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 outputMenu = new JMenu();\r
  81   JMenu pdbMenu = new JMenu();\r
  82   JMenuItem pdbFromFile = new JMenuItem();\r
  83   JMenuItem enterPDB = new JMenuItem();\r
  84   JMenuItem discoverPDB = 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           outputMenu.add(item);\r
 132         }\r
 133 \r
 134 \r
 135         try\r
 136         {\r
 137             jbInit();\r
 138         }\r
 139         catch (Exception e)\r
 140         {\r
 141             e.printStackTrace();\r
 142         }\r
 143 \r
 144 \r
 145         if (seq != null)\r
 146         {\r
 147           JMenuItem menuItem;\r
 148           if( seq.getDatasetSequence().getPDBId() != null)\r
 149           {\r
 150             java.util.Enumeration e = seq.getDatasetSequence().getPDBId().\r
 151                 elements();\r
 152 \r
 153             while (e.hasMoreElements())\r
 154             {\r
 155               final PDBEntry pdb = (PDBEntry) e.nextElement();\r
 156 \r
 157               menuItem = new JMenuItem();\r
 158               menuItem.setText("View PDB entry: " + pdb.getId());\r
 159               menuItem.addActionListener(new java.awt.event.ActionListener()\r
 160               {\r
 161                 public void actionPerformed(ActionEvent e)\r
 162                 {\r
 163                   new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);\r
 164                 }\r
 165               });\r
 166               sequenceMenu.add(menuItem);\r
 167             }\r
 168           }\r
 169 \r
 170           menuItem = new JMenuItem("Hide Sequences");\r
 171           menuItem.addActionListener(new java.awt.event.ActionListener()\r
 172               {\r
 173                 public void actionPerformed(ActionEvent e)\r
 174                 {\r
 175                   hideSequences(false);\r
 176                 }\r
 177               });\r
 178           sequenceMenu.add(menuItem);\r
 179 \r
 180           if(ap.av.getSelectionGroup() !=null\r
 181              && ap.av.getSelectionGroup().getSize(false)>1)\r
 182           {\r
 183             menuItem = new JMenuItem("Represent Group with " + seq.getName());\r
 184             menuItem.addActionListener(new java.awt.event.ActionListener()\r
 185             {\r
 186               public void actionPerformed(ActionEvent e)\r
 187               {\r
 188                 hideSequences(true);\r
 189               }\r
 190             });\r
 191             sequenceMenu.add(menuItem);\r
 192           }\r
 193 \r
 194           if (ap.av.hasHiddenRows)\r
 195           {\r
 196             final int index = ap.av.alignment.findIndex(seq);\r
 197 \r
 198             if (ap.av.adjustForHiddenSeqs(index) -\r
 199                 ap.av.adjustForHiddenSeqs(index - 1) > 1)\r
 200             {\r
 201               menuItem = new JMenuItem("Reveal");\r
 202               menuItem.addActionListener(new ActionListener()\r
 203               {\r
 204                 public void actionPerformed(ActionEvent e)\r
 205                 {\r
 206                   ap.av.showSequence(index);\r
 207                   ap.repaint();\r
 208                   if (ap.overviewPanel != null)\r
 209                     ap.overviewPanel.updateOverviewImage();\r
 210                 }\r
 211               });\r
 212               sequenceMenu.add(menuItem);\r
 213             }\r
 214 \r
 215             menuItem = new JMenuItem("Reveal All");\r
 216             menuItem.addActionListener(new ActionListener()\r
 217                 {\r
 218                   public void actionPerformed(ActionEvent e)\r
 219                   {\r
 220                     ap.av.showAllHiddenSeqs();\r
 221                     ap.repaint();\r
 222                     if (ap.overviewPanel != null)\r
 223                       ap.overviewPanel.updateOverviewImage();\r
 224                       }\r
 225                 });\r
 226 \r
 227             sequenceMenu.add(menuItem);\r
 228 \r
 229 \r
 230 \r
 231           }\r
 232 \r
 233 \r
 234         }\r
 235 \r
 236 \r
 237 \r
 238         SequenceGroup sg = ap.av.getSelectionGroup();\r
 239 \r
 240         if (sg != null)\r
 241         {\r
 242             groupName.setText(sg.getName());\r
 243 \r
 244             if (sg.cs instanceof ZappoColourScheme)\r
 245             {\r
 246                 zappoColour.setSelected(true);\r
 247             }\r
 248             else if (sg.cs instanceof TaylorColourScheme)\r
 249             {\r
 250                 taylorColour.setSelected(true);\r
 251             }\r
 252             else if (sg.cs instanceof PIDColourScheme)\r
 253             {\r
 254                 PIDColour.setSelected(true);\r
 255             }\r
 256             else if (sg.cs instanceof Blosum62ColourScheme)\r
 257             {\r
 258                 BLOSUM62Colour.setSelected(true);\r
 259             }\r
 260             else if (sg.cs instanceof UserColourScheme)\r
 261             {\r
 262                 userDefinedColour.setSelected(true);\r
 263             }\r
 264             else if (sg.cs instanceof HydrophobicColourScheme)\r
 265             {\r
 266                 hydrophobicityColour.setSelected(true);\r
 267             }\r
 268             else if (sg.cs instanceof HelixColourScheme)\r
 269             {\r
 270                 helixColour.setSelected(true);\r
 271             }\r
 272             else if (sg.cs instanceof StrandColourScheme)\r
 273             {\r
 274                 strandColour.setSelected(true);\r
 275             }\r
 276             else if (sg.cs instanceof TurnColourScheme)\r
 277             {\r
 278                 turnColour.setSelected(true);\r
 279             }\r
 280             else if (sg.cs instanceof BuriedColourScheme)\r
 281             {\r
 282                 buriedColour.setSelected(true);\r
 283             }\r
 284             else if (sg.cs instanceof ClustalxColourScheme)\r
 285             {\r
 286                 clustalColour.setSelected(true);\r
 287             }\r
 288             else\r
 289             {\r
 290                 noColourmenuItem.setSelected(true);\r
 291             }\r
 292 \r
 293             if (sg.cs!=null && sg.cs.conservationApplied())\r
 294             {\r
 295                 conservationMenuItem.setSelected(true);\r
 296             }\r
 297 \r
 298             showText.setSelected(sg.getDisplayText());\r
 299             showColourText.setSelected(sg.getColourText());\r
 300             showBoxes.setSelected(sg.getDisplayBoxes());\r
 301         }\r
 302         else\r
 303         {\r
 304           groupMenu.setVisible(false);\r
 305           editMenu.setVisible(false);\r
 306         }\r
 307 \r
 308         if (!ap.av.alignment.getGroups().contains(sg))\r
 309         {\r
 310             unGroupMenuItem.setVisible(false);\r
 311         }\r
 312         else\r
 313         {\r
 314             groupMenu.insertSeparator(3);\r
 315         }\r
 316 \r
 317         if (seq == null)\r
 318         {\r
 319             sequenceMenu.setVisible(false);\r
 320             pdbMenu.setVisible(false);\r
 321         }\r
 322 \r
 323         if(links != null && links.size()>0)\r
 324         {\r
 325           JMenu linkMenu = new JMenu("Link");\r
 326           JMenuItem item;\r
 327           for(int i=0; i<links.size(); i++)\r
 328           {\r
 329             String link = links.elementAt(i).toString();\r
 330             final String label = link.substring(0, link.indexOf("|"));\r
 331             item = new JMenuItem(label);\r
 332             final String url;\r
 333 \r
 334             if (link.indexOf("$SEQUENCE_ID$") > -1)\r
 335             {\r
 336               String id = seq.getName();\r
 337               if (id.indexOf("|") > -1)\r
 338                 id = id.substring(id.lastIndexOf("|") + 1);\r
 339 \r
 340               url = link.substring(link.indexOf("|") + 1,\r
 341                                    link.indexOf("$SEQUENCE_ID$"))\r
 342                   + id +\r
 343                   link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
 344             }\r
 345             else\r
 346               url = link.substring(link.lastIndexOf("|")+1);\r
 347 \r
 348 \r
 349             item.addActionListener(new java.awt.event.ActionListener()\r
 350             {\r
 351                 public void actionPerformed(ActionEvent e)\r
 352                 {\r
 353                     showLink(url);\r
 354                 }\r
 355             });\r
 356 \r
 357             linkMenu.add(item);\r
 358           }\r
 359           add(linkMenu);\r
 360         }\r
 361     }\r
 362 \r
 363 \r
 364     /**\r
 365      * DOCUMENT ME!\r
 366      *\r
 367      * @throws Exception DOCUMENT ME!\r
 368      */\r
 369     private void jbInit() throws Exception\r
 370     {\r
 371         groupMenu.setText("Group");\r
 372         groupMenu.setText("Group");\r
 373         groupName.setText("Name");\r
 374         groupName.addActionListener(new java.awt.event.ActionListener()\r
 375             {\r
 376                 public void actionPerformed(ActionEvent e)\r
 377                 {\r
 378                     groupName_actionPerformed(e);\r
 379                 }\r
 380             });\r
 381         sequenceMenu.setText("Sequence");\r
 382         sequenceName.setText("Edit Name/Description");\r
 383         sequenceName.addActionListener(new java.awt.event.ActionListener()\r
 384             {\r
 385                 public void actionPerformed(ActionEvent e)\r
 386                 {\r
 387                     sequenceName_actionPerformed(e);\r
 388                 }\r
 389             });\r
 390         PIDColour.setFocusPainted(false);\r
 391         unGroupMenuItem.setText("Remove Group");\r
 392         unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 393             {\r
 394                 public void actionPerformed(ActionEvent e)\r
 395                 {\r
 396                     unGroupMenuItem_actionPerformed(e);\r
 397                 }\r
 398             });\r
 399 \r
 400         outline.setText("Border colour");\r
 401         outline.addActionListener(new java.awt.event.ActionListener()\r
 402             {\r
 403                 public void actionPerformed(ActionEvent e)\r
 404                 {\r
 405                     outline_actionPerformed(e);\r
 406                 }\r
 407             });\r
 408         nucleotideMenuItem.setText("Nucleotide");\r
 409         nucleotideMenuItem.addActionListener(new ActionListener()\r
 410             {\r
 411                 public void actionPerformed(ActionEvent e)\r
 412                 {\r
 413                     nucleotideMenuItem_actionPerformed(e);\r
 414                 }\r
 415             });\r
 416         colourMenu.setText("Group Colour");\r
 417         showBoxes.setText("Boxes");\r
 418         showBoxes.setState(true);\r
 419         showBoxes.addActionListener(new ActionListener()\r
 420             {\r
 421                 public void actionPerformed(ActionEvent e)\r
 422                 {\r
 423                     showBoxes_actionPerformed(e);\r
 424                 }\r
 425             });\r
 426         showText.setText("Text");\r
 427         showText.setState(true);\r
 428         showText.addActionListener(new ActionListener()\r
 429             {\r
 430                 public void actionPerformed(ActionEvent e)\r
 431                 {\r
 432                     showText_actionPerformed(e);\r
 433                 }\r
 434             });\r
 435         showColourText.setText("Colour Text");\r
 436         showColourText.addActionListener(new ActionListener()\r
 437             {\r
 438                 public void actionPerformed(ActionEvent e)\r
 439                 {\r
 440                     showColourText_actionPerformed(e);\r
 441                 }\r
 442             });\r
 443     editMenu.setText("Edit");\r
 444     cut.setText("Cut");\r
 445     cut.addActionListener(new ActionListener()\r
 446     {\r
 447       public void actionPerformed(ActionEvent e)\r
 448       {\r
 449         cut_actionPerformed(e);\r
 450       }\r
 451     });\r
 452     upperCase.setText("To Upper Case");\r
 453     upperCase.addActionListener(new ActionListener()\r
 454     {\r
 455       public void actionPerformed(ActionEvent e)\r
 456       {\r
 457         upperCase_actionPerformed(e);\r
 458       }\r
 459     });\r
 460     copy.setText("Copy");\r
 461     copy.addActionListener(new ActionListener()\r
 462     {\r
 463       public void actionPerformed(ActionEvent e)\r
 464       {\r
 465         copy_actionPerformed(e);\r
 466       }\r
 467     });\r
 468     lowerCase.setText("To Lower Case");\r
 469     lowerCase.addActionListener(new ActionListener()\r
 470     {\r
 471       public void actionPerformed(ActionEvent e)\r
 472       {\r
 473         lowerCase_actionPerformed(e);\r
 474       }\r
 475     });\r
 476     toggle.setText("Toggle Case");\r
 477     toggle.addActionListener(new ActionListener()\r
 478     {\r
 479       public void actionPerformed(ActionEvent e)\r
 480       {\r
 481         toggle_actionPerformed(e);\r
 482       }\r
 483     });\r
 484     outputMenu.setText("Output to Textbox...");\r
 485     pdbMenu.setText("Associate Structure with Sequence");\r
 486     pdbFromFile.setText("From File");\r
 487     pdbFromFile.addActionListener(new ActionListener()\r
 488     {\r
 489       public void actionPerformed(ActionEvent e)\r
 490       {\r
 491         pdbFromFile_actionPerformed(e);\r
 492       }\r
 493     });\r
 494     enterPDB.setText("Enter PDB Id");\r
 495     enterPDB.addActionListener(new ActionListener()\r
 496     {\r
 497       public void actionPerformed(ActionEvent e)\r
 498       {\r
 499         enterPDB_actionPerformed(e);\r
 500       }\r
 501     });\r
 502     discoverPDB.setText("Discover PDB ids");\r
 503     discoverPDB.addActionListener(new ActionListener()\r
 504     {\r
 505       public void actionPerformed(ActionEvent e)\r
 506       {\r
 507         discoverPDB_actionPerformed(e);\r
 508       }\r
 509     });\r
 510     add(groupMenu);\r
 511 \r
 512     this.add(editMenu);\r
 513     this.add(outputMenu);\r
 514     add(sequenceMenu);\r
 515     this.add(pdbMenu);\r
 516     groupMenu.add(groupName);\r
 517         groupMenu.addSeparator();\r
 518         groupMenu.add(unGroupMenuItem);\r
 519         groupMenu.add(colourMenu);\r
 520         groupMenu.addSeparator();\r
 521         groupMenu.add(showBoxes);\r
 522         groupMenu.add(showText);\r
 523         groupMenu.add(showColourText);\r
 524         groupMenu.addSeparator();\r
 525         groupMenu.add(outline);\r
 526         sequenceMenu.add(sequenceName);\r
 527         colourMenu.add(noColourmenuItem);\r
 528         colourMenu.add(clustalColour);\r
 529         colourMenu.add(BLOSUM62Colour);\r
 530         colourMenu.add(PIDColour);\r
 531         colourMenu.add(zappoColour);\r
 532         colourMenu.add(taylorColour);\r
 533         colourMenu.add(hydrophobicityColour);\r
 534         colourMenu.add(helixColour);\r
 535         colourMenu.add(strandColour);\r
 536         colourMenu.add(turnColour);\r
 537         colourMenu.add(buriedColour);\r
 538         colourMenu.add(nucleotideMenuItem);\r
 539         colourMenu.add(userDefinedColour);\r
 540 \r
 541         if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
 542         {\r
 543           java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 544               getUserColourSchemes().keys();\r
 545 \r
 546           while (userColours.hasMoreElements())\r
 547           {\r
 548             JMenuItem item = new JMenuItem(userColours.\r
 549                 nextElement().toString());\r
 550             item.addActionListener(new ActionListener()\r
 551             {\r
 552               public void actionPerformed(ActionEvent evt)\r
 553               {\r
 554                 userDefinedColour_actionPerformed(evt);\r
 555               }\r
 556             });\r
 557             colourMenu.add(item);\r
 558           }\r
 559         }\r
 560 \r
 561 \r
 562         colourMenu.addSeparator();\r
 563         colourMenu.add(abovePIDColour);\r
 564         colourMenu.add(conservationMenuItem);\r
 565     editMenu.add(copy);\r
 566     editMenu.add(cut);\r
 567     editMenu.add(upperCase);\r
 568     editMenu.add(lowerCase);\r
 569     editMenu.add(toggle);\r
 570     pdbMenu.add(pdbFromFile);\r
 571     pdbMenu.add(enterPDB);\r
 572     pdbMenu.add(discoverPDB);\r
 573     noColourmenuItem.setText("None");\r
 574         noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 575             {\r
 576                 public void actionPerformed(ActionEvent e)\r
 577                 {\r
 578                     noColourmenuItem_actionPerformed(e);\r
 579                 }\r
 580             });\r
 581 \r
 582         clustalColour.setText("Clustalx colours");\r
 583         clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 584             {\r
 585                 public void actionPerformed(ActionEvent e)\r
 586                 {\r
 587                     clustalColour_actionPerformed(e);\r
 588                 }\r
 589             });\r
 590         zappoColour.setText("Zappo");\r
 591         zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 592             {\r
 593                 public void actionPerformed(ActionEvent e)\r
 594                 {\r
 595                     zappoColour_actionPerformed(e);\r
 596                 }\r
 597             });\r
 598         taylorColour.setText("Taylor");\r
 599         taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 600             {\r
 601                 public void actionPerformed(ActionEvent e)\r
 602                 {\r
 603                     taylorColour_actionPerformed(e);\r
 604                 }\r
 605             });\r
 606         hydrophobicityColour.setText("Hydrophobicity");\r
 607         hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 608             {\r
 609                 public void actionPerformed(ActionEvent e)\r
 610                 {\r
 611                     hydrophobicityColour_actionPerformed(e);\r
 612                 }\r
 613             });\r
 614         helixColour.setText("Helix propensity");\r
 615         helixColour.addActionListener(new java.awt.event.ActionListener()\r
 616             {\r
 617                 public void actionPerformed(ActionEvent e)\r
 618                 {\r
 619                     helixColour_actionPerformed(e);\r
 620                 }\r
 621             });\r
 622         strandColour.setText("Strand propensity");\r
 623         strandColour.addActionListener(new java.awt.event.ActionListener()\r
 624             {\r
 625                 public void actionPerformed(ActionEvent e)\r
 626                 {\r
 627                     strandColour_actionPerformed(e);\r
 628                 }\r
 629             });\r
 630         turnColour.setText("Turn propensity");\r
 631         turnColour.addActionListener(new java.awt.event.ActionListener()\r
 632             {\r
 633                 public void actionPerformed(ActionEvent e)\r
 634                 {\r
 635                     turnColour_actionPerformed(e);\r
 636                 }\r
 637             });\r
 638         buriedColour.setText("Buried Index");\r
 639         buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 640             {\r
 641                 public void actionPerformed(ActionEvent e)\r
 642                 {\r
 643                     buriedColour_actionPerformed(e);\r
 644                 }\r
 645             });\r
 646         abovePIDColour.setText("Above % Identity");\r
 647         abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
 648             {\r
 649                 public void actionPerformed(ActionEvent e)\r
 650                 {\r
 651                     abovePIDColour_actionPerformed(e);\r
 652                 }\r
 653             });\r
 654         userDefinedColour.setText("User Defined...");\r
 655         userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 656             {\r
 657                 public void actionPerformed(ActionEvent e)\r
 658                 {\r
 659                     userDefinedColour_actionPerformed(e);\r
 660                 }\r
 661             });\r
 662         PIDColour.setText("Percentage Identity");\r
 663         PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 664             {\r
 665                 public void actionPerformed(ActionEvent e)\r
 666                 {\r
 667                     PIDColour_actionPerformed(e);\r
 668                 }\r
 669             });\r
 670         BLOSUM62Colour.setText("BLOSUM62");\r
 671         BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 672             {\r
 673                 public void actionPerformed(ActionEvent e)\r
 674                 {\r
 675                     BLOSUM62Colour_actionPerformed(e);\r
 676                 }\r
 677             });\r
 678         conservationMenuItem.setText("Conservation");\r
 679         conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 680             {\r
 681                 public void actionPerformed(ActionEvent e)\r
 682                 {\r
 683                     conservationMenuItem_actionPerformed(e);\r
 684                 }\r
 685             });\r
 686     }\r
 687 \r
 688     /**\r
 689      * DOCUMENT ME!\r
 690      */\r
 691     void refresh()\r
 692     {\r
 693         if (ap.overviewPanel != null)\r
 694           ap.overviewPanel.updateOverviewImage();\r
 695 \r
 696         ap.seqPanel.repaint();\r
 697     }\r
 698 \r
 699     /**\r
 700      * DOCUMENT ME!\r
 701      *\r
 702      * @param e DOCUMENT ME!\r
 703      */\r
 704     protected void clustalColour_actionPerformed(ActionEvent e)\r
 705     {\r
 706         SequenceGroup sg = getGroup();\r
 707         sg.cs = new ClustalxColourScheme(sg.getSequences(true),\r
 708                 ap.av.alignment.getWidth());\r
 709         refresh();\r
 710     }\r
 711 \r
 712     /**\r
 713      * DOCUMENT ME!\r
 714      *\r
 715      * @param e DOCUMENT ME!\r
 716      */\r
 717     protected void zappoColour_actionPerformed(ActionEvent e)\r
 718     {\r
 719         getGroup().cs = new ZappoColourScheme();\r
 720         refresh();\r
 721     }\r
 722 \r
 723     /**\r
 724      * DOCUMENT ME!\r
 725      *\r
 726      * @param e DOCUMENT ME!\r
 727      */\r
 728     protected void taylorColour_actionPerformed(ActionEvent e)\r
 729     {\r
 730         getGroup().cs = new TaylorColourScheme();\r
 731         refresh();\r
 732     }\r
 733 \r
 734     /**\r
 735      * DOCUMENT ME!\r
 736      *\r
 737      * @param e DOCUMENT ME!\r
 738      */\r
 739     protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 740     {\r
 741         getGroup().cs = new HydrophobicColourScheme();\r
 742         refresh();\r
 743     }\r
 744 \r
 745     /**\r
 746      * DOCUMENT ME!\r
 747      *\r
 748      * @param e DOCUMENT ME!\r
 749      */\r
 750     protected void helixColour_actionPerformed(ActionEvent e)\r
 751     {\r
 752         getGroup().cs = new HelixColourScheme();\r
 753         refresh();\r
 754     }\r
 755 \r
 756     /**\r
 757      * DOCUMENT ME!\r
 758      *\r
 759      * @param e DOCUMENT ME!\r
 760      */\r
 761     protected void strandColour_actionPerformed(ActionEvent e)\r
 762     {\r
 763         getGroup().cs = new StrandColourScheme();\r
 764         refresh();\r
 765     }\r
 766 \r
 767     /**\r
 768      * DOCUMENT ME!\r
 769      *\r
 770      * @param e DOCUMENT ME!\r
 771      */\r
 772     protected void turnColour_actionPerformed(ActionEvent e)\r
 773     {\r
 774         getGroup().cs = new TurnColourScheme();\r
 775         refresh();\r
 776     }\r
 777 \r
 778     /**\r
 779      * DOCUMENT ME!\r
 780      *\r
 781      * @param e DOCUMENT ME!\r
 782      */\r
 783     protected void buriedColour_actionPerformed(ActionEvent e)\r
 784     {\r
 785         getGroup().cs = new BuriedColourScheme();\r
 786         refresh();\r
 787     }\r
 788 \r
 789     /**\r
 790      * DOCUMENT ME!\r
 791      *\r
 792      * @param e DOCUMENT ME!\r
 793      */\r
 794     public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
 795     {\r
 796         getGroup().cs = new NucleotideColourScheme();\r
 797         refresh();\r
 798     }\r
 799 \r
 800     /**\r
 801      * DOCUMENT ME!\r
 802      *\r
 803      * @param e DOCUMENT ME!\r
 804      */\r
 805     protected void abovePIDColour_actionPerformed(ActionEvent e)\r
 806     {\r
 807         SequenceGroup sg = getGroup();\r
 808         if(sg.cs==null)\r
 809           return;\r
 810 \r
 811         if (abovePIDColour.isSelected())\r
 812         {\r
 813             sg.cs.setConsensus(AAFrequency.calculate(\r
 814                     sg.getSequences(true), 0,\r
 815                     ap.av.alignment.getWidth()));\r
 816 \r
 817             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
 818                     getGroup().getName());\r
 819 \r
 820            sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
 821 \r
 822             SliderPanel.showPIDSlider();\r
 823         }\r
 824         else // remove PIDColouring\r
 825         {\r
 826             sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
 827         }\r
 828 \r
 829         refresh();\r
 830     }\r
 831 \r
 832     /**\r
 833      * DOCUMENT ME!\r
 834      *\r
 835      * @param e DOCUMENT ME!\r
 836      */\r
 837     protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 838     {\r
 839        SequenceGroup sg = getGroup();\r
 840 \r
 841        if (e.getActionCommand().equals("User Defined..."))\r
 842          new UserDefinedColours(ap, sg);\r
 843        else\r
 844        {\r
 845          UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
 846              getUserColourSchemes().get(e.getActionCommand());\r
 847 \r
 848          sg.cs = udc;\r
 849        }\r
 850      }\r
 851     /**\r
 852      * DOCUMENT ME!\r
 853      *\r
 854      * @param e DOCUMENT ME!\r
 855      */\r
 856     protected void PIDColour_actionPerformed(ActionEvent e)\r
 857     {\r
 858         SequenceGroup sg = getGroup();\r
 859         sg.cs = new PIDColourScheme();\r
 860         sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
 861                 ap.av.alignment.getWidth()));\r
 862         refresh();\r
 863     }\r
 864 \r
 865     /**\r
 866      * DOCUMENT ME!\r
 867      *\r
 868      * @param e DOCUMENT ME!\r
 869      */\r
 870     protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 871     {\r
 872         SequenceGroup sg = getGroup();\r
 873 \r
 874         sg.cs = new Blosum62ColourScheme();\r
 875 \r
 876         sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
 877                 ap.av.alignment.getWidth()));\r
 878 \r
 879         refresh();\r
 880     }\r
 881 \r
 882     /**\r
 883      * DOCUMENT ME!\r
 884      *\r
 885      * @param e DOCUMENT ME!\r
 886      */\r
 887     protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 888     {\r
 889         getGroup().cs = null;\r
 890         refresh();\r
 891     }\r
 892 \r
 893     /**\r
 894      * DOCUMENT ME!\r
 895      *\r
 896      * @param e DOCUMENT ME!\r
 897      */\r
 898     protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
 899     {\r
 900         SequenceGroup sg = getGroup();\r
 901         if(sg.cs==null)\r
 902           return;\r
 903 \r
 904         if (conservationMenuItem.isSelected())\r
 905         {\r
 906             Conservation c = new Conservation("Group",\r
 907                     ResidueProperties.propHash, 3,\r
 908                     sg.getSequences(true), 0,\r
 909                     ap.av.alignment.getWidth());\r
 910 \r
 911             c.calculate();\r
 912             c.verdict(false, ap.av.ConsPercGaps);\r
 913 \r
 914             sg.cs.setConservation(c);\r
 915 \r
 916             SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
 917             SliderPanel.showConservationSlider();\r
 918         }\r
 919         else // remove ConservationColouring\r
 920         {\r
 921             sg.cs.setConservation(null);\r
 922         }\r
 923 \r
 924         refresh();\r
 925     }\r
 926 \r
 927     /**\r
 928      * DOCUMENT ME!\r
 929      *\r
 930      * @param e DOCUMENT ME!\r
 931      */\r
 932     protected void groupName_actionPerformed(ActionEvent e)\r
 933     {\r
 934         SequenceGroup sg = getGroup();\r
 935         String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
 936                 "Enter new group name", "Edit group name",\r
 937                 JOptionPane.QUESTION_MESSAGE);\r
 938 \r
 939         if (reply == null)\r
 940         {\r
 941             return;\r
 942         }\r
 943 \r
 944         sg.setName(reply);\r
 945         groupName.setText(reply);\r
 946     }\r
 947 \r
 948     /**\r
 949      * DOCUMENT ME!\r
 950      *\r
 951      * @param e DOCUMENT ME!\r
 952      */\r
 953     protected void analyze_actionPerformed(ActionEvent e)\r
 954     {\r
 955         CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
 956         JInternalFrame frame = new JInternalFrame();\r
 957         frame.setContentPane(cap);\r
 958         Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
 959 \r
 960         SequenceGroup sg = getGroup();\r
 961         StringBuffer sb = new StringBuffer();\r
 962 \r
 963         for (int i = 0; i < sg.getSize(false); i++)\r
 964         {\r
 965             Sequence tmp = (Sequence) sg.getSequences(false).elementAt(i);\r
 966             sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
 967             sb.append("\n");\r
 968         }\r
 969 \r
 970         sb.append("Something amazing will happen soon");\r
 971         cap.setText(sb.toString());\r
 972     }\r
 973 \r
 974     /**\r
 975      * DOCUMENT ME!\r
 976      *\r
 977      * @return DOCUMENT ME!\r
 978      */\r
 979     SequenceGroup getGroup()\r
 980     {\r
 981         SequenceGroup sg = ap.av.getSelectionGroup();\r
 982       // this method won't add a new group if it already exists\r
 983         if(sg!=null)\r
 984           ap.av.alignment.addGroup(sg);\r
 985 \r
 986         return sg;\r
 987     }\r
 988 \r
 989     /**\r
 990      * DOCUMENT ME!\r
 991      *\r
 992      * @param e DOCUMENT ME!\r
 993      */\r
 994     void sequenceName_actionPerformed(ActionEvent e)\r
 995     {\r
 996       JLabel idlabel = new JLabel(  "       Sequence Name ");\r
 997       JLabel desclabel = new JLabel("Sequence Description ");\r
 998       idlabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
 999       desclabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
1000       JTextField id = new JTextField(sequence.getName(), 40);\r
1001       JTextField description = new JTextField(sequence.getDescription(), 40);\r
1002       JPanel panel = new JPanel(new BorderLayout());\r
1003       JPanel panel2 = new JPanel(new BorderLayout());\r
1004       panel2.add(idlabel, BorderLayout.WEST);\r
1005       panel2.add(id, BorderLayout.CENTER);\r
1006       panel.add(panel2, BorderLayout.NORTH);\r
1007       panel2 = new JPanel(new BorderLayout());\r
1008       panel2.add(desclabel, BorderLayout.WEST);\r
1009       panel2.add(description, BorderLayout.CENTER);\r
1010       panel.add(panel2, BorderLayout.SOUTH);\r
1011 \r
1012 \r
1013        int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
1014           panel, "Edit Sequence Name/Description",\r
1015           JOptionPane.OK_CANCEL_OPTION );\r
1016 \r
1017 \r
1018         if (reply != JOptionPane.OK_OPTION )\r
1019         {\r
1020             return;\r
1021         }\r
1022 \r
1023         String s = id.getText();\r
1024 \r
1025         if (s != null)\r
1026         {\r
1027             if (s.indexOf(" ") > -1)\r
1028             {\r
1029                 JOptionPane.showMessageDialog(ap,\r
1030                     "Spaces have been converted to \"_\"",\r
1031                     "No spaces allowed in Sequence Name",\r
1032                     JOptionPane.WARNING_MESSAGE);\r
1033             }\r
1034 \r
1035             s = s.replace(' ', '_');\r
1036             sequence.getDatasetSequence().setName(s);\r
1037             sequence.setName(s);\r
1038             ap.repaint();\r
1039         }\r
1040 \r
1041         sequence.getDatasetSequence().setDescription(description.getText());\r
1042         sequence.setDescription(description.getText());\r
1043     }\r
1044 \r
1045     /**\r
1046      * DOCUMENT ME!\r
1047      *\r
1048      * @param e DOCUMENT ME!\r
1049      */\r
1050     void unGroupMenuItem_actionPerformed(ActionEvent e)\r
1051     {\r
1052         SequenceGroup sg = ap.av.getSelectionGroup();\r
1053         ap.av.alignment.deleteGroup(sg);\r
1054         ap.av.setSelectionGroup(null);\r
1055         refresh();\r
1056     }\r
1057 \r
1058 \r
1059     /**\r
1060      * DOCUMENT ME!\r
1061      *\r
1062      * @param e DOCUMENT ME!\r
1063      */\r
1064     protected void outline_actionPerformed(ActionEvent e)\r
1065     {\r
1066         SequenceGroup sg = getGroup();\r
1067         Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
1068                 Color.BLUE);\r
1069 \r
1070         if (col != null)\r
1071         {\r
1072             sg.setOutlineColour(col);\r
1073         }\r
1074 \r
1075         refresh();\r
1076     }\r
1077 \r
1078     /**\r
1079      * DOCUMENT ME!\r
1080      *\r
1081      * @param e DOCUMENT ME!\r
1082      */\r
1083     public void showBoxes_actionPerformed(ActionEvent e)\r
1084     {\r
1085         getGroup().setDisplayBoxes(showBoxes.isSelected());\r
1086         refresh();\r
1087     }\r
1088 \r
1089     /**\r
1090      * DOCUMENT ME!\r
1091      *\r
1092      * @param e DOCUMENT ME!\r
1093      */\r
1094     public void showText_actionPerformed(ActionEvent e)\r
1095     {\r
1096         getGroup().setDisplayText(showText.isSelected());\r
1097         refresh();\r
1098     }\r
1099 \r
1100     /**\r
1101      * DOCUMENT ME!\r
1102      *\r
1103      * @param e DOCUMENT ME!\r
1104      */\r
1105     public void showColourText_actionPerformed(ActionEvent e)\r
1106     {\r
1107         getGroup().setColourText(showColourText.isSelected());\r
1108         refresh();\r
1109     }\r
1110 \r
1111     public void showLink(String url)\r
1112     {\r
1113       try\r
1114       {\r
1115         jalview.util.BrowserLauncher.openURL(url);\r
1116       }\r
1117       catch (Exception ex)\r
1118       {\r
1119         JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
1120             "Unixers: Couldn't find default web browser."\r
1121            +"\nAdd the full path to your browser in Preferences.",\r
1122            "Web browser not found", JOptionPane.WARNING_MESSAGE );\r
1123 \r
1124 \r
1125         ex.printStackTrace();\r
1126       }\r
1127     }\r
1128 \r
1129     void hideSequences(boolean representGroup)\r
1130     {\r
1131       SequenceGroup sg = ap.av.getSelectionGroup();\r
1132       if(sg==null || sg.getSize(false)<1)\r
1133       {\r
1134         ap.av.hideSequence(sequence);\r
1135         return;\r
1136       }\r
1137 \r
1138         int index = 0;\r
1139         while(index < sg.getSize(false))\r
1140         {\r
1141           if(representGroup && sg.getSequenceAt(index)!=sequence)\r
1142           {\r
1143             sequence.addHiddenSequence(sg.getSequenceAt(index));\r
1144             ap.av.hideSequence(sg.getSequenceAt(index));\r
1145           }\r
1146           else if(!representGroup)\r
1147           {\r
1148             ap.av.hideSequence(sg.getSequenceAt(index));\r
1149           }\r
1150           index ++;\r
1151         }\r
1152 \r
1153         ap.av.setSelectionGroup(null);\r
1154         refresh();\r
1155     }\r
1156 \r
1157   public void copy_actionPerformed(ActionEvent e)\r
1158   {\r
1159     ap.alignFrame.copy_actionPerformed(null);\r
1160   }\r
1161 \r
1162   public void cut_actionPerformed(ActionEvent e)\r
1163   {\r
1164     ap.alignFrame.cut_actionPerformed(null);\r
1165   }\r
1166 \r
1167   public void upperCase_actionPerformed(ActionEvent e)\r
1168   {\r
1169     SequenceGroup sg = ap.av.getSelectionGroup();\r
1170     if(sg==null)\r
1171       return;\r
1172 \r
1173     for(int g=0; g<sg.getSize(true); g++)\r
1174     {\r
1175     ( (SequenceI)sg.getSequences(true).elementAt(g))\r
1176         .changeCase(true, sg.getStartRes(), sg.getEndRes()+1);\r
1177     }\r
1178     ap.repaint();\r
1179   }\r
1180 \r
1181   public void lowerCase_actionPerformed(ActionEvent e)\r
1182   {\r
1183     SequenceGroup sg = ap.av.getSelectionGroup();\r
1184     if(sg==null)\r
1185       return;\r
1186 \r
1187     for(int g=0; g<sg.getSize(true); g++)\r
1188     {\r
1189        ( (SequenceI)sg.getSequences(true).elementAt(g))\r
1190            .changeCase(false, sg.getStartRes(), sg.getEndRes()+1);\r
1191     }\r
1192     ap.repaint();\r
1193   }\r
1194 \r
1195   public void toggle_actionPerformed(ActionEvent e)\r
1196   {\r
1197     SequenceGroup sg = ap.av.getSelectionGroup();\r
1198     if (sg == null)\r
1199       return;\r
1200 \r
1201     for (int g = 0; g < sg.getSize(true); g++)\r
1202     {\r
1203       ( (SequenceI)sg.getSequences(true).elementAt(g))\r
1204           .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);\r
1205     }\r
1206 \r
1207     ap.repaint();\r
1208   }\r
1209 \r
1210   public void outputText_actionPerformed(ActionEvent e)\r
1211   {\r
1212     CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
1213     Desktop.addInternalFrame(cap,\r
1214                              "Alignment output - " + e.getActionCommand(), 600,\r
1215                              500);\r
1216 \r
1217     String [] omitHidden = null;\r
1218 \r
1219     if(ap.av.hasHiddenColumns)\r
1220     {\r
1221       System.out.println("PROMPT USER HERE");\r
1222       omitHidden = ap.av.getViewAsString(true);\r
1223     }\r
1224 \r
1225     cap.setText(new FormatAdapter().formatSequences(\r
1226         e.getActionCommand(),\r
1227         ap.av.getSelectionAsNewSequence(),\r
1228         omitHidden));\r
1229   }\r
1230 \r
1231 \r
1232   public void pdbFromFile_actionPerformed(ActionEvent e)\r
1233   {\r
1234      jalview.io.JalviewFileChooser chooser\r
1235          = new jalview.io.JalviewFileChooser(jalview.bin.Cache.\r
1236          getProperty(\r
1237              "LAST_DIRECTORY"));\r
1238      chooser.setFileView(new jalview.io.JalviewFileView());\r
1239      chooser.setDialogTitle("Select a PDB file");\r
1240      chooser.setToolTipText("Load a PDB file");\r
1241 \r
1242      int value = chooser.showOpenDialog(null);\r
1243 \r
1244      if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
1245      {\r
1246        PDBEntry entry = new PDBEntry();\r
1247        String choice = chooser.getSelectedFile().getPath();\r
1248        jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
1249        try\r
1250        {\r
1251          MCview.PDBfile pdbfile = new MCview.PDBfile(choice,\r
1252                                        jalview.io.AppletFormatAdapter.FILE);\r
1253 \r
1254          if (pdbfile.id == null)\r
1255          {\r
1256            String reply = JOptionPane.showInternalInputDialog(\r
1257                Desktop.desktop,\r
1258                "Couldn't find a PDB id in the file supplied."\r
1259                + "Please enter an Id to identify this structure.",\r
1260                "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);\r
1261            if (reply == null)\r
1262              return;\r
1263 \r
1264            entry.setId(reply);\r
1265          }\r
1266          else\r
1267            entry.setId(pdbfile.id);\r
1268        }\r
1269        catch (java.io.IOException ex)\r
1270        {\r
1271          ex.printStackTrace();\r
1272        }\r
1273 \r
1274        entry.setFile(choice);\r
1275        sequence.getDatasetSequence().addPDBId(entry);\r
1276      }\r
1277 \r
1278   }\r
1279 \r
1280   public void enterPDB_actionPerformed(ActionEvent e)\r
1281   {\r
1282     int size = (ap.av.getSelectionGroup() == null ? 0 :\r
1283                 ap.av.getSelectionGroup().getSize(false));\r
1284 \r
1285     if (size == 0 || size > 1)\r
1286     {\r
1287       JOptionPane.showInternalMessageDialog(\r
1288           Desktop.desktop,\r
1289           "Select a single sequence to specify a PDB id for first",\r
1290           "Select Single Selected", JOptionPane.WARNING_MESSAGE);\r
1291       return;\r
1292     }\r
1293 \r
1294     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
1295         "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);\r
1296 \r
1297     if (id != null && id.length() > 0)\r
1298     {\r
1299       PDBEntry entry = new PDBEntry();\r
1300       entry.setId(id);\r
1301       ap.av.getSelectionGroup().getSequenceAt(0).getDatasetSequence()\r
1302           .addPDBId(entry);\r
1303     }\r
1304   }\r
1305 \r
1306   public void discoverPDB_actionPerformed(ActionEvent e)\r
1307   {\r
1308     new jalview.io.DBRefFetcher(\r
1309              ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);\r
1310   }\r
1311 }\r