src/jalview/gui/PopupMenu.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer
   3  * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4  *
   5  * This program is free software; you can redistribute it and/or
   6  * modify it under the terms of the GNU General Public License
   7  * as published by the Free Software Foundation; either version 2
   8  * of the License, or (at your option) any later version.
   9  *
  10  * This program is distributed in the hope that it will be useful,
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13  * GNU General Public License for more details.
  14  *
  15  * You should have received a copy of the GNU General Public License
  16  * along with this program; if not, write to the Free Software
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18  */
  19 package jalview.gui;
  20
  21 import MCview.*;
  22
  23 import jalview.analysis.*;
  24
  25 import jalview.datamodel.*;
  26
  27
  28 import jalview.schemes.*;
  29
  30 import java.awt.*;
  31 import java.awt.event.*;
  32
  33 import javax.swing.*;
  34
  35 import java.util.Vector;
  36 import jalview.io.FormatAdapter;
  37
  38
  39 /**
  40  * DOCUMENT ME!
  41  *
  42  * @author $author$
  43  * @version $Revision$
  44  */
  45 public class PopupMenu extends JPopupMenu
  46 {
  47     JMenu groupMenu = new JMenu();
  48     JMenuItem groupName = new JMenuItem();
  49     protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  50     protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  51     protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  52     protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
  53     protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
  54     protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
  55     protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
  56     protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
  57     protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
  58     protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
  59     protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
  60     protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
  61     JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
  62     protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
  63     AlignmentPanel ap;
  64     JMenu sequenceMenu = new JMenu();
  65     JMenuItem sequenceName = new JMenuItem();
  66     Sequence sequence;
  67     JMenuItem unGroupMenuItem = new JMenuItem();
  68     JMenuItem outline = new JMenuItem();
  69     JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
  70     JMenu colourMenu = new JMenu();
  71     JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
  72     JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
  73     JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
  74   JMenu editMenu = new JMenu();
  75   JMenuItem cut = new JMenuItem();
  76   JMenuItem copy = new JMenuItem();
  77   JMenuItem upperCase = new JMenuItem();
  78   JMenuItem lowerCase = new JMenuItem();
  79   JMenuItem toggle = new JMenuItem();
  80   JMenu pdbMenu = new JMenu();
  81   JMenuItem pdbFromFile = new JMenuItem();
  82   JMenuItem enterPDB = new JMenuItem();
  83   JMenuItem discoverPDB = new JMenuItem();
  84   JMenu outputMenu = new JMenu();
  85
  86   /**
  87      * Creates a new PopupMenu object.
  88      *
  89      * @param ap DOCUMENT ME!
  90      * @param seq DOCUMENT ME!
  91      */
  92     public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
  93     {
  94         ///////////////////////////////////////////////////////////
  95         // If this is activated from the sequence panel, the user may want to
  96         // edit or annotate a particular residue. Therefore display the residue menu
  97         //
  98         // If from the IDPanel, we must display the sequence menu
  99         //////////////////////////////////////////////////////////
 100         this.ap = ap;
 101         sequence = seq;
 102
 103         ButtonGroup colours = new ButtonGroup();
 104         colours.add(noColourmenuItem);
 105         colours.add(clustalColour);
 106         colours.add(zappoColour);
 107         colours.add(taylorColour);
 108         colours.add(hydrophobicityColour);
 109         colours.add(helixColour);
 110         colours.add(strandColour);
 111         colours.add(turnColour);
 112         colours.add(buriedColour);
 113         colours.add(abovePIDColour);
 114         colours.add(userDefinedColour);
 115         colours.add(PIDColour);
 116         colours.add(BLOSUM62Colour);
 117
 118         for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 119         {
 120           JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );
 121
 122           item.addActionListener(new java.awt.event.ActionListener()
 123           {
 124             public void actionPerformed(ActionEvent e)
 125             {
 126               outputText_actionPerformed(e);
 127             }
 128           });
 129
 130           outputMenu.add(item);
 131         }
 132
 133
 134         try
 135         {
 136             jbInit();
 137         }
 138         catch (Exception e)
 139         {
 140             e.printStackTrace();
 141         }
 142
 143
 144         if (seq != null)
 145         {
 146           int start = Math.max(sequence.getName().length()-15, 0);
 147           sequenceMenu.setText(sequence.getName().substring(start));
 148
 149           JMenuItem menuItem;
 150           if( seq.getDatasetSequence().getPDBId() != null)
 151           {
 152             java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
 153                 elements();
 154
 155             while (e.hasMoreElements())
 156             {
 157               final PDBEntry pdb = (PDBEntry) e.nextElement();
 158
 159               menuItem = new JMenuItem();
 160               menuItem.setText("View PDB entry: " + pdb.getId());
 161               menuItem.addActionListener(new java.awt.event.ActionListener()
 162               {
 163                 public void actionPerformed(ActionEvent e)
 164                 {
 165                   new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);
 166                 }
 167               });
 168               sequenceMenu.add(menuItem);
 169             }
 170           }
 171
 172           menuItem = new JMenuItem("Hide Sequences");
 173           menuItem.addActionListener(new java.awt.event.ActionListener()
 174               {
 175                 public void actionPerformed(ActionEvent e)
 176                 {
 177                   hideSequences(false);
 178                 }
 179               });
 180           add(menuItem);
 181
 182           if(ap.av.getSelectionGroup() !=null
 183              && ap.av.getSelectionGroup().getSize(false)>1)
 184           {
 185             menuItem = new JMenuItem("Represent Group with " + seq.getName());
 186             menuItem.addActionListener(new java.awt.event.ActionListener()
 187             {
 188               public void actionPerformed(ActionEvent e)
 189               {
 190                 hideSequences(true);
 191               }
 192             });
 193             sequenceMenu.add(menuItem);
 194           }
 195
 196           if (ap.av.hasHiddenRows)
 197           {
 198             final int index = ap.av.alignment.findIndex(seq);
 199
 200             if (ap.av.adjustForHiddenSeqs(index) -
 201                 ap.av.adjustForHiddenSeqs(index - 1) > 1)
 202             {
 203               menuItem = new JMenuItem("Reveal Sequences");
 204               menuItem.addActionListener(new ActionListener()
 205               {
 206                 public void actionPerformed(ActionEvent e)
 207                 {
 208                   ap.av.showSequence(index);
 209                   if (ap.overviewPanel != null)
 210                     ap.overviewPanel.updateOverviewImage();
 211                 }
 212               });
 213               add(menuItem);
 214             }
 215
 216             menuItem = new JMenuItem("Reveal All");
 217             menuItem.addActionListener(new ActionListener()
 218                 {
 219                   public void actionPerformed(ActionEvent e)
 220                   {
 221                     ap.av.showAllHiddenSeqs();
 222                     if (ap.overviewPanel != null)
 223                       ap.overviewPanel.updateOverviewImage();
 224                     }
 225                 });
 226
 227             add(menuItem);
 228           }
 229
 230
 231         }
 232
 233
 234
 235         SequenceGroup sg = ap.av.getSelectionGroup();
 236
 237         if (sg != null)
 238         {
 239             groupName.setText(sg.getName());
 240
 241             if (sg.cs instanceof ZappoColourScheme)
 242             {
 243                 zappoColour.setSelected(true);
 244             }
 245             else if (sg.cs instanceof TaylorColourScheme)
 246             {
 247                 taylorColour.setSelected(true);
 248             }
 249             else if (sg.cs instanceof PIDColourScheme)
 250             {
 251                 PIDColour.setSelected(true);
 252             }
 253             else if (sg.cs instanceof Blosum62ColourScheme)
 254             {
 255                 BLOSUM62Colour.setSelected(true);
 256             }
 257             else if (sg.cs instanceof UserColourScheme)
 258             {
 259                 userDefinedColour.setSelected(true);
 260             }
 261             else if (sg.cs instanceof HydrophobicColourScheme)
 262             {
 263                 hydrophobicityColour.setSelected(true);
 264             }
 265             else if (sg.cs instanceof HelixColourScheme)
 266             {
 267                 helixColour.setSelected(true);
 268             }
 269             else if (sg.cs instanceof StrandColourScheme)
 270             {
 271                 strandColour.setSelected(true);
 272             }
 273             else if (sg.cs instanceof TurnColourScheme)
 274             {
 275                 turnColour.setSelected(true);
 276             }
 277             else if (sg.cs instanceof BuriedColourScheme)
 278             {
 279                 buriedColour.setSelected(true);
 280             }
 281             else if (sg.cs instanceof ClustalxColourScheme)
 282             {
 283                 clustalColour.setSelected(true);
 284             }
 285             else
 286             {
 287                 noColourmenuItem.setSelected(true);
 288             }
 289
 290             if (sg.cs!=null && sg.cs.conservationApplied())
 291             {
 292                 conservationMenuItem.setSelected(true);
 293             }
 294
 295             showText.setSelected(sg.getDisplayText());
 296             showColourText.setSelected(sg.getColourText());
 297             showBoxes.setSelected(sg.getDisplayBoxes());
 298         }
 299         else
 300         {
 301           groupMenu.setVisible(false);
 302           editMenu.setVisible(false);
 303         }
 304
 305         if (!ap.av.alignment.getGroups().contains(sg))
 306         {
 307             unGroupMenuItem.setVisible(false);
 308         }
 309
 310
 311         if (seq == null)
 312         {
 313             sequenceMenu.setVisible(false);
 314             pdbMenu.setVisible(false);
 315         }
 316
 317         if(links != null && links.size()>0)
 318         {
 319           JMenu linkMenu = new JMenu("Link");
 320           JMenuItem item;
 321           for(int i=0; i<links.size(); i++)
 322           {
 323             String link = links.elementAt(i).toString();
 324             final String label = link.substring(0, link.indexOf("|"));
 325             item = new JMenuItem(label);
 326             final String url;
 327
 328             if (link.indexOf("$SEQUENCE_ID$") > -1)
 329             {
 330               String id = seq.getName();
 331               if (id.indexOf("|") > -1)
 332                 id = id.substring(id.lastIndexOf("|") + 1);
 333
 334               url = link.substring(link.indexOf("|") + 1,
 335                                    link.indexOf("$SEQUENCE_ID$"))
 336                   + id +
 337                   link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
 338             }
 339             else
 340               url = link.substring(link.lastIndexOf("|")+1);
 341
 342
 343             item.addActionListener(new java.awt.event.ActionListener()
 344             {
 345                 public void actionPerformed(ActionEvent e)
 346                 {
 347                     showLink(url);
 348                 }
 349             });
 350
 351             linkMenu.add(item);
 352           }
 353           if(sequence!=null)
 354             sequenceMenu.add(linkMenu);
 355           else
 356             add(linkMenu);
 357         }
 358     }
 359
 360
 361     /**
 362      * DOCUMENT ME!
 363      *
 364      * @throws Exception DOCUMENT ME!
 365      */
 366     private void jbInit() throws Exception
 367     {
 368         groupMenu.setText("Group");
 369         groupMenu.setText("Selection");
 370         groupName.setText("Name");
 371         groupName.addActionListener(new java.awt.event.ActionListener()
 372             {
 373                 public void actionPerformed(ActionEvent e)
 374                 {
 375                     groupName_actionPerformed(e);
 376                 }
 377             });
 378         sequenceMenu.setText("Sequence");
 379         sequenceName.setText("Edit Name/Description");
 380         sequenceName.addActionListener(new java.awt.event.ActionListener()
 381             {
 382                 public void actionPerformed(ActionEvent e)
 383                 {
 384                     sequenceName_actionPerformed(e);
 385                 }
 386             });
 387         PIDColour.setFocusPainted(false);
 388         unGroupMenuItem.setText("Remove Group");
 389         unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 390             {
 391                 public void actionPerformed(ActionEvent e)
 392                 {
 393                     unGroupMenuItem_actionPerformed(e);
 394                 }
 395             });
 396
 397         outline.setText("Border colour");
 398         outline.addActionListener(new java.awt.event.ActionListener()
 399             {
 400                 public void actionPerformed(ActionEvent e)
 401                 {
 402                     outline_actionPerformed(e);
 403                 }
 404             });
 405         nucleotideMenuItem.setText("Nucleotide");
 406         nucleotideMenuItem.addActionListener(new ActionListener()
 407             {
 408                 public void actionPerformed(ActionEvent e)
 409                 {
 410                     nucleotideMenuItem_actionPerformed(e);
 411                 }
 412             });
 413         colourMenu.setText("Group Colour");
 414         showBoxes.setText("Boxes");
 415         showBoxes.setState(true);
 416         showBoxes.addActionListener(new ActionListener()
 417             {
 418                 public void actionPerformed(ActionEvent e)
 419                 {
 420                     showBoxes_actionPerformed(e);
 421                 }
 422             });
 423         showText.setText("Text");
 424         showText.setState(true);
 425         showText.addActionListener(new ActionListener()
 426             {
 427                 public void actionPerformed(ActionEvent e)
 428                 {
 429                     showText_actionPerformed(e);
 430                 }
 431             });
 432         showColourText.setText("Colour Text");
 433         showColourText.addActionListener(new ActionListener()
 434             {
 435                 public void actionPerformed(ActionEvent e)
 436                 {
 437                     showColourText_actionPerformed(e);
 438                 }
 439             });
 440     editMenu.setText("Edit");
 441     cut.setText("Cut");
 442     cut.addActionListener(new ActionListener()
 443     {
 444       public void actionPerformed(ActionEvent e)
 445       {
 446         cut_actionPerformed(e);
 447       }
 448     });
 449     upperCase.setText("To Upper Case");
 450     upperCase.addActionListener(new ActionListener()
 451     {
 452       public void actionPerformed(ActionEvent e)
 453       {
 454         upperCase_actionPerformed(e);
 455       }
 456     });
 457     copy.setText("Copy");
 458     copy.addActionListener(new ActionListener()
 459     {
 460       public void actionPerformed(ActionEvent e)
 461       {
 462         copy_actionPerformed(e);
 463       }
 464     });
 465     lowerCase.setText("To Lower Case");
 466     lowerCase.addActionListener(new ActionListener()
 467     {
 468       public void actionPerformed(ActionEvent e)
 469       {
 470         lowerCase_actionPerformed(e);
 471       }
 472     });
 473     toggle.setText("Toggle Case");
 474     toggle.addActionListener(new ActionListener()
 475     {
 476       public void actionPerformed(ActionEvent e)
 477       {
 478         toggle_actionPerformed(e);
 479       }
 480     });
 481     pdbMenu.setText("Associate Structure with Sequence");
 482     pdbFromFile.setText("From File");
 483     pdbFromFile.addActionListener(new ActionListener()
 484     {
 485       public void actionPerformed(ActionEvent e)
 486       {
 487         pdbFromFile_actionPerformed(e);
 488       }
 489     });
 490     enterPDB.setText("Enter PDB Id");
 491     enterPDB.addActionListener(new ActionListener()
 492     {
 493       public void actionPerformed(ActionEvent e)
 494       {
 495         enterPDB_actionPerformed(e);
 496       }
 497     });
 498     discoverPDB.setText("Discover PDB ids");
 499     discoverPDB.addActionListener(new ActionListener()
 500     {
 501       public void actionPerformed(ActionEvent e)
 502       {
 503         discoverPDB_actionPerformed(e);
 504       }
 505     });
 506     outputMenu.setText("Output to Textbox...");
 507     add(groupMenu);
 508
 509     add(sequenceMenu);
 510     groupMenu.add(editMenu);
 511     groupMenu.add(outputMenu);
 512     groupMenu.addSeparator();
 513     groupMenu.add(groupName);
 514     groupMenu.add(unGroupMenuItem);
 515         groupMenu.add(colourMenu);
 516     groupMenu.add(showBoxes);
 517         groupMenu.add(showText);
 518         groupMenu.add(showColourText);
 519     groupMenu.add(outline);
 520         sequenceMenu.add(sequenceName);
 521     sequenceMenu.add(pdbMenu);
 522     colourMenu.add(noColourmenuItem);
 523         colourMenu.add(clustalColour);
 524         colourMenu.add(BLOSUM62Colour);
 525         colourMenu.add(PIDColour);
 526         colourMenu.add(zappoColour);
 527         colourMenu.add(taylorColour);
 528         colourMenu.add(hydrophobicityColour);
 529         colourMenu.add(helixColour);
 530         colourMenu.add(strandColour);
 531         colourMenu.add(turnColour);
 532         colourMenu.add(buriedColour);
 533         colourMenu.add(nucleotideMenuItem);
 534         colourMenu.add(userDefinedColour);
 535
 536         if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
 537         {
 538           java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
 539               getUserColourSchemes().keys();
 540
 541           while (userColours.hasMoreElements())
 542           {
 543             JMenuItem item = new JMenuItem(userColours.
 544                 nextElement().toString());
 545             item.addActionListener(new ActionListener()
 546             {
 547               public void actionPerformed(ActionEvent evt)
 548               {
 549                 userDefinedColour_actionPerformed(evt);
 550               }
 551             });
 552             colourMenu.add(item);
 553           }
 554         }
 555
 556
 557         colourMenu.addSeparator();
 558         colourMenu.add(abovePIDColour);
 559         colourMenu.add(conservationMenuItem);
 560     editMenu.add(copy);
 561     editMenu.add(cut);
 562     editMenu.add(upperCase);
 563     editMenu.add(lowerCase);
 564     editMenu.add(toggle);
 565     pdbMenu.add(pdbFromFile);
 566     pdbMenu.add(enterPDB);
 567     pdbMenu.add(discoverPDB);
 568     noColourmenuItem.setText("None");
 569         noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
 570             {
 571                 public void actionPerformed(ActionEvent e)
 572                 {
 573                     noColourmenuItem_actionPerformed(e);
 574                 }
 575             });
 576
 577         clustalColour.setText("Clustalx colours");
 578         clustalColour.addActionListener(new java.awt.event.ActionListener()
 579             {
 580                 public void actionPerformed(ActionEvent e)
 581                 {
 582                     clustalColour_actionPerformed(e);
 583                 }
 584             });
 585         zappoColour.setText("Zappo");
 586         zappoColour.addActionListener(new java.awt.event.ActionListener()
 587             {
 588                 public void actionPerformed(ActionEvent e)
 589                 {
 590                     zappoColour_actionPerformed(e);
 591                 }
 592             });
 593         taylorColour.setText("Taylor");
 594         taylorColour.addActionListener(new java.awt.event.ActionListener()
 595             {
 596                 public void actionPerformed(ActionEvent e)
 597                 {
 598                     taylorColour_actionPerformed(e);
 599                 }
 600             });
 601         hydrophobicityColour.setText("Hydrophobicity");
 602         hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
 603             {
 604                 public void actionPerformed(ActionEvent e)
 605                 {
 606                     hydrophobicityColour_actionPerformed(e);
 607                 }
 608             });
 609         helixColour.setText("Helix propensity");
 610         helixColour.addActionListener(new java.awt.event.ActionListener()
 611             {
 612                 public void actionPerformed(ActionEvent e)
 613                 {
 614                     helixColour_actionPerformed(e);
 615                 }
 616             });
 617         strandColour.setText("Strand propensity");
 618         strandColour.addActionListener(new java.awt.event.ActionListener()
 619             {
 620                 public void actionPerformed(ActionEvent e)
 621                 {
 622                     strandColour_actionPerformed(e);
 623                 }
 624             });
 625         turnColour.setText("Turn propensity");
 626         turnColour.addActionListener(new java.awt.event.ActionListener()
 627             {
 628                 public void actionPerformed(ActionEvent e)
 629                 {
 630                     turnColour_actionPerformed(e);
 631                 }
 632             });
 633         buriedColour.setText("Buried Index");
 634         buriedColour.addActionListener(new java.awt.event.ActionListener()
 635             {
 636                 public void actionPerformed(ActionEvent e)
 637                 {
 638                     buriedColour_actionPerformed(e);
 639                 }
 640             });
 641         abovePIDColour.setText("Above % Identity");
 642         abovePIDColour.addActionListener(new java.awt.event.ActionListener()
 643             {
 644                 public void actionPerformed(ActionEvent e)
 645                 {
 646                     abovePIDColour_actionPerformed(e);
 647                 }
 648             });
 649         userDefinedColour.setText("User Defined...");
 650         userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 651             {
 652                 public void actionPerformed(ActionEvent e)
 653                 {
 654                     userDefinedColour_actionPerformed(e);
 655                 }
 656             });
 657         PIDColour.setText("Percentage Identity");
 658         PIDColour.addActionListener(new java.awt.event.ActionListener()
 659             {
 660                 public void actionPerformed(ActionEvent e)
 661                 {
 662                     PIDColour_actionPerformed(e);
 663                 }
 664             });
 665         BLOSUM62Colour.setText("BLOSUM62");
 666         BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 667             {
 668                 public void actionPerformed(ActionEvent e)
 669                 {
 670                     BLOSUM62Colour_actionPerformed(e);
 671                 }
 672             });
 673         conservationMenuItem.setText("Conservation");
 674         conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
 675             {
 676                 public void actionPerformed(ActionEvent e)
 677                 {
 678                     conservationMenuItem_actionPerformed(e);
 679                 }
 680             });
 681     }
 682
 683     /**
 684      * DOCUMENT ME!
 685      */
 686     void refresh()
 687     {
 688         if (ap.overviewPanel != null)
 689           ap.overviewPanel.updateOverviewImage();
 690
 691         ap.seqPanel.repaint();
 692     }
 693
 694     /**
 695      * DOCUMENT ME!
 696      *
 697      * @param e DOCUMENT ME!
 698      */
 699     protected void clustalColour_actionPerformed(ActionEvent e)
 700     {
 701         SequenceGroup sg = getGroup();
 702         sg.cs = new ClustalxColourScheme(sg.getSequences(true),
 703                 ap.av.alignment.getWidth());
 704         refresh();
 705     }
 706
 707     /**
 708      * DOCUMENT ME!
 709      *
 710      * @param e DOCUMENT ME!
 711      */
 712     protected void zappoColour_actionPerformed(ActionEvent e)
 713     {
 714         getGroup().cs = new ZappoColourScheme();
 715         refresh();
 716     }
 717
 718     /**
 719      * DOCUMENT ME!
 720      *
 721      * @param e DOCUMENT ME!
 722      */
 723     protected void taylorColour_actionPerformed(ActionEvent e)
 724     {
 725         getGroup().cs = new TaylorColourScheme();
 726         refresh();
 727     }
 728
 729     /**
 730      * DOCUMENT ME!
 731      *
 732      * @param e DOCUMENT ME!
 733      */
 734     protected void hydrophobicityColour_actionPerformed(ActionEvent e)
 735     {
 736         getGroup().cs = new HydrophobicColourScheme();
 737         refresh();
 738     }
 739
 740     /**
 741      * DOCUMENT ME!
 742      *
 743      * @param e DOCUMENT ME!
 744      */
 745     protected void helixColour_actionPerformed(ActionEvent e)
 746     {
 747         getGroup().cs = new HelixColourScheme();
 748         refresh();
 749     }
 750
 751     /**
 752      * DOCUMENT ME!
 753      *
 754      * @param e DOCUMENT ME!
 755      */
 756     protected void strandColour_actionPerformed(ActionEvent e)
 757     {
 758         getGroup().cs = new StrandColourScheme();
 759         refresh();
 760     }
 761
 762     /**
 763      * DOCUMENT ME!
 764      *
 765      * @param e DOCUMENT ME!
 766      */
 767     protected void turnColour_actionPerformed(ActionEvent e)
 768     {
 769         getGroup().cs = new TurnColourScheme();
 770         refresh();
 771     }
 772
 773     /**
 774      * DOCUMENT ME!
 775      *
 776      * @param e DOCUMENT ME!
 777      */
 778     protected void buriedColour_actionPerformed(ActionEvent e)
 779     {
 780         getGroup().cs = new BuriedColourScheme();
 781         refresh();
 782     }
 783
 784     /**
 785      * DOCUMENT ME!
 786      *
 787      * @param e DOCUMENT ME!
 788      */
 789     public void nucleotideMenuItem_actionPerformed(ActionEvent e)
 790     {
 791         getGroup().cs = new NucleotideColourScheme();
 792         refresh();
 793     }
 794
 795     /**
 796      * DOCUMENT ME!
 797      *
 798      * @param e DOCUMENT ME!
 799      */
 800     protected void abovePIDColour_actionPerformed(ActionEvent e)
 801     {
 802         SequenceGroup sg = getGroup();
 803         if(sg.cs==null)
 804           return;
 805
 806         if (abovePIDColour.isSelected())
 807         {
 808             sg.cs.setConsensus(AAFrequency.calculate(
 809                     sg.getSequences(true), 0,
 810                     ap.av.alignment.getWidth()));
 811
 812             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
 813                     getGroup().getName());
 814
 815            sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
 816
 817             SliderPanel.showPIDSlider();
 818         }
 819         else // remove PIDColouring
 820         {
 821             sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
 822         }
 823
 824         refresh();
 825     }
 826
 827     /**
 828      * DOCUMENT ME!
 829      *
 830      * @param e DOCUMENT ME!
 831      */
 832     protected void userDefinedColour_actionPerformed(ActionEvent e)
 833     {
 834        SequenceGroup sg = getGroup();
 835
 836        if (e.getActionCommand().equals("User Defined..."))
 837          new UserDefinedColours(ap, sg);
 838        else
 839        {
 840          UserColourScheme udc = (UserColourScheme) UserDefinedColours.
 841              getUserColourSchemes().get(e.getActionCommand());
 842
 843          sg.cs = udc;
 844        }
 845      }
 846     /**
 847      * DOCUMENT ME!
 848      *
 849      * @param e DOCUMENT ME!
 850      */
 851     protected void PIDColour_actionPerformed(ActionEvent e)
 852     {
 853         SequenceGroup sg = getGroup();
 854         sg.cs = new PIDColourScheme();
 855         sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
 856                 ap.av.alignment.getWidth()));
 857         refresh();
 858     }
 859
 860     /**
 861      * DOCUMENT ME!
 862      *
 863      * @param e DOCUMENT ME!
 864      */
 865     protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
 866     {
 867         SequenceGroup sg = getGroup();
 868
 869         sg.cs = new Blosum62ColourScheme();
 870
 871         sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
 872                 ap.av.alignment.getWidth()));
 873
 874         refresh();
 875     }
 876
 877     /**
 878      * DOCUMENT ME!
 879      *
 880      * @param e DOCUMENT ME!
 881      */
 882     protected void noColourmenuItem_actionPerformed(ActionEvent e)
 883     {
 884         getGroup().cs = null;
 885         refresh();
 886     }
 887
 888     /**
 889      * DOCUMENT ME!
 890      *
 891      * @param e DOCUMENT ME!
 892      */
 893     protected void conservationMenuItem_actionPerformed(ActionEvent e)
 894     {
 895         SequenceGroup sg = getGroup();
 896         if(sg.cs==null)
 897           return;
 898
 899         if (conservationMenuItem.isSelected())
 900         {
 901             Conservation c = new Conservation("Group",
 902                     ResidueProperties.propHash, 3,
 903                     sg.getSequences(true), 0,
 904                     ap.av.alignment.getWidth());
 905
 906             c.calculate();
 907             c.verdict(false, ap.av.ConsPercGaps);
 908
 909             sg.cs.setConservation(c);
 910
 911             SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
 912             SliderPanel.showConservationSlider();
 913         }
 914         else // remove ConservationColouring
 915         {
 916             sg.cs.setConservation(null);
 917         }
 918
 919         refresh();
 920     }
 921
 922     /**
 923      * DOCUMENT ME!
 924      *
 925      * @param e DOCUMENT ME!
 926      */
 927     protected void groupName_actionPerformed(ActionEvent e)
 928     {
 929         SequenceGroup sg = getGroup();
 930         String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
 931                 "Enter new group name", "Edit group name",
 932                 JOptionPane.QUESTION_MESSAGE);
 933
 934         if (reply == null)
 935         {
 936             return;
 937         }
 938
 939         sg.setName(reply);
 940         groupName.setText(reply);
 941     }
 942
 943     /**
 944      * DOCUMENT ME!
 945      *
 946      * @param e DOCUMENT ME!
 947      */
 948     protected void analyze_actionPerformed(ActionEvent e)
 949     {
 950         CutAndPasteTransfer cap = new CutAndPasteTransfer();
 951         JInternalFrame frame = new JInternalFrame();
 952         frame.setContentPane(cap);
 953         Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
 954
 955         SequenceGroup sg = getGroup();
 956         StringBuffer sb = new StringBuffer();
 957
 958         for (int i = 0; i < sg.getSize(false); i++)
 959         {
 960             Sequence tmp = (Sequence) sg.getSequences(false).elementAt(i);
 961             sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
 962             sb.append("\n");
 963         }
 964
 965         sb.append("Something amazing will happen soon");
 966         cap.setText(sb.toString());
 967     }
 968
 969     /**
 970      * DOCUMENT ME!
 971      *
 972      * @return DOCUMENT ME!
 973      */
 974     SequenceGroup getGroup()
 975     {
 976         SequenceGroup sg = ap.av.getSelectionGroup();
 977       // this method won't add a new group if it already exists
 978         if(sg!=null)
 979           ap.av.alignment.addGroup(sg);
 980
 981         return sg;
 982     }
 983
 984     /**
 985      * DOCUMENT ME!
 986      *
 987      * @param e DOCUMENT ME!
 988      */
 989     void sequenceName_actionPerformed(ActionEvent e)
 990     {
 991       JLabel idlabel = new JLabel(  "       Sequence Name ");
 992       JLabel desclabel = new JLabel("Sequence Description ");
 993       idlabel.setFont(new Font("Courier", Font.PLAIN, 12));
 994       desclabel.setFont(new Font("Courier", Font.PLAIN, 12));
 995       JTextField id = new JTextField(sequence.getName(), 40);
 996       JTextField description = new JTextField(sequence.getDescription(), 40);
 997       JPanel panel = new JPanel(new BorderLayout());
 998       JPanel panel2 = new JPanel(new BorderLayout());
 999       panel2.add(idlabel, BorderLayout.WEST);
1000       panel2.add(id, BorderLayout.CENTER);
1001       panel.add(panel2, BorderLayout.NORTH);
1002       panel2 = new JPanel(new BorderLayout());
1003       panel2.add(desclabel, BorderLayout.WEST);
1004       panel2.add(description, BorderLayout.CENTER);
1005       panel.add(panel2, BorderLayout.SOUTH);
1006
1007
1008        int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
1009           panel, "Edit Sequence Name/Description",
1010           JOptionPane.OK_CANCEL_OPTION );
1011
1012
1013         if (reply != JOptionPane.OK_OPTION )
1014         {
1015             return;
1016         }
1017
1018         String s = id.getText();
1019
1020         if (s != null)
1021         {
1022             if (s.indexOf(" ") > -1)
1023             {
1024                 JOptionPane.showMessageDialog(ap,
1025                     "Spaces have been converted to \"_\"",
1026                     "No spaces allowed in Sequence Name",
1027                     JOptionPane.WARNING_MESSAGE);
1028             }
1029
1030             s = s.replace(' ', '_');
1031             sequence.getDatasetSequence().setName(s);
1032             sequence.setName(s);
1033             ap.repaint();
1034         }
1035
1036         sequence.getDatasetSequence().setDescription(description.getText());
1037         sequence.setDescription(description.getText());
1038     }
1039
1040     /**
1041      * DOCUMENT ME!
1042      *
1043      * @param e DOCUMENT ME!
1044      */
1045     void unGroupMenuItem_actionPerformed(ActionEvent e)
1046     {
1047         SequenceGroup sg = ap.av.getSelectionGroup();
1048         ap.av.alignment.deleteGroup(sg);
1049         ap.av.setSelectionGroup(null);
1050         refresh();
1051     }
1052
1053
1054     /**
1055      * DOCUMENT ME!
1056      *
1057      * @param e DOCUMENT ME!
1058      */
1059     protected void outline_actionPerformed(ActionEvent e)
1060     {
1061         SequenceGroup sg = getGroup();
1062         Color col = JColorChooser.showDialog(this, "Select Outline Colour",
1063                 Color.BLUE);
1064
1065         if (col != null)
1066         {
1067             sg.setOutlineColour(col);
1068         }
1069
1070         refresh();
1071     }
1072
1073     /**
1074      * DOCUMENT ME!
1075      *
1076      * @param e DOCUMENT ME!
1077      */
1078     public void showBoxes_actionPerformed(ActionEvent e)
1079     {
1080         getGroup().setDisplayBoxes(showBoxes.isSelected());
1081         refresh();
1082     }
1083
1084     /**
1085      * DOCUMENT ME!
1086      *
1087      * @param e DOCUMENT ME!
1088      */
1089     public void showText_actionPerformed(ActionEvent e)
1090     {
1091         getGroup().setDisplayText(showText.isSelected());
1092         refresh();
1093     }
1094
1095     /**
1096      * DOCUMENT ME!
1097      *
1098      * @param e DOCUMENT ME!
1099      */
1100     public void showColourText_actionPerformed(ActionEvent e)
1101     {
1102         getGroup().setColourText(showColourText.isSelected());
1103         refresh();
1104     }
1105
1106     public void showLink(String url)
1107     {
1108       try
1109       {
1110         jalview.util.BrowserLauncher.openURL(url);
1111       }
1112       catch (Exception ex)
1113       {
1114         JOptionPane.showInternalMessageDialog(Desktop.desktop,
1115             "Unixers: Couldn't find default web browser."
1116            +"\nAdd the full path to your browser in Preferences.",
1117            "Web browser not found", JOptionPane.WARNING_MESSAGE );
1118
1119
1120         ex.printStackTrace();
1121       }
1122     }
1123
1124     void hideSequences(boolean representGroup)
1125     {
1126       SequenceGroup sg = ap.av.getSelectionGroup();
1127       if(sg==null || sg.getSize(false)<1)
1128       {
1129         ap.av.hideSequence(sequence);
1130         return;
1131       }
1132
1133         int index = 0;
1134         while(index < sg.getSize(false))
1135         {
1136           if(representGroup && sg.getSequenceAt(index)!=sequence)
1137           {
1138             sequence.addHiddenSequence(sg.getSequenceAt(index));
1139             ap.av.hideSequence(sg.getSequenceAt(index));
1140           }
1141           else if(!representGroup)
1142           {
1143             ap.av.hideSequence(sg.getSequenceAt(index));
1144           }
1145           index ++;
1146         }
1147
1148         ap.av.setSelectionGroup(null);
1149     }
1150
1151   public void copy_actionPerformed(ActionEvent e)
1152   {
1153     ap.alignFrame.copy_actionPerformed(null);
1154   }
1155
1156   public void cut_actionPerformed(ActionEvent e)
1157   {
1158     ap.alignFrame.cut_actionPerformed(null);
1159   }
1160
1161   public void upperCase_actionPerformed(ActionEvent e)
1162   {
1163     changeCase(e.getSource());
1164   }
1165
1166   public void lowerCase_actionPerformed(ActionEvent e)
1167   {
1168     changeCase(e.getSource());
1169   }
1170
1171   public void toggle_actionPerformed(ActionEvent e)
1172   {
1173     changeCase(e.getSource());
1174   }
1175
1176   void changeCase(Object source)
1177   {
1178     SequenceGroup sg = ap.av.getSelectionGroup();
1179     if (sg != null)
1180     {
1181       for (int g = 0; g < sg.getSize(true); g++)
1182       {
1183         int start = sg.getStartRes();
1184         int end = sg.getEndRes() + 1;
1185
1186         do
1187         {
1188           if (ap.av.hasHiddenColumns)
1189           {
1190             end = ap.av.colSel.getHiddenBoundaryRight(start);
1191             if (start == end)
1192               end = sg.getEndRes() + 1;
1193             if (end > sg.getEndRes())
1194               end = sg.getEndRes() + 1;
1195           }
1196
1197           if (source == toggle)
1198             ( (SequenceI) sg.getSequences(true).elementAt(g))
1199                 .toggleCase(start, end);
1200           else
1201             ( (SequenceI) sg.getSequences(true).elementAt(g))
1202                 .changeCase(source == upperCase, start, end);
1203
1204           if (ap.av.hasHiddenColumns)
1205           {
1206             start = ap.av.colSel.adjustForHiddenColumns(end);
1207             start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
1208           }
1209
1210         }
1211         while (end < sg.getEndRes());
1212       }
1213       ap.repaint();
1214     }
1215   }
1216
1217   public void outputText_actionPerformed(ActionEvent e)
1218   {
1219     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1220     Desktop.addInternalFrame(cap,
1221                              "Alignment output - " + e.getActionCommand(), 600,
1222                              500);
1223
1224     String [] omitHidden = null;
1225
1226     if(ap.av.hasHiddenColumns)
1227     {
1228       System.out.println("PROMPT USER HERE");
1229       omitHidden = ap.av.getViewAsString(true);
1230     }
1231
1232     cap.setText(new FormatAdapter().formatSequences(
1233         e.getActionCommand(),
1234         ap.av.getSelectionAsNewSequence(),
1235         omitHidden));
1236   }
1237
1238
1239   public void pdbFromFile_actionPerformed(ActionEvent e)
1240   {
1241      jalview.io.JalviewFileChooser chooser
1242          = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
1243          getProperty(
1244              "LAST_DIRECTORY"));
1245      chooser.setFileView(new jalview.io.JalviewFileView());
1246      chooser.setDialogTitle("Select a PDB file");
1247      chooser.setToolTipText("Load a PDB file");
1248
1249      int value = chooser.showOpenDialog(null);
1250
1251      if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
1252      {
1253        PDBEntry entry = new PDBEntry();
1254        String choice = chooser.getSelectedFile().getPath();
1255        jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1256        try
1257        {
1258          MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
1259                                        jalview.io.AppletFormatAdapter.FILE);
1260
1261          if (pdbfile.id == null)
1262          {
1263            String reply = JOptionPane.showInternalInputDialog(
1264                Desktop.desktop,
1265                "Couldn't find a PDB id in the file supplied."
1266                + "Please enter an Id to identify this structure.",
1267                "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
1268            if (reply == null)
1269              return;
1270
1271            entry.setId(reply);
1272          }
1273          else
1274            entry.setId(pdbfile.id);
1275        }
1276        catch (java.io.IOException ex)
1277        {
1278          ex.printStackTrace();
1279        }
1280
1281        entry.setFile(choice);
1282        sequence.getDatasetSequence().addPDBId(entry);
1283      }
1284
1285   }
1286
1287   public void enterPDB_actionPerformed(ActionEvent e)
1288   {
1289     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
1290         "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
1291
1292     if (id != null && id.length() > 0)
1293     {
1294       PDBEntry entry = new PDBEntry();
1295       entry.setId(id);
1296       sequence.getDatasetSequence()
1297           .addPDBId(entry);
1298     }
1299   }
1300
1301   public void discoverPDB_actionPerformed(ActionEvent e)
1302   {
1303     new jalview.io.DBRefFetcher(
1304              ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);
1305   }
1306 }