2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
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3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
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5 * This file is part of Jalview.
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7 * Jalview is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License
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9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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11 * Jalview is distributed in the hope that it will be useful, but
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12 * WITHOUT ANY WARRANTY; without even the implied warranty
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13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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14 * PURPOSE. See the GNU General Public License for more details.
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16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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18 package jalview.gui;
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23 import java.awt.event.*;
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25 import javax.swing.*;
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27 import jalview.analysis.*;
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28 import jalview.commands.*;
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29 import jalview.datamodel.*;
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30 import jalview.io.*;
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31 import jalview.schemes.*;
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32 import jalview.util.GroupUrlLink;
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33 import jalview.util.GroupUrlLink.UrlStringTooLongException;
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34 import jalview.util.MessageManager;
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35 import jalview.util.UrlLink;
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41 * @version $Revision: 1.118 $
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43 public class PopupMenu extends JPopupMenu
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45 JMenu groupMenu = new JMenu();
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47 JMenuItem groupName = new JMenuItem();
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49 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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51 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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53 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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55 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
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57 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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59 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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61 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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63 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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65 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
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67 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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69 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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71 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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73 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
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75 // protected JRadioButtonMenuItem covariationColour = new
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76 // JRadioButtonMenuItem();
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78 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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80 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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84 JMenu sequenceMenu = new JMenu();
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86 JMenuItem sequenceName = new JMenuItem();
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88 JMenuItem sequenceDetails = new JMenuItem();
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90 JMenuItem sequenceSelDetails = new JMenuItem();
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93 JMenuItem createGroupMenuItem = new JMenuItem();
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94 JMenuItem unGroupMenuItem = new JMenuItem();
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96 JMenuItem outline = new JMenuItem();
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98 JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
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100 JMenu colourMenu = new JMenu();
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102 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
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104 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
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106 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
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108 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
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110 JMenu editMenu = new JMenu();
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112 JMenuItem cut = new JMenuItem();
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114 JMenuItem copy = new JMenuItem();
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116 JMenuItem upperCase = new JMenuItem();
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118 JMenuItem lowerCase = new JMenuItem();
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120 JMenuItem toggle = new JMenuItem();
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122 JMenu pdbMenu = new JMenu();
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124 JMenuItem pdbFromFile = new JMenuItem();
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126 JMenuItem enterPDB = new JMenuItem();
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128 JMenuItem discoverPDB = new JMenuItem();
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130 JMenu outputMenu = new JMenu();
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132 JMenuItem sequenceFeature = new JMenuItem();
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134 JMenuItem textColour = new JMenuItem();
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136 JMenu jMenu1 = new JMenu();
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138 JMenu structureMenu = new JMenu();
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140 JMenu viewStructureMenu = new JMenu();
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142 // JMenu colStructureMenu = new JMenu();
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143 JMenuItem editSequence = new JMenuItem();
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145 // JMenuItem annotationMenuItem = new JMenuItem();
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147 JMenu groupLinksMenu;
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150 * Creates a new PopupMenu object.
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157 public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
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159 this(ap, seq, links, null);
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167 * @param groupLinks
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169 public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
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170 Vector links, Vector groupLinks)
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172 // /////////////////////////////////////////////////////////
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173 // If this is activated from the sequence panel, the user may want to
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174 // edit or annotate a particular residue. Therefore display the residue menu
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176 // If from the IDPanel, we must display the sequence menu
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177 // ////////////////////////////////////////////////////////
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181 ButtonGroup colours = new ButtonGroup();
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182 colours.add(noColourmenuItem);
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183 colours.add(clustalColour);
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184 colours.add(zappoColour);
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185 colours.add(taylorColour);
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186 colours.add(hydrophobicityColour);
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187 colours.add(helixColour);
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188 colours.add(strandColour);
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189 colours.add(turnColour);
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190 colours.add(buriedColour);
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191 colours.add(abovePIDColour);
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192 colours.add(userDefinedColour);
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193 colours.add(PIDColour);
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194 colours.add(BLOSUM62Colour);
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195 colours.add(purinePyrimidineColour);
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196 // colours.add(covariationColour);
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198 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
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200 JMenuItem item = new JMenuItem(
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201 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
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203 item.addActionListener(new java.awt.event.ActionListener()
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205 public void actionPerformed(ActionEvent e)
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207 outputText_actionPerformed(e);
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211 outputMenu.add(item);
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217 } catch (Exception e)
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219 e.printStackTrace();
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222 JMenuItem menuItem;
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225 sequenceMenu.setText(sequence.getName());
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227 if (seq.getDatasetSequence().getPDBId() != null
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228 && seq.getDatasetSequence().getPDBId().size() > 0)
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230 java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
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233 while (e.hasMoreElements())
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235 final PDBEntry pdb = (PDBEntry) e.nextElement();
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237 menuItem = new JMenuItem();
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238 menuItem.setText(pdb.getId());
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239 menuItem.addActionListener(new java.awt.event.ActionListener()
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241 public void actionPerformed(ActionEvent e)
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243 // TODO re JAL-860: optionally open dialog or provide a menu entry
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244 // allowing user to open just one structure per sequence
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245 new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
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246 { pdb })[0], null, ap);
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247 // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
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251 viewStructureMenu.add(menuItem);
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254 * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
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255 * menuItem.addActionListener(new java.awt.event.ActionListener() {
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256 * public void actionPerformed(ActionEvent e) {
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257 * colourByStructure(pdb.getId()); } });
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258 * colStructureMenu.add(menuItem);
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264 if (ap.av.getAlignment().isNucleotide() == false)
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266 structureMenu.remove(viewStructureMenu);
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268 // structureMenu.remove(colStructureMenu);
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271 if (ap.av.getAlignment().isNucleotide() == true)
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273 AlignmentAnnotation[] aa = ap.av.getAlignment()
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274 .getAlignmentAnnotation();
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275 for (int i = 0; i < aa.length; i++)
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277 if (aa[i].getRNAStruc() != null)
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279 final String rnastruc = aa[i].getRNAStruc();
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280 final String structureLine = aa[i].label;
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281 menuItem = new JMenuItem();
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282 menuItem.setText(MessageManager.formatMessage("label.2d_rna_structure_line", new String[]{structureLine}));
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283 menuItem.addActionListener(new java.awt.event.ActionListener()
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285 public void actionPerformed(ActionEvent e)
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287 new AppVarna(structureLine, seq, seq.getSequenceAsString(),
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288 rnastruc, seq.getName(), ap);
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291 viewStructureMenu.add(menuItem);
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295 // SequenceFeatures[] test = seq.getSequenceFeatures();
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297 if (seq.getAnnotation() != null)
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299 AlignmentAnnotation seqAnno[] = seq.getAnnotation();
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300 for (int i = 0; i < seqAnno.length; i++)
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302 if (seqAnno[i].getRNAStruc() != null)
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304 final String rnastruc = seqAnno[i].getRNAStruc();
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306 // TODO: make rnastrucF a bit more nice
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307 menuItem = new JMenuItem();
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308 menuItem.setText(MessageManager.formatMessage("label.2d_rna_sequence_name", new String[]{seq.getName()}));
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309 menuItem.addActionListener(new java.awt.event.ActionListener()
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311 public void actionPerformed(ActionEvent e)
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313 // TODO: VARNA does'nt print gaps in the sequence
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314 new AppVarna(seq.getName() + " structure", seq, seq
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315 .getSequenceAsString(), rnastruc, seq.getName(),
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319 viewStructureMenu.add(menuItem);
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326 menuItem = new JMenuItem(MessageManager.getString("action.hide_sequences"));
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327 menuItem.addActionListener(new java.awt.event.ActionListener()
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329 public void actionPerformed(ActionEvent e)
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331 hideSequences(false);
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336 if (ap.av.getSelectionGroup() != null
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337 && ap.av.getSelectionGroup().getSize() > 1)
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339 menuItem = new JMenuItem(MessageManager.formatMessage("label.represent_group_with", new String[]{seq.getName()}));
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340 menuItem.addActionListener(new java.awt.event.ActionListener()
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342 public void actionPerformed(ActionEvent e)
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344 hideSequences(true);
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347 sequenceMenu.add(menuItem);
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350 if (ap.av.hasHiddenRows())
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352 final int index = ap.av.getAlignment().findIndex(seq);
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354 if (ap.av.adjustForHiddenSeqs(index)
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355 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
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357 menuItem = new JMenuItem(MessageManager.getString("action.reveal_sequences"));
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358 menuItem.addActionListener(new ActionListener()
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360 public void actionPerformed(ActionEvent e)
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362 ap.av.showSequence(index);
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363 if (ap.overviewPanel != null)
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365 ap.overviewPanel.updateOverviewImage();
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373 // for the case when no sequences are even visible
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374 if (ap.av.hasHiddenRows())
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377 menuItem = new JMenuItem(MessageManager.getString("action.reveal_all"));
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378 menuItem.addActionListener(new ActionListener()
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380 public void actionPerformed(ActionEvent e)
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382 ap.av.showAllHiddenSeqs();
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383 if (ap.overviewPanel != null)
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385 ap.overviewPanel.updateOverviewImage();
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395 SequenceGroup sg = ap.av.getSelectionGroup();
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396 boolean isDefinedGroup = (sg!=null) ? ap.av.getAlignment().getGroups().contains(sg) : false;
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398 if (sg != null && sg.getSize() > 0)
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400 groupName.setText(MessageManager.formatMessage("label.name_param", new String[]{sg.getName()}));
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401 groupName.setText(MessageManager.getString("label.edit_name_and_description_current_group"));
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403 if (sg.cs instanceof ZappoColourScheme)
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405 zappoColour.setSelected(true);
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407 else if (sg.cs instanceof TaylorColourScheme)
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409 taylorColour.setSelected(true);
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411 else if (sg.cs instanceof PIDColourScheme)
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413 PIDColour.setSelected(true);
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415 else if (sg.cs instanceof Blosum62ColourScheme)
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417 BLOSUM62Colour.setSelected(true);
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419 else if (sg.cs instanceof UserColourScheme)
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421 userDefinedColour.setSelected(true);
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423 else if (sg.cs instanceof HydrophobicColourScheme)
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425 hydrophobicityColour.setSelected(true);
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427 else if (sg.cs instanceof HelixColourScheme)
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429 helixColour.setSelected(true);
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431 else if (sg.cs instanceof StrandColourScheme)
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433 strandColour.setSelected(true);
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435 else if (sg.cs instanceof TurnColourScheme)
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437 turnColour.setSelected(true);
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439 else if (sg.cs instanceof BuriedColourScheme)
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441 buriedColour.setSelected(true);
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443 else if (sg.cs instanceof ClustalxColourScheme)
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445 clustalColour.setSelected(true);
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447 else if (sg.cs instanceof PurinePyrimidineColourScheme)
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449 purinePyrimidineColour.setSelected(true);
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452 * else if (sg.cs instanceof CovariationColourScheme) {
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453 * covariationColour.setSelected(true); }
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457 noColourmenuItem.setSelected(true);
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460 if (sg.cs != null && sg.cs.conservationApplied())
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462 conservationMenuItem.setSelected(true);
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464 displayNonconserved.setSelected(sg.getShowNonconserved());
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465 showText.setSelected(sg.getDisplayText());
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466 showColourText.setSelected(sg.getColourText());
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467 showBoxes.setSelected(sg.getDisplayBoxes());
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468 // add any groupURLs to the groupURL submenu and make it visible
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469 if (groupLinks != null && groupLinks.size() > 0)
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471 buildGroupURLMenu(sg, groupLinks);
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473 // Add a 'show all structures' for the current selection
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474 Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>();
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475 SequenceI sqass = null;
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476 for (SequenceI sq : ap.av.getSequenceSelection())
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478 Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence()
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482 for (PDBEntry pe : pes)
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484 pdbe.put(pe.getId(), pe);
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492 if (pdbe.size() > 0)
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494 final PDBEntry[] pe = pdbe.values().toArray(
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495 new PDBEntry[pdbe.size()]);
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496 final JMenuItem gpdbview;
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497 if (pdbe.size() == 1)
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499 structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_structure_for", new String[]{sqass.getDisplayId(false)})));
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503 structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_structures", new String[]{new Integer(pdbe.size()).toString()})));
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505 gpdbview.setToolTipText(MessageManager.getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));
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506 gpdbview.addActionListener(new ActionListener()
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510 public void actionPerformed(ActionEvent e)
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512 new AppJmol(ap, pe, ap.av.collateForPDB(pe));
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519 groupMenu.setVisible(false);
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520 editMenu.setVisible(false);
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523 if (!isDefinedGroup)
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525 createGroupMenuItem.setVisible(true);
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526 unGroupMenuItem.setVisible(false);
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527 jMenu1.setText(MessageManager.getString("action.edit_new_group"));
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529 createGroupMenuItem.setVisible(false);
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530 unGroupMenuItem.setVisible(true);
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531 jMenu1.setText(MessageManager.getString("action.edit_group"));
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536 sequenceMenu.setVisible(false);
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537 structureMenu.setVisible(false);
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540 if (links != null && links.size() > 0)
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543 JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
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544 Vector linkset = new Vector();
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545 for (int i = 0; i < links.size(); i++)
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547 String link = links.elementAt(i).toString();
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548 UrlLink urlLink = null;
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551 urlLink = new UrlLink(link);
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552 } catch (Exception foo)
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554 jalview.bin.Cache.log.error("Exception for URLLink '" + link
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559 if (!urlLink.isValid())
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561 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
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564 final String label = urlLink.getLabel();
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565 if (seq != null && urlLink.isDynamic())
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568 // collect matching db-refs
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569 DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
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570 seq.getDBRef(), new String[]
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571 { urlLink.getTarget() });
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572 // collect id string too
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573 String id = seq.getName();
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574 String descr = seq.getDescription();
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575 if (descr != null && descr.length() < 1)
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582 for (int r = 0; r < dbr.length; r++)
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584 if (id != null && dbr[r].getAccessionId().equals(id))
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586 // suppress duplicate link creation for the bare sequence ID
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587 // string with this link
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590 // create Bare ID link for this RUL
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591 String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
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595 for (int u = 0; u < urls.length; u += 2)
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597 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
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599 linkset.addElement(urls[u] + "|" + urls[u + 1]);
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600 addshowLink(linkMenu, label + "|" + urls[u],
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609 // create Bare ID link for this RUL
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610 String[] urls = urlLink.makeUrls(id, true);
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613 for (int u = 0; u < urls.length; u += 2)
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615 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
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617 linkset.addElement(urls[u] + "|" + urls[u + 1]);
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618 addshowLink(linkMenu, label, urls[u + 1]);
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623 // Create urls from description but only for URL links which are regex
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625 if (descr != null && urlLink.getRegexReplace() != null)
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627 // create link for this URL from description where regex matches
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628 String[] urls = urlLink.makeUrls(descr, true);
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631 for (int u = 0; u < urls.length; u += 2)
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633 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
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635 linkset.addElement(urls[u] + "|" + urls[u + 1]);
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636 addshowLink(linkMenu, label, urls[u + 1]);
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644 if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
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646 linkset.addElement(label + "|" + urlLink.getUrl_prefix());
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647 // Add a non-dynamic link
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648 addshowLink(linkMenu, label, urlLink.getUrl_prefix());
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652 if (sequence != null)
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654 sequenceMenu.add(linkMenu);
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663 private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
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666 // TODO: usability: thread off the generation of group url content so root
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667 // menu appears asap
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668 // sequence only URLs
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669 // ID/regex match URLs
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670 groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));
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671 JMenu[] linkMenus = new JMenu[]
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672 { null, new JMenu(MessageManager.getString("action.ids")), new JMenu(MessageManager.getString("action.sequences")),
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673 new JMenu(MessageManager.getString("action.ids_sequences")) }; // three types of url that might be
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675 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
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676 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
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677 Hashtable commonDbrefs = new Hashtable();
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678 for (int sq = 0; sq < seqs.length; sq++)
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681 int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
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682 .findPosition(sg.getEndRes());
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683 // just collect ids from dataset sequence
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684 // TODO: check if IDs collected from selecton group intersects with the
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685 // current selection, too
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686 SequenceI sqi = seqs[sq];
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687 while (sqi.getDatasetSequence() != null)
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689 sqi = sqi.getDatasetSequence();
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691 DBRefEntry[] dbr = sqi.getDBRef();
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692 if (dbr != null && dbr.length > 0)
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694 for (int d = 0; d < dbr.length; d++)
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696 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
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697 Object[] sarray = (Object[]) commonDbrefs.get(src);
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698 if (sarray == null)
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700 sarray = new Object[2];
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701 sarray[0] = new int[]
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703 sarray[1] = new String[seqs.length];
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705 commonDbrefs.put(src, sarray);
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708 if (((String[]) sarray[1])[sq] == null)
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710 if (!dbr[d].hasMap()
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711 || (dbr[d].getMap().locateMappedRange(start, end) != null))
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713 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
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714 ((int[]) sarray[0])[0]++;
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720 // now create group links for all distinct ID/sequence sets.
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721 boolean addMenu = false; // indicates if there are any group links to give
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723 for (int i = 0; i < groupLinks.size(); i++)
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725 String link = groupLinks.elementAt(i).toString();
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726 GroupUrlLink urlLink = null;
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729 urlLink = new GroupUrlLink(link);
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730 } catch (Exception foo)
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732 jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
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737 if (!urlLink.isValid())
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739 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
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742 final String label = urlLink.getLabel();
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743 boolean usingNames = false;
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744 // Now see which parts of the group apply for this URL
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745 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
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746 Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
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747 String[] seqstr, ids; // input to makeUrl
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750 int numinput = ((int[]) idset[0])[0];
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751 String[] allids = ((String[]) idset[1]);
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752 seqstr = new String[numinput];
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753 ids = new String[numinput];
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754 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
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756 if (allids[sq] != null)
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758 ids[idcount] = allids[sq];
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759 seqstr[idcount++] = idandseqs[1][sq];
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765 // just use the id/seq set
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766 seqstr = idandseqs[1];
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767 ids = idandseqs[0];
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770 // and try and make the groupURL!
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772 Object[] urlset = null;
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775 urlset = urlLink.makeUrlStubs(ids, seqstr,
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776 "FromJalview" + System.currentTimeMillis(), false);
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777 } catch (UrlStringTooLongException e)
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780 if (urlset != null)
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782 int type = urlLink.getGroupURLType() & 3;
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783 // System.out.println(urlLink.getGroupURLType()
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784 // +" "+((String[])urlset[3])[0]);
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785 // first two bits ofurlLink type bitfield are sequenceids and sequences
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786 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
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787 addshowLink(linkMenus[type], label
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788 + (((type & 1) == 1) ? ("("
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789 + (usingNames ? "Names" : ltarget) + ")") : ""),
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796 groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));
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797 for (int m = 0; m < linkMenus.length; m++)
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799 if (linkMenus[m] != null
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800 && linkMenus[m].getMenuComponentCount() > 0)
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802 groupLinksMenu.add(linkMenus[m]);
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806 groupMenu.add(groupLinksMenu);
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811 * add a show URL menu item to the given linkMenu
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815 * - menu label string
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819 private void addshowLink(JMenu linkMenu, String label, final String url)
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821 JMenuItem item = new JMenuItem(label);
\r
822 item.setToolTipText(MessageManager.formatMessage("label.open_url_param", new String[]{url}));
\r
823 item.addActionListener(new java.awt.event.ActionListener()
\r
825 public void actionPerformed(ActionEvent e)
\r
827 new Thread(new Runnable()
\r
839 linkMenu.add(item);
\r
843 * add a late bound groupURL item to the given linkMenu
\r
847 * - menu label string
\r
848 * @param urlgenerator
\r
849 * GroupURLLink used to generate URL
\r
851 * Object array returned from the makeUrlStubs function.
\r
853 private void addshowLink(JMenu linkMenu, String label,
\r
854 final GroupUrlLink urlgenerator, final Object[] urlstub)
\r
856 JMenuItem item = new JMenuItem(label);
\r
857 item.setToolTipText(MessageManager.formatMessage("label.open_url_seqs_param", new Object[]{urlgenerator.getUrl_prefix(),urlgenerator.getNumberInvolved(urlstub)}));
\r
858 // TODO: put in info about what is being sent.
\r
859 item.addActionListener(new java.awt.event.ActionListener()
\r
861 public void actionPerformed(ActionEvent e)
\r
863 new Thread(new Runnable()
\r
870 showLink(urlgenerator.constructFrom(urlstub));
\r
871 } catch (UrlStringTooLongException e)
\r
880 linkMenu.add(item);
\r
886 * @throws Exception
\r
889 private void jbInit() throws Exception
\r
891 groupMenu.setText(MessageManager.getString("label.group"));
\r
892 groupMenu.setText(MessageManager.getString("label.selection"));
\r
893 groupName.setText(MessageManager.getString("label.name"));
\r
894 groupName.addActionListener(new java.awt.event.ActionListener()
\r
896 public void actionPerformed(ActionEvent e)
\r
898 groupName_actionPerformed();
\r
901 sequenceMenu.setText(MessageManager.getString("label.sequence"));
\r
902 sequenceName.setText(MessageManager.getString("label.edit_name_description"));
\r
903 sequenceName.addActionListener(new java.awt.event.ActionListener()
\r
905 public void actionPerformed(ActionEvent e)
\r
907 sequenceName_actionPerformed();
\r
910 sequenceDetails.setText(MessageManager.getString("label.sequence_details") + "...");
\r
911 sequenceDetails.addActionListener(new java.awt.event.ActionListener()
\r
913 public void actionPerformed(ActionEvent e)
\r
915 sequenceDetails_actionPerformed();
\r
918 sequenceSelDetails.setText(MessageManager.getString("label.sequence_details") + "...");
\r
920 .addActionListener(new java.awt.event.ActionListener()
\r
922 public void actionPerformed(ActionEvent e)
\r
924 sequenceSelectionDetails_actionPerformed();
\r
927 PIDColour.setFocusPainted(false);
\r
928 unGroupMenuItem.setText(MessageManager.getString("action.remove_group"));
\r
929 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
931 public void actionPerformed(ActionEvent e)
\r
933 unGroupMenuItem_actionPerformed();
\r
936 createGroupMenuItem.setText(MessageManager.getString("action.create_group"));
\r
937 createGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
939 public void actionPerformed(ActionEvent e)
\r
941 createGroupMenuItem_actionPerformed();
\r
945 outline.setText(MessageManager.getString("action.border_colour"));
\r
946 outline.addActionListener(new java.awt.event.ActionListener()
\r
948 public void actionPerformed(ActionEvent e)
\r
950 outline_actionPerformed();
\r
953 nucleotideMenuItem.setText(MessageManager.getString("label.nucleotide"));
\r
954 nucleotideMenuItem.addActionListener(new ActionListener()
\r
956 public void actionPerformed(ActionEvent e)
\r
958 nucleotideMenuItem_actionPerformed();
\r
961 colourMenu.setText(MessageManager.getString("label.group_colour"));
\r
962 showBoxes.setText(MessageManager.getString("action.boxes"));
\r
963 showBoxes.setState(true);
\r
964 showBoxes.addActionListener(new ActionListener()
\r
966 public void actionPerformed(ActionEvent e)
\r
968 showBoxes_actionPerformed();
\r
971 showText.setText(MessageManager.getString("action.text"));
\r
972 showText.setState(true);
\r
973 showText.addActionListener(new ActionListener()
\r
975 public void actionPerformed(ActionEvent e)
\r
977 showText_actionPerformed();
\r
980 showColourText.setText(MessageManager.getString("label.colour_text"));
\r
981 showColourText.addActionListener(new ActionListener()
\r
983 public void actionPerformed(ActionEvent e)
\r
985 showColourText_actionPerformed();
\r
988 displayNonconserved.setText(MessageManager.getString("label.show_non_conversed"));
\r
989 displayNonconserved.setState(true);
\r
990 displayNonconserved.addActionListener(new ActionListener()
\r
992 public void actionPerformed(ActionEvent e)
\r
994 showNonconserved_actionPerformed();
\r
997 editMenu.setText(MessageManager.getString("action.edit"));
\r
998 cut.setText(MessageManager.getString("action.cut"));
\r
999 cut.addActionListener(new ActionListener()
\r
1001 public void actionPerformed(ActionEvent e)
\r
1003 cut_actionPerformed();
\r
1006 upperCase.setText(MessageManager.getString("label.to_upper_case"));
\r
1007 upperCase.addActionListener(new ActionListener()
\r
1009 public void actionPerformed(ActionEvent e)
\r
1014 copy.setText(MessageManager.getString("action.copy"));
\r
1015 copy.addActionListener(new ActionListener()
\r
1017 public void actionPerformed(ActionEvent e)
\r
1019 copy_actionPerformed();
\r
1022 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
\r
1023 lowerCase.addActionListener(new ActionListener()
\r
1025 public void actionPerformed(ActionEvent e)
\r
1030 toggle.setText(MessageManager.getString("label.toggle_case"));
\r
1031 toggle.addActionListener(new ActionListener()
\r
1033 public void actionPerformed(ActionEvent e)
\r
1038 pdbMenu.setText(MessageManager.getString("label.associate_structure_with_sequence"));
\r
1039 pdbFromFile.setText(MessageManager.getString("label.from_file"));
\r
1040 pdbFromFile.addActionListener(new ActionListener()
\r
1042 public void actionPerformed(ActionEvent e)
\r
1044 pdbFromFile_actionPerformed();
\r
1047 enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
\r
1048 enterPDB.addActionListener(new ActionListener()
\r
1050 public void actionPerformed(ActionEvent e)
\r
1052 enterPDB_actionPerformed();
\r
1055 discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));
\r
1056 discoverPDB.addActionListener(new ActionListener()
\r
1058 public void actionPerformed(ActionEvent e)
\r
1060 discoverPDB_actionPerformed();
\r
1063 outputMenu.setText(MessageManager.getString("label.out_to_textbox") + "...");
\r
1064 sequenceFeature.setText(MessageManager.getString("label.create_sequence_feature"));
\r
1065 sequenceFeature.addActionListener(new ActionListener()
\r
1067 public void actionPerformed(ActionEvent e)
\r
1069 sequenceFeature_actionPerformed();
\r
1072 textColour.setText(MessageManager.getString("label.text_colour"));
\r
1073 textColour.addActionListener(new ActionListener()
\r
1075 public void actionPerformed(ActionEvent e)
\r
1077 textColour_actionPerformed();
\r
1080 jMenu1.setText(MessageManager.getString("label.group"));
\r
1081 structureMenu.setText(MessageManager.getString("label.structure"));
\r
1082 viewStructureMenu.setText(MessageManager.getString("label.view_structure"));
\r
1083 // colStructureMenu.setText("Colour By Structure");
\r
1084 editSequence.setText(MessageManager.getString("label.edit_sequence") + "...");
\r
1085 editSequence.addActionListener(new ActionListener()
\r
1087 public void actionPerformed(ActionEvent actionEvent)
\r
1089 editSequence_actionPerformed(actionEvent);
\r
1094 * annotationMenuItem.setText("By Annotation");
\r
1095 * annotationMenuItem.addActionListener(new ActionListener() { public void
\r
1096 * actionPerformed(ActionEvent actionEvent) {
\r
1097 * annotationMenuItem_actionPerformed(actionEvent); } });
\r
1099 groupMenu.add(sequenceSelDetails);
\r
1101 add(sequenceMenu);
\r
1102 this.add(structureMenu);
\r
1103 groupMenu.add(editMenu);
\r
1104 groupMenu.add(outputMenu);
\r
1105 groupMenu.add(sequenceFeature);
\r
1106 groupMenu.add(createGroupMenuItem);
\r
1107 groupMenu.add(unGroupMenuItem);
\r
1108 groupMenu.add(jMenu1);
\r
1109 sequenceMenu.add(sequenceName);
\r
1110 sequenceMenu.add(sequenceDetails);
\r
1111 colourMenu.add(textColour);
\r
1112 colourMenu.add(noColourmenuItem);
\r
1113 colourMenu.add(clustalColour);
\r
1114 colourMenu.add(BLOSUM62Colour);
\r
1115 colourMenu.add(PIDColour);
\r
1116 colourMenu.add(zappoColour);
\r
1117 colourMenu.add(taylorColour);
\r
1118 colourMenu.add(hydrophobicityColour);
\r
1119 colourMenu.add(helixColour);
\r
1120 colourMenu.add(strandColour);
\r
1121 colourMenu.add(turnColour);
\r
1122 colourMenu.add(buriedColour);
\r
1123 colourMenu.add(nucleotideMenuItem);
\r
1124 if (ap.getAlignment().isNucleotide())
\r
1126 colourMenu.add(purinePyrimidineColour);
\r
1128 // colourMenu.add(covariationColour);
\r
1129 colourMenu.add(userDefinedColour);
\r
1131 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
\r
1133 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
\r
1134 .getUserColourSchemes().keys();
\r
1136 while (userColours.hasMoreElements())
\r
1138 JMenuItem item = new JMenuItem(userColours.nextElement().toString());
\r
1139 item.addActionListener(new ActionListener()
\r
1141 public void actionPerformed(ActionEvent evt)
\r
1143 userDefinedColour_actionPerformed(evt);
\r
1146 colourMenu.add(item);
\r
1150 colourMenu.addSeparator();
\r
1151 colourMenu.add(abovePIDColour);
\r
1152 colourMenu.add(conservationMenuItem);
\r
1153 // colourMenu.add(annotationMenuItem);
\r
1154 editMenu.add(copy);
\r
1155 editMenu.add(cut);
\r
1156 editMenu.add(editSequence);
\r
1157 editMenu.add(upperCase);
\r
1158 editMenu.add(lowerCase);
\r
1159 editMenu.add(toggle);
\r
1160 pdbMenu.add(pdbFromFile);
\r
1161 pdbMenu.add(enterPDB);
\r
1162 pdbMenu.add(discoverPDB);
\r
1163 jMenu1.add(groupName);
\r
1164 jMenu1.add(colourMenu);
\r
1165 jMenu1.add(showBoxes);
\r
1166 jMenu1.add(showText);
\r
1167 jMenu1.add(showColourText);
\r
1168 jMenu1.add(outline);
\r
1169 jMenu1.add(displayNonconserved);
\r
1170 structureMenu.add(pdbMenu);
\r
1171 structureMenu.add(viewStructureMenu);
\r
1172 // structureMenu.add(colStructureMenu);
\r
1173 noColourmenuItem.setText(MessageManager.getString("label.none"));
\r
1174 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
\r
1176 public void actionPerformed(ActionEvent e)
\r
1178 noColourmenuItem_actionPerformed();
\r
1182 clustalColour.setText(MessageManager.getString("label.clustalx_colours"));
\r
1183 clustalColour.addActionListener(new java.awt.event.ActionListener()
\r
1185 public void actionPerformed(ActionEvent e)
\r
1187 clustalColour_actionPerformed();
\r
1190 zappoColour.setText(MessageManager.getString("label.zappo"));
\r
1191 zappoColour.addActionListener(new java.awt.event.ActionListener()
\r
1193 public void actionPerformed(ActionEvent e)
\r
1195 zappoColour_actionPerformed();
\r
1198 taylorColour.setText(MessageManager.getString("label.taylor"));
\r
1199 taylorColour.addActionListener(new java.awt.event.ActionListener()
\r
1201 public void actionPerformed(ActionEvent e)
\r
1203 taylorColour_actionPerformed();
\r
1206 hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));
\r
1207 hydrophobicityColour
\r
1208 .addActionListener(new java.awt.event.ActionListener()
\r
1210 public void actionPerformed(ActionEvent e)
\r
1212 hydrophobicityColour_actionPerformed();
\r
1215 helixColour.setText(MessageManager.getString("label.helix_propensity"));
\r
1216 helixColour.addActionListener(new java.awt.event.ActionListener()
\r
1218 public void actionPerformed(ActionEvent e)
\r
1220 helixColour_actionPerformed();
\r
1223 strandColour.setText(MessageManager.getString("label.strand_propensity"));
\r
1224 strandColour.addActionListener(new java.awt.event.ActionListener()
\r
1226 public void actionPerformed(ActionEvent e)
\r
1228 strandColour_actionPerformed();
\r
1231 turnColour.setText(MessageManager.getString("label.turn_propensity"));
\r
1232 turnColour.addActionListener(new java.awt.event.ActionListener()
\r
1234 public void actionPerformed(ActionEvent e)
\r
1236 turnColour_actionPerformed();
\r
1239 buriedColour.setText(MessageManager.getString("label.buried_index"));
\r
1240 buriedColour.addActionListener(new java.awt.event.ActionListener()
\r
1242 public void actionPerformed(ActionEvent e)
\r
1244 buriedColour_actionPerformed();
\r
1247 abovePIDColour.setText(MessageManager.getString("label.above_identity_percentage"));
\r
1248 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
\r
1250 public void actionPerformed(ActionEvent e)
\r
1252 abovePIDColour_actionPerformed();
\r
1255 userDefinedColour.setText(MessageManager.getString("action.user_defined"));
\r
1256 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
\r
1258 public void actionPerformed(ActionEvent e)
\r
1260 userDefinedColour_actionPerformed(e);
\r
1263 PIDColour.setText(MessageManager.getString("label.percentage_identity"));
\r
1264 PIDColour.addActionListener(new java.awt.event.ActionListener()
\r
1266 public void actionPerformed(ActionEvent e)
\r
1268 PIDColour_actionPerformed();
\r
1271 BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
\r
1272 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
\r
1274 public void actionPerformed(ActionEvent e)
\r
1276 BLOSUM62Colour_actionPerformed();
\r
1279 purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));
\r
1280 purinePyrimidineColour
\r
1281 .addActionListener(new java.awt.event.ActionListener()
\r
1283 public void actionPerformed(ActionEvent e)
\r
1285 purinePyrimidineColour_actionPerformed();
\r
1289 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
\r
1290 * public void actionPerformed(ActionEvent e) {
\r
1291 * covariationColour_actionPerformed(); } });
\r
1294 conservationMenuItem.setText(MessageManager.getString("label.conservation"));
\r
1295 conservationMenuItem
\r
1296 .addActionListener(new java.awt.event.ActionListener()
\r
1298 public void actionPerformed(ActionEvent e)
\r
1300 conservationMenuItem_actionPerformed();
\r
1305 protected void sequenceSelectionDetails_actionPerformed()
\r
1307 createSequenceDetailsReport(ap.av.getSequenceSelection());
\r
1310 protected void sequenceDetails_actionPerformed()
\r
1312 createSequenceDetailsReport(new SequenceI[]
\r
1316 public void createSequenceDetailsReport(SequenceI[] sequences)
\r
1318 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
\r
1319 StringBuffer contents = new StringBuffer();
\r
1320 for (SequenceI seq : sequences)
\r
1322 contents.append("<p><h2>" + MessageManager.formatMessage("label.create_sequence_details_report_annotation_for", new String[]{seq.getDisplayId(true)})
\r
1323 + "</h2></p><p>");
\r
1324 new SequenceAnnotationReport(null)
\r
1325 .createSequenceAnnotationReport(
\r
1331 (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
\r
1333 contents.append("</p>");
\r
1335 cap.setText("<html>" + contents.toString() + "</html>");
\r
1337 Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage("label.sequece_details_for", (sequences.length == 1 ? new String[]{sequences[0].getDisplayId(true)}: new String[]{MessageManager.getString("label.selection")}))
\r
1342 protected void showNonconserved_actionPerformed()
\r
1344 getGroup().setShowNonconserved(displayNonconserved.isSelected());
\r
1349 * call to refresh view after settings change
\r
1353 ap.updateAnnotation();
\r
1354 ap.paintAlignment(true);
\r
1356 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
\r
1365 protected void clustalColour_actionPerformed()
\r
1367 SequenceGroup sg = getGroup();
\r
1368 sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
\r
1378 protected void zappoColour_actionPerformed()
\r
1380 getGroup().cs = new ZappoColourScheme();
\r
1390 protected void taylorColour_actionPerformed()
\r
1392 getGroup().cs = new TaylorColourScheme();
\r
1402 protected void hydrophobicityColour_actionPerformed()
\r
1404 getGroup().cs = new HydrophobicColourScheme();
\r
1414 protected void helixColour_actionPerformed()
\r
1416 getGroup().cs = new HelixColourScheme();
\r
1426 protected void strandColour_actionPerformed()
\r
1428 getGroup().cs = new StrandColourScheme();
\r
1438 protected void turnColour_actionPerformed()
\r
1440 getGroup().cs = new TurnColourScheme();
\r
1450 protected void buriedColour_actionPerformed()
\r
1452 getGroup().cs = new BuriedColourScheme();
\r
1462 public void nucleotideMenuItem_actionPerformed()
\r
1464 getGroup().cs = new NucleotideColourScheme();
\r
1468 protected void purinePyrimidineColour_actionPerformed()
\r
1470 getGroup().cs = new PurinePyrimidineColourScheme();
\r
1475 * protected void covariationColour_actionPerformed() { getGroup().cs = new
\r
1476 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
\r
1484 protected void abovePIDColour_actionPerformed()
\r
1486 SequenceGroup sg = getGroup();
\r
1487 if (sg.cs == null)
\r
1492 if (abovePIDColour.isSelected())
\r
1494 sg.cs.setConsensus(AAFrequency.calculate(
\r
1495 sg.getSequences(ap.av.getHiddenRepSequences()),
\r
1496 sg.getStartRes(), sg.getEndRes() + 1));
\r
1498 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
\r
1501 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
\r
1503 SliderPanel.showPIDSlider();
\r
1506 // remove PIDColouring
\r
1508 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
\r
1520 protected void userDefinedColour_actionPerformed(ActionEvent e)
\r
1522 SequenceGroup sg = getGroup();
\r
1524 if (e.getSource().equals(userDefinedColour))
\r
1526 new UserDefinedColours(ap, sg);
\r
1530 UserColourScheme udc = (UserColourScheme) UserDefinedColours
\r
1531 .getUserColourSchemes().get(e.getActionCommand());
\r
1544 protected void PIDColour_actionPerformed()
\r
1546 SequenceGroup sg = getGroup();
\r
1547 sg.cs = new PIDColourScheme();
\r
1548 sg.cs.setConsensus(AAFrequency.calculate(
\r
1549 sg.getSequences(ap.av.getHiddenRepSequences()),
\r
1550 sg.getStartRes(), sg.getEndRes() + 1));
\r
1560 protected void BLOSUM62Colour_actionPerformed()
\r
1562 SequenceGroup sg = getGroup();
\r
1564 sg.cs = new Blosum62ColourScheme();
\r
1566 sg.cs.setConsensus(AAFrequency.calculate(
\r
1567 sg.getSequences(ap.av.getHiddenRepSequences()),
\r
1568 sg.getStartRes(), sg.getEndRes() + 1));
\r
1579 protected void noColourmenuItem_actionPerformed()
\r
1581 getGroup().cs = null;
\r
1591 protected void conservationMenuItem_actionPerformed()
\r
1593 SequenceGroup sg = getGroup();
\r
1594 if (sg.cs == null)
\r
1599 if (conservationMenuItem.isSelected())
\r
1601 Conservation c = new Conservation(MessageManager.getString("label.group"),
\r
1602 ResidueProperties.propHash, 3, sg.getSequences(ap.av
\r
1603 .getHiddenRepSequences()), sg.getStartRes(),
\r
1604 sg.getEndRes() + 1);
\r
1607 c.verdict(false, ap.av.getConsPercGaps());
\r
1609 sg.cs.setConservation(c);
\r
1611 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
\r
1612 SliderPanel.showConservationSlider();
\r
1615 // remove ConservationColouring
\r
1617 sg.cs.setConservation(null);
\r
1623 public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
\r
1625 SequenceGroup sg = getGroup();
\r
1631 AnnotationColourGradient acg = new AnnotationColourGradient(
\r
1632 sequence.getAnnotation()[0], null,
\r
1633 AnnotationColourGradient.NO_THRESHOLD);
\r
1635 acg.setPredefinedColours(true);
\r
1647 protected void groupName_actionPerformed()
\r
1650 SequenceGroup sg = getGroup();
\r
1651 EditNameDialog dialog = new EditNameDialog(sg.getName(),
\r
1652 sg.getDescription(), " " + MessageManager.getString("label.group_name") + " ",
\r
1653 MessageManager.getString("label.group_description") + " ", MessageManager.getString("label.edit_group_name_description"),
\r
1656 if (!dialog.accept)
\r
1661 sg.setName(dialog.getName());
\r
1662 sg.setDescription(dialog.getDescription());
\r
1667 * Get selection group - adding it to the alignment if necessary.
\r
1669 * @return sequence group to operate on
\r
1671 SequenceGroup getGroup()
\r
1673 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1674 // this method won't add a new group if it already exists
\r
1677 ap.av.getAlignment().addGroup(sg);
\r
1689 void sequenceName_actionPerformed()
\r
1691 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
\r
1692 sequence.getDescription(), " " + MessageManager.getString("label.sequence_name") + " ",
\r
1693 MessageManager.getString("label.sequence_description") + " ", MessageManager.getString("label.edit_sequence_name_description"),
\r
1696 if (!dialog.accept)
\r
1701 if (dialog.getName() != null)
\r
1703 if (dialog.getName().indexOf(" ") > -1)
\r
1705 JOptionPane.showMessageDialog(ap,
\r
1706 MessageManager.getString("label.spaces_converted_to_backslashes"),
\r
1707 MessageManager.getString("label.no_spaces_allowed_sequence_name"),
\r
1708 JOptionPane.WARNING_MESSAGE);
\r
1711 sequence.setName(dialog.getName().replace(' ', '_'));
\r
1712 ap.paintAlignment(false);
\r
1715 sequence.setDescription(dialog.getDescription());
\r
1717 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
\r
1728 void unGroupMenuItem_actionPerformed()
\r
1730 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1731 ap.av.getAlignment().deleteGroup(sg);
\r
1732 ap.av.setSelectionGroup(null);
\r
1735 void createGroupMenuItem_actionPerformed()
\r
1737 getGroup(); // implicitly creates group - note - should apply defaults / use standard alignment window logic for this
\r
1747 protected void outline_actionPerformed()
\r
1749 SequenceGroup sg = getGroup();
\r
1750 Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_outline_colour"),
\r
1755 sg.setOutlineColour(col);
\r
1767 public void showBoxes_actionPerformed()
\r
1769 getGroup().setDisplayBoxes(showBoxes.isSelected());
\r
1779 public void showText_actionPerformed()
\r
1781 getGroup().setDisplayText(showText.isSelected());
\r
1791 public void showColourText_actionPerformed()
\r
1793 getGroup().setColourText(showColourText.isSelected());
\r
1797 public void showLink(String url)
\r
1801 jalview.util.BrowserLauncher.openURL(url);
\r
1802 } catch (Exception ex)
\r
1805 .showInternalMessageDialog(
\r
1807 MessageManager.getString("label.web_browser_not_found_unix"),
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1808 MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE);
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1810 ex.printStackTrace();
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1814 void hideSequences(boolean representGroup)
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1816 SequenceGroup sg = ap.av.getSelectionGroup();
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1817 if (sg == null || sg.getSize() < 1)
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1819 ap.av.hideSequence(new SequenceI[]
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1824 ap.av.setSelectionGroup(null);
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1826 if (representGroup)
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1828 ap.av.hideRepSequences(sequence, sg);
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1833 int gsize = sg.getSize();
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1834 SequenceI[] hseqs;
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1836 hseqs = new SequenceI[gsize];
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1839 for (int i = 0; i < gsize; i++)
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1841 hseqs[index++] = sg.getSequenceAt(i);
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1844 ap.av.hideSequence(hseqs);
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1845 // refresh(); TODO: ? needed ?
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1846 ap.av.sendSelection();
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1849 public void copy_actionPerformed()
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1851 ap.alignFrame.copy_actionPerformed(null);
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1854 public void cut_actionPerformed()
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1856 ap.alignFrame.cut_actionPerformed(null);
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1859 void changeCase(ActionEvent e)
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1861 Object source = e.getSource();
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1862 SequenceGroup sg = ap.av.getSelectionGroup();
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1866 int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
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1867 sg.getEndRes() + 1);
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1869 String description;
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1872 if (source == toggle)
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1874 description = MessageManager.getString("label.toggle_case");
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1875 caseChange = ChangeCaseCommand.TOGGLE_CASE;
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1877 else if (source == upperCase)
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1879 description = MessageManager.getString("label.to_upper_case");
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1880 caseChange = ChangeCaseCommand.TO_UPPER;
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1884 description = MessageManager.getString("label.to_lower_case");
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1885 caseChange = ChangeCaseCommand.TO_LOWER;
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1888 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
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1889 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
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1890 startEnd, caseChange);
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1892 ap.alignFrame.addHistoryItem(caseCommand);
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1894 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
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1900 public void outputText_actionPerformed(ActionEvent e)
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1902 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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1903 cap.setForInput(null);
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1904 Desktop.addInternalFrame(cap,
\r
1905 MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500);
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1907 String[] omitHidden = null;
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1909 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
\r
1910 // or we simply trust the user wants
\r
1911 // wysiwig behaviour
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1912 SequenceGroup sg = ap.av.getSelectionGroup();
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1913 ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
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1914 omitHidden = ap.av.getViewAsString(true);
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1915 Alignment oal = new Alignment(ap.av.getSequenceSelection());
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1916 AlignmentAnnotation[] nala = ap.av.getAlignment()
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1917 .getAlignmentAnnotation();
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1920 for (int i = 0; i < nala.length; i++)
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1922 AlignmentAnnotation na = nala[i];
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1923 oal.addAnnotation(na);
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1926 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
\r
1927 oal, omitHidden, csel, sg));
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1931 public void pdbFromFile_actionPerformed()
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1933 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
\r
1934 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
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1935 chooser.setFileView(new jalview.io.JalviewFileView());
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1936 chooser.setDialogTitle(MessageManager.formatMessage("label.select_pdb_file_for", new String[]{sequence.getDisplayId(false)}));
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1937 chooser.setToolTipText(MessageManager.formatMessage("label.load_pdb_file_associate_with_sequence", new String[]{new Integer(sequence.getDisplayId(false)).toString()}));
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1939 int value = chooser.showOpenDialog(null);
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1941 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
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1943 String choice = chooser.getSelectedFile().getPath();
\r
1944 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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1945 new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
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1946 jalview.io.AppletFormatAdapter.FILE, sequence, true);
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1951 public void enterPDB_actionPerformed()
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1953 String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
\r
1954 MessageManager.getString("label.enter_pdb_id"), MessageManager.getString("label.enter_pdb_id"), JOptionPane.QUESTION_MESSAGE);
\r
1956 if (id != null && id.length() > 0)
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1958 PDBEntry entry = new PDBEntry();
\r
1959 entry.setId(id.toUpperCase());
\r
1960 sequence.getDatasetSequence().addPDBId(entry);
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1964 public void discoverPDB_actionPerformed()
\r
1967 final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
\r
1969 : ap.av.getSequenceSelection());
\r
1970 Thread discpdb = new Thread(new Runnable()
\r
1975 new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
\r
1976 .fetchDBRefs(false);
\r
1983 public void sequenceFeature_actionPerformed()
\r
1985 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1991 int rsize = 0, gSize = sg.getSize();
\r
1992 SequenceI[] rseqs, seqs = new SequenceI[gSize];
\r
1993 SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
\r
1995 for (int i = 0; i < gSize; i++)
\r
1997 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
\r
1998 int end = sg.findEndRes(sg.getSequenceAt(i));
\r
2001 seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
\r
2002 features[rsize] = new SequenceFeature(null, null, null, start, end,
\r
2007 rseqs = new SequenceI[rsize];
\r
2008 tfeatures = new SequenceFeature[rsize];
\r
2009 System.arraycopy(seqs, 0, rseqs, 0, rsize);
\r
2010 System.arraycopy(features, 0, tfeatures, 0, rsize);
\r
2011 features = tfeatures;
\r
2013 if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
\r
2014 features, true, ap))
\r
2016 ap.alignFrame.setShowSeqFeatures(true);
\r
2017 ap.highlightSearchResults(null);
\r
2021 public void textColour_actionPerformed()
\r
2023 SequenceGroup sg = getGroup();
\r
2026 new TextColourChooser().chooseColour(ap, sg);
\r
2030 public void colourByStructure(String pdbid)
\r
2032 Annotation[] anots = ap.av.getStructureSelectionManager()
\r
2033 .colourSequenceFromStructure(sequence, pdbid);
\r
2035 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
\r
2036 "Coloured by " + pdbid, anots);
\r
2038 ap.av.getAlignment().addAnnotation(an);
\r
2039 an.createSequenceMapping(sequence, 0, true);
\r
2040 // an.adjustForAlignment();
\r
2041 ap.av.getAlignment().setAnnotationIndex(an, 0);
\r
2043 ap.adjustAnnotationHeight();
\r
2045 sequence.addAlignmentAnnotation(an);
\r
2049 public void editSequence_actionPerformed(ActionEvent actionEvent)
\r
2051 SequenceGroup sg = ap.av.getSelectionGroup();
\r
2055 if (sequence == null)
\r
2056 sequence = (Sequence) sg.getSequenceAt(0);
\r
2058 EditNameDialog dialog = new EditNameDialog(
\r
2059 sequence.getSequenceAsString(sg.getStartRes(),
\r
2060 sg.getEndRes() + 1), null, MessageManager.getString("label.edit_sequence"), null,
\r
2061 MessageManager.getString("label.edit_sequence"), ap.alignFrame);
\r
2063 if (dialog.accept)
\r
2065 EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"),
\r
2066 EditCommand.REPLACE, dialog.getName().replace(' ',
\r
2067 ap.av.getGapCharacter()),
\r
2068 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
\r
2069 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
\r
2071 ap.alignFrame.addHistoryItem(editCommand);
\r
2073 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
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