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 import javax.swing.event.ChangeListener;\r
  36 import javax.swing.event.ChangeEvent;\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   JMenuItem textColour = new JMenuItem();\r
  87   JMenu jMenu1 = new JMenu();\r
  88 \r
  89   /**\r
  90      * Creates a new PopupMenu object.\r
  91      *\r
  92      * @param ap DOCUMENT ME!\r
  93      * @param seq DOCUMENT ME!\r
  94      */\r
  95     public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)\r
  96     {\r
  97         ///////////////////////////////////////////////////////////\r
  98         // If this is activated from the sequence panel, the user may want to\r
  99         // edit or annotate a particular residue. Therefore display the residue menu\r
 100         //\r
 101         // If from the IDPanel, we must display the sequence menu\r
 102         //////////////////////////////////////////////////////////\r
 103         this.ap = ap;\r
 104         sequence = seq;\r
 105 \r
 106         ButtonGroup colours = new ButtonGroup();\r
 107         colours.add(noColourmenuItem);\r
 108         colours.add(clustalColour);\r
 109         colours.add(zappoColour);\r
 110         colours.add(taylorColour);\r
 111         colours.add(hydrophobicityColour);\r
 112         colours.add(helixColour);\r
 113         colours.add(strandColour);\r
 114         colours.add(turnColour);\r
 115         colours.add(buriedColour);\r
 116         colours.add(abovePIDColour);\r
 117         colours.add(userDefinedColour);\r
 118         colours.add(PIDColour);\r
 119         colours.add(BLOSUM62Colour);\r
 120 \r
 121         for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)\r
 122         {\r
 123           JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );\r
 124 \r
 125           item.addActionListener(new java.awt.event.ActionListener()\r
 126           {\r
 127             public void actionPerformed(ActionEvent e)\r
 128             {\r
 129               outputText_actionPerformed(e);\r
 130             }\r
 131           });\r
 132 \r
 133           outputMenu.add(item);\r
 134         }\r
 135 \r
 136 \r
 137         try\r
 138         {\r
 139             jbInit();\r
 140         }\r
 141         catch (Exception e)\r
 142         {\r
 143             e.printStackTrace();\r
 144         }\r
 145 \r
 146 \r
 147         if (seq != null)\r
 148         {\r
 149           sequenceMenu.setText(sequence.getName());\r
 150 \r
 151           JMenuItem menuItem;\r
 152           if( seq.getDatasetSequence().getPDBId() != null)\r
 153           {\r
 154             java.util.Enumeration e = seq.getDatasetSequence().getPDBId().\r
 155                 elements();\r
 156 \r
 157             while (e.hasMoreElements())\r
 158             {\r
 159               final PDBEntry pdb = (PDBEntry) e.nextElement();\r
 160 \r
 161               menuItem = new JMenuItem();\r
 162               menuItem.setText("View PDB entry: " + pdb.getId());\r
 163               menuItem.addActionListener(new java.awt.event.ActionListener()\r
 164               {\r
 165                 public void actionPerformed(ActionEvent e)\r
 166                 {\r
 167                   new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);\r
 168                 }\r
 169               });\r
 170               sequenceMenu.add(menuItem);\r
 171             }\r
 172           }\r
 173 \r
 174           menuItem = new JMenuItem("Hide Sequences");\r
 175           menuItem.addActionListener(new java.awt.event.ActionListener()\r
 176               {\r
 177                 public void actionPerformed(ActionEvent e)\r
 178                 {\r
 179                   hideSequences(false);\r
 180                 }\r
 181               });\r
 182           add(menuItem);\r
 183 \r
 184           if(ap.av.getSelectionGroup() !=null\r
 185              && ap.av.getSelectionGroup().getSize(false)>1)\r
 186           {\r
 187             menuItem = new JMenuItem("Represent Group with " + seq.getName());\r
 188             menuItem.addActionListener(new java.awt.event.ActionListener()\r
 189             {\r
 190               public void actionPerformed(ActionEvent e)\r
 191               {\r
 192                 hideSequences(true);\r
 193               }\r
 194             });\r
 195             sequenceMenu.add(menuItem);\r
 196           }\r
 197 \r
 198           if (ap.av.hasHiddenRows)\r
 199           {\r
 200             final int index = ap.av.alignment.findIndex(seq);\r
 201 \r
 202             if (ap.av.adjustForHiddenSeqs(index) -\r
 203                 ap.av.adjustForHiddenSeqs(index - 1) > 1)\r
 204             {\r
 205               menuItem = new JMenuItem("Reveal Sequences");\r
 206               menuItem.addActionListener(new ActionListener()\r
 207               {\r
 208                 public void actionPerformed(ActionEvent e)\r
 209                 {\r
 210                   ap.av.showSequence(index);\r
 211                   if (ap.overviewPanel != null)\r
 212                     ap.overviewPanel.updateOverviewImage();\r
 213                 }\r
 214               });\r
 215               add(menuItem);\r
 216             }\r
 217 \r
 218             menuItem = new JMenuItem("Reveal All");\r
 219             menuItem.addActionListener(new ActionListener()\r
 220                 {\r
 221                   public void actionPerformed(ActionEvent e)\r
 222                   {\r
 223                     ap.av.showAllHiddenSeqs();\r
 224                     if (ap.overviewPanel != null)\r
 225                       ap.overviewPanel.updateOverviewImage();\r
 226                     }\r
 227                 });\r
 228 \r
 229             add(menuItem);\r
 230           }\r
 231 \r
 232 \r
 233         }\r
 234 \r
 235 \r
 236 \r
 237         SequenceGroup sg = ap.av.getSelectionGroup();\r
 238 \r
 239         if (sg != null)\r
 240         {\r
 241             groupName.setText(sg.getName());\r
 242 \r
 243             if (sg.cs instanceof ZappoColourScheme)\r
 244             {\r
 245                 zappoColour.setSelected(true);\r
 246             }\r
 247             else if (sg.cs instanceof TaylorColourScheme)\r
 248             {\r
 249                 taylorColour.setSelected(true);\r
 250             }\r
 251             else if (sg.cs instanceof PIDColourScheme)\r
 252             {\r
 253                 PIDColour.setSelected(true);\r
 254             }\r
 255             else if (sg.cs instanceof Blosum62ColourScheme)\r
 256             {\r
 257                 BLOSUM62Colour.setSelected(true);\r
 258             }\r
 259             else if (sg.cs instanceof UserColourScheme)\r
 260             {\r
 261                 userDefinedColour.setSelected(true);\r
 262             }\r
 263             else if (sg.cs instanceof HydrophobicColourScheme)\r
 264             {\r
 265                 hydrophobicityColour.setSelected(true);\r
 266             }\r
 267             else if (sg.cs instanceof HelixColourScheme)\r
 268             {\r
 269                 helixColour.setSelected(true);\r
 270             }\r
 271             else if (sg.cs instanceof StrandColourScheme)\r
 272             {\r
 273                 strandColour.setSelected(true);\r
 274             }\r
 275             else if (sg.cs instanceof TurnColourScheme)\r
 276             {\r
 277                 turnColour.setSelected(true);\r
 278             }\r
 279             else if (sg.cs instanceof BuriedColourScheme)\r
 280             {\r
 281                 buriedColour.setSelected(true);\r
 282             }\r
 283             else if (sg.cs instanceof ClustalxColourScheme)\r
 284             {\r
 285                 clustalColour.setSelected(true);\r
 286             }\r
 287             else\r
 288             {\r
 289                 noColourmenuItem.setSelected(true);\r
 290             }\r
 291 \r
 292             if (sg.cs!=null && sg.cs.conservationApplied())\r
 293             {\r
 294                 conservationMenuItem.setSelected(true);\r
 295             }\r
 296 \r
 297             showText.setSelected(sg.getDisplayText());\r
 298             showColourText.setSelected(sg.getColourText());\r
 299             showBoxes.setSelected(sg.getDisplayBoxes());\r
 300         }\r
 301         else\r
 302         {\r
 303           groupMenu.setVisible(false);\r
 304           editMenu.setVisible(false);\r
 305         }\r
 306 \r
 307         if (!ap.av.alignment.getGroups().contains(sg))\r
 308         {\r
 309             unGroupMenuItem.setVisible(false);\r
 310         }\r
 311 \r
 312 \r
 313         if (seq == null)\r
 314         {\r
 315             sequenceMenu.setVisible(false);\r
 316             pdbMenu.setVisible(false);\r
 317         }\r
 318 \r
 319         if(links != null && links.size()>0)\r
 320         {\r
 321           JMenu linkMenu = new JMenu("Link");\r
 322           JMenuItem item;\r
 323           for(int i=0; i<links.size(); i++)\r
 324           {\r
 325             String link = links.elementAt(i).toString();\r
 326             final String label = link.substring(0, link.indexOf("|"));\r
 327             item = new JMenuItem(label);\r
 328             final String url;\r
 329 \r
 330             if (link.indexOf("$SEQUENCE_ID$") > -1)\r
 331             {\r
 332               String id = seq.getName();\r
 333               if (id.indexOf("|") > -1)\r
 334                 id = id.substring(id.lastIndexOf("|") + 1);\r
 335 \r
 336               url = link.substring(link.indexOf("|") + 1,\r
 337                                    link.indexOf("$SEQUENCE_ID$"))\r
 338                   + id +\r
 339                   link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
 340             }\r
 341             else\r
 342               url = link.substring(link.lastIndexOf("|")+1);\r
 343 \r
 344 \r
 345             item.addActionListener(new java.awt.event.ActionListener()\r
 346             {\r
 347                 public void actionPerformed(ActionEvent e)\r
 348                 {\r
 349                     showLink(url);\r
 350                 }\r
 351             });\r
 352 \r
 353             linkMenu.add(item);\r
 354           }\r
 355           if(sequence!=null)\r
 356             sequenceMenu.add(linkMenu);\r
 357           else\r
 358             add(linkMenu);\r
 359         }\r
 360     }\r
 361 \r
 362 \r
 363     /**\r
 364      * DOCUMENT ME!\r
 365      *\r
 366      * @throws Exception DOCUMENT ME!\r
 367      */\r
 368     private void jbInit() throws Exception\r
 369     {\r
 370         groupMenu.setText("Group");\r
 371         groupMenu.setText("Selection");\r
 372         groupName.setText("Name");\r
 373         groupName.addActionListener(new java.awt.event.ActionListener()\r
 374             {\r
 375                 public void actionPerformed(ActionEvent e)\r
 376                 {\r
 377                     groupName_actionPerformed(e);\r
 378                 }\r
 379             });\r
 380         sequenceMenu.setText("Sequence");\r
 381         sequenceName.setText("Edit Name/Description");\r
 382         sequenceName.addActionListener(new java.awt.event.ActionListener()\r
 383             {\r
 384                 public void actionPerformed(ActionEvent e)\r
 385                 {\r
 386                     sequenceName_actionPerformed(e);\r
 387                 }\r
 388             });\r
 389         PIDColour.setFocusPainted(false);\r
 390         unGroupMenuItem.setText("Remove Group");\r
 391         unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 392             {\r
 393                 public void actionPerformed(ActionEvent e)\r
 394                 {\r
 395                     unGroupMenuItem_actionPerformed(e);\r
 396                 }\r
 397             });\r
 398 \r
 399         outline.setText("Border colour");\r
 400         outline.addActionListener(new java.awt.event.ActionListener()\r
 401             {\r
 402                 public void actionPerformed(ActionEvent e)\r
 403                 {\r
 404                     outline_actionPerformed(e);\r
 405                 }\r
 406             });\r
 407         nucleotideMenuItem.setText("Nucleotide");\r
 408         nucleotideMenuItem.addActionListener(new ActionListener()\r
 409             {\r
 410                 public void actionPerformed(ActionEvent e)\r
 411                 {\r
 412                     nucleotideMenuItem_actionPerformed(e);\r
 413                 }\r
 414             });\r
 415         colourMenu.setText("Group Colour");\r
 416         showBoxes.setText("Boxes");\r
 417         showBoxes.setState(true);\r
 418         showBoxes.addActionListener(new ActionListener()\r
 419             {\r
 420                 public void actionPerformed(ActionEvent e)\r
 421                 {\r
 422                     showBoxes_actionPerformed(e);\r
 423                 }\r
 424             });\r
 425         showText.setText("Text");\r
 426         showText.setState(true);\r
 427         showText.addActionListener(new ActionListener()\r
 428             {\r
 429                 public void actionPerformed(ActionEvent e)\r
 430                 {\r
 431                     showText_actionPerformed(e);\r
 432                 }\r
 433             });\r
 434         showColourText.setText("Colour Text");\r
 435         showColourText.addActionListener(new ActionListener()\r
 436             {\r
 437                 public void actionPerformed(ActionEvent e)\r
 438                 {\r
 439                     showColourText_actionPerformed(e);\r
 440                 }\r
 441             });\r
 442     editMenu.setText("Edit");\r
 443     cut.setText("Cut");\r
 444     cut.addActionListener(new ActionListener()\r
 445     {\r
 446       public void actionPerformed(ActionEvent e)\r
 447       {\r
 448         cut_actionPerformed(e);\r
 449       }\r
 450     });\r
 451     upperCase.setText("To Upper Case");\r
 452     upperCase.addActionListener(new ActionListener()\r
 453     {\r
 454       public void actionPerformed(ActionEvent e)\r
 455       {\r
 456         changeCase(e);\r
 457       }\r
 458     });\r
 459     copy.setText("Copy");\r
 460     copy.addActionListener(new ActionListener()\r
 461     {\r
 462       public void actionPerformed(ActionEvent e)\r
 463       {\r
 464         copy_actionPerformed(e);\r
 465       }\r
 466     });\r
 467     lowerCase.setText("To Lower Case");\r
 468     lowerCase.addActionListener(new ActionListener()\r
 469     {\r
 470       public void actionPerformed(ActionEvent e)\r
 471       {\r
 472         changeCase(e);\r
 473       }\r
 474     });\r
 475     toggle.setText("Toggle Case");\r
 476     toggle.addActionListener(new ActionListener()\r
 477     {\r
 478       public void actionPerformed(ActionEvent e)\r
 479       {\r
 480         changeCase(e);\r
 481       }\r
 482     });\r
 483     pdbMenu.setText("Associate Structure with Sequence");\r
 484     pdbFromFile.setText("From File");\r
 485     pdbFromFile.addActionListener(new ActionListener()\r
 486     {\r
 487       public void actionPerformed(ActionEvent e)\r
 488       {\r
 489         pdbFromFile_actionPerformed(e);\r
 490       }\r
 491     });\r
 492     enterPDB.setText("Enter PDB Id");\r
 493     enterPDB.addActionListener(new ActionListener()\r
 494     {\r
 495       public void actionPerformed(ActionEvent e)\r
 496       {\r
 497         enterPDB_actionPerformed(e);\r
 498       }\r
 499     });\r
 500     discoverPDB.setText("Discover PDB ids");\r
 501     discoverPDB.addActionListener(new ActionListener()\r
 502     {\r
 503       public void actionPerformed(ActionEvent e)\r
 504       {\r
 505         discoverPDB_actionPerformed(e);\r
 506       }\r
 507     });\r
 508     outputMenu.setText("Output to Textbox...");\r
 509     sequenceFeature.setText("Create Sequence Feature");\r
 510     sequenceFeature.addActionListener(new ActionListener()\r
 511     {\r
 512       public void actionPerformed(ActionEvent e)\r
 513       {\r
 514         sequenceFeature_actionPerformed(e);\r
 515       }\r
 516     });\r
 517     textColour.setText("Text Colour");\r
 518     textColour.addActionListener(new ActionListener()\r
 519     {\r
 520       public void actionPerformed(ActionEvent e)\r
 521       {\r
 522         textColour_actionPerformed(e);\r
 523       }\r
 524     });\r
 525     jMenu1.setText("Group");\r
 526     add(groupMenu);\r
 527 \r
 528     add(sequenceMenu);\r
 529     groupMenu.add(editMenu);\r
 530     groupMenu.add(outputMenu);\r
 531     groupMenu.add(sequenceFeature);\r
 532     groupMenu.add(jMenu1);\r
 533     sequenceMenu.add(sequenceName);\r
 534     sequenceMenu.add(pdbMenu);\r
 535     colourMenu.add(textColour);\r
 536     colourMenu.add(noColourmenuItem);\r
 537         colourMenu.add(clustalColour);\r
 538         colourMenu.add(BLOSUM62Colour);\r
 539         colourMenu.add(PIDColour);\r
 540         colourMenu.add(zappoColour);\r
 541         colourMenu.add(taylorColour);\r
 542         colourMenu.add(hydrophobicityColour);\r
 543         colourMenu.add(helixColour);\r
 544         colourMenu.add(strandColour);\r
 545         colourMenu.add(turnColour);\r
 546         colourMenu.add(buriedColour);\r
 547         colourMenu.add(nucleotideMenuItem);\r
 548         colourMenu.add(userDefinedColour);\r
 549 \r
 550         if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
 551         {\r
 552           java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 553               getUserColourSchemes().keys();\r
 554 \r
 555           while (userColours.hasMoreElements())\r
 556           {\r
 557             JMenuItem item = new JMenuItem(userColours.\r
 558                 nextElement().toString());\r
 559             item.addActionListener(new ActionListener()\r
 560             {\r
 561               public void actionPerformed(ActionEvent evt)\r
 562               {\r
 563                 userDefinedColour_actionPerformed(evt);\r
 564               }\r
 565             });\r
 566             colourMenu.add(item);\r
 567           }\r
 568         }\r
 569 \r
 570 \r
 571         colourMenu.addSeparator();\r
 572         colourMenu.add(abovePIDColour);\r
 573         colourMenu.add(conservationMenuItem);\r
 574     editMenu.add(copy);\r
 575     editMenu.add(cut);\r
 576     editMenu.add(upperCase);\r
 577     editMenu.add(lowerCase);\r
 578     editMenu.add(toggle);\r
 579     pdbMenu.add(pdbFromFile);\r
 580     pdbMenu.add(enterPDB);\r
 581     pdbMenu.add(discoverPDB);\r
 582     jMenu1.add(groupName);\r
 583     jMenu1.add(unGroupMenuItem);\r
 584     jMenu1.add(colourMenu);\r
 585     jMenu1.add(showBoxes);\r
 586     jMenu1.add(showText);\r
 587     jMenu1.add(showColourText);\r
 588     jMenu1.add(outline);\r
 589     noColourmenuItem.setText("None");\r
 590         noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 591             {\r
 592                 public void actionPerformed(ActionEvent e)\r
 593                 {\r
 594                     noColourmenuItem_actionPerformed(e);\r
 595                 }\r
 596             });\r
 597 \r
 598         clustalColour.setText("Clustalx colours");\r
 599         clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 600             {\r
 601                 public void actionPerformed(ActionEvent e)\r
 602                 {\r
 603                     clustalColour_actionPerformed(e);\r
 604                 }\r
 605             });\r
 606         zappoColour.setText("Zappo");\r
 607         zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 608             {\r
 609                 public void actionPerformed(ActionEvent e)\r
 610                 {\r
 611                     zappoColour_actionPerformed(e);\r
 612                 }\r
 613             });\r
 614         taylorColour.setText("Taylor");\r
 615         taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 616             {\r
 617                 public void actionPerformed(ActionEvent e)\r
 618                 {\r
 619                     taylorColour_actionPerformed(e);\r
 620                 }\r
 621             });\r
 622         hydrophobicityColour.setText("Hydrophobicity");\r
 623         hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 624             {\r
 625                 public void actionPerformed(ActionEvent e)\r
 626                 {\r
 627                     hydrophobicityColour_actionPerformed(e);\r
 628                 }\r
 629             });\r
 630         helixColour.setText("Helix propensity");\r
 631         helixColour.addActionListener(new java.awt.event.ActionListener()\r
 632             {\r
 633                 public void actionPerformed(ActionEvent e)\r
 634                 {\r
 635                     helixColour_actionPerformed(e);\r
 636                 }\r
 637             });\r
 638         strandColour.setText("Strand propensity");\r
 639         strandColour.addActionListener(new java.awt.event.ActionListener()\r
 640             {\r
 641                 public void actionPerformed(ActionEvent e)\r
 642                 {\r
 643                     strandColour_actionPerformed(e);\r
 644                 }\r
 645             });\r
 646         turnColour.setText("Turn propensity");\r
 647         turnColour.addActionListener(new java.awt.event.ActionListener()\r
 648             {\r
 649                 public void actionPerformed(ActionEvent e)\r
 650                 {\r
 651                     turnColour_actionPerformed(e);\r
 652                 }\r
 653             });\r
 654         buriedColour.setText("Buried Index");\r
 655         buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 656             {\r
 657                 public void actionPerformed(ActionEvent e)\r
 658                 {\r
 659                     buriedColour_actionPerformed(e);\r
 660                 }\r
 661             });\r
 662         abovePIDColour.setText("Above % Identity");\r
 663         abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
 664             {\r
 665                 public void actionPerformed(ActionEvent e)\r
 666                 {\r
 667                     abovePIDColour_actionPerformed(e);\r
 668                 }\r
 669             });\r
 670         userDefinedColour.setText("User Defined...");\r
 671         userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 672             {\r
 673                 public void actionPerformed(ActionEvent e)\r
 674                 {\r
 675                     userDefinedColour_actionPerformed(e);\r
 676                 }\r
 677             });\r
 678         PIDColour.setText("Percentage Identity");\r
 679         PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 680             {\r
 681                 public void actionPerformed(ActionEvent e)\r
 682                 {\r
 683                     PIDColour_actionPerformed(e);\r
 684                 }\r
 685             });\r
 686         BLOSUM62Colour.setText("BLOSUM62");\r
 687         BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 688             {\r
 689                 public void actionPerformed(ActionEvent e)\r
 690                 {\r
 691                     BLOSUM62Colour_actionPerformed(e);\r
 692                 }\r
 693             });\r
 694         conservationMenuItem.setText("Conservation");\r
 695         conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 696             {\r
 697                 public void actionPerformed(ActionEvent e)\r
 698                 {\r
 699                     conservationMenuItem_actionPerformed(e);\r
 700                 }\r
 701             });\r
 702     }\r
 703 \r
 704     /**\r
 705      * DOCUMENT ME!\r
 706      */\r
 707     void refresh()\r
 708     {\r
 709         if (ap.overviewPanel != null)\r
 710           ap.overviewPanel.updateOverviewImage();\r
 711 \r
 712         PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
 713     }\r
 714 \r
 715     /**\r
 716      * DOCUMENT ME!\r
 717      *\r
 718      * @param e DOCUMENT ME!\r
 719      */\r
 720     protected void clustalColour_actionPerformed(ActionEvent e)\r
 721     {\r
 722         SequenceGroup sg = getGroup();\r
 723         sg.cs = new ClustalxColourScheme(sg.getSequences(true),\r
 724                 ap.av.alignment.getWidth());\r
 725         refresh();\r
 726     }\r
 727 \r
 728     /**\r
 729      * DOCUMENT ME!\r
 730      *\r
 731      * @param e DOCUMENT ME!\r
 732      */\r
 733     protected void zappoColour_actionPerformed(ActionEvent e)\r
 734     {\r
 735         getGroup().cs = new ZappoColourScheme();\r
 736         refresh();\r
 737     }\r
 738 \r
 739     /**\r
 740      * DOCUMENT ME!\r
 741      *\r
 742      * @param e DOCUMENT ME!\r
 743      */\r
 744     protected void taylorColour_actionPerformed(ActionEvent e)\r
 745     {\r
 746         getGroup().cs = new TaylorColourScheme();\r
 747         refresh();\r
 748     }\r
 749 \r
 750     /**\r
 751      * DOCUMENT ME!\r
 752      *\r
 753      * @param e DOCUMENT ME!\r
 754      */\r
 755     protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 756     {\r
 757         getGroup().cs = new HydrophobicColourScheme();\r
 758         refresh();\r
 759     }\r
 760 \r
 761     /**\r
 762      * DOCUMENT ME!\r
 763      *\r
 764      * @param e DOCUMENT ME!\r
 765      */\r
 766     protected void helixColour_actionPerformed(ActionEvent e)\r
 767     {\r
 768         getGroup().cs = new HelixColourScheme();\r
 769         refresh();\r
 770     }\r
 771 \r
 772     /**\r
 773      * DOCUMENT ME!\r
 774      *\r
 775      * @param e DOCUMENT ME!\r
 776      */\r
 777     protected void strandColour_actionPerformed(ActionEvent e)\r
 778     {\r
 779         getGroup().cs = new StrandColourScheme();\r
 780         refresh();\r
 781     }\r
 782 \r
 783     /**\r
 784      * DOCUMENT ME!\r
 785      *\r
 786      * @param e DOCUMENT ME!\r
 787      */\r
 788     protected void turnColour_actionPerformed(ActionEvent e)\r
 789     {\r
 790         getGroup().cs = new TurnColourScheme();\r
 791         refresh();\r
 792     }\r
 793 \r
 794     /**\r
 795      * DOCUMENT ME!\r
 796      *\r
 797      * @param e DOCUMENT ME!\r
 798      */\r
 799     protected void buriedColour_actionPerformed(ActionEvent e)\r
 800     {\r
 801         getGroup().cs = new BuriedColourScheme();\r
 802         refresh();\r
 803     }\r
 804 \r
 805     /**\r
 806      * DOCUMENT ME!\r
 807      *\r
 808      * @param e DOCUMENT ME!\r
 809      */\r
 810     public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
 811     {\r
 812         getGroup().cs = new NucleotideColourScheme();\r
 813         refresh();\r
 814     }\r
 815 \r
 816     /**\r
 817      * DOCUMENT ME!\r
 818      *\r
 819      * @param e DOCUMENT ME!\r
 820      */\r
 821     protected void abovePIDColour_actionPerformed(ActionEvent e)\r
 822     {\r
 823         SequenceGroup sg = getGroup();\r
 824         if(sg.cs==null)\r
 825           return;\r
 826 \r
 827         if (abovePIDColour.isSelected())\r
 828         {\r
 829           sg.cs.setConsensus(AAFrequency.calculate(\r
 830               sg.getSequences(true), sg.getStartRes(),\r
 831               sg.getEndRes() + 1));\r
 832 \r
 833             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
 834                     getGroup().getName());\r
 835 \r
 836            sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
 837 \r
 838             SliderPanel.showPIDSlider();\r
 839         }\r
 840         else // remove PIDColouring\r
 841         {\r
 842             sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
 843         }\r
 844 \r
 845         refresh();\r
 846     }\r
 847 \r
 848     /**\r
 849      * DOCUMENT ME!\r
 850      *\r
 851      * @param e DOCUMENT ME!\r
 852      */\r
 853     protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 854     {\r
 855        SequenceGroup sg = getGroup();\r
 856 \r
 857        if (e.getActionCommand().equals("User Defined..."))\r
 858          new UserDefinedColours(ap, sg);\r
 859        else\r
 860        {\r
 861          UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
 862              getUserColourSchemes().get(e.getActionCommand());\r
 863 \r
 864          sg.cs = udc;\r
 865        }\r
 866        refresh();\r
 867      }\r
 868     /**\r
 869      * DOCUMENT ME!\r
 870      *\r
 871      * @param e DOCUMENT ME!\r
 872      */\r
 873     protected void PIDColour_actionPerformed(ActionEvent e)\r
 874     {\r
 875         SequenceGroup sg = getGroup();\r
 876         sg.cs = new PIDColourScheme();\r
 877         sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),\r
 878                                                  sg.getStartRes(),\r
 879                                                  sg.getEndRes() + 1));\r
 880         refresh();\r
 881     }\r
 882 \r
 883     /**\r
 884      * DOCUMENT ME!\r
 885      *\r
 886      * @param e DOCUMENT ME!\r
 887      */\r
 888     protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 889     {\r
 890         SequenceGroup sg = getGroup();\r
 891 \r
 892         sg.cs = new Blosum62ColourScheme();\r
 893 \r
 894         sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),\r
 895                                                  sg.getStartRes(),\r
 896                                                  sg.getEndRes() + 1));\r
 897 \r
 898         refresh();\r
 899     }\r
 900 \r
 901     /**\r
 902      * DOCUMENT ME!\r
 903      *\r
 904      * @param e DOCUMENT ME!\r
 905      */\r
 906     protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 907     {\r
 908         getGroup().cs = null;\r
 909         refresh();\r
 910     }\r
 911 \r
 912     /**\r
 913      * DOCUMENT ME!\r
 914      *\r
 915      * @param e DOCUMENT ME!\r
 916      */\r
 917     protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
 918     {\r
 919         SequenceGroup sg = getGroup();\r
 920         if(sg.cs==null)\r
 921           return;\r
 922 \r
 923         if (conservationMenuItem.isSelected())\r
 924         {\r
 925             Conservation c = new Conservation("Group",\r
 926                     ResidueProperties.propHash, 3,\r
 927                     sg.getSequences(true),\r
 928                     sg.getStartRes(),\r
 929                     sg.getEndRes() + 1);\r
 930 \r
 931             c.calculate();\r
 932             c.verdict(false, ap.av.ConsPercGaps);\r
 933 \r
 934             sg.cs.setConservation(c);\r
 935 \r
 936             SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
 937             SliderPanel.showConservationSlider();\r
 938         }\r
 939         else // remove ConservationColouring\r
 940         {\r
 941             sg.cs.setConservation(null);\r
 942         }\r
 943 \r
 944         refresh();\r
 945     }\r
 946 \r
 947     /**\r
 948      * DOCUMENT ME!\r
 949      *\r
 950      * @param e DOCUMENT ME!\r
 951      */\r
 952     protected void groupName_actionPerformed(ActionEvent e)\r
 953     {\r
 954         SequenceGroup sg = getGroup();\r
 955         String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
 956                 "Enter new group name", "Edit group name",\r
 957                 JOptionPane.QUESTION_MESSAGE);\r
 958 \r
 959         if (reply == null)\r
 960         {\r
 961             return;\r
 962         }\r
 963 \r
 964         sg.setName(reply);\r
 965         groupName.setText(reply);\r
 966     }\r
 967 \r
 968 \r
 969     /**\r
 970      * DOCUMENT ME!\r
 971      *\r
 972      * @return DOCUMENT ME!\r
 973      */\r
 974     SequenceGroup getGroup()\r
 975     {\r
 976         SequenceGroup sg = ap.av.getSelectionGroup();\r
 977       // this method won't add a new group if it already exists\r
 978         if(sg!=null)\r
 979           ap.av.alignment.addGroup(sg);\r
 980 \r
 981         return sg;\r
 982     }\r
 983 \r
 984     /**\r
 985      * DOCUMENT ME!\r
 986      *\r
 987      * @param e DOCUMENT ME!\r
 988      */\r
 989     void sequenceName_actionPerformed(ActionEvent e)\r
 990     {\r
 991       JLabel idlabel = new JLabel(  "       Sequence Name ");\r
 992       JLabel desclabel = new JLabel("Sequence Description ");\r
 993       idlabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
 994       desclabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
 995       JTextField id = new JTextField(sequence.getName(), 40);\r
 996       JTextField description = new JTextField(sequence.getDescription(), 40);\r
 997       JPanel panel = new JPanel(new BorderLayout());\r
 998       JPanel panel2 = new JPanel(new BorderLayout());\r
 999       panel2.add(idlabel, BorderLayout.WEST);\r
1000       panel2.add(id, BorderLayout.CENTER);\r
1001       panel.add(panel2, BorderLayout.NORTH);\r
1002       panel2 = new JPanel(new BorderLayout());\r
1003       panel2.add(desclabel, BorderLayout.WEST);\r
1004       panel2.add(description, BorderLayout.CENTER);\r
1005       panel.add(panel2, BorderLayout.SOUTH);\r
1006 \r
1007 \r
1008        int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
1009           panel, "Edit Sequence Name/Description",\r
1010           JOptionPane.OK_CANCEL_OPTION );\r
1011 \r
1012 \r
1013         if (reply != JOptionPane.OK_OPTION )\r
1014         {\r
1015             return;\r
1016         }\r
1017 \r
1018         String s = id.getText();\r
1019 \r
1020         if (s != null)\r
1021         {\r
1022             if (s.indexOf(" ") > -1)\r
1023             {\r
1024                 JOptionPane.showMessageDialog(ap,\r
1025                     "Spaces have been converted to \"_\"",\r
1026                     "No spaces allowed in Sequence Name",\r
1027                     JOptionPane.WARNING_MESSAGE);\r
1028             }\r
1029 \r
1030             s = s.replace(' ', '_');\r
1031             sequence.setName(s);\r
1032             ap.repaint();\r
1033         }\r
1034 \r
1035         sequence.setDescription(description.getText());\r
1036 \r
1037         ap.av.firePropertyChange("alignment", null,\r
1038                                   ap.av.getAlignment().getSequences());\r
1039 \r
1040     }\r
1041 \r
1042     /**\r
1043      * DOCUMENT ME!\r
1044      *\r
1045      * @param e DOCUMENT ME!\r
1046      */\r
1047     void unGroupMenuItem_actionPerformed(ActionEvent e)\r
1048     {\r
1049         SequenceGroup sg = ap.av.getSelectionGroup();\r
1050         ap.av.alignment.deleteGroup(sg);\r
1051         ap.av.setSelectionGroup(null);\r
1052         refresh();\r
1053     }\r
1054 \r
1055 \r
1056     /**\r
1057      * DOCUMENT ME!\r
1058      *\r
1059      * @param e DOCUMENT ME!\r
1060      */\r
1061     protected void outline_actionPerformed(ActionEvent e)\r
1062     {\r
1063         SequenceGroup sg = getGroup();\r
1064         Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
1065                 Color.BLUE);\r
1066 \r
1067         if (col != null)\r
1068         {\r
1069             sg.setOutlineColour(col);\r
1070         }\r
1071 \r
1072         refresh();\r
1073     }\r
1074 \r
1075     /**\r
1076      * DOCUMENT ME!\r
1077      *\r
1078      * @param e DOCUMENT ME!\r
1079      */\r
1080     public void showBoxes_actionPerformed(ActionEvent e)\r
1081     {\r
1082         getGroup().setDisplayBoxes(showBoxes.isSelected());\r
1083         refresh();\r
1084     }\r
1085 \r
1086     /**\r
1087      * DOCUMENT ME!\r
1088      *\r
1089      * @param e DOCUMENT ME!\r
1090      */\r
1091     public void showText_actionPerformed(ActionEvent e)\r
1092     {\r
1093         getGroup().setDisplayText(showText.isSelected());\r
1094         refresh();\r
1095     }\r
1096 \r
1097     /**\r
1098      * DOCUMENT ME!\r
1099      *\r
1100      * @param e DOCUMENT ME!\r
1101      */\r
1102     public void showColourText_actionPerformed(ActionEvent e)\r
1103     {\r
1104         getGroup().setColourText(showColourText.isSelected());\r
1105         refresh();\r
1106     }\r
1107 \r
1108     public void showLink(String url)\r
1109     {\r
1110       try\r
1111       {\r
1112         jalview.util.BrowserLauncher.openURL(url);\r
1113       }\r
1114       catch (Exception ex)\r
1115       {\r
1116         JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
1117             "Unixers: Couldn't find default web browser."\r
1118            +"\nAdd the full path to your browser in Preferences.",\r
1119            "Web browser not found", JOptionPane.WARNING_MESSAGE );\r
1120 \r
1121 \r
1122         ex.printStackTrace();\r
1123       }\r
1124     }\r
1125 \r
1126     void hideSequences(boolean representGroup)\r
1127     {\r
1128       SequenceGroup sg = ap.av.getSelectionGroup();\r
1129       if(sg==null || sg.getSize(false)<1)\r
1130       {\r
1131         ap.av.hideSequence(new SequenceI[]{sequence});\r
1132         return;\r
1133       }\r
1134 \r
1135       int gsize = sg.getSize(false);\r
1136       SequenceI [] hseqs;\r
1137 \r
1138       hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ];\r
1139 \r
1140         int index = 0;\r
1141         for(int i=0; i<gsize; i++)\r
1142         {\r
1143           if(representGroup && sg.getSequenceAt(i)!=sequence)\r
1144           {\r
1145             sequence.addHiddenSequence(sg.getSequenceAt(i));\r
1146             hseqs[index++] = sg.getSequenceAt(i);\r
1147           }\r
1148           else if(!representGroup)\r
1149           {\r
1150             hseqs[index++] = sg.getSequenceAt(i);\r
1151           }\r
1152         }\r
1153 \r
1154         ap.av.hideSequence(hseqs);\r
1155 \r
1156         ap.av.setSelectionGroup(null);\r
1157     }\r
1158 \r
1159   public void copy_actionPerformed(ActionEvent e)\r
1160   {\r
1161     ap.alignFrame.copy_actionPerformed(null);\r
1162   }\r
1163 \r
1164   public void cut_actionPerformed(ActionEvent e)\r
1165   {\r
1166     ap.alignFrame.cut_actionPerformed(null);\r
1167   }\r
1168 \r
1169   void changeCase(ActionEvent e)\r
1170   {\r
1171     Object source = e.getSource();\r
1172     SequenceGroup sg = ap.av.getSelectionGroup();\r
1173     Vector regions = new Vector();\r
1174     if (sg != null)\r
1175     {\r
1176       int start = sg.getStartRes();\r
1177       int end = sg.getEndRes() + 1;\r
1178 \r
1179       do\r
1180       {\r
1181         if (ap.av.hasHiddenColumns)\r
1182         {\r
1183           if(start==0)\r
1184             start = ap.av.colSel.adjustForHiddenColumns(start);\r
1185 \r
1186           end = ap.av.colSel.getHiddenBoundaryRight(start);\r
1187           if (start == end)\r
1188             end = sg.getEndRes() + 1;\r
1189           if (end > sg.getEndRes())\r
1190             end = sg.getEndRes() + 1;\r
1191         }\r
1192 \r
1193         regions.addElement(new int[]\r
1194                            {start, end});\r
1195 \r
1196         if (ap.av.hasHiddenColumns)\r
1197         {\r
1198           start = ap.av.colSel.adjustForHiddenColumns(end);\r
1199           start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;\r
1200         }\r
1201       }\r
1202       while (end < sg.getEndRes());\r
1203 \r
1204       int[][] startEnd = new int[regions.size()][2];\r
1205       for (int i = 0; i < regions.size(); i++)\r
1206       {\r
1207         startEnd[i] = (int[]) regions.elementAt(i);\r
1208       }\r
1209 \r
1210 \r
1211       String description;\r
1212       int caseChange;\r
1213 \r
1214       if(source==toggle)\r
1215       {\r
1216         description = "Toggle Case";\r
1217         caseChange = ChangeCaseCommand.TOGGLE_CASE;\r
1218       }\r
1219       else if(source==upperCase)\r
1220       {\r
1221         description = "To Upper Case";\r
1222         caseChange = ChangeCaseCommand.TO_UPPER;\r
1223       }\r
1224       else\r
1225       {\r
1226         description = "To Lower Case";\r
1227         caseChange = ChangeCaseCommand.TO_LOWER;\r
1228       }\r
1229 \r
1230       ChangeCaseCommand caseCommand = new ChangeCaseCommand(\r
1231           description, sg.getSequencesAsArray(true), startEnd, caseChange\r
1232           );\r
1233 \r
1234       ap.alignFrame.addHistoryItem(caseCommand);\r
1235 \r
1236 \r
1237       ap.av.firePropertyChange("alignment", null,\r
1238                                 ap.av.getAlignment().getSequences());\r
1239 \r
1240     }\r
1241   }\r
1242 \r
1243   public void outputText_actionPerformed(ActionEvent e)\r
1244   {\r
1245     CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
1246     cap.setForInput(null);\r
1247     Desktop.addInternalFrame(cap,\r
1248                              "Alignment output - " + e.getActionCommand(), 600,\r
1249                              500);\r
1250 \r
1251     String [] omitHidden = null;\r
1252 \r
1253     if(ap.av.hasHiddenColumns)\r
1254     {\r
1255       System.out.println("PROMPT USER HERE");\r
1256       omitHidden = ap.av.getViewAsString(true);\r
1257     }\r
1258 \r
1259     cap.setText(new FormatAdapter().formatSequences(\r
1260         e.getActionCommand(),\r
1261         ap.av.getSelectionAsNewSequence(),\r
1262         omitHidden));\r
1263   }\r
1264 \r
1265 \r
1266   public void pdbFromFile_actionPerformed(ActionEvent e)\r
1267   {\r
1268      jalview.io.JalviewFileChooser chooser\r
1269          = new jalview.io.JalviewFileChooser(jalview.bin.Cache.\r
1270          getProperty(\r
1271              "LAST_DIRECTORY"));\r
1272      chooser.setFileView(new jalview.io.JalviewFileView());\r
1273      chooser.setDialogTitle("Select a PDB file");\r
1274      chooser.setToolTipText("Load a PDB file");\r
1275 \r
1276      int value = chooser.showOpenDialog(null);\r
1277 \r
1278      if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
1279      {\r
1280        PDBEntry entry = new PDBEntry();\r
1281        String choice = chooser.getSelectedFile().getPath();\r
1282        jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
1283        try\r
1284        {\r
1285          MCview.PDBfile pdbfile = new MCview.PDBfile(choice,\r
1286                                        jalview.io.AppletFormatAdapter.FILE);\r
1287 \r
1288          if (pdbfile.id == null)\r
1289          {\r
1290            String reply = JOptionPane.showInternalInputDialog(\r
1291                Desktop.desktop,\r
1292                "Couldn't find a PDB id in the file supplied."\r
1293                + "Please enter an Id to identify this structure.",\r
1294                "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);\r
1295            if (reply == null)\r
1296              return;\r
1297 \r
1298            entry.setId(reply);\r
1299          }\r
1300          else\r
1301            entry.setId(pdbfile.id);\r
1302        }\r
1303        catch (java.io.IOException ex)\r
1304        {\r
1305          ex.printStackTrace();\r
1306        }\r
1307 \r
1308        entry.setFile(choice);\r
1309        sequence.getDatasetSequence().addPDBId(entry);\r
1310      }\r
1311 \r
1312   }\r
1313 \r
1314   public void enterPDB_actionPerformed(ActionEvent e)\r
1315   {\r
1316     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
1317         "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);\r
1318 \r
1319     if (id != null && id.length() > 0)\r
1320     {\r
1321       PDBEntry entry = new PDBEntry();\r
1322       entry.setId(id);\r
1323       sequence.getDatasetSequence()\r
1324           .addPDBId(entry);\r
1325     }\r
1326   }\r
1327 \r
1328   public void discoverPDB_actionPerformed(ActionEvent e)\r
1329   {\r
1330     new jalview.io.DBRefFetcher(\r
1331              ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);\r
1332   }\r
1333 \r
1334   public void sequenceFeature_actionPerformed(ActionEvent e)\r
1335   {\r
1336     SequenceGroup sg = ap.av.getSelectionGroup();\r
1337     if(sg==null)\r
1338       return;\r
1339 \r
1340     int gSize= sg.getSize(false);\r
1341     SequenceI [] seqs = new SequenceI[gSize];\r
1342     SequenceFeature [] features = new SequenceFeature[gSize];\r
1343 \r
1344     for (int i = 0; i < gSize; i++)\r
1345     {\r
1346       seqs[i] = sg.getSequenceAt(i).getDatasetSequence();\r
1347       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());\r
1348       int end = sg.findEndRes(sg.getSequenceAt(i));\r
1349       features[i] = new SequenceFeature(null,null, null,start,end,"Jalview");\r
1350     }\r
1351 \r
1352     if (ap.seqPanel.seqCanvas.getFeatureRenderer()\r
1353         .createNewFeatures(seqs, features))\r
1354     {\r
1355       ap.alignFrame.showSeqFeatures.setSelected(true);\r
1356       ap.av.setShowSequenceFeatures(true);\r
1357       ap.highlightSearchResults(null);\r
1358     }\r
1359   }\r
1360 \r
1361   public void textColour_actionPerformed(ActionEvent e)\r
1362   {\r
1363     SequenceGroup sg = getGroup();\r
1364     if (sg != null)\r
1365       new TextColourChooser().chooseColour(ap, sg);\r
1366   }\r
1367 }\r