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   JMenuItem textColour = new JMenuItem();\r
  85   JMenu jMenu1 = new JMenu();\r
  86 \r
  87   /**\r
  88      * Creates a new PopupMenu object.\r
  89      *\r
  90      * @param ap DOCUMENT ME!\r
  91      * @param seq DOCUMENT ME!\r
  92      */\r
  93     public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)\r
  94     {\r
  95         ///////////////////////////////////////////////////////////\r
  96         // If this is activated from the sequence panel, the user may want to\r
  97         // edit or annotate a particular residue. Therefore display the residue menu\r
  98         //\r
  99         // If from the IDPanel, we must display the sequence menu\r
 100         //////////////////////////////////////////////////////////\r
 101         this.ap = ap;\r
 102         sequence = seq;\r
 103 \r
 104         ButtonGroup colours = new ButtonGroup();\r
 105         colours.add(noColourmenuItem);\r
 106         colours.add(clustalColour);\r
 107         colours.add(zappoColour);\r
 108         colours.add(taylorColour);\r
 109         colours.add(hydrophobicityColour);\r
 110         colours.add(helixColour);\r
 111         colours.add(strandColour);\r
 112         colours.add(turnColour);\r
 113         colours.add(buriedColour);\r
 114         colours.add(abovePIDColour);\r
 115         colours.add(userDefinedColour);\r
 116         colours.add(PIDColour);\r
 117         colours.add(BLOSUM62Colour);\r
 118 \r
 119         for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)\r
 120         {\r
 121           JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );\r
 122 \r
 123           item.addActionListener(new java.awt.event.ActionListener()\r
 124           {\r
 125             public void actionPerformed(ActionEvent e)\r
 126             {\r
 127               outputText_actionPerformed(e);\r
 128             }\r
 129           });\r
 130 \r
 131           outputMenu.add(item);\r
 132         }\r
 133 \r
 134 \r
 135         try\r
 136         {\r
 137             jbInit();\r
 138         }\r
 139         catch (Exception e)\r
 140         {\r
 141             e.printStackTrace();\r
 142         }\r
 143 \r
 144 \r
 145         if (seq != null)\r
 146         {\r
 147           sequenceMenu.setText(sequence.getName());\r
 148 \r
 149           JMenuItem menuItem;\r
 150           if( seq.getDatasetSequence().getPDBId() != null)\r
 151           {\r
 152             java.util.Enumeration e = seq.getDatasetSequence().getPDBId().\r
 153                 elements();\r
 154 \r
 155             while (e.hasMoreElements())\r
 156             {\r
 157               final PDBEntry pdb = (PDBEntry) e.nextElement();\r
 158 \r
 159               menuItem = new JMenuItem();\r
 160               menuItem.setText("View PDB entry: " + pdb.getId());\r
 161               menuItem.addActionListener(new java.awt.event.ActionListener()\r
 162               {\r
 163                 public void actionPerformed(ActionEvent e)\r
 164                 {\r
 165                   new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);\r
 166                 }\r
 167               });\r
 168               sequenceMenu.add(menuItem);\r
 169             }\r
 170           }\r
 171 \r
 172           menuItem = new JMenuItem("Hide Sequences");\r
 173           menuItem.addActionListener(new java.awt.event.ActionListener()\r
 174               {\r
 175                 public void actionPerformed(ActionEvent e)\r
 176                 {\r
 177                   hideSequences(false);\r
 178                 }\r
 179               });\r
 180           add(menuItem);\r
 181 \r
 182           if(ap.av.getSelectionGroup() !=null\r
 183              && ap.av.getSelectionGroup().getSize(false)>1)\r
 184           {\r
 185             menuItem = new JMenuItem("Represent Group with " + seq.getName());\r
 186             menuItem.addActionListener(new java.awt.event.ActionListener()\r
 187             {\r
 188               public void actionPerformed(ActionEvent e)\r
 189               {\r
 190                 hideSequences(true);\r
 191               }\r
 192             });\r
 193             sequenceMenu.add(menuItem);\r
 194           }\r
 195 \r
 196           if (ap.av.hasHiddenRows)\r
 197           {\r
 198             final int index = ap.av.alignment.findIndex(seq);\r
 199 \r
 200             if (ap.av.adjustForHiddenSeqs(index) -\r
 201                 ap.av.adjustForHiddenSeqs(index - 1) > 1)\r
 202             {\r
 203               menuItem = new JMenuItem("Reveal Sequences");\r
 204               menuItem.addActionListener(new ActionListener()\r
 205               {\r
 206                 public void actionPerformed(ActionEvent e)\r
 207                 {\r
 208                   ap.av.showSequence(index);\r
 209                   if (ap.overviewPanel != null)\r
 210                     ap.overviewPanel.updateOverviewImage();\r
 211                 }\r
 212               });\r
 213               add(menuItem);\r
 214             }\r
 215 \r
 216             menuItem = new JMenuItem("Reveal All");\r
 217             menuItem.addActionListener(new ActionListener()\r
 218                 {\r
 219                   public void actionPerformed(ActionEvent e)\r
 220                   {\r
 221                     ap.av.showAllHiddenSeqs();\r
 222                     if (ap.overviewPanel != null)\r
 223                       ap.overviewPanel.updateOverviewImage();\r
 224                     }\r
 225                 });\r
 226 \r
 227             add(menuItem);\r
 228           }\r
 229 \r
 230 \r
 231         }\r
 232 \r
 233 \r
 234 \r
 235         SequenceGroup sg = ap.av.getSelectionGroup();\r
 236 \r
 237         if (sg != null)\r
 238         {\r
 239             groupName.setText(sg.getName());\r
 240 \r
 241             if (sg.cs instanceof ZappoColourScheme)\r
 242             {\r
 243                 zappoColour.setSelected(true);\r
 244             }\r
 245             else if (sg.cs instanceof TaylorColourScheme)\r
 246             {\r
 247                 taylorColour.setSelected(true);\r
 248             }\r
 249             else if (sg.cs instanceof PIDColourScheme)\r
 250             {\r
 251                 PIDColour.setSelected(true);\r
 252             }\r
 253             else if (sg.cs instanceof Blosum62ColourScheme)\r
 254             {\r
 255                 BLOSUM62Colour.setSelected(true);\r
 256             }\r
 257             else if (sg.cs instanceof UserColourScheme)\r
 258             {\r
 259                 userDefinedColour.setSelected(true);\r
 260             }\r
 261             else if (sg.cs instanceof HydrophobicColourScheme)\r
 262             {\r
 263                 hydrophobicityColour.setSelected(true);\r
 264             }\r
 265             else if (sg.cs instanceof HelixColourScheme)\r
 266             {\r
 267                 helixColour.setSelected(true);\r
 268             }\r
 269             else if (sg.cs instanceof StrandColourScheme)\r
 270             {\r
 271                 strandColour.setSelected(true);\r
 272             }\r
 273             else if (sg.cs instanceof TurnColourScheme)\r
 274             {\r
 275                 turnColour.setSelected(true);\r
 276             }\r
 277             else if (sg.cs instanceof BuriedColourScheme)\r
 278             {\r
 279                 buriedColour.setSelected(true);\r
 280             }\r
 281             else if (sg.cs instanceof ClustalxColourScheme)\r
 282             {\r
 283                 clustalColour.setSelected(true);\r
 284             }\r
 285             else\r
 286             {\r
 287                 noColourmenuItem.setSelected(true);\r
 288             }\r
 289 \r
 290             if (sg.cs!=null && sg.cs.conservationApplied())\r
 291             {\r
 292                 conservationMenuItem.setSelected(true);\r
 293             }\r
 294 \r
 295             showText.setSelected(sg.getDisplayText());\r
 296             showColourText.setSelected(sg.getColourText());\r
 297             showBoxes.setSelected(sg.getDisplayBoxes());\r
 298         }\r
 299         else\r
 300         {\r
 301           groupMenu.setVisible(false);\r
 302           editMenu.setVisible(false);\r
 303         }\r
 304 \r
 305         if (!ap.av.alignment.getGroups().contains(sg))\r
 306         {\r
 307             unGroupMenuItem.setVisible(false);\r
 308         }\r
 309 \r
 310 \r
 311         if (seq == null)\r
 312         {\r
 313             sequenceMenu.setVisible(false);\r
 314             pdbMenu.setVisible(false);\r
 315         }\r
 316 \r
 317         if(links != null && links.size()>0)\r
 318         {\r
 319           JMenu linkMenu = new JMenu("Link");\r
 320           JMenuItem item;\r
 321           for(int i=0; i<links.size(); i++)\r
 322           {\r
 323             String link = links.elementAt(i).toString();\r
 324             final String label = link.substring(0, link.indexOf("|"));\r
 325             item = new JMenuItem(label);\r
 326             final String url;\r
 327 \r
 328             if (link.indexOf("$SEQUENCE_ID$") > -1)\r
 329             {\r
 330               String id = seq.getName();\r
 331               if (id.indexOf("|") > -1)\r
 332                 id = id.substring(id.lastIndexOf("|") + 1);\r
 333 \r
 334               url = link.substring(link.indexOf("|") + 1,\r
 335                                    link.indexOf("$SEQUENCE_ID$"))\r
 336                   + id +\r
 337                   link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
 338             }\r
 339             else\r
 340               url = link.substring(link.lastIndexOf("|")+1);\r
 341 \r
 342 \r
 343             item.addActionListener(new java.awt.event.ActionListener()\r
 344             {\r
 345                 public void actionPerformed(ActionEvent e)\r
 346                 {\r
 347                     showLink(url);\r
 348                 }\r
 349             });\r
 350 \r
 351             linkMenu.add(item);\r
 352           }\r
 353           if(sequence!=null)\r
 354             sequenceMenu.add(linkMenu);\r
 355           else\r
 356             add(linkMenu);\r
 357         }\r
 358     }\r
 359 \r
 360 \r
 361     /**\r
 362      * DOCUMENT ME!\r
 363      *\r
 364      * @throws Exception DOCUMENT ME!\r
 365      */\r
 366     private void jbInit() throws Exception\r
 367     {\r
 368         groupMenu.setText("Group");\r
 369         groupMenu.setText("Selection");\r
 370         groupName.setText("Name");\r
 371         groupName.addActionListener(new java.awt.event.ActionListener()\r
 372             {\r
 373                 public void actionPerformed(ActionEvent e)\r
 374                 {\r
 375                     groupName_actionPerformed(e);\r
 376                 }\r
 377             });\r
 378         sequenceMenu.setText("Sequence");\r
 379         sequenceName.setText("Edit Name/Description");\r
 380         sequenceName.addActionListener(new java.awt.event.ActionListener()\r
 381             {\r
 382                 public void actionPerformed(ActionEvent e)\r
 383                 {\r
 384                     sequenceName_actionPerformed(e);\r
 385                 }\r
 386             });\r
 387         PIDColour.setFocusPainted(false);\r
 388         unGroupMenuItem.setText("Remove Group");\r
 389         unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 390             {\r
 391                 public void actionPerformed(ActionEvent e)\r
 392                 {\r
 393                     unGroupMenuItem_actionPerformed(e);\r
 394                 }\r
 395             });\r
 396 \r
 397         outline.setText("Border colour");\r
 398         outline.addActionListener(new java.awt.event.ActionListener()\r
 399             {\r
 400                 public void actionPerformed(ActionEvent e)\r
 401                 {\r
 402                     outline_actionPerformed(e);\r
 403                 }\r
 404             });\r
 405         nucleotideMenuItem.setText("Nucleotide");\r
 406         nucleotideMenuItem.addActionListener(new ActionListener()\r
 407             {\r
 408                 public void actionPerformed(ActionEvent e)\r
 409                 {\r
 410                     nucleotideMenuItem_actionPerformed(e);\r
 411                 }\r
 412             });\r
 413         colourMenu.setText("Group Colour");\r
 414         showBoxes.setText("Boxes");\r
 415         showBoxes.setState(true);\r
 416         showBoxes.addActionListener(new ActionListener()\r
 417             {\r
 418                 public void actionPerformed(ActionEvent e)\r
 419                 {\r
 420                     showBoxes_actionPerformed(e);\r
 421                 }\r
 422             });\r
 423         showText.setText("Text");\r
 424         showText.setState(true);\r
 425         showText.addActionListener(new ActionListener()\r
 426             {\r
 427                 public void actionPerformed(ActionEvent e)\r
 428                 {\r
 429                     showText_actionPerformed(e);\r
 430                 }\r
 431             });\r
 432         showColourText.setText("Colour Text");\r
 433         showColourText.addActionListener(new ActionListener()\r
 434             {\r
 435                 public void actionPerformed(ActionEvent e)\r
 436                 {\r
 437                     showColourText_actionPerformed(e);\r
 438                 }\r
 439             });\r
 440     editMenu.setText("Edit");\r
 441     cut.setText("Cut");\r
 442     cut.addActionListener(new ActionListener()\r
 443     {\r
 444       public void actionPerformed(ActionEvent e)\r
 445       {\r
 446         cut_actionPerformed(e);\r
 447       }\r
 448     });\r
 449     upperCase.setText("To Upper Case");\r
 450     upperCase.addActionListener(new ActionListener()\r
 451     {\r
 452       public void actionPerformed(ActionEvent e)\r
 453       {\r
 454         changeCase(e);\r
 455       }\r
 456     });\r
 457     copy.setText("Copy");\r
 458     copy.addActionListener(new ActionListener()\r
 459     {\r
 460       public void actionPerformed(ActionEvent e)\r
 461       {\r
 462         copy_actionPerformed(e);\r
 463       }\r
 464     });\r
 465     lowerCase.setText("To Lower Case");\r
 466     lowerCase.addActionListener(new ActionListener()\r
 467     {\r
 468       public void actionPerformed(ActionEvent e)\r
 469       {\r
 470         changeCase(e);\r
 471       }\r
 472     });\r
 473     toggle.setText("Toggle Case");\r
 474     toggle.addActionListener(new ActionListener()\r
 475     {\r
 476       public void actionPerformed(ActionEvent e)\r
 477       {\r
 478         changeCase(e);\r
 479       }\r
 480     });\r
 481     pdbMenu.setText("Associate Structure with Sequence");\r
 482     pdbFromFile.setText("From File");\r
 483     pdbFromFile.addActionListener(new ActionListener()\r
 484     {\r
 485       public void actionPerformed(ActionEvent e)\r
 486       {\r
 487         pdbFromFile_actionPerformed(e);\r
 488       }\r
 489     });\r
 490     enterPDB.setText("Enter PDB Id");\r
 491     enterPDB.addActionListener(new ActionListener()\r
 492     {\r
 493       public void actionPerformed(ActionEvent e)\r
 494       {\r
 495         enterPDB_actionPerformed(e);\r
 496       }\r
 497     });\r
 498     discoverPDB.setText("Discover PDB ids");\r
 499     discoverPDB.addActionListener(new ActionListener()\r
 500     {\r
 501       public void actionPerformed(ActionEvent e)\r
 502       {\r
 503         discoverPDB_actionPerformed(e);\r
 504       }\r
 505     });\r
 506     outputMenu.setText("Output to Textbox...");\r
 507     sequenceFeature.setText("Create Sequence Feature");\r
 508     sequenceFeature.addActionListener(new ActionListener()\r
 509     {\r
 510       public void actionPerformed(ActionEvent e)\r
 511       {\r
 512         sequenceFeature_actionPerformed(e);\r
 513       }\r
 514     });\r
 515     textColour.setText("Text Colour");\r
 516     textColour.addActionListener(new ActionListener()\r
 517     {\r
 518       public void actionPerformed(ActionEvent e)\r
 519       {\r
 520         textColour_actionPerformed(e);\r
 521       }\r
 522     });\r
 523     jMenu1.setText("Group");\r
 524     add(groupMenu);\r
 525 \r
 526     add(sequenceMenu);\r
 527     groupMenu.add(editMenu);\r
 528     groupMenu.add(outputMenu);\r
 529     groupMenu.add(sequenceFeature);\r
 530     groupMenu.add(jMenu1);\r
 531     sequenceMenu.add(sequenceName);\r
 532     sequenceMenu.add(pdbMenu);\r
 533     colourMenu.add(textColour);\r
 534     colourMenu.add(noColourmenuItem);\r
 535         colourMenu.add(clustalColour);\r
 536         colourMenu.add(BLOSUM62Colour);\r
 537         colourMenu.add(PIDColour);\r
 538         colourMenu.add(zappoColour);\r
 539         colourMenu.add(taylorColour);\r
 540         colourMenu.add(hydrophobicityColour);\r
 541         colourMenu.add(helixColour);\r
 542         colourMenu.add(strandColour);\r
 543         colourMenu.add(turnColour);\r
 544         colourMenu.add(buriedColour);\r
 545         colourMenu.add(nucleotideMenuItem);\r
 546         colourMenu.add(userDefinedColour);\r
 547 \r
 548         if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
 549         {\r
 550           java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 551               getUserColourSchemes().keys();\r
 552 \r
 553           while (userColours.hasMoreElements())\r
 554           {\r
 555             JMenuItem item = new JMenuItem(userColours.\r
 556                 nextElement().toString());\r
 557             item.addActionListener(new ActionListener()\r
 558             {\r
 559               public void actionPerformed(ActionEvent evt)\r
 560               {\r
 561                 userDefinedColour_actionPerformed(evt);\r
 562               }\r
 563             });\r
 564             colourMenu.add(item);\r
 565           }\r
 566         }\r
 567 \r
 568 \r
 569         colourMenu.addSeparator();\r
 570         colourMenu.add(abovePIDColour);\r
 571         colourMenu.add(conservationMenuItem);\r
 572     editMenu.add(copy);\r
 573     editMenu.add(cut);\r
 574     editMenu.add(upperCase);\r
 575     editMenu.add(lowerCase);\r
 576     editMenu.add(toggle);\r
 577     pdbMenu.add(pdbFromFile);\r
 578     pdbMenu.add(enterPDB);\r
 579     pdbMenu.add(discoverPDB);\r
 580     jMenu1.add(groupName);\r
 581     jMenu1.add(unGroupMenuItem);\r
 582     jMenu1.add(colourMenu);\r
 583     jMenu1.add(showBoxes);\r
 584     jMenu1.add(showText);\r
 585     jMenu1.add(showColourText);\r
 586     jMenu1.add(outline);\r
 587     noColourmenuItem.setText("None");\r
 588         noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 589             {\r
 590                 public void actionPerformed(ActionEvent e)\r
 591                 {\r
 592                     noColourmenuItem_actionPerformed(e);\r
 593                 }\r
 594             });\r
 595 \r
 596         clustalColour.setText("Clustalx colours");\r
 597         clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 598             {\r
 599                 public void actionPerformed(ActionEvent e)\r
 600                 {\r
 601                     clustalColour_actionPerformed(e);\r
 602                 }\r
 603             });\r
 604         zappoColour.setText("Zappo");\r
 605         zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 606             {\r
 607                 public void actionPerformed(ActionEvent e)\r
 608                 {\r
 609                     zappoColour_actionPerformed(e);\r
 610                 }\r
 611             });\r
 612         taylorColour.setText("Taylor");\r
 613         taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 614             {\r
 615                 public void actionPerformed(ActionEvent e)\r
 616                 {\r
 617                     taylorColour_actionPerformed(e);\r
 618                 }\r
 619             });\r
 620         hydrophobicityColour.setText("Hydrophobicity");\r
 621         hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 622             {\r
 623                 public void actionPerformed(ActionEvent e)\r
 624                 {\r
 625                     hydrophobicityColour_actionPerformed(e);\r
 626                 }\r
 627             });\r
 628         helixColour.setText("Helix propensity");\r
 629         helixColour.addActionListener(new java.awt.event.ActionListener()\r
 630             {\r
 631                 public void actionPerformed(ActionEvent e)\r
 632                 {\r
 633                     helixColour_actionPerformed(e);\r
 634                 }\r
 635             });\r
 636         strandColour.setText("Strand propensity");\r
 637         strandColour.addActionListener(new java.awt.event.ActionListener()\r
 638             {\r
 639                 public void actionPerformed(ActionEvent e)\r
 640                 {\r
 641                     strandColour_actionPerformed(e);\r
 642                 }\r
 643             });\r
 644         turnColour.setText("Turn propensity");\r
 645         turnColour.addActionListener(new java.awt.event.ActionListener()\r
 646             {\r
 647                 public void actionPerformed(ActionEvent e)\r
 648                 {\r
 649                     turnColour_actionPerformed(e);\r
 650                 }\r
 651             });\r
 652         buriedColour.setText("Buried Index");\r
 653         buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 654             {\r
 655                 public void actionPerformed(ActionEvent e)\r
 656                 {\r
 657                     buriedColour_actionPerformed(e);\r
 658                 }\r
 659             });\r
 660         abovePIDColour.setText("Above % Identity");\r
 661         abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
 662             {\r
 663                 public void actionPerformed(ActionEvent e)\r
 664                 {\r
 665                     abovePIDColour_actionPerformed(e);\r
 666                 }\r
 667             });\r
 668         userDefinedColour.setText("User Defined...");\r
 669         userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 670             {\r
 671                 public void actionPerformed(ActionEvent e)\r
 672                 {\r
 673                     userDefinedColour_actionPerformed(e);\r
 674                 }\r
 675             });\r
 676         PIDColour.setText("Percentage Identity");\r
 677         PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 678             {\r
 679                 public void actionPerformed(ActionEvent e)\r
 680                 {\r
 681                     PIDColour_actionPerformed(e);\r
 682                 }\r
 683             });\r
 684         BLOSUM62Colour.setText("BLOSUM62");\r
 685         BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 686             {\r
 687                 public void actionPerformed(ActionEvent e)\r
 688                 {\r
 689                     BLOSUM62Colour_actionPerformed(e);\r
 690                 }\r
 691             });\r
 692         conservationMenuItem.setText("Conservation");\r
 693         conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 694             {\r
 695                 public void actionPerformed(ActionEvent e)\r
 696                 {\r
 697                     conservationMenuItem_actionPerformed(e);\r
 698                 }\r
 699             });\r
 700     }\r
 701 \r
 702     /**\r
 703      * DOCUMENT ME!\r
 704      */\r
 705     void refresh()\r
 706     {\r
 707         if (ap.overviewPanel != null)\r
 708           ap.overviewPanel.updateOverviewImage();\r
 709 \r
 710         PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
 711     }\r
 712 \r
 713     /**\r
 714      * DOCUMENT ME!\r
 715      *\r
 716      * @param e DOCUMENT ME!\r
 717      */\r
 718     protected void clustalColour_actionPerformed(ActionEvent e)\r
 719     {\r
 720         SequenceGroup sg = getGroup();\r
 721         sg.cs = new ClustalxColourScheme(sg.getSequences(true),\r
 722                 ap.av.alignment.getWidth());\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 zappoColour_actionPerformed(ActionEvent e)\r
 732     {\r
 733         getGroup().cs = new ZappoColourScheme();\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 taylorColour_actionPerformed(ActionEvent e)\r
 743     {\r
 744         getGroup().cs = new TaylorColourScheme();\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 hydrophobicityColour_actionPerformed(ActionEvent e)\r
 754     {\r
 755         getGroup().cs = new HydrophobicColourScheme();\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 helixColour_actionPerformed(ActionEvent e)\r
 765     {\r
 766         getGroup().cs = new HelixColourScheme();\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 strandColour_actionPerformed(ActionEvent e)\r
 776     {\r
 777         getGroup().cs = new StrandColourScheme();\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 turnColour_actionPerformed(ActionEvent e)\r
 787     {\r
 788         getGroup().cs = new TurnColourScheme();\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     protected void buriedColour_actionPerformed(ActionEvent e)\r
 798     {\r
 799         getGroup().cs = new BuriedColourScheme();\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     public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
 809     {\r
 810         getGroup().cs = new NucleotideColourScheme();\r
 811         refresh();\r
 812     }\r
 813 \r
 814     /**\r
 815      * DOCUMENT ME!\r
 816      *\r
 817      * @param e DOCUMENT ME!\r
 818      */\r
 819     protected void abovePIDColour_actionPerformed(ActionEvent e)\r
 820     {\r
 821         SequenceGroup sg = getGroup();\r
 822         if(sg.cs==null)\r
 823           return;\r
 824 \r
 825         if (abovePIDColour.isSelected())\r
 826         {\r
 827           sg.cs.setConsensus(AAFrequency.calculate(\r
 828               sg.getSequences(true), sg.getStartRes(),\r
 829               sg.getEndRes() + 1));\r
 830 \r
 831             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
 832                     getGroup().getName());\r
 833 \r
 834            sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
 835 \r
 836             SliderPanel.showPIDSlider();\r
 837         }\r
 838         else // remove PIDColouring\r
 839         {\r
 840             sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
 841         }\r
 842 \r
 843         refresh();\r
 844     }\r
 845 \r
 846     /**\r
 847      * DOCUMENT ME!\r
 848      *\r
 849      * @param e DOCUMENT ME!\r
 850      */\r
 851     protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 852     {\r
 853        SequenceGroup sg = getGroup();\r
 854 \r
 855        if (e.getActionCommand().equals("User Defined..."))\r
 856          new UserDefinedColours(ap, sg);\r
 857        else\r
 858        {\r
 859          UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
 860              getUserColourSchemes().get(e.getActionCommand());\r
 861 \r
 862          sg.cs = udc;\r
 863        }\r
 864        refresh();\r
 865      }\r
 866     /**\r
 867      * DOCUMENT ME!\r
 868      *\r
 869      * @param e DOCUMENT ME!\r
 870      */\r
 871     protected void PIDColour_actionPerformed(ActionEvent e)\r
 872     {\r
 873         SequenceGroup sg = getGroup();\r
 874         sg.cs = new PIDColourScheme();\r
 875         sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),\r
 876                                                  sg.getStartRes(),\r
 877                                                  sg.getEndRes() + 1));\r
 878         refresh();\r
 879     }\r
 880 \r
 881     /**\r
 882      * DOCUMENT ME!\r
 883      *\r
 884      * @param e DOCUMENT ME!\r
 885      */\r
 886     protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 887     {\r
 888         SequenceGroup sg = getGroup();\r
 889 \r
 890         sg.cs = new Blosum62ColourScheme();\r
 891 \r
 892         sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),\r
 893                                                  sg.getStartRes(),\r
 894                                                  sg.getEndRes() + 1));\r
 895 \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 noColourmenuItem_actionPerformed(ActionEvent e)\r
 905     {\r
 906         getGroup().cs = null;\r
 907         refresh();\r
 908     }\r
 909 \r
 910     /**\r
 911      * DOCUMENT ME!\r
 912      *\r
 913      * @param e DOCUMENT ME!\r
 914      */\r
 915     protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
 916     {\r
 917         SequenceGroup sg = getGroup();\r
 918         if(sg.cs==null)\r
 919           return;\r
 920 \r
 921         if (conservationMenuItem.isSelected())\r
 922         {\r
 923             Conservation c = new Conservation("Group",\r
 924                     ResidueProperties.propHash, 3,\r
 925                     sg.getSequences(true),\r
 926                     sg.getStartRes(),\r
 927                     sg.getEndRes() + 1);\r
 928 \r
 929             c.calculate();\r
 930             c.verdict(false, ap.av.ConsPercGaps);\r
 931 \r
 932             sg.cs.setConservation(c);\r
 933 \r
 934             SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
 935             SliderPanel.showConservationSlider();\r
 936         }\r
 937         else // remove ConservationColouring\r
 938         {\r
 939             sg.cs.setConservation(null);\r
 940         }\r
 941 \r
 942         refresh();\r
 943     }\r
 944 \r
 945     /**\r
 946      * DOCUMENT ME!\r
 947      *\r
 948      * @param e DOCUMENT ME!\r
 949      */\r
 950     protected void groupName_actionPerformed(ActionEvent e)\r
 951     {\r
 952         SequenceGroup sg = getGroup();\r
 953         String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
 954                 "Enter new group name", "Edit group name",\r
 955                 JOptionPane.QUESTION_MESSAGE);\r
 956 \r
 957         if (reply == null)\r
 958         {\r
 959             return;\r
 960         }\r
 961 \r
 962         sg.setName(reply);\r
 963         groupName.setText(reply);\r
 964     }\r
 965 \r
 966 \r
 967     /**\r
 968      * DOCUMENT ME!\r
 969      *\r
 970      * @return DOCUMENT ME!\r
 971      */\r
 972     SequenceGroup getGroup()\r
 973     {\r
 974         SequenceGroup sg = ap.av.getSelectionGroup();\r
 975       // this method won't add a new group if it already exists\r
 976         if(sg!=null)\r
 977           ap.av.alignment.addGroup(sg);\r
 978 \r
 979         return sg;\r
 980     }\r
 981 \r
 982     /**\r
 983      * DOCUMENT ME!\r
 984      *\r
 985      * @param e DOCUMENT ME!\r
 986      */\r
 987     void sequenceName_actionPerformed(ActionEvent e)\r
 988     {\r
 989       JLabel idlabel = new JLabel(  "       Sequence Name ");\r
 990       JLabel desclabel = new JLabel("Sequence Description ");\r
 991       idlabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
 992       desclabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
 993       JTextField id = new JTextField(sequence.getName(), 40);\r
 994       JTextField description = new JTextField(sequence.getDescription(), 40);\r
 995       JPanel panel = new JPanel(new BorderLayout());\r
 996       JPanel panel2 = new JPanel(new BorderLayout());\r
 997       panel2.add(idlabel, BorderLayout.WEST);\r
 998       panel2.add(id, BorderLayout.CENTER);\r
 999       panel.add(panel2, BorderLayout.NORTH);\r
1000       panel2 = new JPanel(new BorderLayout());\r
1001       panel2.add(desclabel, BorderLayout.WEST);\r
1002       panel2.add(description, BorderLayout.CENTER);\r
1003       panel.add(panel2, BorderLayout.SOUTH);\r
1004 \r
1005 \r
1006        int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
1007           panel, "Edit Sequence Name/Description",\r
1008           JOptionPane.OK_CANCEL_OPTION );\r
1009 \r
1010 \r
1011         if (reply != JOptionPane.OK_OPTION )\r
1012         {\r
1013             return;\r
1014         }\r
1015 \r
1016         String s = id.getText();\r
1017 \r
1018         if (s != null)\r
1019         {\r
1020             if (s.indexOf(" ") > -1)\r
1021             {\r
1022                 JOptionPane.showMessageDialog(ap,\r
1023                     "Spaces have been converted to \"_\"",\r
1024                     "No spaces allowed in Sequence Name",\r
1025                     JOptionPane.WARNING_MESSAGE);\r
1026             }\r
1027 \r
1028             s = s.replace(' ', '_');\r
1029             sequence.setName(s);\r
1030             ap.repaint();\r
1031         }\r
1032 \r
1033         sequence.setDescription(description.getText());\r
1034 \r
1035         ap.av.firePropertyChange("alignment", null,\r
1036                                   ap.av.getAlignment().getSequences());\r
1037 \r
1038     }\r
1039 \r
1040     /**\r
1041      * DOCUMENT ME!\r
1042      *\r
1043      * @param e DOCUMENT ME!\r
1044      */\r
1045     void unGroupMenuItem_actionPerformed(ActionEvent e)\r
1046     {\r
1047         SequenceGroup sg = ap.av.getSelectionGroup();\r
1048         ap.av.alignment.deleteGroup(sg);\r
1049         ap.av.setSelectionGroup(null);\r
1050         refresh();\r
1051     }\r
1052 \r
1053 \r
1054     /**\r
1055      * DOCUMENT ME!\r
1056      *\r
1057      * @param e DOCUMENT ME!\r
1058      */\r
1059     protected void outline_actionPerformed(ActionEvent e)\r
1060     {\r
1061         SequenceGroup sg = getGroup();\r
1062         Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
1063                 Color.BLUE);\r
1064 \r
1065         if (col != null)\r
1066         {\r
1067             sg.setOutlineColour(col);\r
1068         }\r
1069 \r
1070         refresh();\r
1071     }\r
1072 \r
1073     /**\r
1074      * DOCUMENT ME!\r
1075      *\r
1076      * @param e DOCUMENT ME!\r
1077      */\r
1078     public void showBoxes_actionPerformed(ActionEvent e)\r
1079     {\r
1080         getGroup().setDisplayBoxes(showBoxes.isSelected());\r
1081         refresh();\r
1082     }\r
1083 \r
1084     /**\r
1085      * DOCUMENT ME!\r
1086      *\r
1087      * @param e DOCUMENT ME!\r
1088      */\r
1089     public void showText_actionPerformed(ActionEvent e)\r
1090     {\r
1091         getGroup().setDisplayText(showText.isSelected());\r
1092         refresh();\r
1093     }\r
1094 \r
1095     /**\r
1096      * DOCUMENT ME!\r
1097      *\r
1098      * @param e DOCUMENT ME!\r
1099      */\r
1100     public void showColourText_actionPerformed(ActionEvent e)\r
1101     {\r
1102         getGroup().setColourText(showColourText.isSelected());\r
1103         refresh();\r
1104     }\r
1105 \r
1106     public void showLink(String url)\r
1107     {\r
1108       try\r
1109       {\r
1110         jalview.util.BrowserLauncher.openURL(url);\r
1111       }\r
1112       catch (Exception ex)\r
1113       {\r
1114         JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
1115             "Unixers: Couldn't find default web browser."\r
1116            +"\nAdd the full path to your browser in Preferences.",\r
1117            "Web browser not found", JOptionPane.WARNING_MESSAGE );\r
1118 \r
1119 \r
1120         ex.printStackTrace();\r
1121       }\r
1122     }\r
1123 \r
1124     void hideSequences(boolean representGroup)\r
1125     {\r
1126       SequenceGroup sg = ap.av.getSelectionGroup();\r
1127       if(sg==null || sg.getSize(false)<1)\r
1128       {\r
1129         ap.av.hideSequence(new SequenceI[]{sequence});\r
1130         return;\r
1131       }\r
1132 \r
1133       int gsize = sg.getSize(false);\r
1134       SequenceI [] hseqs;\r
1135 \r
1136       hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ];\r
1137 \r
1138         int index = 0;\r
1139         for(int i=0; i<gsize; i++)\r
1140         {\r
1141           if(representGroup && sg.getSequenceAt(i)!=sequence)\r
1142           {\r
1143             sequence.addHiddenSequence(sg.getSequenceAt(i));\r
1144             hseqs[index++] = sg.getSequenceAt(i);\r
1145           }\r
1146           else if(!representGroup)\r
1147           {\r
1148             hseqs[index++] = sg.getSequenceAt(i);\r
1149           }\r
1150         }\r
1151 \r
1152         ap.av.hideSequence(hseqs);\r
1153 \r
1154         ap.av.setSelectionGroup(null);\r
1155     }\r
1156 \r
1157   public void copy_actionPerformed(ActionEvent e)\r
1158   {\r
1159     ap.alignFrame.copy_actionPerformed(null);\r
1160   }\r
1161 \r
1162   public void cut_actionPerformed(ActionEvent e)\r
1163   {\r
1164     ap.alignFrame.cut_actionPerformed(null);\r
1165   }\r
1166 \r
1167   void changeCase(ActionEvent e)\r
1168   {\r
1169     Object source = e.getSource();\r
1170     SequenceGroup sg = ap.av.getSelectionGroup();\r
1171     Vector regions = new Vector();\r
1172     if (sg != null)\r
1173     {\r
1174       int start = sg.getStartRes();\r
1175       int end = sg.getEndRes() + 1;\r
1176 \r
1177       do\r
1178       {\r
1179         if (ap.av.hasHiddenColumns)\r
1180         {\r
1181           if(start==0)\r
1182             start = ap.av.colSel.adjustForHiddenColumns(start);\r
1183 \r
1184           end = ap.av.colSel.getHiddenBoundaryRight(start);\r
1185           if (start == end)\r
1186             end = sg.getEndRes() + 1;\r
1187           if (end > sg.getEndRes())\r
1188             end = sg.getEndRes() + 1;\r
1189         }\r
1190 \r
1191         regions.addElement(new int[]\r
1192                            {start, end});\r
1193 \r
1194         if (ap.av.hasHiddenColumns)\r
1195         {\r
1196           start = ap.av.colSel.adjustForHiddenColumns(end);\r
1197           start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;\r
1198         }\r
1199       }\r
1200       while (end < sg.getEndRes());\r
1201 \r
1202       int[][] startEnd = new int[regions.size()][2];\r
1203       for (int i = 0; i < regions.size(); i++)\r
1204       {\r
1205         startEnd[i] = (int[]) regions.elementAt(i);\r
1206       }\r
1207 \r
1208 \r
1209       String description;\r
1210       int caseChange;\r
1211 \r
1212       if(source==toggle)\r
1213       {\r
1214         description = "Toggle Case";\r
1215         caseChange = ChangeCaseCommand.TOGGLE_CASE;\r
1216       }\r
1217       else if(source==upperCase)\r
1218       {\r
1219         description = "To Upper Case";\r
1220         caseChange = ChangeCaseCommand.TO_UPPER;\r
1221       }\r
1222       else\r
1223       {\r
1224         description = "To Lower Case";\r
1225         caseChange = ChangeCaseCommand.TO_LOWER;\r
1226       }\r
1227 \r
1228       ChangeCaseCommand caseCommand = new ChangeCaseCommand(\r
1229           description, sg.getSequencesAsArray(true), startEnd, caseChange\r
1230           );\r
1231 \r
1232       ap.alignFrame.addHistoryItem(caseCommand);\r
1233 \r
1234 \r
1235       ap.av.firePropertyChange("alignment", null,\r
1236                                 ap.av.getAlignment().getSequences());\r
1237 \r
1238     }\r
1239   }\r
1240 \r
1241   public void outputText_actionPerformed(ActionEvent e)\r
1242   {\r
1243     CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
1244     cap.setForInput(null);\r
1245     Desktop.addInternalFrame(cap,\r
1246                              "Alignment output - " + e.getActionCommand(), 600,\r
1247                              500);\r
1248 \r
1249     String [] omitHidden = null;\r
1250 \r
1251     if(ap.av.hasHiddenColumns)\r
1252     {\r
1253       System.out.println("PROMPT USER HERE");\r
1254       omitHidden = ap.av.getViewAsString(true);\r
1255     }\r
1256 \r
1257     cap.setText(new FormatAdapter().formatSequences(\r
1258         e.getActionCommand(),\r
1259         ap.av.getSelectionAsNewSequence(),\r
1260         omitHidden));\r
1261   }\r
1262 \r
1263 \r
1264   public void pdbFromFile_actionPerformed(ActionEvent e)\r
1265   {\r
1266      jalview.io.JalviewFileChooser chooser\r
1267          = new jalview.io.JalviewFileChooser(jalview.bin.Cache.\r
1268          getProperty(\r
1269              "LAST_DIRECTORY"));\r
1270      chooser.setFileView(new jalview.io.JalviewFileView());\r
1271      chooser.setDialogTitle("Select a PDB file");\r
1272      chooser.setToolTipText("Load a PDB file");\r
1273 \r
1274      int value = chooser.showOpenDialog(null);\r
1275 \r
1276      if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
1277      {\r
1278        PDBEntry entry = new PDBEntry();\r
1279        String choice = chooser.getSelectedFile().getPath();\r
1280        jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
1281        try\r
1282        {\r
1283          MCview.PDBfile pdbfile = new MCview.PDBfile(choice,\r
1284                                        jalview.io.AppletFormatAdapter.FILE);\r
1285 \r
1286          if (pdbfile.id == null)\r
1287          {\r
1288            String reply = JOptionPane.showInternalInputDialog(\r
1289                Desktop.desktop,\r
1290                "Couldn't find a PDB id in the file supplied."\r
1291                + "Please enter an Id to identify this structure.",\r
1292                "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);\r
1293            if (reply == null)\r
1294              return;\r
1295 \r
1296            entry.setId(reply);\r
1297          }\r
1298          else\r
1299            entry.setId(pdbfile.id);\r
1300        }\r
1301        catch (java.io.IOException ex)\r
1302        {\r
1303          ex.printStackTrace();\r
1304        }\r
1305 \r
1306        entry.setFile(choice);\r
1307        sequence.getDatasetSequence().addPDBId(entry);\r
1308      }\r
1309 \r
1310   }\r
1311 \r
1312   public void enterPDB_actionPerformed(ActionEvent e)\r
1313   {\r
1314     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
1315         "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);\r
1316 \r
1317     if (id != null && id.length() > 0)\r
1318     {\r
1319       PDBEntry entry = new PDBEntry();\r
1320       entry.setId(id);\r
1321       sequence.getDatasetSequence()\r
1322           .addPDBId(entry);\r
1323     }\r
1324   }\r
1325 \r
1326   public void discoverPDB_actionPerformed(ActionEvent e)\r
1327   {\r
1328     new jalview.io.DBRefFetcher(\r
1329              ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);\r
1330   }\r
1331 \r
1332   public void sequenceFeature_actionPerformed(ActionEvent e)\r
1333   {\r
1334     SequenceGroup sg = ap.av.getSelectionGroup();\r
1335     if(sg==null)\r
1336       return;\r
1337 \r
1338     int gSize= sg.getSize(false);\r
1339     SequenceI [] seqs = new SequenceI[gSize];\r
1340     SequenceFeature [] features = new SequenceFeature[gSize];\r
1341 \r
1342     for (int i = 0; i < gSize; i++)\r
1343     {\r
1344       seqs[i] = sg.getSequenceAt(i).getDatasetSequence();\r
1345       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());\r
1346       int end = sg.findEndRes(sg.getSequenceAt(i));\r
1347       features[i] = new SequenceFeature(null,null, null,start,end,"Jalview");\r
1348     }\r
1349 \r
1350     if (ap.seqPanel.seqCanvas.getFeatureRenderer()\r
1351         .createNewFeatures(seqs, features))\r
1352     {\r
1353       ap.alignFrame.showSeqFeatures.setSelected(true);\r
1354       ap.av.setShowSequenceFeatures(true);\r
1355       ap.highlightSearchResults(null);\r
1356     }\r
1357   }\r
1358 \r
1359   public void textColour_actionPerformed(ActionEvent e)\r
1360   {\r
1361     SequenceGroup sg = getGroup();\r
1362     if (sg != null)\r
1363       new TextColourChooser().chooseColour(ap, sg);\r
1364   }\r
1365 }\r