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