)
\r
920 showGroupConservation_actionPerformed();
\r
922 else if (source == showSequenceLogo)
\r
924 showSequenceLogo_actionPerformed();
\r
926 else if (source == showConsensusHistogram)
\r
928 showConsensusHistogram_actionPerformed();
\r
930 else if (source == applyAutoAnnotationSettings)
\r
932 applyAutoAnnotationSettings_actionPerformed();
\r
934 else if (source == featureSettings)
\r
936 new FeatureSettings(alignPanel);
\r
938 else if (source == alProperties)
\r
940 StringBuffer contents = new jalview.io.AlignmentProperties(
\r
941 viewport.getAlignment()).formatAsString();
\r
942 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
943 cap.setText(contents.toString());
\r
944 Frame frame = new Frame();
\r
946 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
\r
947 + getTitle(), 400, 250);
\r
949 else if (source == overviewMenuItem)
\r
951 overviewMenuItem_actionPerformed();
\r
953 else if (source == noColourmenuItem)
\r
955 changeColour(null);
\r
957 else if (source == clustalColour)
\r
959 abovePIDThreshold.setState(false);
\r
960 changeColour(new ClustalxColourScheme(viewport.getAlignment(),null));
\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 / T-coffee score 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 String outputAnnotations(boolean displayTextbox)
\r
1117 String annotation = new AnnotationFile().printAnnotations(
\r
1118 viewport.showAnnotation ? viewport.getAlignment()
\r
1119 .getAlignmentAnnotation() : null, viewport.getAlignment()
\r
1121 ((Alignment) viewport.getAlignment()).alignmentProperties);
\r
1123 if (displayTextbox)
\r
1125 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
1126 Frame frame = new Frame();
\r
1128 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
\r
1129 cap.setText(annotation);
\r
1132 return annotation;
\r
1135 private Hashtable getDisplayedFeatureCols()
\r
1137 if (alignPanel.getFeatureRenderer() != null && viewport.featuresDisplayed!=null)
\r
1139 FeatureRenderer fr = alignPanel.getFeatureRenderer();
\r
1140 Hashtable fcols = new Hashtable();
\r
1141 Enumeration en = viewport.featuresDisplayed.keys();
\r
1142 while (en.hasMoreElements())
\r
1144 Object col = en.nextElement();
\r
1145 fcols.put(col, fr.featureColours.get(col));
\r
1152 public String outputFeatures(boolean displayTextbox, String format)
\r
1155 if (format.equalsIgnoreCase("Jalview"))
\r
1157 features = new FeaturesFile().printJalviewFormat(
\r
1158 viewport.getAlignment().getSequencesArray(),
\r
1159 getDisplayedFeatureCols());
\r
1163 features = new FeaturesFile().printGFFFormat(
\r
1164 viewport.getAlignment().getSequencesArray(),
\r
1165 getDisplayedFeatureCols());
\r
1168 if (displayTextbox)
\r
1170 boolean frimport=false;
\r
1171 if (features==null || features.equals("No Features Visible"))
\r
1173 features = "# No features visible - paste some and import them here.";
\r
1177 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
\r
1180 cap.setAnnotationImport();
\r
1182 Frame frame = new Frame();
\r
1184 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
\r
1185 cap.setText(features);
\r
1187 if (features==null)
\r
1194 void launchFullApplication()
\r
1196 StringBuffer url = new StringBuffer(jalviewServletURL);
\r
1198 url.append("?open="
\r
1199 + appendProtocol(viewport.applet.getParameter("file")));
\r
1201 if (viewport.applet.getParameter("features") != null)
\r
1203 url.append("&features=");
\r
1204 url.append(appendProtocol(viewport.applet.getParameter("features")));
\r
1207 if (viewport.applet.getParameter("annotations") != null)
\r
1209 url.append("&annotations=");
\r
1210 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
\r
1213 if (viewport.applet.getParameter("jnetfile") != null)
\r
1215 url.append("&annotations=");
\r
1216 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
\r
1219 if (viewport.applet.getParameter("defaultColour") != null)
\r
1221 url.append("&colour="
\r
1222 + removeWhiteSpace(viewport.applet
\r
1223 .getParameter("defaultColour")));
\r
1226 if (viewport.applet.getParameter("userDefinedColour") != null)
\r
1228 url.append("&colour="
\r
1229 + removeWhiteSpace(viewport.applet
\r
1230 .getParameter("userDefinedColour")));
\r
1232 if (viewport.applet.getParameter("tree") != null)
\r
1234 url.append("&tree="
\r
1235 + appendProtocol(viewport.applet.getParameter("tree")));
\r
1237 if (viewport.applet.getParameter("treeFile") != null)
\r
1239 url.append("&tree="
\r
1240 + appendProtocol(viewport.applet.getParameter("treeFile")));
\r
1243 showURL(url.toString(), "FULL_APP");
\r
1246 String removeWhiteSpace(String colour)
\r
1248 StringBuffer sb = new StringBuffer();
\r
1249 for (int i = 0; i < colour.length(); i++)
\r
1251 if (Character.isWhitespace(colour.charAt(i)))
\r
1257 sb.append(colour.charAt(i));
\r
1261 return sb.toString();
\r
1264 String appendProtocol(String url)
\r
1269 url = URLEncoder.encode(url);
\r
1272 * When we finally deprecate 1.1 compatibility, we can start to use
\r
1273 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
\r
1274 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
\r
1275 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
\r
1276 * ex.printStackTrace(); }
\r
1278 catch (java.net.MalformedURLException ex)
\r
1280 url = viewport.applet.getCodeBase() + url;
\r
1285 public void closeMenuItem_actionPerformed()
\r
1287 PaintRefresher.RemoveComponent(alignPanel);
\r
1288 if (alignPanel.seqPanel!=null && alignPanel.seqPanel.seqCanvas!=null)
\r
1290 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
\r
1292 if (alignPanel.idPanel!=null && alignPanel.idPanel.idCanvas!=null) {
\r
1293 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
1341 public void addHistoryItem(CommandI command)
\r
1343 if (command.getSize() > 0)
\r
1345 viewport.historyList.push(command);
\r
1346 viewport.redoList.removeAllElements();
\r
1347 updateEditMenuBar();
\r
1348 viewport.updateHiddenColumns();
\r
1359 protected void undoMenuItem_actionPerformed()
\r
1361 if (viewport.historyList.size() < 1)
\r
1366 CommandI command = (CommandI) viewport.historyList.pop();
\r
1367 viewport.redoList.push(command);
\r
1368 command.undoCommand(null);
\r
1370 AlignViewport originalSource = getOriginatingSource(command);
\r
1372 if (originalSource!=viewport) {
\r
1373 System.err.println("Warning: Viewport object mismatch whilst undoing");
\r
1375 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns = viewport.getColumnSelection().getHiddenColumns() != null;
\r
1376 updateEditMenuBar();
\r
1377 originalSource.firePropertyChange("alignment", null,
\r
1378 originalSource.getAlignment().getSequences());
\r
1388 protected void redoMenuItem_actionPerformed()
\r
1390 if (viewport.redoList.size() < 1)
\r
1395 CommandI command = (CommandI) viewport.redoList.pop();
\r
1396 viewport.historyList.push(command);
\r
1397 command.doCommand(null);
\r
1399 AlignViewport originalSource = getOriginatingSource(command);
\r
1401 if (originalSource!=viewport) {
\r
1402 System.err.println("Warning: Viewport object mismatch whilst re-doing");
\r
1404 originalSource.updateHiddenColumns(); //sethasHiddenColumns(); = viewport.getColumnSelection().getHiddenColumns() != null;
\r
1406 updateEditMenuBar();
\r
1407 originalSource.firePropertyChange("alignment", null,
\r
1408 originalSource.getAlignment().getSequences());
\r
1411 AlignViewport getOriginatingSource(CommandI command)
\r
1413 AlignViewport originalSource = null;
\r
1414 // For sequence removal and addition, we need to fire
\r
1415 // the property change event FROM the viewport where the
\r
1416 // original alignment was altered
\r
1417 AlignmentI al = null;
\r
1418 if (command instanceof EditCommand)
\r
1420 EditCommand editCommand = (EditCommand) command;
\r
1421 al = editCommand.getAlignment();
\r
1422 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
1423 .getSequenceSetId());
\r
1424 for (int i = 0; i < comps.size(); i++)
\r
1426 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
1428 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
\r
1430 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
\r
1437 if (originalSource == null)
\r
1439 // The original view is closed, we must validate
\r
1440 // the current view against the closed view first
\r
1443 PaintRefresher.validateSequences(al, viewport.getAlignment());
\r
1446 originalSource = viewport;
\r
1449 return originalSource;
\r
1452 public void moveSelectedSequences(boolean up)
\r
1454 SequenceGroup sg = viewport.getSelectionGroup();
\r
1462 for (int i = 1; i < viewport.getAlignment().getHeight(); i++)
\r
1464 SequenceI seq = viewport.getAlignment().getSequenceAt(i);
\r
1465 if (!sg.getSequences(null).contains(seq))
\r
1470 SequenceI temp = viewport.getAlignment().getSequenceAt(i - 1);
\r
1471 if (sg.getSequences(null).contains(temp))
\r
1476 viewport.getAlignment().getSequences().setElementAt(temp, i);
\r
1477 viewport.getAlignment().getSequences().setElementAt(seq, i - 1);
\r
1482 for (int i = viewport.getAlignment().getHeight() - 2; i > -1; i--)
\r
1484 SequenceI seq = viewport.getAlignment().getSequenceAt(i);
\r
1485 if (!sg.getSequences(viewport.getHiddenRepSequences()).contains(seq))
\r
1490 SequenceI temp = viewport.getAlignment().getSequenceAt(i + 1);
\r
1491 if (sg.getSequences(viewport.getHiddenRepSequences()).contains(temp))
\r
1496 viewport.getAlignment().getSequences().setElementAt(temp, i);
\r
1497 viewport.getAlignment().getSequences().setElementAt(seq, i + 1);
\r
1501 alignPanel.paintAlignment(true);
\r
1504 synchronized void slideSequences(boolean right, int size)
\r
1506 List<SequenceI>sg = new Vector<SequenceI>();
\r
1507 if (viewport.cursorMode)
\r
1509 sg.add(viewport.getAlignment()
\r
1510 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
\r
1512 else if (viewport.getSelectionGroup() != null
\r
1513 && viewport.getSelectionGroup().getSize() != viewport.getAlignment()
\r
1516 sg = viewport.getSelectionGroup().getSequences(
\r
1517 viewport.getHiddenRepSequences());
\r
1520 if (sg.size() < 1)
\r
1525 Vector<SequenceI> invertGroup = new Vector();
\r
1527 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
\r
1529 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
\r
1530 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
\r
1533 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
\r
1535 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup.size()]);
\r
1536 for (int i = 0; i < invertGroup.size(); i++)
\r
1537 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
\r
1539 SlideSequencesCommand ssc;
\r
1541 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
\r
1542 size, viewport.getGapCharacter());
\r
1544 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
\r
1545 size, viewport.getGapCharacter());
\r
1547 int groupAdjustment = 0;
\r
1548 if (ssc.getGapsInsertedBegin() && right)
\r
1550 if (viewport.cursorMode)
\r
1551 alignPanel.seqPanel.moveCursor(size, 0);
\r
1553 groupAdjustment = size;
\r
1555 else if (!ssc.getGapsInsertedBegin() && !right)
\r
1557 if (viewport.cursorMode)
\r
1558 alignPanel.seqPanel.moveCursor(-size, 0);
\r
1560 groupAdjustment = -size;
\r
1563 if (groupAdjustment != 0)
\r
1565 viewport.getSelectionGroup().setStartRes(
\r
1566 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
\r
1567 viewport.getSelectionGroup().setEndRes(
\r
1568 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
\r
1571 boolean appendHistoryItem = false;
\r
1572 if (viewport.historyList != null && viewport.historyList.size() > 0
\r
1573 && viewport.historyList.peek() instanceof SlideSequencesCommand)
\r
1575 appendHistoryItem = ssc
\r
1576 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
\r
1580 if (!appendHistoryItem)
\r
1581 addHistoryItem(ssc);
\r
1586 static StringBuffer copiedSequences;
\r
1588 static Vector copiedHiddenColumns;
\r
1590 protected void copy_actionPerformed()
\r
1592 if (viewport.getSelectionGroup() == null)
\r
1597 SequenceGroup sg = viewport.getSelectionGroup();
\r
1598 copiedSequences = new StringBuffer();
\r
1599 Hashtable orderedSeqs = new Hashtable();
\r
1600 for (int i = 0; i < sg.getSize(); i++)
\r
1602 SequenceI seq = sg.getSequenceAt(i);
\r
1603 int index = viewport.getAlignment().findIndex(seq);
\r
1604 orderedSeqs.put(index + "", seq);
\r
1607 int index = 0, startRes, endRes;
\r
1610 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
\r
1612 copiedHiddenColumns = new Vector();
\r
1613 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
\r
1614 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
\r
1617 int[] region = (int[]) viewport.getColumnSelection()
\r
1618 .getHiddenColumns().elementAt(i);
\r
1620 copiedHiddenColumns.addElement(new int[]
\r
1621 { region[0] - hiddenOffset, region[1] - hiddenOffset });
\r
1626 copiedHiddenColumns = null;
\r
1629 for (int i = 0; i < sg.getSize(); i++)
\r
1631 SequenceI seq = null;
\r
1633 while (seq == null)
\r
1635 if (orderedSeqs.containsKey(index + ""))
\r
1637 seq = (SequenceI) orderedSeqs.get(index + "");
\r
1649 // Returns residue following index if gap
\r
1650 startRes = seq.findPosition(sg.getStartRes());
\r
1653 // Need to find the residue preceeding index if gap
\r
1656 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
\r
1658 ch = seq.getCharAt(j);
\r
1659 if (!jalview.util.Comparison.isGap((ch)))
\r
1667 endRes += seq.getStart() - 1;
\r
1670 copiedSequences.append(seq.getName()
\r
1676 + seq.getSequenceAsString(sg.getStartRes(),
\r
1677 sg.getEndRes() + 1) + "\n");
\r
1682 protected void pasteNew_actionPerformed()
\r
1687 protected void pasteThis_actionPerformed()
\r
1692 void paste(boolean newAlignment)
\r
1697 if (copiedSequences == null)
\r
1702 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
1703 Vector seqs = new Vector();
\r
1704 while (st.hasMoreElements())
\r
1706 String name = st.nextToken();
\r
1707 int start = Integer.parseInt(st.nextToken());
\r
1708 int end = Integer.parseInt(st.nextToken());
\r
1709 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
\r
1711 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
1712 for (int i = 0; i < seqs.size(); i++)
\r
1714 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
1719 String newtitle = new String("Copied sequences");
\r
1720 if (getTitle().startsWith("Copied sequences"))
\r
1722 newtitle = getTitle();
\r
1726 newtitle = newtitle.concat("- from " + getTitle());
\r
1728 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
1729 viewport.applet, newtitle, false);
\r
1730 if (copiedHiddenColumns != null)
\r
1732 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
1734 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
1735 af.viewport.hideColumns(region[0], region[1]);
\r
1739 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
\r
1744 addSequences(newSeqs);
\r
1747 } catch (Exception ex)
\r
1749 } // could be anything being pasted in here
\r
1753 void addSequences(SequenceI[] seqs)
\r
1755 for (int i = 0; i < seqs.length; i++)
\r
1757 viewport.getAlignment().addSequence(seqs[i]);
\r
1761 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
\r
1762 seqs, 0, viewport.getAlignment().getWidth(), viewport.getAlignment()));
\r
1764 viewport.setEndSeq(viewport.getAlignment().getHeight());
\r
1765 viewport.getAlignment().getWidth();
\r
1766 viewport.firePropertyChange("alignment", null,
\r
1767 viewport.getAlignment().getSequences());
\r
1771 protected void cut_actionPerformed()
\r
1773 copy_actionPerformed();
\r
1774 delete_actionPerformed();
\r
1777 protected void delete_actionPerformed()
\r
1780 SequenceGroup sg = viewport.getSelectionGroup();
\r
1786 Vector seqs = new Vector();
\r
1788 for (int i = 0; i < sg.getSize(); i++)
\r
1790 seq = sg.getSequenceAt(i);
\r
1791 seqs.addElement(seq);
\r
1794 // If the cut affects all sequences, remove highlighted columns
\r
1795 if (sg.getSize() == viewport.getAlignment().getHeight())
\r
1797 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
1798 sg.getEndRes() + 1);
\r
1801 SequenceI[] cut = new SequenceI[seqs.size()];
\r
1802 for (int i = 0; i < seqs.size(); i++)
\r
1804 cut[i] = (SequenceI) seqs.elementAt(i);
\r
1808 * //ADD HISTORY ITEM
\r
1810 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
\r
1811 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
\r
1812 viewport.getAlignment()));
\r
1814 viewport.setSelectionGroup(null);
\r
1815 viewport.getAlignment().deleteGroup(sg);
\r
1817 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1820 if (viewport.getAlignment().getHeight() < 1)
\r
1822 this.setVisible(false);
\r
1824 viewport.sendSelection();
\r
1828 * group consensus toggled
\r
1831 protected void showGroupConsensus_actionPerformed()
\r
1833 viewport.setShowGroupConsensus(showGroupConsensus.getState());
\r
1834 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1839 * group conservation toggled.
\r
1841 protected void showGroupConservation_actionPerformed()
\r
1843 viewport.setShowGroupConservation(showGroupConservation.getState());
\r
1844 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1851 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
\r
1852 * .event.ActionEvent)
\r
1854 protected void showConsensusHistogram_actionPerformed()
\r
1856 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
\r
1857 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1863 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
\r
1864 * .event.ActionEvent)
\r
1866 protected void showSequenceLogo_actionPerformed()
\r
1868 viewport.setShowSequenceLogo(showSequenceLogo.getState());
\r
1869 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1872 protected void applyAutoAnnotationSettings_actionPerformed()
\r
1874 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1877 protected void makeGrpsFromSelection_actionPerformed()
\r
1879 if (viewport.getSelectionGroup() != null)
\r
1881 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
\r
1882 viewport.getSequenceSelection(),
\r
1883 viewport.getAlignmentView(true).getSequenceStrings(
\r
1884 viewport.getGapCharacter()),
\r
1885 viewport.getAlignment().getGroups());
\r
1886 viewport.getAlignment().deleteAllGroups();
\r
1887 viewport.sequenceColours = null;
\r
1888 viewport.setSelectionGroup(null);
\r
1889 // set view properties for each group
\r
1890 for (int g = 0; g < gps.length; g++)
\r
1892 // gps[g].setShowunconserved(viewport.getShowUnconserved());
\r
1893 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
\r
1894 viewport.getAlignment().addGroup(gps[g]);
\r
1895 Color col = new Color((int) (Math.random() * 255),
\r
1896 (int) (Math.random() * 255), (int) (Math.random() * 255));
\r
1897 col = col.brighter();
\r
1898 for (SequenceI sq : gps[g].getSequences(null))
\r
1899 viewport.setSequenceColour(
\r
1903 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
\r
1904 alignPanel.updateAnnotation();
\r
1905 alignPanel.paintAlignment(true);
\r
1909 protected void deleteGroups_actionPerformed()
\r
1911 viewport.getAlignment().deleteAllGroups();
\r
1912 viewport.sequenceColours = null;
\r
1913 viewport.setSelectionGroup(null);
\r
1915 alignPanel.paintAlignment(true);
\r
1918 public void selectAllSequenceMenuItem_actionPerformed()
\r
1920 SequenceGroup sg = new SequenceGroup();
\r
1921 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1923 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
1925 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
\r
1926 viewport.setSelectionGroup(sg);
\r
1927 alignPanel.paintAlignment(true);
\r
1928 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1929 viewport.sendSelection();
\r
1932 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1934 if (viewport.cursorMode)
\r
1936 alignPanel.seqPanel.keyboardNo1 = null;
\r
1937 alignPanel.seqPanel.keyboardNo2 = null;
\r
1939 viewport.setSelectionGroup(null);
\r
1940 viewport.getColumnSelection().clear();
\r
1941 viewport.setSelectionGroup(null);
\r
1942 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1943 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1944 alignPanel.paintAlignment(true);
\r
1945 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1946 viewport.sendSelection();
\r
1949 public void invertSequenceMenuItem_actionPerformed()
\r
1951 SequenceGroup sg = viewport.getSelectionGroup();
\r
1952 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1954 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1957 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1958 viewport.sendSelection();
\r
1961 public void invertColSel_actionPerformed()
\r
1963 viewport.invertColumnSelection();
\r
1964 alignPanel.paintAlignment(true);
\r
1965 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1966 viewport.sendSelection();
\r
1969 void trimAlignment(boolean trimLeft)
\r
1971 ColumnSelection colSel = viewport.getColumnSelection();
\r
1974 if (colSel.size() > 0)
\r
1978 column = colSel.getMin();
\r
1982 column = colSel.getMax();
\r
1986 if (viewport.getSelectionGroup() != null)
\r
1988 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
1989 viewport.getHiddenRepSequences());
\r
1993 seqs = viewport.getAlignment().getSequencesArray();
\r
1996 TrimRegionCommand trimRegion;
\r
1999 trimRegion = new TrimRegionCommand("Remove Left",
\r
2000 TrimRegionCommand.TRIM_LEFT, seqs, column,
\r
2001 viewport.getAlignment(), viewport.getColumnSelection(),
\r
2002 viewport.getSelectionGroup());
\r
2003 viewport.setStartRes(0);
\r
2007 trimRegion = new TrimRegionCommand("Remove Right",
\r
2008 TrimRegionCommand.TRIM_RIGHT, seqs, column,
\r
2009 viewport.getAlignment(), viewport.getColumnSelection(),
\r
2010 viewport.getSelectionGroup());
\r
2013 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
\r
2015 addHistoryItem(trimRegion);
\r
2019 for (SequenceGroup sg:viewport.getAlignment().getGroups())
\r
2021 if ((trimLeft && !sg.adjustForRemoveLeft(column))
\r
2022 || (!trimLeft && !sg.adjustForRemoveRight(column)))
\r
2024 viewport.getAlignment().deleteGroup(sg);
\r
2028 viewport.firePropertyChange("alignment", null, viewport
\r
2029 .getAlignment().getSequences());
\r
2033 public void removeGappedColumnMenuItem_actionPerformed()
\r
2035 int start = 0, end = viewport.getAlignment().getWidth() - 1;
\r
2038 if (viewport.getSelectionGroup() != null)
\r
2040 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2041 viewport.getHiddenRepSequences());
\r
2042 start = viewport.getSelectionGroup().getStartRes();
\r
2043 end = viewport.getSelectionGroup().getEndRes();
\r
2047 seqs = viewport.getAlignment().getSequencesArray();
\r
2050 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
\r
2051 "Remove Gapped Columns", seqs, start, end, viewport.getAlignment());
\r
2053 addHistoryItem(removeGapCols);
\r
2055 statusBar.setText("Removed " + removeGapCols.getSize()
\r
2056 + " empty columns.");
\r
2058 // This is to maintain viewport position on first residue
\r
2059 // of first sequence
\r
2060 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
\r
2061 int startRes = seq.findPosition(viewport.startRes);
\r
2062 // ShiftList shifts;
\r
2063 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
\r
2064 // edit.alColumnChanges=shifts.getInverse();
\r
2065 // if (viewport.hasHiddenColumns)
\r
2066 // viewport.getColumnSelection().compensateForEdits(shifts);
\r
2067 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
2068 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
2073 public void removeAllGapsMenuItem_actionPerformed()
\r
2075 int start = 0, end = viewport.getAlignment().getWidth() - 1;
\r
2078 if (viewport.getSelectionGroup() != null)
\r
2080 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2081 viewport.getHiddenRepSequences());
\r
2082 start = viewport.getSelectionGroup().getStartRes();
\r
2083 end = viewport.getSelectionGroup().getEndRes();
\r
2087 seqs = viewport.getAlignment().getSequencesArray();
\r
2090 // This is to maintain viewport position on first residue
\r
2091 // of first sequence
\r
2092 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
\r
2093 int startRes = seq.findPosition(viewport.startRes);
\r
2095 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
\r
2096 viewport.getAlignment()));
\r
2098 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
2100 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
2105 public void findMenuItem_actionPerformed()
\r
2107 new Finder(alignPanel);
\r
2111 * create a new view derived from the current view
\r
2113 * @param viewtitle
\r
2114 * @return frame for the new view
\r
2116 public AlignFrame newView(String viewtitle)
\r
2119 if (viewport.hasHiddenRows())
\r
2121 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
\r
2122 .getFullAlignment().getSequencesArray());
\r
2126 newal = new Alignment(viewport.getAlignment().getSequencesArray());
\r
2129 if (viewport.getAlignment().getAlignmentAnnotation() != null)
\r
2131 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
\r
2133 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
\r
2135 newal.addAnnotation(viewport.getAlignment().getAlignmentAnnotation()[i]);
\r
2140 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
\r
2142 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
\r
2143 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
\r
2144 PaintRefresher.Register(newaf.alignPanel,
\r
2145 newaf.alignPanel.av.getSequenceSetId());
\r
2147 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
\r
2148 newaf.alignPanel.av.getSequenceSetId());
\r
2149 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
\r
2150 newaf.alignPanel.av.getSequenceSetId());
\r
2152 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
2153 .getSequenceSetId());
\r
2154 int viewSize = -1;
\r
2155 for (int i = 0; i < comps.size(); i++)
\r
2157 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
2163 String title = new String(this.getTitle());
\r
2164 if (viewtitle != null)
\r
2166 title = viewtitle + " ( " + title + ")";
\r
2170 if (title.indexOf("(View") > -1)
\r
2172 title = title.substring(0, title.indexOf("(View"));
\r
2174 title += "(View " + viewSize + ")";
\r
2177 newaf.setTitle(title.toString());
\r
2179 newaf.viewport.historyList = viewport.historyList;
\r
2180 newaf.viewport.redoList = viewport.redoList;
\r
2186 * @return list of feature groups on the view
\r
2188 public String[] getFeatureGroups()
\r
2190 FeatureRenderer fr = null;
\r
2191 if (alignPanel != null
\r
2192 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2194 return fr.getGroups();
\r
2200 * get sequence feature groups that are hidden or shown
\r
2206 public String[] getFeatureGroupsOfState(boolean visible)
\r
2208 FeatureRenderer fr = null;
\r
2209 if (alignPanel != null
\r
2210 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2212 return fr.getGroups(visible);
\r
2218 * Change the display state for the given feature groups
\r
2221 * list of group strings
\r
2223 * visible or invisible
\r
2225 public void setFeatureGroupState(String[] groups, boolean state)
\r
2227 FeatureRenderer fr = null;
\r
2228 this.sequenceFeatures.setState(true);
\r
2229 viewport.showSequenceFeatures(true);
\r
2230 if (alignPanel != null
\r
2231 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2233 fr.setGroupState(groups, state);
\r
2234 alignPanel.seqPanel.seqCanvas.repaint();
\r
2235 if (alignPanel.overviewPanel != null)
\r
2237 alignPanel.overviewPanel.updateOverviewImage();
\r
2242 public void seqLimits_itemStateChanged()
\r
2244 viewport.setShowJVSuffix(seqLimits.getState());
\r
2245 alignPanel.fontChanged();
\r
2246 alignPanel.paintAlignment(true);
\r
2249 protected void colourTextMenuItem_actionPerformed()
\r
2251 viewport.setColourText(colourTextMenuItem.getState());
\r
2252 alignPanel.paintAlignment(true);
\r
2255 protected void displayNonconservedMenuItem_actionPerformed()
\r
2257 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
\r
2258 alignPanel.paintAlignment(true);
\r
2261 protected void wrapMenuItem_actionPerformed()
\r
2263 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
2264 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
2265 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
2266 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
2267 scaleRight.setEnabled(wrapMenuItem.getState());
\r
2268 alignPanel.paintAlignment(true);
\r
2271 public void overviewMenuItem_actionPerformed()
\r
2273 if (alignPanel.overviewPanel != null)
\r
2278 Frame frame = new Frame();
\r
2279 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
2280 frame.add(overview);
\r
2281 // +50 must allow for applet frame window
\r
2282 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
2283 overview.getPreferredSize().width,
\r
2284 overview.getPreferredSize().height + 50);
\r
2287 final AlignmentPanel ap=alignPanel;
\r
2288 frame.addWindowListener(new WindowAdapter()
\r
2290 public void windowClosing(WindowEvent e)
\r
2293 ap.setOverviewPanel(null);
\r
2298 alignPanel.setOverviewPanel(overview);
\r
2302 void changeColour(ColourSchemeI cs)
\r
2304 int threshold = 0;
\r
2308 if (viewport.getAbovePIDThreshold())
\r
2310 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
2313 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2315 viewport.setGlobalColourScheme(cs);
\r
2319 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2322 if (viewport.getConservationSelected())
\r
2325 Alignment al = (Alignment) viewport.getAlignment();
\r
2326 Conservation c = new Conservation("All",
\r
2327 ResidueProperties.propHash, 3, al.getSequences(), 0,
\r
2328 al.getWidth() - 1);
\r
2331 c.verdict(false, viewport.getConsPercGaps());
\r
2333 cs.setConservation(c);
\r
2335 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
\r
2336 cs, "Background"));
\r
2341 cs.setConservation(null);
\r
2344 cs.setConsensus(viewport.getSequenceConsensusHash());
\r
2347 viewport.setGlobalColourScheme(cs);
\r
2350 if (alignPanel.getOverviewPanel() != null)
\r
2352 alignPanel.getOverviewPanel().updateOverviewImage();
\r
2355 jalview.structure.StructureSelectionManager
\r
2356 .getStructureSelectionManager(viewport.applet).sequenceColoursChanged(
\r
2359 alignPanel.paintAlignment(true);
\r
2362 protected void modifyPID_actionPerformed()
\r
2364 if (viewport.getAbovePIDThreshold()
\r
2365 && viewport.getGlobalColourScheme() != null)
\r
2367 SliderPanel.setPIDSliderSource(alignPanel,
\r
2368 viewport.getGlobalColourScheme(), "Background");
\r
2369 SliderPanel.showPIDSlider();
\r
2373 protected void modifyConservation_actionPerformed()
\r
2375 if (viewport.getConservationSelected()
\r
2376 && viewport.getGlobalColourScheme() != null)
\r
2378 SliderPanel.setConservationSlider(alignPanel,
\r
2379 viewport.getGlobalColourScheme(), "Background");
\r
2380 SliderPanel.showConservationSlider();
\r
2384 protected void conservationMenuItem_actionPerformed()
\r
2386 viewport.setConservationSelected(conservationMenuItem.getState());
\r
2388 viewport.setAbovePIDThreshold(false);
\r
2389 abovePIDThreshold.setState(false);
\r
2391 changeColour(viewport.getGlobalColourScheme());
\r
2393 modifyConservation_actionPerformed();
\r
2396 public void abovePIDThreshold_actionPerformed()
\r
2398 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
2400 conservationMenuItem.setState(false);
\r
2401 viewport.setConservationSelected(false);
\r
2403 changeColour(viewport.getGlobalColourScheme());
\r
2405 modifyPID_actionPerformed();
\r
2408 public void sortPairwiseMenuItem_actionPerformed()
\r
2410 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2411 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
\r
2412 .getAlignment().getSequenceAt(0), null);
\r
2414 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
\r
2415 viewport.getAlignment()));
\r
2416 alignPanel.paintAlignment(true);
\r
2419 public void sortIDMenuItem_actionPerformed()
\r
2421 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2422 AlignmentSorter.sortByID(viewport.getAlignment());
\r
2423 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
\r
2424 alignPanel.paintAlignment(true);
\r
2427 public void sortLengthMenuItem_actionPerformed()
\r
2429 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2430 AlignmentSorter.sortByLength(viewport.getAlignment());
\r
2431 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
\r
2432 viewport.getAlignment()));
\r
2433 alignPanel.paintAlignment(true);
\r
2436 public void sortGroupMenuItem_actionPerformed()
\r
2438 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2439 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
2440 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
\r
2441 viewport.getAlignment()));
\r
2442 alignPanel.paintAlignment(true);
\r
2446 public void removeRedundancyMenuItem_actionPerformed()
\r
2448 new RedundancyPanel(alignPanel);
\r
2451 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
2453 if (viewport.getSelectionGroup() != null
\r
2454 && viewport.getSelectionGroup().getSize() > 1)
\r
2456 Frame frame = new Frame();
\r
2457 frame.add(new PairwiseAlignPanel(alignPanel));
\r
2458 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
\r
2463 public void PCAMenuItem_actionPerformed()
\r
2465 // are the sequences aligned?
\r
2466 if (!viewport.getAlignment().isAligned(false))
\r
2468 SequenceI current;
\r
2469 int Width = viewport.getAlignment().getWidth();
\r
2471 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2473 current = viewport.getAlignment().getSequenceAt(i);
\r
2475 if (current.getLength() < Width)
\r
2477 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2480 alignPanel.paintAlignment(true);
\r
2483 if ((viewport.getSelectionGroup() != null
\r
2484 && viewport.getSelectionGroup().getSize() < 4 && viewport
\r
2485 .getSelectionGroup().getSize() > 0)
\r
2486 || viewport.getAlignment().getHeight() < 4)
\r
2493 new PCAPanel(viewport);
\r
2494 } catch (java.lang.OutOfMemoryError ex)
\r
2500 public void averageDistanceTreeMenuItem_actionPerformed()
\r
2502 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
2505 public void neighbourTreeMenuItem_actionPerformed()
\r
2507 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
2510 protected void njTreeBlosumMenuItem_actionPerformed()
\r
2512 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2515 protected void avTreeBlosumMenuItem_actionPerformed()
\r
2517 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2520 void NewTreePanel(String type, String pwType, String title)
\r
2522 // are the sequences aligned?
\r
2523 if (!viewport.getAlignment().isAligned(false))
\r
2525 SequenceI current;
\r
2526 int Width = viewport.getAlignment().getWidth();
\r
2528 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2530 current = viewport.getAlignment().getSequenceAt(i);
\r
2532 if (current.getLength() < Width)
\r
2534 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2537 alignPanel.paintAlignment(true);
\r
2541 if ((viewport.getSelectionGroup() != null && viewport
\r
2542 .getSelectionGroup().getSize() > 1)
\r
2543 || (viewport.getSelectionGroup() == null && viewport.getAlignment()
\r
2544 .getHeight() > 1))
\r
2546 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
\r
2548 addTreeMenuItem(tp, title);
\r
2550 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
2554 void loadTree_actionPerformed()
\r
2556 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
2557 cap.setText("Paste your Newick tree file here.");
\r
2558 cap.setTreeImport();
\r
2559 Frame frame = new Frame();
\r
2561 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
2564 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
2566 TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
\r
2567 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
2568 addTreeMenuItem(tp, treeFile);
\r
2572 * sort the alignment using the given treePanel
\r
2574 * @param treePanel
\r
2575 * tree used to sort view
\r
2577 * string used for undo event name
\r
2579 public void sortByTree(TreePanel treePanel, String title)
\r
2581 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2583 .sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
2584 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2585 // HistoryItem.SORT));
\r
2586 addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
\r
2587 viewport.getAlignment()));
\r
2588 alignPanel.paintAlignment(true);
\r
2592 * Do any automatic reordering of the alignment and add the necessary bits to
\r
2593 * the menu structure for the new tree
\r
2595 * @param treePanel
\r
2598 protected void addTreeMenuItem(final TreePanel treePanel,
\r
2599 final String title)
\r
2601 final MenuItem item = new MenuItem(title);
\r
2602 sortByTreeMenu.add(item);
\r
2603 item.addActionListener(new java.awt.event.ActionListener()
\r
2605 public void actionPerformed(ActionEvent evt)
\r
2607 sortByTree(treePanel, title); // treePanel.getTitle());
\r
2611 treePanel.addWindowListener(new WindowAdapter()
\r
2613 public void windowOpened(WindowEvent e)
\r
2615 if (viewport.sortByTree)
\r
2617 sortByTree(treePanel, title);
\r
2619 super.windowOpened(e);
\r
2622 public void windowClosing(WindowEvent e)
\r
2624 sortByTreeMenu.remove(item);
\r
2628 public boolean sortBy(AlignmentOrder alorder, String undoname)
\r
2630 SequenceI[] oldOrder = viewport.getAlignment()
\r
2631 .getSequencesArray();
\r
2632 if (viewport.applet.debug)
\r
2634 System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");
\r
2636 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
\r
2637 if (undoname!=null)
\r
2639 addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.getAlignment()));
\r
2641 alignPanel.paintAlignment(true);
\r
2645 protected void documentation_actionPerformed()
\r
2647 alignPanel.av.applet.openJalviewHelpUrl();
\r
2650 protected void about_actionPerformed()
\r
2653 class AboutPanel extends Canvas
\r
2659 public AboutPanel(String version, String builddate)
\r
2661 this.version = version;
\r
2662 this.builddate = builddate;
\r
2665 public void paint(Graphics g)
\r
2667 g.setColor(Color.white);
\r
2668 g.fillRect(0, 0, getSize().width, getSize().height);
\r
2669 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2670 FontMetrics fm = g.getFontMetrics();
\r
2671 int fh = fm.getHeight();
\r
2673 g.setColor(Color.black);
\r
2674 // TODO: update this text for each release or centrally store it for
\r
2675 // lite and application
\r
2676 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
2677 g.drawString("JalviewLite - Release " + version, x, y += fh);
\r
2678 g.setFont(new Font("Helvetica", Font.BOLD, 12));
\r
2679 g.drawString("Build date: " + builddate, x, y += fh);
\r
2680 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2682 "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",
\r
2683 x, y += fh * 1.5);
\r
2684 g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
\r
2686 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
\r
2689 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
\r
2691 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
\r
2693 "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
\r
2696 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
\r
2698 g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
\r
2703 Frame frame = new Frame();
\r
2704 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
\r
2705 .getBuildDate()));
\r
2706 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
\r
2710 public void showURL(String url, String target)
\r
2712 if (viewport.applet == null)
\r
2714 System.out.println("Not running as applet - no browser available.");
\r
2718 viewport.applet.showURL(url, target);
\r
2722 // ////////////////////////////////////////////////////////////////////////////////
\r
2723 // JBuilder Graphics here
\r
2725 MenuBar alignFrameMenuBar = new MenuBar();
\r
2727 Menu fileMenu = new Menu("File");
\r
2729 MenuItem loadApplication = new MenuItem("View in Full Application");
\r
2731 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
\r
2733 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
\r
2735 MenuItem outputFeatures = new MenuItem("Export Features ...");
\r
2737 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
\r
2739 MenuItem closeMenuItem = new MenuItem("Close");
\r
2741 Menu editMenu = new Menu("Edit");
\r
2743 Menu viewMenu = new Menu("View");
\r
2745 Menu colourMenu = new Menu("Colour");
\r
2747 Menu calculateMenu = new Menu("Calculate");
\r
2749 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
2751 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
2753 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
2755 MenuItem remove2LeftMenuItem = new MenuItem();
\r
2757 MenuItem remove2RightMenuItem = new MenuItem();
\r
2759 MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
2761 MenuItem removeAllGapsMenuItem = new MenuItem();
\r
2763 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
2765 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
2767 MenuItem sortPairwiseMenuItem = new MenuItem();
\r
2769 MenuItem sortIDMenuItem = new MenuItem();
\r
2771 MenuItem sortLengthMenuItem = new MenuItem();
\r
2773 MenuItem sortGroupMenuItem = new MenuItem();
\r
2775 MenuItem removeRedundancyMenuItem = new MenuItem();
\r
2777 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
2779 MenuItem PCAMenuItem = new MenuItem();
\r
2781 MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
2783 MenuItem neighbourTreeMenuItem = new MenuItem();
\r
2785 BorderLayout borderLayout1 = new BorderLayout();
\r
2787 public Label statusBar = new Label();
\r
2789 Menu outputTextboxMenu = new Menu();
\r
2791 MenuItem clustalColour = new MenuItem();
\r
2793 MenuItem zappoColour = new MenuItem();
\r
2795 MenuItem taylorColour = new MenuItem();
\r
2797 MenuItem hydrophobicityColour = new MenuItem();
\r
2799 MenuItem helixColour = new MenuItem();
\r
2801 MenuItem strandColour = new MenuItem();
\r
2803 MenuItem turnColour = new MenuItem();
\r
2805 MenuItem buriedColour = new MenuItem();
\r
2807 MenuItem purinePyrimidineColour = new MenuItem();
\r
2808 MenuItem RNAHelixColour = new MenuItem();
\r
2810 MenuItem userDefinedColour = new MenuItem();
\r
2812 MenuItem PIDColour = new MenuItem();
\r
2814 MenuItem BLOSUM62Colour = new MenuItem();
\r
2816 MenuItem tcoffeeColour = new MenuItem();
\r
2818 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
2820 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
2822 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
2824 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
2826 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
\r
2828 MenuItem alProperties = new MenuItem("Alignment Properties...");
\r
2830 MenuItem overviewMenuItem = new MenuItem();
\r
2832 MenuItem undoMenuItem = new MenuItem();
\r
2834 MenuItem redoMenuItem = new MenuItem();
\r
2836 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
2838 MenuItem noColourmenuItem = new MenuItem();
\r
2840 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
2842 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
2844 MenuItem findMenuItem = new MenuItem();
\r
2846 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
2848 MenuItem nucleotideColour = new MenuItem();
\r
2850 MenuItem deleteGroups = new MenuItem();
\r
2852 MenuItem grpsFromSelection = new MenuItem();
\r
2854 MenuItem delete = new MenuItem();
\r
2856 MenuItem copy = new MenuItem();
\r
2858 MenuItem cut = new MenuItem();
\r
2860 Menu pasteMenu = new Menu();
\r
2862 MenuItem pasteNew = new MenuItem();
\r
2864 MenuItem pasteThis = new MenuItem();
\r
2866 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
2868 MenuItem font = new MenuItem();
\r
2870 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
2872 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
2874 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
2876 MenuItem modifyPID = new MenuItem();
\r
2878 MenuItem modifyConservation = new MenuItem();
\r
2880 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
\r
2881 "Autocalculate Consensus", true);
\r
2883 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
\r
2884 "Sort Alignment With New Tree", true);
\r
2886 Menu sortByTreeMenu = new Menu();
\r
2888 Menu sort = new Menu();
\r
2890 Menu calculate = new Menu();
\r
2892 MenuItem inputText = new MenuItem();
\r
2894 Menu helpMenu = new Menu();
\r
2896 MenuItem documentation = new MenuItem();
\r
2898 MenuItem about = new MenuItem();
\r
2900 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
2902 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
\r
2904 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
\r
2905 Menu autoAnnMenu=new Menu();
\r
2906 CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();
\r
2907 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
\r
2908 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
\r
2909 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
\r
2910 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
\r
2912 private void jbInit() throws Exception
\r
2915 setMenuBar(alignFrameMenuBar);
\r
2919 // dynamically fill save as menu with available formats
\r
2920 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
2923 item = new MenuItem(
\r
2924 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
2926 item.addActionListener(new java.awt.event.ActionListener()
\r
2928 public void actionPerformed(ActionEvent e)
\r
2930 outputText_actionPerformed(e);
\r
2934 outputTextboxMenu.add(item);
\r
2936 closeMenuItem.addActionListener(this);
\r
2937 loadApplication.addActionListener(this);
\r
2939 loadTree.addActionListener(this);
\r
2940 loadAnnotations.addActionListener(this);
\r
2941 outputFeatures.addActionListener(this);
\r
2942 outputAnnotations.addActionListener(this);
\r
2943 selectAllSequenceMenuItem.addActionListener(this);
\r
2944 deselectAllSequenceMenuItem.addActionListener(this);
\r
2945 invertSequenceMenuItem.addActionListener(this);
\r
2946 remove2LeftMenuItem.setLabel("Remove Left");
\r
2947 remove2LeftMenuItem.addActionListener(this);
\r
2948 remove2RightMenuItem.setLabel("Remove Right");
\r
2949 remove2RightMenuItem.addActionListener(this);
\r
2950 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
2951 removeGappedColumnMenuItem.addActionListener(this);
\r
2952 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
2953 removeAllGapsMenuItem.addActionListener(this);
\r
2954 viewBoxesMenuItem.setLabel("Boxes");
\r
2955 viewBoxesMenuItem.setState(true);
\r
2956 viewBoxesMenuItem.addItemListener(this);
\r
2957 viewTextMenuItem.setLabel("Text");
\r
2958 viewTextMenuItem.setState(true);
\r
2959 viewTextMenuItem.addItemListener(this);
\r
2960 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
2961 sortPairwiseMenuItem.addActionListener(this);
\r
2962 sortIDMenuItem.setLabel("by ID");
\r
2963 sortIDMenuItem.addActionListener(this);
\r
2964 sortLengthMenuItem.setLabel("by Length");
\r
2965 sortLengthMenuItem.addActionListener(this);
\r
2966 sortGroupMenuItem.setLabel("by Group");
\r
2967 sortGroupMenuItem.addActionListener(this);
\r
2968 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
2969 removeRedundancyMenuItem.addActionListener(this);
\r
2970 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
2971 pairwiseAlignmentMenuItem.addActionListener(this);
\r
2972 PCAMenuItem.setLabel("Principal Component Analysis");
\r
2973 PCAMenuItem.addActionListener(this);
\r
2974 averageDistanceTreeMenuItem
\r
2975 .setLabel("Average Distance Using % Identity");
\r
2976 averageDistanceTreeMenuItem.addActionListener(this);
\r
2977 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
2978 neighbourTreeMenuItem.addActionListener(this);
\r
2979 statusBar.setBackground(Color.white);
\r
2980 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
2981 statusBar.setText("Status bar");
\r
2982 outputTextboxMenu.setLabel("Output to Textbox");
\r
2983 clustalColour.setLabel("Clustalx");
\r
2985 clustalColour.addActionListener(this);
\r
2986 zappoColour.setLabel("Zappo");
\r
2987 zappoColour.addActionListener(this);
\r
2988 taylorColour.setLabel("Taylor");
\r
2989 taylorColour.addActionListener(this);
\r
2990 hydrophobicityColour.setLabel("Hydrophobicity");
\r
2991 hydrophobicityColour.addActionListener(this);
\r
2992 helixColour.setLabel("Helix Propensity");
\r
2993 helixColour.addActionListener(this);
\r
2994 strandColour.setLabel("Strand Propensity");
\r
2995 strandColour.addActionListener(this);
\r
2996 turnColour.setLabel("Turn Propensity");
\r
2997 turnColour.addActionListener(this);
\r
2998 buriedColour.setLabel("Buried Index");
\r
2999 buriedColour.addActionListener(this);
\r
3000 purinePyrimidineColour.setLabel("Purine/Pyrimidine");
\r
3001 purinePyrimidineColour.addActionListener(this);
\r
3002 RNAHelixColour.setLabel("by RNA Helices");
\r
3003 RNAHelixColour.addActionListener(this);
\r
3004 userDefinedColour.setLabel("User Defined...");
\r
3005 userDefinedColour.addActionListener(this);
\r
3006 PIDColour.setLabel("Percentage Identity");
\r
3007 PIDColour.addActionListener(this);
\r
3008 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
3009 BLOSUM62Colour.addActionListener(this);
\r
3010 tcoffeeColour.setLabel("T-Coffee Scores");
\r
3011 tcoffeeColour.setEnabled(false); // it will enabled only if a score file is provided
\r
3012 tcoffeeColour.addActionListener(this);
\r
3013 avDistanceTreeBlosumMenuItem .setLabel("Average Distance Using BLOSUM62");
\r
3014 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
3015 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
3016 njTreeBlosumMenuItem.addActionListener(this);
\r
3017 annotationPanelMenuItem.setLabel("Show Annotations");
\r
3018 annotationPanelMenuItem.addItemListener(this);
\r
3019 colourTextMenuItem.setLabel("Colour Text");
\r
3020 colourTextMenuItem.addItemListener(this);
\r
3021 displayNonconservedMenuItem.setLabel("Show nonconserved");
\r
3022 displayNonconservedMenuItem.addItemListener(this);
\r
3023 alProperties.addActionListener(this);
\r
3024 overviewMenuItem.setLabel("Overview Window");
\r
3025 overviewMenuItem.addActionListener(this);
\r
3026 undoMenuItem.setEnabled(false);
\r
3027 undoMenuItem.setLabel("Undo");
\r
3028 undoMenuItem.addActionListener(this);
\r
3029 redoMenuItem.setEnabled(false);
\r
3030 redoMenuItem.setLabel("Redo");
\r
3031 redoMenuItem.addActionListener(this);
\r
3032 conservationMenuItem.setLabel("by Conservation");
\r
3033 conservationMenuItem.addItemListener(this);
\r
3034 noColourmenuItem.setLabel("None");
\r
3035 noColourmenuItem.addActionListener(this);
\r
3036 wrapMenuItem.setLabel("Wrap");
\r
3037 wrapMenuItem.addItemListener(this);
\r
3038 renderGapsMenuItem.setLabel("Show Gaps");
\r
3039 renderGapsMenuItem.setState(true);
\r
3040 renderGapsMenuItem.addItemListener(this);
\r
3041 findMenuItem.setLabel("Find...");
\r
3042 findMenuItem.addActionListener(this);
\r
3043 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
3044 abovePIDThreshold.addItemListener(this);
\r
3045 nucleotideColour.setLabel("Nucleotide");
\r
3046 nucleotideColour.addActionListener(this);
\r
3047 deleteGroups.setLabel("Undefine Groups");
\r
3048 deleteGroups.addActionListener(this);
\r
3049 grpsFromSelection.setLabel("Make Groups for selection");
\r
3050 grpsFromSelection.addActionListener(this);
\r
3051 copy.setLabel("Copy");
\r
3052 copy.addActionListener(this);
\r
3053 cut.setLabel("Cut");
\r
3054 cut.addActionListener(this);
\r
3055 delete.setLabel("Delete");
\r
3056 delete.addActionListener(this);
\r
3057 pasteMenu.setLabel("Paste");
\r
3058 pasteNew.setLabel("To New Alignment");
\r
3059 pasteNew.addActionListener(this);
\r
3060 pasteThis.setLabel("Add To This Alignment");
\r
3061 pasteThis.addActionListener(this);
\r
3062 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
3063 applyToAllGroups.setState(true);
\r
3064 applyToAllGroups.addItemListener(this);
\r
3065 font.setLabel("Font...");
\r
3066 font.addActionListener(this);
\r
3067 scaleAbove.setLabel("Scale Above");
\r
3068 scaleAbove.setState(true);
\r
3069 scaleAbove.setEnabled(false);
\r
3070 scaleAbove.addItemListener(this);
\r
3071 scaleLeft.setEnabled(false);
\r
3072 scaleLeft.setState(true);
\r
3073 scaleLeft.setLabel("Scale Left");
\r
3074 scaleLeft.addItemListener(this);
\r
3075 scaleRight.setEnabled(false);
\r
3076 scaleRight.setState(true);
\r
3077 scaleRight.setLabel("Scale Right");
\r
3078 scaleRight.addItemListener(this);
\r
3079 modifyPID.setLabel("Modify Identity Threshold...");
\r
3080 modifyPID.addActionListener(this);
\r
3081 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
3082 modifyConservation.addActionListener(this);
\r
3083 sortByTreeMenu.setLabel("By Tree Order");
\r
3084 sort.setLabel("Sort");
\r
3085 calculate.setLabel("Calculate Tree");
\r
3086 autoCalculate.addItemListener(this);
\r
3087 sortByTree.addItemListener(this);
\r
3088 inputText.setLabel("Input from textbox");
\r
3089 inputText.addActionListener(this);
\r
3090 centreColumnLabelFlag.setLabel("Centre column labels");
\r
3091 centreColumnLabelFlag.addItemListener(this);
\r
3092 followMouseOverFlag.setLabel("Automatic Scrolling");
\r
3093 followMouseOverFlag.addItemListener(this);
\r
3094 helpMenu.setLabel("Help");
\r
3095 documentation.setLabel("Documentation");
\r
3096 documentation.addActionListener(this);
\r
3098 about.setLabel("About...");
\r
3099 about.addActionListener(this);
\r
3100 seqLimits.setState(true);
\r
3101 seqLimits.setLabel("Show Sequence Limits");
\r
3102 seqLimits.addItemListener(this);
\r
3103 featureSettings.setLabel("Feature Settings...");
\r
3104 featureSettings.addActionListener(this);
\r
3105 sequenceFeatures.setLabel("Sequence Features");
\r
3106 sequenceFeatures.addItemListener(this);
\r
3107 sequenceFeatures.setState(false);
\r
3108 annotationColour.setLabel("by Annotation...");
\r
3109 annotationColour.addActionListener(this);
\r
3110 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
3111 invertColSel.setLabel("Invert Column Selection");
\r
3112 menu1.setLabel("Show");
\r
3113 showColumns.setLabel("All Columns ");
\r
3114 showSeqs.setLabel("All Sequences");
\r
3115 menu2.setLabel("Hide");
\r
3116 hideColumns.setLabel("Selected Columns");
\r
3117 hideSequences.setLabel("Selected Sequences");
\r
3118 hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
\r
3119 hideAllSelection.setLabel("Selected Region");
\r
3120 showAllHidden.setLabel("All Sequences and Columns");
\r
3121 showGroupConsensus.setLabel("Group Consensus");
\r
3122 showGroupConservation.setLabel("Group Conservation");
\r
3123 showConsensusHistogram.setLabel("Show Consensus Histogram");
\r
3124 showSequenceLogo.setLabel("Show Consensus Logo");
\r
3125 applyAutoAnnotationSettings.setLabel("Apply to all groups");
\r
3126 applyAutoAnnotationSettings.setState(true);
\r
3127 autoAnnMenu.setLabel("Autocalculated Annotation");
\r
3129 invertColSel.addActionListener(this);
\r
3130 showColumns.addActionListener(this);
\r
3131 showSeqs.addActionListener(this);
\r
3132 hideColumns.addActionListener(this);
\r
3133 hideSequences.addActionListener(this);
\r
3134 hideAllButSelection.addActionListener(this);
\r
3135 hideAllSelection.addActionListener(this);
\r
3136 showAllHidden.addActionListener(this);
\r
3137 showGroupConsensus.addItemListener(this);
\r
3138 showGroupConservation.addItemListener(this);
\r
3139 showConsensusHistogram.addItemListener(this);
\r
3140 showSequenceLogo.addItemListener(this);
\r
3141 applyAutoAnnotationSettings.addItemListener(this);
\r
3142 formatMenu.setLabel("Format");
\r
3143 selectMenu.setLabel("Select");
\r
3144 newView.setLabel("New View");
\r
3145 newView.addActionListener(this);
\r
3146 alignFrameMenuBar.add(fileMenu);
\r
3147 alignFrameMenuBar.add(editMenu);
\r
3148 alignFrameMenuBar.add(selectMenu);
\r
3149 alignFrameMenuBar.add(viewMenu);
\r
3150 alignFrameMenuBar.add(formatMenu);
\r
3151 alignFrameMenuBar.add(colourMenu);
\r
3152 alignFrameMenuBar.add(calculateMenu);
\r
3153 alignFrameMenuBar.add(helpMenu);
\r
3155 fileMenu.add(inputText);
\r
3156 fileMenu.add(loadTree);
\r
3157 fileMenu.add(loadAnnotations);
\r
3159 fileMenu.addSeparator();
\r
3160 fileMenu.add(outputTextboxMenu);
\r
3161 fileMenu.add(outputFeatures);
\r
3162 fileMenu.add(outputAnnotations);
\r
3164 if (jalviewServletURL != null)
\r
3166 fileMenu.add(loadApplication);
\r
3169 fileMenu.addSeparator();
\r
3170 fileMenu.add(closeMenuItem);
\r
3172 editMenu.add(undoMenuItem);
\r
3173 editMenu.add(redoMenuItem);
\r
3174 editMenu.add(cut);
\r
3175 editMenu.add(copy);
\r
3176 editMenu.add(pasteMenu);
\r
3177 editMenu.add(delete);
\r
3178 editMenu.addSeparator();
\r
3179 editMenu.add(remove2LeftMenuItem);
\r
3180 editMenu.add(remove2RightMenuItem);
\r
3181 editMenu.add(removeGappedColumnMenuItem);
\r
3182 editMenu.add(removeAllGapsMenuItem);
\r
3183 editMenu.add(removeRedundancyMenuItem);
\r
3184 viewMenu.add(newView);
\r
3185 viewMenu.addSeparator();
\r
3186 viewMenu.add(menu1);
\r
3187 viewMenu.add(menu2);
\r
3188 viewMenu.addSeparator();
\r
3189 viewMenu.add(followMouseOverFlag);
\r
3190 viewMenu.add(annotationPanelMenuItem);
\r
3191 autoAnnMenu.add(applyAutoAnnotationSettings);
\r
3192 autoAnnMenu.add(showConsensusHistogram);
\r
3193 autoAnnMenu.add(showSequenceLogo);
\r
3194 autoAnnMenu.addSeparator();
\r
3195 autoAnnMenu.add(showGroupConservation);
\r
3196 autoAnnMenu.add(showGroupConsensus);
\r
3197 viewMenu.add(autoAnnMenu);
\r
3198 viewMenu.addSeparator();
\r
3199 viewMenu.add(sequenceFeatures);
\r
3200 viewMenu.add(featureSettings);
\r
3201 viewMenu.addSeparator();
\r
3202 viewMenu.add(alProperties);
\r
3203 viewMenu.addSeparator();
\r
3204 viewMenu.add(overviewMenuItem);
\r
3205 colourMenu.add(applyToAllGroups);
\r
3206 colourMenu.addSeparator();
\r
3207 colourMenu.add(noColourmenuItem);
\r
3208 colourMenu.add(clustalColour);
\r
3209 colourMenu.add(BLOSUM62Colour);
\r
3210 colourMenu.add(PIDColour);
\r
3211 colourMenu.add(zappoColour);
\r
3212 colourMenu.add(taylorColour);
\r
3213 colourMenu.add(hydrophobicityColour);
\r
3214 colourMenu.add(helixColour);
\r
3215 colourMenu.add(strandColour);
\r
3216 colourMenu.add(turnColour);
\r
3217 colourMenu.add(buriedColour);
\r
3218 colourMenu.add(nucleotideColour);
\r
3219 colourMenu.add(purinePyrimidineColour);
\r
3220 colourMenu.add(tcoffeeColour);
\r
3221 colourMenu.add(userDefinedColour);
\r
3222 colourMenu.addSeparator();
\r
3223 colourMenu.add(conservationMenuItem);
\r
3224 colourMenu.add(modifyConservation);
\r
3225 colourMenu.add(abovePIDThreshold);
\r
3226 colourMenu.add(modifyPID);
\r
3227 colourMenu.add(annotationColour);
\r
3228 colourMenu.add(RNAHelixColour);
\r
3229 calculateMenu.add(sort);
\r
3230 calculateMenu.add(calculate);
\r
3231 calculateMenu.addSeparator();
\r
3232 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
3233 calculateMenu.add(PCAMenuItem);
\r
3234 calculateMenu.add(autoCalculate);
\r
3235 calculateMenu.add(sortByTree);
\r
3236 this.add(statusBar, BorderLayout.SOUTH);
\r
3237 pasteMenu.add(pasteNew);
\r
3238 pasteMenu.add(pasteThis);
\r
3239 sort.add(sortIDMenuItem);
\r
3240 sort.add(sortLengthMenuItem);
\r
3241 sort.add(sortByTreeMenu);
\r
3242 sort.add(sortGroupMenuItem);
\r
3243 sort.add(sortPairwiseMenuItem);
\r
3244 calculate.add(averageDistanceTreeMenuItem);
\r
3245 calculate.add(neighbourTreeMenuItem);
\r
3246 calculate.add(avDistanceTreeBlosumMenuItem);
\r
3247 calculate.add(njTreeBlosumMenuItem);
\r
3248 helpMenu.add(documentation);
\r
3249 helpMenu.add(about);
\r
3250 menu1.add(showColumns);
\r
3251 menu1.add(showSeqs);
\r
3252 menu1.add(showAllHidden);
\r
3253 menu2.add(hideColumns);
\r
3254 menu2.add(hideSequences);
\r
3255 menu2.add(hideAllSelection);
\r
3256 menu2.add(hideAllButSelection);
\r
3257 formatMenu.add(font);
\r
3258 formatMenu.add(seqLimits);
\r
3259 formatMenu.add(wrapMenuItem);
\r
3260 formatMenu.add(scaleAbove);
\r
3261 formatMenu.add(scaleLeft);
\r
3262 formatMenu.add(scaleRight);
\r
3263 formatMenu.add(viewBoxesMenuItem);
\r
3264 formatMenu.add(viewTextMenuItem);
\r
3265 formatMenu.add(colourTextMenuItem);
\r
3266 formatMenu.add(displayNonconservedMenuItem);
\r
3267 formatMenu.add(renderGapsMenuItem);
\r
3268 formatMenu.add(centreColumnLabelFlag);
\r
3269 selectMenu.add(findMenuItem);
\r
3270 selectMenu.addSeparator();
\r
3271 selectMenu.add(selectAllSequenceMenuItem);
\r
3272 selectMenu.add(deselectAllSequenceMenuItem);
\r
3273 selectMenu.add(invertSequenceMenuItem);
\r
3274 selectMenu.add(invertColSel);
\r
3275 selectMenu.add(grpsFromSelection);
\r
3276 selectMenu.add(deleteGroups);
\r
3280 MenuItem featureSettings = new MenuItem();
\r
3282 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
3284 MenuItem annotationColour = new MenuItem();
\r
3286 MenuItem invertColSel = new MenuItem();
\r
3288 Menu menu1 = new Menu();
\r
3290 MenuItem showColumns = new MenuItem();
\r
3292 MenuItem showSeqs = new MenuItem();
\r
3294 Menu menu2 = new Menu();
\r
3296 MenuItem hideColumns = new MenuItem();
\r
3298 MenuItem hideSequences = new MenuItem();
\r
3300 MenuItem hideAllButSelection = new MenuItem();
\r
3302 MenuItem hideAllSelection = new MenuItem();
\r
3304 MenuItem showAllHidden = new MenuItem();
\r
3306 Menu formatMenu = new Menu();
\r
3308 Menu selectMenu = new Menu();
\r
3310 MenuItem newView = new MenuItem();
\r
3313 * Attach the alignFrame panels after embedding menus, if necessary. This used
\r
3314 * to be called setEmbedded, but is now creates the dropdown menus in a
\r
3315 * platform independent manner to avoid OSX/Mac menu appendage daftness.
\r
3317 * @param reallyEmbedded
\r
3318 * true to attach the view to the applet area on the page rather than
\r
3321 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
\r
3323 if (reallyEmbedded)
\r
3326 // Explicly build the embedded menu panel for the on-page applet
\r
3328 // view cannot be closed if its actually on the page
\r
3329 fileMenu.remove(closeMenuItem);
\r
3330 fileMenu.remove(3); // Remove Seperator
\r
3331 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
\r
3332 Font.PLAIN, 10, false); // use our own fonts.
\r
3333 // and actually add the components to the applet area
\r
3334 viewport.applet.setLayout(new BorderLayout());
\r
3335 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
\r
3336 viewport.applet.add(statusBar, BorderLayout.SOUTH);
\r
3337 alignPanel.setSize(viewport.applet.getSize().width,
\r
3338 viewport.applet.getSize().height - embeddedMenu.HEIGHT
\r
3339 - statusBar.HEIGHT);
\r
3340 viewport.applet.add(alignPanel, BorderLayout.CENTER);
\r
3341 final AlignFrame me = this;
\r
3342 viewport.applet.addFocusListener(new FocusListener()
\r
3346 public void focusLost(FocusEvent e)
\r
3348 if (me.viewport.applet.currentAlignFrame==me) {
\r
3349 me.viewport.applet.currentAlignFrame = null;
\r
3353 public void focusGained(FocusEvent e)
\r
3355 me.viewport.applet.currentAlignFrame = me;
\r
3358 viewport.applet.validate();
\r
3363 // test and embed menu bar if necessary.
\r
3365 if (embedMenuIfNeeded(alignPanel))
\r
3367 // adjust for status bar height too
\r
3368 alignPanel.setSize(getSize().width, getSize().height
\r
3369 - statusBar.HEIGHT);
\r
3371 add(statusBar, BorderLayout.SOUTH);
\r
3372 add(alignPanel, BorderLayout.CENTER);
\r
3373 // and register with the applet so it can pass external API calls to us
\r
3374 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
\r
3380 * create a new binding between structures in an existing jmol viewer instance
\r
3381 * and an alignpanel with sequences that have existing PDBFile entries. Note,
\r
3382 * this does not open a new Jmol window, or modify the display of the
\r
3383 * structures in the original jmol window. Note This method doesn't work
\r
3384 * without an additional javascript library to exchange messages between the
\r
3385 * distinct applets. See http://issues.jalview.org/browse/JAL-621
\r
3388 * JmolViewer instance
\r
3389 * @param sequenceIds
\r
3390 * - sequence Ids to search for associations
\r
3392 public SequenceStructureBinding addStructureViewInstance(
\r
3393 Object jmolviewer, String[] sequenceIds)
\r
3395 org.jmol.api.JmolViewer viewer = null;
\r
3398 viewer = (org.jmol.api.JmolViewer) jmolviewer;
\r
3399 } catch (ClassCastException ex)
\r
3401 System.err.println("Unsupported viewer object :"
\r
3402 + jmolviewer.getClass());
\r
3404 if (viewer == null)
\r
3406 System.err.println("Can't use this object as a structure viewer:"
\r
3407 + jmolviewer.getClass());
\r
3410 SequenceI[] seqs = null;
\r
3411 if (sequenceIds == null || sequenceIds.length == 0)
\r
3413 seqs = viewport.getAlignment().getSequencesArray();
\r
3417 Vector sqi = new Vector();
\r
3418 AlignmentI al = viewport.getAlignment();
\r
3419 for (int sid = 0; sid < sequenceIds.length; sid++)
\r
3421 SequenceI sq = al.findName(sequenceIds[sid]);
\r
3424 sqi.addElement(sq);
\r
3427 if (sqi.size() > 0)
\r
3429 seqs = new SequenceI[sqi.size()];
\r
3430 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
\r
3432 seqs[sid] = (SequenceI) sqi.elementAt(sid);
\r
3440 ExtJmol jmv = null;
\r
3441 // TODO: search for a jmv that involves viewer
\r
3443 { // create a new viewer/jalview binding.
\r
3444 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs});
\r
3450 * bind a pdb file to a sequence in the current view
\r
3452 * @param sequenceId
\r
3453 * - sequenceId within the dataset.
\r
3454 * @param pdbEntryString
\r
3455 * - the short name for the PDB file
\r
3457 * - pdb file - either a URL or a valid PDB file.
\r
3458 * @return true if binding was as success TODO: consider making an exception
\r
3459 * structure for indicating when PDB parsing or sequenceId location
\r
3462 public boolean addPdbFile(String sequenceId, String pdbEntryString,
\r
3465 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
\r
3466 boolean needtoadd = false;
\r
3467 if (toaddpdb != null)
\r
3469 Vector pdbe = toaddpdb.getPDBId();
\r
3470 PDBEntry pdbentry = null;
\r
3471 if (pdbe != null && pdbe.size() > 0)
\r
3473 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
\r
3475 pdbentry = (PDBEntry) pdbe.elementAt(pe);
\r
3476 if (!pdbentry.getId().equals(pdbEntryString)
\r
3477 && !pdbentry.getFile().equals(pdbFile))
\r
3487 if (pdbentry == null)
\r
3489 pdbentry = new PDBEntry();
\r
3490 pdbentry.setId(pdbEntryString);
\r
3491 pdbentry.setFile(pdbFile);
\r
3492 needtoadd = true; // add this new entry to sequence.
\r
3494 // resolve data source
\r
3495 // TODO: this code should be a refactored to an io package
\r
3496 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
\r
3497 if (protocol == null)
\r
3503 // make a note of the access mode and add
\r
3504 if (pdbentry.getProperty() == null)
\r
3506 pdbentry.setProperty(new Hashtable());
\r
3508 pdbentry.getProperty().put("protocol", protocol);
\r
3509 toaddpdb.addPDBId(pdbentry);
\r
3515 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
\r
3519 Vector sequences = new Vector();
\r
3520 for (int i = 0; i < seqs.length; i++)
\r
3522 if (seqs[i] != null)
\r
3524 sequences.addElement(new Object[]
\r
3525 { seqs[i], (chains != null) ? chains[i] : null });
\r
3528 seqs = new SequenceI[sequences.size()];
\r
3529 chains = new String[sequences.size()];
\r
3530 for (int i = 0, isize = sequences.size(); i < isize; i++)
\r
3532 Object[] oj = (Object[]) sequences.elementAt(i);
\r
3534 seqs[i] = (SequenceI) oj[0];
\r
3535 chains[i] = (String) oj[1];
\r
3538 return new Object[]
\r
3543 public void newStructureView(JalviewLite applet, PDBEntry pdb,
\r
3544 SequenceI[] seqs, String[] chains, String protocol)
\r
3546 // Scrub any null sequences from the array
\r
3547 Object[] sqch = cleanSeqChainArrays(seqs, chains);
\r
3548 seqs = (SequenceI[]) sqch[0];
\r
3549 chains = (String[]) sqch[1];
\r
3550 if (seqs == null || seqs.length == 0)
\r
3553 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
\r
3555 if (protocol == null || protocol.trim().length() == 0
\r
3556 || protocol.equals("null"))
\r
3558 protocol = (String) pdb.getProperty().get("protocol");
\r
3559 if (protocol == null)
\r
3561 System.err.println("Couldn't work out protocol to open structure: "
\r
3566 if (applet.useXtrnalSviewer)
\r
3568 // register the association(s) and quit, don't create any windows.
\r
3569 if (StructureSelectionManager.getStructureSelectionManager(applet).setMapping(seqs, chains, pdb.getFile(), protocol)==null) {
\r
3570 System.err.println("Failed to map "+pdb.getFile()+" ("+protocol+") to any sequences");
\r
3574 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
\r
3576 // can only do alignments with Jmol
\r
3577 // find the last jmol window assigned to this alignment
\r
3578 jalview.appletgui.AppletJmol ajm = null, tajm;
\r
3579 Vector jmols = applet
\r
3580 .getAppletWindow(jalview.appletgui.AppletJmol.class);
\r
3581 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
\r
3583 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
\r
3584 if (tajm.ap.alignFrame == this)
\r
3593 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
\r
3594 // try and add the pdb structure
\r
3599 // otherwise, create a new window
\r
3600 if (applet.jmolAvailable)
\r
3602 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
\r
3604 applet.lastFrameX += 40;
\r
3605 applet.lastFrameY += 40;
\r
3609 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
\r
3614 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
\r
3615 SequenceI[][] seqs, String[][] chains, String[] protocols)
\r
3617 // TODO Auto-generated method stub
\r
3618 System.err.println("Aligned Structure View: Not yet implemented.");
\r
3622 * modify the current selection, providing the user has not made a selection already.
\r
3623 * @param sel - sequences from this alignment
\r
3624 * @param csel - columns to be selected on the alignment
\r
3626 public void select(SequenceGroup sel, ColumnSelection csel)
\r
3628 alignPanel.seqPanel.selection(sel, csel, null);
\r
3631 public void scrollTo(int row, int column)
\r
3633 alignPanel.seqPanel.scrollTo(row, column);
\r
3635 public void scrollToRow(int row)
\r
3637 alignPanel.seqPanel.scrollToRow(row);
\r
3639 public void scrollToColumn(int column)
\r
3641 alignPanel.seqPanel.scrollToColumn(column);
\r
3644 * @return the alignments unique ID.
\r
3646 public String getSequenceSetId() {
\r
3647 return viewport.getSequenceSetId();
\r
3652 * Load the (T-Coffee) score file from the specified url
\r
3654 * @param source File/URL/T-COFFEE score file contents
\r
3655 * @throws IOException
\r
3656 * @return true if alignment was annotated with data from source
\r
3658 public boolean loadScoreFile( String source ) throws IOException {
\r
3660 TCoffeeScoreFile file = new TCoffeeScoreFile(source, AppletFormatAdapter.checkProtocol(source));
\r
3661 if( !file.isValid()) {
\r
3662 // TODO: raise dialog for gui
\r
3663 System.err.println("Problems parsing T-Coffee scores: "+file.getWarningMessage());
\r
3664 System.err.println("Origin was:\n"+source);
\r
3669 * check that the score matrix matches the alignment dimensions
\r
3672 if( (aln=viewport.getAlignment()) != null && (aln.getHeight() != file.getHeight() || aln.getWidth() != file.getWidth()) ) {
\r
3673 // TODO: raise a dialog box here rather than bomb out.
\r
3674 System.err.println("The scores matrix does not match the alignment dimensions");
\r
3678 // TODO add parameter to indicate if matching should be done
\r
3679 if (file.annotateAlignment(alignPanel.getAlignment(), false))
\r
3681 alignPanel.fontChanged();
\r
3682 tcoffeeColour.setEnabled(true);
\r
3683 // switch to this color
\r
3684 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
\r
3687 System.err.println("Problems resolving T-Coffee scores:");
\r
3688 if (file.getWarningMessage()!=null) {
\r
3689 System.err.println(file.getWarningMessage());
\r