src/jalview/gui/PopupMenu.java

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