src/jalview/gui/PopupMenu.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer
   3  * Copyright (C) 2007 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
  34 /**
  35  * DOCUMENT ME!
  36  *
  37  * @author $author$
  38  * @version $Revision$
  39  */
  40 public class PopupMenu
  41     extends JPopupMenu
  42 {
  43   JMenu groupMenu = new JMenu();
  44   JMenuItem groupName = new JMenuItem();
  45   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  46   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  47   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  48   protected JRadioButtonMenuItem hydrophobicityColour = new
  49       JRadioButtonMenuItem();
  50   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
  51   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
  52   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
  53   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
  54   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
  55   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
  56   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
  57   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
  58   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
  59   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
  60   AlignmentPanel ap;
  61   JMenu sequenceMenu = new JMenu();
  62   JMenuItem sequenceName = new JMenuItem();
  63   Sequence sequence;
  64   JMenuItem unGroupMenuItem = new JMenuItem();
  65   JMenuItem outline = new JMenuItem();
  66   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
  67   JMenu colourMenu = new JMenu();
  68   JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
  69   JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
  70   JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
  71   JMenu editMenu = new JMenu();
  72   JMenuItem cut = new JMenuItem();
  73   JMenuItem copy = new JMenuItem();
  74   JMenuItem upperCase = new JMenuItem();
  75   JMenuItem lowerCase = new JMenuItem();
  76   JMenuItem toggle = new JMenuItem();
  77   JMenu pdbMenu = new JMenu();
  78   JMenuItem pdbFromFile = new JMenuItem();
  79   JMenuItem enterPDB = new JMenuItem();
  80   JMenuItem discoverPDB = new JMenuItem();
  81   JMenu outputMenu = new JMenu();
  82   JMenuItem sequenceFeature = new JMenuItem();
  83   JMenuItem textColour = new JMenuItem();
  84   JMenu jMenu1 = new JMenu();
  85   JMenu structureMenu = new JMenu();
  86   JMenu viewStructureMenu = new JMenu();
  87  // JMenu colStructureMenu = new JMenu();
  88   JMenuItem editSequence = new JMenuItem();
  89  // JMenuItem annotationMenuItem = new JMenuItem();
  90
  91   /**
  92    * Creates a new PopupMenu object.
  93    *
  94    * @param ap DOCUMENT ME!
  95    * @param seq DOCUMENT ME!
  96    */
  97   public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
  98   {
  99     ///////////////////////////////////////////////////////////
 100     // If this is activated from the sequence panel, the user may want to
 101     // edit or annotate a particular residue. Therefore display the residue menu
 102     //
 103     // If from the IDPanel, we must display the sequence menu
 104     //////////////////////////////////////////////////////////
 105     this.ap = ap;
 106     sequence = seq;
 107
 108     ButtonGroup colours = new ButtonGroup();
 109     colours.add(noColourmenuItem);
 110     colours.add(clustalColour);
 111     colours.add(zappoColour);
 112     colours.add(taylorColour);
 113     colours.add(hydrophobicityColour);
 114     colours.add(helixColour);
 115     colours.add(strandColour);
 116     colours.add(turnColour);
 117     colours.add(buriedColour);
 118     colours.add(abovePIDColour);
 119     colours.add(userDefinedColour);
 120     colours.add(PIDColour);
 121     colours.add(BLOSUM62Colour);
 122
 123     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 124     {
 125       JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.WRITEABLE_FORMATS[
 126                                      i]);
 127
 128       item.addActionListener(new java.awt.event.ActionListener()
 129       {
 130         public void actionPerformed(ActionEvent e)
 131         {
 132           outputText_actionPerformed(e);
 133         }
 134       });
 135
 136       outputMenu.add(item);
 137     }
 138
 139     try
 140     {
 141       jbInit();
 142     }
 143     catch (Exception e)
 144     {
 145       e.printStackTrace();
 146     }
 147
 148     if (seq != null)
 149     {
 150       sequenceMenu.setText(sequence.getName());
 151
 152       JMenuItem menuItem;
 153       if (seq.getDatasetSequence().getPDBId() != null
 154           && seq.getDatasetSequence().getPDBId().size()>0)
 155       {
 156         java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
 157             elements();
 158
 159         while (e.hasMoreElements())
 160         {
 161           final PDBEntry pdb = (PDBEntry) e.nextElement();
 162
 163           menuItem = new JMenuItem();
 164           menuItem.setText(pdb.getId());
 165           menuItem.addActionListener(new java.awt.event.ActionListener()
 166           {
 167             public void actionPerformed(ActionEvent e)
 168             {
 169               Vector seqs = new Vector();
 170               for (int i = 0; i < ap.av.alignment.getHeight(); i++)
 171               {
 172                 Vector pdbs = ap.av.alignment.getSequenceAt(i).getDatasetSequence().getPDBId();
 173                 if(pdbs==null)
 174                   continue;
 175
 176                 for(int p=0; p<pdbs.size(); p++)
 177                 {
 178                   PDBEntry p1 = (PDBEntry)pdbs.elementAt(p);
 179                   if(p1.getId().equals(pdb.getId()))
 180                   {
 181                     if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))
 182                         seqs.addElement(ap.av.alignment.getSequenceAt(i));
 183
 184                       continue;
 185                   }
 186                 }
 187               }
 188
 189               SequenceI [] seqs2 = new SequenceI[seqs.size()];
 190               seqs.toArray(seqs2);
 191
 192               new AppJmol(pdb, seqs2, null, ap);
 193               //  new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
 194             }
 195           });
 196           viewStructureMenu.add(menuItem);
 197
 198        /*   menuItem = new JMenuItem();
 199           menuItem.setText(pdb.getId());
 200           menuItem.addActionListener(new java.awt.event.ActionListener()
 201           {
 202             public void actionPerformed(ActionEvent e)
 203             {
 204               colourByStructure(pdb.getId());
 205             }
 206           });
 207           colStructureMenu.add(menuItem);*/
 208         }
 209       }
 210       else
 211       {
 212         structureMenu.remove(viewStructureMenu);
 213        // structureMenu.remove(colStructureMenu);
 214       }
 215
 216       menuItem = new JMenuItem("Hide Sequences");
 217       menuItem.addActionListener(new java.awt.event.ActionListener()
 218       {
 219         public void actionPerformed(ActionEvent e)
 220         {
 221           hideSequences(false);
 222         }
 223       });
 224       add(menuItem);
 225
 226       if (ap.av.getSelectionGroup() != null
 227           && ap.av.getSelectionGroup().getSize() > 1)
 228       {
 229         menuItem = new JMenuItem("Represent Group with " + seq.getName());
 230         menuItem.addActionListener(new java.awt.event.ActionListener()
 231         {
 232           public void actionPerformed(ActionEvent e)
 233           {
 234             hideSequences(true);
 235           }
 236         });
 237         sequenceMenu.add(menuItem);
 238       }
 239
 240       if (ap.av.hasHiddenRows)
 241       {
 242         final int index = ap.av.alignment.findIndex(seq);
 243
 244         if (ap.av.adjustForHiddenSeqs(index) -
 245             ap.av.adjustForHiddenSeqs(index - 1) > 1)
 246         {
 247           menuItem = new JMenuItem("Reveal Sequences");
 248           menuItem.addActionListener(new ActionListener()
 249           {
 250             public void actionPerformed(ActionEvent e)
 251             {
 252               ap.av.showSequence(index);
 253               if (ap.overviewPanel != null)
 254               {
 255                 ap.overviewPanel.updateOverviewImage();
 256               }
 257             }
 258           });
 259           add(menuItem);
 260         }
 261
 262         menuItem = new JMenuItem("Reveal All");
 263         menuItem.addActionListener(new ActionListener()
 264         {
 265           public void actionPerformed(ActionEvent e)
 266           {
 267             ap.av.showAllHiddenSeqs();
 268             if (ap.overviewPanel != null)
 269             {
 270               ap.overviewPanel.updateOverviewImage();
 271             }
 272           }
 273         });
 274
 275         add(menuItem);
 276       }
 277
 278     }
 279
 280     SequenceGroup sg = ap.av.getSelectionGroup();
 281
 282     if (sg != null)
 283     {
 284       groupName.setText(sg.getName());
 285
 286       if (sg.cs instanceof ZappoColourScheme)
 287       {
 288         zappoColour.setSelected(true);
 289       }
 290       else if (sg.cs instanceof TaylorColourScheme)
 291       {
 292         taylorColour.setSelected(true);
 293       }
 294       else if (sg.cs instanceof PIDColourScheme)
 295       {
 296         PIDColour.setSelected(true);
 297       }
 298       else if (sg.cs instanceof Blosum62ColourScheme)
 299       {
 300         BLOSUM62Colour.setSelected(true);
 301       }
 302       else if (sg.cs instanceof UserColourScheme)
 303       {
 304         userDefinedColour.setSelected(true);
 305       }
 306       else if (sg.cs instanceof HydrophobicColourScheme)
 307       {
 308         hydrophobicityColour.setSelected(true);
 309       }
 310       else if (sg.cs instanceof HelixColourScheme)
 311       {
 312         helixColour.setSelected(true);
 313       }
 314       else if (sg.cs instanceof StrandColourScheme)
 315       {
 316         strandColour.setSelected(true);
 317       }
 318       else if (sg.cs instanceof TurnColourScheme)
 319       {
 320         turnColour.setSelected(true);
 321       }
 322       else if (sg.cs instanceof BuriedColourScheme)
 323       {
 324         buriedColour.setSelected(true);
 325       }
 326       else if (sg.cs instanceof ClustalxColourScheme)
 327       {
 328         clustalColour.setSelected(true);
 329       }
 330       else
 331       {
 332         noColourmenuItem.setSelected(true);
 333       }
 334
 335       if (sg.cs != null && sg.cs.conservationApplied())
 336       {
 337         conservationMenuItem.setSelected(true);
 338       }
 339
 340       showText.setSelected(sg.getDisplayText());
 341       showColourText.setSelected(sg.getColourText());
 342       showBoxes.setSelected(sg.getDisplayBoxes());
 343     }
 344     else
 345     {
 346       groupMenu.setVisible(false);
 347       editMenu.setVisible(false);
 348     }
 349
 350     if (!ap.av.alignment.getGroups().contains(sg))
 351     {
 352       unGroupMenuItem.setVisible(false);
 353     }
 354
 355     if (seq == null)
 356     {
 357       sequenceMenu.setVisible(false);
 358       structureMenu.setVisible(false);
 359     }
 360
 361     if (links != null && links.size() > 0)
 362     {
 363       JMenu linkMenu = new JMenu("Link");
 364       JMenuItem item;
 365       for (int i = 0; i < links.size(); i++)
 366       {
 367         String link = links.elementAt(i).toString();
 368         final String label = link.substring(0, link.indexOf("|"));
 369         item = new JMenuItem(label);
 370         final String url;
 371
 372         if (link.indexOf("$SEQUENCE_ID$") > -1)
 373         {
 374           String id = seq.getName();
 375           if (id.indexOf("|") > -1)
 376           {
 377             id = id.substring(id.lastIndexOf("|") + 1);
 378           }
 379
 380           url = link.substring(link.indexOf("|") + 1,
 381                                link.indexOf("$SEQUENCE_ID$"))
 382               + id +
 383               link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
 384         }
 385         else
 386         {
 387           url = link.substring(link.lastIndexOf("|") + 1);
 388         }
 389
 390         item.addActionListener(new java.awt.event.ActionListener()
 391         {
 392           public void actionPerformed(ActionEvent e)
 393           {
 394             showLink(url);
 395           }
 396         });
 397
 398         linkMenu.add(item);
 399       }
 400       if (sequence != null)
 401       {
 402         sequenceMenu.add(linkMenu);
 403       }
 404       else
 405       {
 406         add(linkMenu);
 407       }
 408     }
 409   }
 410
 411   /**
 412    * DOCUMENT ME!
 413    *
 414    * @throws Exception DOCUMENT ME!
 415    */
 416   private void jbInit()
 417       throws Exception
 418   {
 419     groupMenu.setText("Group");
 420     groupMenu.setText("Selection");
 421     groupName.setText("Name");
 422     groupName.addActionListener(new java.awt.event.ActionListener()
 423     {
 424       public void actionPerformed(ActionEvent e)
 425       {
 426         groupName_actionPerformed();
 427       }
 428     });
 429     sequenceMenu.setText("Sequence");
 430     sequenceName.setText("Edit Name/Description");
 431     sequenceName.addActionListener(new java.awt.event.ActionListener()
 432     {
 433       public void actionPerformed(ActionEvent e)
 434       {
 435         sequenceName_actionPerformed();
 436       }
 437     });
 438     PIDColour.setFocusPainted(false);
 439     unGroupMenuItem.setText("Remove Group");
 440     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 441     {
 442       public void actionPerformed(ActionEvent e)
 443       {
 444         unGroupMenuItem_actionPerformed();
 445       }
 446     });
 447
 448     outline.setText("Border colour");
 449     outline.addActionListener(new java.awt.event.ActionListener()
 450     {
 451       public void actionPerformed(ActionEvent e)
 452       {
 453         outline_actionPerformed();
 454       }
 455     });
 456     nucleotideMenuItem.setText("Nucleotide");
 457     nucleotideMenuItem.addActionListener(new ActionListener()
 458     {
 459       public void actionPerformed(ActionEvent e)
 460       {
 461         nucleotideMenuItem_actionPerformed();
 462       }
 463     });
 464     colourMenu.setText("Group Colour");
 465     showBoxes.setText("Boxes");
 466     showBoxes.setState(true);
 467     showBoxes.addActionListener(new ActionListener()
 468     {
 469       public void actionPerformed(ActionEvent e)
 470       {
 471         showBoxes_actionPerformed();
 472       }
 473     });
 474     showText.setText("Text");
 475     showText.setState(true);
 476     showText.addActionListener(new ActionListener()
 477     {
 478       public void actionPerformed(ActionEvent e)
 479       {
 480         showText_actionPerformed();
 481       }
 482     });
 483     showColourText.setText("Colour Text");
 484     showColourText.addActionListener(new ActionListener()
 485     {
 486       public void actionPerformed(ActionEvent e)
 487       {
 488         showColourText_actionPerformed();
 489       }
 490     });
 491     editMenu.setText("Edit");
 492     cut.setText("Cut");
 493     cut.addActionListener(new ActionListener()
 494     {
 495       public void actionPerformed(ActionEvent e)
 496       {
 497         cut_actionPerformed();
 498       }
 499     });
 500     upperCase.setText("To Upper Case");
 501     upperCase.addActionListener(new ActionListener()
 502     {
 503       public void actionPerformed(ActionEvent e)
 504       {
 505         changeCase(e);
 506       }
 507     });
 508     copy.setText("Copy");
 509     copy.addActionListener(new ActionListener()
 510     {
 511       public void actionPerformed(ActionEvent e)
 512       {
 513         copy_actionPerformed();
 514       }
 515     });
 516     lowerCase.setText("To Lower Case");
 517     lowerCase.addActionListener(new ActionListener()
 518     {
 519       public void actionPerformed(ActionEvent e)
 520       {
 521         changeCase(e);
 522       }
 523     });
 524     toggle.setText("Toggle Case");
 525     toggle.addActionListener(new ActionListener()
 526     {
 527       public void actionPerformed(ActionEvent e)
 528       {
 529         changeCase(e);
 530       }
 531     });
 532     pdbMenu.setText("Associate Structure with Sequence");
 533     pdbFromFile.setText("From File");
 534     pdbFromFile.addActionListener(new ActionListener()
 535     {
 536       public void actionPerformed(ActionEvent e)
 537       {
 538         pdbFromFile_actionPerformed();
 539       }
 540     });
 541     enterPDB.setText("Enter PDB Id");
 542     enterPDB.addActionListener(new ActionListener()
 543     {
 544       public void actionPerformed(ActionEvent e)
 545       {
 546         enterPDB_actionPerformed();
 547       }
 548     });
 549     discoverPDB.setText("Discover PDB ids");
 550     discoverPDB.addActionListener(new ActionListener()
 551     {
 552       public void actionPerformed(ActionEvent e)
 553       {
 554         discoverPDB_actionPerformed();
 555       }
 556     });
 557     outputMenu.setText("Output to Textbox...");
 558     sequenceFeature.setText("Create Sequence Feature");
 559     sequenceFeature.addActionListener(new ActionListener()
 560     {
 561       public void actionPerformed(ActionEvent e)
 562       {
 563         sequenceFeature_actionPerformed();
 564       }
 565     });
 566     textColour.setText("Text Colour");
 567     textColour.addActionListener(new ActionListener()
 568     {
 569       public void actionPerformed(ActionEvent e)
 570       {
 571         textColour_actionPerformed();
 572       }
 573     });
 574     jMenu1.setText("Group");
 575     structureMenu.setText("Structure");
 576     viewStructureMenu.setText("View Structure");
 577   //  colStructureMenu.setText("Colour By Structure");
 578     editSequence.setText("Edit Sequence...");
 579     editSequence.addActionListener(new ActionListener()
 580     {
 581       public void actionPerformed(ActionEvent actionEvent)
 582       {
 583         editSequence_actionPerformed(actionEvent);
 584       }
 585     });
 586    /* annotationMenuItem.setText("By Annotation");
 587     annotationMenuItem.addActionListener(new ActionListener()
 588     {
 589       public void actionPerformed(ActionEvent actionEvent)
 590       {
 591         annotationMenuItem_actionPerformed(actionEvent);
 592       }
 593     });*/
 594
 595     add(groupMenu);
 596
 597     add(sequenceMenu);
 598     this.add(structureMenu);
 599     groupMenu.add(editMenu);
 600     groupMenu.add(outputMenu);
 601     groupMenu.add(sequenceFeature);
 602     groupMenu.add(jMenu1);
 603     sequenceMenu.add(sequenceName);
 604     colourMenu.add(textColour);
 605     colourMenu.add(noColourmenuItem);
 606     colourMenu.add(clustalColour);
 607     colourMenu.add(BLOSUM62Colour);
 608     colourMenu.add(PIDColour);
 609     colourMenu.add(zappoColour);
 610     colourMenu.add(taylorColour);
 611     colourMenu.add(hydrophobicityColour);
 612     colourMenu.add(helixColour);
 613     colourMenu.add(strandColour);
 614     colourMenu.add(turnColour);
 615     colourMenu.add(buriedColour);
 616     colourMenu.add(nucleotideMenuItem);
 617     colourMenu.add(userDefinedColour);
 618
 619     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 620     {
 621       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
 622           getUserColourSchemes().keys();
 623
 624       while (userColours.hasMoreElements())
 625       {
 626         JMenuItem item = new JMenuItem(userColours.
 627                                        nextElement().toString());
 628         item.addActionListener(new ActionListener()
 629         {
 630           public void actionPerformed(ActionEvent evt)
 631           {
 632             userDefinedColour_actionPerformed(evt);
 633           }
 634         });
 635         colourMenu.add(item);
 636       }
 637     }
 638
 639     colourMenu.addSeparator();
 640     colourMenu.add(abovePIDColour);
 641     colourMenu.add(conservationMenuItem);
 642     //colourMenu.add(annotationMenuItem);
 643     editMenu.add(copy);
 644     editMenu.add(cut);
 645     editMenu.add(editSequence);
 646     editMenu.add(upperCase);
 647     editMenu.add(lowerCase);
 648     editMenu.add(toggle);
 649     pdbMenu.add(pdbFromFile);
 650     pdbMenu.add(enterPDB);
 651     pdbMenu.add(discoverPDB);
 652     jMenu1.add(groupName);
 653     jMenu1.add(unGroupMenuItem);
 654     jMenu1.add(colourMenu);
 655     jMenu1.add(showBoxes);
 656     jMenu1.add(showText);
 657     jMenu1.add(showColourText);
 658     jMenu1.add(outline);
 659     structureMenu.add(pdbMenu);
 660     structureMenu.add(viewStructureMenu);
 661    // structureMenu.add(colStructureMenu);
 662     noColourmenuItem.setText("None");
 663     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
 664     {
 665       public void actionPerformed(ActionEvent e)
 666       {
 667         noColourmenuItem_actionPerformed();
 668       }
 669     });
 670
 671     clustalColour.setText("Clustalx colours");
 672     clustalColour.addActionListener(new java.awt.event.ActionListener()
 673     {
 674       public void actionPerformed(ActionEvent e)
 675       {
 676         clustalColour_actionPerformed();
 677       }
 678     });
 679     zappoColour.setText("Zappo");
 680     zappoColour.addActionListener(new java.awt.event.ActionListener()
 681     {
 682       public void actionPerformed(ActionEvent e)
 683       {
 684         zappoColour_actionPerformed();
 685       }
 686     });
 687     taylorColour.setText("Taylor");
 688     taylorColour.addActionListener(new java.awt.event.ActionListener()
 689     {
 690       public void actionPerformed(ActionEvent e)
 691       {
 692         taylorColour_actionPerformed();
 693       }
 694     });
 695     hydrophobicityColour.setText("Hydrophobicity");
 696     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
 697     {
 698       public void actionPerformed(ActionEvent e)
 699       {
 700         hydrophobicityColour_actionPerformed();
 701       }
 702     });
 703     helixColour.setText("Helix propensity");
 704     helixColour.addActionListener(new java.awt.event.ActionListener()
 705     {
 706       public void actionPerformed(ActionEvent e)
 707       {
 708         helixColour_actionPerformed();
 709       }
 710     });
 711     strandColour.setText("Strand propensity");
 712     strandColour.addActionListener(new java.awt.event.ActionListener()
 713     {
 714       public void actionPerformed(ActionEvent e)
 715       {
 716         strandColour_actionPerformed();
 717       }
 718     });
 719     turnColour.setText("Turn propensity");
 720     turnColour.addActionListener(new java.awt.event.ActionListener()
 721     {
 722       public void actionPerformed(ActionEvent e)
 723       {
 724         turnColour_actionPerformed();
 725       }
 726     });
 727     buriedColour.setText("Buried Index");
 728     buriedColour.addActionListener(new java.awt.event.ActionListener()
 729     {
 730       public void actionPerformed(ActionEvent e)
 731       {
 732         buriedColour_actionPerformed();
 733       }
 734     });
 735     abovePIDColour.setText("Above % Identity");
 736     abovePIDColour.addActionListener(new java.awt.event.ActionListener()
 737     {
 738       public void actionPerformed(ActionEvent e)
 739       {
 740         abovePIDColour_actionPerformed();
 741       }
 742     });
 743     userDefinedColour.setText("User Defined...");
 744     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 745     {
 746       public void actionPerformed(ActionEvent e)
 747       {
 748         userDefinedColour_actionPerformed(e);
 749       }
 750     });
 751     PIDColour.setText("Percentage Identity");
 752     PIDColour.addActionListener(new java.awt.event.ActionListener()
 753     {
 754       public void actionPerformed(ActionEvent e)
 755       {
 756         PIDColour_actionPerformed();
 757       }
 758     });
 759     BLOSUM62Colour.setText("BLOSUM62");
 760     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 761     {
 762       public void actionPerformed(ActionEvent e)
 763       {
 764         BLOSUM62Colour_actionPerformed();
 765       }
 766     });
 767     conservationMenuItem.setText("Conservation");
 768     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
 769     {
 770       public void actionPerformed(ActionEvent e)
 771       {
 772         conservationMenuItem_actionPerformed();
 773       }
 774     });
 775   }
 776
 777   /**
 778    * DOCUMENT ME!
 779    */
 780   void refresh()
 781   {
 782     ap.paintAlignment(true);
 783
 784     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
 785   }
 786
 787   /**
 788    * DOCUMENT ME!
 789    *
 790    * @param e DOCUMENT ME!
 791    */
 792   protected void clustalColour_actionPerformed()
 793   {
 794     SequenceGroup sg = getGroup();
 795     sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
 796                                      ap.av.alignment.getWidth());
 797     refresh();
 798   }
 799
 800   /**
 801    * DOCUMENT ME!
 802    *
 803    * @param e DOCUMENT ME!
 804    */
 805   protected void zappoColour_actionPerformed()
 806   {
 807     getGroup().cs = new ZappoColourScheme();
 808     refresh();
 809   }
 810
 811   /**
 812    * DOCUMENT ME!
 813    *
 814    * @param e DOCUMENT ME!
 815    */
 816   protected void taylorColour_actionPerformed()
 817   {
 818     getGroup().cs = new TaylorColourScheme();
 819     refresh();
 820   }
 821
 822   /**
 823    * DOCUMENT ME!
 824    *
 825    * @param e DOCUMENT ME!
 826    */
 827   protected void hydrophobicityColour_actionPerformed()
 828   {
 829     getGroup().cs = new HydrophobicColourScheme();
 830     refresh();
 831   }
 832
 833   /**
 834    * DOCUMENT ME!
 835    *
 836    * @param e DOCUMENT ME!
 837    */
 838   protected void helixColour_actionPerformed()
 839   {
 840     getGroup().cs = new HelixColourScheme();
 841     refresh();
 842   }
 843
 844   /**
 845    * DOCUMENT ME!
 846    *
 847    * @param e DOCUMENT ME!
 848    */
 849   protected void strandColour_actionPerformed()
 850   {
 851     getGroup().cs = new StrandColourScheme();
 852     refresh();
 853   }
 854
 855   /**
 856    * DOCUMENT ME!
 857    *
 858    * @param e DOCUMENT ME!
 859    */
 860   protected void turnColour_actionPerformed()
 861   {
 862     getGroup().cs = new TurnColourScheme();
 863     refresh();
 864   }
 865
 866   /**
 867    * DOCUMENT ME!
 868    *
 869    * @param e DOCUMENT ME!
 870    */
 871   protected void buriedColour_actionPerformed()
 872   {
 873     getGroup().cs = new BuriedColourScheme();
 874     refresh();
 875   }
 876
 877   /**
 878    * DOCUMENT ME!
 879    *
 880    * @param e DOCUMENT ME!
 881    */
 882   public void nucleotideMenuItem_actionPerformed()
 883   {
 884     getGroup().cs = new NucleotideColourScheme();
 885     refresh();
 886   }
 887
 888   /**
 889    * DOCUMENT ME!
 890    *
 891    * @param e DOCUMENT ME!
 892    */
 893   protected void abovePIDColour_actionPerformed()
 894   {
 895     SequenceGroup sg = getGroup();
 896     if (sg.cs == null)
 897     {
 898       return;
 899     }
 900
 901     if (abovePIDColour.isSelected())
 902     {
 903       sg.cs.setConsensus(AAFrequency.calculate(
 904           sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
 905           sg.getEndRes() + 1));
 906
 907       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
 908           getGroup().getName());
 909
 910       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
 911
 912       SliderPanel.showPIDSlider();
 913     }
 914     else // remove PIDColouring
 915     {
 916       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
 917     }
 918
 919     refresh();
 920   }
 921
 922   /**
 923    * DOCUMENT ME!
 924    *
 925    * @param e DOCUMENT ME!
 926    */
 927   protected void userDefinedColour_actionPerformed(ActionEvent e)
 928   {
 929     SequenceGroup sg = getGroup();
 930
 931     if (e.getActionCommand().equals("User Defined..."))
 932     {
 933       new UserDefinedColours(ap, sg);
 934     }
 935     else
 936     {
 937       UserColourScheme udc = (UserColourScheme) UserDefinedColours.
 938           getUserColourSchemes().get(e.getActionCommand());
 939
 940       sg.cs = udc;
 941     }
 942     refresh();
 943   }
 944
 945   /**
 946    * DOCUMENT ME!
 947    *
 948    * @param e DOCUMENT ME!
 949    */
 950   protected void PIDColour_actionPerformed()
 951   {
 952     SequenceGroup sg = getGroup();
 953     sg.cs = new PIDColourScheme();
 954     sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
 955         hiddenRepSequences),
 956                                              sg.getStartRes(),
 957                                              sg.getEndRes() + 1));
 958     refresh();
 959   }
 960
 961   /**
 962    * DOCUMENT ME!
 963    *
 964    * @param e DOCUMENT ME!
 965    */
 966   protected void BLOSUM62Colour_actionPerformed()
 967   {
 968     SequenceGroup sg = getGroup();
 969
 970     sg.cs = new Blosum62ColourScheme();
 971
 972     sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
 973         hiddenRepSequences),
 974                                              sg.getStartRes(),
 975                                              sg.getEndRes() + 1));
 976
 977     refresh();
 978   }
 979
 980   /**
 981    * DOCUMENT ME!
 982    *
 983    * @param e DOCUMENT ME!
 984    */
 985   protected void noColourmenuItem_actionPerformed()
 986   {
 987     getGroup().cs = null;
 988     refresh();
 989   }
 990
 991   /**
 992    * DOCUMENT ME!
 993    *
 994    * @param e DOCUMENT ME!
 995    */
 996   protected void conservationMenuItem_actionPerformed()
 997   {
 998     SequenceGroup sg = getGroup();
 999     if (sg.cs == null)
1000     {
1001       return;
1002     }
1003
1004     if (conservationMenuItem.isSelected())
1005     {
1006       Conservation c = new Conservation("Group",
1007                                         ResidueProperties.propHash, 3,
1008                                         sg.getSequences(ap.av.
1009           hiddenRepSequences),
1010                                         sg.getStartRes(),
1011                                         sg.getEndRes() + 1);
1012
1013       c.calculate();
1014       c.verdict(false, ap.av.ConsPercGaps);
1015
1016       sg.cs.setConservation(c);
1017
1018       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1019       SliderPanel.showConservationSlider();
1020     }
1021     else // remove ConservationColouring
1022     {
1023       sg.cs.setConservation(null);
1024     }
1025
1026     refresh();
1027   }
1028
1029   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1030   {
1031     SequenceGroup sg = getGroup();
1032     if (sg == null)
1033     {
1034       return;
1035     }
1036
1037     AnnotationColourGradient acg = new AnnotationColourGradient(
1038         sequence.getAnnotation()[0], null, AnnotationColourGradient.NO_THRESHOLD);
1039
1040     acg.predefinedColours = true;
1041     sg.cs = acg;
1042
1043     refresh();
1044   }
1045
1046   /**
1047    * DOCUMENT ME!
1048    *
1049    * @param e DOCUMENT ME!
1050    */
1051   protected void groupName_actionPerformed()
1052   {
1053
1054     SequenceGroup sg = getGroup();
1055     EditNameDialog dialog = new EditNameDialog(sg.getName(),
1056                                                sg.getDescription(),
1057                                                "       Group Name ",
1058                                                "Group Description ",
1059                                                "Edit Group Name/Description");
1060
1061     if (!dialog.accept)
1062     {
1063       return;
1064     }
1065
1066     sg.setName(dialog.getName());
1067     sg.setDescription(dialog.getDescription());
1068   }
1069
1070   /**
1071    * DOCUMENT ME!
1072    *
1073    * @return DOCUMENT ME!
1074    */
1075   SequenceGroup getGroup()
1076   {
1077     SequenceGroup sg = ap.av.getSelectionGroup();
1078     // this method won't add a new group if it already exists
1079     if (sg != null)
1080     {
1081       ap.av.alignment.addGroup(sg);
1082     }
1083
1084     return sg;
1085   }
1086
1087   /**
1088    * DOCUMENT ME!
1089    *
1090    * @param e DOCUMENT ME!
1091    */
1092   void sequenceName_actionPerformed()
1093   {
1094     EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1095                                                sequence.getDescription(),
1096                                                "       Sequence Name ",
1097                                                "Sequence Description ",
1098                                                "Edit Sequence Name/Description");
1099
1100     if (!dialog.accept)
1101     {
1102       return;
1103     }
1104
1105     if (dialog.getName() != null)
1106     {
1107       if (dialog.getName().indexOf(" ") > -1)
1108       {
1109         JOptionPane.showMessageDialog(ap,
1110                                       "Spaces have been converted to \"_\"",
1111                                       "No spaces allowed in Sequence Name",
1112                                       JOptionPane.WARNING_MESSAGE);
1113       }
1114
1115       sequence.setName(dialog.getName().replace(' ', '_'));
1116       ap.paintAlignment(false);
1117     }
1118
1119     sequence.setDescription(dialog.getDescription());
1120
1121     ap.av.firePropertyChange("alignment", null,
1122                              ap.av.getAlignment().getSequences());
1123
1124   }
1125
1126   /**
1127    * DOCUMENT ME!
1128    *
1129    * @param e DOCUMENT ME!
1130    */
1131   void unGroupMenuItem_actionPerformed()
1132   {
1133     SequenceGroup sg = ap.av.getSelectionGroup();
1134     ap.av.alignment.deleteGroup(sg);
1135     ap.av.setSelectionGroup(null);
1136     refresh();
1137   }
1138
1139   /**
1140    * DOCUMENT ME!
1141    *
1142    * @param e DOCUMENT ME!
1143    */
1144   protected void outline_actionPerformed()
1145   {
1146     SequenceGroup sg = getGroup();
1147     Color col = JColorChooser.showDialog(this, "Select Outline Colour",
1148                                          Color.BLUE);
1149
1150     if (col != null)
1151     {
1152       sg.setOutlineColour(col);
1153     }
1154
1155     refresh();
1156   }
1157
1158   /**
1159    * DOCUMENT ME!
1160    *
1161    * @param e DOCUMENT ME!
1162    */
1163   public void showBoxes_actionPerformed()
1164   {
1165     getGroup().setDisplayBoxes(showBoxes.isSelected());
1166     refresh();
1167   }
1168
1169   /**
1170    * DOCUMENT ME!
1171    *
1172    * @param e DOCUMENT ME!
1173    */
1174   public void showText_actionPerformed()
1175   {
1176     getGroup().setDisplayText(showText.isSelected());
1177     refresh();
1178   }
1179
1180   /**
1181    * DOCUMENT ME!
1182    *
1183    * @param e DOCUMENT ME!
1184    */
1185   public void showColourText_actionPerformed()
1186   {
1187     getGroup().setColourText(showColourText.isSelected());
1188     refresh();
1189   }
1190
1191   public void showLink(String url)
1192   {
1193     try
1194     {
1195       jalview.util.BrowserLauncher.openURL(url);
1196     }
1197     catch (Exception ex)
1198     {
1199       JOptionPane.showInternalMessageDialog(Desktop.desktop,
1200                                             "Unixers: Couldn't find default web browser."
1201                                             +
1202           "\nAdd the full path to your browser in Preferences.",
1203                                             "Web browser not found",
1204                                             JOptionPane.WARNING_MESSAGE);
1205
1206       ex.printStackTrace();
1207     }
1208   }
1209
1210   void hideSequences(boolean representGroup)
1211   {
1212     SequenceGroup sg = ap.av.getSelectionGroup();
1213     if (sg == null || sg.getSize() < 1)
1214     {
1215       ap.av.hideSequence(new SequenceI[]
1216                          {sequence});
1217       return;
1218     }
1219
1220     ap.av.setSelectionGroup(null);
1221
1222     if (representGroup)
1223     {
1224       ap.av.hideRepSequences(sequence, sg);
1225
1226       return;
1227     }
1228
1229     int gsize = sg.getSize();
1230     SequenceI[] hseqs;
1231
1232     hseqs = new SequenceI[gsize];
1233
1234     int index = 0;
1235     for (int i = 0; i < gsize; i++)
1236     {
1237       hseqs[index++] = sg.getSequenceAt(i);
1238     }
1239
1240     ap.av.hideSequence(hseqs);
1241   }
1242
1243   public void copy_actionPerformed()
1244   {
1245     ap.alignFrame.copy_actionPerformed(null);
1246   }
1247
1248   public void cut_actionPerformed()
1249   {
1250     ap.alignFrame.cut_actionPerformed(null);
1251   }
1252
1253   void changeCase(ActionEvent e)
1254   {
1255     Object source = e.getSource();
1256     SequenceGroup sg = ap.av.getSelectionGroup();
1257
1258     if (sg != null)
1259     {
1260       int[][] startEnd = ap.av.getVisibleRegionBoundaries(
1261           sg.getStartRes(), sg.getEndRes() + 1);
1262
1263       String description;
1264       int caseChange;
1265
1266       if (source == toggle)
1267       {
1268         description = "Toggle Case";
1269         caseChange = ChangeCaseCommand.TOGGLE_CASE;
1270       }
1271       else if (source == upperCase)
1272       {
1273         description = "To Upper Case";
1274         caseChange = ChangeCaseCommand.TO_UPPER;
1275       }
1276       else
1277       {
1278         description = "To Lower Case";
1279         caseChange = ChangeCaseCommand.TO_LOWER;
1280       }
1281
1282       ChangeCaseCommand caseCommand = new ChangeCaseCommand(
1283           description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),
1284           startEnd, caseChange
1285           );
1286
1287       ap.alignFrame.addHistoryItem(caseCommand);
1288
1289       ap.av.firePropertyChange("alignment", null,
1290                                ap.av.getAlignment().getSequences());
1291
1292     }
1293   }
1294
1295   public void outputText_actionPerformed(ActionEvent e)
1296   {
1297     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1298     cap.setForInput(null);
1299     Desktop.addInternalFrame(cap,
1300                              "Alignment output - " + e.getActionCommand(), 600,
1301                              500);
1302
1303     String[] omitHidden = null;
1304
1305     if (ap.av.hasHiddenColumns)
1306     {
1307       System.out.println("PROMPT USER HERE");
1308       omitHidden = ap.av.getViewAsString(true);
1309     }
1310
1311     cap.setText(new FormatAdapter().formatSequences(
1312         e.getActionCommand(),
1313         ap.av.getSelectionAsNewSequence(),
1314         omitHidden));
1315   }
1316
1317   public void pdbFromFile_actionPerformed()
1318   {
1319     jalview.io.JalviewFileChooser chooser
1320         = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
1321                                             getProperty(
1322                                                 "LAST_DIRECTORY"));
1323     chooser.setFileView(new jalview.io.JalviewFileView());
1324     chooser.setDialogTitle("Select a PDB file");
1325     chooser.setToolTipText("Load a PDB file");
1326
1327     int value = chooser.showOpenDialog(null);
1328
1329     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
1330     {
1331       PDBEntry entry = new PDBEntry();
1332       String choice = chooser.getSelectedFile().getPath();
1333       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1334       try
1335       {
1336         MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
1337             jalview.io.AppletFormatAdapter.FILE);
1338
1339         if (pdbfile.id == null)
1340         {
1341           String reply = JOptionPane.showInternalInputDialog(
1342               Desktop.desktop,
1343               "Couldn't find a PDB id in the file supplied."
1344               + "Please enter an Id to identify this structure.",
1345               "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
1346           if (reply == null)
1347           {
1348             return;
1349           }
1350
1351           entry.setId(reply);
1352         }
1353         else
1354         {
1355           entry.setId(pdbfile.id);
1356         }
1357       }
1358       catch (java.io.IOException ex)
1359       {
1360         ex.printStackTrace();
1361       }
1362
1363       entry.setFile(choice);
1364       sequence.getDatasetSequence().addPDBId(entry);
1365     }
1366
1367   }
1368
1369   public void enterPDB_actionPerformed()
1370   {
1371     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
1372         "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
1373
1374     if (id != null && id.length() > 0)
1375     {
1376       PDBEntry entry = new PDBEntry();
1377       entry.setId(id.toUpperCase());
1378       sequence.getDatasetSequence()
1379           .addPDBId(entry);
1380     }
1381   }
1382
1383   public void discoverPDB_actionPerformed()
1384   {
1385     SequenceI[] sequences =
1386          ap.av.selectionGroup == null ?
1387            new Sequence[]{sequence}
1388          : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment);
1389
1390     new jalview.ws.DBRefFetcher(sequences,
1391         ap.alignFrame).fetchDBRefs(false);
1392   }
1393
1394   public void sequenceFeature_actionPerformed()
1395   {
1396     SequenceGroup sg = ap.av.getSelectionGroup();
1397     if (sg == null)
1398     {
1399       return;
1400     }
1401
1402     int gSize = sg.getSize();
1403     SequenceI[] seqs = new SequenceI[gSize];
1404     SequenceFeature[] features = new SequenceFeature[gSize];
1405
1406     for (int i = 0; i < gSize; i++)
1407     {
1408       seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
1409       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
1410       int end = sg.findEndRes(sg.getSequenceAt(i));
1411       features[i] = new SequenceFeature(null, null, null, start, end, "Jalview");
1412     }
1413
1414     if (ap.seqPanel.seqCanvas.getFeatureRenderer()
1415         .amendFeatures(seqs, features, true, ap))
1416     {
1417       ap.alignFrame.showSeqFeatures.setSelected(true);
1418       ap.av.setShowSequenceFeatures(true);
1419       ap.highlightSearchResults(null);
1420     }
1421   }
1422
1423   public void textColour_actionPerformed()
1424   {
1425     SequenceGroup sg = getGroup();
1426     if (sg != null)
1427     {
1428       new TextColourChooser().chooseColour(ap, sg);
1429     }
1430   }
1431
1432   public void colourByStructure(String pdbid)
1433   {
1434     Annotation [] anots = jalview.structure.StructureSelectionManager.getStructureSelectionManager()
1435         .colourSequenceFromStructure(sequence, pdbid);
1436
1437     AlignmentAnnotation an = new AlignmentAnnotation(
1438       "Structure", "Coloured by "+pdbid, anots);
1439
1440     ap.av.alignment.addAnnotation(an);
1441     an.createSequenceMapping(sequence, 0, true);
1442     //an.adjustForAlignment();
1443     ap.av.alignment.setAnnotationIndex(an,0);
1444
1445     ap.adjustAnnotationHeight();
1446
1447     sequence.addAlignmentAnnotation(an);
1448
1449     }
1450
1451   public void editSequence_actionPerformed(ActionEvent actionEvent)
1452   {
1453       SequenceGroup sg = ap.av.getSelectionGroup();
1454
1455       if(sg!=null)
1456       {
1457         if (sequence == null)
1458           sequence = (Sequence) sg.getSequenceAt(0);
1459
1460         EditNameDialog dialog = new EditNameDialog(
1461             sequence.getSequenceAsString(
1462                 sg.getStartRes(),
1463                 sg.getEndRes() + 1),
1464             null,
1465             "Edit Sequence ",
1466             null,
1467             "Edit Sequence");
1468
1469         if (dialog.accept)
1470         {
1471           EditCommand editCommand = new EditCommand(
1472               "Edit Sequences", EditCommand.REPLACE,
1473               dialog.getName().replace(' ', ap.av.getGapCharacter()),
1474               sg.getSequencesAsArray(ap.av.hiddenRepSequences),
1475               sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment
1476               );
1477
1478           ap.alignFrame.addHistoryItem(editCommand);
1479
1480           ap.av.firePropertyChange("alignment", null,
1481                                    ap.av.getAlignment().getSequences());
1482         }
1483       }
1484   }
1485
1486
1487 }