src/jalview/gui/PopupMenu.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2006 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 import jalview.datamodel.*;\r
  25 import jalview.schemes.*;\r
  26 import jalview.commands.ChangeCaseCommand;\r
  27 \r
  28 import java.awt.*;\r
  29 import java.awt.event.*;\r
  30 \r
  31 import javax.swing.*;\r
  32 \r
  33 import java.util.Vector;\r
  34 import jalview.io.FormatAdapter;\r
  35 \r
  36 \r
  37 /**\r
  38  * DOCUMENT ME!\r
  39  *\r
  40  * @author $author$\r
  41  * @version $Revision$\r
  42  */\r
  43 public class PopupMenu extends JPopupMenu\r
  44 {\r
  45     JMenu groupMenu = new JMenu();\r
  46     JMenuItem groupName = new JMenuItem();\r
  47     protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  48     protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  49     protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  50     protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
  51     protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  52     protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  53     protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  54     protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  55     protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();\r
  56     protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  57     protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  58     protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  59     JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  60     protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  61     AlignmentPanel ap;\r
  62     JMenu sequenceMenu = new JMenu();\r
  63     JMenuItem sequenceName = new JMenuItem();\r
  64     Sequence sequence;\r
  65     JMenuItem unGroupMenuItem = new JMenuItem();\r
  66     JMenuItem outline = new JMenuItem();\r
  67     JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();\r
  68     JMenu colourMenu = new JMenu();\r
  69     JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();\r
  70     JCheckBoxMenuItem showText = new JCheckBoxMenuItem();\r
  71     JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();\r
  72   JMenu editMenu = new JMenu();\r
  73   JMenuItem cut = new JMenuItem();\r
  74   JMenuItem copy = new JMenuItem();\r
  75   JMenuItem upperCase = new JMenuItem();\r
  76   JMenuItem lowerCase = new JMenuItem();\r
  77   JMenuItem toggle = new JMenuItem();\r
  78   JMenu pdbMenu = new JMenu();\r
  79   JMenuItem pdbFromFile = new JMenuItem();\r
  80   JMenuItem enterPDB = new JMenuItem();\r
  81   JMenuItem discoverPDB = new JMenuItem();\r
  82   JMenu outputMenu = new JMenu();\r
  83   JMenuItem sequenceFeature = new JMenuItem();\r
  84 \r
  85   /**\r
  86      * Creates a new PopupMenu object.\r
  87      *\r
  88      * @param ap DOCUMENT ME!\r
  89      * @param seq DOCUMENT ME!\r
  90      */\r
  91     public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)\r
  92     {\r
  93         ///////////////////////////////////////////////////////////\r
  94         // If this is activated from the sequence panel, the user may want to\r
  95         // edit or annotate a particular residue. Therefore display the residue menu\r
  96         //\r
  97         // If from the IDPanel, we must display the sequence menu\r
  98         //////////////////////////////////////////////////////////\r
  99         this.ap = ap;\r
 100         sequence = seq;\r
 101 \r
 102         ButtonGroup colours = new ButtonGroup();\r
 103         colours.add(noColourmenuItem);\r
 104         colours.add(clustalColour);\r
 105         colours.add(zappoColour);\r
 106         colours.add(taylorColour);\r
 107         colours.add(hydrophobicityColour);\r
 108         colours.add(helixColour);\r
 109         colours.add(strandColour);\r
 110         colours.add(turnColour);\r
 111         colours.add(buriedColour);\r
 112         colours.add(abovePIDColour);\r
 113         colours.add(userDefinedColour);\r
 114         colours.add(PIDColour);\r
 115         colours.add(BLOSUM62Colour);\r
 116 \r
 117         for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)\r
 118         {\r
 119           JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );\r
 120 \r
 121           item.addActionListener(new java.awt.event.ActionListener()\r
 122           {\r
 123             public void actionPerformed(ActionEvent e)\r
 124             {\r
 125               outputText_actionPerformed(e);\r
 126             }\r
 127           });\r
 128 \r
 129           outputMenu.add(item);\r
 130         }\r
 131 \r
 132 \r
 133         try\r
 134         {\r
 135             jbInit();\r
 136         }\r
 137         catch (Exception e)\r
 138         {\r
 139             e.printStackTrace();\r
 140         }\r
 141 \r
 142 \r
 143         if (seq != null)\r
 144         {\r
 145           sequenceMenu.setText(sequence.getName());\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           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 Sequences");\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                   if (ap.overviewPanel != null)\r
 208                     ap.overviewPanel.updateOverviewImage();\r
 209                 }\r
 210               });\r
 211               add(menuItem);\r
 212             }\r
 213 \r
 214             menuItem = new JMenuItem("Reveal All");\r
 215             menuItem.addActionListener(new ActionListener()\r
 216                 {\r
 217                   public void actionPerformed(ActionEvent e)\r
 218                   {\r
 219                     ap.av.showAllHiddenSeqs();\r
 220                     if (ap.overviewPanel != null)\r
 221                       ap.overviewPanel.updateOverviewImage();\r
 222                     }\r
 223                 });\r
 224 \r
 225             add(menuItem);\r
 226           }\r
 227 \r
 228 \r
 229         }\r
 230 \r
 231 \r
 232 \r
 233         SequenceGroup sg = ap.av.getSelectionGroup();\r
 234 \r
 235         if (sg != null)\r
 236         {\r
 237             groupName.setText(sg.getName());\r
 238 \r
 239             if (sg.cs instanceof ZappoColourScheme)\r
 240             {\r
 241                 zappoColour.setSelected(true);\r
 242             }\r
 243             else if (sg.cs instanceof TaylorColourScheme)\r
 244             {\r
 245                 taylorColour.setSelected(true);\r
 246             }\r
 247             else if (sg.cs instanceof PIDColourScheme)\r
 248             {\r
 249                 PIDColour.setSelected(true);\r
 250             }\r
 251             else if (sg.cs instanceof Blosum62ColourScheme)\r
 252             {\r
 253                 BLOSUM62Colour.setSelected(true);\r
 254             }\r
 255             else if (sg.cs instanceof UserColourScheme)\r
 256             {\r
 257                 userDefinedColour.setSelected(true);\r
 258             }\r
 259             else if (sg.cs instanceof HydrophobicColourScheme)\r
 260             {\r
 261                 hydrophobicityColour.setSelected(true);\r
 262             }\r
 263             else if (sg.cs instanceof HelixColourScheme)\r
 264             {\r
 265                 helixColour.setSelected(true);\r
 266             }\r
 267             else if (sg.cs instanceof StrandColourScheme)\r
 268             {\r
 269                 strandColour.setSelected(true);\r
 270             }\r
 271             else if (sg.cs instanceof TurnColourScheme)\r
 272             {\r
 273                 turnColour.setSelected(true);\r
 274             }\r
 275             else if (sg.cs instanceof BuriedColourScheme)\r
 276             {\r
 277                 buriedColour.setSelected(true);\r
 278             }\r
 279             else if (sg.cs instanceof ClustalxColourScheme)\r
 280             {\r
 281                 clustalColour.setSelected(true);\r
 282             }\r
 283             else\r
 284             {\r
 285                 noColourmenuItem.setSelected(true);\r
 286             }\r
 287 \r
 288             if (sg.cs!=null && sg.cs.conservationApplied())\r
 289             {\r
 290                 conservationMenuItem.setSelected(true);\r
 291             }\r
 292 \r
 293             showText.setSelected(sg.getDisplayText());\r
 294             showColourText.setSelected(sg.getColourText());\r
 295             showBoxes.setSelected(sg.getDisplayBoxes());\r
 296         }\r
 297         else\r
 298         {\r
 299           groupMenu.setVisible(false);\r
 300           editMenu.setVisible(false);\r
 301         }\r
 302 \r
 303         if (!ap.av.alignment.getGroups().contains(sg))\r
 304         {\r
 305             unGroupMenuItem.setVisible(false);\r
 306         }\r
 307 \r
 308 \r
 309         if (seq == null)\r
 310         {\r
 311             sequenceMenu.setVisible(false);\r
 312             pdbMenu.setVisible(false);\r
 313         }\r
 314 \r
 315         if(links != null && links.size()>0)\r
 316         {\r
 317           JMenu linkMenu = new JMenu("Link");\r
 318           JMenuItem item;\r
 319           for(int i=0; i<links.size(); i++)\r
 320           {\r
 321             String link = links.elementAt(i).toString();\r
 322             final String label = link.substring(0, link.indexOf("|"));\r
 323             item = new JMenuItem(label);\r
 324             final String url;\r
 325 \r
 326             if (link.indexOf("$SEQUENCE_ID$") > -1)\r
 327             {\r
 328               String id = seq.getName();\r
 329               if (id.indexOf("|") > -1)\r
 330                 id = id.substring(id.lastIndexOf("|") + 1);\r
 331 \r
 332               url = link.substring(link.indexOf("|") + 1,\r
 333                                    link.indexOf("$SEQUENCE_ID$"))\r
 334                   + id +\r
 335                   link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
 336             }\r
 337             else\r
 338               url = link.substring(link.lastIndexOf("|")+1);\r
 339 \r
 340 \r
 341             item.addActionListener(new java.awt.event.ActionListener()\r
 342             {\r
 343                 public void actionPerformed(ActionEvent e)\r
 344                 {\r
 345                     showLink(url);\r
 346                 }\r
 347             });\r
 348 \r
 349             linkMenu.add(item);\r
 350           }\r
 351           if(sequence!=null)\r
 352             sequenceMenu.add(linkMenu);\r
 353           else\r
 354             add(linkMenu);\r
 355         }\r
 356     }\r
 357 \r
 358 \r
 359     /**\r
 360      * DOCUMENT ME!\r
 361      *\r
 362      * @throws Exception DOCUMENT ME!\r
 363      */\r
 364     private void jbInit() throws Exception\r
 365     {\r
 366         groupMenu.setText("Group");\r
 367         groupMenu.setText("Selection");\r
 368         groupName.setText("Name");\r
 369         groupName.addActionListener(new java.awt.event.ActionListener()\r
 370             {\r
 371                 public void actionPerformed(ActionEvent e)\r
 372                 {\r
 373                     groupName_actionPerformed(e);\r
 374                 }\r
 375             });\r
 376         sequenceMenu.setText("Sequence");\r
 377         sequenceName.setText("Edit Name/Description");\r
 378         sequenceName.addActionListener(new java.awt.event.ActionListener()\r
 379             {\r
 380                 public void actionPerformed(ActionEvent e)\r
 381                 {\r
 382                     sequenceName_actionPerformed(e);\r
 383                 }\r
 384             });\r
 385         PIDColour.setFocusPainted(false);\r
 386         unGroupMenuItem.setText("Remove Group");\r
 387         unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 388             {\r
 389                 public void actionPerformed(ActionEvent e)\r
 390                 {\r
 391                     unGroupMenuItem_actionPerformed(e);\r
 392                 }\r
 393             });\r
 394 \r
 395         outline.setText("Border colour");\r
 396         outline.addActionListener(new java.awt.event.ActionListener()\r
 397             {\r
 398                 public void actionPerformed(ActionEvent e)\r
 399                 {\r
 400                     outline_actionPerformed(e);\r
 401                 }\r
 402             });\r
 403         nucleotideMenuItem.setText("Nucleotide");\r
 404         nucleotideMenuItem.addActionListener(new ActionListener()\r
 405             {\r
 406                 public void actionPerformed(ActionEvent e)\r
 407                 {\r
 408                     nucleotideMenuItem_actionPerformed(e);\r
 409                 }\r
 410             });\r
 411         colourMenu.setText("Group Colour");\r
 412         showBoxes.setText("Boxes");\r
 413         showBoxes.setState(true);\r
 414         showBoxes.addActionListener(new ActionListener()\r
 415             {\r
 416                 public void actionPerformed(ActionEvent e)\r
 417                 {\r
 418                     showBoxes_actionPerformed(e);\r
 419                 }\r
 420             });\r
 421         showText.setText("Text");\r
 422         showText.setState(true);\r
 423         showText.addActionListener(new ActionListener()\r
 424             {\r
 425                 public void actionPerformed(ActionEvent e)\r
 426                 {\r
 427                     showText_actionPerformed(e);\r
 428                 }\r
 429             });\r
 430         showColourText.setText("Colour Text");\r
 431         showColourText.addActionListener(new ActionListener()\r
 432             {\r
 433                 public void actionPerformed(ActionEvent e)\r
 434                 {\r
 435                     showColourText_actionPerformed(e);\r
 436                 }\r
 437             });\r
 438     editMenu.setText("Edit");\r
 439     cut.setText("Cut");\r
 440     cut.addActionListener(new ActionListener()\r
 441     {\r
 442       public void actionPerformed(ActionEvent e)\r
 443       {\r
 444         cut_actionPerformed(e);\r
 445       }\r
 446     });\r
 447     upperCase.setText("To Upper Case");\r
 448     upperCase.addActionListener(new ActionListener()\r
 449     {\r
 450       public void actionPerformed(ActionEvent e)\r
 451       {\r
 452         changeCase(e);\r
 453       }\r
 454     });\r
 455     copy.setText("Copy");\r
 456     copy.addActionListener(new ActionListener()\r
 457     {\r
 458       public void actionPerformed(ActionEvent e)\r
 459       {\r
 460         copy_actionPerformed(e);\r
 461       }\r
 462     });\r
 463     lowerCase.setText("To Lower Case");\r
 464     lowerCase.addActionListener(new ActionListener()\r
 465     {\r
 466       public void actionPerformed(ActionEvent e)\r
 467       {\r
 468         changeCase(e);\r
 469       }\r
 470     });\r
 471     toggle.setText("Toggle Case");\r
 472     toggle.addActionListener(new ActionListener()\r
 473     {\r
 474       public void actionPerformed(ActionEvent e)\r
 475       {\r
 476         changeCase(e);\r
 477       }\r
 478     });\r
 479     pdbMenu.setText("Associate Structure with Sequence");\r
 480     pdbFromFile.setText("From File");\r
 481     pdbFromFile.addActionListener(new ActionListener()\r
 482     {\r
 483       public void actionPerformed(ActionEvent e)\r
 484       {\r
 485         pdbFromFile_actionPerformed(e);\r
 486       }\r
 487     });\r
 488     enterPDB.setText("Enter PDB Id");\r
 489     enterPDB.addActionListener(new ActionListener()\r
 490     {\r
 491       public void actionPerformed(ActionEvent e)\r
 492       {\r
 493         enterPDB_actionPerformed(e);\r
 494       }\r
 495     });\r
 496     discoverPDB.setText("Discover PDB ids");\r
 497     discoverPDB.addActionListener(new ActionListener()\r
 498     {\r
 499       public void actionPerformed(ActionEvent e)\r
 500       {\r
 501         discoverPDB_actionPerformed(e);\r
 502       }\r
 503     });\r
 504     outputMenu.setText("Output to Textbox...");\r
 505     sequenceFeature.setText("Create Sequence Feature");\r
 506     sequenceFeature.addActionListener(new ActionListener()\r
 507     {\r
 508       public void actionPerformed(ActionEvent e)\r
 509       {\r
 510         sequenceFeature_actionPerformed(e);\r
 511       }\r
 512     });\r
 513     add(groupMenu);\r
 514 \r
 515     add(sequenceMenu);\r
 516     groupMenu.add(editMenu);\r
 517     groupMenu.add(outputMenu);\r
 518     groupMenu.addSeparator();\r
 519     groupMenu.add(sequenceFeature);\r
 520     groupMenu.addSeparator();\r
 521     groupMenu.add(groupName);\r
 522     groupMenu.add(unGroupMenuItem);\r
 523     groupMenu.add(colourMenu);\r
 524     groupMenu.add(showBoxes);\r
 525     groupMenu.add(showText);\r
 526     groupMenu.add(showColourText);\r
 527     groupMenu.add(outline);\r
 528     sequenceMenu.add(sequenceName);\r
 529     sequenceMenu.add(pdbMenu);\r
 530     colourMenu.add(noColourmenuItem);\r
 531         colourMenu.add(clustalColour);\r
 532         colourMenu.add(BLOSUM62Colour);\r
 533         colourMenu.add(PIDColour);\r
 534         colourMenu.add(zappoColour);\r
 535         colourMenu.add(taylorColour);\r
 536         colourMenu.add(hydrophobicityColour);\r
 537         colourMenu.add(helixColour);\r
 538         colourMenu.add(strandColour);\r
 539         colourMenu.add(turnColour);\r
 540         colourMenu.add(buriedColour);\r
 541         colourMenu.add(nucleotideMenuItem);\r
 542         colourMenu.add(userDefinedColour);\r
 543 \r
 544         if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
 545         {\r
 546           java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 547               getUserColourSchemes().keys();\r
 548 \r
 549           while (userColours.hasMoreElements())\r
 550           {\r
 551             JMenuItem item = new JMenuItem(userColours.\r
 552                 nextElement().toString());\r
 553             item.addActionListener(new ActionListener()\r
 554             {\r
 555               public void actionPerformed(ActionEvent evt)\r
 556               {\r
 557                 userDefinedColour_actionPerformed(evt);\r
 558               }\r
 559             });\r
 560             colourMenu.add(item);\r
 561           }\r
 562         }\r
 563 \r
 564 \r
 565         colourMenu.addSeparator();\r
 566         colourMenu.add(abovePIDColour);\r
 567         colourMenu.add(conservationMenuItem);\r
 568     editMenu.add(copy);\r
 569     editMenu.add(cut);\r
 570     editMenu.add(upperCase);\r
 571     editMenu.add(lowerCase);\r
 572     editMenu.add(toggle);\r
 573     pdbMenu.add(pdbFromFile);\r
 574     pdbMenu.add(enterPDB);\r
 575     pdbMenu.add(discoverPDB);\r
 576     noColourmenuItem.setText("None");\r
 577         noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 578             {\r
 579                 public void actionPerformed(ActionEvent e)\r
 580                 {\r
 581                     noColourmenuItem_actionPerformed(e);\r
 582                 }\r
 583             });\r
 584 \r
 585         clustalColour.setText("Clustalx colours");\r
 586         clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 587             {\r
 588                 public void actionPerformed(ActionEvent e)\r
 589                 {\r
 590                     clustalColour_actionPerformed(e);\r
 591                 }\r
 592             });\r
 593         zappoColour.setText("Zappo");\r
 594         zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 595             {\r
 596                 public void actionPerformed(ActionEvent e)\r
 597                 {\r
 598                     zappoColour_actionPerformed(e);\r
 599                 }\r
 600             });\r
 601         taylorColour.setText("Taylor");\r
 602         taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 603             {\r
 604                 public void actionPerformed(ActionEvent e)\r
 605                 {\r
 606                     taylorColour_actionPerformed(e);\r
 607                 }\r
 608             });\r
 609         hydrophobicityColour.setText("Hydrophobicity");\r
 610         hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 611             {\r
 612                 public void actionPerformed(ActionEvent e)\r
 613                 {\r
 614                     hydrophobicityColour_actionPerformed(e);\r
 615                 }\r
 616             });\r
 617         helixColour.setText("Helix propensity");\r
 618         helixColour.addActionListener(new java.awt.event.ActionListener()\r
 619             {\r
 620                 public void actionPerformed(ActionEvent e)\r
 621                 {\r
 622                     helixColour_actionPerformed(e);\r
 623                 }\r
 624             });\r
 625         strandColour.setText("Strand propensity");\r
 626         strandColour.addActionListener(new java.awt.event.ActionListener()\r
 627             {\r
 628                 public void actionPerformed(ActionEvent e)\r
 629                 {\r
 630                     strandColour_actionPerformed(e);\r
 631                 }\r
 632             });\r
 633         turnColour.setText("Turn propensity");\r
 634         turnColour.addActionListener(new java.awt.event.ActionListener()\r
 635             {\r
 636                 public void actionPerformed(ActionEvent e)\r
 637                 {\r
 638                     turnColour_actionPerformed(e);\r
 639                 }\r
 640             });\r
 641         buriedColour.setText("Buried Index");\r
 642         buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 643             {\r
 644                 public void actionPerformed(ActionEvent e)\r
 645                 {\r
 646                     buriedColour_actionPerformed(e);\r
 647                 }\r
 648             });\r
 649         abovePIDColour.setText("Above % Identity");\r
 650         abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
 651             {\r
 652                 public void actionPerformed(ActionEvent e)\r
 653                 {\r
 654                     abovePIDColour_actionPerformed(e);\r
 655                 }\r
 656             });\r
 657         userDefinedColour.setText("User Defined...");\r
 658         userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 659             {\r
 660                 public void actionPerformed(ActionEvent e)\r
 661                 {\r
 662                     userDefinedColour_actionPerformed(e);\r
 663                 }\r
 664             });\r
 665         PIDColour.setText("Percentage Identity");\r
 666         PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 667             {\r
 668                 public void actionPerformed(ActionEvent e)\r
 669                 {\r
 670                     PIDColour_actionPerformed(e);\r
 671                 }\r
 672             });\r
 673         BLOSUM62Colour.setText("BLOSUM62");\r
 674         BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 675             {\r
 676                 public void actionPerformed(ActionEvent e)\r
 677                 {\r
 678                     BLOSUM62Colour_actionPerformed(e);\r
 679                 }\r
 680             });\r
 681         conservationMenuItem.setText("Conservation");\r
 682         conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 683             {\r
 684                 public void actionPerformed(ActionEvent e)\r
 685                 {\r
 686                     conservationMenuItem_actionPerformed(e);\r
 687                 }\r
 688             });\r
 689     }\r
 690 \r
 691     /**\r
 692      * DOCUMENT ME!\r
 693      */\r
 694     void refresh()\r
 695     {\r
 696         if (ap.overviewPanel != null)\r
 697           ap.overviewPanel.updateOverviewImage();\r
 698 \r
 699         PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
 700     }\r
 701 \r
 702     /**\r
 703      * DOCUMENT ME!\r
 704      *\r
 705      * @param e DOCUMENT ME!\r
 706      */\r
 707     protected void clustalColour_actionPerformed(ActionEvent e)\r
 708     {\r
 709         SequenceGroup sg = getGroup();\r
 710         sg.cs = new ClustalxColourScheme(sg.getSequences(true),\r
 711                 ap.av.alignment.getWidth());\r
 712         refresh();\r
 713     }\r
 714 \r
 715     /**\r
 716      * DOCUMENT ME!\r
 717      *\r
 718      * @param e DOCUMENT ME!\r
 719      */\r
 720     protected void zappoColour_actionPerformed(ActionEvent e)\r
 721     {\r
 722         getGroup().cs = new ZappoColourScheme();\r
 723         refresh();\r
 724     }\r
 725 \r
 726     /**\r
 727      * DOCUMENT ME!\r
 728      *\r
 729      * @param e DOCUMENT ME!\r
 730      */\r
 731     protected void taylorColour_actionPerformed(ActionEvent e)\r
 732     {\r
 733         getGroup().cs = new TaylorColourScheme();\r
 734         refresh();\r
 735     }\r
 736 \r
 737     /**\r
 738      * DOCUMENT ME!\r
 739      *\r
 740      * @param e DOCUMENT ME!\r
 741      */\r
 742     protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 743     {\r
 744         getGroup().cs = new HydrophobicColourScheme();\r
 745         refresh();\r
 746     }\r
 747 \r
 748     /**\r
 749      * DOCUMENT ME!\r
 750      *\r
 751      * @param e DOCUMENT ME!\r
 752      */\r
 753     protected void helixColour_actionPerformed(ActionEvent e)\r
 754     {\r
 755         getGroup().cs = new HelixColourScheme();\r
 756         refresh();\r
 757     }\r
 758 \r
 759     /**\r
 760      * DOCUMENT ME!\r
 761      *\r
 762      * @param e DOCUMENT ME!\r
 763      */\r
 764     protected void strandColour_actionPerformed(ActionEvent e)\r
 765     {\r
 766         getGroup().cs = new StrandColourScheme();\r
 767         refresh();\r
 768     }\r
 769 \r
 770     /**\r
 771      * DOCUMENT ME!\r
 772      *\r
 773      * @param e DOCUMENT ME!\r
 774      */\r
 775     protected void turnColour_actionPerformed(ActionEvent e)\r
 776     {\r
 777         getGroup().cs = new TurnColourScheme();\r
 778         refresh();\r
 779     }\r
 780 \r
 781     /**\r
 782      * DOCUMENT ME!\r
 783      *\r
 784      * @param e DOCUMENT ME!\r
 785      */\r
 786     protected void buriedColour_actionPerformed(ActionEvent e)\r
 787     {\r
 788         getGroup().cs = new BuriedColourScheme();\r
 789         refresh();\r
 790     }\r
 791 \r
 792     /**\r
 793      * DOCUMENT ME!\r
 794      *\r
 795      * @param e DOCUMENT ME!\r
 796      */\r
 797     public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
 798     {\r
 799         getGroup().cs = new NucleotideColourScheme();\r
 800         refresh();\r
 801     }\r
 802 \r
 803     /**\r
 804      * DOCUMENT ME!\r
 805      *\r
 806      * @param e DOCUMENT ME!\r
 807      */\r
 808     protected void abovePIDColour_actionPerformed(ActionEvent e)\r
 809     {\r
 810         SequenceGroup sg = getGroup();\r
 811         if(sg.cs==null)\r
 812           return;\r
 813 \r
 814         if (abovePIDColour.isSelected())\r
 815         {\r
 816           sg.cs.setConsensus(AAFrequency.calculate(\r
 817               sg.getSequences(true), sg.getStartRes(),\r
 818               sg.getEndRes() + 1));\r
 819 \r
 820             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
 821                     getGroup().getName());\r
 822 \r
 823            sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
 824 \r
 825             SliderPanel.showPIDSlider();\r
 826         }\r
 827         else // remove PIDColouring\r
 828         {\r
 829             sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
 830         }\r
 831 \r
 832         refresh();\r
 833     }\r
 834 \r
 835     /**\r
 836      * DOCUMENT ME!\r
 837      *\r
 838      * @param e DOCUMENT ME!\r
 839      */\r
 840     protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 841     {\r
 842        SequenceGroup sg = getGroup();\r
 843 \r
 844        if (e.getActionCommand().equals("User Defined..."))\r
 845          new UserDefinedColours(ap, sg);\r
 846        else\r
 847        {\r
 848          UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
 849              getUserColourSchemes().get(e.getActionCommand());\r
 850 \r
 851          sg.cs = udc;\r
 852        }\r
 853        refresh();\r
 854      }\r
 855     /**\r
 856      * DOCUMENT ME!\r
 857      *\r
 858      * @param e DOCUMENT ME!\r
 859      */\r
 860     protected void PIDColour_actionPerformed(ActionEvent e)\r
 861     {\r
 862         SequenceGroup sg = getGroup();\r
 863         sg.cs = new PIDColourScheme();\r
 864         sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),\r
 865                                                  sg.getStartRes(),\r
 866                                                  sg.getEndRes() + 1));\r
 867         refresh();\r
 868     }\r
 869 \r
 870     /**\r
 871      * DOCUMENT ME!\r
 872      *\r
 873      * @param e DOCUMENT ME!\r
 874      */\r
 875     protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 876     {\r
 877         SequenceGroup sg = getGroup();\r
 878 \r
 879         sg.cs = new Blosum62ColourScheme();\r
 880 \r
 881         sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),\r
 882                                                  sg.getStartRes(),\r
 883                                                  sg.getEndRes() + 1));\r
 884 \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 noColourmenuItem_actionPerformed(ActionEvent e)\r
 894     {\r
 895         getGroup().cs = null;\r
 896         refresh();\r
 897     }\r
 898 \r
 899     /**\r
 900      * DOCUMENT ME!\r
 901      *\r
 902      * @param e DOCUMENT ME!\r
 903      */\r
 904     protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
 905     {\r
 906         SequenceGroup sg = getGroup();\r
 907         if(sg.cs==null)\r
 908           return;\r
 909 \r
 910         if (conservationMenuItem.isSelected())\r
 911         {\r
 912             Conservation c = new Conservation("Group",\r
 913                     ResidueProperties.propHash, 3,\r
 914                     sg.getSequences(true),\r
 915                     sg.getStartRes(),\r
 916                     sg.getEndRes() + 1);\r
 917 \r
 918             c.calculate();\r
 919             c.verdict(false, ap.av.ConsPercGaps);\r
 920 \r
 921             sg.cs.setConservation(c);\r
 922 \r
 923             SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
 924             SliderPanel.showConservationSlider();\r
 925         }\r
 926         else // remove ConservationColouring\r
 927         {\r
 928             sg.cs.setConservation(null);\r
 929         }\r
 930 \r
 931         refresh();\r
 932     }\r
 933 \r
 934     /**\r
 935      * DOCUMENT ME!\r
 936      *\r
 937      * @param e DOCUMENT ME!\r
 938      */\r
 939     protected void groupName_actionPerformed(ActionEvent e)\r
 940     {\r
 941         SequenceGroup sg = getGroup();\r
 942         String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
 943                 "Enter new group name", "Edit group name",\r
 944                 JOptionPane.QUESTION_MESSAGE);\r
 945 \r
 946         if (reply == null)\r
 947         {\r
 948             return;\r
 949         }\r
 950 \r
 951         sg.setName(reply);\r
 952         groupName.setText(reply);\r
 953     }\r
 954 \r
 955 \r
 956     /**\r
 957      * DOCUMENT ME!\r
 958      *\r
 959      * @return DOCUMENT ME!\r
 960      */\r
 961     SequenceGroup getGroup()\r
 962     {\r
 963         SequenceGroup sg = ap.av.getSelectionGroup();\r
 964       // this method won't add a new group if it already exists\r
 965         if(sg!=null)\r
 966           ap.av.alignment.addGroup(sg);\r
 967 \r
 968         return sg;\r
 969     }\r
 970 \r
 971     /**\r
 972      * DOCUMENT ME!\r
 973      *\r
 974      * @param e DOCUMENT ME!\r
 975      */\r
 976     void sequenceName_actionPerformed(ActionEvent e)\r
 977     {\r
 978       JLabel idlabel = new JLabel(  "       Sequence Name ");\r
 979       JLabel desclabel = new JLabel("Sequence Description ");\r
 980       idlabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
 981       desclabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
 982       JTextField id = new JTextField(sequence.getName(), 40);\r
 983       JTextField description = new JTextField(sequence.getDescription(), 40);\r
 984       JPanel panel = new JPanel(new BorderLayout());\r
 985       JPanel panel2 = new JPanel(new BorderLayout());\r
 986       panel2.add(idlabel, BorderLayout.WEST);\r
 987       panel2.add(id, BorderLayout.CENTER);\r
 988       panel.add(panel2, BorderLayout.NORTH);\r
 989       panel2 = new JPanel(new BorderLayout());\r
 990       panel2.add(desclabel, BorderLayout.WEST);\r
 991       panel2.add(description, BorderLayout.CENTER);\r
 992       panel.add(panel2, BorderLayout.SOUTH);\r
 993 \r
 994 \r
 995        int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
 996           panel, "Edit Sequence Name/Description",\r
 997           JOptionPane.OK_CANCEL_OPTION );\r
 998 \r
 999 \r
1000         if (reply != JOptionPane.OK_OPTION )\r
1001         {\r
1002             return;\r
1003         }\r
1004 \r
1005         String s = id.getText();\r
1006 \r
1007         if (s != null)\r
1008         {\r
1009             if (s.indexOf(" ") > -1)\r
1010             {\r
1011                 JOptionPane.showMessageDialog(ap,\r
1012                     "Spaces have been converted to \"_\"",\r
1013                     "No spaces allowed in Sequence Name",\r
1014                     JOptionPane.WARNING_MESSAGE);\r
1015             }\r
1016 \r
1017             s = s.replace(' ', '_');\r
1018             sequence.setName(s);\r
1019             ap.repaint();\r
1020         }\r
1021 \r
1022         sequence.setDescription(description.getText());\r
1023 \r
1024         ap.av.firePropertyChange("alignment", null,\r
1025                                   ap.av.getAlignment().getSequences());\r
1026 \r
1027     }\r
1028 \r
1029     /**\r
1030      * DOCUMENT ME!\r
1031      *\r
1032      * @param e DOCUMENT ME!\r
1033      */\r
1034     void unGroupMenuItem_actionPerformed(ActionEvent e)\r
1035     {\r
1036         SequenceGroup sg = ap.av.getSelectionGroup();\r
1037         ap.av.alignment.deleteGroup(sg);\r
1038         ap.av.setSelectionGroup(null);\r
1039         refresh();\r
1040     }\r
1041 \r
1042 \r
1043     /**\r
1044      * DOCUMENT ME!\r
1045      *\r
1046      * @param e DOCUMENT ME!\r
1047      */\r
1048     protected void outline_actionPerformed(ActionEvent e)\r
1049     {\r
1050         SequenceGroup sg = getGroup();\r
1051         Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
1052                 Color.BLUE);\r
1053 \r
1054         if (col != null)\r
1055         {\r
1056             sg.setOutlineColour(col);\r
1057         }\r
1058 \r
1059         refresh();\r
1060     }\r
1061 \r
1062     /**\r
1063      * DOCUMENT ME!\r
1064      *\r
1065      * @param e DOCUMENT ME!\r
1066      */\r
1067     public void showBoxes_actionPerformed(ActionEvent e)\r
1068     {\r
1069         getGroup().setDisplayBoxes(showBoxes.isSelected());\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 showText_actionPerformed(ActionEvent e)\r
1079     {\r
1080         getGroup().setDisplayText(showText.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 showColourText_actionPerformed(ActionEvent e)\r
1090     {\r
1091         getGroup().setColourText(showColourText.isSelected());\r
1092         refresh();\r
1093     }\r
1094 \r
1095     public void showLink(String url)\r
1096     {\r
1097       try\r
1098       {\r
1099         jalview.util.BrowserLauncher.openURL(url);\r
1100       }\r
1101       catch (Exception ex)\r
1102       {\r
1103         JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
1104             "Unixers: Couldn't find default web browser."\r
1105            +"\nAdd the full path to your browser in Preferences.",\r
1106            "Web browser not found", JOptionPane.WARNING_MESSAGE );\r
1107 \r
1108 \r
1109         ex.printStackTrace();\r
1110       }\r
1111     }\r
1112 \r
1113     void hideSequences(boolean representGroup)\r
1114     {\r
1115       SequenceGroup sg = ap.av.getSelectionGroup();\r
1116       if(sg==null || sg.getSize(false)<1)\r
1117       {\r
1118         ap.av.hideSequence(new SequenceI[]{sequence});\r
1119         return;\r
1120       }\r
1121 \r
1122       int gsize = sg.getSize(false);\r
1123       SequenceI [] hseqs;\r
1124 \r
1125       hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ];\r
1126 \r
1127         int index = 0;\r
1128         for(int i=0; i<gsize; i++)\r
1129         {\r
1130           if(representGroup && sg.getSequenceAt(i)!=sequence)\r
1131           {\r
1132             sequence.addHiddenSequence(sg.getSequenceAt(i));\r
1133             hseqs[index++] = sg.getSequenceAt(i);\r
1134           }\r
1135           else if(!representGroup)\r
1136           {\r
1137             hseqs[index++] = sg.getSequenceAt(i);\r
1138           }\r
1139         }\r
1140 \r
1141         ap.av.hideSequence(hseqs);\r
1142 \r
1143         ap.av.setSelectionGroup(null);\r
1144     }\r
1145 \r
1146   public void copy_actionPerformed(ActionEvent e)\r
1147   {\r
1148     ap.alignFrame.copy_actionPerformed(null);\r
1149   }\r
1150 \r
1151   public void cut_actionPerformed(ActionEvent e)\r
1152   {\r
1153     ap.alignFrame.cut_actionPerformed(null);\r
1154   }\r
1155 \r
1156   void changeCase(ActionEvent e)\r
1157   {\r
1158     Object source = e.getSource();\r
1159     SequenceGroup sg = ap.av.getSelectionGroup();\r
1160     Vector regions = new Vector();\r
1161     if (sg != null)\r
1162     {\r
1163       int start = sg.getStartRes();\r
1164       int end = sg.getEndRes() + 1;\r
1165 \r
1166       do\r
1167       {\r
1168         if (ap.av.hasHiddenColumns)\r
1169         {\r
1170           if(start==0)\r
1171             start = ap.av.colSel.adjustForHiddenColumns(start);\r
1172 \r
1173           end = ap.av.colSel.getHiddenBoundaryRight(start);\r
1174           if (start == end)\r
1175             end = sg.getEndRes() + 1;\r
1176           if (end > sg.getEndRes())\r
1177             end = sg.getEndRes() + 1;\r
1178         }\r
1179 \r
1180         regions.addElement(new int[]\r
1181                            {start, end});\r
1182 \r
1183         if (ap.av.hasHiddenColumns)\r
1184         {\r
1185           start = ap.av.colSel.adjustForHiddenColumns(end);\r
1186           start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;\r
1187         }\r
1188       }\r
1189       while (end < sg.getEndRes());\r
1190 \r
1191       int[][] startEnd = new int[regions.size()][2];\r
1192       for (int i = 0; i < regions.size(); i++)\r
1193       {\r
1194         startEnd[i] = (int[]) regions.elementAt(i);\r
1195       }\r
1196 \r
1197 \r
1198       String description;\r
1199       int caseChange;\r
1200 \r
1201       if(source==toggle)\r
1202       {\r
1203         description = "Toggle Case";\r
1204         caseChange = ChangeCaseCommand.TOGGLE_CASE;\r
1205       }\r
1206       else if(source==upperCase)\r
1207       {\r
1208         description = "To Upper Case";\r
1209         caseChange = ChangeCaseCommand.TO_UPPER;\r
1210       }\r
1211       else\r
1212       {\r
1213         description = "To Lower Case";\r
1214         caseChange = ChangeCaseCommand.TO_LOWER;\r
1215       }\r
1216 \r
1217       ChangeCaseCommand caseCommand = new ChangeCaseCommand(\r
1218           description, sg.getSequencesAsArray(true), startEnd, caseChange\r
1219           );\r
1220 \r
1221       ap.alignFrame.addHistoryItem(caseCommand);\r
1222 \r
1223 \r
1224       ap.av.firePropertyChange("alignment", null,\r
1225                                 ap.av.getAlignment().getSequences());\r
1226 \r
1227     }\r
1228   }\r
1229 \r
1230   public void outputText_actionPerformed(ActionEvent e)\r
1231   {\r
1232     CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
1233     cap.setForInput(null);\r
1234     Desktop.addInternalFrame(cap,\r
1235                              "Alignment output - " + e.getActionCommand(), 600,\r
1236                              500);\r
1237 \r
1238     String [] omitHidden = null;\r
1239 \r
1240     if(ap.av.hasHiddenColumns)\r
1241     {\r
1242       System.out.println("PROMPT USER HERE");\r
1243       omitHidden = ap.av.getViewAsString(true);\r
1244     }\r
1245 \r
1246     cap.setText(new FormatAdapter().formatSequences(\r
1247         e.getActionCommand(),\r
1248         ap.av.getSelectionAsNewSequence(),\r
1249         omitHidden));\r
1250   }\r
1251 \r
1252 \r
1253   public void pdbFromFile_actionPerformed(ActionEvent e)\r
1254   {\r
1255      jalview.io.JalviewFileChooser chooser\r
1256          = new jalview.io.JalviewFileChooser(jalview.bin.Cache.\r
1257          getProperty(\r
1258              "LAST_DIRECTORY"));\r
1259      chooser.setFileView(new jalview.io.JalviewFileView());\r
1260      chooser.setDialogTitle("Select a PDB file");\r
1261      chooser.setToolTipText("Load a PDB file");\r
1262 \r
1263      int value = chooser.showOpenDialog(null);\r
1264 \r
1265      if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
1266      {\r
1267        PDBEntry entry = new PDBEntry();\r
1268        String choice = chooser.getSelectedFile().getPath();\r
1269        jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
1270        try\r
1271        {\r
1272          MCview.PDBfile pdbfile = new MCview.PDBfile(choice,\r
1273                                        jalview.io.AppletFormatAdapter.FILE);\r
1274 \r
1275          if (pdbfile.id == null)\r
1276          {\r
1277            String reply = JOptionPane.showInternalInputDialog(\r
1278                Desktop.desktop,\r
1279                "Couldn't find a PDB id in the file supplied."\r
1280                + "Please enter an Id to identify this structure.",\r
1281                "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);\r
1282            if (reply == null)\r
1283              return;\r
1284 \r
1285            entry.setId(reply);\r
1286          }\r
1287          else\r
1288            entry.setId(pdbfile.id);\r
1289        }\r
1290        catch (java.io.IOException ex)\r
1291        {\r
1292          ex.printStackTrace();\r
1293        }\r
1294 \r
1295        entry.setFile(choice);\r
1296        sequence.getDatasetSequence().addPDBId(entry);\r
1297      }\r
1298 \r
1299   }\r
1300 \r
1301   public void enterPDB_actionPerformed(ActionEvent e)\r
1302   {\r
1303     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
1304         "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);\r
1305 \r
1306     if (id != null && id.length() > 0)\r
1307     {\r
1308       PDBEntry entry = new PDBEntry();\r
1309       entry.setId(id);\r
1310       sequence.getDatasetSequence()\r
1311           .addPDBId(entry);\r
1312     }\r
1313   }\r
1314 \r
1315   public void discoverPDB_actionPerformed(ActionEvent e)\r
1316   {\r
1317     new jalview.io.DBRefFetcher(\r
1318              ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);\r
1319   }\r
1320 \r
1321   public void sequenceFeature_actionPerformed(ActionEvent e)\r
1322   {\r
1323     SequenceGroup sg = ap.av.getSelectionGroup();\r
1324     if(sg==null)\r
1325       return;\r
1326 \r
1327     int gSize= sg.getSize(false);\r
1328     SequenceI [] seqs = new SequenceI[gSize];\r
1329     SequenceFeature [] features = new SequenceFeature[gSize];\r
1330 \r
1331     for (int i = 0; i < gSize; i++)\r
1332     {\r
1333       seqs[i] = sg.getSequenceAt(i).getDatasetSequence();\r
1334       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());\r
1335       int end = sg.findEndRes(sg.getSequenceAt(i));\r
1336       features[i] = new SequenceFeature(null,null, null,start,end,"Jalview");\r
1337     }\r
1338 \r
1339     if (ap.seqPanel.seqCanvas.getFeatureRenderer()\r
1340         .createNewFeatures(seqs, features))\r
1341     {\r
1342       ap.alignFrame.showSeqFeatures.setSelected(true);\r
1343       ap.av.setShowSequenceFeatures(true);\r
1344       ap.highlightSearchResults(null);\r
1345     }\r
1346   }\r
1347 }\r