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!=null && sg.cs.conservationApplied())\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 \r
 343         if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
 344         {\r
 345           java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 346               getUserColourSchemes().keys();\r
 347 \r
 348           while (userColours.hasMoreElements())\r
 349           {\r
 350             JMenuItem item = new JMenuItem(userColours.\r
 351                 nextElement().toString());\r
 352             item.addActionListener(new ActionListener()\r
 353             {\r
 354               public void actionPerformed(ActionEvent evt)\r
 355               {\r
 356                 userDefinedColour_actionPerformed(evt);\r
 357               }\r
 358             });\r
 359             colourMenu.add(item);\r
 360           }\r
 361         }\r
 362 \r
 363 \r
 364         colourMenu.addSeparator();\r
 365         colourMenu.add(abovePIDColour);\r
 366         colourMenu.add(conservationMenuItem);\r
 367         noColourmenuItem.setText("None");\r
 368         noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 369             {\r
 370                 public void actionPerformed(ActionEvent e)\r
 371                 {\r
 372                     noColourmenuItem_actionPerformed(e);\r
 373                 }\r
 374             });\r
 375 \r
 376         clustalColour.setText("Clustalx colours");\r
 377         clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 378             {\r
 379                 public void actionPerformed(ActionEvent e)\r
 380                 {\r
 381                     clustalColour_actionPerformed(e);\r
 382                 }\r
 383             });\r
 384         zappoColour.setText("Zappo");\r
 385         zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 386             {\r
 387                 public void actionPerformed(ActionEvent e)\r
 388                 {\r
 389                     zappoColour_actionPerformed(e);\r
 390                 }\r
 391             });\r
 392         taylorColour.setText("Taylor");\r
 393         taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 394             {\r
 395                 public void actionPerformed(ActionEvent e)\r
 396                 {\r
 397                     taylorColour_actionPerformed(e);\r
 398                 }\r
 399             });\r
 400         hydrophobicityColour.setText("Hydrophobicity");\r
 401         hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 402             {\r
 403                 public void actionPerformed(ActionEvent e)\r
 404                 {\r
 405                     hydrophobicityColour_actionPerformed(e);\r
 406                 }\r
 407             });\r
 408         helixColour.setText("Helix propensity");\r
 409         helixColour.addActionListener(new java.awt.event.ActionListener()\r
 410             {\r
 411                 public void actionPerformed(ActionEvent e)\r
 412                 {\r
 413                     helixColour_actionPerformed(e);\r
 414                 }\r
 415             });\r
 416         strandColour.setText("Strand propensity");\r
 417         strandColour.addActionListener(new java.awt.event.ActionListener()\r
 418             {\r
 419                 public void actionPerformed(ActionEvent e)\r
 420                 {\r
 421                     strandColour_actionPerformed(e);\r
 422                 }\r
 423             });\r
 424         turnColour.setText("Turn propensity");\r
 425         turnColour.addActionListener(new java.awt.event.ActionListener()\r
 426             {\r
 427                 public void actionPerformed(ActionEvent e)\r
 428                 {\r
 429                     turnColour_actionPerformed(e);\r
 430                 }\r
 431             });\r
 432         buriedColour.setText("Buried Index");\r
 433         buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 434             {\r
 435                 public void actionPerformed(ActionEvent e)\r
 436                 {\r
 437                     buriedColour_actionPerformed(e);\r
 438                 }\r
 439             });\r
 440         abovePIDColour.setText("Above % Identity");\r
 441         abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
 442             {\r
 443                 public void actionPerformed(ActionEvent e)\r
 444                 {\r
 445                     abovePIDColour_actionPerformed(e);\r
 446                 }\r
 447             });\r
 448         userDefinedColour.setText("User Defined...");\r
 449         userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 450             {\r
 451                 public void actionPerformed(ActionEvent e)\r
 452                 {\r
 453                     userDefinedColour_actionPerformed(e);\r
 454                 }\r
 455             });\r
 456         PIDColour.setText("Percentage Identity");\r
 457         PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 458             {\r
 459                 public void actionPerformed(ActionEvent e)\r
 460                 {\r
 461                     PIDColour_actionPerformed(e);\r
 462                 }\r
 463             });\r
 464         BLOSUM62Colour.setText("BLOSUM62");\r
 465         BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 466             {\r
 467                 public void actionPerformed(ActionEvent e)\r
 468                 {\r
 469                     BLOSUM62Colour_actionPerformed(e);\r
 470                 }\r
 471             });\r
 472         conservationMenuItem.setText("Conservation");\r
 473         conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 474             {\r
 475                 public void actionPerformed(ActionEvent e)\r
 476                 {\r
 477                     conservationMenuItem_actionPerformed(e);\r
 478                 }\r
 479             });\r
 480     }\r
 481 \r
 482     /**\r
 483      * DOCUMENT ME!\r
 484      */\r
 485     void refresh()\r
 486     {\r
 487         SequenceGroup sg = getGroup();\r
 488         if(sg!=null)\r
 489         {\r
 490           SuperGroup superG = ap.av.alignment.getSuperGroup(sg);\r
 491 \r
 492           if (superG != null)\r
 493           {\r
 494             superG.setSuperGroupProperties(sg);\r
 495           }\r
 496         }\r
 497         ap.seqPanel.repaint();\r
 498     }\r
 499 \r
 500     /**\r
 501      * DOCUMENT ME!\r
 502      *\r
 503      * @param e DOCUMENT ME!\r
 504      */\r
 505     protected void clustalColour_actionPerformed(ActionEvent e)\r
 506     {\r
 507         SequenceGroup sg = getGroup();\r
 508         sg.cs = new ClustalxColourScheme(sg.sequences,\r
 509                 ap.av.alignment.getWidth());\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 zappoColour_actionPerformed(ActionEvent e)\r
 519     {\r
 520         getGroup().cs = new ZappoColourScheme();\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 taylorColour_actionPerformed(ActionEvent e)\r
 530     {\r
 531         getGroup().cs = new TaylorColourScheme();\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 hydrophobicityColour_actionPerformed(ActionEvent e)\r
 541     {\r
 542         getGroup().cs = new HydrophobicColourScheme();\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 helixColour_actionPerformed(ActionEvent e)\r
 552     {\r
 553         getGroup().cs = new HelixColourScheme();\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 strandColour_actionPerformed(ActionEvent e)\r
 563     {\r
 564         getGroup().cs = new StrandColourScheme();\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     protected void turnColour_actionPerformed(ActionEvent e)\r
 574     {\r
 575         getGroup().cs = new TurnColourScheme();\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 buriedColour_actionPerformed(ActionEvent e)\r
 585     {\r
 586         getGroup().cs = new BuriedColourScheme();\r
 587         refresh();\r
 588     }\r
 589 \r
 590     /**\r
 591      * DOCUMENT ME!\r
 592      *\r
 593      * @param e DOCUMENT ME!\r
 594      */\r
 595     public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
 596     {\r
 597         getGroup().cs = new NucleotideColourScheme();\r
 598         refresh();\r
 599     }\r
 600 \r
 601     /**\r
 602      * DOCUMENT ME!\r
 603      *\r
 604      * @param e DOCUMENT ME!\r
 605      */\r
 606     protected void abovePIDColour_actionPerformed(ActionEvent e)\r
 607     {\r
 608         SequenceGroup sg = getGroup();\r
 609 \r
 610         if (abovePIDColour.isSelected())\r
 611         {\r
 612             sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 613                     ap.av.alignment.getWidth()));\r
 614 \r
 615             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
 616                     getGroup().getName());\r
 617 \r
 618            sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
 619 \r
 620             SliderPanel.showPIDSlider();\r
 621         }\r
 622         else // remove PIDColouring\r
 623         {\r
 624             sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
 625         }\r
 626 \r
 627         refresh();\r
 628     }\r
 629 \r
 630     /**\r
 631      * DOCUMENT ME!\r
 632      *\r
 633      * @param e DOCUMENT ME!\r
 634      */\r
 635     protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 636     {\r
 637        SequenceGroup sg = getGroup();\r
 638 \r
 639        if (e.getActionCommand().equals("User Defined..."))\r
 640          new UserDefinedColours(ap, sg);\r
 641        else\r
 642        {\r
 643          UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
 644              getUserColourSchemes().get(e.getActionCommand());\r
 645 \r
 646          sg.cs = udc;\r
 647        }\r
 648      }\r
 649     /**\r
 650      * DOCUMENT ME!\r
 651      *\r
 652      * @param e DOCUMENT ME!\r
 653      */\r
 654     protected void PIDColour_actionPerformed(ActionEvent e)\r
 655     {\r
 656         SequenceGroup sg = getGroup();\r
 657         sg.cs = new PIDColourScheme();\r
 658         sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 659                 ap.av.alignment.getWidth()));\r
 660         refresh();\r
 661     }\r
 662 \r
 663     /**\r
 664      * DOCUMENT ME!\r
 665      *\r
 666      * @param e DOCUMENT ME!\r
 667      */\r
 668     protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 669     {\r
 670         SequenceGroup sg = getGroup();\r
 671 \r
 672         sg.cs = new Blosum62ColourScheme();\r
 673 \r
 674         sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 675                 ap.av.alignment.getWidth()));\r
 676 \r
 677         refresh();\r
 678     }\r
 679 \r
 680     /**\r
 681      * DOCUMENT ME!\r
 682      *\r
 683      * @param e DOCUMENT ME!\r
 684      */\r
 685     protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 686     {\r
 687         getGroup().cs = null;\r
 688         refresh();\r
 689     }\r
 690 \r
 691     /**\r
 692      * DOCUMENT ME!\r
 693      *\r
 694      * @param e DOCUMENT ME!\r
 695      */\r
 696     protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
 697     {\r
 698         SequenceGroup sg = getGroup();\r
 699 \r
 700         if (conservationMenuItem.isSelected())\r
 701         {\r
 702             Conservation c = new Conservation("Group",\r
 703                     ResidueProperties.propHash, 3, sg.sequences, 0,\r
 704                     ap.av.alignment.getWidth());\r
 705 \r
 706             c.calculate();\r
 707             c.verdict(false, ap.av.ConsPercGaps);\r
 708 \r
 709             sg.cs.setConservation(c);\r
 710 \r
 711             SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
 712             SliderPanel.showConservationSlider();\r
 713         }\r
 714         else // remove ConservationColouring\r
 715         {\r
 716             sg.cs.setConservation(null);\r
 717         }\r
 718 \r
 719         refresh();\r
 720     }\r
 721 \r
 722     /**\r
 723      * DOCUMENT ME!\r
 724      *\r
 725      * @param e DOCUMENT ME!\r
 726      */\r
 727     protected void groupName_actionPerformed(ActionEvent e)\r
 728     {\r
 729         SequenceGroup sg = getGroup();\r
 730         String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
 731                 "Enter new group name", "Edit group name",\r
 732                 JOptionPane.QUESTION_MESSAGE);\r
 733 \r
 734         if (reply == null)\r
 735         {\r
 736             return;\r
 737         }\r
 738 \r
 739         sg.setName(reply);\r
 740         groupName.setText(reply);\r
 741     }\r
 742 \r
 743     /**\r
 744      * DOCUMENT ME!\r
 745      *\r
 746      * @param e DOCUMENT ME!\r
 747      */\r
 748     protected void analyze_actionPerformed(ActionEvent e)\r
 749     {\r
 750         CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
 751         JInternalFrame frame = new JInternalFrame();\r
 752         frame.setContentPane(cap);\r
 753         Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
 754 \r
 755         SequenceGroup sg = getGroup();\r
 756         StringBuffer sb = new StringBuffer();\r
 757 \r
 758         for (int i = 0; i < sg.sequences.size(); i++)\r
 759         {\r
 760             Sequence tmp = (Sequence) sg.sequences.get(i);\r
 761             sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
 762             sb.append("\n");\r
 763         }\r
 764 \r
 765         sb.append("Something amazing will happen soon");\r
 766         cap.setText(sb.toString());\r
 767     }\r
 768 \r
 769     /**\r
 770      * DOCUMENT ME!\r
 771      *\r
 772      * @return DOCUMENT ME!\r
 773      */\r
 774     SequenceGroup getGroup()\r
 775     {\r
 776         SequenceGroup sg = ap.av.getSelectionGroup();\r
 777       // this method won't add a new group if it already exists\r
 778         if(sg!=null)\r
 779           ap.av.alignment.addGroup(sg);\r
 780 \r
 781         return sg;\r
 782     }\r
 783 \r
 784     /**\r
 785      * DOCUMENT ME!\r
 786      *\r
 787      * @param e DOCUMENT ME!\r
 788      */\r
 789     void sequenceName_actionPerformed(ActionEvent e)\r
 790     {\r
 791         String id = sequence.getName();\r
 792         String s = (String) JOptionPane.showInternalInputDialog(ap,\r
 793                 "Edit sequence name",\r
 794                 "Edit sequence name (" + sequence.getName() + ")",\r
 795                 JOptionPane.PLAIN_MESSAGE, null, null, id);\r
 796 \r
 797         if (s != null)\r
 798         {\r
 799             if (s.indexOf(" ") > -1)\r
 800             {\r
 801                 JOptionPane.showMessageDialog(ap,\r
 802                     "Spaces have been converted to \"_\"",\r
 803                     "No spaces allowed in Sequence Name",\r
 804                     JOptionPane.WARNING_MESSAGE);\r
 805             }\r
 806 \r
 807             s = s.replace(' ', '_');\r
 808             sequence.setName(s);\r
 809             ap.repaint();\r
 810         }\r
 811     }\r
 812 \r
 813     /**\r
 814      * DOCUMENT ME!\r
 815      *\r
 816      * @param e DOCUMENT ME!\r
 817      */\r
 818     void unGroupMenuItem_actionPerformed(ActionEvent e)\r
 819     {\r
 820         SequenceGroup sg = ap.av.getSelectionGroup();\r
 821         ap.av.alignment.deleteGroup(sg);\r
 822         ap.av.setSelectionGroup(null);\r
 823         refresh();\r
 824     }\r
 825 \r
 826     /**\r
 827      * DOCUMENT ME!\r
 828      *\r
 829      * @param e DOCUMENT ME!\r
 830      */\r
 831     void pdbMenuItem_actionPerformed(ActionEvent e)\r
 832     {\r
 833         if (sequence.getPDBId() == null)\r
 834         {\r
 835             return;\r
 836         }\r
 837 \r
 838         try\r
 839         {\r
 840             EBIFetchClient ebi = new EBIFetchClient();\r
 841             String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null,\r
 842                     null);\r
 843 \r
 844             PDBfile pdb = new PDBfile(result);\r
 845 \r
 846             rotCanvas rc = new rotCanvas(pdb, sequence, ap.av);\r
 847             JInternalFrame frame = new JInternalFrame();\r
 848             frame.setContentPane(rc);\r
 849             Desktop.addInternalFrame(frame,\r
 850                 sequence.getName() + " " + sequence.getPDBId(), 400, 400);\r
 851         }\r
 852         catch (Exception ex)\r
 853         {\r
 854             ex.printStackTrace();\r
 855         }\r
 856     }\r
 857 \r
 858     /**\r
 859      * DOCUMENT ME!\r
 860      *\r
 861      * @param e DOCUMENT ME!\r
 862      */\r
 863     protected void outline_actionPerformed(ActionEvent e)\r
 864     {\r
 865         SequenceGroup sg = getGroup();\r
 866         Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
 867                 Color.BLUE);\r
 868 \r
 869         if (col != null)\r
 870         {\r
 871             sg.setOutlineColour(col);\r
 872         }\r
 873 \r
 874         refresh();\r
 875     }\r
 876 \r
 877     /**\r
 878      * DOCUMENT ME!\r
 879      *\r
 880      * @param e DOCUMENT ME!\r
 881      */\r
 882     public void showBoxes_actionPerformed(ActionEvent e)\r
 883     {\r
 884         getGroup().setDisplayBoxes(showBoxes.isSelected());\r
 885         refresh();\r
 886     }\r
 887 \r
 888     /**\r
 889      * DOCUMENT ME!\r
 890      *\r
 891      * @param e DOCUMENT ME!\r
 892      */\r
 893     public void showText_actionPerformed(ActionEvent e)\r
 894     {\r
 895         getGroup().setDisplayText(showText.isSelected());\r
 896         refresh();\r
 897     }\r
 898 \r
 899     /**\r
 900      * DOCUMENT ME!\r
 901      *\r
 902      * @param e DOCUMENT ME!\r
 903      */\r
 904     public void showColourText_actionPerformed(ActionEvent e)\r
 905     {\r
 906         getGroup().setColourText(showColourText.isSelected());\r
 907         refresh();\r
 908     }\r
 909 \r
 910     public void showLink(String url)\r
 911     {\r
 912       try\r
 913       {\r
 914         jalview.util.BrowserLauncher.openURL(url);\r
 915       }\r
 916       catch (Exception ex)\r
 917       {\r
 918         JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 919             "Unixers: Couldn't find default web browser."\r
 920            +"\nAdd the full path to your browser in Preferences.",\r
 921            "Web browser not found", JOptionPane.WARNING_MESSAGE );\r
 922 \r
 923 \r
 924         ex.printStackTrace();\r
 925       }\r
 926     }\r
 927 }\r