src/jalview/gui/PopupMenu.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 package jalview.gui;\r
  20 \r
  21 import MCview.*;\r
  22 \r
  23 import jalview.analysis.*;\r
  24 \r
  25 import jalview.datamodel.*;\r
  26 \r
  27 \r
  28 import jalview.schemes.*;\r
  29 \r
  30 import java.awt.*;\r
  31 import java.awt.event.*;\r
  32 \r
  33 import javax.swing.*;\r
  34 \r
  35 \r
  36 /**\r
  37  * DOCUMENT ME!\r
  38  *\r
  39  * @author $author$\r
  40  * @version $Revision$\r
  41  */\r
  42 public class PopupMenu extends JPopupMenu\r
  43 {\r
  44     JMenu groupMenu = new JMenu();\r
  45     JMenuItem groupName = new JMenuItem();\r
  46     protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  47     protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  48     protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  49     protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
  50     protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  51     protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  52     protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  53     protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  54     protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();\r
  55     protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  56     protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  57     protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  58     JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  59     protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  60     AlignmentPanel ap;\r
  61     JMenu sequenceMenu = new JMenu();\r
  62     JMenuItem sequenceName = new JMenuItem();\r
  63     Sequence sequence;\r
  64     JMenuItem unGroupMenuItem = new JMenuItem();\r
  65     JMenuItem outline = new JMenuItem();\r
  66     JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();\r
  67     JMenu colourMenu = new JMenu();\r
  68     JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();\r
  69     JCheckBoxMenuItem showText = new JCheckBoxMenuItem();\r
  70     JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();\r
  71 \r
  72     /**\r
  73      * Creates a new PopupMenu object.\r
  74      *\r
  75      * @param ap DOCUMENT ME!\r
  76      * @param seq DOCUMENT ME!\r
  77      */\r
  78     public PopupMenu(final AlignmentPanel ap, Sequence seq)\r
  79     {\r
  80         ///////////////////////////////////////////////////////////\r
  81         // If this is activated from the sequence panel, the user may want to\r
  82         // edit or annotate a particular residue. Therefore display the residue menu\r
  83         //\r
  84         // If from the IDPanel, we must display the sequence menu\r
  85         //////////////////////////////////////////////////////////\r
  86         this.ap = ap;\r
  87         sequence = seq;\r
  88 \r
  89         ButtonGroup colours = new ButtonGroup();\r
  90         colours.add(noColourmenuItem);\r
  91         colours.add(clustalColour);\r
  92         colours.add(zappoColour);\r
  93         colours.add(taylorColour);\r
  94         colours.add(hydrophobicityColour);\r
  95         colours.add(helixColour);\r
  96         colours.add(strandColour);\r
  97         colours.add(turnColour);\r
  98         colours.add(buriedColour);\r
  99         colours.add(abovePIDColour);\r
 100         colours.add(userDefinedColour);\r
 101         colours.add(PIDColour);\r
 102         colours.add(BLOSUM62Colour);\r
 103 \r
 104         try\r
 105         {\r
 106             jbInit();\r
 107         }\r
 108         catch (Exception e)\r
 109         {\r
 110             e.printStackTrace();\r
 111         }\r
 112 \r
 113 \r
 114         if (seq != null)\r
 115         {\r
 116           JMenuItem menuItem;\r
 117           if( seq.getDatasetSequence().getPDBId() != null)\r
 118           {\r
 119             java.util.Enumeration e = seq.getDatasetSequence().getPDBId().\r
 120                 elements();\r
 121             while (e.hasMoreElements())\r
 122             {\r
 123               final PDBEntry pdb = (PDBEntry) e.nextElement();\r
 124 \r
 125               menuItem = new JMenuItem();\r
 126               menuItem.setText("View PDB entry: " + pdb.getId());\r
 127               menuItem.addActionListener(new java.awt.event.ActionListener()\r
 128               {\r
 129                 public void actionPerformed(ActionEvent e)\r
 130                 {\r
 131                   new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);\r
 132                 }\r
 133               });\r
 134               sequenceMenu.add(menuItem);\r
 135             }\r
 136           }\r
 137 \r
 138           menuItem = new JMenuItem("Hide Sequences");\r
 139           menuItem.addActionListener(new java.awt.event.ActionListener()\r
 140               {\r
 141                 public void actionPerformed(ActionEvent e)\r
 142                 {\r
 143                   hideSequences(false);\r
 144                 }\r
 145               });\r
 146           sequenceMenu.add(menuItem);\r
 147 \r
 148           if(ap.av.getSelectionGroup() !=null && ap.av.getSelectionGroup().getSize()>1)\r
 149           {\r
 150             menuItem = new JMenuItem("Represent Group with " + seq.getName());\r
 151             menuItem.addActionListener(new java.awt.event.ActionListener()\r
 152             {\r
 153               public void actionPerformed(ActionEvent e)\r
 154               {\r
 155                 hideSequences(true);\r
 156               }\r
 157             });\r
 158             sequenceMenu.add(menuItem);\r
 159           }\r
 160 \r
 161 \r
 162         }\r
 163 \r
 164 \r
 165 \r
 166         SequenceGroup sg = ap.av.getSelectionGroup();\r
 167 \r
 168         if (sg != null)\r
 169         {\r
 170             groupName.setText(sg.getName());\r
 171 \r
 172             if (sg.cs instanceof ZappoColourScheme)\r
 173             {\r
 174                 zappoColour.setSelected(true);\r
 175             }\r
 176             else if (sg.cs instanceof TaylorColourScheme)\r
 177             {\r
 178                 taylorColour.setSelected(true);\r
 179             }\r
 180             else if (sg.cs instanceof PIDColourScheme)\r
 181             {\r
 182                 PIDColour.setSelected(true);\r
 183             }\r
 184             else if (sg.cs instanceof Blosum62ColourScheme)\r
 185             {\r
 186                 BLOSUM62Colour.setSelected(true);\r
 187             }\r
 188             else if (sg.cs instanceof UserColourScheme)\r
 189             {\r
 190                 userDefinedColour.setSelected(true);\r
 191             }\r
 192             else if (sg.cs instanceof HydrophobicColourScheme)\r
 193             {\r
 194                 hydrophobicityColour.setSelected(true);\r
 195             }\r
 196             else if (sg.cs instanceof HelixColourScheme)\r
 197             {\r
 198                 helixColour.setSelected(true);\r
 199             }\r
 200             else if (sg.cs instanceof StrandColourScheme)\r
 201             {\r
 202                 strandColour.setSelected(true);\r
 203             }\r
 204             else if (sg.cs instanceof TurnColourScheme)\r
 205             {\r
 206                 turnColour.setSelected(true);\r
 207             }\r
 208             else if (sg.cs instanceof BuriedColourScheme)\r
 209             {\r
 210                 buriedColour.setSelected(true);\r
 211             }\r
 212             else if (sg.cs instanceof ClustalxColourScheme)\r
 213             {\r
 214                 clustalColour.setSelected(true);\r
 215             }\r
 216             else\r
 217             {\r
 218                 noColourmenuItem.setSelected(true);\r
 219             }\r
 220 \r
 221             if (sg.cs!=null && sg.cs.conservationApplied())\r
 222             {\r
 223                 conservationMenuItem.setSelected(true);\r
 224             }\r
 225 \r
 226             showText.setSelected(sg.getDisplayText());\r
 227             showColourText.setSelected(sg.getColourText());\r
 228             showBoxes.setSelected(sg.getDisplayBoxes());\r
 229         }\r
 230 \r
 231         if (!ap.av.alignment.getGroups().contains(sg))\r
 232         {\r
 233             unGroupMenuItem.setVisible(false);\r
 234         }\r
 235         else\r
 236         {\r
 237             groupMenu.insertSeparator(3);\r
 238         }\r
 239 \r
 240         if (seq == null)\r
 241         {\r
 242             sequenceMenu.setVisible(false);\r
 243         }\r
 244         else\r
 245         {\r
 246           java.util.Vector links = Preferences.sequenceURLLinks;\r
 247 \r
 248           JMenu linkMenu = new JMenu("Link");\r
 249           JMenuItem item;\r
 250           for(int i=0; i<links.size(); i++)\r
 251           {\r
 252             String link = links.elementAt(i).toString();\r
 253 \r
 254             item = new JMenuItem(link.substring(0, link.indexOf("|")));\r
 255             String id = sequence.getName();\r
 256             if(id.indexOf("|")>-1)\r
 257               id = id.substring(id.lastIndexOf("|")+1);\r
 258 \r
 259             final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))\r
 260                 + id +\r
 261                 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
 262 \r
 263 \r
 264             item.addActionListener(new java.awt.event.ActionListener()\r
 265             {\r
 266                 public void actionPerformed(ActionEvent e)\r
 267                 {\r
 268                     showLink(url);\r
 269                 }\r
 270             });\r
 271 \r
 272             linkMenu.add(item);\r
 273           }\r
 274           add(linkMenu);\r
 275         }\r
 276     }\r
 277 \r
 278 \r
 279     /**\r
 280      * DOCUMENT ME!\r
 281      *\r
 282      * @throws Exception DOCUMENT ME!\r
 283      */\r
 284     private void jbInit() throws Exception\r
 285     {\r
 286         groupMenu.setText("Group");\r
 287         groupMenu.setText("Define");\r
 288         groupName.setText("Name");\r
 289         groupName.addActionListener(new java.awt.event.ActionListener()\r
 290             {\r
 291                 public void actionPerformed(ActionEvent e)\r
 292                 {\r
 293                     groupName_actionPerformed(e);\r
 294                 }\r
 295             });\r
 296         sequenceMenu.setText("Sequence");\r
 297         sequenceName.setText("Edit Name/Desciption");\r
 298         sequenceName.addActionListener(new java.awt.event.ActionListener()\r
 299             {\r
 300                 public void actionPerformed(ActionEvent e)\r
 301                 {\r
 302                     sequenceName_actionPerformed(e);\r
 303                 }\r
 304             });\r
 305         PIDColour.setFocusPainted(false);\r
 306         unGroupMenuItem.setText("Remove Group");\r
 307         unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 308             {\r
 309                 public void actionPerformed(ActionEvent e)\r
 310                 {\r
 311                     unGroupMenuItem_actionPerformed(e);\r
 312                 }\r
 313             });\r
 314 \r
 315         outline.setText("Border colour");\r
 316         outline.addActionListener(new java.awt.event.ActionListener()\r
 317             {\r
 318                 public void actionPerformed(ActionEvent e)\r
 319                 {\r
 320                     outline_actionPerformed(e);\r
 321                 }\r
 322             });\r
 323         nucleotideMenuItem.setText("Nucleotide");\r
 324         nucleotideMenuItem.addActionListener(new ActionListener()\r
 325             {\r
 326                 public void actionPerformed(ActionEvent e)\r
 327                 {\r
 328                     nucleotideMenuItem_actionPerformed(e);\r
 329                 }\r
 330             });\r
 331         colourMenu.setText("Group Colour");\r
 332         showBoxes.setText("Boxes");\r
 333         showBoxes.setState(true);\r
 334         showBoxes.addActionListener(new ActionListener()\r
 335             {\r
 336                 public void actionPerformed(ActionEvent e)\r
 337                 {\r
 338                     showBoxes_actionPerformed(e);\r
 339                 }\r
 340             });\r
 341         showText.setText("Text");\r
 342         showText.setState(true);\r
 343         showText.addActionListener(new ActionListener()\r
 344             {\r
 345                 public void actionPerformed(ActionEvent e)\r
 346                 {\r
 347                     showText_actionPerformed(e);\r
 348                 }\r
 349             });\r
 350         showColourText.setText("Colour Text");\r
 351         showColourText.addActionListener(new ActionListener()\r
 352             {\r
 353                 public void actionPerformed(ActionEvent e)\r
 354                 {\r
 355                     showColourText_actionPerformed(e);\r
 356                 }\r
 357             });\r
 358         add(groupMenu);\r
 359         add(sequenceMenu);\r
 360         groupMenu.add(groupName);\r
 361         groupMenu.addSeparator();\r
 362         groupMenu.add(unGroupMenuItem);\r
 363         groupMenu.add(colourMenu);\r
 364         groupMenu.addSeparator();\r
 365         groupMenu.add(showBoxes);\r
 366         groupMenu.add(showText);\r
 367         groupMenu.add(showColourText);\r
 368         groupMenu.addSeparator();\r
 369         groupMenu.add(outline);\r
 370         sequenceMenu.add(sequenceName);\r
 371         colourMenu.add(noColourmenuItem);\r
 372         colourMenu.add(clustalColour);\r
 373         colourMenu.add(BLOSUM62Colour);\r
 374         colourMenu.add(PIDColour);\r
 375         colourMenu.add(zappoColour);\r
 376         colourMenu.add(taylorColour);\r
 377         colourMenu.add(hydrophobicityColour);\r
 378         colourMenu.add(helixColour);\r
 379         colourMenu.add(strandColour);\r
 380         colourMenu.add(turnColour);\r
 381         colourMenu.add(buriedColour);\r
 382         colourMenu.add(nucleotideMenuItem);\r
 383         colourMenu.add(userDefinedColour);\r
 384 \r
 385         if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
 386         {\r
 387           java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 388               getUserColourSchemes().keys();\r
 389 \r
 390           while (userColours.hasMoreElements())\r
 391           {\r
 392             JMenuItem item = new JMenuItem(userColours.\r
 393                 nextElement().toString());\r
 394             item.addActionListener(new ActionListener()\r
 395             {\r
 396               public void actionPerformed(ActionEvent evt)\r
 397               {\r
 398                 userDefinedColour_actionPerformed(evt);\r
 399               }\r
 400             });\r
 401             colourMenu.add(item);\r
 402           }\r
 403         }\r
 404 \r
 405 \r
 406         colourMenu.addSeparator();\r
 407         colourMenu.add(abovePIDColour);\r
 408         colourMenu.add(conservationMenuItem);\r
 409         noColourmenuItem.setText("None");\r
 410         noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 411             {\r
 412                 public void actionPerformed(ActionEvent e)\r
 413                 {\r
 414                     noColourmenuItem_actionPerformed(e);\r
 415                 }\r
 416             });\r
 417 \r
 418         clustalColour.setText("Clustalx colours");\r
 419         clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 420             {\r
 421                 public void actionPerformed(ActionEvent e)\r
 422                 {\r
 423                     clustalColour_actionPerformed(e);\r
 424                 }\r
 425             });\r
 426         zappoColour.setText("Zappo");\r
 427         zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 428             {\r
 429                 public void actionPerformed(ActionEvent e)\r
 430                 {\r
 431                     zappoColour_actionPerformed(e);\r
 432                 }\r
 433             });\r
 434         taylorColour.setText("Taylor");\r
 435         taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 436             {\r
 437                 public void actionPerformed(ActionEvent e)\r
 438                 {\r
 439                     taylorColour_actionPerformed(e);\r
 440                 }\r
 441             });\r
 442         hydrophobicityColour.setText("Hydrophobicity");\r
 443         hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 444             {\r
 445                 public void actionPerformed(ActionEvent e)\r
 446                 {\r
 447                     hydrophobicityColour_actionPerformed(e);\r
 448                 }\r
 449             });\r
 450         helixColour.setText("Helix propensity");\r
 451         helixColour.addActionListener(new java.awt.event.ActionListener()\r
 452             {\r
 453                 public void actionPerformed(ActionEvent e)\r
 454                 {\r
 455                     helixColour_actionPerformed(e);\r
 456                 }\r
 457             });\r
 458         strandColour.setText("Strand propensity");\r
 459         strandColour.addActionListener(new java.awt.event.ActionListener()\r
 460             {\r
 461                 public void actionPerformed(ActionEvent e)\r
 462                 {\r
 463                     strandColour_actionPerformed(e);\r
 464                 }\r
 465             });\r
 466         turnColour.setText("Turn propensity");\r
 467         turnColour.addActionListener(new java.awt.event.ActionListener()\r
 468             {\r
 469                 public void actionPerformed(ActionEvent e)\r
 470                 {\r
 471                     turnColour_actionPerformed(e);\r
 472                 }\r
 473             });\r
 474         buriedColour.setText("Buried Index");\r
 475         buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 476             {\r
 477                 public void actionPerformed(ActionEvent e)\r
 478                 {\r
 479                     buriedColour_actionPerformed(e);\r
 480                 }\r
 481             });\r
 482         abovePIDColour.setText("Above % Identity");\r
 483         abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
 484             {\r
 485                 public void actionPerformed(ActionEvent e)\r
 486                 {\r
 487                     abovePIDColour_actionPerformed(e);\r
 488                 }\r
 489             });\r
 490         userDefinedColour.setText("User Defined...");\r
 491         userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 492             {\r
 493                 public void actionPerformed(ActionEvent e)\r
 494                 {\r
 495                     userDefinedColour_actionPerformed(e);\r
 496                 }\r
 497             });\r
 498         PIDColour.setText("Percentage Identity");\r
 499         PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 500             {\r
 501                 public void actionPerformed(ActionEvent e)\r
 502                 {\r
 503                     PIDColour_actionPerformed(e);\r
 504                 }\r
 505             });\r
 506         BLOSUM62Colour.setText("BLOSUM62");\r
 507         BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 508             {\r
 509                 public void actionPerformed(ActionEvent e)\r
 510                 {\r
 511                     BLOSUM62Colour_actionPerformed(e);\r
 512                 }\r
 513             });\r
 514         conservationMenuItem.setText("Conservation");\r
 515         conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 516             {\r
 517                 public void actionPerformed(ActionEvent e)\r
 518                 {\r
 519                     conservationMenuItem_actionPerformed(e);\r
 520                 }\r
 521             });\r
 522     }\r
 523 \r
 524     /**\r
 525      * DOCUMENT ME!\r
 526      */\r
 527     void refresh()\r
 528     {\r
 529         if (ap.overviewPanel != null)\r
 530           ap.overviewPanel.updateOverviewImage();\r
 531 \r
 532         ap.seqPanel.repaint();\r
 533     }\r
 534 \r
 535     /**\r
 536      * DOCUMENT ME!\r
 537      *\r
 538      * @param e DOCUMENT ME!\r
 539      */\r
 540     protected void clustalColour_actionPerformed(ActionEvent e)\r
 541     {\r
 542         SequenceGroup sg = getGroup();\r
 543         sg.cs = new ClustalxColourScheme(sg.sequences,\r
 544                 ap.av.alignment.getWidth());\r
 545         refresh();\r
 546     }\r
 547 \r
 548     /**\r
 549      * DOCUMENT ME!\r
 550      *\r
 551      * @param e DOCUMENT ME!\r
 552      */\r
 553     protected void zappoColour_actionPerformed(ActionEvent e)\r
 554     {\r
 555         getGroup().cs = new ZappoColourScheme();\r
 556         refresh();\r
 557     }\r
 558 \r
 559     /**\r
 560      * DOCUMENT ME!\r
 561      *\r
 562      * @param e DOCUMENT ME!\r
 563      */\r
 564     protected void taylorColour_actionPerformed(ActionEvent e)\r
 565     {\r
 566         getGroup().cs = new TaylorColourScheme();\r
 567         refresh();\r
 568     }\r
 569 \r
 570     /**\r
 571      * DOCUMENT ME!\r
 572      *\r
 573      * @param e DOCUMENT ME!\r
 574      */\r
 575     protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 576     {\r
 577         getGroup().cs = new HydrophobicColourScheme();\r
 578         refresh();\r
 579     }\r
 580 \r
 581     /**\r
 582      * DOCUMENT ME!\r
 583      *\r
 584      * @param e DOCUMENT ME!\r
 585      */\r
 586     protected void helixColour_actionPerformed(ActionEvent e)\r
 587     {\r
 588         getGroup().cs = new HelixColourScheme();\r
 589         refresh();\r
 590     }\r
 591 \r
 592     /**\r
 593      * DOCUMENT ME!\r
 594      *\r
 595      * @param e DOCUMENT ME!\r
 596      */\r
 597     protected void strandColour_actionPerformed(ActionEvent e)\r
 598     {\r
 599         getGroup().cs = new StrandColourScheme();\r
 600         refresh();\r
 601     }\r
 602 \r
 603     /**\r
 604      * DOCUMENT ME!\r
 605      *\r
 606      * @param e DOCUMENT ME!\r
 607      */\r
 608     protected void turnColour_actionPerformed(ActionEvent e)\r
 609     {\r
 610         getGroup().cs = new TurnColourScheme();\r
 611         refresh();\r
 612     }\r
 613 \r
 614     /**\r
 615      * DOCUMENT ME!\r
 616      *\r
 617      * @param e DOCUMENT ME!\r
 618      */\r
 619     protected void buriedColour_actionPerformed(ActionEvent e)\r
 620     {\r
 621         getGroup().cs = new BuriedColourScheme();\r
 622         refresh();\r
 623     }\r
 624 \r
 625     /**\r
 626      * DOCUMENT ME!\r
 627      *\r
 628      * @param e DOCUMENT ME!\r
 629      */\r
 630     public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
 631     {\r
 632         getGroup().cs = new NucleotideColourScheme();\r
 633         refresh();\r
 634     }\r
 635 \r
 636     /**\r
 637      * DOCUMENT ME!\r
 638      *\r
 639      * @param e DOCUMENT ME!\r
 640      */\r
 641     protected void abovePIDColour_actionPerformed(ActionEvent e)\r
 642     {\r
 643         SequenceGroup sg = getGroup();\r
 644         if(sg.cs==null)\r
 645           return;\r
 646 \r
 647         if (abovePIDColour.isSelected())\r
 648         {\r
 649             sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 650                     ap.av.alignment.getWidth()));\r
 651 \r
 652             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
 653                     getGroup().getName());\r
 654 \r
 655            sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
 656 \r
 657             SliderPanel.showPIDSlider();\r
 658         }\r
 659         else // remove PIDColouring\r
 660         {\r
 661             sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
 662         }\r
 663 \r
 664         refresh();\r
 665     }\r
 666 \r
 667     /**\r
 668      * DOCUMENT ME!\r
 669      *\r
 670      * @param e DOCUMENT ME!\r
 671      */\r
 672     protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 673     {\r
 674        SequenceGroup sg = getGroup();\r
 675 \r
 676        if (e.getActionCommand().equals("User Defined..."))\r
 677          new UserDefinedColours(ap, sg);\r
 678        else\r
 679        {\r
 680          UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
 681              getUserColourSchemes().get(e.getActionCommand());\r
 682 \r
 683          sg.cs = udc;\r
 684        }\r
 685      }\r
 686     /**\r
 687      * DOCUMENT ME!\r
 688      *\r
 689      * @param e DOCUMENT ME!\r
 690      */\r
 691     protected void PIDColour_actionPerformed(ActionEvent e)\r
 692     {\r
 693         SequenceGroup sg = getGroup();\r
 694         sg.cs = new PIDColourScheme();\r
 695         sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 696                 ap.av.alignment.getWidth()));\r
 697         refresh();\r
 698     }\r
 699 \r
 700     /**\r
 701      * DOCUMENT ME!\r
 702      *\r
 703      * @param e DOCUMENT ME!\r
 704      */\r
 705     protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 706     {\r
 707         SequenceGroup sg = getGroup();\r
 708 \r
 709         sg.cs = new Blosum62ColourScheme();\r
 710 \r
 711         sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 712                 ap.av.alignment.getWidth()));\r
 713 \r
 714         refresh();\r
 715     }\r
 716 \r
 717     /**\r
 718      * DOCUMENT ME!\r
 719      *\r
 720      * @param e DOCUMENT ME!\r
 721      */\r
 722     protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 723     {\r
 724         getGroup().cs = null;\r
 725         refresh();\r
 726     }\r
 727 \r
 728     /**\r
 729      * DOCUMENT ME!\r
 730      *\r
 731      * @param e DOCUMENT ME!\r
 732      */\r
 733     protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
 734     {\r
 735         SequenceGroup sg = getGroup();\r
 736         if(sg.cs==null)\r
 737           return;\r
 738 \r
 739         if (conservationMenuItem.isSelected())\r
 740         {\r
 741             Conservation c = new Conservation("Group",\r
 742                     ResidueProperties.propHash, 3, sg.sequences, 0,\r
 743                     ap.av.alignment.getWidth());\r
 744 \r
 745             c.calculate();\r
 746             c.verdict(false, ap.av.ConsPercGaps);\r
 747 \r
 748             sg.cs.setConservation(c);\r
 749 \r
 750             SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
 751             SliderPanel.showConservationSlider();\r
 752         }\r
 753         else // remove ConservationColouring\r
 754         {\r
 755             sg.cs.setConservation(null);\r
 756         }\r
 757 \r
 758         refresh();\r
 759     }\r
 760 \r
 761     /**\r
 762      * DOCUMENT ME!\r
 763      *\r
 764      * @param e DOCUMENT ME!\r
 765      */\r
 766     protected void groupName_actionPerformed(ActionEvent e)\r
 767     {\r
 768         SequenceGroup sg = getGroup();\r
 769         String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
 770                 "Enter new group name", "Edit group name",\r
 771                 JOptionPane.QUESTION_MESSAGE);\r
 772 \r
 773         if (reply == null)\r
 774         {\r
 775             return;\r
 776         }\r
 777 \r
 778         sg.setName(reply);\r
 779         groupName.setText(reply);\r
 780     }\r
 781 \r
 782     /**\r
 783      * DOCUMENT ME!\r
 784      *\r
 785      * @param e DOCUMENT ME!\r
 786      */\r
 787     protected void analyze_actionPerformed(ActionEvent e)\r
 788     {\r
 789         CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
 790         JInternalFrame frame = new JInternalFrame();\r
 791         frame.setContentPane(cap);\r
 792         Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
 793 \r
 794         SequenceGroup sg = getGroup();\r
 795         StringBuffer sb = new StringBuffer();\r
 796 \r
 797         for (int i = 0; i < sg.sequences.size(); i++)\r
 798         {\r
 799             Sequence tmp = (Sequence) sg.sequences.get(i);\r
 800             sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
 801             sb.append("\n");\r
 802         }\r
 803 \r
 804         sb.append("Something amazing will happen soon");\r
 805         cap.setText(sb.toString());\r
 806     }\r
 807 \r
 808     /**\r
 809      * DOCUMENT ME!\r
 810      *\r
 811      * @return DOCUMENT ME!\r
 812      */\r
 813     SequenceGroup getGroup()\r
 814     {\r
 815         SequenceGroup sg = ap.av.getSelectionGroup();\r
 816       // this method won't add a new group if it already exists\r
 817         if(sg!=null)\r
 818           ap.av.alignment.addGroup(sg);\r
 819 \r
 820         return sg;\r
 821     }\r
 822 \r
 823     /**\r
 824      * DOCUMENT ME!\r
 825      *\r
 826      * @param e DOCUMENT ME!\r
 827      */\r
 828     void sequenceName_actionPerformed(ActionEvent e)\r
 829     {\r
 830       JLabel idlabel = new JLabel(  "       Sequence Name ");\r
 831       JLabel desclabel = new JLabel("Sequence Description ");\r
 832       idlabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
 833       desclabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
 834       JTextField id = new JTextField(sequence.getName(), 40);\r
 835       JTextField description = new JTextField(sequence.getDescription(), 40);\r
 836       JPanel panel = new JPanel(new BorderLayout());\r
 837       JPanel panel2 = new JPanel(new BorderLayout());\r
 838       panel2.add(idlabel, BorderLayout.WEST);\r
 839       panel2.add(id, BorderLayout.CENTER);\r
 840       panel.add(panel2, BorderLayout.NORTH);\r
 841       panel2 = new JPanel(new BorderLayout());\r
 842       panel2.add(desclabel, BorderLayout.WEST);\r
 843       panel2.add(description, BorderLayout.CENTER);\r
 844       panel.add(panel2, BorderLayout.SOUTH);\r
 845 \r
 846 \r
 847        int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
 848           panel, "Edit Sequence Name/Description",\r
 849           JOptionPane.OK_CANCEL_OPTION );\r
 850 \r
 851 \r
 852         if (reply != JOptionPane.OK_OPTION )\r
 853         {\r
 854             return;\r
 855         }\r
 856 \r
 857         String s = id.getText();\r
 858 \r
 859         if (s != null)\r
 860         {\r
 861             if (s.indexOf(" ") > -1)\r
 862             {\r
 863                 JOptionPane.showMessageDialog(ap,\r
 864                     "Spaces have been converted to \"_\"",\r
 865                     "No spaces allowed in Sequence Name",\r
 866                     JOptionPane.WARNING_MESSAGE);\r
 867             }\r
 868 \r
 869             s = s.replace(' ', '_');\r
 870             sequence.getDatasetSequence().setName(s);\r
 871             sequence.setName(s);\r
 872             ap.repaint();\r
 873         }\r
 874 \r
 875         sequence.getDatasetSequence().setDescription(description.getText());\r
 876         sequence.setDescription(description.getText());\r
 877     }\r
 878 \r
 879     /**\r
 880      * DOCUMENT ME!\r
 881      *\r
 882      * @param e DOCUMENT ME!\r
 883      */\r
 884     void unGroupMenuItem_actionPerformed(ActionEvent e)\r
 885     {\r
 886         SequenceGroup sg = ap.av.getSelectionGroup();\r
 887         ap.av.alignment.deleteGroup(sg);\r
 888         ap.av.setSelectionGroup(null);\r
 889         refresh();\r
 890     }\r
 891 \r
 892 \r
 893     /**\r
 894      * DOCUMENT ME!\r
 895      *\r
 896      * @param e DOCUMENT ME!\r
 897      */\r
 898     protected void outline_actionPerformed(ActionEvent e)\r
 899     {\r
 900         SequenceGroup sg = getGroup();\r
 901         Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
 902                 Color.BLUE);\r
 903 \r
 904         if (col != null)\r
 905         {\r
 906             sg.setOutlineColour(col);\r
 907         }\r
 908 \r
 909         refresh();\r
 910     }\r
 911 \r
 912     /**\r
 913      * DOCUMENT ME!\r
 914      *\r
 915      * @param e DOCUMENT ME!\r
 916      */\r
 917     public void showBoxes_actionPerformed(ActionEvent e)\r
 918     {\r
 919         getGroup().setDisplayBoxes(showBoxes.isSelected());\r
 920         refresh();\r
 921     }\r
 922 \r
 923     /**\r
 924      * DOCUMENT ME!\r
 925      *\r
 926      * @param e DOCUMENT ME!\r
 927      */\r
 928     public void showText_actionPerformed(ActionEvent e)\r
 929     {\r
 930         getGroup().setDisplayText(showText.isSelected());\r
 931         refresh();\r
 932     }\r
 933 \r
 934     /**\r
 935      * DOCUMENT ME!\r
 936      *\r
 937      * @param e DOCUMENT ME!\r
 938      */\r
 939     public void showColourText_actionPerformed(ActionEvent e)\r
 940     {\r
 941         getGroup().setColourText(showColourText.isSelected());\r
 942         refresh();\r
 943     }\r
 944 \r
 945     public void showLink(String url)\r
 946     {\r
 947       try\r
 948       {\r
 949         jalview.util.BrowserLauncher.openURL(url);\r
 950       }\r
 951       catch (Exception ex)\r
 952       {\r
 953         JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 954             "Unixers: Couldn't find default web browser."\r
 955            +"\nAdd the full path to your browser in Preferences.",\r
 956            "Web browser not found", JOptionPane.WARNING_MESSAGE );\r
 957 \r
 958 \r
 959         ex.printStackTrace();\r
 960       }\r
 961     }\r
 962 \r
 963     void hideSequences(boolean representGroup)\r
 964     {\r
 965       SequenceGroup sg = ap.av.getSelectionGroup();\r
 966       if(sg==null || sg.getSize()<1)\r
 967       {\r
 968         ap.av.hideSequence(sequence);\r
 969         return;\r
 970       }\r
 971 \r
 972         int index = 0;\r
 973         while(index < sg.sequences.size())\r
 974         {\r
 975           if(representGroup && sg.getSequenceAt(index)!=sequence)\r
 976           {\r
 977             sequence.addHiddenSequence(sg.getSequenceAt(index));\r
 978             ap.av.hideSequence(sg.getSequenceAt(index));\r
 979           }\r
 980           else if(!representGroup)\r
 981           {\r
 982             ap.av.hideSequence(sg.getSequenceAt(index));\r
 983           }\r
 984           index ++;\r
 985         }\r
 986 \r
 987         ap.av.setSelectionGroup(null);\r
 988         refresh();\r
 989     }\r
 990 \r
 991 }\r