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 = new PDBEntry();\r
 121             pdb.setId("pdb");\r
 122 \r
 123 \r
 124               //  (PDBEntry)e.nextElement();\r
 125             JMenuItem pdbMenuItem = new JMenuItem();\r
 126             pdbMenuItem.setText("View PDB entry: "+pdb.getId());\r
 127             pdbMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 128             {\r
 129                 public void actionPerformed(ActionEvent e)\r
 130                 {\r
 131                   new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);\r
 132                 }\r
 133             });\r
 134             sequenceMenu.add(pdbMenuItem);\r
 135           }\r
 136 \r
 137         }\r
 138 \r
 139         SequenceGroup sg = ap.av.getSelectionGroup();\r
 140 \r
 141         if (sg != null)\r
 142         {\r
 143             groupName.setText(sg.getName());\r
 144 \r
 145             if (sg.cs instanceof ZappoColourScheme)\r
 146             {\r
 147                 zappoColour.setSelected(true);\r
 148             }\r
 149             else if (sg.cs instanceof TaylorColourScheme)\r
 150             {\r
 151                 taylorColour.setSelected(true);\r
 152             }\r
 153             else if (sg.cs instanceof PIDColourScheme)\r
 154             {\r
 155                 PIDColour.setSelected(true);\r
 156             }\r
 157             else if (sg.cs instanceof Blosum62ColourScheme)\r
 158             {\r
 159                 BLOSUM62Colour.setSelected(true);\r
 160             }\r
 161             else if (sg.cs instanceof UserColourScheme)\r
 162             {\r
 163                 userDefinedColour.setSelected(true);\r
 164             }\r
 165             else if (sg.cs instanceof HydrophobicColourScheme)\r
 166             {\r
 167                 hydrophobicityColour.setSelected(true);\r
 168             }\r
 169             else if (sg.cs instanceof HelixColourScheme)\r
 170             {\r
 171                 helixColour.setSelected(true);\r
 172             }\r
 173             else if (sg.cs instanceof StrandColourScheme)\r
 174             {\r
 175                 strandColour.setSelected(true);\r
 176             }\r
 177             else if (sg.cs instanceof TurnColourScheme)\r
 178             {\r
 179                 turnColour.setSelected(true);\r
 180             }\r
 181             else if (sg.cs instanceof BuriedColourScheme)\r
 182             {\r
 183                 buriedColour.setSelected(true);\r
 184             }\r
 185             else if (sg.cs instanceof ClustalxColourScheme)\r
 186             {\r
 187                 clustalColour.setSelected(true);\r
 188             }\r
 189             else\r
 190             {\r
 191                 noColourmenuItem.setSelected(true);\r
 192             }\r
 193 \r
 194             if (sg.cs!=null && sg.cs.conservationApplied())\r
 195             {\r
 196                 conservationMenuItem.setSelected(true);\r
 197             }\r
 198 \r
 199             showText.setSelected(sg.getDisplayText());\r
 200             showColourText.setSelected(sg.getColourText());\r
 201             showBoxes.setSelected(sg.getDisplayBoxes());\r
 202         }\r
 203 \r
 204         if (!ap.av.alignment.getGroups().contains(sg))\r
 205         {\r
 206             unGroupMenuItem.setVisible(false);\r
 207         }\r
 208         else\r
 209         {\r
 210             groupMenu.insertSeparator(3);\r
 211         }\r
 212 \r
 213         if (seq == null)\r
 214         {\r
 215             sequenceMenu.setVisible(false);\r
 216         }\r
 217         else\r
 218         {\r
 219           java.util.Vector links = Preferences.sequenceURLLinks;\r
 220 \r
 221           JMenu linkMenu = new JMenu("Link");\r
 222           JMenuItem item;\r
 223           for(int i=0; i<links.size(); i++)\r
 224           {\r
 225             String link = links.elementAt(i).toString();\r
 226 \r
 227             item = new JMenuItem(link.substring(0, link.indexOf("|")));\r
 228 \r
 229             final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))\r
 230                 + sequence.getName() +\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");\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         SequenceGroup sg = getGroup();\r
 499         if(sg!=null)\r
 500         {\r
 501           SuperGroup superG = ap.av.alignment.getSuperGroup(sg);\r
 502 \r
 503           if (superG != null)\r
 504           {\r
 505             superG.setSuperGroupProperties(sg);\r
 506           }\r
 507         }\r
 508         if (ap.overviewPanel != null)\r
 509           ap.overviewPanel.updateOverviewImage();\r
 510 \r
 511         ap.seqPanel.repaint();\r
 512     }\r
 513 \r
 514     /**\r
 515      * DOCUMENT ME!\r
 516      *\r
 517      * @param e DOCUMENT ME!\r
 518      */\r
 519     protected void clustalColour_actionPerformed(ActionEvent e)\r
 520     {\r
 521         SequenceGroup sg = getGroup();\r
 522         sg.cs = new ClustalxColourScheme(sg.sequences,\r
 523                 ap.av.alignment.getWidth());\r
 524         refresh();\r
 525     }\r
 526 \r
 527     /**\r
 528      * DOCUMENT ME!\r
 529      *\r
 530      * @param e DOCUMENT ME!\r
 531      */\r
 532     protected void zappoColour_actionPerformed(ActionEvent e)\r
 533     {\r
 534         getGroup().cs = new ZappoColourScheme();\r
 535         refresh();\r
 536     }\r
 537 \r
 538     /**\r
 539      * DOCUMENT ME!\r
 540      *\r
 541      * @param e DOCUMENT ME!\r
 542      */\r
 543     protected void taylorColour_actionPerformed(ActionEvent e)\r
 544     {\r
 545         getGroup().cs = new TaylorColourScheme();\r
 546         refresh();\r
 547     }\r
 548 \r
 549     /**\r
 550      * DOCUMENT ME!\r
 551      *\r
 552      * @param e DOCUMENT ME!\r
 553      */\r
 554     protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 555     {\r
 556         getGroup().cs = new HydrophobicColourScheme();\r
 557         refresh();\r
 558     }\r
 559 \r
 560     /**\r
 561      * DOCUMENT ME!\r
 562      *\r
 563      * @param e DOCUMENT ME!\r
 564      */\r
 565     protected void helixColour_actionPerformed(ActionEvent e)\r
 566     {\r
 567         getGroup().cs = new HelixColourScheme();\r
 568         refresh();\r
 569     }\r
 570 \r
 571     /**\r
 572      * DOCUMENT ME!\r
 573      *\r
 574      * @param e DOCUMENT ME!\r
 575      */\r
 576     protected void strandColour_actionPerformed(ActionEvent e)\r
 577     {\r
 578         getGroup().cs = new StrandColourScheme();\r
 579         refresh();\r
 580     }\r
 581 \r
 582     /**\r
 583      * DOCUMENT ME!\r
 584      *\r
 585      * @param e DOCUMENT ME!\r
 586      */\r
 587     protected void turnColour_actionPerformed(ActionEvent e)\r
 588     {\r
 589         getGroup().cs = new TurnColourScheme();\r
 590         refresh();\r
 591     }\r
 592 \r
 593     /**\r
 594      * DOCUMENT ME!\r
 595      *\r
 596      * @param e DOCUMENT ME!\r
 597      */\r
 598     protected void buriedColour_actionPerformed(ActionEvent e)\r
 599     {\r
 600         getGroup().cs = new BuriedColourScheme();\r
 601         refresh();\r
 602     }\r
 603 \r
 604     /**\r
 605      * DOCUMENT ME!\r
 606      *\r
 607      * @param e DOCUMENT ME!\r
 608      */\r
 609     public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
 610     {\r
 611         getGroup().cs = new NucleotideColourScheme();\r
 612         refresh();\r
 613     }\r
 614 \r
 615     /**\r
 616      * DOCUMENT ME!\r
 617      *\r
 618      * @param e DOCUMENT ME!\r
 619      */\r
 620     protected void abovePIDColour_actionPerformed(ActionEvent e)\r
 621     {\r
 622         SequenceGroup sg = getGroup();\r
 623         if(sg.cs==null)\r
 624           return;\r
 625 \r
 626         if (abovePIDColour.isSelected())\r
 627         {\r
 628             sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 629                     ap.av.alignment.getWidth()));\r
 630 \r
 631             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
 632                     getGroup().getName());\r
 633 \r
 634            sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
 635 \r
 636             SliderPanel.showPIDSlider();\r
 637         }\r
 638         else // remove PIDColouring\r
 639         {\r
 640             sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
 641         }\r
 642 \r
 643         refresh();\r
 644     }\r
 645 \r
 646     /**\r
 647      * DOCUMENT ME!\r
 648      *\r
 649      * @param e DOCUMENT ME!\r
 650      */\r
 651     protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 652     {\r
 653        SequenceGroup sg = getGroup();\r
 654 \r
 655        if (e.getActionCommand().equals("User Defined..."))\r
 656          new UserDefinedColours(ap, sg);\r
 657        else\r
 658        {\r
 659          UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
 660              getUserColourSchemes().get(e.getActionCommand());\r
 661 \r
 662          sg.cs = udc;\r
 663        }\r
 664      }\r
 665     /**\r
 666      * DOCUMENT ME!\r
 667      *\r
 668      * @param e DOCUMENT ME!\r
 669      */\r
 670     protected void PIDColour_actionPerformed(ActionEvent e)\r
 671     {\r
 672         SequenceGroup sg = getGroup();\r
 673         sg.cs = new PIDColourScheme();\r
 674         sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 675                 ap.av.alignment.getWidth()));\r
 676         refresh();\r
 677     }\r
 678 \r
 679     /**\r
 680      * DOCUMENT ME!\r
 681      *\r
 682      * @param e DOCUMENT ME!\r
 683      */\r
 684     protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 685     {\r
 686         SequenceGroup sg = getGroup();\r
 687 \r
 688         sg.cs = new Blosum62ColourScheme();\r
 689 \r
 690         sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 691                 ap.av.alignment.getWidth()));\r
 692 \r
 693         refresh();\r
 694     }\r
 695 \r
 696     /**\r
 697      * DOCUMENT ME!\r
 698      *\r
 699      * @param e DOCUMENT ME!\r
 700      */\r
 701     protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 702     {\r
 703         getGroup().cs = null;\r
 704         refresh();\r
 705     }\r
 706 \r
 707     /**\r
 708      * DOCUMENT ME!\r
 709      *\r
 710      * @param e DOCUMENT ME!\r
 711      */\r
 712     protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
 713     {\r
 714         SequenceGroup sg = getGroup();\r
 715         if(sg.cs==null)\r
 716           return;\r
 717 \r
 718         if (conservationMenuItem.isSelected())\r
 719         {\r
 720             Conservation c = new Conservation("Group",\r
 721                     ResidueProperties.propHash, 3, sg.sequences, 0,\r
 722                     ap.av.alignment.getWidth());\r
 723 \r
 724             c.calculate();\r
 725             c.verdict(false, ap.av.ConsPercGaps);\r
 726 \r
 727             sg.cs.setConservation(c);\r
 728 \r
 729             SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
 730             SliderPanel.showConservationSlider();\r
 731         }\r
 732         else // remove ConservationColouring\r
 733         {\r
 734             sg.cs.setConservation(null);\r
 735         }\r
 736 \r
 737         refresh();\r
 738     }\r
 739 \r
 740     /**\r
 741      * DOCUMENT ME!\r
 742      *\r
 743      * @param e DOCUMENT ME!\r
 744      */\r
 745     protected void groupName_actionPerformed(ActionEvent e)\r
 746     {\r
 747         SequenceGroup sg = getGroup();\r
 748         String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
 749                 "Enter new group name", "Edit group name",\r
 750                 JOptionPane.QUESTION_MESSAGE);\r
 751 \r
 752         if (reply == null)\r
 753         {\r
 754             return;\r
 755         }\r
 756 \r
 757         sg.setName(reply);\r
 758         groupName.setText(reply);\r
 759     }\r
 760 \r
 761     /**\r
 762      * DOCUMENT ME!\r
 763      *\r
 764      * @param e DOCUMENT ME!\r
 765      */\r
 766     protected void analyze_actionPerformed(ActionEvent e)\r
 767     {\r
 768         CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
 769         JInternalFrame frame = new JInternalFrame();\r
 770         frame.setContentPane(cap);\r
 771         Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
 772 \r
 773         SequenceGroup sg = getGroup();\r
 774         StringBuffer sb = new StringBuffer();\r
 775 \r
 776         for (int i = 0; i < sg.sequences.size(); i++)\r
 777         {\r
 778             Sequence tmp = (Sequence) sg.sequences.get(i);\r
 779             sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
 780             sb.append("\n");\r
 781         }\r
 782 \r
 783         sb.append("Something amazing will happen soon");\r
 784         cap.setText(sb.toString());\r
 785     }\r
 786 \r
 787     /**\r
 788      * DOCUMENT ME!\r
 789      *\r
 790      * @return DOCUMENT ME!\r
 791      */\r
 792     SequenceGroup getGroup()\r
 793     {\r
 794         SequenceGroup sg = ap.av.getSelectionGroup();\r
 795       // this method won't add a new group if it already exists\r
 796         if(sg!=null)\r
 797           ap.av.alignment.addGroup(sg);\r
 798 \r
 799         return sg;\r
 800     }\r
 801 \r
 802     /**\r
 803      * DOCUMENT ME!\r
 804      *\r
 805      * @param e DOCUMENT ME!\r
 806      */\r
 807     void sequenceName_actionPerformed(ActionEvent e)\r
 808     {\r
 809         String id = sequence.getName();\r
 810         String s = (String) JOptionPane.showInternalInputDialog(ap,\r
 811                 "Edit sequence name",\r
 812                 "Edit sequence name (" + sequence.getName() + ")",\r
 813                 JOptionPane.PLAIN_MESSAGE, null, null, id);\r
 814 \r
 815         if (s != null)\r
 816         {\r
 817             if (s.indexOf(" ") > -1)\r
 818             {\r
 819                 JOptionPane.showMessageDialog(ap,\r
 820                     "Spaces have been converted to \"_\"",\r
 821                     "No spaces allowed in Sequence Name",\r
 822                     JOptionPane.WARNING_MESSAGE);\r
 823             }\r
 824 \r
 825             s = s.replace(' ', '_');\r
 826             sequence.setName(s);\r
 827             ap.repaint();\r
 828         }\r
 829     }\r
 830 \r
 831     /**\r
 832      * DOCUMENT ME!\r
 833      *\r
 834      * @param e DOCUMENT ME!\r
 835      */\r
 836     void unGroupMenuItem_actionPerformed(ActionEvent e)\r
 837     {\r
 838         SequenceGroup sg = ap.av.getSelectionGroup();\r
 839         ap.av.alignment.deleteGroup(sg);\r
 840         ap.av.setSelectionGroup(null);\r
 841         refresh();\r
 842     }\r
 843 \r
 844 \r
 845     /**\r
 846      * DOCUMENT ME!\r
 847      *\r
 848      * @param e DOCUMENT ME!\r
 849      */\r
 850     protected void outline_actionPerformed(ActionEvent e)\r
 851     {\r
 852         SequenceGroup sg = getGroup();\r
 853         Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
 854                 Color.BLUE);\r
 855 \r
 856         if (col != null)\r
 857         {\r
 858             sg.setOutlineColour(col);\r
 859         }\r
 860 \r
 861         refresh();\r
 862     }\r
 863 \r
 864     /**\r
 865      * DOCUMENT ME!\r
 866      *\r
 867      * @param e DOCUMENT ME!\r
 868      */\r
 869     public void showBoxes_actionPerformed(ActionEvent e)\r
 870     {\r
 871         getGroup().setDisplayBoxes(showBoxes.isSelected());\r
 872         refresh();\r
 873     }\r
 874 \r
 875     /**\r
 876      * DOCUMENT ME!\r
 877      *\r
 878      * @param e DOCUMENT ME!\r
 879      */\r
 880     public void showText_actionPerformed(ActionEvent e)\r
 881     {\r
 882         getGroup().setDisplayText(showText.isSelected());\r
 883         refresh();\r
 884     }\r
 885 \r
 886     /**\r
 887      * DOCUMENT ME!\r
 888      *\r
 889      * @param e DOCUMENT ME!\r
 890      */\r
 891     public void showColourText_actionPerformed(ActionEvent e)\r
 892     {\r
 893         getGroup().setColourText(showColourText.isSelected());\r
 894         refresh();\r
 895     }\r
 896 \r
 897     public void showLink(String url)\r
 898     {\r
 899       try\r
 900       {\r
 901         jalview.util.BrowserLauncher.openURL(url);\r
 902       }\r
 903       catch (Exception ex)\r
 904       {\r
 905         JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 906             "Unixers: Couldn't find default web browser."\r
 907            +"\nAdd the full path to your browser in Preferences.",\r
 908            "Web browser not found", JOptionPane.WARNING_MESSAGE );\r
 909 \r
 910 \r
 911         ex.printStackTrace();\r
 912       }\r
 913     }\r
 914 }\r