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