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