src/jalview/gui/PopupMenu.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
   3  * Copyright (C) 2008 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 java.util.*;
  22
  23 import java.awt.*;
  24 import java.awt.event.*;
  25 import javax.swing.*;
  26
  27 import MCview.*;
  28 import jalview.analysis.*;
  29 import jalview.commands.*;
  30 import jalview.datamodel.*;
  31 import jalview.io.*;
  32 import jalview.schemes.*;
  33 import jalview.util.UrlLink;
  34
  35 /**
  36  * DOCUMENT ME!
  37  *
  38  * @author $author$
  39  * @version $Revision$
  40  */
  41 public class PopupMenu extends JPopupMenu
  42 {
  43   JMenu groupMenu = new JMenu();
  44
  45   JMenuItem groupName = new JMenuItem();
  46
  47   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  48
  49   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  50
  51   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  52
  53   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
  54
  55   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
  56
  57   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
  58
  59   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
  60
  61   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
  62
  63   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
  64
  65   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
  66
  67   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
  68
  69   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
  70
  71   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
  72
  73   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
  74
  75   AlignmentPanel ap;
  76
  77   JMenu sequenceMenu = new JMenu();
  78
  79   JMenuItem sequenceName = new JMenuItem();
  80
  81   Sequence sequence;
  82
  83   JMenuItem unGroupMenuItem = new JMenuItem();
  84
  85   JMenuItem outline = new JMenuItem();
  86
  87   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
  88
  89   JMenu colourMenu = new JMenu();
  90
  91   JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
  92
  93   JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
  94
  95   JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
  96
  97   JMenu editMenu = new JMenu();
  98
  99   JMenuItem cut = new JMenuItem();
 100
 101   JMenuItem copy = new JMenuItem();
 102
 103   JMenuItem upperCase = new JMenuItem();
 104
 105   JMenuItem lowerCase = new JMenuItem();
 106
 107   JMenuItem toggle = new JMenuItem();
 108
 109   JMenu pdbMenu = new JMenu();
 110
 111   JMenuItem pdbFromFile = new JMenuItem();
 112
 113   JMenuItem enterPDB = new JMenuItem();
 114
 115   JMenuItem discoverPDB = new JMenuItem();
 116
 117   JMenu outputMenu = new JMenu();
 118
 119   JMenuItem sequenceFeature = new JMenuItem();
 120
 121   JMenuItem textColour = new JMenuItem();
 122
 123   JMenu jMenu1 = new JMenu();
 124
 125   JMenu structureMenu = new JMenu();
 126
 127   JMenu viewStructureMenu = new JMenu();
 128
 129   // JMenu colStructureMenu = new JMenu();
 130   JMenuItem editSequence = new JMenuItem();
 131
 132   // JMenuItem annotationMenuItem = new JMenuItem();
 133
 134   /**
 135    * Creates a new PopupMenu object.
 136    *
 137    * @param ap
 138    *                DOCUMENT ME!
 139    * @param seq
 140    *                DOCUMENT ME!
 141    */
 142   public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
 143   {
 144     // /////////////////////////////////////////////////////////
 145     // If this is activated from the sequence panel, the user may want to
 146     // edit or annotate a particular residue. Therefore display the residue menu
 147     //
 148     // If from the IDPanel, we must display the sequence menu
 149     // ////////////////////////////////////////////////////////
 150     this.ap = ap;
 151     sequence = seq;
 152
 153     ButtonGroup colours = new ButtonGroup();
 154     colours.add(noColourmenuItem);
 155     colours.add(clustalColour);
 156     colours.add(zappoColour);
 157     colours.add(taylorColour);
 158     colours.add(hydrophobicityColour);
 159     colours.add(helixColour);
 160     colours.add(strandColour);
 161     colours.add(turnColour);
 162     colours.add(buriedColour);
 163     colours.add(abovePIDColour);
 164     colours.add(userDefinedColour);
 165     colours.add(PIDColour);
 166     colours.add(BLOSUM62Colour);
 167
 168     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 169     {
 170       JMenuItem item = new JMenuItem(
 171               jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 172
 173       item.addActionListener(new java.awt.event.ActionListener()
 174       {
 175         public void actionPerformed(ActionEvent e)
 176         {
 177           outputText_actionPerformed(e);
 178         }
 179       });
 180
 181       outputMenu.add(item);
 182     }
 183
 184     try
 185     {
 186       jbInit();
 187     } catch (Exception e)
 188     {
 189       e.printStackTrace();
 190     }
 191
 192     if (seq != null)
 193     {
 194       sequenceMenu.setText(sequence.getName());
 195
 196       JMenuItem menuItem;
 197       if (seq.getDatasetSequence().getPDBId() != null
 198               && seq.getDatasetSequence().getPDBId().size() > 0)
 199       {
 200         java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
 201                 .elements();
 202
 203         while (e.hasMoreElements())
 204         {
 205           final PDBEntry pdb = (PDBEntry) e.nextElement();
 206
 207           menuItem = new JMenuItem();
 208           menuItem.setText(pdb.getId());
 209           menuItem.addActionListener(new java.awt.event.ActionListener()
 210           {
 211             public void actionPerformed(ActionEvent e)
 212             {
 213               Vector seqs = new Vector();
 214               for (int i = 0; i < ap.av.alignment.getHeight(); i++)
 215               {
 216                 Vector pdbs = ap.av.alignment.getSequenceAt(i)
 217                         .getDatasetSequence().getPDBId();
 218                 if (pdbs == null)
 219                   continue;
 220
 221                 for (int p = 0; p < pdbs.size(); p++)
 222                 {
 223                   PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
 224                   if (p1.getId().equals(pdb.getId()))
 225                   {
 226                     if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))
 227                       seqs.addElement(ap.av.alignment.getSequenceAt(i));
 228
 229                     continue;
 230                   }
 231                 }
 232               }
 233
 234               SequenceI[] seqs2 = new SequenceI[seqs.size()];
 235               seqs.toArray(seqs2);
 236
 237               new AppJmol(pdb, seqs2, null, ap);
 238               // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
 239             }
 240           });
 241           viewStructureMenu.add(menuItem);
 242
 243           /*
 244            * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
 245            * menuItem.addActionListener(new java.awt.event.ActionListener() {
 246            * public void actionPerformed(ActionEvent e) {
 247            * colourByStructure(pdb.getId()); } });
 248            * colStructureMenu.add(menuItem);
 249            */
 250         }
 251       }
 252       else
 253       {
 254         structureMenu.remove(viewStructureMenu);
 255         // structureMenu.remove(colStructureMenu);
 256       }
 257
 258       menuItem = new JMenuItem("Hide Sequences");
 259       menuItem.addActionListener(new java.awt.event.ActionListener()
 260       {
 261         public void actionPerformed(ActionEvent e)
 262         {
 263           hideSequences(false);
 264         }
 265       });
 266       add(menuItem);
 267
 268       if (ap.av.getSelectionGroup() != null
 269               && ap.av.getSelectionGroup().getSize() > 1)
 270       {
 271         menuItem = new JMenuItem("Represent Group with " + seq.getName());
 272         menuItem.addActionListener(new java.awt.event.ActionListener()
 273         {
 274           public void actionPerformed(ActionEvent e)
 275           {
 276             hideSequences(true);
 277           }
 278         });
 279         sequenceMenu.add(menuItem);
 280       }
 281
 282       if (ap.av.hasHiddenRows)
 283       {
 284         final int index = ap.av.alignment.findIndex(seq);
 285
 286         if (ap.av.adjustForHiddenSeqs(index)
 287                 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
 288         {
 289           menuItem = new JMenuItem("Reveal Sequences");
 290           menuItem.addActionListener(new ActionListener()
 291           {
 292             public void actionPerformed(ActionEvent e)
 293             {
 294               ap.av.showSequence(index);
 295               if (ap.overviewPanel != null)
 296               {
 297                 ap.overviewPanel.updateOverviewImage();
 298               }
 299             }
 300           });
 301           add(menuItem);
 302         }
 303
 304         menuItem = new JMenuItem("Reveal All");
 305         menuItem.addActionListener(new ActionListener()
 306         {
 307           public void actionPerformed(ActionEvent e)
 308           {
 309             ap.av.showAllHiddenSeqs();
 310             if (ap.overviewPanel != null)
 311             {
 312               ap.overviewPanel.updateOverviewImage();
 313             }
 314           }
 315         });
 316
 317         add(menuItem);
 318       }
 319
 320     }
 321
 322     SequenceGroup sg = ap.av.getSelectionGroup();
 323
 324     if (sg != null)
 325     {
 326       groupName.setText(sg.getName());
 327
 328       if (sg.cs instanceof ZappoColourScheme)
 329       {
 330         zappoColour.setSelected(true);
 331       }
 332       else if (sg.cs instanceof TaylorColourScheme)
 333       {
 334         taylorColour.setSelected(true);
 335       }
 336       else if (sg.cs instanceof PIDColourScheme)
 337       {
 338         PIDColour.setSelected(true);
 339       }
 340       else if (sg.cs instanceof Blosum62ColourScheme)
 341       {
 342         BLOSUM62Colour.setSelected(true);
 343       }
 344       else if (sg.cs instanceof UserColourScheme)
 345       {
 346         userDefinedColour.setSelected(true);
 347       }
 348       else if (sg.cs instanceof HydrophobicColourScheme)
 349       {
 350         hydrophobicityColour.setSelected(true);
 351       }
 352       else if (sg.cs instanceof HelixColourScheme)
 353       {
 354         helixColour.setSelected(true);
 355       }
 356       else if (sg.cs instanceof StrandColourScheme)
 357       {
 358         strandColour.setSelected(true);
 359       }
 360       else if (sg.cs instanceof TurnColourScheme)
 361       {
 362         turnColour.setSelected(true);
 363       }
 364       else if (sg.cs instanceof BuriedColourScheme)
 365       {
 366         buriedColour.setSelected(true);
 367       }
 368       else if (sg.cs instanceof ClustalxColourScheme)
 369       {
 370         clustalColour.setSelected(true);
 371       }
 372       else
 373       {
 374         noColourmenuItem.setSelected(true);
 375       }
 376
 377       if (sg.cs != null && sg.cs.conservationApplied())
 378       {
 379         conservationMenuItem.setSelected(true);
 380       }
 381
 382       showText.setSelected(sg.getDisplayText());
 383       showColourText.setSelected(sg.getColourText());
 384       showBoxes.setSelected(sg.getDisplayBoxes());
 385     }
 386     else
 387     {
 388       groupMenu.setVisible(false);
 389       editMenu.setVisible(false);
 390     }
 391
 392     if (!ap.av.alignment.getGroups().contains(sg))
 393     {
 394       unGroupMenuItem.setVisible(false);
 395     }
 396
 397     if (seq == null)
 398     {
 399       sequenceMenu.setVisible(false);
 400       structureMenu.setVisible(false);
 401     }
 402
 403     if (links != null && links.size() > 0)
 404     {
 405       JMenu linkMenu = new JMenu("Link");
 406
 407       for (int i = 0; i < links.size(); i++)
 408       {
 409         String link = links.elementAt(i).toString();
 410         UrlLink urlLink = null;
 411         try
 412         {
 413           urlLink = new UrlLink(link);
 414         } catch (Exception foo)
 415         {
 416           jalview.bin.Cache.log.error("Exception for URLLink '" + link
 417                   + "'", foo);
 418           continue;
 419         }
 420         ;
 421         if (!urlLink.isValid())
 422         {
 423           jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 424           continue;
 425         }
 426         final String label = urlLink.getLabel();
 427         if (urlLink.isDynamic())
 428         {
 429
 430           // collect matching db-refs
 431           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq
 432                   .getDBRef(), new String[]
 433           { urlLink.getTarget() });
 434           // collect id string too
 435           String id = seq.getName();
 436           String descr = seq.getDescription();
 437           if (descr!=null && descr.length()<1)
 438           {
 439             descr = null;
 440           }
 441
 442           if (dbr != null)
 443           {
 444             for (int r = 0; r < dbr.length; r++)
 445             {
 446               if (id != null && dbr[r].getAccessionId().equals(id))
 447               {
 448                 // suppress duplicate link creation for the bare sequence ID
 449                 // string with this link
 450                 id = null;
 451               }
 452               // create Bare ID link for this RUL
 453               String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
 454                       true);
 455               if (urls != null)
 456               {
 457                 for (int u = 0; u < urls.length; u += 2)
 458                 {
 459                   addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
 460                 }
 461               }
 462             }
 463           }
 464           if (id != null)
 465           {
 466             // create Bare ID link for this RUL
 467             String[] urls = urlLink.makeUrls(id, true);
 468             if (urls != null)
 469             {
 470               for (int u = 0; u < urls.length; u += 2)
 471               {
 472                 addshowLink(linkMenu, label, urls[u + 1]);
 473               }
 474             }
 475           }
 476           // Create urls from description but only for URL links which are regex links
 477           if (descr != null && urlLink.getRegexReplace()!=null)
 478           {
 479             // create link for this URL from description where regex matches
 480             String[] urls = urlLink.makeUrls(descr, true);
 481             if (urls != null)
 482             {
 483               for (int u = 0; u < urls.length; u += 2)
 484               {
 485                 addshowLink(linkMenu, label, urls[u + 1]);
 486               }
 487             }
 488           }
 489         }
 490         else
 491         {
 492           // Add a non-dynamic link
 493           addshowLink(linkMenu, label, urlLink.getUrl_prefix());
 494         }
 495       }
 496       if (sequence != null)
 497       {
 498         sequenceMenu.add(linkMenu);
 499       }
 500       else
 501       {
 502         add(linkMenu);
 503       }
 504     }
 505   }
 506
 507   /**
 508    * add a show URL menu item to the given linkMenu
 509    *
 510    * @param linkMenu
 511    * @param label -
 512    *                menu label string
 513    * @param url -
 514    *                url to open
 515    */
 516   private void addshowLink(JMenu linkMenu, String label, final String url)
 517   {
 518     JMenuItem item = new JMenuItem(label);
 519     item.setToolTipText("open URL: " + url);
 520     item.addActionListener(new java.awt.event.ActionListener()
 521     {
 522       public void actionPerformed(ActionEvent e)
 523       {
 524         new Thread(new Runnable()
 525         {
 526
 527           public void run()
 528           {
 529             showLink(url);
 530           }
 531
 532         }).start();
 533       }
 534     });
 535
 536     linkMenu.add(item);
 537   }
 538
 539   /**
 540    * DOCUMENT ME!
 541    *
 542    * @throws Exception
 543    *                 DOCUMENT ME!
 544    */
 545   private void jbInit() throws Exception
 546   {
 547     groupMenu.setText("Group");
 548     groupMenu.setText("Selection");
 549     groupName.setText("Name");
 550     groupName.addActionListener(new java.awt.event.ActionListener()
 551     {
 552       public void actionPerformed(ActionEvent e)
 553       {
 554         groupName_actionPerformed();
 555       }
 556     });
 557     sequenceMenu.setText("Sequence");
 558     sequenceName.setText("Edit Name/Description");
 559     sequenceName.addActionListener(new java.awt.event.ActionListener()
 560     {
 561       public void actionPerformed(ActionEvent e)
 562       {
 563         sequenceName_actionPerformed();
 564       }
 565     });
 566     PIDColour.setFocusPainted(false);
 567     unGroupMenuItem.setText("Remove Group");
 568     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 569     {
 570       public void actionPerformed(ActionEvent e)
 571       {
 572         unGroupMenuItem_actionPerformed();
 573       }
 574     });
 575
 576     outline.setText("Border colour");
 577     outline.addActionListener(new java.awt.event.ActionListener()
 578     {
 579       public void actionPerformed(ActionEvent e)
 580       {
 581         outline_actionPerformed();
 582       }
 583     });
 584     nucleotideMenuItem.setText("Nucleotide");
 585     nucleotideMenuItem.addActionListener(new ActionListener()
 586     {
 587       public void actionPerformed(ActionEvent e)
 588       {
 589         nucleotideMenuItem_actionPerformed();
 590       }
 591     });
 592     colourMenu.setText("Group Colour");
 593     showBoxes.setText("Boxes");
 594     showBoxes.setState(true);
 595     showBoxes.addActionListener(new ActionListener()
 596     {
 597       public void actionPerformed(ActionEvent e)
 598       {
 599         showBoxes_actionPerformed();
 600       }
 601     });
 602     showText.setText("Text");
 603     showText.setState(true);
 604     showText.addActionListener(new ActionListener()
 605     {
 606       public void actionPerformed(ActionEvent e)
 607       {
 608         showText_actionPerformed();
 609       }
 610     });
 611     showColourText.setText("Colour Text");
 612     showColourText.addActionListener(new ActionListener()
 613     {
 614       public void actionPerformed(ActionEvent e)
 615       {
 616         showColourText_actionPerformed();
 617       }
 618     });
 619     editMenu.setText("Edit");
 620     cut.setText("Cut");
 621     cut.addActionListener(new ActionListener()
 622     {
 623       public void actionPerformed(ActionEvent e)
 624       {
 625         cut_actionPerformed();
 626       }
 627     });
 628     upperCase.setText("To Upper Case");
 629     upperCase.addActionListener(new ActionListener()
 630     {
 631       public void actionPerformed(ActionEvent e)
 632       {
 633         changeCase(e);
 634       }
 635     });
 636     copy.setText("Copy");
 637     copy.addActionListener(new ActionListener()
 638     {
 639       public void actionPerformed(ActionEvent e)
 640       {
 641         copy_actionPerformed();
 642       }
 643     });
 644     lowerCase.setText("To Lower Case");
 645     lowerCase.addActionListener(new ActionListener()
 646     {
 647       public void actionPerformed(ActionEvent e)
 648       {
 649         changeCase(e);
 650       }
 651     });
 652     toggle.setText("Toggle Case");
 653     toggle.addActionListener(new ActionListener()
 654     {
 655       public void actionPerformed(ActionEvent e)
 656       {
 657         changeCase(e);
 658       }
 659     });
 660     pdbMenu.setText("Associate Structure with Sequence");
 661     pdbFromFile.setText("From File");
 662     pdbFromFile.addActionListener(new ActionListener()
 663     {
 664       public void actionPerformed(ActionEvent e)
 665       {
 666         pdbFromFile_actionPerformed();
 667       }
 668     });
 669     enterPDB.setText("Enter PDB Id");
 670     enterPDB.addActionListener(new ActionListener()
 671     {
 672       public void actionPerformed(ActionEvent e)
 673       {
 674         enterPDB_actionPerformed();
 675       }
 676     });
 677     discoverPDB.setText("Discover PDB ids");
 678     discoverPDB.addActionListener(new ActionListener()
 679     {
 680       public void actionPerformed(ActionEvent e)
 681       {
 682         discoverPDB_actionPerformed();
 683       }
 684     });
 685     outputMenu.setText("Output to Textbox...");
 686     sequenceFeature.setText("Create Sequence Feature");
 687     sequenceFeature.addActionListener(new ActionListener()
 688     {
 689       public void actionPerformed(ActionEvent e)
 690       {
 691         sequenceFeature_actionPerformed();
 692       }
 693     });
 694     textColour.setText("Text Colour");
 695     textColour.addActionListener(new ActionListener()
 696     {
 697       public void actionPerformed(ActionEvent e)
 698       {
 699         textColour_actionPerformed();
 700       }
 701     });
 702     jMenu1.setText("Group");
 703     structureMenu.setText("Structure");
 704     viewStructureMenu.setText("View Structure");
 705     // colStructureMenu.setText("Colour By Structure");
 706     editSequence.setText("Edit Sequence...");
 707     editSequence.addActionListener(new ActionListener()
 708     {
 709       public void actionPerformed(ActionEvent actionEvent)
 710       {
 711         editSequence_actionPerformed(actionEvent);
 712       }
 713     });
 714     /*
 715      * annotationMenuItem.setText("By Annotation");
 716      * annotationMenuItem.addActionListener(new ActionListener() { public void
 717      * actionPerformed(ActionEvent actionEvent) {
 718      * annotationMenuItem_actionPerformed(actionEvent); } });
 719      */
 720
 721     add(groupMenu);
 722
 723     add(sequenceMenu);
 724     this.add(structureMenu);
 725     groupMenu.add(editMenu);
 726     groupMenu.add(outputMenu);
 727     groupMenu.add(sequenceFeature);
 728     groupMenu.add(jMenu1);
 729     sequenceMenu.add(sequenceName);
 730     colourMenu.add(textColour);
 731     colourMenu.add(noColourmenuItem);
 732     colourMenu.add(clustalColour);
 733     colourMenu.add(BLOSUM62Colour);
 734     colourMenu.add(PIDColour);
 735     colourMenu.add(zappoColour);
 736     colourMenu.add(taylorColour);
 737     colourMenu.add(hydrophobicityColour);
 738     colourMenu.add(helixColour);
 739     colourMenu.add(strandColour);
 740     colourMenu.add(turnColour);
 741     colourMenu.add(buriedColour);
 742     colourMenu.add(nucleotideMenuItem);
 743     colourMenu.add(userDefinedColour);
 744
 745     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 746     {
 747       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 748               .getUserColourSchemes().keys();
 749
 750       while (userColours.hasMoreElements())
 751       {
 752         JMenuItem item = new JMenuItem(userColours.nextElement().toString());
 753         item.addActionListener(new ActionListener()
 754         {
 755           public void actionPerformed(ActionEvent evt)
 756           {
 757             userDefinedColour_actionPerformed(evt);
 758           }
 759         });
 760         colourMenu.add(item);
 761       }
 762     }
 763
 764     colourMenu.addSeparator();
 765     colourMenu.add(abovePIDColour);
 766     colourMenu.add(conservationMenuItem);
 767     // colourMenu.add(annotationMenuItem);
 768     editMenu.add(copy);
 769     editMenu.add(cut);
 770     editMenu.add(editSequence);
 771     editMenu.add(upperCase);
 772     editMenu.add(lowerCase);
 773     editMenu.add(toggle);
 774     pdbMenu.add(pdbFromFile);
 775     pdbMenu.add(enterPDB);
 776     pdbMenu.add(discoverPDB);
 777     jMenu1.add(groupName);
 778     jMenu1.add(unGroupMenuItem);
 779     jMenu1.add(colourMenu);
 780     jMenu1.add(showBoxes);
 781     jMenu1.add(showText);
 782     jMenu1.add(showColourText);
 783     jMenu1.add(outline);
 784     structureMenu.add(pdbMenu);
 785     structureMenu.add(viewStructureMenu);
 786     // structureMenu.add(colStructureMenu);
 787     noColourmenuItem.setText("None");
 788     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
 789     {
 790       public void actionPerformed(ActionEvent e)
 791       {
 792         noColourmenuItem_actionPerformed();
 793       }
 794     });
 795
 796     clustalColour.setText("Clustalx colours");
 797     clustalColour.addActionListener(new java.awt.event.ActionListener()
 798     {
 799       public void actionPerformed(ActionEvent e)
 800       {
 801         clustalColour_actionPerformed();
 802       }
 803     });
 804     zappoColour.setText("Zappo");
 805     zappoColour.addActionListener(new java.awt.event.ActionListener()
 806     {
 807       public void actionPerformed(ActionEvent e)
 808       {
 809         zappoColour_actionPerformed();
 810       }
 811     });
 812     taylorColour.setText("Taylor");
 813     taylorColour.addActionListener(new java.awt.event.ActionListener()
 814     {
 815       public void actionPerformed(ActionEvent e)
 816       {
 817         taylorColour_actionPerformed();
 818       }
 819     });
 820     hydrophobicityColour.setText("Hydrophobicity");
 821     hydrophobicityColour
 822             .addActionListener(new java.awt.event.ActionListener()
 823             {
 824               public void actionPerformed(ActionEvent e)
 825               {
 826                 hydrophobicityColour_actionPerformed();
 827               }
 828             });
 829     helixColour.setText("Helix propensity");
 830     helixColour.addActionListener(new java.awt.event.ActionListener()
 831     {
 832       public void actionPerformed(ActionEvent e)
 833       {
 834         helixColour_actionPerformed();
 835       }
 836     });
 837     strandColour.setText("Strand propensity");
 838     strandColour.addActionListener(new java.awt.event.ActionListener()
 839     {
 840       public void actionPerformed(ActionEvent e)
 841       {
 842         strandColour_actionPerformed();
 843       }
 844     });
 845     turnColour.setText("Turn propensity");
 846     turnColour.addActionListener(new java.awt.event.ActionListener()
 847     {
 848       public void actionPerformed(ActionEvent e)
 849       {
 850         turnColour_actionPerformed();
 851       }
 852     });
 853     buriedColour.setText("Buried Index");
 854     buriedColour.addActionListener(new java.awt.event.ActionListener()
 855     {
 856       public void actionPerformed(ActionEvent e)
 857       {
 858         buriedColour_actionPerformed();
 859       }
 860     });
 861     abovePIDColour.setText("Above % Identity");
 862     abovePIDColour.addActionListener(new java.awt.event.ActionListener()
 863     {
 864       public void actionPerformed(ActionEvent e)
 865       {
 866         abovePIDColour_actionPerformed();
 867       }
 868     });
 869     userDefinedColour.setText("User Defined...");
 870     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 871     {
 872       public void actionPerformed(ActionEvent e)
 873       {
 874         userDefinedColour_actionPerformed(e);
 875       }
 876     });
 877     PIDColour.setText("Percentage Identity");
 878     PIDColour.addActionListener(new java.awt.event.ActionListener()
 879     {
 880       public void actionPerformed(ActionEvent e)
 881       {
 882         PIDColour_actionPerformed();
 883       }
 884     });
 885     BLOSUM62Colour.setText("BLOSUM62");
 886     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 887     {
 888       public void actionPerformed(ActionEvent e)
 889       {
 890         BLOSUM62Colour_actionPerformed();
 891       }
 892     });
 893     conservationMenuItem.setText("Conservation");
 894     conservationMenuItem
 895             .addActionListener(new java.awt.event.ActionListener()
 896             {
 897               public void actionPerformed(ActionEvent e)
 898               {
 899                 conservationMenuItem_actionPerformed();
 900               }
 901             });
 902   }
 903
 904   /**
 905    * DOCUMENT ME!
 906    */
 907   void refresh()
 908   {
 909     ap.paintAlignment(true);
 910
 911     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
 912   }
 913
 914   /**
 915    * DOCUMENT ME!
 916    *
 917    * @param e
 918    *                DOCUMENT ME!
 919    */
 920   protected void clustalColour_actionPerformed()
 921   {
 922     SequenceGroup sg = getGroup();
 923     sg.cs = new ClustalxColourScheme(sg
 924             .getSequences(ap.av.hiddenRepSequences), ap.av.alignment
 925             .getWidth());
 926     refresh();
 927   }
 928
 929   /**
 930    * DOCUMENT ME!
 931    *
 932    * @param e
 933    *                DOCUMENT ME!
 934    */
 935   protected void zappoColour_actionPerformed()
 936   {
 937     getGroup().cs = new ZappoColourScheme();
 938     refresh();
 939   }
 940
 941   /**
 942    * DOCUMENT ME!
 943    *
 944    * @param e
 945    *                DOCUMENT ME!
 946    */
 947   protected void taylorColour_actionPerformed()
 948   {
 949     getGroup().cs = new TaylorColourScheme();
 950     refresh();
 951   }
 952
 953   /**
 954    * DOCUMENT ME!
 955    *
 956    * @param e
 957    *                DOCUMENT ME!
 958    */
 959   protected void hydrophobicityColour_actionPerformed()
 960   {
 961     getGroup().cs = new HydrophobicColourScheme();
 962     refresh();
 963   }
 964
 965   /**
 966    * DOCUMENT ME!
 967    *
 968    * @param e
 969    *                DOCUMENT ME!
 970    */
 971   protected void helixColour_actionPerformed()
 972   {
 973     getGroup().cs = new HelixColourScheme();
 974     refresh();
 975   }
 976
 977   /**
 978    * DOCUMENT ME!
 979    *
 980    * @param e
 981    *                DOCUMENT ME!
 982    */
 983   protected void strandColour_actionPerformed()
 984   {
 985     getGroup().cs = new StrandColourScheme();
 986     refresh();
 987   }
 988
 989   /**
 990    * DOCUMENT ME!
 991    *
 992    * @param e
 993    *                DOCUMENT ME!
 994    */
 995   protected void turnColour_actionPerformed()
 996   {
 997     getGroup().cs = new TurnColourScheme();
 998     refresh();
 999   }
1000
1001   /**
1002    * DOCUMENT ME!
1003    *
1004    * @param e
1005    *                DOCUMENT ME!
1006    */
1007   protected void buriedColour_actionPerformed()
1008   {
1009     getGroup().cs = new BuriedColourScheme();
1010     refresh();
1011   }
1012
1013   /**
1014    * DOCUMENT ME!
1015    *
1016    * @param e
1017    *                DOCUMENT ME!
1018    */
1019   public void nucleotideMenuItem_actionPerformed()
1020   {
1021     getGroup().cs = new NucleotideColourScheme();
1022     refresh();
1023   }
1024
1025   /**
1026    * DOCUMENT ME!
1027    *
1028    * @param e
1029    *                DOCUMENT ME!
1030    */
1031   protected void abovePIDColour_actionPerformed()
1032   {
1033     SequenceGroup sg = getGroup();
1034     if (sg.cs == null)
1035     {
1036       return;
1037     }
1038
1039     if (abovePIDColour.isSelected())
1040     {
1041       sg.cs.setConsensus(AAFrequency.calculate(sg
1042               .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
1043               .getEndRes() + 1));
1044
1045       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1046               .getName());
1047
1048       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1049
1050       SliderPanel.showPIDSlider();
1051     }
1052     else
1053     // remove PIDColouring
1054     {
1055       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1056     }
1057
1058     refresh();
1059   }
1060
1061   /**
1062    * DOCUMENT ME!
1063    *
1064    * @param e
1065    *                DOCUMENT ME!
1066    */
1067   protected void userDefinedColour_actionPerformed(ActionEvent e)
1068   {
1069     SequenceGroup sg = getGroup();
1070
1071     if (e.getActionCommand().equals("User Defined..."))
1072     {
1073       new UserDefinedColours(ap, sg);
1074     }
1075     else
1076     {
1077       UserColourScheme udc = (UserColourScheme) UserDefinedColours
1078               .getUserColourSchemes().get(e.getActionCommand());
1079
1080       sg.cs = udc;
1081     }
1082     refresh();
1083   }
1084
1085   /**
1086    * DOCUMENT ME!
1087    *
1088    * @param e
1089    *                DOCUMENT ME!
1090    */
1091   protected void PIDColour_actionPerformed()
1092   {
1093     SequenceGroup sg = getGroup();
1094     sg.cs = new PIDColourScheme();
1095     sg.cs.setConsensus(AAFrequency.calculate(sg
1096             .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
1097             .getEndRes() + 1));
1098     refresh();
1099   }
1100
1101   /**
1102    * DOCUMENT ME!
1103    *
1104    * @param e
1105    *                DOCUMENT ME!
1106    */
1107   protected void BLOSUM62Colour_actionPerformed()
1108   {
1109     SequenceGroup sg = getGroup();
1110
1111     sg.cs = new Blosum62ColourScheme();
1112
1113     sg.cs.setConsensus(AAFrequency.calculate(sg
1114             .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
1115             .getEndRes() + 1));
1116
1117     refresh();
1118   }
1119
1120   /**
1121    * DOCUMENT ME!
1122    *
1123    * @param e
1124    *                DOCUMENT ME!
1125    */
1126   protected void noColourmenuItem_actionPerformed()
1127   {
1128     getGroup().cs = null;
1129     refresh();
1130   }
1131
1132   /**
1133    * DOCUMENT ME!
1134    *
1135    * @param e
1136    *                DOCUMENT ME!
1137    */
1138   protected void conservationMenuItem_actionPerformed()
1139   {
1140     SequenceGroup sg = getGroup();
1141     if (sg.cs == null)
1142     {
1143       return;
1144     }
1145
1146     if (conservationMenuItem.isSelected())
1147     {
1148       Conservation c = new Conservation("Group",
1149               ResidueProperties.propHash, 3, sg
1150                       .getSequences(ap.av.hiddenRepSequences), sg
1151                       .getStartRes(), sg.getEndRes() + 1);
1152
1153       c.calculate();
1154       c.verdict(false, ap.av.ConsPercGaps);
1155
1156       sg.cs.setConservation(c);
1157
1158       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1159       SliderPanel.showConservationSlider();
1160     }
1161     else
1162     // remove ConservationColouring
1163     {
1164       sg.cs.setConservation(null);
1165     }
1166
1167     refresh();
1168   }
1169
1170   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1171   {
1172     SequenceGroup sg = getGroup();
1173     if (sg == null)
1174     {
1175       return;
1176     }
1177
1178     AnnotationColourGradient acg = new AnnotationColourGradient(sequence
1179             .getAnnotation()[0], null,
1180             AnnotationColourGradient.NO_THRESHOLD);
1181
1182     acg.predefinedColours = true;
1183     sg.cs = acg;
1184
1185     refresh();
1186   }
1187
1188   /**
1189    * DOCUMENT ME!
1190    *
1191    * @param e
1192    *                DOCUMENT ME!
1193    */
1194   protected void groupName_actionPerformed()
1195   {
1196
1197     SequenceGroup sg = getGroup();
1198     EditNameDialog dialog = new EditNameDialog(sg.getName(), sg
1199             .getDescription(), "       Group Name ", "Group Description ",
1200             "Edit Group Name/Description");
1201
1202     if (!dialog.accept)
1203     {
1204       return;
1205     }
1206
1207     sg.setName(dialog.getName());
1208     sg.setDescription(dialog.getDescription());
1209   }
1210
1211   /**
1212    * DOCUMENT ME!
1213    *
1214    * @return DOCUMENT ME!
1215    */
1216   SequenceGroup getGroup()
1217   {
1218     SequenceGroup sg = ap.av.getSelectionGroup();
1219     // this method won't add a new group if it already exists
1220     if (sg != null)
1221     {
1222       ap.av.alignment.addGroup(sg);
1223     }
1224
1225     return sg;
1226   }
1227
1228   /**
1229    * DOCUMENT ME!
1230    *
1231    * @param e
1232    *                DOCUMENT ME!
1233    */
1234   void sequenceName_actionPerformed()
1235   {
1236     EditNameDialog dialog = new EditNameDialog(sequence.getName(), sequence
1237             .getDescription(), "       Sequence Name ",
1238             "Sequence Description ", "Edit Sequence Name/Description");
1239
1240     if (!dialog.accept)
1241     {
1242       return;
1243     }
1244
1245     if (dialog.getName() != null)
1246     {
1247       if (dialog.getName().indexOf(" ") > -1)
1248       {
1249         JOptionPane.showMessageDialog(ap,
1250                 "Spaces have been converted to \"_\"",
1251                 "No spaces allowed in Sequence Name",
1252                 JOptionPane.WARNING_MESSAGE);
1253       }
1254
1255       sequence.setName(dialog.getName().replace(' ', '_'));
1256       ap.paintAlignment(false);
1257     }
1258
1259     sequence.setDescription(dialog.getDescription());
1260
1261     ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1262             .getSequences());
1263
1264   }
1265
1266   /**
1267    * DOCUMENT ME!
1268    *
1269    * @param e
1270    *                DOCUMENT ME!
1271    */
1272   void unGroupMenuItem_actionPerformed()
1273   {
1274     SequenceGroup sg = ap.av.getSelectionGroup();
1275     ap.av.alignment.deleteGroup(sg);
1276     ap.av.setSelectionGroup(null);
1277     refresh();
1278   }
1279
1280   /**
1281    * DOCUMENT ME!
1282    *
1283    * @param e
1284    *                DOCUMENT ME!
1285    */
1286   protected void outline_actionPerformed()
1287   {
1288     SequenceGroup sg = getGroup();
1289     Color col = JColorChooser.showDialog(this, "Select Outline Colour",
1290             Color.BLUE);
1291
1292     if (col != null)
1293     {
1294       sg.setOutlineColour(col);
1295     }
1296
1297     refresh();
1298   }
1299
1300   /**
1301    * DOCUMENT ME!
1302    *
1303    * @param e
1304    *                DOCUMENT ME!
1305    */
1306   public void showBoxes_actionPerformed()
1307   {
1308     getGroup().setDisplayBoxes(showBoxes.isSelected());
1309     refresh();
1310   }
1311
1312   /**
1313    * DOCUMENT ME!
1314    *
1315    * @param e
1316    *                DOCUMENT ME!
1317    */
1318   public void showText_actionPerformed()
1319   {
1320     getGroup().setDisplayText(showText.isSelected());
1321     refresh();
1322   }
1323
1324   /**
1325    * DOCUMENT ME!
1326    *
1327    * @param e
1328    *                DOCUMENT ME!
1329    */
1330   public void showColourText_actionPerformed()
1331   {
1332     getGroup().setColourText(showColourText.isSelected());
1333     refresh();
1334   }
1335
1336   public void showLink(String url)
1337   {
1338     try
1339     {
1340       jalview.util.BrowserLauncher.openURL(url);
1341     } catch (Exception ex)
1342     {
1343       JOptionPane
1344               .showInternalMessageDialog(
1345                       Desktop.desktop,
1346                       "Unixers: Couldn't find default web browser."
1347                               + "\nAdd the full path to your browser in Preferences.",
1348                       "Web browser not found", JOptionPane.WARNING_MESSAGE);
1349
1350       ex.printStackTrace();
1351     }
1352   }
1353
1354   void hideSequences(boolean representGroup)
1355   {
1356     SequenceGroup sg = ap.av.getSelectionGroup();
1357     if (sg == null || sg.getSize() < 1)
1358     {
1359       ap.av.hideSequence(new SequenceI[]
1360       { sequence });
1361       return;
1362     }
1363
1364     ap.av.setSelectionGroup(null);
1365
1366     if (representGroup)
1367     {
1368       ap.av.hideRepSequences(sequence, sg);
1369
1370       return;
1371     }
1372
1373     int gsize = sg.getSize();
1374     SequenceI[] hseqs;
1375
1376     hseqs = new SequenceI[gsize];
1377
1378     int index = 0;
1379     for (int i = 0; i < gsize; i++)
1380     {
1381       hseqs[index++] = sg.getSequenceAt(i);
1382     }
1383
1384     ap.av.hideSequence(hseqs);
1385   }
1386
1387   public void copy_actionPerformed()
1388   {
1389     ap.alignFrame.copy_actionPerformed(null);
1390   }
1391
1392   public void cut_actionPerformed()
1393   {
1394     ap.alignFrame.cut_actionPerformed(null);
1395   }
1396
1397   void changeCase(ActionEvent e)
1398   {
1399     Object source = e.getSource();
1400     SequenceGroup sg = ap.av.getSelectionGroup();
1401
1402     if (sg != null)
1403     {
1404       int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
1405               sg.getEndRes() + 1);
1406
1407       String description;
1408       int caseChange;
1409
1410       if (source == toggle)
1411       {
1412         description = "Toggle Case";
1413         caseChange = ChangeCaseCommand.TOGGLE_CASE;
1414       }
1415       else if (source == upperCase)
1416       {
1417         description = "To Upper Case";
1418         caseChange = ChangeCaseCommand.TO_UPPER;
1419       }
1420       else
1421       {
1422         description = "To Lower Case";
1423         caseChange = ChangeCaseCommand.TO_LOWER;
1424       }
1425
1426       ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, sg
1427               .getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
1428               caseChange);
1429
1430       ap.alignFrame.addHistoryItem(caseCommand);
1431
1432       ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1433               .getSequences());
1434
1435     }
1436   }
1437
1438   public void outputText_actionPerformed(ActionEvent e)
1439   {
1440     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1441     cap.setForInput(null);
1442     Desktop.addInternalFrame(cap, "Alignment output - "
1443             + e.getActionCommand(), 600, 500);
1444
1445     String[] omitHidden = null;
1446
1447     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1448                                             // or we simply trust the user wants
1449                                             // wysiwig behaviour
1450     SequenceGroup sg = ap.av.getSelectionGroup();
1451     ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1452     omitHidden = ap.av.getViewAsString(true);
1453     Alignment oal = new Alignment(ap.av.getSequenceSelection());
1454     AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
1455     for (int i = 0; i < nala.length; i++)
1456     {
1457       AlignmentAnnotation na = nala[i];
1458       oal.addAnnotation(na);
1459     }
1460     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1461             oal, omitHidden, csel, sg));
1462     oal = null;
1463   }
1464
1465   public void pdbFromFile_actionPerformed()
1466   {
1467     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
1468             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1469     chooser.setFileView(new jalview.io.JalviewFileView());
1470     chooser.setDialogTitle("Select a PDB file");
1471     chooser.setToolTipText("Load a PDB file");
1472
1473     int value = chooser.showOpenDialog(null);
1474
1475     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
1476     {
1477       PDBEntry entry = new PDBEntry();
1478       String choice = chooser.getSelectedFile().getPath();
1479       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1480       try
1481       {
1482         MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
1483                 jalview.io.AppletFormatAdapter.FILE);
1484
1485         if (pdbfile.id == null)
1486         {
1487           String reply = JOptionPane
1488                   .showInternalInputDialog(
1489                           Desktop.desktop,
1490                           "Couldn't find a PDB id in the file supplied."
1491                                   + "Please enter an Id to identify this structure.",
1492                           "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
1493           if (reply == null)
1494           {
1495             return;
1496           }
1497
1498           entry.setId(reply);
1499         }
1500         else
1501         {
1502           entry.setId(pdbfile.id);
1503         }
1504       } catch (java.io.IOException ex)
1505       {
1506         ex.printStackTrace();
1507       }
1508
1509       entry.setFile(choice);
1510       sequence.getDatasetSequence().addPDBId(entry);
1511     }
1512
1513   }
1514
1515   public void enterPDB_actionPerformed()
1516   {
1517     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
1518             "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
1519
1520     if (id != null && id.length() > 0)
1521     {
1522       PDBEntry entry = new PDBEntry();
1523       entry.setId(id.toUpperCase());
1524       sequence.getDatasetSequence().addPDBId(entry);
1525     }
1526   }
1527
1528   public void discoverPDB_actionPerformed()
1529   {
1530
1531     final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new Sequence[]
1532     { sequence }
1533             : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
1534     Thread discpdb = new Thread(new Runnable()
1535     {
1536       public void run()
1537       {
1538
1539         new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
1540                 .fetchDBRefs(false);
1541       }
1542
1543     });
1544     discpdb.start();
1545   }
1546
1547   public void sequenceFeature_actionPerformed()
1548   {
1549     SequenceGroup sg = ap.av.getSelectionGroup();
1550     if (sg == null)
1551     {
1552       return;
1553     }
1554
1555     int gSize = sg.getSize();
1556     SequenceI[] seqs = new SequenceI[gSize];
1557     SequenceFeature[] features = new SequenceFeature[gSize];
1558
1559     for (int i = 0; i < gSize; i++)
1560     {
1561       seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
1562       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
1563       int end = sg.findEndRes(sg.getSequenceAt(i));
1564       features[i] = new SequenceFeature(null, null, null, start, end,
1565               "Jalview");
1566     }
1567
1568     if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
1569             features, true, ap))
1570     {
1571       ap.alignFrame.showSeqFeatures.setSelected(true);
1572       ap.av.setShowSequenceFeatures(true);
1573       ap.highlightSearchResults(null);
1574     }
1575   }
1576
1577   public void textColour_actionPerformed()
1578   {
1579     SequenceGroup sg = getGroup();
1580     if (sg != null)
1581     {
1582       new TextColourChooser().chooseColour(ap, sg);
1583     }
1584   }
1585
1586   public void colourByStructure(String pdbid)
1587   {
1588     Annotation[] anots = jalview.structure.StructureSelectionManager
1589             .getStructureSelectionManager().colourSequenceFromStructure(
1590                     sequence, pdbid);
1591
1592     AlignmentAnnotation an = new AlignmentAnnotation("Structure",
1593             "Coloured by " + pdbid, anots);
1594
1595     ap.av.alignment.addAnnotation(an);
1596     an.createSequenceMapping(sequence, 0, true);
1597     // an.adjustForAlignment();
1598     ap.av.alignment.setAnnotationIndex(an, 0);
1599
1600     ap.adjustAnnotationHeight();
1601
1602     sequence.addAlignmentAnnotation(an);
1603
1604   }
1605
1606   public void editSequence_actionPerformed(ActionEvent actionEvent)
1607   {
1608     SequenceGroup sg = ap.av.getSelectionGroup();
1609
1610     if (sg != null)
1611     {
1612       if (sequence == null)
1613         sequence = (Sequence) sg.getSequenceAt(0);
1614
1615       EditNameDialog dialog = new EditNameDialog(sequence
1616               .getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1),
1617               null, "Edit Sequence ", null, "Edit Sequence");
1618
1619       if (dialog.accept)
1620       {
1621         EditCommand editCommand = new EditCommand("Edit Sequences",
1622                 EditCommand.REPLACE, dialog.getName().replace(' ',
1623                         ap.av.getGapCharacter()), sg
1624                         .getSequencesAsArray(ap.av.hiddenRepSequences), sg
1625                         .getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
1626
1627         ap.alignFrame.addHistoryItem(editCommand);
1628
1629         ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1630                 .getSequences());
1631       }
1632     }
1633   }
1634
1635 }