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   JMenu outputMenu = new JMenu();\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()-1; 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           int start = Math.max(sequence.getName().length()-15, 0);\r
 148           sequenceMenu.setText(sequence.getName().substring(start));\r
 149 \r
 150           JMenuItem menuItem;\r
 151           if( seq.getDatasetSequence().getPDBId() != null)\r
 152           {\r
 153             java.util.Enumeration e = seq.getDatasetSequence().getPDBId().\r
 154                 elements();\r
 155 \r
 156             while (e.hasMoreElements())\r
 157             {\r
 158               final PDBEntry pdb = (PDBEntry) e.nextElement();\r
 159 \r
 160               menuItem = new JMenuItem();\r
 161               menuItem.setText("View PDB entry: " + pdb.getId());\r
 162               menuItem.addActionListener(new java.awt.event.ActionListener()\r
 163               {\r
 164                 public void actionPerformed(ActionEvent e)\r
 165                 {\r
 166                   new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);\r
 167                 }\r
 168               });\r
 169               sequenceMenu.add(menuItem);\r
 170             }\r
 171           }\r
 172 \r
 173           menuItem = new JMenuItem("Hide Sequences");\r
 174           menuItem.addActionListener(new java.awt.event.ActionListener()\r
 175               {\r
 176                 public void actionPerformed(ActionEvent e)\r
 177                 {\r
 178                   hideSequences(false);\r
 179                 }\r
 180               });\r
 181           add(menuItem);\r
 182 \r
 183           if(ap.av.getSelectionGroup() !=null\r
 184              && ap.av.getSelectionGroup().getSize(false)>1)\r
 185           {\r
 186             menuItem = new JMenuItem("Represent Group with " + seq.getName());\r
 187             menuItem.addActionListener(new java.awt.event.ActionListener()\r
 188             {\r
 189               public void actionPerformed(ActionEvent e)\r
 190               {\r
 191                 hideSequences(true);\r
 192               }\r
 193             });\r
 194             sequenceMenu.add(menuItem);\r
 195           }\r
 196 \r
 197           if (ap.av.hasHiddenRows)\r
 198           {\r
 199             final int index = ap.av.alignment.findIndex(seq);\r
 200 \r
 201             if (ap.av.adjustForHiddenSeqs(index) -\r
 202                 ap.av.adjustForHiddenSeqs(index - 1) > 1)\r
 203             {\r
 204               menuItem = new JMenuItem("Reveal Sequences");\r
 205               menuItem.addActionListener(new ActionListener()\r
 206               {\r
 207                 public void actionPerformed(ActionEvent e)\r
 208                 {\r
 209                   ap.av.showSequence(index);\r
 210                   ap.repaint();\r
 211                   if (ap.overviewPanel != null)\r
 212                     ap.overviewPanel.updateOverviewImage();\r
 213                 }\r
 214               });\r
 215               add(menuItem);\r
 216             }\r
 217 \r
 218             menuItem = new JMenuItem("Reveal All");\r
 219             menuItem.addActionListener(new ActionListener()\r
 220                 {\r
 221                   public void actionPerformed(ActionEvent e)\r
 222                   {\r
 223                     ap.av.showAllHiddenSeqs();\r
 224                     ap.repaint();\r
 225                     if (ap.overviewPanel != null)\r
 226                       ap.overviewPanel.updateOverviewImage();\r
 227                       }\r
 228                 });\r
 229 \r
 230             add(menuItem);\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 \r
 313 \r
 314         if (seq == null)\r
 315         {\r
 316             sequenceMenu.setVisible(false);\r
 317             pdbMenu.setVisible(false);\r
 318         }\r
 319 \r
 320         if(links != null && links.size()>0)\r
 321         {\r
 322           JMenu linkMenu = new JMenu("Link");\r
 323           JMenuItem item;\r
 324           for(int i=0; i<links.size(); i++)\r
 325           {\r
 326             String link = links.elementAt(i).toString();\r
 327             final String label = link.substring(0, link.indexOf("|"));\r
 328             item = new JMenuItem(label);\r
 329             final String url;\r
 330 \r
 331             if (link.indexOf("$SEQUENCE_ID$") > -1)\r
 332             {\r
 333               String id = seq.getName();\r
 334               if (id.indexOf("|") > -1)\r
 335                 id = id.substring(id.lastIndexOf("|") + 1);\r
 336 \r
 337               url = link.substring(link.indexOf("|") + 1,\r
 338                                    link.indexOf("$SEQUENCE_ID$"))\r
 339                   + id +\r
 340                   link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
 341             }\r
 342             else\r
 343               url = link.substring(link.lastIndexOf("|")+1);\r
 344 \r
 345 \r
 346             item.addActionListener(new java.awt.event.ActionListener()\r
 347             {\r
 348                 public void actionPerformed(ActionEvent e)\r
 349                 {\r
 350                     showLink(url);\r
 351                 }\r
 352             });\r
 353 \r
 354             linkMenu.add(item);\r
 355           }\r
 356           sequenceMenu.add(linkMenu);\r
 357         }\r
 358     }\r
 359 \r
 360 \r
 361     /**\r
 362      * DOCUMENT ME!\r
 363      *\r
 364      * @throws Exception DOCUMENT ME!\r
 365      */\r
 366     private void jbInit() throws Exception\r
 367     {\r
 368         groupMenu.setText("Group");\r
 369         groupMenu.setText("Selection");\r
 370         groupName.setText("Name");\r
 371         groupName.addActionListener(new java.awt.event.ActionListener()\r
 372             {\r
 373                 public void actionPerformed(ActionEvent e)\r
 374                 {\r
 375                     groupName_actionPerformed(e);\r
 376                 }\r
 377             });\r
 378         sequenceMenu.setText("Sequence");\r
 379         sequenceName.setText("Edit Name/Description");\r
 380         sequenceName.addActionListener(new java.awt.event.ActionListener()\r
 381             {\r
 382                 public void actionPerformed(ActionEvent e)\r
 383                 {\r
 384                     sequenceName_actionPerformed(e);\r
 385                 }\r
 386             });\r
 387         PIDColour.setFocusPainted(false);\r
 388         unGroupMenuItem.setText("Remove Group");\r
 389         unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 390             {\r
 391                 public void actionPerformed(ActionEvent e)\r
 392                 {\r
 393                     unGroupMenuItem_actionPerformed(e);\r
 394                 }\r
 395             });\r
 396 \r
 397         outline.setText("Border colour");\r
 398         outline.addActionListener(new java.awt.event.ActionListener()\r
 399             {\r
 400                 public void actionPerformed(ActionEvent e)\r
 401                 {\r
 402                     outline_actionPerformed(e);\r
 403                 }\r
 404             });\r
 405         nucleotideMenuItem.setText("Nucleotide");\r
 406         nucleotideMenuItem.addActionListener(new ActionListener()\r
 407             {\r
 408                 public void actionPerformed(ActionEvent e)\r
 409                 {\r
 410                     nucleotideMenuItem_actionPerformed(e);\r
 411                 }\r
 412             });\r
 413         colourMenu.setText("Group Colour");\r
 414         showBoxes.setText("Boxes");\r
 415         showBoxes.setState(true);\r
 416         showBoxes.addActionListener(new ActionListener()\r
 417             {\r
 418                 public void actionPerformed(ActionEvent e)\r
 419                 {\r
 420                     showBoxes_actionPerformed(e);\r
 421                 }\r
 422             });\r
 423         showText.setText("Text");\r
 424         showText.setState(true);\r
 425         showText.addActionListener(new ActionListener()\r
 426             {\r
 427                 public void actionPerformed(ActionEvent e)\r
 428                 {\r
 429                     showText_actionPerformed(e);\r
 430                 }\r
 431             });\r
 432         showColourText.setText("Colour Text");\r
 433         showColourText.addActionListener(new ActionListener()\r
 434             {\r
 435                 public void actionPerformed(ActionEvent e)\r
 436                 {\r
 437                     showColourText_actionPerformed(e);\r
 438                 }\r
 439             });\r
 440     editMenu.setText("Edit");\r
 441     cut.setText("Cut");\r
 442     cut.addActionListener(new ActionListener()\r
 443     {\r
 444       public void actionPerformed(ActionEvent e)\r
 445       {\r
 446         cut_actionPerformed(e);\r
 447       }\r
 448     });\r
 449     upperCase.setText("To Upper Case");\r
 450     upperCase.addActionListener(new ActionListener()\r
 451     {\r
 452       public void actionPerformed(ActionEvent e)\r
 453       {\r
 454         upperCase_actionPerformed(e);\r
 455       }\r
 456     });\r
 457     copy.setText("Copy");\r
 458     copy.addActionListener(new ActionListener()\r
 459     {\r
 460       public void actionPerformed(ActionEvent e)\r
 461       {\r
 462         copy_actionPerformed(e);\r
 463       }\r
 464     });\r
 465     lowerCase.setText("To Lower Case");\r
 466     lowerCase.addActionListener(new ActionListener()\r
 467     {\r
 468       public void actionPerformed(ActionEvent e)\r
 469       {\r
 470         lowerCase_actionPerformed(e);\r
 471       }\r
 472     });\r
 473     toggle.setText("Toggle Case");\r
 474     toggle.addActionListener(new ActionListener()\r
 475     {\r
 476       public void actionPerformed(ActionEvent e)\r
 477       {\r
 478         toggle_actionPerformed(e);\r
 479       }\r
 480     });\r
 481     pdbMenu.setText("Associate Structure with Sequence");\r
 482     pdbFromFile.setText("From File");\r
 483     pdbFromFile.addActionListener(new ActionListener()\r
 484     {\r
 485       public void actionPerformed(ActionEvent e)\r
 486       {\r
 487         pdbFromFile_actionPerformed(e);\r
 488       }\r
 489     });\r
 490     enterPDB.setText("Enter PDB Id");\r
 491     enterPDB.addActionListener(new ActionListener()\r
 492     {\r
 493       public void actionPerformed(ActionEvent e)\r
 494       {\r
 495         enterPDB_actionPerformed(e);\r
 496       }\r
 497     });\r
 498     discoverPDB.setText("Discover PDB ids");\r
 499     discoverPDB.addActionListener(new ActionListener()\r
 500     {\r
 501       public void actionPerformed(ActionEvent e)\r
 502       {\r
 503         discoverPDB_actionPerformed(e);\r
 504       }\r
 505     });\r
 506     outputMenu.setText("Output to Textbox...");\r
 507     add(groupMenu);\r
 508 \r
 509     add(sequenceMenu);\r
 510     groupMenu.add(editMenu);\r
 511     groupMenu.add(outputMenu);\r
 512     groupMenu.addSeparator();\r
 513     groupMenu.add(groupName);\r
 514     groupMenu.add(unGroupMenuItem);\r
 515         groupMenu.add(colourMenu);\r
 516     groupMenu.add(showBoxes);\r
 517         groupMenu.add(showText);\r
 518         groupMenu.add(showColourText);\r
 519     groupMenu.add(outline);\r
 520         sequenceMenu.add(sequenceName);\r
 521     sequenceMenu.add(pdbMenu);\r
 522     colourMenu.add(noColourmenuItem);\r
 523         colourMenu.add(clustalColour);\r
 524         colourMenu.add(BLOSUM62Colour);\r
 525         colourMenu.add(PIDColour);\r
 526         colourMenu.add(zappoColour);\r
 527         colourMenu.add(taylorColour);\r
 528         colourMenu.add(hydrophobicityColour);\r
 529         colourMenu.add(helixColour);\r
 530         colourMenu.add(strandColour);\r
 531         colourMenu.add(turnColour);\r
 532         colourMenu.add(buriedColour);\r
 533         colourMenu.add(nucleotideMenuItem);\r
 534         colourMenu.add(userDefinedColour);\r
 535 \r
 536         if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
 537         {\r
 538           java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 539               getUserColourSchemes().keys();\r
 540 \r
 541           while (userColours.hasMoreElements())\r
 542           {\r
 543             JMenuItem item = new JMenuItem(userColours.\r
 544                 nextElement().toString());\r
 545             item.addActionListener(new ActionListener()\r
 546             {\r
 547               public void actionPerformed(ActionEvent evt)\r
 548               {\r
 549                 userDefinedColour_actionPerformed(evt);\r
 550               }\r
 551             });\r
 552             colourMenu.add(item);\r
 553           }\r
 554         }\r
 555 \r
 556 \r
 557         colourMenu.addSeparator();\r
 558         colourMenu.add(abovePIDColour);\r
 559         colourMenu.add(conservationMenuItem);\r
 560     editMenu.add(copy);\r
 561     editMenu.add(cut);\r
 562     editMenu.add(upperCase);\r
 563     editMenu.add(lowerCase);\r
 564     editMenu.add(toggle);\r
 565     pdbMenu.add(pdbFromFile);\r
 566     pdbMenu.add(enterPDB);\r
 567     pdbMenu.add(discoverPDB);\r
 568     noColourmenuItem.setText("None");\r
 569         noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 570             {\r
 571                 public void actionPerformed(ActionEvent e)\r
 572                 {\r
 573                     noColourmenuItem_actionPerformed(e);\r
 574                 }\r
 575             });\r
 576 \r
 577         clustalColour.setText("Clustalx colours");\r
 578         clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 579             {\r
 580                 public void actionPerformed(ActionEvent e)\r
 581                 {\r
 582                     clustalColour_actionPerformed(e);\r
 583                 }\r
 584             });\r
 585         zappoColour.setText("Zappo");\r
 586         zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 587             {\r
 588                 public void actionPerformed(ActionEvent e)\r
 589                 {\r
 590                     zappoColour_actionPerformed(e);\r
 591                 }\r
 592             });\r
 593         taylorColour.setText("Taylor");\r
 594         taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 595             {\r
 596                 public void actionPerformed(ActionEvent e)\r
 597                 {\r
 598                     taylorColour_actionPerformed(e);\r
 599                 }\r
 600             });\r
 601         hydrophobicityColour.setText("Hydrophobicity");\r
 602         hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 603             {\r
 604                 public void actionPerformed(ActionEvent e)\r
 605                 {\r
 606                     hydrophobicityColour_actionPerformed(e);\r
 607                 }\r
 608             });\r
 609         helixColour.setText("Helix propensity");\r
 610         helixColour.addActionListener(new java.awt.event.ActionListener()\r
 611             {\r
 612                 public void actionPerformed(ActionEvent e)\r
 613                 {\r
 614                     helixColour_actionPerformed(e);\r
 615                 }\r
 616             });\r
 617         strandColour.setText("Strand propensity");\r
 618         strandColour.addActionListener(new java.awt.event.ActionListener()\r
 619             {\r
 620                 public void actionPerformed(ActionEvent e)\r
 621                 {\r
 622                     strandColour_actionPerformed(e);\r
 623                 }\r
 624             });\r
 625         turnColour.setText("Turn propensity");\r
 626         turnColour.addActionListener(new java.awt.event.ActionListener()\r
 627             {\r
 628                 public void actionPerformed(ActionEvent e)\r
 629                 {\r
 630                     turnColour_actionPerformed(e);\r
 631                 }\r
 632             });\r
 633         buriedColour.setText("Buried Index");\r
 634         buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 635             {\r
 636                 public void actionPerformed(ActionEvent e)\r
 637                 {\r
 638                     buriedColour_actionPerformed(e);\r
 639                 }\r
 640             });\r
 641         abovePIDColour.setText("Above % Identity");\r
 642         abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
 643             {\r
 644                 public void actionPerformed(ActionEvent e)\r
 645                 {\r
 646                     abovePIDColour_actionPerformed(e);\r
 647                 }\r
 648             });\r
 649         userDefinedColour.setText("User Defined...");\r
 650         userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 651             {\r
 652                 public void actionPerformed(ActionEvent e)\r
 653                 {\r
 654                     userDefinedColour_actionPerformed(e);\r
 655                 }\r
 656             });\r
 657         PIDColour.setText("Percentage Identity");\r
 658         PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 659             {\r
 660                 public void actionPerformed(ActionEvent e)\r
 661                 {\r
 662                     PIDColour_actionPerformed(e);\r
 663                 }\r
 664             });\r
 665         BLOSUM62Colour.setText("BLOSUM62");\r
 666         BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 667             {\r
 668                 public void actionPerformed(ActionEvent e)\r
 669                 {\r
 670                     BLOSUM62Colour_actionPerformed(e);\r
 671                 }\r
 672             });\r
 673         conservationMenuItem.setText("Conservation");\r
 674         conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 675             {\r
 676                 public void actionPerformed(ActionEvent e)\r
 677                 {\r
 678                     conservationMenuItem_actionPerformed(e);\r
 679                 }\r
 680             });\r
 681     }\r
 682 \r
 683     /**\r
 684      * DOCUMENT ME!\r
 685      */\r
 686     void refresh()\r
 687     {\r
 688         if (ap.overviewPanel != null)\r
 689           ap.overviewPanel.updateOverviewImage();\r
 690 \r
 691         ap.seqPanel.repaint();\r
 692     }\r
 693 \r
 694     /**\r
 695      * DOCUMENT ME!\r
 696      *\r
 697      * @param e DOCUMENT ME!\r
 698      */\r
 699     protected void clustalColour_actionPerformed(ActionEvent e)\r
 700     {\r
 701         SequenceGroup sg = getGroup();\r
 702         sg.cs = new ClustalxColourScheme(sg.getSequences(true),\r
 703                 ap.av.alignment.getWidth());\r
 704         refresh();\r
 705     }\r
 706 \r
 707     /**\r
 708      * DOCUMENT ME!\r
 709      *\r
 710      * @param e DOCUMENT ME!\r
 711      */\r
 712     protected void zappoColour_actionPerformed(ActionEvent e)\r
 713     {\r
 714         getGroup().cs = new ZappoColourScheme();\r
 715         refresh();\r
 716     }\r
 717 \r
 718     /**\r
 719      * DOCUMENT ME!\r
 720      *\r
 721      * @param e DOCUMENT ME!\r
 722      */\r
 723     protected void taylorColour_actionPerformed(ActionEvent e)\r
 724     {\r
 725         getGroup().cs = new TaylorColourScheme();\r
 726         refresh();\r
 727     }\r
 728 \r
 729     /**\r
 730      * DOCUMENT ME!\r
 731      *\r
 732      * @param e DOCUMENT ME!\r
 733      */\r
 734     protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 735     {\r
 736         getGroup().cs = new HydrophobicColourScheme();\r
 737         refresh();\r
 738     }\r
 739 \r
 740     /**\r
 741      * DOCUMENT ME!\r
 742      *\r
 743      * @param e DOCUMENT ME!\r
 744      */\r
 745     protected void helixColour_actionPerformed(ActionEvent e)\r
 746     {\r
 747         getGroup().cs = new HelixColourScheme();\r
 748         refresh();\r
 749     }\r
 750 \r
 751     /**\r
 752      * DOCUMENT ME!\r
 753      *\r
 754      * @param e DOCUMENT ME!\r
 755      */\r
 756     protected void strandColour_actionPerformed(ActionEvent e)\r
 757     {\r
 758         getGroup().cs = new StrandColourScheme();\r
 759         refresh();\r
 760     }\r
 761 \r
 762     /**\r
 763      * DOCUMENT ME!\r
 764      *\r
 765      * @param e DOCUMENT ME!\r
 766      */\r
 767     protected void turnColour_actionPerformed(ActionEvent e)\r
 768     {\r
 769         getGroup().cs = new TurnColourScheme();\r
 770         refresh();\r
 771     }\r
 772 \r
 773     /**\r
 774      * DOCUMENT ME!\r
 775      *\r
 776      * @param e DOCUMENT ME!\r
 777      */\r
 778     protected void buriedColour_actionPerformed(ActionEvent e)\r
 779     {\r
 780         getGroup().cs = new BuriedColourScheme();\r
 781         refresh();\r
 782     }\r
 783 \r
 784     /**\r
 785      * DOCUMENT ME!\r
 786      *\r
 787      * @param e DOCUMENT ME!\r
 788      */\r
 789     public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
 790     {\r
 791         getGroup().cs = new NucleotideColourScheme();\r
 792         refresh();\r
 793     }\r
 794 \r
 795     /**\r
 796      * DOCUMENT ME!\r
 797      *\r
 798      * @param e DOCUMENT ME!\r
 799      */\r
 800     protected void abovePIDColour_actionPerformed(ActionEvent e)\r
 801     {\r
 802         SequenceGroup sg = getGroup();\r
 803         if(sg.cs==null)\r
 804           return;\r
 805 \r
 806         if (abovePIDColour.isSelected())\r
 807         {\r
 808             sg.cs.setConsensus(AAFrequency.calculate(\r
 809                     sg.getSequences(true), 0,\r
 810                     ap.av.alignment.getWidth()));\r
 811 \r
 812             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
 813                     getGroup().getName());\r
 814 \r
 815            sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
 816 \r
 817             SliderPanel.showPIDSlider();\r
 818         }\r
 819         else // remove PIDColouring\r
 820         {\r
 821             sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
 822         }\r
 823 \r
 824         refresh();\r
 825     }\r
 826 \r
 827     /**\r
 828      * DOCUMENT ME!\r
 829      *\r
 830      * @param e DOCUMENT ME!\r
 831      */\r
 832     protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 833     {\r
 834        SequenceGroup sg = getGroup();\r
 835 \r
 836        if (e.getActionCommand().equals("User Defined..."))\r
 837          new UserDefinedColours(ap, sg);\r
 838        else\r
 839        {\r
 840          UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
 841              getUserColourSchemes().get(e.getActionCommand());\r
 842 \r
 843          sg.cs = udc;\r
 844        }\r
 845      }\r
 846     /**\r
 847      * DOCUMENT ME!\r
 848      *\r
 849      * @param e DOCUMENT ME!\r
 850      */\r
 851     protected void PIDColour_actionPerformed(ActionEvent e)\r
 852     {\r
 853         SequenceGroup sg = getGroup();\r
 854         sg.cs = new PIDColourScheme();\r
 855         sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
 856                 ap.av.alignment.getWidth()));\r
 857         refresh();\r
 858     }\r
 859 \r
 860     /**\r
 861      * DOCUMENT ME!\r
 862      *\r
 863      * @param e DOCUMENT ME!\r
 864      */\r
 865     protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 866     {\r
 867         SequenceGroup sg = getGroup();\r
 868 \r
 869         sg.cs = new Blosum62ColourScheme();\r
 870 \r
 871         sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
 872                 ap.av.alignment.getWidth()));\r
 873 \r
 874         refresh();\r
 875     }\r
 876 \r
 877     /**\r
 878      * DOCUMENT ME!\r
 879      *\r
 880      * @param e DOCUMENT ME!\r
 881      */\r
 882     protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 883     {\r
 884         getGroup().cs = null;\r
 885         refresh();\r
 886     }\r
 887 \r
 888     /**\r
 889      * DOCUMENT ME!\r
 890      *\r
 891      * @param e DOCUMENT ME!\r
 892      */\r
 893     protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
 894     {\r
 895         SequenceGroup sg = getGroup();\r
 896         if(sg.cs==null)\r
 897           return;\r
 898 \r
 899         if (conservationMenuItem.isSelected())\r
 900         {\r
 901             Conservation c = new Conservation("Group",\r
 902                     ResidueProperties.propHash, 3,\r
 903                     sg.getSequences(true), 0,\r
 904                     ap.av.alignment.getWidth());\r
 905 \r
 906             c.calculate();\r
 907             c.verdict(false, ap.av.ConsPercGaps);\r
 908 \r
 909             sg.cs.setConservation(c);\r
 910 \r
 911             SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
 912             SliderPanel.showConservationSlider();\r
 913         }\r
 914         else // remove ConservationColouring\r
 915         {\r
 916             sg.cs.setConservation(null);\r
 917         }\r
 918 \r
 919         refresh();\r
 920     }\r
 921 \r
 922     /**\r
 923      * DOCUMENT ME!\r
 924      *\r
 925      * @param e DOCUMENT ME!\r
 926      */\r
 927     protected void groupName_actionPerformed(ActionEvent e)\r
 928     {\r
 929         SequenceGroup sg = getGroup();\r
 930         String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
 931                 "Enter new group name", "Edit group name",\r
 932                 JOptionPane.QUESTION_MESSAGE);\r
 933 \r
 934         if (reply == null)\r
 935         {\r
 936             return;\r
 937         }\r
 938 \r
 939         sg.setName(reply);\r
 940         groupName.setText(reply);\r
 941     }\r
 942 \r
 943     /**\r
 944      * DOCUMENT ME!\r
 945      *\r
 946      * @param e DOCUMENT ME!\r
 947      */\r
 948     protected void analyze_actionPerformed(ActionEvent e)\r
 949     {\r
 950         CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
 951         JInternalFrame frame = new JInternalFrame();\r
 952         frame.setContentPane(cap);\r
 953         Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
 954 \r
 955         SequenceGroup sg = getGroup();\r
 956         StringBuffer sb = new StringBuffer();\r
 957 \r
 958         for (int i = 0; i < sg.getSize(false); i++)\r
 959         {\r
 960             Sequence tmp = (Sequence) sg.getSequences(false).elementAt(i);\r
 961             sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
 962             sb.append("\n");\r
 963         }\r
 964 \r
 965         sb.append("Something amazing will happen soon");\r
 966         cap.setText(sb.toString());\r
 967     }\r
 968 \r
 969     /**\r
 970      * DOCUMENT ME!\r
 971      *\r
 972      * @return DOCUMENT ME!\r
 973      */\r
 974     SequenceGroup getGroup()\r
 975     {\r
 976         SequenceGroup sg = ap.av.getSelectionGroup();\r
 977       // this method won't add a new group if it already exists\r
 978         if(sg!=null)\r
 979           ap.av.alignment.addGroup(sg);\r
 980 \r
 981         return sg;\r
 982     }\r
 983 \r
 984     /**\r
 985      * DOCUMENT ME!\r
 986      *\r
 987      * @param e DOCUMENT ME!\r
 988      */\r
 989     void sequenceName_actionPerformed(ActionEvent e)\r
 990     {\r
 991       JLabel idlabel = new JLabel(  "       Sequence Name ");\r
 992       JLabel desclabel = new JLabel("Sequence Description ");\r
 993       idlabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
 994       desclabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
 995       JTextField id = new JTextField(sequence.getName(), 40);\r
 996       JTextField description = new JTextField(sequence.getDescription(), 40);\r
 997       JPanel panel = new JPanel(new BorderLayout());\r
 998       JPanel panel2 = new JPanel(new BorderLayout());\r
 999       panel2.add(idlabel, BorderLayout.WEST);\r
1000       panel2.add(id, BorderLayout.CENTER);\r
1001       panel.add(panel2, BorderLayout.NORTH);\r
1002       panel2 = new JPanel(new BorderLayout());\r
1003       panel2.add(desclabel, BorderLayout.WEST);\r
1004       panel2.add(description, BorderLayout.CENTER);\r
1005       panel.add(panel2, BorderLayout.SOUTH);\r
1006 \r
1007 \r
1008        int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
1009           panel, "Edit Sequence Name/Description",\r
1010           JOptionPane.OK_CANCEL_OPTION );\r
1011 \r
1012 \r
1013         if (reply != JOptionPane.OK_OPTION )\r
1014         {\r
1015             return;\r
1016         }\r
1017 \r
1018         String s = id.getText();\r
1019 \r
1020         if (s != null)\r
1021         {\r
1022             if (s.indexOf(" ") > -1)\r
1023             {\r
1024                 JOptionPane.showMessageDialog(ap,\r
1025                     "Spaces have been converted to \"_\"",\r
1026                     "No spaces allowed in Sequence Name",\r
1027                     JOptionPane.WARNING_MESSAGE);\r
1028             }\r
1029 \r
1030             s = s.replace(' ', '_');\r
1031             sequence.getDatasetSequence().setName(s);\r
1032             sequence.setName(s);\r
1033             ap.repaint();\r
1034         }\r
1035 \r
1036         sequence.getDatasetSequence().setDescription(description.getText());\r
1037         sequence.setDescription(description.getText());\r
1038     }\r
1039 \r
1040     /**\r
1041      * DOCUMENT ME!\r
1042      *\r
1043      * @param e DOCUMENT ME!\r
1044      */\r
1045     void unGroupMenuItem_actionPerformed(ActionEvent e)\r
1046     {\r
1047         SequenceGroup sg = ap.av.getSelectionGroup();\r
1048         ap.av.alignment.deleteGroup(sg);\r
1049         ap.av.setSelectionGroup(null);\r
1050         refresh();\r
1051     }\r
1052 \r
1053 \r
1054     /**\r
1055      * DOCUMENT ME!\r
1056      *\r
1057      * @param e DOCUMENT ME!\r
1058      */\r
1059     protected void outline_actionPerformed(ActionEvent e)\r
1060     {\r
1061         SequenceGroup sg = getGroup();\r
1062         Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
1063                 Color.BLUE);\r
1064 \r
1065         if (col != null)\r
1066         {\r
1067             sg.setOutlineColour(col);\r
1068         }\r
1069 \r
1070         refresh();\r
1071     }\r
1072 \r
1073     /**\r
1074      * DOCUMENT ME!\r
1075      *\r
1076      * @param e DOCUMENT ME!\r
1077      */\r
1078     public void showBoxes_actionPerformed(ActionEvent e)\r
1079     {\r
1080         getGroup().setDisplayBoxes(showBoxes.isSelected());\r
1081         refresh();\r
1082     }\r
1083 \r
1084     /**\r
1085      * DOCUMENT ME!\r
1086      *\r
1087      * @param e DOCUMENT ME!\r
1088      */\r
1089     public void showText_actionPerformed(ActionEvent e)\r
1090     {\r
1091         getGroup().setDisplayText(showText.isSelected());\r
1092         refresh();\r
1093     }\r
1094 \r
1095     /**\r
1096      * DOCUMENT ME!\r
1097      *\r
1098      * @param e DOCUMENT ME!\r
1099      */\r
1100     public void showColourText_actionPerformed(ActionEvent e)\r
1101     {\r
1102         getGroup().setColourText(showColourText.isSelected());\r
1103         refresh();\r
1104     }\r
1105 \r
1106     public void showLink(String url)\r
1107     {\r
1108       try\r
1109       {\r
1110         jalview.util.BrowserLauncher.openURL(url);\r
1111       }\r
1112       catch (Exception ex)\r
1113       {\r
1114         JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
1115             "Unixers: Couldn't find default web browser."\r
1116            +"\nAdd the full path to your browser in Preferences.",\r
1117            "Web browser not found", JOptionPane.WARNING_MESSAGE );\r
1118 \r
1119 \r
1120         ex.printStackTrace();\r
1121       }\r
1122     }\r
1123 \r
1124     void hideSequences(boolean representGroup)\r
1125     {\r
1126       SequenceGroup sg = ap.av.getSelectionGroup();\r
1127       if(sg==null || sg.getSize(false)<1)\r
1128       {\r
1129         ap.av.hideSequence(sequence);\r
1130         return;\r
1131       }\r
1132 \r
1133         int index = 0;\r
1134         while(index < sg.getSize(false))\r
1135         {\r
1136           if(representGroup && sg.getSequenceAt(index)!=sequence)\r
1137           {\r
1138             sequence.addHiddenSequence(sg.getSequenceAt(index));\r
1139             ap.av.hideSequence(sg.getSequenceAt(index));\r
1140           }\r
1141           else if(!representGroup)\r
1142           {\r
1143             ap.av.hideSequence(sg.getSequenceAt(index));\r
1144           }\r
1145           index ++;\r
1146         }\r
1147 \r
1148         ap.av.setSelectionGroup(null);\r
1149         ap.repaint();\r
1150         refresh();\r
1151     }\r
1152 \r
1153   public void copy_actionPerformed(ActionEvent e)\r
1154   {\r
1155     ap.alignFrame.copy_actionPerformed(null);\r
1156   }\r
1157 \r
1158   public void cut_actionPerformed(ActionEvent e)\r
1159   {\r
1160     ap.alignFrame.cut_actionPerformed(null);\r
1161   }\r
1162 \r
1163   public void upperCase_actionPerformed(ActionEvent e)\r
1164   {\r
1165     SequenceGroup sg = ap.av.getSelectionGroup();\r
1166     if(sg==null)\r
1167       return;\r
1168 \r
1169     for(int g=0; g<sg.getSize(true); g++)\r
1170     {\r
1171     ( (SequenceI)sg.getSequences(true).elementAt(g))\r
1172         .changeCase(true, sg.getStartRes(), sg.getEndRes()+1);\r
1173     }\r
1174     ap.repaint();\r
1175   }\r
1176 \r
1177   public void lowerCase_actionPerformed(ActionEvent e)\r
1178   {\r
1179     SequenceGroup sg = ap.av.getSelectionGroup();\r
1180     if(sg==null)\r
1181       return;\r
1182 \r
1183     for(int g=0; g<sg.getSize(true); g++)\r
1184     {\r
1185        ( (SequenceI)sg.getSequences(true).elementAt(g))\r
1186            .changeCase(false, sg.getStartRes(), sg.getEndRes()+1);\r
1187     }\r
1188     ap.repaint();\r
1189   }\r
1190 \r
1191   public void toggle_actionPerformed(ActionEvent e)\r
1192   {\r
1193     SequenceGroup sg = ap.av.getSelectionGroup();\r
1194     if (sg == null)\r
1195       return;\r
1196 \r
1197     for (int g = 0; g < sg.getSize(true); g++)\r
1198     {\r
1199       ( (SequenceI)sg.getSequences(true).elementAt(g))\r
1200           .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);\r
1201     }\r
1202 \r
1203     ap.repaint();\r
1204   }\r
1205 \r
1206   public void outputText_actionPerformed(ActionEvent e)\r
1207   {\r
1208     CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
1209     Desktop.addInternalFrame(cap,\r
1210                              "Alignment output - " + e.getActionCommand(), 600,\r
1211                              500);\r
1212 \r
1213     String [] omitHidden = null;\r
1214 \r
1215     if(ap.av.hasHiddenColumns)\r
1216     {\r
1217       System.out.println("PROMPT USER HERE");\r
1218       omitHidden = ap.av.getViewAsString(true);\r
1219     }\r
1220 \r
1221     cap.setText(new FormatAdapter().formatSequences(\r
1222         e.getActionCommand(),\r
1223         ap.av.getSelectionAsNewSequence(),\r
1224         omitHidden));\r
1225   }\r
1226 \r
1227 \r
1228   public void pdbFromFile_actionPerformed(ActionEvent e)\r
1229   {\r
1230      jalview.io.JalviewFileChooser chooser\r
1231          = new jalview.io.JalviewFileChooser(jalview.bin.Cache.\r
1232          getProperty(\r
1233              "LAST_DIRECTORY"));\r
1234      chooser.setFileView(new jalview.io.JalviewFileView());\r
1235      chooser.setDialogTitle("Select a PDB file");\r
1236      chooser.setToolTipText("Load a PDB file");\r
1237 \r
1238      int value = chooser.showOpenDialog(null);\r
1239 \r
1240      if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
1241      {\r
1242        PDBEntry entry = new PDBEntry();\r
1243        String choice = chooser.getSelectedFile().getPath();\r
1244        jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
1245        try\r
1246        {\r
1247          MCview.PDBfile pdbfile = new MCview.PDBfile(choice,\r
1248                                        jalview.io.AppletFormatAdapter.FILE);\r
1249 \r
1250          if (pdbfile.id == null)\r
1251          {\r
1252            String reply = JOptionPane.showInternalInputDialog(\r
1253                Desktop.desktop,\r
1254                "Couldn't find a PDB id in the file supplied."\r
1255                + "Please enter an Id to identify this structure.",\r
1256                "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);\r
1257            if (reply == null)\r
1258              return;\r
1259 \r
1260            entry.setId(reply);\r
1261          }\r
1262          else\r
1263            entry.setId(pdbfile.id);\r
1264        }\r
1265        catch (java.io.IOException ex)\r
1266        {\r
1267          ex.printStackTrace();\r
1268        }\r
1269 \r
1270        entry.setFile(choice);\r
1271        sequence.getDatasetSequence().addPDBId(entry);\r
1272      }\r
1273 \r
1274   }\r
1275 \r
1276   public void enterPDB_actionPerformed(ActionEvent e)\r
1277   {\r
1278     int size = (ap.av.getSelectionGroup() == null ? 0 :\r
1279                 ap.av.getSelectionGroup().getSize(false));\r
1280 \r
1281     if (size == 0 || size > 1)\r
1282     {\r
1283       JOptionPane.showInternalMessageDialog(\r
1284           Desktop.desktop,\r
1285           "Select a single sequence to specify a PDB id for first",\r
1286           "Select Single Selected", JOptionPane.WARNING_MESSAGE);\r
1287       return;\r
1288     }\r
1289 \r
1290     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
1291         "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);\r
1292 \r
1293     if (id != null && id.length() > 0)\r
1294     {\r
1295       PDBEntry entry = new PDBEntry();\r
1296       entry.setId(id);\r
1297       ap.av.getSelectionGroup().getSequenceAt(0).getDatasetSequence()\r
1298           .addPDBId(entry);\r
1299     }\r
1300   }\r
1301 \r
1302   public void discoverPDB_actionPerformed(ActionEvent e)\r
1303   {\r
1304     new jalview.io.DBRefFetcher(\r
1305              ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);\r
1306   }\r
1307 }\r