src/jalview/gui/PopupMenu.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
   3  * Copyright (C) 2009 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.GroupUrlLink;
  34 import jalview.util.UrlLink;
  35
  36 /**
  37  * DOCUMENT ME!
  38  *
  39  * @author $author$
  40  * @version $Revision$
  41  */
  42 public class PopupMenu extends JPopupMenu
  43 {
  44   JMenu groupMenu = new JMenu();
  45
  46   JMenuItem groupName = new JMenuItem();
  47
  48   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  49
  50   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  51
  52   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  53
  54   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
  55
  56   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
  57
  58   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
  59
  60   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
  61
  62   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
  63
  64   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
  65
  66   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
  67
  68   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
  69
  70   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
  71
  72   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
  73
  74   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
  75
  76   AlignmentPanel ap;
  77
  78   JMenu sequenceMenu = new JMenu();
  79
  80   JMenuItem sequenceName = new JMenuItem();
  81
  82   Sequence sequence;
  83
  84   JMenuItem unGroupMenuItem = new JMenuItem();
  85
  86   JMenuItem outline = new JMenuItem();
  87
  88   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
  89
  90   JMenu colourMenu = new JMenu();
  91
  92   JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
  93
  94   JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
  95
  96   JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
  97
  98   JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
  99
 100   JMenu editMenu = new JMenu();
 101
 102   JMenuItem cut = new JMenuItem();
 103
 104   JMenuItem copy = new JMenuItem();
 105
 106   JMenuItem upperCase = new JMenuItem();
 107
 108   JMenuItem lowerCase = new JMenuItem();
 109
 110   JMenuItem toggle = new JMenuItem();
 111
 112   JMenu pdbMenu = new JMenu();
 113
 114   JMenuItem pdbFromFile = new JMenuItem();
 115
 116   JMenuItem enterPDB = new JMenuItem();
 117
 118   JMenuItem discoverPDB = new JMenuItem();
 119
 120   JMenu outputMenu = new JMenu();
 121
 122   JMenuItem sequenceFeature = new JMenuItem();
 123
 124   JMenuItem textColour = new JMenuItem();
 125
 126   JMenu jMenu1 = new JMenu();
 127
 128   JMenu structureMenu = new JMenu();
 129
 130   JMenu viewStructureMenu = new JMenu();
 131
 132   // JMenu colStructureMenu = new JMenu();
 133   JMenuItem editSequence = new JMenuItem();
 134
 135   // JMenuItem annotationMenuItem = new JMenuItem();
 136
 137   JMenu groupLinksMenu;
 138
 139   /**
 140    * Creates a new PopupMenu object.
 141    *
 142    * @param ap
 143    *                DOCUMENT ME!
 144    * @param seq
 145    *                DOCUMENT ME!
 146    */
 147   public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
 148   {
 149     this(ap, seq, links, null);
 150   }
 151   /**
 152    *
 153    * @param ap
 154    * @param seq
 155    * @param links
 156    * @param groupLinks
 157    */
 158   public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links, Vector groupLinks)
 159   {
 160     // /////////////////////////////////////////////////////////
 161     // If this is activated from the sequence panel, the user may want to
 162     // edit or annotate a particular residue. Therefore display the residue menu
 163     //
 164     // If from the IDPanel, we must display the sequence menu
 165     // ////////////////////////////////////////////////////////
 166     this.ap = ap;
 167     sequence = seq;
 168
 169     ButtonGroup colours = new ButtonGroup();
 170     colours.add(noColourmenuItem);
 171     colours.add(clustalColour);
 172     colours.add(zappoColour);
 173     colours.add(taylorColour);
 174     colours.add(hydrophobicityColour);
 175     colours.add(helixColour);
 176     colours.add(strandColour);
 177     colours.add(turnColour);
 178     colours.add(buriedColour);
 179     colours.add(abovePIDColour);
 180     colours.add(userDefinedColour);
 181     colours.add(PIDColour);
 182     colours.add(BLOSUM62Colour);
 183
 184     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 185     {
 186       JMenuItem item = new JMenuItem(
 187               jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 188
 189       item.addActionListener(new java.awt.event.ActionListener()
 190       {
 191         public void actionPerformed(ActionEvent e)
 192         {
 193           outputText_actionPerformed(e);
 194         }
 195       });
 196
 197       outputMenu.add(item);
 198     }
 199
 200     try
 201     {
 202       jbInit();
 203     } catch (Exception e)
 204     {
 205       e.printStackTrace();
 206     }
 207
 208     if (seq != null)
 209     {
 210       sequenceMenu.setText(sequence.getName());
 211
 212       JMenuItem menuItem;
 213       if (seq.getDatasetSequence().getPDBId() != null
 214               && seq.getDatasetSequence().getPDBId().size() > 0)
 215       {
 216         java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
 217                 .elements();
 218
 219         while (e.hasMoreElements())
 220         {
 221           final PDBEntry pdb = (PDBEntry) e.nextElement();
 222
 223           menuItem = new JMenuItem();
 224           menuItem.setText(pdb.getId());
 225           menuItem.addActionListener(new java.awt.event.ActionListener()
 226           {
 227             public void actionPerformed(ActionEvent e)
 228             {
 229               Vector seqs = new Vector();
 230               for (int i = 0; i < ap.av.alignment.getHeight(); i++)
 231               {
 232                 Vector pdbs = ap.av.alignment.getSequenceAt(i)
 233                         .getDatasetSequence().getPDBId();
 234                 if (pdbs == null)
 235                   continue;
 236
 237                 for (int p = 0; p < pdbs.size(); p++)
 238                 {
 239                   PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
 240                   if (p1.getId().equals(pdb.getId()))
 241                   {
 242                     if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))
 243                       seqs.addElement(ap.av.alignment.getSequenceAt(i));
 244
 245                     continue;
 246                   }
 247                 }
 248               }
 249
 250               SequenceI[] seqs2 = new SequenceI[seqs.size()];
 251               seqs.toArray(seqs2);
 252
 253               new AppJmol(pdb, seqs2, null, ap);
 254               // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
 255             }
 256           });
 257           viewStructureMenu.add(menuItem);
 258
 259           /*
 260            * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
 261            * menuItem.addActionListener(new java.awt.event.ActionListener() {
 262            * public void actionPerformed(ActionEvent e) {
 263            * colourByStructure(pdb.getId()); } });
 264            * colStructureMenu.add(menuItem);
 265            */
 266         }
 267       }
 268       else
 269       {
 270         structureMenu.remove(viewStructureMenu);
 271         // structureMenu.remove(colStructureMenu);
 272       }
 273
 274       menuItem = new JMenuItem("Hide Sequences");
 275       menuItem.addActionListener(new java.awt.event.ActionListener()
 276       {
 277         public void actionPerformed(ActionEvent e)
 278         {
 279           hideSequences(false);
 280         }
 281       });
 282       add(menuItem);
 283
 284       if (ap.av.getSelectionGroup() != null
 285               && ap.av.getSelectionGroup().getSize() > 1)
 286       {
 287         menuItem = new JMenuItem("Represent Group with " + seq.getName());
 288         menuItem.addActionListener(new java.awt.event.ActionListener()
 289         {
 290           public void actionPerformed(ActionEvent e)
 291           {
 292             hideSequences(true);
 293           }
 294         });
 295         sequenceMenu.add(menuItem);
 296       }
 297
 298       if (ap.av.hasHiddenRows)
 299       {
 300         final int index = ap.av.alignment.findIndex(seq);
 301
 302         if (ap.av.adjustForHiddenSeqs(index)
 303                 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
 304         {
 305           menuItem = new JMenuItem("Reveal Sequences");
 306           menuItem.addActionListener(new ActionListener()
 307           {
 308             public void actionPerformed(ActionEvent e)
 309             {
 310               ap.av.showSequence(index);
 311               if (ap.overviewPanel != null)
 312               {
 313                 ap.overviewPanel.updateOverviewImage();
 314               }
 315             }
 316           });
 317           add(menuItem);
 318         }
 319
 320         menuItem = new JMenuItem("Reveal All");
 321         menuItem.addActionListener(new ActionListener()
 322         {
 323           public void actionPerformed(ActionEvent e)
 324           {
 325             ap.av.showAllHiddenSeqs();
 326             if (ap.overviewPanel != null)
 327             {
 328               ap.overviewPanel.updateOverviewImage();
 329             }
 330           }
 331         });
 332
 333         add(menuItem);
 334       }
 335
 336     }
 337
 338     SequenceGroup sg = ap.av.getSelectionGroup();
 339
 340     if (sg != null)
 341     {
 342       groupName.setText(sg.getName());
 343
 344       if (sg.cs instanceof ZappoColourScheme)
 345       {
 346         zappoColour.setSelected(true);
 347       }
 348       else if (sg.cs instanceof TaylorColourScheme)
 349       {
 350         taylorColour.setSelected(true);
 351       }
 352       else if (sg.cs instanceof PIDColourScheme)
 353       {
 354         PIDColour.setSelected(true);
 355       }
 356       else if (sg.cs instanceof Blosum62ColourScheme)
 357       {
 358         BLOSUM62Colour.setSelected(true);
 359       }
 360       else if (sg.cs instanceof UserColourScheme)
 361       {
 362         userDefinedColour.setSelected(true);
 363       }
 364       else if (sg.cs instanceof HydrophobicColourScheme)
 365       {
 366         hydrophobicityColour.setSelected(true);
 367       }
 368       else if (sg.cs instanceof HelixColourScheme)
 369       {
 370         helixColour.setSelected(true);
 371       }
 372       else if (sg.cs instanceof StrandColourScheme)
 373       {
 374         strandColour.setSelected(true);
 375       }
 376       else if (sg.cs instanceof TurnColourScheme)
 377       {
 378         turnColour.setSelected(true);
 379       }
 380       else if (sg.cs instanceof BuriedColourScheme)
 381       {
 382         buriedColour.setSelected(true);
 383       }
 384       else if (sg.cs instanceof ClustalxColourScheme)
 385       {
 386         clustalColour.setSelected(true);
 387       }
 388       else
 389       {
 390         noColourmenuItem.setSelected(true);
 391       }
 392
 393       if (sg.cs != null && sg.cs.conservationApplied())
 394       {
 395         conservationMenuItem.setSelected(true);
 396       }
 397       displayNonconserved.setSelected(sg.getShowunconserved());
 398       showText.setSelected(sg.getDisplayText());
 399       showColourText.setSelected(sg.getColourText());
 400       showBoxes.setSelected(sg.getDisplayBoxes());
 401       // add any groupURLs to the groupURL submenu and make it visible
 402       if (groupLinks!=null && groupLinks.size()>0) {
 403         buildGroupURLMenu(sg, groupLinks);
 404       }
 405     }
 406     else
 407     {
 408       groupMenu.setVisible(false);
 409       editMenu.setVisible(false);
 410     }
 411
 412     if (!ap.av.alignment.getGroups().contains(sg))
 413     {
 414       unGroupMenuItem.setVisible(false);
 415     }
 416
 417     if (seq == null)
 418     {
 419       sequenceMenu.setVisible(false);
 420       structureMenu.setVisible(false);
 421     }
 422
 423     if (links != null && links.size() > 0)
 424     {
 425
 426       JMenu linkMenu = new JMenu("Link");
 427       Vector linkset = new Vector();
 428       for (int i = 0; i < links.size(); i++)
 429       {
 430         String link = links.elementAt(i).toString();
 431         UrlLink urlLink = null;
 432         try
 433         {
 434           urlLink = new UrlLink(link);
 435         } catch (Exception foo)
 436         {
 437           jalview.bin.Cache.log.error("Exception for URLLink '" + link
 438                   + "'", foo);
 439           continue;
 440         }
 441         ;
 442         if (!urlLink.isValid())
 443         {
 444           jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 445           continue;
 446         }
 447         final String label = urlLink.getLabel();
 448         if (urlLink.isDynamic())
 449         {
 450
 451           // collect matching db-refs
 452           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq
 453                   .getDBRef(), new String[]
 454           { urlLink.getTarget() });
 455           // collect id string too
 456           String id = seq.getName();
 457           String descr = seq.getDescription();
 458           if (descr!=null && descr.length()<1)
 459           {
 460             descr = null;
 461           }
 462
 463           if (dbr != null)
 464           {
 465             for (int r = 0; r < dbr.length; r++)
 466             {
 467               if (id != null && dbr[r].getAccessionId().equals(id))
 468               {
 469                 // suppress duplicate link creation for the bare sequence ID
 470                 // string with this link
 471                 id = null;
 472               }
 473               // create Bare ID link for this RUL
 474               String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
 475                       true);
 476               if (urls != null)
 477               {
 478                 for (int u = 0; u < urls.length; u += 2)
 479                 {
 480                   if (!linkset.contains(urls[u]+"|"+urls[u+1]))
 481                   {
 482                     linkset.addElement(urls[u]+"|"+urls[u+1]);
 483                     addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
 484                   }
 485                 }
 486               }
 487             }
 488           }
 489           if (id != null)
 490           {
 491             // create Bare ID link for this RUL
 492             String[] urls = urlLink.makeUrls(id, true);
 493             if (urls != null)
 494             {
 495               for (int u = 0; u < urls.length; u += 2)
 496               {
 497                 if (!linkset.contains(urls[u]+"|"+urls[u+1]))
 498                 {
 499                   linkset.addElement(urls[u]+"|"+urls[u+1]);
 500                   addshowLink(linkMenu, label, urls[u + 1]);
 501                 }
 502               }
 503             }
 504           }
 505           // Create urls from description but only for URL links which are regex links
 506           if (descr != null && urlLink.getRegexReplace()!=null)
 507           {
 508             // create link for this URL from description where regex matches
 509             String[] urls = urlLink.makeUrls(descr, true);
 510             if (urls != null)
 511             {
 512               for (int u = 0; u < urls.length; u += 2)
 513               {
 514                 if (!linkset.contains(urls[u]+"|"+urls[u+1]))
 515                 {
 516                   linkset.addElement(urls[u]+"|"+urls[u+1]);
 517                   addshowLink(linkMenu, label, urls[u + 1]);
 518                 }
 519               }
 520             }
 521           }
 522         }
 523         else
 524         {
 525           if (!linkset.contains(label+"|"+urlLink.getUrl_prefix()))
 526           {
 527             linkset.addElement(label+"|"+urlLink.getUrl_prefix());
 528             // Add a non-dynamic link
 529             addshowLink(linkMenu, label, urlLink.getUrl_prefix());
 530           }
 531         }
 532       }
 533       if (sequence != null)
 534       {
 535         sequenceMenu.add(linkMenu);
 536       }
 537       else
 538       {
 539         add(linkMenu);
 540       }
 541     }
 542   }
 543
 544   private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
 545   {
 546
 547     // TODO: usability: thread off the generation of group url content so root menu appears asap
 548     // sequence only URLs
 549     // ID/regex match URLs
 550     groupLinksMenu = new JMenu("Group Link");
 551     JMenu[] linkMenus = new JMenu[] { null, new JMenu("IDS"), new JMenu("Sequences"), new JMenu("IDS and Sequences")}; // three types of url that might be created.
 552     SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
 553     String[][] idandseqs = GroupUrlLink.formStrings(seqs);
 554     Hashtable commonDbrefs = new Hashtable();
 555     for (int sq = 0; sq<seqs.length;sq++) {
 556
 557       int start = seqs[sq].findPosition(sg.getStartRes()),end=seqs[sq].findPosition(sg.getEndRes());
 558       // just collect ids from dataset sequence
 559       // TODO: check if IDs collected from selecton group intersects with the current selection, too
 560       SequenceI sqi = seqs[sq];
 561       while (sqi.getDatasetSequence()!=null) {
 562         sqi = sqi.getDatasetSequence(); }
 563       DBRefEntry[] dbr = sqi.getDBRef();
 564       if (dbr!=null && dbr.length>0)
 565       {
 566         for (int d=0;d<dbr.length;d++)
 567         {
 568           String src =dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
 569           Object[] sarray = (Object[]) commonDbrefs.get(src);
 570           if (sarray==null)
 571           {
 572             sarray = new Object[2];
 573             sarray[0] = new int[] { 0 };
 574             sarray[1] = new String[seqs.length];
 575
 576             commonDbrefs.put(src,sarray);
 577           }
 578
 579           if (((String[])sarray[1])[sq]==null) {
 580             if (!dbr[d].hasMap() || (dbr[d].getMap().locateMappedRange(start, end)!=null)) {
 581               ((String[])sarray[1])[sq] = dbr[d].getAccessionId();
 582               ((int[])sarray[0])[0]++;
 583             }
 584           }
 585         }
 586       }
 587     }
 588     // now create group links for all distinct ID/sequence sets.
 589     boolean addMenu = false; // indicates if there are any group links to give to user
 590     for (int i = 0; i < groupLinks.size(); i++) {
 591         String link = groupLinks.elementAt(i).toString();
 592         GroupUrlLink urlLink = null;
 593         try
 594         {
 595           urlLink = new GroupUrlLink(link);
 596         } catch (Exception foo)
 597         {
 598           jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
 599                   + "'", foo);
 600           continue;
 601         }
 602         ;
 603         if (!urlLink.isValid())
 604         {
 605           jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 606           continue;
 607         }
 608         final String label = urlLink.getLabel();
 609         boolean usingNames = false;
 610         // Now see which parts of the group apply for this URL
 611         String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
 612         Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
 613         String[] seqstr,ids; // input to makeUrl
 614         if (idset!=null)
 615         {
 616           int numinput = ((int[])idset[0])[0];
 617           String[] allids = ((String[])idset[1]);
 618           seqstr = new String[numinput];
 619           ids = new String[numinput];
 620           for (int sq=0,idcount=0;sq<seqs.length;sq++)
 621           {
 622             if (allids[sq]!=null) {
 623               ids[idcount] = allids[sq];
 624               seqstr[idcount++] = idandseqs[1][sq];
 625             }
 626           }
 627         } else {
 628           // just use the id/seq set
 629           seqstr = idandseqs[1];
 630           ids = idandseqs[0];
 631           usingNames=true;
 632         }
 633         // and try and make the groupURL!
 634
 635         Object[] urlset = urlLink.makeUrlStubs(ids,seqstr, "FromJalview"+System.currentTimeMillis(),false);
 636         if (urlset!=null)
 637         {
 638           int type = urlLink.getGroupURLType() & 3;
 639           //System.out.println(urlLink.getGroupURLType() +" "+((String[])urlset[3])[0]);
 640           // first two bits ofurlLink type bitfield are sequenceids and sequences
 641           // TODO: FUTURE: ensure the groupURL menu structure can be generalised
 642           addshowLink(linkMenus[type], label + (((type & 1)==1) ? ("("+(usingNames ? "Names" : ltarget)+")") : ""), urlLink, urlset);
 643           addMenu = true;
 644         }
 645       }
 646     if (addMenu)
 647     {
 648       groupLinksMenu = new JMenu("Group Links");
 649       for (int m=0;m<linkMenus.length; m++)
 650       {
 651         if (linkMenus[m]!=null && linkMenus[m].getMenuComponentCount()>0)
 652         {
 653           groupLinksMenu.add(linkMenus[m]);
 654         }
 655       }
 656
 657       groupMenu.add(groupLinksMenu);
 658     }
 659   }
 660
 661   /**
 662    * add a show URL menu item to the given linkMenu
 663    *
 664    * @param linkMenu
 665    * @param label -
 666    *                menu label string
 667    * @param url -
 668    *                url to open
 669    */
 670   private void addshowLink(JMenu linkMenu, String label, final String url)
 671   {
 672     JMenuItem item = new JMenuItem(label);
 673     item.setToolTipText("open URL: " + url);
 674     item.addActionListener(new java.awt.event.ActionListener()
 675     {
 676       public void actionPerformed(ActionEvent e)
 677       {
 678         new Thread(new Runnable()
 679         {
 680
 681           public void run()
 682           {
 683             showLink(url);
 684           }
 685
 686         }).start();
 687       }
 688     });
 689
 690     linkMenu.add(item);
 691   }
 692   /**
 693    * add a late bound groupURL item to the given linkMenu
 694    *
 695    * @param linkMenu
 696    * @param label -
 697    *                menu label string
 698    * @param urlgenerator GroupURLLink used to generate URL
 699    * @param urlstub Object array returned from the makeUrlStubs function.
 700    */
 701   private void addshowLink(JMenu linkMenu, String label, final GroupUrlLink urlgenerator, final Object[] urlstub)
 702   {
 703     JMenuItem item = new JMenuItem(label);
 704     item.setToolTipText("open URL ("+urlgenerator.getUrl_prefix()+"..) ("+urlgenerator.getNumberInvolved(urlstub)+" seqs)"); // TODO: put in info about what is being sent.
 705     item.addActionListener(new java.awt.event.ActionListener()
 706     {
 707       public void actionPerformed(ActionEvent e)
 708       {
 709         new Thread(new Runnable()
 710         {
 711
 712           public void run()
 713           {
 714             showLink(urlgenerator.constructFrom(urlstub));
 715           }
 716
 717         }).start();
 718       }
 719     });
 720
 721     linkMenu.add(item);
 722   }
 723   /**
 724    * DOCUMENT ME!
 725    *
 726    * @throws Exception
 727    *                 DOCUMENT ME!
 728    */
 729   private void jbInit() throws Exception
 730   {
 731     groupMenu.setText("Group");
 732     groupMenu.setText("Selection");
 733     groupName.setText("Name");
 734     groupName.addActionListener(new java.awt.event.ActionListener()
 735     {
 736       public void actionPerformed(ActionEvent e)
 737       {
 738         groupName_actionPerformed();
 739       }
 740     });
 741     sequenceMenu.setText("Sequence");
 742     sequenceName.setText("Edit Name/Description");
 743     sequenceName.addActionListener(new java.awt.event.ActionListener()
 744     {
 745       public void actionPerformed(ActionEvent e)
 746       {
 747         sequenceName_actionPerformed();
 748       }
 749     });
 750     PIDColour.setFocusPainted(false);
 751     unGroupMenuItem.setText("Remove Group");
 752     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 753     {
 754       public void actionPerformed(ActionEvent e)
 755       {
 756         unGroupMenuItem_actionPerformed();
 757       }
 758     });
 759
 760     outline.setText("Border colour");
 761     outline.addActionListener(new java.awt.event.ActionListener()
 762     {
 763       public void actionPerformed(ActionEvent e)
 764       {
 765         outline_actionPerformed();
 766       }
 767     });
 768     nucleotideMenuItem.setText("Nucleotide");
 769     nucleotideMenuItem.addActionListener(new ActionListener()
 770     {
 771       public void actionPerformed(ActionEvent e)
 772       {
 773         nucleotideMenuItem_actionPerformed();
 774       }
 775     });
 776     colourMenu.setText("Group Colour");
 777     showBoxes.setText("Boxes");
 778     showBoxes.setState(true);
 779     showBoxes.addActionListener(new ActionListener()
 780     {
 781       public void actionPerformed(ActionEvent e)
 782       {
 783         showBoxes_actionPerformed();
 784       }
 785     });
 786     showText.setText("Text");
 787     showText.setState(true);
 788     showText.addActionListener(new ActionListener()
 789     {
 790       public void actionPerformed(ActionEvent e)
 791       {
 792         showText_actionPerformed();
 793       }
 794     });
 795     showColourText.setText("Colour Text");
 796     showColourText.addActionListener(new ActionListener()
 797     {
 798       public void actionPerformed(ActionEvent e)
 799       {
 800         showColourText_actionPerformed();
 801       }
 802     });
 803     displayNonconserved.setText("Show Nonconserved");
 804     displayNonconserved.setState(true);
 805     displayNonconserved.addActionListener(new ActionListener()
 806     {
 807       public void actionPerformed(ActionEvent e)
 808       {
 809         showNonconserved_actionPerformed();
 810       }
 811     });
 812     editMenu.setText("Edit");
 813     cut.setText("Cut");
 814     cut.addActionListener(new ActionListener()
 815     {
 816       public void actionPerformed(ActionEvent e)
 817       {
 818         cut_actionPerformed();
 819       }
 820     });
 821     upperCase.setText("To Upper Case");
 822     upperCase.addActionListener(new ActionListener()
 823     {
 824       public void actionPerformed(ActionEvent e)
 825       {
 826         changeCase(e);
 827       }
 828     });
 829     copy.setText("Copy");
 830     copy.addActionListener(new ActionListener()
 831     {
 832       public void actionPerformed(ActionEvent e)
 833       {
 834         copy_actionPerformed();
 835       }
 836     });
 837     lowerCase.setText("To Lower Case");
 838     lowerCase.addActionListener(new ActionListener()
 839     {
 840       public void actionPerformed(ActionEvent e)
 841       {
 842         changeCase(e);
 843       }
 844     });
 845     toggle.setText("Toggle Case");
 846     toggle.addActionListener(new ActionListener()
 847     {
 848       public void actionPerformed(ActionEvent e)
 849       {
 850         changeCase(e);
 851       }
 852     });
 853     pdbMenu.setText("Associate Structure with Sequence");
 854     pdbFromFile.setText("From File");
 855     pdbFromFile.addActionListener(new ActionListener()
 856     {
 857       public void actionPerformed(ActionEvent e)
 858       {
 859         pdbFromFile_actionPerformed();
 860       }
 861     });
 862     enterPDB.setText("Enter PDB Id");
 863     enterPDB.addActionListener(new ActionListener()
 864     {
 865       public void actionPerformed(ActionEvent e)
 866       {
 867         enterPDB_actionPerformed();
 868       }
 869     });
 870     discoverPDB.setText("Discover PDB ids");
 871     discoverPDB.addActionListener(new ActionListener()
 872     {
 873       public void actionPerformed(ActionEvent e)
 874       {
 875         discoverPDB_actionPerformed();
 876       }
 877     });
 878     outputMenu.setText("Output to Textbox...");
 879     sequenceFeature.setText("Create Sequence Feature");
 880     sequenceFeature.addActionListener(new ActionListener()
 881     {
 882       public void actionPerformed(ActionEvent e)
 883       {
 884         sequenceFeature_actionPerformed();
 885       }
 886     });
 887     textColour.setText("Text Colour");
 888     textColour.addActionListener(new ActionListener()
 889     {
 890       public void actionPerformed(ActionEvent e)
 891       {
 892         textColour_actionPerformed();
 893       }
 894     });
 895     jMenu1.setText("Group");
 896     structureMenu.setText("Structure");
 897     viewStructureMenu.setText("View Structure");
 898     // colStructureMenu.setText("Colour By Structure");
 899     editSequence.setText("Edit Sequence...");
 900     editSequence.addActionListener(new ActionListener()
 901     {
 902       public void actionPerformed(ActionEvent actionEvent)
 903       {
 904         editSequence_actionPerformed(actionEvent);
 905       }
 906     });
 907     /*
 908      * annotationMenuItem.setText("By Annotation");
 909      * annotationMenuItem.addActionListener(new ActionListener() { public void
 910      * actionPerformed(ActionEvent actionEvent) {
 911      * annotationMenuItem_actionPerformed(actionEvent); } });
 912      */
 913
 914     add(groupMenu);
 915
 916     add(sequenceMenu);
 917     this.add(structureMenu);
 918     groupMenu.add(editMenu);
 919     groupMenu.add(outputMenu);
 920     groupMenu.add(sequenceFeature);
 921     groupMenu.add(jMenu1);
 922     sequenceMenu.add(sequenceName);
 923     colourMenu.add(textColour);
 924     colourMenu.add(noColourmenuItem);
 925     colourMenu.add(clustalColour);
 926     colourMenu.add(BLOSUM62Colour);
 927     colourMenu.add(PIDColour);
 928     colourMenu.add(zappoColour);
 929     colourMenu.add(taylorColour);
 930     colourMenu.add(hydrophobicityColour);
 931     colourMenu.add(helixColour);
 932     colourMenu.add(strandColour);
 933     colourMenu.add(turnColour);
 934     colourMenu.add(buriedColour);
 935     colourMenu.add(nucleotideMenuItem);
 936     colourMenu.add(userDefinedColour);
 937
 938     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 939     {
 940       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 941               .getUserColourSchemes().keys();
 942
 943       while (userColours.hasMoreElements())
 944       {
 945         JMenuItem item = new JMenuItem(userColours.nextElement().toString());
 946         item.addActionListener(new ActionListener()
 947         {
 948           public void actionPerformed(ActionEvent evt)
 949           {
 950             userDefinedColour_actionPerformed(evt);
 951           }
 952         });
 953         colourMenu.add(item);
 954       }
 955     }
 956
 957     colourMenu.addSeparator();
 958     colourMenu.add(abovePIDColour);
 959     colourMenu.add(conservationMenuItem);
 960     // colourMenu.add(annotationMenuItem);
 961     editMenu.add(copy);
 962     editMenu.add(cut);
 963     editMenu.add(editSequence);
 964     editMenu.add(upperCase);
 965     editMenu.add(lowerCase);
 966     editMenu.add(toggle);
 967     pdbMenu.add(pdbFromFile);
 968     pdbMenu.add(enterPDB);
 969     pdbMenu.add(discoverPDB);
 970     jMenu1.add(groupName);
 971     jMenu1.add(unGroupMenuItem);
 972     jMenu1.add(colourMenu);
 973     jMenu1.add(showBoxes);
 974     jMenu1.add(showText);
 975     jMenu1.add(showColourText);
 976     jMenu1.add(outline);
 977     jMenu1.add(displayNonconserved);
 978     structureMenu.add(pdbMenu);
 979     structureMenu.add(viewStructureMenu);
 980     // structureMenu.add(colStructureMenu);
 981     noColourmenuItem.setText("None");
 982     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
 983     {
 984       public void actionPerformed(ActionEvent e)
 985       {
 986         noColourmenuItem_actionPerformed();
 987       }
 988     });
 989
 990     clustalColour.setText("Clustalx colours");
 991     clustalColour.addActionListener(new java.awt.event.ActionListener()
 992     {
 993       public void actionPerformed(ActionEvent e)
 994       {
 995         clustalColour_actionPerformed();
 996       }
 997     });
 998     zappoColour.setText("Zappo");
 999     zappoColour.addActionListener(new java.awt.event.ActionListener()
1000     {
1001       public void actionPerformed(ActionEvent e)
1002       {
1003         zappoColour_actionPerformed();
1004       }
1005     });
1006     taylorColour.setText("Taylor");
1007     taylorColour.addActionListener(new java.awt.event.ActionListener()
1008     {
1009       public void actionPerformed(ActionEvent e)
1010       {
1011         taylorColour_actionPerformed();
1012       }
1013     });
1014     hydrophobicityColour.setText("Hydrophobicity");
1015     hydrophobicityColour
1016             .addActionListener(new java.awt.event.ActionListener()
1017             {
1018               public void actionPerformed(ActionEvent e)
1019               {
1020                 hydrophobicityColour_actionPerformed();
1021               }
1022             });
1023     helixColour.setText("Helix propensity");
1024     helixColour.addActionListener(new java.awt.event.ActionListener()
1025     {
1026       public void actionPerformed(ActionEvent e)
1027       {
1028         helixColour_actionPerformed();
1029       }
1030     });
1031     strandColour.setText("Strand propensity");
1032     strandColour.addActionListener(new java.awt.event.ActionListener()
1033     {
1034       public void actionPerformed(ActionEvent e)
1035       {
1036         strandColour_actionPerformed();
1037       }
1038     });
1039     turnColour.setText("Turn propensity");
1040     turnColour.addActionListener(new java.awt.event.ActionListener()
1041     {
1042       public void actionPerformed(ActionEvent e)
1043       {
1044         turnColour_actionPerformed();
1045       }
1046     });
1047     buriedColour.setText("Buried Index");
1048     buriedColour.addActionListener(new java.awt.event.ActionListener()
1049     {
1050       public void actionPerformed(ActionEvent e)
1051       {
1052         buriedColour_actionPerformed();
1053       }
1054     });
1055     abovePIDColour.setText("Above % Identity");
1056     abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1057     {
1058       public void actionPerformed(ActionEvent e)
1059       {
1060         abovePIDColour_actionPerformed();
1061       }
1062     });
1063     userDefinedColour.setText("User Defined...");
1064     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1065     {
1066       public void actionPerformed(ActionEvent e)
1067       {
1068         userDefinedColour_actionPerformed(e);
1069       }
1070     });
1071     PIDColour.setText("Percentage Identity");
1072     PIDColour.addActionListener(new java.awt.event.ActionListener()
1073     {
1074       public void actionPerformed(ActionEvent e)
1075       {
1076         PIDColour_actionPerformed();
1077       }
1078     });
1079     BLOSUM62Colour.setText("BLOSUM62");
1080     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1081     {
1082       public void actionPerformed(ActionEvent e)
1083       {
1084         BLOSUM62Colour_actionPerformed();
1085       }
1086     });
1087     conservationMenuItem.setText("Conservation");
1088     conservationMenuItem
1089             .addActionListener(new java.awt.event.ActionListener()
1090             {
1091               public void actionPerformed(ActionEvent e)
1092               {
1093                 conservationMenuItem_actionPerformed();
1094               }
1095             });
1096   }
1097
1098   protected void showNonconserved_actionPerformed()
1099   {
1100     getGroup().setShowunconserved(displayNonconserved.isSelected());
1101     refresh();
1102   }
1103
1104   /**
1105    * call to refresh view after settings change
1106    */
1107   void refresh()
1108   {
1109     ap.updateAnnotation();
1110     ap.paintAlignment(true);
1111
1112     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1113   }
1114
1115   /**
1116    * DOCUMENT ME!
1117    *
1118    * @param e
1119    *                DOCUMENT ME!
1120    */
1121   protected void clustalColour_actionPerformed()
1122   {
1123     SequenceGroup sg = getGroup();
1124     sg.cs = new ClustalxColourScheme(sg
1125             .getSequences(ap.av.hiddenRepSequences), ap.av.alignment
1126             .getWidth());
1127     refresh();
1128   }
1129
1130   /**
1131    * DOCUMENT ME!
1132    *
1133    * @param e
1134    *                DOCUMENT ME!
1135    */
1136   protected void zappoColour_actionPerformed()
1137   {
1138     getGroup().cs = new ZappoColourScheme();
1139     refresh();
1140   }
1141
1142   /**
1143    * DOCUMENT ME!
1144    *
1145    * @param e
1146    *                DOCUMENT ME!
1147    */
1148   protected void taylorColour_actionPerformed()
1149   {
1150     getGroup().cs = new TaylorColourScheme();
1151     refresh();
1152   }
1153
1154   /**
1155    * DOCUMENT ME!
1156    *
1157    * @param e
1158    *                DOCUMENT ME!
1159    */
1160   protected void hydrophobicityColour_actionPerformed()
1161   {
1162     getGroup().cs = new HydrophobicColourScheme();
1163     refresh();
1164   }
1165
1166   /**
1167    * DOCUMENT ME!
1168    *
1169    * @param e
1170    *                DOCUMENT ME!
1171    */
1172   protected void helixColour_actionPerformed()
1173   {
1174     getGroup().cs = new HelixColourScheme();
1175     refresh();
1176   }
1177
1178   /**
1179    * DOCUMENT ME!
1180    *
1181    * @param e
1182    *                DOCUMENT ME!
1183    */
1184   protected void strandColour_actionPerformed()
1185   {
1186     getGroup().cs = new StrandColourScheme();
1187     refresh();
1188   }
1189
1190   /**
1191    * DOCUMENT ME!
1192    *
1193    * @param e
1194    *                DOCUMENT ME!
1195    */
1196   protected void turnColour_actionPerformed()
1197   {
1198     getGroup().cs = new TurnColourScheme();
1199     refresh();
1200   }
1201
1202   /**
1203    * DOCUMENT ME!
1204    *
1205    * @param e
1206    *                DOCUMENT ME!
1207    */
1208   protected void buriedColour_actionPerformed()
1209   {
1210     getGroup().cs = new BuriedColourScheme();
1211     refresh();
1212   }
1213
1214   /**
1215    * DOCUMENT ME!
1216    *
1217    * @param e
1218    *                DOCUMENT ME!
1219    */
1220   public void nucleotideMenuItem_actionPerformed()
1221   {
1222     getGroup().cs = new NucleotideColourScheme();
1223     refresh();
1224   }
1225
1226   /**
1227    * DOCUMENT ME!
1228    *
1229    * @param e
1230    *                DOCUMENT ME!
1231    */
1232   protected void abovePIDColour_actionPerformed()
1233   {
1234     SequenceGroup sg = getGroup();
1235     if (sg.cs == null)
1236     {
1237       return;
1238     }
1239
1240     if (abovePIDColour.isSelected())
1241     {
1242       sg.cs.setConsensus(AAFrequency.calculate(sg
1243               .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
1244               .getEndRes() + 1));
1245
1246       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1247               .getName());
1248
1249       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1250
1251       SliderPanel.showPIDSlider();
1252     }
1253     else
1254     // remove PIDColouring
1255     {
1256       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1257     }
1258
1259     refresh();
1260   }
1261
1262   /**
1263    * DOCUMENT ME!
1264    *
1265    * @param e
1266    *                DOCUMENT ME!
1267    */
1268   protected void userDefinedColour_actionPerformed(ActionEvent e)
1269   {
1270     SequenceGroup sg = getGroup();
1271
1272     if (e.getActionCommand().equals("User Defined..."))
1273     {
1274       new UserDefinedColours(ap, sg);
1275     }
1276     else
1277     {
1278       UserColourScheme udc = (UserColourScheme) UserDefinedColours
1279               .getUserColourSchemes().get(e.getActionCommand());
1280
1281       sg.cs = udc;
1282     }
1283     refresh();
1284   }
1285
1286   /**
1287    * DOCUMENT ME!
1288    *
1289    * @param e
1290    *                DOCUMENT ME!
1291    */
1292   protected void PIDColour_actionPerformed()
1293   {
1294     SequenceGroup sg = getGroup();
1295     sg.cs = new PIDColourScheme();
1296     sg.cs.setConsensus(AAFrequency.calculate(sg
1297             .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
1298             .getEndRes() + 1));
1299     refresh();
1300   }
1301
1302   /**
1303    * DOCUMENT ME!
1304    *
1305    * @param e
1306    *                DOCUMENT ME!
1307    */
1308   protected void BLOSUM62Colour_actionPerformed()
1309   {
1310     SequenceGroup sg = getGroup();
1311
1312     sg.cs = new Blosum62ColourScheme();
1313
1314     sg.cs.setConsensus(AAFrequency.calculate(sg
1315             .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
1316             .getEndRes() + 1));
1317
1318     refresh();
1319   }
1320
1321   /**
1322    * DOCUMENT ME!
1323    *
1324    * @param e
1325    *                DOCUMENT ME!
1326    */
1327   protected void noColourmenuItem_actionPerformed()
1328   {
1329     getGroup().cs = null;
1330     refresh();
1331   }
1332
1333   /**
1334    * DOCUMENT ME!
1335    *
1336    * @param e
1337    *                DOCUMENT ME!
1338    */
1339   protected void conservationMenuItem_actionPerformed()
1340   {
1341     SequenceGroup sg = getGroup();
1342     if (sg.cs == null)
1343     {
1344       return;
1345     }
1346
1347     if (conservationMenuItem.isSelected())
1348     {
1349       Conservation c = new Conservation("Group",
1350               ResidueProperties.propHash, 3, sg
1351                       .getSequences(ap.av.hiddenRepSequences), sg
1352                       .getStartRes(), sg.getEndRes() + 1);
1353
1354       c.calculate();
1355       c.verdict(false, ap.av.ConsPercGaps);
1356
1357       sg.cs.setConservation(c);
1358
1359       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1360       SliderPanel.showConservationSlider();
1361     }
1362     else
1363     // remove ConservationColouring
1364     {
1365       sg.cs.setConservation(null);
1366     }
1367
1368     refresh();
1369   }
1370
1371   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1372   {
1373     SequenceGroup sg = getGroup();
1374     if (sg == null)
1375     {
1376       return;
1377     }
1378
1379     AnnotationColourGradient acg = new AnnotationColourGradient(sequence
1380             .getAnnotation()[0], null,
1381             AnnotationColourGradient.NO_THRESHOLD);
1382
1383     acg.predefinedColours = true;
1384     sg.cs = acg;
1385
1386     refresh();
1387   }
1388
1389   /**
1390    * DOCUMENT ME!
1391    *
1392    * @param e
1393    *                DOCUMENT ME!
1394    */
1395   protected void groupName_actionPerformed()
1396   {
1397
1398     SequenceGroup sg = getGroup();
1399     EditNameDialog dialog = new EditNameDialog(sg.getName(), sg
1400             .getDescription(), "       Group Name ", "Group Description ",
1401             "Edit Group Name/Description");
1402
1403     if (!dialog.accept)
1404     {
1405       return;
1406     }
1407
1408     sg.setName(dialog.getName());
1409     sg.setDescription(dialog.getDescription());
1410     refresh();
1411   }
1412
1413   /**
1414    * Get selection group - adding it to the alignment if necessary.
1415    *
1416    * @return sequence group to operate on
1417    */
1418   SequenceGroup getGroup()
1419   {
1420     SequenceGroup sg = ap.av.getSelectionGroup();
1421     // this method won't add a new group if it already exists
1422     if (sg != null)
1423     {
1424       ap.av.alignment.addGroup(sg);
1425     }
1426
1427     return sg;
1428   }
1429
1430   /**
1431    * DOCUMENT ME!
1432    *
1433    * @param e
1434    *                DOCUMENT ME!
1435    */
1436   void sequenceName_actionPerformed()
1437   {
1438     EditNameDialog dialog = new EditNameDialog(sequence.getName(), sequence
1439             .getDescription(), "       Sequence Name ",
1440             "Sequence Description ", "Edit Sequence Name/Description");
1441
1442     if (!dialog.accept)
1443     {
1444       return;
1445     }
1446
1447     if (dialog.getName() != null)
1448     {
1449       if (dialog.getName().indexOf(" ") > -1)
1450       {
1451         JOptionPane.showMessageDialog(ap,
1452                 "Spaces have been converted to \"_\"",
1453                 "No spaces allowed in Sequence Name",
1454                 JOptionPane.WARNING_MESSAGE);
1455       }
1456
1457       sequence.setName(dialog.getName().replace(' ', '_'));
1458       ap.paintAlignment(false);
1459     }
1460
1461     sequence.setDescription(dialog.getDescription());
1462
1463     ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1464             .getSequences());
1465
1466   }
1467
1468   /**
1469    * DOCUMENT ME!
1470    *
1471    * @param e
1472    *                DOCUMENT ME!
1473    */
1474   void unGroupMenuItem_actionPerformed()
1475   {
1476     SequenceGroup sg = ap.av.getSelectionGroup();
1477     ap.av.alignment.deleteGroup(sg);
1478     ap.av.setSelectionGroup(null);
1479     refresh();
1480   }
1481
1482   /**
1483    * DOCUMENT ME!
1484    *
1485    * @param e
1486    *                DOCUMENT ME!
1487    */
1488   protected void outline_actionPerformed()
1489   {
1490     SequenceGroup sg = getGroup();
1491     Color col = JColorChooser.showDialog(this, "Select Outline Colour",
1492             Color.BLUE);
1493
1494     if (col != null)
1495     {
1496       sg.setOutlineColour(col);
1497     }
1498
1499     refresh();
1500   }
1501
1502   /**
1503    * DOCUMENT ME!
1504    *
1505    * @param e
1506    *                DOCUMENT ME!
1507    */
1508   public void showBoxes_actionPerformed()
1509   {
1510     getGroup().setDisplayBoxes(showBoxes.isSelected());
1511     refresh();
1512   }
1513
1514   /**
1515    * DOCUMENT ME!
1516    *
1517    * @param e
1518    *                DOCUMENT ME!
1519    */
1520   public void showText_actionPerformed()
1521   {
1522     getGroup().setDisplayText(showText.isSelected());
1523     refresh();
1524   }
1525
1526   /**
1527    * DOCUMENT ME!
1528    *
1529    * @param e
1530    *                DOCUMENT ME!
1531    */
1532   public void showColourText_actionPerformed()
1533   {
1534     getGroup().setColourText(showColourText.isSelected());
1535     refresh();
1536   }
1537
1538   public void showLink(String url)
1539   {
1540     try
1541     {
1542       jalview.util.BrowserLauncher.openURL(url);
1543     } catch (Exception ex)
1544     {
1545       JOptionPane
1546               .showInternalMessageDialog(
1547                       Desktop.desktop,
1548                       "Unixers: Couldn't find default web browser."
1549                               + "\nAdd the full path to your browser in Preferences.",
1550                       "Web browser not found", JOptionPane.WARNING_MESSAGE);
1551
1552       ex.printStackTrace();
1553     }
1554   }
1555
1556   void hideSequences(boolean representGroup)
1557   {
1558     SequenceGroup sg = ap.av.getSelectionGroup();
1559     if (sg == null || sg.getSize() < 1)
1560     {
1561       ap.av.hideSequence(new SequenceI[]
1562       { sequence });
1563       return;
1564     }
1565
1566     ap.av.setSelectionGroup(null);
1567
1568     if (representGroup)
1569     {
1570       ap.av.hideRepSequences(sequence, sg);
1571
1572       return;
1573     }
1574
1575     int gsize = sg.getSize();
1576     SequenceI[] hseqs;
1577
1578     hseqs = new SequenceI[gsize];
1579
1580     int index = 0;
1581     for (int i = 0; i < gsize; i++)
1582     {
1583       hseqs[index++] = sg.getSequenceAt(i);
1584     }
1585
1586     ap.av.hideSequence(hseqs);
1587     // refresh(); TODO: ? needed ?
1588     ap.av.sendSelection();
1589   }
1590
1591   public void copy_actionPerformed()
1592   {
1593     ap.alignFrame.copy_actionPerformed(null);
1594   }
1595
1596   public void cut_actionPerformed()
1597   {
1598     ap.alignFrame.cut_actionPerformed(null);
1599   }
1600
1601   void changeCase(ActionEvent e)
1602   {
1603     Object source = e.getSource();
1604     SequenceGroup sg = ap.av.getSelectionGroup();
1605
1606     if (sg != null)
1607     {
1608       int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
1609               sg.getEndRes() + 1);
1610
1611       String description;
1612       int caseChange;
1613
1614       if (source == toggle)
1615       {
1616         description = "Toggle Case";
1617         caseChange = ChangeCaseCommand.TOGGLE_CASE;
1618       }
1619       else if (source == upperCase)
1620       {
1621         description = "To Upper Case";
1622         caseChange = ChangeCaseCommand.TO_UPPER;
1623       }
1624       else
1625       {
1626         description = "To Lower Case";
1627         caseChange = ChangeCaseCommand.TO_LOWER;
1628       }
1629
1630       ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, sg
1631               .getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
1632               caseChange);
1633
1634       ap.alignFrame.addHistoryItem(caseCommand);
1635
1636       ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1637               .getSequences());
1638
1639     }
1640   }
1641
1642   public void outputText_actionPerformed(ActionEvent e)
1643   {
1644     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1645     cap.setForInput(null);
1646     Desktop.addInternalFrame(cap, "Alignment output - "
1647             + e.getActionCommand(), 600, 500);
1648
1649     String[] omitHidden = null;
1650
1651     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1652                                             // or we simply trust the user wants
1653                                             // wysiwig behaviour
1654     SequenceGroup sg = ap.av.getSelectionGroup();
1655     ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1656     omitHidden = ap.av.getViewAsString(true);
1657     Alignment oal = new Alignment(ap.av.getSequenceSelection());
1658     AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
1659     for (int i = 0; i < nala.length; i++)
1660     {
1661       AlignmentAnnotation na = nala[i];
1662       oal.addAnnotation(na);
1663     }
1664     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1665             oal, omitHidden, csel, sg));
1666     oal = null;
1667   }
1668
1669   public void pdbFromFile_actionPerformed()
1670   {
1671     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
1672             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1673     chooser.setFileView(new jalview.io.JalviewFileView());
1674     chooser.setDialogTitle("Select a PDB file");
1675     chooser.setToolTipText("Load a PDB file");
1676
1677     int value = chooser.showOpenDialog(null);
1678
1679     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
1680     {
1681       PDBEntry entry = new PDBEntry();
1682       String choice = chooser.getSelectedFile().getPath();
1683       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1684       try
1685       {
1686         MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
1687                 jalview.io.AppletFormatAdapter.FILE);
1688
1689         if (pdbfile.id == null)
1690         {
1691           String reply = JOptionPane
1692                   .showInternalInputDialog(
1693                           Desktop.desktop,
1694                           "Couldn't find a PDB id in the file supplied."
1695                                   + "Please enter an Id to identify this structure.",
1696                           "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
1697           if (reply == null)
1698           {
1699             return;
1700           }
1701
1702           entry.setId(reply);
1703         }
1704         else
1705         {
1706           entry.setId(pdbfile.id);
1707         }
1708       } catch (java.io.IOException ex)
1709       {
1710         ex.printStackTrace();
1711       }
1712
1713       entry.setFile(choice);
1714       sequence.getDatasetSequence().addPDBId(entry);
1715     }
1716
1717   }
1718
1719   public void enterPDB_actionPerformed()
1720   {
1721     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
1722             "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
1723
1724     if (id != null && id.length() > 0)
1725     {
1726       PDBEntry entry = new PDBEntry();
1727       entry.setId(id.toUpperCase());
1728       sequence.getDatasetSequence().addPDBId(entry);
1729     }
1730   }
1731
1732   public void discoverPDB_actionPerformed()
1733   {
1734
1735     final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new Sequence[]
1736     { sequence }
1737             : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
1738     Thread discpdb = new Thread(new Runnable()
1739     {
1740       public void run()
1741       {
1742
1743         new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
1744                 .fetchDBRefs(false);
1745       }
1746
1747     });
1748     discpdb.start();
1749   }
1750
1751   public void sequenceFeature_actionPerformed()
1752   {
1753     SequenceGroup sg = ap.av.getSelectionGroup();
1754     if (sg == null)
1755     {
1756       return;
1757     }
1758
1759     int rsize=0,gSize = sg.getSize();
1760     SequenceI[] rseqs,seqs = new SequenceI[gSize];
1761     SequenceFeature[] tfeatures,features = new SequenceFeature[gSize];
1762
1763     for (int i = 0; i < gSize; i++)
1764     {
1765       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
1766       int end = sg.findEndRes(sg.getSequenceAt(i));
1767       if (start<=end)
1768       {
1769         seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
1770         features[rsize] = new SequenceFeature(null, null, null, start, end,
1771               "Jalview");
1772         rsize++;
1773       }
1774     }
1775     rseqs = new SequenceI[rsize];
1776     tfeatures = new SequenceFeature[rsize];
1777     System.arraycopy(seqs,0,rseqs, 0, rsize);
1778     System.arraycopy(features, 0, tfeatures, 0, rsize);
1779     features = tfeatures;
1780     seqs = rseqs;
1781     if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
1782             features, true, ap))
1783     {
1784       ap.alignFrame.setShowSeqFeatures(true);
1785       ap.highlightSearchResults(null);
1786     }
1787   }
1788
1789   public void textColour_actionPerformed()
1790   {
1791     SequenceGroup sg = getGroup();
1792     if (sg != null)
1793     {
1794       new TextColourChooser().chooseColour(ap, sg);
1795     }
1796   }
1797
1798   public void colourByStructure(String pdbid)
1799   {
1800     Annotation[] anots = jalview.structure.StructureSelectionManager
1801             .getStructureSelectionManager().colourSequenceFromStructure(
1802                     sequence, pdbid);
1803
1804     AlignmentAnnotation an = new AlignmentAnnotation("Structure",
1805             "Coloured by " + pdbid, anots);
1806
1807     ap.av.alignment.addAnnotation(an);
1808     an.createSequenceMapping(sequence, 0, true);
1809     // an.adjustForAlignment();
1810     ap.av.alignment.setAnnotationIndex(an, 0);
1811
1812     ap.adjustAnnotationHeight();
1813
1814     sequence.addAlignmentAnnotation(an);
1815
1816   }
1817
1818   public void editSequence_actionPerformed(ActionEvent actionEvent)
1819   {
1820     SequenceGroup sg = ap.av.getSelectionGroup();
1821
1822     if (sg != null)
1823     {
1824       if (sequence == null)
1825         sequence = (Sequence) sg.getSequenceAt(0);
1826
1827       EditNameDialog dialog = new EditNameDialog(sequence
1828               .getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1),
1829               null, "Edit Sequence ", null, "Edit Sequence");
1830
1831       if (dialog.accept)
1832       {
1833         EditCommand editCommand = new EditCommand("Edit Sequences",
1834                 EditCommand.REPLACE, dialog.getName().replace(' ',
1835                         ap.av.getGapCharacter()), sg
1836                         .getSequencesAsArray(ap.av.hiddenRepSequences), sg
1837                         .getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
1838
1839         ap.alignFrame.addHistoryItem(editCommand);
1840
1841         ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1842                 .getSequences());
1843       }
1844     }
1845   }
1846
1847 }