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           int start = Math.max(sequence.getName().length()-15, 0);\r
 146           sequenceMenu.setText(sequence.getName().substring(start));\r
 147 \r
 148           JMenuItem menuItem;\r
 149           if( seq.getDatasetSequence().getPDBId() != null)\r
 150           {\r
 151             java.util.Enumeration e = seq.getDatasetSequence().getPDBId().\r
 152                 elements();\r
 153 \r
 154             while (e.hasMoreElements())\r
 155             {\r
 156               final PDBEntry pdb = (PDBEntry) e.nextElement();\r
 157 \r
 158               menuItem = new JMenuItem();\r
 159               menuItem.setText("View PDB entry: " + pdb.getId());\r
 160               menuItem.addActionListener(new java.awt.event.ActionListener()\r
 161               {\r
 162                 public void actionPerformed(ActionEvent e)\r
 163                 {\r
 164                   new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);\r
 165                 }\r
 166               });\r
 167               sequenceMenu.add(menuItem);\r
 168             }\r
 169           }\r
 170 \r
 171           menuItem = new JMenuItem("Hide Sequences");\r
 172           menuItem.addActionListener(new java.awt.event.ActionListener()\r
 173               {\r
 174                 public void actionPerformed(ActionEvent e)\r
 175                 {\r
 176                   hideSequences(false);\r
 177                 }\r
 178               });\r
 179           add(menuItem);\r
 180 \r
 181           if(ap.av.getSelectionGroup() !=null\r
 182              && ap.av.getSelectionGroup().getSize(false)>1)\r
 183           {\r
 184             menuItem = new JMenuItem("Represent Group with " + seq.getName());\r
 185             menuItem.addActionListener(new java.awt.event.ActionListener()\r
 186             {\r
 187               public void actionPerformed(ActionEvent e)\r
 188               {\r
 189                 hideSequences(true);\r
 190               }\r
 191             });\r
 192             sequenceMenu.add(menuItem);\r
 193           }\r
 194 \r
 195           if (ap.av.hasHiddenRows)\r
 196           {\r
 197             final int index = ap.av.alignment.findIndex(seq);\r
 198 \r
 199             if (ap.av.adjustForHiddenSeqs(index) -\r
 200                 ap.av.adjustForHiddenSeqs(index - 1) > 1)\r
 201             {\r
 202               menuItem = new JMenuItem("Reveal Sequences");\r
 203               menuItem.addActionListener(new ActionListener()\r
 204               {\r
 205                 public void actionPerformed(ActionEvent e)\r
 206                 {\r
 207                   ap.av.showSequence(index);\r
 208                   if (ap.overviewPanel != null)\r
 209                     ap.overviewPanel.updateOverviewImage();\r
 210                 }\r
 211               });\r
 212               add(menuItem);\r
 213             }\r
 214 \r
 215             menuItem = new JMenuItem("Reveal All");\r
 216             menuItem.addActionListener(new ActionListener()\r
 217                 {\r
 218                   public void actionPerformed(ActionEvent e)\r
 219                   {\r
 220                     ap.av.showAllHiddenSeqs();\r
 221                     if (ap.overviewPanel != null)\r
 222                       ap.overviewPanel.updateOverviewImage();\r
 223                     }\r
 224                 });\r
 225 \r
 226             add(menuItem);\r
 227           }\r
 228 \r
 229 \r
 230         }\r
 231 \r
 232 \r
 233 \r
 234         SequenceGroup sg = ap.av.getSelectionGroup();\r
 235 \r
 236         if (sg != null)\r
 237         {\r
 238             groupName.setText(sg.getName());\r
 239 \r
 240             if (sg.cs instanceof ZappoColourScheme)\r
 241             {\r
 242                 zappoColour.setSelected(true);\r
 243             }\r
 244             else if (sg.cs instanceof TaylorColourScheme)\r
 245             {\r
 246                 taylorColour.setSelected(true);\r
 247             }\r
 248             else if (sg.cs instanceof PIDColourScheme)\r
 249             {\r
 250                 PIDColour.setSelected(true);\r
 251             }\r
 252             else if (sg.cs instanceof Blosum62ColourScheme)\r
 253             {\r
 254                 BLOSUM62Colour.setSelected(true);\r
 255             }\r
 256             else if (sg.cs instanceof UserColourScheme)\r
 257             {\r
 258                 userDefinedColour.setSelected(true);\r
 259             }\r
 260             else if (sg.cs instanceof HydrophobicColourScheme)\r
 261             {\r
 262                 hydrophobicityColour.setSelected(true);\r
 263             }\r
 264             else if (sg.cs instanceof HelixColourScheme)\r
 265             {\r
 266                 helixColour.setSelected(true);\r
 267             }\r
 268             else if (sg.cs instanceof StrandColourScheme)\r
 269             {\r
 270                 strandColour.setSelected(true);\r
 271             }\r
 272             else if (sg.cs instanceof TurnColourScheme)\r
 273             {\r
 274                 turnColour.setSelected(true);\r
 275             }\r
 276             else if (sg.cs instanceof BuriedColourScheme)\r
 277             {\r
 278                 buriedColour.setSelected(true);\r
 279             }\r
 280             else if (sg.cs instanceof ClustalxColourScheme)\r
 281             {\r
 282                 clustalColour.setSelected(true);\r
 283             }\r
 284             else\r
 285             {\r
 286                 noColourmenuItem.setSelected(true);\r
 287             }\r
 288 \r
 289             if (sg.cs!=null && sg.cs.conservationApplied())\r
 290             {\r
 291                 conservationMenuItem.setSelected(true);\r
 292             }\r
 293 \r
 294             showText.setSelected(sg.getDisplayText());\r
 295             showColourText.setSelected(sg.getColourText());\r
 296             showBoxes.setSelected(sg.getDisplayBoxes());\r
 297         }\r
 298         else\r
 299         {\r
 300           groupMenu.setVisible(false);\r
 301           editMenu.setVisible(false);\r
 302         }\r
 303 \r
 304         if (!ap.av.alignment.getGroups().contains(sg))\r
 305         {\r
 306             unGroupMenuItem.setVisible(false);\r
 307         }\r
 308 \r
 309 \r
 310         if (seq == null)\r
 311         {\r
 312             sequenceMenu.setVisible(false);\r
 313             pdbMenu.setVisible(false);\r
 314         }\r
 315 \r
 316         if(links != null && links.size()>0)\r
 317         {\r
 318           JMenu linkMenu = new JMenu("Link");\r
 319           JMenuItem item;\r
 320           for(int i=0; i<links.size(); i++)\r
 321           {\r
 322             String link = links.elementAt(i).toString();\r
 323             final String label = link.substring(0, link.indexOf("|"));\r
 324             item = new JMenuItem(label);\r
 325             final String url;\r
 326 \r
 327             if (link.indexOf("$SEQUENCE_ID$") > -1)\r
 328             {\r
 329               String id = seq.getName();\r
 330               if (id.indexOf("|") > -1)\r
 331                 id = id.substring(id.lastIndexOf("|") + 1);\r
 332 \r
 333               url = link.substring(link.indexOf("|") + 1,\r
 334                                    link.indexOf("$SEQUENCE_ID$"))\r
 335                   + id +\r
 336                   link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
 337             }\r
 338             else\r
 339               url = link.substring(link.lastIndexOf("|")+1);\r
 340 \r
 341 \r
 342             item.addActionListener(new java.awt.event.ActionListener()\r
 343             {\r
 344                 public void actionPerformed(ActionEvent e)\r
 345                 {\r
 346                     showLink(url);\r
 347                 }\r
 348             });\r
 349 \r
 350             linkMenu.add(item);\r
 351           }\r
 352           if(sequence!=null)\r
 353             sequenceMenu.add(linkMenu);\r
 354           else\r
 355             add(linkMenu);\r
 356         }\r
 357     }\r
 358 \r
 359 \r
 360     /**\r
 361      * DOCUMENT ME!\r
 362      *\r
 363      * @throws Exception DOCUMENT ME!\r
 364      */\r
 365     private void jbInit() throws Exception\r
 366     {\r
 367         groupMenu.setText("Group");\r
 368         groupMenu.setText("Selection");\r
 369         groupName.setText("Name");\r
 370         groupName.addActionListener(new java.awt.event.ActionListener()\r
 371             {\r
 372                 public void actionPerformed(ActionEvent e)\r
 373                 {\r
 374                     groupName_actionPerformed(e);\r
 375                 }\r
 376             });\r
 377         sequenceMenu.setText("Sequence");\r
 378         sequenceName.setText("Edit Name/Description");\r
 379         sequenceName.addActionListener(new java.awt.event.ActionListener()\r
 380             {\r
 381                 public void actionPerformed(ActionEvent e)\r
 382                 {\r
 383                     sequenceName_actionPerformed(e);\r
 384                 }\r
 385             });\r
 386         PIDColour.setFocusPainted(false);\r
 387         unGroupMenuItem.setText("Remove Group");\r
 388         unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 389             {\r
 390                 public void actionPerformed(ActionEvent e)\r
 391                 {\r
 392                     unGroupMenuItem_actionPerformed(e);\r
 393                 }\r
 394             });\r
 395 \r
 396         outline.setText("Border colour");\r
 397         outline.addActionListener(new java.awt.event.ActionListener()\r
 398             {\r
 399                 public void actionPerformed(ActionEvent e)\r
 400                 {\r
 401                     outline_actionPerformed(e);\r
 402                 }\r
 403             });\r
 404         nucleotideMenuItem.setText("Nucleotide");\r
 405         nucleotideMenuItem.addActionListener(new ActionListener()\r
 406             {\r
 407                 public void actionPerformed(ActionEvent e)\r
 408                 {\r
 409                     nucleotideMenuItem_actionPerformed(e);\r
 410                 }\r
 411             });\r
 412         colourMenu.setText("Group Colour");\r
 413         showBoxes.setText("Boxes");\r
 414         showBoxes.setState(true);\r
 415         showBoxes.addActionListener(new ActionListener()\r
 416             {\r
 417                 public void actionPerformed(ActionEvent e)\r
 418                 {\r
 419                     showBoxes_actionPerformed(e);\r
 420                 }\r
 421             });\r
 422         showText.setText("Text");\r
 423         showText.setState(true);\r
 424         showText.addActionListener(new ActionListener()\r
 425             {\r
 426                 public void actionPerformed(ActionEvent e)\r
 427                 {\r
 428                     showText_actionPerformed(e);\r
 429                 }\r
 430             });\r
 431         showColourText.setText("Colour Text");\r
 432         showColourText.addActionListener(new ActionListener()\r
 433             {\r
 434                 public void actionPerformed(ActionEvent e)\r
 435                 {\r
 436                     showColourText_actionPerformed(e);\r
 437                 }\r
 438             });\r
 439     editMenu.setText("Edit");\r
 440     cut.setText("Cut");\r
 441     cut.addActionListener(new ActionListener()\r
 442     {\r
 443       public void actionPerformed(ActionEvent e)\r
 444       {\r
 445         cut_actionPerformed(e);\r
 446       }\r
 447     });\r
 448     upperCase.setText("To Upper Case");\r
 449     upperCase.addActionListener(new ActionListener()\r
 450     {\r
 451       public void actionPerformed(ActionEvent e)\r
 452       {\r
 453         upperCase_actionPerformed(e);\r
 454       }\r
 455     });\r
 456     copy.setText("Copy");\r
 457     copy.addActionListener(new ActionListener()\r
 458     {\r
 459       public void actionPerformed(ActionEvent e)\r
 460       {\r
 461         copy_actionPerformed(e);\r
 462       }\r
 463     });\r
 464     lowerCase.setText("To Lower Case");\r
 465     lowerCase.addActionListener(new ActionListener()\r
 466     {\r
 467       public void actionPerformed(ActionEvent e)\r
 468       {\r
 469         lowerCase_actionPerformed(e);\r
 470       }\r
 471     });\r
 472     toggle.setText("Toggle Case");\r
 473     toggle.addActionListener(new ActionListener()\r
 474     {\r
 475       public void actionPerformed(ActionEvent e)\r
 476       {\r
 477         toggle_actionPerformed(e);\r
 478       }\r
 479     });\r
 480     pdbMenu.setText("Associate Structure with Sequence");\r
 481     pdbFromFile.setText("From File");\r
 482     pdbFromFile.addActionListener(new ActionListener()\r
 483     {\r
 484       public void actionPerformed(ActionEvent e)\r
 485       {\r
 486         pdbFromFile_actionPerformed(e);\r
 487       }\r
 488     });\r
 489     enterPDB.setText("Enter PDB Id");\r
 490     enterPDB.addActionListener(new ActionListener()\r
 491     {\r
 492       public void actionPerformed(ActionEvent e)\r
 493       {\r
 494         enterPDB_actionPerformed(e);\r
 495       }\r
 496     });\r
 497     discoverPDB.setText("Discover PDB ids");\r
 498     discoverPDB.addActionListener(new ActionListener()\r
 499     {\r
 500       public void actionPerformed(ActionEvent e)\r
 501       {\r
 502         discoverPDB_actionPerformed(e);\r
 503       }\r
 504     });\r
 505     outputMenu.setText("Output to Textbox...");\r
 506     sequenceFeature.setText("Create Sequence Feature");\r
 507     sequenceFeature.addActionListener(new ActionListener()\r
 508     {\r
 509       public void actionPerformed(ActionEvent e)\r
 510       {\r
 511         sequenceFeature_actionPerformed(e);\r
 512       }\r
 513     });\r
 514     add(groupMenu);\r
 515 \r
 516     add(sequenceMenu);\r
 517     groupMenu.add(editMenu);\r
 518     groupMenu.add(outputMenu);\r
 519     groupMenu.addSeparator();\r
 520     groupMenu.add(sequenceFeature);\r
 521     groupMenu.addSeparator();\r
 522     groupMenu.add(groupName);\r
 523     groupMenu.add(unGroupMenuItem);\r
 524         groupMenu.add(colourMenu);\r
 525     groupMenu.add(showBoxes);\r
 526         groupMenu.add(showText);\r
 527         groupMenu.add(showColourText);\r
 528     groupMenu.add(outline);\r
 529         sequenceMenu.add(sequenceName);\r
 530     sequenceMenu.add(pdbMenu);\r
 531     colourMenu.add(noColourmenuItem);\r
 532         colourMenu.add(clustalColour);\r
 533         colourMenu.add(BLOSUM62Colour);\r
 534         colourMenu.add(PIDColour);\r
 535         colourMenu.add(zappoColour);\r
 536         colourMenu.add(taylorColour);\r
 537         colourMenu.add(hydrophobicityColour);\r
 538         colourMenu.add(helixColour);\r
 539         colourMenu.add(strandColour);\r
 540         colourMenu.add(turnColour);\r
 541         colourMenu.add(buriedColour);\r
 542         colourMenu.add(nucleotideMenuItem);\r
 543         colourMenu.add(userDefinedColour);\r
 544 \r
 545         if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
 546         {\r
 547           java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 548               getUserColourSchemes().keys();\r
 549 \r
 550           while (userColours.hasMoreElements())\r
 551           {\r
 552             JMenuItem item = new JMenuItem(userColours.\r
 553                 nextElement().toString());\r
 554             item.addActionListener(new ActionListener()\r
 555             {\r
 556               public void actionPerformed(ActionEvent evt)\r
 557               {\r
 558                 userDefinedColour_actionPerformed(evt);\r
 559               }\r
 560             });\r
 561             colourMenu.add(item);\r
 562           }\r
 563         }\r
 564 \r
 565 \r
 566         colourMenu.addSeparator();\r
 567         colourMenu.add(abovePIDColour);\r
 568         colourMenu.add(conservationMenuItem);\r
 569     editMenu.add(copy);\r
 570     editMenu.add(cut);\r
 571     editMenu.add(upperCase);\r
 572     editMenu.add(lowerCase);\r
 573     editMenu.add(toggle);\r
 574     pdbMenu.add(pdbFromFile);\r
 575     pdbMenu.add(enterPDB);\r
 576     pdbMenu.add(discoverPDB);\r
 577     noColourmenuItem.setText("None");\r
 578         noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 579             {\r
 580                 public void actionPerformed(ActionEvent e)\r
 581                 {\r
 582                     noColourmenuItem_actionPerformed(e);\r
 583                 }\r
 584             });\r
 585 \r
 586         clustalColour.setText("Clustalx colours");\r
 587         clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 588             {\r
 589                 public void actionPerformed(ActionEvent e)\r
 590                 {\r
 591                     clustalColour_actionPerformed(e);\r
 592                 }\r
 593             });\r
 594         zappoColour.setText("Zappo");\r
 595         zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 596             {\r
 597                 public void actionPerformed(ActionEvent e)\r
 598                 {\r
 599                     zappoColour_actionPerformed(e);\r
 600                 }\r
 601             });\r
 602         taylorColour.setText("Taylor");\r
 603         taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 604             {\r
 605                 public void actionPerformed(ActionEvent e)\r
 606                 {\r
 607                     taylorColour_actionPerformed(e);\r
 608                 }\r
 609             });\r
 610         hydrophobicityColour.setText("Hydrophobicity");\r
 611         hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 612             {\r
 613                 public void actionPerformed(ActionEvent e)\r
 614                 {\r
 615                     hydrophobicityColour_actionPerformed(e);\r
 616                 }\r
 617             });\r
 618         helixColour.setText("Helix propensity");\r
 619         helixColour.addActionListener(new java.awt.event.ActionListener()\r
 620             {\r
 621                 public void actionPerformed(ActionEvent e)\r
 622                 {\r
 623                     helixColour_actionPerformed(e);\r
 624                 }\r
 625             });\r
 626         strandColour.setText("Strand propensity");\r
 627         strandColour.addActionListener(new java.awt.event.ActionListener()\r
 628             {\r
 629                 public void actionPerformed(ActionEvent e)\r
 630                 {\r
 631                     strandColour_actionPerformed(e);\r
 632                 }\r
 633             });\r
 634         turnColour.setText("Turn propensity");\r
 635         turnColour.addActionListener(new java.awt.event.ActionListener()\r
 636             {\r
 637                 public void actionPerformed(ActionEvent e)\r
 638                 {\r
 639                     turnColour_actionPerformed(e);\r
 640                 }\r
 641             });\r
 642         buriedColour.setText("Buried Index");\r
 643         buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 644             {\r
 645                 public void actionPerformed(ActionEvent e)\r
 646                 {\r
 647                     buriedColour_actionPerformed(e);\r
 648                 }\r
 649             });\r
 650         abovePIDColour.setText("Above % Identity");\r
 651         abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
 652             {\r
 653                 public void actionPerformed(ActionEvent e)\r
 654                 {\r
 655                     abovePIDColour_actionPerformed(e);\r
 656                 }\r
 657             });\r
 658         userDefinedColour.setText("User Defined...");\r
 659         userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 660             {\r
 661                 public void actionPerformed(ActionEvent e)\r
 662                 {\r
 663                     userDefinedColour_actionPerformed(e);\r
 664                 }\r
 665             });\r
 666         PIDColour.setText("Percentage Identity");\r
 667         PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 668             {\r
 669                 public void actionPerformed(ActionEvent e)\r
 670                 {\r
 671                     PIDColour_actionPerformed(e);\r
 672                 }\r
 673             });\r
 674         BLOSUM62Colour.setText("BLOSUM62");\r
 675         BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 676             {\r
 677                 public void actionPerformed(ActionEvent e)\r
 678                 {\r
 679                     BLOSUM62Colour_actionPerformed(e);\r
 680                 }\r
 681             });\r
 682         conservationMenuItem.setText("Conservation");\r
 683         conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 684             {\r
 685                 public void actionPerformed(ActionEvent e)\r
 686                 {\r
 687                     conservationMenuItem_actionPerformed(e);\r
 688                 }\r
 689             });\r
 690     }\r
 691 \r
 692     /**\r
 693      * DOCUMENT ME!\r
 694      */\r
 695     void refresh()\r
 696     {\r
 697         if (ap.overviewPanel != null)\r
 698           ap.overviewPanel.updateOverviewImage();\r
 699 \r
 700         PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
 701     }\r
 702 \r
 703     /**\r
 704      * DOCUMENT ME!\r
 705      *\r
 706      * @param e DOCUMENT ME!\r
 707      */\r
 708     protected void clustalColour_actionPerformed(ActionEvent e)\r
 709     {\r
 710         SequenceGroup sg = getGroup();\r
 711         sg.cs = new ClustalxColourScheme(sg.getSequences(true),\r
 712                 ap.av.alignment.getWidth());\r
 713         refresh();\r
 714     }\r
 715 \r
 716     /**\r
 717      * DOCUMENT ME!\r
 718      *\r
 719      * @param e DOCUMENT ME!\r
 720      */\r
 721     protected void zappoColour_actionPerformed(ActionEvent e)\r
 722     {\r
 723         getGroup().cs = new ZappoColourScheme();\r
 724         refresh();\r
 725     }\r
 726 \r
 727     /**\r
 728      * DOCUMENT ME!\r
 729      *\r
 730      * @param e DOCUMENT ME!\r
 731      */\r
 732     protected void taylorColour_actionPerformed(ActionEvent e)\r
 733     {\r
 734         getGroup().cs = new TaylorColourScheme();\r
 735         refresh();\r
 736     }\r
 737 \r
 738     /**\r
 739      * DOCUMENT ME!\r
 740      *\r
 741      * @param e DOCUMENT ME!\r
 742      */\r
 743     protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 744     {\r
 745         getGroup().cs = new HydrophobicColourScheme();\r
 746         refresh();\r
 747     }\r
 748 \r
 749     /**\r
 750      * DOCUMENT ME!\r
 751      *\r
 752      * @param e DOCUMENT ME!\r
 753      */\r
 754     protected void helixColour_actionPerformed(ActionEvent e)\r
 755     {\r
 756         getGroup().cs = new HelixColourScheme();\r
 757         refresh();\r
 758     }\r
 759 \r
 760     /**\r
 761      * DOCUMENT ME!\r
 762      *\r
 763      * @param e DOCUMENT ME!\r
 764      */\r
 765     protected void strandColour_actionPerformed(ActionEvent e)\r
 766     {\r
 767         getGroup().cs = new StrandColourScheme();\r
 768         refresh();\r
 769     }\r
 770 \r
 771     /**\r
 772      * DOCUMENT ME!\r
 773      *\r
 774      * @param e DOCUMENT ME!\r
 775      */\r
 776     protected void turnColour_actionPerformed(ActionEvent e)\r
 777     {\r
 778         getGroup().cs = new TurnColourScheme();\r
 779         refresh();\r
 780     }\r
 781 \r
 782     /**\r
 783      * DOCUMENT ME!\r
 784      *\r
 785      * @param e DOCUMENT ME!\r
 786      */\r
 787     protected void buriedColour_actionPerformed(ActionEvent e)\r
 788     {\r
 789         getGroup().cs = new BuriedColourScheme();\r
 790         refresh();\r
 791     }\r
 792 \r
 793     /**\r
 794      * DOCUMENT ME!\r
 795      *\r
 796      * @param e DOCUMENT ME!\r
 797      */\r
 798     public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
 799     {\r
 800         getGroup().cs = new NucleotideColourScheme();\r
 801         refresh();\r
 802     }\r
 803 \r
 804     /**\r
 805      * DOCUMENT ME!\r
 806      *\r
 807      * @param e DOCUMENT ME!\r
 808      */\r
 809     protected void abovePIDColour_actionPerformed(ActionEvent e)\r
 810     {\r
 811         SequenceGroup sg = getGroup();\r
 812         if(sg.cs==null)\r
 813           return;\r
 814 \r
 815         if (abovePIDColour.isSelected())\r
 816         {\r
 817             sg.cs.setConsensus(AAFrequency.calculate(\r
 818                     sg.getSequences(true), 0,\r
 819                     ap.av.alignment.getWidth()));\r
 820 \r
 821             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
 822                     getGroup().getName());\r
 823 \r
 824            sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
 825 \r
 826             SliderPanel.showPIDSlider();\r
 827         }\r
 828         else // remove PIDColouring\r
 829         {\r
 830             sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
 831         }\r
 832 \r
 833         refresh();\r
 834     }\r
 835 \r
 836     /**\r
 837      * DOCUMENT ME!\r
 838      *\r
 839      * @param e DOCUMENT ME!\r
 840      */\r
 841     protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 842     {\r
 843        SequenceGroup sg = getGroup();\r
 844 \r
 845        if (e.getActionCommand().equals("User Defined..."))\r
 846          new UserDefinedColours(ap, sg);\r
 847        else\r
 848        {\r
 849          UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
 850              getUserColourSchemes().get(e.getActionCommand());\r
 851 \r
 852          sg.cs = udc;\r
 853        }\r
 854        refresh();\r
 855      }\r
 856     /**\r
 857      * DOCUMENT ME!\r
 858      *\r
 859      * @param e DOCUMENT ME!\r
 860      */\r
 861     protected void PIDColour_actionPerformed(ActionEvent e)\r
 862     {\r
 863         SequenceGroup sg = getGroup();\r
 864         sg.cs = new PIDColourScheme();\r
 865         sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
 866                 ap.av.alignment.getWidth()));\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), 0,\r
 882                 ap.av.alignment.getWidth()));\r
 883 \r
 884         refresh();\r
 885     }\r
 886 \r
 887     /**\r
 888      * DOCUMENT ME!\r
 889      *\r
 890      * @param e DOCUMENT ME!\r
 891      */\r
 892     protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 893     {\r
 894         getGroup().cs = null;\r
 895         refresh();\r
 896     }\r
 897 \r
 898     /**\r
 899      * DOCUMENT ME!\r
 900      *\r
 901      * @param e DOCUMENT ME!\r
 902      */\r
 903     protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
 904     {\r
 905         SequenceGroup sg = getGroup();\r
 906         if(sg.cs==null)\r
 907           return;\r
 908 \r
 909         if (conservationMenuItem.isSelected())\r
 910         {\r
 911             Conservation c = new Conservation("Group",\r
 912                     ResidueProperties.propHash, 3,\r
 913                     sg.getSequences(true), 0,\r
 914                     ap.av.alignment.getWidth());\r
 915 \r
 916             c.calculate();\r
 917             c.verdict(false, ap.av.ConsPercGaps);\r
 918 \r
 919             sg.cs.setConservation(c);\r
 920 \r
 921             SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
 922             SliderPanel.showConservationSlider();\r
 923         }\r
 924         else // remove ConservationColouring\r
 925         {\r
 926             sg.cs.setConservation(null);\r
 927         }\r
 928 \r
 929         refresh();\r
 930     }\r
 931 \r
 932     /**\r
 933      * DOCUMENT ME!\r
 934      *\r
 935      * @param e DOCUMENT ME!\r
 936      */\r
 937     protected void groupName_actionPerformed(ActionEvent e)\r
 938     {\r
 939         SequenceGroup sg = getGroup();\r
 940         String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
 941                 "Enter new group name", "Edit group name",\r
 942                 JOptionPane.QUESTION_MESSAGE);\r
 943 \r
 944         if (reply == null)\r
 945         {\r
 946             return;\r
 947         }\r
 948 \r
 949         sg.setName(reply);\r
 950         groupName.setText(reply);\r
 951     }\r
 952 \r
 953     /**\r
 954      * DOCUMENT ME!\r
 955      *\r
 956      * @param e DOCUMENT ME!\r
 957      */\r
 958     protected void analyze_actionPerformed(ActionEvent e)\r
 959     {\r
 960         CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
 961         JInternalFrame frame = new JInternalFrame();\r
 962         frame.setContentPane(cap);\r
 963         Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
 964 \r
 965         SequenceGroup sg = getGroup();\r
 966         StringBuffer sb = new StringBuffer();\r
 967 \r
 968         for (int i = 0; i < sg.getSize(false); i++)\r
 969         {\r
 970             Sequence tmp = (Sequence) sg.getSequences(false).elementAt(i);\r
 971             sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
 972             sb.append("\n");\r
 973         }\r
 974 \r
 975         sb.append("Something amazing will happen soon");\r
 976         cap.setText(sb.toString());\r
 977     }\r
 978 \r
 979     /**\r
 980      * DOCUMENT ME!\r
 981      *\r
 982      * @return DOCUMENT ME!\r
 983      */\r
 984     SequenceGroup getGroup()\r
 985     {\r
 986         SequenceGroup sg = ap.av.getSelectionGroup();\r
 987       // this method won't add a new group if it already exists\r
 988         if(sg!=null)\r
 989           ap.av.alignment.addGroup(sg);\r
 990 \r
 991         return sg;\r
 992     }\r
 993 \r
 994     /**\r
 995      * DOCUMENT ME!\r
 996      *\r
 997      * @param e DOCUMENT ME!\r
 998      */\r
 999     void sequenceName_actionPerformed(ActionEvent e)\r
1000     {\r
1001       JLabel idlabel = new JLabel(  "       Sequence Name ");\r
1002       JLabel desclabel = new JLabel("Sequence Description ");\r
1003       idlabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
1004       desclabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
1005       JTextField id = new JTextField(sequence.getName(), 40);\r
1006       JTextField description = new JTextField(sequence.getDescription(), 40);\r
1007       JPanel panel = new JPanel(new BorderLayout());\r
1008       JPanel panel2 = new JPanel(new BorderLayout());\r
1009       panel2.add(idlabel, BorderLayout.WEST);\r
1010       panel2.add(id, BorderLayout.CENTER);\r
1011       panel.add(panel2, BorderLayout.NORTH);\r
1012       panel2 = new JPanel(new BorderLayout());\r
1013       panel2.add(desclabel, BorderLayout.WEST);\r
1014       panel2.add(description, BorderLayout.CENTER);\r
1015       panel.add(panel2, BorderLayout.SOUTH);\r
1016 \r
1017 \r
1018        int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
1019           panel, "Edit Sequence Name/Description",\r
1020           JOptionPane.OK_CANCEL_OPTION );\r
1021 \r
1022 \r
1023         if (reply != JOptionPane.OK_OPTION )\r
1024         {\r
1025             return;\r
1026         }\r
1027 \r
1028         String s = id.getText();\r
1029 \r
1030         if (s != null)\r
1031         {\r
1032             if (s.indexOf(" ") > -1)\r
1033             {\r
1034                 JOptionPane.showMessageDialog(ap,\r
1035                     "Spaces have been converted to \"_\"",\r
1036                     "No spaces allowed in Sequence Name",\r
1037                     JOptionPane.WARNING_MESSAGE);\r
1038             }\r
1039 \r
1040             s = s.replace(' ', '_');\r
1041             sequence.getDatasetSequence().setName(s);\r
1042             sequence.setName(s);\r
1043             ap.repaint();\r
1044         }\r
1045 \r
1046         sequence.getDatasetSequence().setDescription(description.getText());\r
1047         sequence.setDescription(description.getText());\r
1048     }\r
1049 \r
1050     /**\r
1051      * DOCUMENT ME!\r
1052      *\r
1053      * @param e DOCUMENT ME!\r
1054      */\r
1055     void unGroupMenuItem_actionPerformed(ActionEvent e)\r
1056     {\r
1057         SequenceGroup sg = ap.av.getSelectionGroup();\r
1058         ap.av.alignment.deleteGroup(sg);\r
1059         ap.av.setSelectionGroup(null);\r
1060         refresh();\r
1061     }\r
1062 \r
1063 \r
1064     /**\r
1065      * DOCUMENT ME!\r
1066      *\r
1067      * @param e DOCUMENT ME!\r
1068      */\r
1069     protected void outline_actionPerformed(ActionEvent e)\r
1070     {\r
1071         SequenceGroup sg = getGroup();\r
1072         Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
1073                 Color.BLUE);\r
1074 \r
1075         if (col != null)\r
1076         {\r
1077             sg.setOutlineColour(col);\r
1078         }\r
1079 \r
1080         refresh();\r
1081     }\r
1082 \r
1083     /**\r
1084      * DOCUMENT ME!\r
1085      *\r
1086      * @param e DOCUMENT ME!\r
1087      */\r
1088     public void showBoxes_actionPerformed(ActionEvent e)\r
1089     {\r
1090         getGroup().setDisplayBoxes(showBoxes.isSelected());\r
1091         refresh();\r
1092     }\r
1093 \r
1094     /**\r
1095      * DOCUMENT ME!\r
1096      *\r
1097      * @param e DOCUMENT ME!\r
1098      */\r
1099     public void showText_actionPerformed(ActionEvent e)\r
1100     {\r
1101         getGroup().setDisplayText(showText.isSelected());\r
1102         refresh();\r
1103     }\r
1104 \r
1105     /**\r
1106      * DOCUMENT ME!\r
1107      *\r
1108      * @param e DOCUMENT ME!\r
1109      */\r
1110     public void showColourText_actionPerformed(ActionEvent e)\r
1111     {\r
1112         getGroup().setColourText(showColourText.isSelected());\r
1113         refresh();\r
1114     }\r
1115 \r
1116     public void showLink(String url)\r
1117     {\r
1118       try\r
1119       {\r
1120         jalview.util.BrowserLauncher.openURL(url);\r
1121       }\r
1122       catch (Exception ex)\r
1123       {\r
1124         JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
1125             "Unixers: Couldn't find default web browser."\r
1126            +"\nAdd the full path to your browser in Preferences.",\r
1127            "Web browser not found", JOptionPane.WARNING_MESSAGE );\r
1128 \r
1129 \r
1130         ex.printStackTrace();\r
1131       }\r
1132     }\r
1133 \r
1134     void hideSequences(boolean representGroup)\r
1135     {\r
1136       SequenceGroup sg = ap.av.getSelectionGroup();\r
1137       if(sg==null || sg.getSize(false)<1)\r
1138       {\r
1139         ap.av.hideSequence(new SequenceI[]{sequence});\r
1140         return;\r
1141       }\r
1142 \r
1143       int gsize = sg.getSize(false);\r
1144       SequenceI [] hseqs;\r
1145 \r
1146       hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ];\r
1147 \r
1148         int index = 0;\r
1149         for(int i=0; i<gsize; i++)\r
1150         {\r
1151           if(representGroup && sg.getSequenceAt(i)!=sequence)\r
1152           {\r
1153             sequence.addHiddenSequence(sg.getSequenceAt(i));\r
1154             hseqs[index++] = sg.getSequenceAt(i);\r
1155           }\r
1156           else if(!representGroup)\r
1157           {\r
1158             hseqs[index++] = sg.getSequenceAt(i);\r
1159           }\r
1160         }\r
1161 \r
1162         ap.av.hideSequence(hseqs);\r
1163 \r
1164         ap.av.setSelectionGroup(null);\r
1165     }\r
1166 \r
1167   public void copy_actionPerformed(ActionEvent e)\r
1168   {\r
1169     ap.alignFrame.copy_actionPerformed(null);\r
1170   }\r
1171 \r
1172   public void cut_actionPerformed(ActionEvent e)\r
1173   {\r
1174     ap.alignFrame.cut_actionPerformed(null);\r
1175   }\r
1176 \r
1177   public void upperCase_actionPerformed(ActionEvent e)\r
1178   {\r
1179     changeCase(e.getSource());\r
1180   }\r
1181 \r
1182   public void lowerCase_actionPerformed(ActionEvent e)\r
1183   {\r
1184     changeCase(e.getSource());\r
1185   }\r
1186 \r
1187   public void toggle_actionPerformed(ActionEvent e)\r
1188   {\r
1189     changeCase(e.getSource());\r
1190   }\r
1191 \r
1192   void changeCase(Object source)\r
1193   {\r
1194     SequenceGroup sg = ap.av.getSelectionGroup();\r
1195     Vector regions = new Vector();\r
1196     if (sg != null)\r
1197     {\r
1198       int start = sg.getStartRes();\r
1199       int end = sg.getEndRes() + 1;\r
1200 \r
1201       do\r
1202       {\r
1203         if (ap.av.hasHiddenColumns)\r
1204         {\r
1205           if(start==0)\r
1206             start = ap.av.colSel.adjustForHiddenColumns(start);\r
1207 \r
1208           end = ap.av.colSel.getHiddenBoundaryRight(start);\r
1209           if (start == end)\r
1210             end = sg.getEndRes() + 1;\r
1211           if (end > sg.getEndRes())\r
1212             end = sg.getEndRes() + 1;\r
1213         }\r
1214 \r
1215         regions.addElement(new int[]\r
1216                            {start, end});\r
1217 \r
1218         if (ap.av.hasHiddenColumns)\r
1219         {\r
1220           start = ap.av.colSel.adjustForHiddenColumns(end);\r
1221           start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;\r
1222         }\r
1223       }\r
1224       while (end < sg.getEndRes());\r
1225 \r
1226       int[][] startEnd = new int[regions.size()][2];\r
1227       for (int i = 0; i < regions.size(); i++)\r
1228       {\r
1229         startEnd[i] = (int[]) regions.elementAt(i);\r
1230       }\r
1231 \r
1232 \r
1233       String description;\r
1234       int caseChange;\r
1235 \r
1236       if(source==toggle)\r
1237       {\r
1238         description = "Toggle Case";\r
1239         caseChange = ChangeCaseCommand.TOGGLE_CASE;\r
1240       }\r
1241       else if(source==upperCase)\r
1242       {\r
1243         description = "To Upper Case";\r
1244         caseChange = ChangeCaseCommand.TO_UPPER;\r
1245       }\r
1246       else\r
1247       {\r
1248         description = "To Lower Case";\r
1249         caseChange = ChangeCaseCommand.TO_LOWER;\r
1250       }\r
1251 \r
1252       ChangeCaseCommand caseCommand = new ChangeCaseCommand(\r
1253           description, sg.getSequencesAsArray(true), startEnd, caseChange\r
1254           );\r
1255 \r
1256       ap.alignFrame.addHistoryItem(caseCommand);\r
1257 \r
1258 \r
1259       PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
1260     }\r
1261   }\r
1262 \r
1263   public void outputText_actionPerformed(ActionEvent e)\r
1264   {\r
1265     CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
1266     Desktop.addInternalFrame(cap,\r
1267                              "Alignment output - " + e.getActionCommand(), 600,\r
1268                              500);\r
1269 \r
1270     String [] omitHidden = null;\r
1271 \r
1272     if(ap.av.hasHiddenColumns)\r
1273     {\r
1274       System.out.println("PROMPT USER HERE");\r
1275       omitHidden = ap.av.getViewAsString(true);\r
1276     }\r
1277 \r
1278     cap.setText(new FormatAdapter().formatSequences(\r
1279         e.getActionCommand(),\r
1280         ap.av.getSelectionAsNewSequence(),\r
1281         omitHidden));\r
1282   }\r
1283 \r
1284 \r
1285   public void pdbFromFile_actionPerformed(ActionEvent e)\r
1286   {\r
1287      jalview.io.JalviewFileChooser chooser\r
1288          = new jalview.io.JalviewFileChooser(jalview.bin.Cache.\r
1289          getProperty(\r
1290              "LAST_DIRECTORY"));\r
1291      chooser.setFileView(new jalview.io.JalviewFileView());\r
1292      chooser.setDialogTitle("Select a PDB file");\r
1293      chooser.setToolTipText("Load a PDB file");\r
1294 \r
1295      int value = chooser.showOpenDialog(null);\r
1296 \r
1297      if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
1298      {\r
1299        PDBEntry entry = new PDBEntry();\r
1300        String choice = chooser.getSelectedFile().getPath();\r
1301        jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
1302        try\r
1303        {\r
1304          MCview.PDBfile pdbfile = new MCview.PDBfile(choice,\r
1305                                        jalview.io.AppletFormatAdapter.FILE);\r
1306 \r
1307          if (pdbfile.id == null)\r
1308          {\r
1309            String reply = JOptionPane.showInternalInputDialog(\r
1310                Desktop.desktop,\r
1311                "Couldn't find a PDB id in the file supplied."\r
1312                + "Please enter an Id to identify this structure.",\r
1313                "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);\r
1314            if (reply == null)\r
1315              return;\r
1316 \r
1317            entry.setId(reply);\r
1318          }\r
1319          else\r
1320            entry.setId(pdbfile.id);\r
1321        }\r
1322        catch (java.io.IOException ex)\r
1323        {\r
1324          ex.printStackTrace();\r
1325        }\r
1326 \r
1327        entry.setFile(choice);\r
1328        sequence.getDatasetSequence().addPDBId(entry);\r
1329      }\r
1330 \r
1331   }\r
1332 \r
1333   public void enterPDB_actionPerformed(ActionEvent e)\r
1334   {\r
1335     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
1336         "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);\r
1337 \r
1338     if (id != null && id.length() > 0)\r
1339     {\r
1340       PDBEntry entry = new PDBEntry();\r
1341       entry.setId(id);\r
1342       sequence.getDatasetSequence()\r
1343           .addPDBId(entry);\r
1344     }\r
1345   }\r
1346 \r
1347   public void discoverPDB_actionPerformed(ActionEvent e)\r
1348   {\r
1349     new jalview.io.DBRefFetcher(\r
1350              ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);\r
1351   }\r
1352 \r
1353   public void sequenceFeature_actionPerformed(ActionEvent e)\r
1354   {\r
1355     SequenceGroup sg = ap.av.getSelectionGroup();\r
1356     if(sg==null)\r
1357       return;\r
1358 \r
1359     int gSize= sg.getSize(false);\r
1360     SequenceI [] seqs = new SequenceI[gSize];\r
1361     SequenceFeature [] features = new SequenceFeature[gSize];\r
1362 \r
1363     for (int i = 0; i < gSize; i++)\r
1364     {\r
1365       seqs[i] = sg.getSequenceAt(i).getDatasetSequence();\r
1366       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());\r
1367       int end = sg.findEndRes(sg.getSequenceAt(i));\r
1368       features[i] = new SequenceFeature(null,null, null,start,end,"Jalview");\r
1369     }\r
1370 \r
1371     if (ap.seqPanel.seqCanvas.getFeatureRenderer()\r
1372         .createNewFeatures(seqs, features))\r
1373     {\r
1374       ap.alignFrame.showSeqFeatures.setSelected(true);\r
1375       ap.av.setShowSequenceFeatures(true);\r
1376       ap.highlightSearchResults(null);\r
1377     }\r
1378   }\r
1379 }\r