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      * DOCUMENT ME!\r
 957      *\r
 958      * @param e DOCUMENT ME!\r
 959      */\r
 960     protected void analyze_actionPerformed(ActionEvent e)\r
 961     {\r
 962         CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
 963         JInternalFrame frame = new JInternalFrame();\r
 964         frame.setContentPane(cap);\r
 965         Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
 966 \r
 967         SequenceGroup sg = getGroup();\r
 968         StringBuffer sb = new StringBuffer();\r
 969 \r
 970         for (int i = 0; i < sg.getSize(false); i++)\r
 971         {\r
 972             Sequence tmp = (Sequence) sg.getSequences(false).elementAt(i);\r
 973             sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
 974             sb.append("\n");\r
 975         }\r
 976 \r
 977         sb.append("Something amazing will happen soon");\r
 978         cap.setText(sb.toString());\r
 979     }\r
 980 \r
 981     /**\r
 982      * DOCUMENT ME!\r
 983      *\r
 984      * @return DOCUMENT ME!\r
 985      */\r
 986     SequenceGroup getGroup()\r
 987     {\r
 988         SequenceGroup sg = ap.av.getSelectionGroup();\r
 989       // this method won't add a new group if it already exists\r
 990         if(sg!=null)\r
 991           ap.av.alignment.addGroup(sg);\r
 992 \r
 993         return sg;\r
 994     }\r
 995 \r
 996     /**\r
 997      * DOCUMENT ME!\r
 998      *\r
 999      * @param e DOCUMENT ME!\r
1000      */\r
1001     void sequenceName_actionPerformed(ActionEvent e)\r
1002     {\r
1003       JLabel idlabel = new JLabel(  "       Sequence Name ");\r
1004       JLabel desclabel = new JLabel("Sequence Description ");\r
1005       idlabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
1006       desclabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
1007       JTextField id = new JTextField(sequence.getName(), 40);\r
1008       JTextField description = new JTextField(sequence.getDescription(), 40);\r
1009       JPanel panel = new JPanel(new BorderLayout());\r
1010       JPanel panel2 = new JPanel(new BorderLayout());\r
1011       panel2.add(idlabel, BorderLayout.WEST);\r
1012       panel2.add(id, BorderLayout.CENTER);\r
1013       panel.add(panel2, BorderLayout.NORTH);\r
1014       panel2 = new JPanel(new BorderLayout());\r
1015       panel2.add(desclabel, BorderLayout.WEST);\r
1016       panel2.add(description, BorderLayout.CENTER);\r
1017       panel.add(panel2, BorderLayout.SOUTH);\r
1018 \r
1019 \r
1020        int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
1021           panel, "Edit Sequence Name/Description",\r
1022           JOptionPane.OK_CANCEL_OPTION );\r
1023 \r
1024 \r
1025         if (reply != JOptionPane.OK_OPTION )\r
1026         {\r
1027             return;\r
1028         }\r
1029 \r
1030         String s = id.getText();\r
1031 \r
1032         if (s != null)\r
1033         {\r
1034             if (s.indexOf(" ") > -1)\r
1035             {\r
1036                 JOptionPane.showMessageDialog(ap,\r
1037                     "Spaces have been converted to \"_\"",\r
1038                     "No spaces allowed in Sequence Name",\r
1039                     JOptionPane.WARNING_MESSAGE);\r
1040             }\r
1041 \r
1042             s = s.replace(' ', '_');\r
1043             sequence.setName(s);\r
1044             ap.repaint();\r
1045         }\r
1046 \r
1047         sequence.setDescription(description.getText());\r
1048 \r
1049         ap.av.firePropertyChange("alignment", null,\r
1050                                   ap.av.getAlignment().getSequences());\r
1051 \r
1052     }\r
1053 \r
1054     /**\r
1055      * DOCUMENT ME!\r
1056      *\r
1057      * @param e DOCUMENT ME!\r
1058      */\r
1059     void unGroupMenuItem_actionPerformed(ActionEvent e)\r
1060     {\r
1061         SequenceGroup sg = ap.av.getSelectionGroup();\r
1062         ap.av.alignment.deleteGroup(sg);\r
1063         ap.av.setSelectionGroup(null);\r
1064         refresh();\r
1065     }\r
1066 \r
1067 \r
1068     /**\r
1069      * DOCUMENT ME!\r
1070      *\r
1071      * @param e DOCUMENT ME!\r
1072      */\r
1073     protected void outline_actionPerformed(ActionEvent e)\r
1074     {\r
1075         SequenceGroup sg = getGroup();\r
1076         Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
1077                 Color.BLUE);\r
1078 \r
1079         if (col != null)\r
1080         {\r
1081             sg.setOutlineColour(col);\r
1082         }\r
1083 \r
1084         refresh();\r
1085     }\r
1086 \r
1087     /**\r
1088      * DOCUMENT ME!\r
1089      *\r
1090      * @param e DOCUMENT ME!\r
1091      */\r
1092     public void showBoxes_actionPerformed(ActionEvent e)\r
1093     {\r
1094         getGroup().setDisplayBoxes(showBoxes.isSelected());\r
1095         refresh();\r
1096     }\r
1097 \r
1098     /**\r
1099      * DOCUMENT ME!\r
1100      *\r
1101      * @param e DOCUMENT ME!\r
1102      */\r
1103     public void showText_actionPerformed(ActionEvent e)\r
1104     {\r
1105         getGroup().setDisplayText(showText.isSelected());\r
1106         refresh();\r
1107     }\r
1108 \r
1109     /**\r
1110      * DOCUMENT ME!\r
1111      *\r
1112      * @param e DOCUMENT ME!\r
1113      */\r
1114     public void showColourText_actionPerformed(ActionEvent e)\r
1115     {\r
1116         getGroup().setColourText(showColourText.isSelected());\r
1117         refresh();\r
1118     }\r
1119 \r
1120     public void showLink(String url)\r
1121     {\r
1122       try\r
1123       {\r
1124         jalview.util.BrowserLauncher.openURL(url);\r
1125       }\r
1126       catch (Exception ex)\r
1127       {\r
1128         JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
1129             "Unixers: Couldn't find default web browser."\r
1130            +"\nAdd the full path to your browser in Preferences.",\r
1131            "Web browser not found", JOptionPane.WARNING_MESSAGE );\r
1132 \r
1133 \r
1134         ex.printStackTrace();\r
1135       }\r
1136     }\r
1137 \r
1138     void hideSequences(boolean representGroup)\r
1139     {\r
1140       SequenceGroup sg = ap.av.getSelectionGroup();\r
1141       if(sg==null || sg.getSize(false)<1)\r
1142       {\r
1143         ap.av.hideSequence(new SequenceI[]{sequence});\r
1144         return;\r
1145       }\r
1146 \r
1147       int gsize = sg.getSize(false);\r
1148       SequenceI [] hseqs;\r
1149 \r
1150       hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ];\r
1151 \r
1152         int index = 0;\r
1153         for(int i=0; i<gsize; i++)\r
1154         {\r
1155           if(representGroup && sg.getSequenceAt(i)!=sequence)\r
1156           {\r
1157             sequence.addHiddenSequence(sg.getSequenceAt(i));\r
1158             hseqs[index++] = sg.getSequenceAt(i);\r
1159           }\r
1160           else if(!representGroup)\r
1161           {\r
1162             hseqs[index++] = sg.getSequenceAt(i);\r
1163           }\r
1164         }\r
1165 \r
1166         ap.av.hideSequence(hseqs);\r
1167 \r
1168         ap.av.setSelectionGroup(null);\r
1169     }\r
1170 \r
1171   public void copy_actionPerformed(ActionEvent e)\r
1172   {\r
1173     ap.alignFrame.copy_actionPerformed(null);\r
1174   }\r
1175 \r
1176   public void cut_actionPerformed(ActionEvent e)\r
1177   {\r
1178     ap.alignFrame.cut_actionPerformed(null);\r
1179   }\r
1180 \r
1181   void changeCase(ActionEvent e)\r
1182   {\r
1183     Object source = e.getSource();\r
1184     SequenceGroup sg = ap.av.getSelectionGroup();\r
1185     Vector regions = new Vector();\r
1186     if (sg != null)\r
1187     {\r
1188       int start = sg.getStartRes();\r
1189       int end = sg.getEndRes() + 1;\r
1190 \r
1191       do\r
1192       {\r
1193         if (ap.av.hasHiddenColumns)\r
1194         {\r
1195           if(start==0)\r
1196             start = ap.av.colSel.adjustForHiddenColumns(start);\r
1197 \r
1198           end = ap.av.colSel.getHiddenBoundaryRight(start);\r
1199           if (start == end)\r
1200             end = sg.getEndRes() + 1;\r
1201           if (end > sg.getEndRes())\r
1202             end = sg.getEndRes() + 1;\r
1203         }\r
1204 \r
1205         regions.addElement(new int[]\r
1206                            {start, end});\r
1207 \r
1208         if (ap.av.hasHiddenColumns)\r
1209         {\r
1210           start = ap.av.colSel.adjustForHiddenColumns(end);\r
1211           start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;\r
1212         }\r
1213       }\r
1214       while (end < sg.getEndRes());\r
1215 \r
1216       int[][] startEnd = new int[regions.size()][2];\r
1217       for (int i = 0; i < regions.size(); i++)\r
1218       {\r
1219         startEnd[i] = (int[]) regions.elementAt(i);\r
1220       }\r
1221 \r
1222 \r
1223       String description;\r
1224       int caseChange;\r
1225 \r
1226       if(source==toggle)\r
1227       {\r
1228         description = "Toggle Case";\r
1229         caseChange = ChangeCaseCommand.TOGGLE_CASE;\r
1230       }\r
1231       else if(source==upperCase)\r
1232       {\r
1233         description = "To Upper Case";\r
1234         caseChange = ChangeCaseCommand.TO_UPPER;\r
1235       }\r
1236       else\r
1237       {\r
1238         description = "To Lower Case";\r
1239         caseChange = ChangeCaseCommand.TO_LOWER;\r
1240       }\r
1241 \r
1242       ChangeCaseCommand caseCommand = new ChangeCaseCommand(\r
1243           description, sg.getSequencesAsArray(true), startEnd, caseChange\r
1244           );\r
1245 \r
1246       ap.alignFrame.addHistoryItem(caseCommand);\r
1247 \r
1248 \r
1249       ap.av.firePropertyChange("alignment", null,\r
1250                                 ap.av.getAlignment().getSequences());\r
1251 \r
1252     }\r
1253   }\r
1254 \r
1255   public void outputText_actionPerformed(ActionEvent e)\r
1256   {\r
1257     CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
1258     Desktop.addInternalFrame(cap,\r
1259                              "Alignment output - " + e.getActionCommand(), 600,\r
1260                              500);\r
1261 \r
1262     String [] omitHidden = null;\r
1263 \r
1264     if(ap.av.hasHiddenColumns)\r
1265     {\r
1266       System.out.println("PROMPT USER HERE");\r
1267       omitHidden = ap.av.getViewAsString(true);\r
1268     }\r
1269 \r
1270     cap.setText(new FormatAdapter().formatSequences(\r
1271         e.getActionCommand(),\r
1272         ap.av.getSelectionAsNewSequence(),\r
1273         omitHidden));\r
1274   }\r
1275 \r
1276 \r
1277   public void pdbFromFile_actionPerformed(ActionEvent e)\r
1278   {\r
1279      jalview.io.JalviewFileChooser chooser\r
1280          = new jalview.io.JalviewFileChooser(jalview.bin.Cache.\r
1281          getProperty(\r
1282              "LAST_DIRECTORY"));\r
1283      chooser.setFileView(new jalview.io.JalviewFileView());\r
1284      chooser.setDialogTitle("Select a PDB file");\r
1285      chooser.setToolTipText("Load a PDB file");\r
1286 \r
1287      int value = chooser.showOpenDialog(null);\r
1288 \r
1289      if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
1290      {\r
1291        PDBEntry entry = new PDBEntry();\r
1292        String choice = chooser.getSelectedFile().getPath();\r
1293        jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
1294        try\r
1295        {\r
1296          MCview.PDBfile pdbfile = new MCview.PDBfile(choice,\r
1297                                        jalview.io.AppletFormatAdapter.FILE);\r
1298 \r
1299          if (pdbfile.id == null)\r
1300          {\r
1301            String reply = JOptionPane.showInternalInputDialog(\r
1302                Desktop.desktop,\r
1303                "Couldn't find a PDB id in the file supplied."\r
1304                + "Please enter an Id to identify this structure.",\r
1305                "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);\r
1306            if (reply == null)\r
1307              return;\r
1308 \r
1309            entry.setId(reply);\r
1310          }\r
1311          else\r
1312            entry.setId(pdbfile.id);\r
1313        }\r
1314        catch (java.io.IOException ex)\r
1315        {\r
1316          ex.printStackTrace();\r
1317        }\r
1318 \r
1319        entry.setFile(choice);\r
1320        sequence.getDatasetSequence().addPDBId(entry);\r
1321      }\r
1322 \r
1323   }\r
1324 \r
1325   public void enterPDB_actionPerformed(ActionEvent e)\r
1326   {\r
1327     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
1328         "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);\r
1329 \r
1330     if (id != null && id.length() > 0)\r
1331     {\r
1332       PDBEntry entry = new PDBEntry();\r
1333       entry.setId(id);\r
1334       sequence.getDatasetSequence()\r
1335           .addPDBId(entry);\r
1336     }\r
1337   }\r
1338 \r
1339   public void discoverPDB_actionPerformed(ActionEvent e)\r
1340   {\r
1341     new jalview.io.DBRefFetcher(\r
1342              ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);\r
1343   }\r
1344 \r
1345   public void sequenceFeature_actionPerformed(ActionEvent e)\r
1346   {\r
1347     SequenceGroup sg = ap.av.getSelectionGroup();\r
1348     if(sg==null)\r
1349       return;\r
1350 \r
1351     int gSize= sg.getSize(false);\r
1352     SequenceI [] seqs = new SequenceI[gSize];\r
1353     SequenceFeature [] features = new SequenceFeature[gSize];\r
1354 \r
1355     for (int i = 0; i < gSize; i++)\r
1356     {\r
1357       seqs[i] = sg.getSequenceAt(i).getDatasetSequence();\r
1358       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());\r
1359       int end = sg.findEndRes(sg.getSequenceAt(i));\r
1360       features[i] = new SequenceFeature(null,null, null,start,end,"Jalview");\r
1361     }\r
1362 \r
1363     if (ap.seqPanel.seqCanvas.getFeatureRenderer()\r
1364         .createNewFeatures(seqs, features))\r
1365     {\r
1366       ap.alignFrame.showSeqFeatures.setSelected(true);\r
1367       ap.av.setShowSequenceFeatures(true);\r
1368       ap.highlightSearchResults(null);\r
1369     }\r
1370   }\r
1371 }\r