src/jalview/gui/PopupMenu.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 package jalview.gui;\r
  20 \r
  21 import MCview.*;\r
  22 \r
  23 import jalview.analysis.*;\r
  24 \r
  25 import jalview.datamodel.*;\r
  26 \r
  27 \r
  28 import jalview.schemes.*;\r
  29 \r
  30 import java.awt.*;\r
  31 import java.awt.event.*;\r
  32 \r
  33 import javax.swing.*;\r
  34 \r
  35 import java.util.Vector;\r
  36 import jalview.io.FormatAdapter;\r
  37 \r
  38 \r
  39 /**\r
  40  * DOCUMENT ME!\r
  41  *\r
  42  * @author $author$\r
  43  * @version $Revision$\r
  44  */\r
  45 public class PopupMenu extends JPopupMenu\r
  46 {\r
  47     JMenu groupMenu = new JMenu();\r
  48     JMenuItem groupName = new JMenuItem();\r
  49     protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  50     protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  51     protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  52     protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
  53     protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  54     protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  55     protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  56     protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  57     protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();\r
  58     protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  59     protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  60     protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  61     JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  62     protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  63     AlignmentPanel ap;\r
  64     JMenu sequenceMenu = new JMenu();\r
  65     JMenuItem sequenceName = new JMenuItem();\r
  66     Sequence sequence;\r
  67     JMenuItem unGroupMenuItem = new JMenuItem();\r
  68     JMenuItem outline = new JMenuItem();\r
  69     JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();\r
  70     JMenu colourMenu = new JMenu();\r
  71     JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();\r
  72     JCheckBoxMenuItem showText = new JCheckBoxMenuItem();\r
  73     JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();\r
  74   JMenu editMenu = new JMenu();\r
  75   JMenuItem cut = new JMenuItem();\r
  76   JMenuItem copy = new JMenuItem();\r
  77   JMenuItem upperCase = new JMenuItem();\r
  78   JMenuItem lowerCase = new JMenuItem();\r
  79   JMenuItem toggle = new JMenuItem();\r
  80   JMenu pdbMenu = new JMenu();\r
  81   JMenuItem pdbFromFile = new JMenuItem();\r
  82   JMenuItem enterPDB = new JMenuItem();\r
  83   JMenuItem discoverPDB = new JMenuItem();\r
  84   JMenuItem jMenuItem1 = new JMenuItem();\r
  85 \r
  86   /**\r
  87      * Creates a new PopupMenu object.\r
  88      *\r
  89      * @param ap DOCUMENT ME!\r
  90      * @param seq DOCUMENT ME!\r
  91      */\r
  92     public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)\r
  93     {\r
  94         ///////////////////////////////////////////////////////////\r
  95         // If this is activated from the sequence panel, the user may want to\r
  96         // edit or annotate a particular residue. Therefore display the residue menu\r
  97         //\r
  98         // If from the IDPanel, we must display the sequence menu\r
  99         //////////////////////////////////////////////////////////\r
 100         this.ap = ap;\r
 101         sequence = seq;\r
 102 \r
 103         ButtonGroup colours = new ButtonGroup();\r
 104         colours.add(noColourmenuItem);\r
 105         colours.add(clustalColour);\r
 106         colours.add(zappoColour);\r
 107         colours.add(taylorColour);\r
 108         colours.add(hydrophobicityColour);\r
 109         colours.add(helixColour);\r
 110         colours.add(strandColour);\r
 111         colours.add(turnColour);\r
 112         colours.add(buriedColour);\r
 113         colours.add(abovePIDColour);\r
 114         colours.add(userDefinedColour);\r
 115         colours.add(PIDColour);\r
 116         colours.add(BLOSUM62Colour);\r
 117 \r
 118         for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)\r
 119         {\r
 120           JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
 121                                          elementAt(\r
 122                                              i));\r
 123           item.addActionListener(new java.awt.event.ActionListener()\r
 124           {\r
 125             public void actionPerformed(ActionEvent e)\r
 126             {\r
 127               outputText_actionPerformed(e);\r
 128             }\r
 129           });\r
 130 \r
 131     }\r
 132 \r
 133 \r
 134         try\r
 135         {\r
 136             jbInit();\r
 137         }\r
 138         catch (Exception e)\r
 139         {\r
 140             e.printStackTrace();\r
 141         }\r
 142 \r
 143 \r
 144         if (seq != null)\r
 145         {\r
 146           int start = Math.max(sequence.getName().length()-15, 0);\r
 147           sequenceMenu.setText(sequence.getName().substring(start));\r
 148 \r
 149           JMenuItem menuItem;\r
 150           if( seq.getDatasetSequence().getPDBId() != null)\r
 151           {\r
 152             java.util.Enumeration e = seq.getDatasetSequence().getPDBId().\r
 153                 elements();\r
 154 \r
 155             while (e.hasMoreElements())\r
 156             {\r
 157               final PDBEntry pdb = (PDBEntry) e.nextElement();\r
 158 \r
 159               menuItem = new JMenuItem();\r
 160               menuItem.setText("View PDB entry: " + pdb.getId());\r
 161               menuItem.addActionListener(new java.awt.event.ActionListener()\r
 162               {\r
 163                 public void actionPerformed(ActionEvent e)\r
 164                 {\r
 165                   new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);\r
 166                 }\r
 167               });\r
 168               sequenceMenu.add(menuItem);\r
 169             }\r
 170           }\r
 171 \r
 172           menuItem = new JMenuItem("Hide Sequences");\r
 173           menuItem.addActionListener(new java.awt.event.ActionListener()\r
 174               {\r
 175                 public void actionPerformed(ActionEvent e)\r
 176                 {\r
 177                   hideSequences(false);\r
 178                 }\r
 179               });\r
 180           add(menuItem);\r
 181 \r
 182           if(ap.av.getSelectionGroup() !=null\r
 183              && ap.av.getSelectionGroup().getSize(false)>1)\r
 184           {\r
 185             menuItem = new JMenuItem("Represent Group with " + seq.getName());\r
 186             menuItem.addActionListener(new java.awt.event.ActionListener()\r
 187             {\r
 188               public void actionPerformed(ActionEvent e)\r
 189               {\r
 190                 hideSequences(true);\r
 191               }\r
 192             });\r
 193             sequenceMenu.add(menuItem);\r
 194           }\r
 195 \r
 196           if (ap.av.hasHiddenRows)\r
 197           {\r
 198             final int index = ap.av.alignment.findIndex(seq);\r
 199 \r
 200             if (ap.av.adjustForHiddenSeqs(index) -\r
 201                 ap.av.adjustForHiddenSeqs(index - 1) > 1)\r
 202             {\r
 203               menuItem = new JMenuItem("Reveal Sequences");\r
 204               menuItem.addActionListener(new ActionListener()\r
 205               {\r
 206                 public void actionPerformed(ActionEvent e)\r
 207                 {\r
 208                   ap.av.showSequence(index);\r
 209                   ap.repaint();\r
 210                   if (ap.overviewPanel != null)\r
 211                     ap.overviewPanel.updateOverviewImage();\r
 212                 }\r
 213               });\r
 214               add(menuItem);\r
 215             }\r
 216 \r
 217             menuItem = new JMenuItem("Reveal All");\r
 218             menuItem.addActionListener(new ActionListener()\r
 219                 {\r
 220                   public void actionPerformed(ActionEvent e)\r
 221                   {\r
 222                     ap.av.showAllHiddenSeqs();\r
 223                     ap.repaint();\r
 224                     if (ap.overviewPanel != null)\r
 225                       ap.overviewPanel.updateOverviewImage();\r
 226                       }\r
 227                 });\r
 228 \r
 229             add(menuItem);\r
 230           }\r
 231 \r
 232 \r
 233         }\r
 234 \r
 235 \r
 236 \r
 237         SequenceGroup sg = ap.av.getSelectionGroup();\r
 238 \r
 239         if (sg != null)\r
 240         {\r
 241             groupName.setText(sg.getName());\r
 242 \r
 243             if (sg.cs instanceof ZappoColourScheme)\r
 244             {\r
 245                 zappoColour.setSelected(true);\r
 246             }\r
 247             else if (sg.cs instanceof TaylorColourScheme)\r
 248             {\r
 249                 taylorColour.setSelected(true);\r
 250             }\r
 251             else if (sg.cs instanceof PIDColourScheme)\r
 252             {\r
 253                 PIDColour.setSelected(true);\r
 254             }\r
 255             else if (sg.cs instanceof Blosum62ColourScheme)\r
 256             {\r
 257                 BLOSUM62Colour.setSelected(true);\r
 258             }\r
 259             else if (sg.cs instanceof UserColourScheme)\r
 260             {\r
 261                 userDefinedColour.setSelected(true);\r
 262             }\r
 263             else if (sg.cs instanceof HydrophobicColourScheme)\r
 264             {\r
 265                 hydrophobicityColour.setSelected(true);\r
 266             }\r
 267             else if (sg.cs instanceof HelixColourScheme)\r
 268             {\r
 269                 helixColour.setSelected(true);\r
 270             }\r
 271             else if (sg.cs instanceof StrandColourScheme)\r
 272             {\r
 273                 strandColour.setSelected(true);\r
 274             }\r
 275             else if (sg.cs instanceof TurnColourScheme)\r
 276             {\r
 277                 turnColour.setSelected(true);\r
 278             }\r
 279             else if (sg.cs instanceof BuriedColourScheme)\r
 280             {\r
 281                 buriedColour.setSelected(true);\r
 282             }\r
 283             else if (sg.cs instanceof ClustalxColourScheme)\r
 284             {\r
 285                 clustalColour.setSelected(true);\r
 286             }\r
 287             else\r
 288             {\r
 289                 noColourmenuItem.setSelected(true);\r
 290             }\r
 291 \r
 292             if (sg.cs!=null && sg.cs.conservationApplied())\r
 293             {\r
 294                 conservationMenuItem.setSelected(true);\r
 295             }\r
 296 \r
 297             showText.setSelected(sg.getDisplayText());\r
 298             showColourText.setSelected(sg.getColourText());\r
 299             showBoxes.setSelected(sg.getDisplayBoxes());\r
 300         }\r
 301         else\r
 302         {\r
 303           groupMenu.setVisible(false);\r
 304           editMenu.setVisible(false);\r
 305         }\r
 306 \r
 307         if (!ap.av.alignment.getGroups().contains(sg))\r
 308         {\r
 309             unGroupMenuItem.setVisible(false);\r
 310         }\r
 311 \r
 312 \r
 313         if (seq == null)\r
 314         {\r
 315             sequenceMenu.setVisible(false);\r
 316             pdbMenu.setVisible(false);\r
 317         }\r
 318 \r
 319         if(links != null && links.size()>0)\r
 320         {\r
 321           JMenu linkMenu = new JMenu("Link");\r
 322           JMenuItem item;\r
 323           for(int i=0; i<links.size(); i++)\r
 324           {\r
 325             String link = links.elementAt(i).toString();\r
 326             final String label = link.substring(0, link.indexOf("|"));\r
 327             item = new JMenuItem(label);\r
 328             final String url;\r
 329 \r
 330             if (link.indexOf("$SEQUENCE_ID$") > -1)\r
 331             {\r
 332               String id = seq.getName();\r
 333               if (id.indexOf("|") > -1)\r
 334                 id = id.substring(id.lastIndexOf("|") + 1);\r
 335 \r
 336               url = link.substring(link.indexOf("|") + 1,\r
 337                                    link.indexOf("$SEQUENCE_ID$"))\r
 338                   + id +\r
 339                   link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
 340             }\r
 341             else\r
 342               url = link.substring(link.lastIndexOf("|")+1);\r
 343 \r
 344 \r
 345             item.addActionListener(new java.awt.event.ActionListener()\r
 346             {\r
 347                 public void actionPerformed(ActionEvent e)\r
 348                 {\r
 349                     showLink(url);\r
 350                 }\r
 351             });\r
 352 \r
 353             linkMenu.add(item);\r
 354           }\r
 355           sequenceMenu.add(linkMenu);\r
 356         }\r
 357     }\r
 358 \r
 359 \r
 360     /**\r
 361      * DOCUMENT ME!\r
 362      *\r
 363      * @throws Exception DOCUMENT ME!\r
 364      */\r
 365     private void jbInit() throws Exception\r
 366     {\r
 367         groupMenu.setText("Group");\r
 368         groupMenu.setText("Selection");\r
 369         groupName.setText("Name");\r
 370         groupName.addActionListener(new java.awt.event.ActionListener()\r
 371             {\r
 372                 public void actionPerformed(ActionEvent e)\r
 373                 {\r
 374                     groupName_actionPerformed(e);\r
 375                 }\r
 376             });\r
 377         sequenceMenu.setText("Sequence");\r
 378         sequenceName.setText("Edit Name/Description");\r
 379         sequenceName.addActionListener(new java.awt.event.ActionListener()\r
 380             {\r
 381                 public void actionPerformed(ActionEvent e)\r
 382                 {\r
 383                     sequenceName_actionPerformed(e);\r
 384                 }\r
 385             });\r
 386         PIDColour.setFocusPainted(false);\r
 387         unGroupMenuItem.setText("Remove Group");\r
 388         unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 389             {\r
 390                 public void actionPerformed(ActionEvent e)\r
 391                 {\r
 392                     unGroupMenuItem_actionPerformed(e);\r
 393                 }\r
 394             });\r
 395 \r
 396         outline.setText("Border colour");\r
 397         outline.addActionListener(new java.awt.event.ActionListener()\r
 398             {\r
 399                 public void actionPerformed(ActionEvent e)\r
 400                 {\r
 401                     outline_actionPerformed(e);\r
 402                 }\r
 403             });\r
 404         nucleotideMenuItem.setText("Nucleotide");\r
 405         nucleotideMenuItem.addActionListener(new ActionListener()\r
 406             {\r
 407                 public void actionPerformed(ActionEvent e)\r
 408                 {\r
 409                     nucleotideMenuItem_actionPerformed(e);\r
 410                 }\r
 411             });\r
 412         colourMenu.setText("Group Colour");\r
 413         showBoxes.setText("Boxes");\r
 414         showBoxes.setState(true);\r
 415         showBoxes.addActionListener(new ActionListener()\r
 416             {\r
 417                 public void actionPerformed(ActionEvent e)\r
 418                 {\r
 419                     showBoxes_actionPerformed(e);\r
 420                 }\r
 421             });\r
 422         showText.setText("Text");\r
 423         showText.setState(true);\r
 424         showText.addActionListener(new ActionListener()\r
 425             {\r
 426                 public void actionPerformed(ActionEvent e)\r
 427                 {\r
 428                     showText_actionPerformed(e);\r
 429                 }\r
 430             });\r
 431         showColourText.setText("Colour Text");\r
 432         showColourText.addActionListener(new ActionListener()\r
 433             {\r
 434                 public void actionPerformed(ActionEvent e)\r
 435                 {\r
 436                     showColourText_actionPerformed(e);\r
 437                 }\r
 438             });\r
 439     editMenu.setText("Edit");\r
 440     cut.setText("Cut");\r
 441     cut.addActionListener(new ActionListener()\r
 442     {\r
 443       public void actionPerformed(ActionEvent e)\r
 444       {\r
 445         cut_actionPerformed(e);\r
 446       }\r
 447     });\r
 448     upperCase.setText("To Upper Case");\r
 449     upperCase.addActionListener(new ActionListener()\r
 450     {\r
 451       public void actionPerformed(ActionEvent e)\r
 452       {\r
 453         upperCase_actionPerformed(e);\r
 454       }\r
 455     });\r
 456     copy.setText("Copy");\r
 457     copy.addActionListener(new ActionListener()\r
 458     {\r
 459       public void actionPerformed(ActionEvent e)\r
 460       {\r
 461         copy_actionPerformed(e);\r
 462       }\r
 463     });\r
 464     lowerCase.setText("To Lower Case");\r
 465     lowerCase.addActionListener(new ActionListener()\r
 466     {\r
 467       public void actionPerformed(ActionEvent e)\r
 468       {\r
 469         lowerCase_actionPerformed(e);\r
 470       }\r
 471     });\r
 472     toggle.setText("Toggle Case");\r
 473     toggle.addActionListener(new ActionListener()\r
 474     {\r
 475       public void actionPerformed(ActionEvent e)\r
 476       {\r
 477         toggle_actionPerformed(e);\r
 478       }\r
 479     });\r
 480     pdbMenu.setText("Associate Structure with Sequence");\r
 481     pdbFromFile.setText("From File");\r
 482     pdbFromFile.addActionListener(new ActionListener()\r
 483     {\r
 484       public void actionPerformed(ActionEvent e)\r
 485       {\r
 486         pdbFromFile_actionPerformed(e);\r
 487       }\r
 488     });\r
 489     enterPDB.setText("Enter PDB Id");\r
 490     enterPDB.addActionListener(new ActionListener()\r
 491     {\r
 492       public void actionPerformed(ActionEvent e)\r
 493       {\r
 494         enterPDB_actionPerformed(e);\r
 495       }\r
 496     });\r
 497     discoverPDB.setText("Discover PDB ids");\r
 498     discoverPDB.addActionListener(new ActionListener()\r
 499     {\r
 500       public void actionPerformed(ActionEvent e)\r
 501       {\r
 502         discoverPDB_actionPerformed(e);\r
 503       }\r
 504     });\r
 505     jMenuItem1.setText("Output to Textbox...");\r
 506     add(groupMenu);\r
 507 \r
 508     add(sequenceMenu);\r
 509     groupMenu.add(editMenu);\r
 510     groupMenu.add(jMenuItem1);\r
 511     groupMenu.addSeparator();\r
 512     groupMenu.add(groupName);\r
 513     groupMenu.add(unGroupMenuItem);\r
 514         groupMenu.add(colourMenu);\r
 515     groupMenu.add(showBoxes);\r
 516         groupMenu.add(showText);\r
 517         groupMenu.add(showColourText);\r
 518     groupMenu.add(outline);\r
 519         sequenceMenu.add(sequenceName);\r
 520     sequenceMenu.add(pdbMenu);\r
 521     colourMenu.add(noColourmenuItem);\r
 522         colourMenu.add(clustalColour);\r
 523         colourMenu.add(BLOSUM62Colour);\r
 524         colourMenu.add(PIDColour);\r
 525         colourMenu.add(zappoColour);\r
 526         colourMenu.add(taylorColour);\r
 527         colourMenu.add(hydrophobicityColour);\r
 528         colourMenu.add(helixColour);\r
 529         colourMenu.add(strandColour);\r
 530         colourMenu.add(turnColour);\r
 531         colourMenu.add(buriedColour);\r
 532         colourMenu.add(nucleotideMenuItem);\r
 533         colourMenu.add(userDefinedColour);\r
 534 \r
 535         if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
 536         {\r
 537           java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 538               getUserColourSchemes().keys();\r
 539 \r
 540           while (userColours.hasMoreElements())\r
 541           {\r
 542             JMenuItem item = new JMenuItem(userColours.\r
 543                 nextElement().toString());\r
 544             item.addActionListener(new ActionListener()\r
 545             {\r
 546               public void actionPerformed(ActionEvent evt)\r
 547               {\r
 548                 userDefinedColour_actionPerformed(evt);\r
 549               }\r
 550             });\r
 551             colourMenu.add(item);\r
 552           }\r
 553         }\r
 554 \r
 555 \r
 556         colourMenu.addSeparator();\r
 557         colourMenu.add(abovePIDColour);\r
 558         colourMenu.add(conservationMenuItem);\r
 559     editMenu.add(copy);\r
 560     editMenu.add(cut);\r
 561     editMenu.add(upperCase);\r
 562     editMenu.add(lowerCase);\r
 563     editMenu.add(toggle);\r
 564     pdbMenu.add(pdbFromFile);\r
 565     pdbMenu.add(enterPDB);\r
 566     pdbMenu.add(discoverPDB);\r
 567     noColourmenuItem.setText("None");\r
 568         noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 569             {\r
 570                 public void actionPerformed(ActionEvent e)\r
 571                 {\r
 572                     noColourmenuItem_actionPerformed(e);\r
 573                 }\r
 574             });\r
 575 \r
 576         clustalColour.setText("Clustalx colours");\r
 577         clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 578             {\r
 579                 public void actionPerformed(ActionEvent e)\r
 580                 {\r
 581                     clustalColour_actionPerformed(e);\r
 582                 }\r
 583             });\r
 584         zappoColour.setText("Zappo");\r
 585         zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 586             {\r
 587                 public void actionPerformed(ActionEvent e)\r
 588                 {\r
 589                     zappoColour_actionPerformed(e);\r
 590                 }\r
 591             });\r
 592         taylorColour.setText("Taylor");\r
 593         taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 594             {\r
 595                 public void actionPerformed(ActionEvent e)\r
 596                 {\r
 597                     taylorColour_actionPerformed(e);\r
 598                 }\r
 599             });\r
 600         hydrophobicityColour.setText("Hydrophobicity");\r
 601         hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 602             {\r
 603                 public void actionPerformed(ActionEvent e)\r
 604                 {\r
 605                     hydrophobicityColour_actionPerformed(e);\r
 606                 }\r
 607             });\r
 608         helixColour.setText("Helix propensity");\r
 609         helixColour.addActionListener(new java.awt.event.ActionListener()\r
 610             {\r
 611                 public void actionPerformed(ActionEvent e)\r
 612                 {\r
 613                     helixColour_actionPerformed(e);\r
 614                 }\r
 615             });\r
 616         strandColour.setText("Strand propensity");\r
 617         strandColour.addActionListener(new java.awt.event.ActionListener()\r
 618             {\r
 619                 public void actionPerformed(ActionEvent e)\r
 620                 {\r
 621                     strandColour_actionPerformed(e);\r
 622                 }\r
 623             });\r
 624         turnColour.setText("Turn propensity");\r
 625         turnColour.addActionListener(new java.awt.event.ActionListener()\r
 626             {\r
 627                 public void actionPerformed(ActionEvent e)\r
 628                 {\r
 629                     turnColour_actionPerformed(e);\r
 630                 }\r
 631             });\r
 632         buriedColour.setText("Buried Index");\r
 633         buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 634             {\r
 635                 public void actionPerformed(ActionEvent e)\r
 636                 {\r
 637                     buriedColour_actionPerformed(e);\r
 638                 }\r
 639             });\r
 640         abovePIDColour.setText("Above % Identity");\r
 641         abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
 642             {\r
 643                 public void actionPerformed(ActionEvent e)\r
 644                 {\r
 645                     abovePIDColour_actionPerformed(e);\r
 646                 }\r
 647             });\r
 648         userDefinedColour.setText("User Defined...");\r
 649         userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 650             {\r
 651                 public void actionPerformed(ActionEvent e)\r
 652                 {\r
 653                     userDefinedColour_actionPerformed(e);\r
 654                 }\r
 655             });\r
 656         PIDColour.setText("Percentage Identity");\r
 657         PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 658             {\r
 659                 public void actionPerformed(ActionEvent e)\r
 660                 {\r
 661                     PIDColour_actionPerformed(e);\r
 662                 }\r
 663             });\r
 664         BLOSUM62Colour.setText("BLOSUM62");\r
 665         BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 666             {\r
 667                 public void actionPerformed(ActionEvent e)\r
 668                 {\r
 669                     BLOSUM62Colour_actionPerformed(e);\r
 670                 }\r
 671             });\r
 672         conservationMenuItem.setText("Conservation");\r
 673         conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 674             {\r
 675                 public void actionPerformed(ActionEvent e)\r
 676                 {\r
 677                     conservationMenuItem_actionPerformed(e);\r
 678                 }\r
 679             });\r
 680     }\r
 681 \r
 682     /**\r
 683      * DOCUMENT ME!\r
 684      */\r
 685     void refresh()\r
 686     {\r
 687         if (ap.overviewPanel != null)\r
 688           ap.overviewPanel.updateOverviewImage();\r
 689 \r
 690         ap.seqPanel.repaint();\r
 691     }\r
 692 \r
 693     /**\r
 694      * DOCUMENT ME!\r
 695      *\r
 696      * @param e DOCUMENT ME!\r
 697      */\r
 698     protected void clustalColour_actionPerformed(ActionEvent e)\r
 699     {\r
 700         SequenceGroup sg = getGroup();\r
 701         sg.cs = new ClustalxColourScheme(sg.getSequences(true),\r
 702                 ap.av.alignment.getWidth());\r
 703         refresh();\r
 704     }\r
 705 \r
 706     /**\r
 707      * DOCUMENT ME!\r
 708      *\r
 709      * @param e DOCUMENT ME!\r
 710      */\r
 711     protected void zappoColour_actionPerformed(ActionEvent e)\r
 712     {\r
 713         getGroup().cs = new ZappoColourScheme();\r
 714         refresh();\r
 715     }\r
 716 \r
 717     /**\r
 718      * DOCUMENT ME!\r
 719      *\r
 720      * @param e DOCUMENT ME!\r
 721      */\r
 722     protected void taylorColour_actionPerformed(ActionEvent e)\r
 723     {\r
 724         getGroup().cs = new TaylorColourScheme();\r
 725         refresh();\r
 726     }\r
 727 \r
 728     /**\r
 729      * DOCUMENT ME!\r
 730      *\r
 731      * @param e DOCUMENT ME!\r
 732      */\r
 733     protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 734     {\r
 735         getGroup().cs = new HydrophobicColourScheme();\r
 736         refresh();\r
 737     }\r
 738 \r
 739     /**\r
 740      * DOCUMENT ME!\r
 741      *\r
 742      * @param e DOCUMENT ME!\r
 743      */\r
 744     protected void helixColour_actionPerformed(ActionEvent e)\r
 745     {\r
 746         getGroup().cs = new HelixColourScheme();\r
 747         refresh();\r
 748     }\r
 749 \r
 750     /**\r
 751      * DOCUMENT ME!\r
 752      *\r
 753      * @param e DOCUMENT ME!\r
 754      */\r
 755     protected void strandColour_actionPerformed(ActionEvent e)\r
 756     {\r
 757         getGroup().cs = new StrandColourScheme();\r
 758         refresh();\r
 759     }\r
 760 \r
 761     /**\r
 762      * DOCUMENT ME!\r
 763      *\r
 764      * @param e DOCUMENT ME!\r
 765      */\r
 766     protected void turnColour_actionPerformed(ActionEvent e)\r
 767     {\r
 768         getGroup().cs = new TurnColourScheme();\r
 769         refresh();\r
 770     }\r
 771 \r
 772     /**\r
 773      * DOCUMENT ME!\r
 774      *\r
 775      * @param e DOCUMENT ME!\r
 776      */\r
 777     protected void buriedColour_actionPerformed(ActionEvent e)\r
 778     {\r
 779         getGroup().cs = new BuriedColourScheme();\r
 780         refresh();\r
 781     }\r
 782 \r
 783     /**\r
 784      * DOCUMENT ME!\r
 785      *\r
 786      * @param e DOCUMENT ME!\r
 787      */\r
 788     public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
 789     {\r
 790         getGroup().cs = new NucleotideColourScheme();\r
 791         refresh();\r
 792     }\r
 793 \r
 794     /**\r
 795      * DOCUMENT ME!\r
 796      *\r
 797      * @param e DOCUMENT ME!\r
 798      */\r
 799     protected void abovePIDColour_actionPerformed(ActionEvent e)\r
 800     {\r
 801         SequenceGroup sg = getGroup();\r
 802         if(sg.cs==null)\r
 803           return;\r
 804 \r
 805         if (abovePIDColour.isSelected())\r
 806         {\r
 807             sg.cs.setConsensus(AAFrequency.calculate(\r
 808                     sg.getSequences(true), 0,\r
 809                     ap.av.alignment.getWidth()));\r
 810 \r
 811             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
 812                     getGroup().getName());\r
 813 \r
 814            sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
 815 \r
 816             SliderPanel.showPIDSlider();\r
 817         }\r
 818         else // remove PIDColouring\r
 819         {\r
 820             sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
 821         }\r
 822 \r
 823         refresh();\r
 824     }\r
 825 \r
 826     /**\r
 827      * DOCUMENT ME!\r
 828      *\r
 829      * @param e DOCUMENT ME!\r
 830      */\r
 831     protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 832     {\r
 833        SequenceGroup sg = getGroup();\r
 834 \r
 835        if (e.getActionCommand().equals("User Defined..."))\r
 836          new UserDefinedColours(ap, sg);\r
 837        else\r
 838        {\r
 839          UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
 840              getUserColourSchemes().get(e.getActionCommand());\r
 841 \r
 842          sg.cs = udc;\r
 843        }\r
 844      }\r
 845     /**\r
 846      * DOCUMENT ME!\r
 847      *\r
 848      * @param e DOCUMENT ME!\r
 849      */\r
 850     protected void PIDColour_actionPerformed(ActionEvent e)\r
 851     {\r
 852         SequenceGroup sg = getGroup();\r
 853         sg.cs = new PIDColourScheme();\r
 854         sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
 855                 ap.av.alignment.getWidth()));\r
 856         refresh();\r
 857     }\r
 858 \r
 859     /**\r
 860      * DOCUMENT ME!\r
 861      *\r
 862      * @param e DOCUMENT ME!\r
 863      */\r
 864     protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 865     {\r
 866         SequenceGroup sg = getGroup();\r
 867 \r
 868         sg.cs = new Blosum62ColourScheme();\r
 869 \r
 870         sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
 871                 ap.av.alignment.getWidth()));\r
 872 \r
 873         refresh();\r
 874     }\r
 875 \r
 876     /**\r
 877      * DOCUMENT ME!\r
 878      *\r
 879      * @param e DOCUMENT ME!\r
 880      */\r
 881     protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 882     {\r
 883         getGroup().cs = null;\r
 884         refresh();\r
 885     }\r
 886 \r
 887     /**\r
 888      * DOCUMENT ME!\r
 889      *\r
 890      * @param e DOCUMENT ME!\r
 891      */\r
 892     protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
 893     {\r
 894         SequenceGroup sg = getGroup();\r
 895         if(sg.cs==null)\r
 896           return;\r
 897 \r
 898         if (conservationMenuItem.isSelected())\r
 899         {\r
 900             Conservation c = new Conservation("Group",\r
 901                     ResidueProperties.propHash, 3,\r
 902                     sg.getSequences(true), 0,\r
 903                     ap.av.alignment.getWidth());\r
 904 \r
 905             c.calculate();\r
 906             c.verdict(false, ap.av.ConsPercGaps);\r
 907 \r
 908             sg.cs.setConservation(c);\r
 909 \r
 910             SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
 911             SliderPanel.showConservationSlider();\r
 912         }\r
 913         else // remove ConservationColouring\r
 914         {\r
 915             sg.cs.setConservation(null);\r
 916         }\r
 917 \r
 918         refresh();\r
 919     }\r
 920 \r
 921     /**\r
 922      * DOCUMENT ME!\r
 923      *\r
 924      * @param e DOCUMENT ME!\r
 925      */\r
 926     protected void groupName_actionPerformed(ActionEvent e)\r
 927     {\r
 928         SequenceGroup sg = getGroup();\r
 929         String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
 930                 "Enter new group name", "Edit group name",\r
 931                 JOptionPane.QUESTION_MESSAGE);\r
 932 \r
 933         if (reply == null)\r
 934         {\r
 935             return;\r
 936         }\r
 937 \r
 938         sg.setName(reply);\r
 939         groupName.setText(reply);\r
 940     }\r
 941 \r
 942     /**\r
 943      * DOCUMENT ME!\r
 944      *\r
 945      * @param e DOCUMENT ME!\r
 946      */\r
 947     protected void analyze_actionPerformed(ActionEvent e)\r
 948     {\r
 949         CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
 950         JInternalFrame frame = new JInternalFrame();\r
 951         frame.setContentPane(cap);\r
 952         Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
 953 \r
 954         SequenceGroup sg = getGroup();\r
 955         StringBuffer sb = new StringBuffer();\r
 956 \r
 957         for (int i = 0; i < sg.getSize(false); i++)\r
 958         {\r
 959             Sequence tmp = (Sequence) sg.getSequences(false).elementAt(i);\r
 960             sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
 961             sb.append("\n");\r
 962         }\r
 963 \r
 964         sb.append("Something amazing will happen soon");\r
 965         cap.setText(sb.toString());\r
 966     }\r
 967 \r
 968     /**\r
 969      * DOCUMENT ME!\r
 970      *\r
 971      * @return DOCUMENT ME!\r
 972      */\r
 973     SequenceGroup getGroup()\r
 974     {\r
 975         SequenceGroup sg = ap.av.getSelectionGroup();\r
 976       // this method won't add a new group if it already exists\r
 977         if(sg!=null)\r
 978           ap.av.alignment.addGroup(sg);\r
 979 \r
 980         return sg;\r
 981     }\r
 982 \r
 983     /**\r
 984      * DOCUMENT ME!\r
 985      *\r
 986      * @param e DOCUMENT ME!\r
 987      */\r
 988     void sequenceName_actionPerformed(ActionEvent e)\r
 989     {\r
 990       JLabel idlabel = new JLabel(  "       Sequence Name ");\r
 991       JLabel desclabel = new JLabel("Sequence Description ");\r
 992       idlabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
 993       desclabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
 994       JTextField id = new JTextField(sequence.getName(), 40);\r
 995       JTextField description = new JTextField(sequence.getDescription(), 40);\r
 996       JPanel panel = new JPanel(new BorderLayout());\r
 997       JPanel panel2 = new JPanel(new BorderLayout());\r
 998       panel2.add(idlabel, BorderLayout.WEST);\r
 999       panel2.add(id, BorderLayout.CENTER);\r
1000       panel.add(panel2, BorderLayout.NORTH);\r
1001       panel2 = new JPanel(new BorderLayout());\r
1002       panel2.add(desclabel, BorderLayout.WEST);\r
1003       panel2.add(description, BorderLayout.CENTER);\r
1004       panel.add(panel2, BorderLayout.SOUTH);\r
1005 \r
1006 \r
1007        int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
1008           panel, "Edit Sequence Name/Description",\r
1009           JOptionPane.OK_CANCEL_OPTION );\r
1010 \r
1011 \r
1012         if (reply != JOptionPane.OK_OPTION )\r
1013         {\r
1014             return;\r
1015         }\r
1016 \r
1017         String s = id.getText();\r
1018 \r
1019         if (s != null)\r
1020         {\r
1021             if (s.indexOf(" ") > -1)\r
1022             {\r
1023                 JOptionPane.showMessageDialog(ap,\r
1024                     "Spaces have been converted to \"_\"",\r
1025                     "No spaces allowed in Sequence Name",\r
1026                     JOptionPane.WARNING_MESSAGE);\r
1027             }\r
1028 \r
1029             s = s.replace(' ', '_');\r
1030             sequence.getDatasetSequence().setName(s);\r
1031             sequence.setName(s);\r
1032             ap.repaint();\r
1033         }\r
1034 \r
1035         sequence.getDatasetSequence().setDescription(description.getText());\r
1036         sequence.setDescription(description.getText());\r
1037     }\r
1038 \r
1039     /**\r
1040      * DOCUMENT ME!\r
1041      *\r
1042      * @param e DOCUMENT ME!\r
1043      */\r
1044     void unGroupMenuItem_actionPerformed(ActionEvent e)\r
1045     {\r
1046         SequenceGroup sg = ap.av.getSelectionGroup();\r
1047         ap.av.alignment.deleteGroup(sg);\r
1048         ap.av.setSelectionGroup(null);\r
1049         refresh();\r
1050     }\r
1051 \r
1052 \r
1053     /**\r
1054      * DOCUMENT ME!\r
1055      *\r
1056      * @param e DOCUMENT ME!\r
1057      */\r
1058     protected void outline_actionPerformed(ActionEvent e)\r
1059     {\r
1060         SequenceGroup sg = getGroup();\r
1061         Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
1062                 Color.BLUE);\r
1063 \r
1064         if (col != null)\r
1065         {\r
1066             sg.setOutlineColour(col);\r
1067         }\r
1068 \r
1069         refresh();\r
1070     }\r
1071 \r
1072     /**\r
1073      * DOCUMENT ME!\r
1074      *\r
1075      * @param e DOCUMENT ME!\r
1076      */\r
1077     public void showBoxes_actionPerformed(ActionEvent e)\r
1078     {\r
1079         getGroup().setDisplayBoxes(showBoxes.isSelected());\r
1080         refresh();\r
1081     }\r
1082 \r
1083     /**\r
1084      * DOCUMENT ME!\r
1085      *\r
1086      * @param e DOCUMENT ME!\r
1087      */\r
1088     public void showText_actionPerformed(ActionEvent e)\r
1089     {\r
1090         getGroup().setDisplayText(showText.isSelected());\r
1091         refresh();\r
1092     }\r
1093 \r
1094     /**\r
1095      * DOCUMENT ME!\r
1096      *\r
1097      * @param e DOCUMENT ME!\r
1098      */\r
1099     public void showColourText_actionPerformed(ActionEvent e)\r
1100     {\r
1101         getGroup().setColourText(showColourText.isSelected());\r
1102         refresh();\r
1103     }\r
1104 \r
1105     public void showLink(String url)\r
1106     {\r
1107       try\r
1108       {\r
1109         jalview.util.BrowserLauncher.openURL(url);\r
1110       }\r
1111       catch (Exception ex)\r
1112       {\r
1113         JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
1114             "Unixers: Couldn't find default web browser."\r
1115            +"\nAdd the full path to your browser in Preferences.",\r
1116            "Web browser not found", JOptionPane.WARNING_MESSAGE );\r
1117 \r
1118 \r
1119         ex.printStackTrace();\r
1120       }\r
1121     }\r
1122 \r
1123     void hideSequences(boolean representGroup)\r
1124     {\r
1125       SequenceGroup sg = ap.av.getSelectionGroup();\r
1126       if(sg==null || sg.getSize(false)<1)\r
1127       {\r
1128         ap.av.hideSequence(sequence);\r
1129         return;\r
1130       }\r
1131 \r
1132         int index = 0;\r
1133         while(index < sg.getSize(false))\r
1134         {\r
1135           if(representGroup && sg.getSequenceAt(index)!=sequence)\r
1136           {\r
1137             sequence.addHiddenSequence(sg.getSequenceAt(index));\r
1138             ap.av.hideSequence(sg.getSequenceAt(index));\r
1139           }\r
1140           else if(!representGroup)\r
1141           {\r
1142             ap.av.hideSequence(sg.getSequenceAt(index));\r
1143           }\r
1144           index ++;\r
1145         }\r
1146 \r
1147         ap.av.setSelectionGroup(null);\r
1148         ap.repaint();\r
1149         refresh();\r
1150     }\r
1151 \r
1152   public void copy_actionPerformed(ActionEvent e)\r
1153   {\r
1154     ap.alignFrame.copy_actionPerformed(null);\r
1155   }\r
1156 \r
1157   public void cut_actionPerformed(ActionEvent e)\r
1158   {\r
1159     ap.alignFrame.cut_actionPerformed(null);\r
1160   }\r
1161 \r
1162   public void upperCase_actionPerformed(ActionEvent e)\r
1163   {\r
1164     SequenceGroup sg = ap.av.getSelectionGroup();\r
1165     if(sg==null)\r
1166       return;\r
1167 \r
1168     for(int g=0; g<sg.getSize(true); g++)\r
1169     {\r
1170     ( (SequenceI)sg.getSequences(true).elementAt(g))\r
1171         .changeCase(true, sg.getStartRes(), sg.getEndRes()+1);\r
1172     }\r
1173     ap.repaint();\r
1174   }\r
1175 \r
1176   public void lowerCase_actionPerformed(ActionEvent e)\r
1177   {\r
1178     SequenceGroup sg = ap.av.getSelectionGroup();\r
1179     if(sg==null)\r
1180       return;\r
1181 \r
1182     for(int g=0; g<sg.getSize(true); g++)\r
1183     {\r
1184        ( (SequenceI)sg.getSequences(true).elementAt(g))\r
1185            .changeCase(false, sg.getStartRes(), sg.getEndRes()+1);\r
1186     }\r
1187     ap.repaint();\r
1188   }\r
1189 \r
1190   public void toggle_actionPerformed(ActionEvent e)\r
1191   {\r
1192     SequenceGroup sg = ap.av.getSelectionGroup();\r
1193     if (sg == null)\r
1194       return;\r
1195 \r
1196     for (int g = 0; g < sg.getSize(true); g++)\r
1197     {\r
1198       ( (SequenceI)sg.getSequences(true).elementAt(g))\r
1199           .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);\r
1200     }\r
1201 \r
1202     ap.repaint();\r
1203   }\r
1204 \r
1205   public void outputText_actionPerformed(ActionEvent e)\r
1206   {\r
1207     CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
1208     Desktop.addInternalFrame(cap,\r
1209                              "Alignment output - " + e.getActionCommand(), 600,\r
1210                              500);\r
1211 \r
1212     String [] omitHidden = null;\r
1213 \r
1214     if(ap.av.hasHiddenColumns)\r
1215     {\r
1216       System.out.println("PROMPT USER HERE");\r
1217       omitHidden = ap.av.getViewAsString(true);\r
1218     }\r
1219 \r
1220     cap.setText(new FormatAdapter().formatSequences(\r
1221         e.getActionCommand(),\r
1222         ap.av.getSelectionAsNewSequence(),\r
1223         omitHidden));\r
1224   }\r
1225 \r
1226 \r
1227   public void pdbFromFile_actionPerformed(ActionEvent e)\r
1228   {\r
1229      jalview.io.JalviewFileChooser chooser\r
1230          = new jalview.io.JalviewFileChooser(jalview.bin.Cache.\r
1231          getProperty(\r
1232              "LAST_DIRECTORY"));\r
1233      chooser.setFileView(new jalview.io.JalviewFileView());\r
1234      chooser.setDialogTitle("Select a PDB file");\r
1235      chooser.setToolTipText("Load a PDB file");\r
1236 \r
1237      int value = chooser.showOpenDialog(null);\r
1238 \r
1239      if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
1240      {\r
1241        PDBEntry entry = new PDBEntry();\r
1242        String choice = chooser.getSelectedFile().getPath();\r
1243        jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
1244        try\r
1245        {\r
1246          MCview.PDBfile pdbfile = new MCview.PDBfile(choice,\r
1247                                        jalview.io.AppletFormatAdapter.FILE);\r
1248 \r
1249          if (pdbfile.id == null)\r
1250          {\r
1251            String reply = JOptionPane.showInternalInputDialog(\r
1252                Desktop.desktop,\r
1253                "Couldn't find a PDB id in the file supplied."\r
1254                + "Please enter an Id to identify this structure.",\r
1255                "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);\r
1256            if (reply == null)\r
1257              return;\r
1258 \r
1259            entry.setId(reply);\r
1260          }\r
1261          else\r
1262            entry.setId(pdbfile.id);\r
1263        }\r
1264        catch (java.io.IOException ex)\r
1265        {\r
1266          ex.printStackTrace();\r
1267        }\r
1268 \r
1269        entry.setFile(choice);\r
1270        sequence.getDatasetSequence().addPDBId(entry);\r
1271      }\r
1272 \r
1273   }\r
1274 \r
1275   public void enterPDB_actionPerformed(ActionEvent e)\r
1276   {\r
1277     int size = (ap.av.getSelectionGroup() == null ? 0 :\r
1278                 ap.av.getSelectionGroup().getSize(false));\r
1279 \r
1280     if (size == 0 || size > 1)\r
1281     {\r
1282       JOptionPane.showInternalMessageDialog(\r
1283           Desktop.desktop,\r
1284           "Select a single sequence to specify a PDB id for first",\r
1285           "Select Single Selected", JOptionPane.WARNING_MESSAGE);\r
1286       return;\r
1287     }\r
1288 \r
1289     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
1290         "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);\r
1291 \r
1292     if (id != null && id.length() > 0)\r
1293     {\r
1294       PDBEntry entry = new PDBEntry();\r
1295       entry.setId(id);\r
1296       ap.av.getSelectionGroup().getSequenceAt(0).getDatasetSequence()\r
1297           .addPDBId(entry);\r
1298     }\r
1299   }\r
1300 \r
1301   public void discoverPDB_actionPerformed(ActionEvent e)\r
1302   {\r
1303     new jalview.io.DBRefFetcher(\r
1304              ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);\r
1305   }\r
1306 }\r