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   JMenu editMenu = new JMenu();\r
  72   JMenuItem cut = new JMenuItem();\r
  73   JMenuItem copy = new JMenuItem();\r
  74   JMenuItem upperCase = new JMenuItem();\r
  75   JMenuItem lowerCase = new JMenuItem();\r
  76 \r
  77   /**\r
  78      * Creates a new PopupMenu object.\r
  79      *\r
  80      * @param ap DOCUMENT ME!\r
  81      * @param seq DOCUMENT ME!\r
  82      */\r
  83     public PopupMenu(final AlignmentPanel ap, Sequence seq)\r
  84     {\r
  85         ///////////////////////////////////////////////////////////\r
  86         // If this is activated from the sequence panel, the user may want to\r
  87         // edit or annotate a particular residue. Therefore display the residue menu\r
  88         //\r
  89         // If from the IDPanel, we must display the sequence menu\r
  90         //////////////////////////////////////////////////////////\r
  91         this.ap = ap;\r
  92         sequence = seq;\r
  93 \r
  94         ButtonGroup colours = new ButtonGroup();\r
  95         colours.add(noColourmenuItem);\r
  96         colours.add(clustalColour);\r
  97         colours.add(zappoColour);\r
  98         colours.add(taylorColour);\r
  99         colours.add(hydrophobicityColour);\r
 100         colours.add(helixColour);\r
 101         colours.add(strandColour);\r
 102         colours.add(turnColour);\r
 103         colours.add(buriedColour);\r
 104         colours.add(abovePIDColour);\r
 105         colours.add(userDefinedColour);\r
 106         colours.add(PIDColour);\r
 107         colours.add(BLOSUM62Colour);\r
 108 \r
 109         try\r
 110         {\r
 111             jbInit();\r
 112         }\r
 113         catch (Exception e)\r
 114         {\r
 115             e.printStackTrace();\r
 116         }\r
 117 \r
 118 \r
 119         if (seq != null)\r
 120         {\r
 121           JMenuItem menuItem;\r
 122           if( seq.getDatasetSequence().getPDBId() != null)\r
 123           {\r
 124             java.util.Enumeration e = seq.getDatasetSequence().getPDBId().\r
 125                 elements();\r
 126             while (e.hasMoreElements())\r
 127             {\r
 128               final PDBEntry pdb = (PDBEntry) e.nextElement();\r
 129 \r
 130               menuItem = new JMenuItem();\r
 131               menuItem.setText("View PDB entry: " + pdb.getId());\r
 132               menuItem.addActionListener(new java.awt.event.ActionListener()\r
 133               {\r
 134                 public void actionPerformed(ActionEvent e)\r
 135                 {\r
 136                   new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);\r
 137                 }\r
 138               });\r
 139               sequenceMenu.add(menuItem);\r
 140             }\r
 141           }\r
 142 \r
 143        /*   menuItem = new JMenuItem("Hide Sequences");\r
 144           menuItem.addActionListener(new java.awt.event.ActionListener()\r
 145               {\r
 146                 public void actionPerformed(ActionEvent e)\r
 147                 {\r
 148                   hideSequences(false);\r
 149                 }\r
 150               });\r
 151           sequenceMenu.add(menuItem);\r
 152 \r
 153           if(ap.av.getSelectionGroup() !=null && ap.av.getSelectionGroup().getSize()>1)\r
 154           {\r
 155             menuItem = new JMenuItem("Represent Group with " + seq.getName());\r
 156             menuItem.addActionListener(new java.awt.event.ActionListener()\r
 157             {\r
 158               public void actionPerformed(ActionEvent e)\r
 159               {\r
 160                 hideSequences(true);\r
 161               }\r
 162             });\r
 163             sequenceMenu.add(menuItem);\r
 164           }*/\r
 165 \r
 166 \r
 167         }\r
 168 \r
 169 \r
 170 \r
 171         SequenceGroup sg = ap.av.getSelectionGroup();\r
 172 \r
 173         if (sg != null)\r
 174         {\r
 175             groupName.setText(sg.getName());\r
 176 \r
 177             if (sg.cs instanceof ZappoColourScheme)\r
 178             {\r
 179                 zappoColour.setSelected(true);\r
 180             }\r
 181             else if (sg.cs instanceof TaylorColourScheme)\r
 182             {\r
 183                 taylorColour.setSelected(true);\r
 184             }\r
 185             else if (sg.cs instanceof PIDColourScheme)\r
 186             {\r
 187                 PIDColour.setSelected(true);\r
 188             }\r
 189             else if (sg.cs instanceof Blosum62ColourScheme)\r
 190             {\r
 191                 BLOSUM62Colour.setSelected(true);\r
 192             }\r
 193             else if (sg.cs instanceof UserColourScheme)\r
 194             {\r
 195                 userDefinedColour.setSelected(true);\r
 196             }\r
 197             else if (sg.cs instanceof HydrophobicColourScheme)\r
 198             {\r
 199                 hydrophobicityColour.setSelected(true);\r
 200             }\r
 201             else if (sg.cs instanceof HelixColourScheme)\r
 202             {\r
 203                 helixColour.setSelected(true);\r
 204             }\r
 205             else if (sg.cs instanceof StrandColourScheme)\r
 206             {\r
 207                 strandColour.setSelected(true);\r
 208             }\r
 209             else if (sg.cs instanceof TurnColourScheme)\r
 210             {\r
 211                 turnColour.setSelected(true);\r
 212             }\r
 213             else if (sg.cs instanceof BuriedColourScheme)\r
 214             {\r
 215                 buriedColour.setSelected(true);\r
 216             }\r
 217             else if (sg.cs instanceof ClustalxColourScheme)\r
 218             {\r
 219                 clustalColour.setSelected(true);\r
 220             }\r
 221             else\r
 222             {\r
 223                 noColourmenuItem.setSelected(true);\r
 224             }\r
 225 \r
 226             if (sg.cs!=null && sg.cs.conservationApplied())\r
 227             {\r
 228                 conservationMenuItem.setSelected(true);\r
 229             }\r
 230 \r
 231             showText.setSelected(sg.getDisplayText());\r
 232             showColourText.setSelected(sg.getColourText());\r
 233             showBoxes.setSelected(sg.getDisplayBoxes());\r
 234         }\r
 235         else\r
 236         {\r
 237           groupMenu.setVisible(false);\r
 238           editMenu.setVisible(false);\r
 239         }\r
 240 \r
 241         if (!ap.av.alignment.getGroups().contains(sg))\r
 242         {\r
 243             unGroupMenuItem.setVisible(false);\r
 244         }\r
 245         else\r
 246         {\r
 247             groupMenu.insertSeparator(3);\r
 248         }\r
 249 \r
 250         if (seq == null)\r
 251         {\r
 252             sequenceMenu.setVisible(false);\r
 253         }\r
 254         else\r
 255         {\r
 256           java.util.Vector links = Preferences.sequenceURLLinks;\r
 257 \r
 258           JMenu linkMenu = new JMenu("Link");\r
 259           JMenuItem item;\r
 260           for(int i=0; i<links.size(); i++)\r
 261           {\r
 262             String link = links.elementAt(i).toString();\r
 263 \r
 264             item = new JMenuItem(link.substring(0, link.indexOf("|")));\r
 265             String id = sequence.getName();\r
 266             if(id.indexOf("|")>-1)\r
 267               id = id.substring(id.lastIndexOf("|")+1);\r
 268 \r
 269             final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))\r
 270                 + id +\r
 271                 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
 272 \r
 273 \r
 274             item.addActionListener(new java.awt.event.ActionListener()\r
 275             {\r
 276                 public void actionPerformed(ActionEvent e)\r
 277                 {\r
 278                     showLink(url);\r
 279                 }\r
 280             });\r
 281 \r
 282             linkMenu.add(item);\r
 283           }\r
 284           add(linkMenu);\r
 285         }\r
 286     }\r
 287 \r
 288 \r
 289     /**\r
 290      * DOCUMENT ME!\r
 291      *\r
 292      * @throws Exception DOCUMENT ME!\r
 293      */\r
 294     private void jbInit() throws Exception\r
 295     {\r
 296         groupMenu.setText("Group");\r
 297         groupMenu.setText("Group");\r
 298         groupName.setText("Name");\r
 299         groupName.addActionListener(new java.awt.event.ActionListener()\r
 300             {\r
 301                 public void actionPerformed(ActionEvent e)\r
 302                 {\r
 303                     groupName_actionPerformed(e);\r
 304                 }\r
 305             });\r
 306         sequenceMenu.setText("Sequence");\r
 307         sequenceName.setText("Edit Name/Description");\r
 308         sequenceName.addActionListener(new java.awt.event.ActionListener()\r
 309             {\r
 310                 public void actionPerformed(ActionEvent e)\r
 311                 {\r
 312                     sequenceName_actionPerformed(e);\r
 313                 }\r
 314             });\r
 315         PIDColour.setFocusPainted(false);\r
 316         unGroupMenuItem.setText("Remove Group");\r
 317         unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 318             {\r
 319                 public void actionPerformed(ActionEvent e)\r
 320                 {\r
 321                     unGroupMenuItem_actionPerformed(e);\r
 322                 }\r
 323             });\r
 324 \r
 325         outline.setText("Border colour");\r
 326         outline.addActionListener(new java.awt.event.ActionListener()\r
 327             {\r
 328                 public void actionPerformed(ActionEvent e)\r
 329                 {\r
 330                     outline_actionPerformed(e);\r
 331                 }\r
 332             });\r
 333         nucleotideMenuItem.setText("Nucleotide");\r
 334         nucleotideMenuItem.addActionListener(new ActionListener()\r
 335             {\r
 336                 public void actionPerformed(ActionEvent e)\r
 337                 {\r
 338                     nucleotideMenuItem_actionPerformed(e);\r
 339                 }\r
 340             });\r
 341         colourMenu.setText("Group Colour");\r
 342         showBoxes.setText("Boxes");\r
 343         showBoxes.setState(true);\r
 344         showBoxes.addActionListener(new ActionListener()\r
 345             {\r
 346                 public void actionPerformed(ActionEvent e)\r
 347                 {\r
 348                     showBoxes_actionPerformed(e);\r
 349                 }\r
 350             });\r
 351         showText.setText("Text");\r
 352         showText.setState(true);\r
 353         showText.addActionListener(new ActionListener()\r
 354             {\r
 355                 public void actionPerformed(ActionEvent e)\r
 356                 {\r
 357                     showText_actionPerformed(e);\r
 358                 }\r
 359             });\r
 360         showColourText.setText("Colour Text");\r
 361         showColourText.addActionListener(new ActionListener()\r
 362             {\r
 363                 public void actionPerformed(ActionEvent e)\r
 364                 {\r
 365                     showColourText_actionPerformed(e);\r
 366                 }\r
 367             });\r
 368     editMenu.setText("Edit");\r
 369     cut.setText("Cut");\r
 370     cut.addActionListener(new ActionListener()\r
 371     {\r
 372       public void actionPerformed(ActionEvent e)\r
 373       {\r
 374         cut_actionPerformed(e);\r
 375       }\r
 376     });\r
 377     upperCase.setText("To Upper Case");\r
 378     upperCase.addActionListener(new ActionListener()\r
 379     {\r
 380       public void actionPerformed(ActionEvent e)\r
 381       {\r
 382         upperCase_actionPerformed(e);\r
 383       }\r
 384     });\r
 385     copy.setText("Copy");\r
 386     copy.addActionListener(new ActionListener()\r
 387     {\r
 388       public void actionPerformed(ActionEvent e)\r
 389       {\r
 390         copy_actionPerformed(e);\r
 391       }\r
 392     });\r
 393     lowerCase.setText("To Lower Case");\r
 394     lowerCase.addActionListener(new ActionListener()\r
 395     {\r
 396       public void actionPerformed(ActionEvent e)\r
 397       {\r
 398         lowerCase_actionPerformed(e);\r
 399       }\r
 400     });\r
 401     add(groupMenu);\r
 402         add(sequenceMenu);\r
 403     this.add(editMenu);\r
 404     groupMenu.add(groupName);\r
 405         groupMenu.addSeparator();\r
 406         groupMenu.add(unGroupMenuItem);\r
 407         groupMenu.add(colourMenu);\r
 408         groupMenu.addSeparator();\r
 409         groupMenu.add(showBoxes);\r
 410         groupMenu.add(showText);\r
 411         groupMenu.add(showColourText);\r
 412         groupMenu.addSeparator();\r
 413         groupMenu.add(outline);\r
 414         sequenceMenu.add(sequenceName);\r
 415         colourMenu.add(noColourmenuItem);\r
 416         colourMenu.add(clustalColour);\r
 417         colourMenu.add(BLOSUM62Colour);\r
 418         colourMenu.add(PIDColour);\r
 419         colourMenu.add(zappoColour);\r
 420         colourMenu.add(taylorColour);\r
 421         colourMenu.add(hydrophobicityColour);\r
 422         colourMenu.add(helixColour);\r
 423         colourMenu.add(strandColour);\r
 424         colourMenu.add(turnColour);\r
 425         colourMenu.add(buriedColour);\r
 426         colourMenu.add(nucleotideMenuItem);\r
 427         colourMenu.add(userDefinedColour);\r
 428 \r
 429         if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
 430         {\r
 431           java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 432               getUserColourSchemes().keys();\r
 433 \r
 434           while (userColours.hasMoreElements())\r
 435           {\r
 436             JMenuItem item = new JMenuItem(userColours.\r
 437                 nextElement().toString());\r
 438             item.addActionListener(new ActionListener()\r
 439             {\r
 440               public void actionPerformed(ActionEvent evt)\r
 441               {\r
 442                 userDefinedColour_actionPerformed(evt);\r
 443               }\r
 444             });\r
 445             colourMenu.add(item);\r
 446           }\r
 447         }\r
 448 \r
 449 \r
 450         colourMenu.addSeparator();\r
 451         colourMenu.add(abovePIDColour);\r
 452         colourMenu.add(conservationMenuItem);\r
 453     editMenu.add(copy);\r
 454     editMenu.add(cut);\r
 455     editMenu.add(upperCase);\r
 456     editMenu.add(lowerCase);\r
 457     noColourmenuItem.setText("None");\r
 458         noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 459             {\r
 460                 public void actionPerformed(ActionEvent e)\r
 461                 {\r
 462                     noColourmenuItem_actionPerformed(e);\r
 463                 }\r
 464             });\r
 465 \r
 466         clustalColour.setText("Clustalx colours");\r
 467         clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 468             {\r
 469                 public void actionPerformed(ActionEvent e)\r
 470                 {\r
 471                     clustalColour_actionPerformed(e);\r
 472                 }\r
 473             });\r
 474         zappoColour.setText("Zappo");\r
 475         zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 476             {\r
 477                 public void actionPerformed(ActionEvent e)\r
 478                 {\r
 479                     zappoColour_actionPerformed(e);\r
 480                 }\r
 481             });\r
 482         taylorColour.setText("Taylor");\r
 483         taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 484             {\r
 485                 public void actionPerformed(ActionEvent e)\r
 486                 {\r
 487                     taylorColour_actionPerformed(e);\r
 488                 }\r
 489             });\r
 490         hydrophobicityColour.setText("Hydrophobicity");\r
 491         hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 492             {\r
 493                 public void actionPerformed(ActionEvent e)\r
 494                 {\r
 495                     hydrophobicityColour_actionPerformed(e);\r
 496                 }\r
 497             });\r
 498         helixColour.setText("Helix propensity");\r
 499         helixColour.addActionListener(new java.awt.event.ActionListener()\r
 500             {\r
 501                 public void actionPerformed(ActionEvent e)\r
 502                 {\r
 503                     helixColour_actionPerformed(e);\r
 504                 }\r
 505             });\r
 506         strandColour.setText("Strand propensity");\r
 507         strandColour.addActionListener(new java.awt.event.ActionListener()\r
 508             {\r
 509                 public void actionPerformed(ActionEvent e)\r
 510                 {\r
 511                     strandColour_actionPerformed(e);\r
 512                 }\r
 513             });\r
 514         turnColour.setText("Turn propensity");\r
 515         turnColour.addActionListener(new java.awt.event.ActionListener()\r
 516             {\r
 517                 public void actionPerformed(ActionEvent e)\r
 518                 {\r
 519                     turnColour_actionPerformed(e);\r
 520                 }\r
 521             });\r
 522         buriedColour.setText("Buried Index");\r
 523         buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 524             {\r
 525                 public void actionPerformed(ActionEvent e)\r
 526                 {\r
 527                     buriedColour_actionPerformed(e);\r
 528                 }\r
 529             });\r
 530         abovePIDColour.setText("Above % Identity");\r
 531         abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
 532             {\r
 533                 public void actionPerformed(ActionEvent e)\r
 534                 {\r
 535                     abovePIDColour_actionPerformed(e);\r
 536                 }\r
 537             });\r
 538         userDefinedColour.setText("User Defined...");\r
 539         userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 540             {\r
 541                 public void actionPerformed(ActionEvent e)\r
 542                 {\r
 543                     userDefinedColour_actionPerformed(e);\r
 544                 }\r
 545             });\r
 546         PIDColour.setText("Percentage Identity");\r
 547         PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 548             {\r
 549                 public void actionPerformed(ActionEvent e)\r
 550                 {\r
 551                     PIDColour_actionPerformed(e);\r
 552                 }\r
 553             });\r
 554         BLOSUM62Colour.setText("BLOSUM62");\r
 555         BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 556             {\r
 557                 public void actionPerformed(ActionEvent e)\r
 558                 {\r
 559                     BLOSUM62Colour_actionPerformed(e);\r
 560                 }\r
 561             });\r
 562         conservationMenuItem.setText("Conservation");\r
 563         conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 564             {\r
 565                 public void actionPerformed(ActionEvent e)\r
 566                 {\r
 567                     conservationMenuItem_actionPerformed(e);\r
 568                 }\r
 569             });\r
 570     }\r
 571 \r
 572     /**\r
 573      * DOCUMENT ME!\r
 574      */\r
 575     void refresh()\r
 576     {\r
 577         if (ap.overviewPanel != null)\r
 578           ap.overviewPanel.updateOverviewImage();\r
 579 \r
 580         ap.seqPanel.repaint();\r
 581     }\r
 582 \r
 583     /**\r
 584      * DOCUMENT ME!\r
 585      *\r
 586      * @param e DOCUMENT ME!\r
 587      */\r
 588     protected void clustalColour_actionPerformed(ActionEvent e)\r
 589     {\r
 590         SequenceGroup sg = getGroup();\r
 591         sg.cs = new ClustalxColourScheme(sg.sequences,\r
 592                 ap.av.alignment.getWidth());\r
 593         refresh();\r
 594     }\r
 595 \r
 596     /**\r
 597      * DOCUMENT ME!\r
 598      *\r
 599      * @param e DOCUMENT ME!\r
 600      */\r
 601     protected void zappoColour_actionPerformed(ActionEvent e)\r
 602     {\r
 603         getGroup().cs = new ZappoColourScheme();\r
 604         refresh();\r
 605     }\r
 606 \r
 607     /**\r
 608      * DOCUMENT ME!\r
 609      *\r
 610      * @param e DOCUMENT ME!\r
 611      */\r
 612     protected void taylorColour_actionPerformed(ActionEvent e)\r
 613     {\r
 614         getGroup().cs = new TaylorColourScheme();\r
 615         refresh();\r
 616     }\r
 617 \r
 618     /**\r
 619      * DOCUMENT ME!\r
 620      *\r
 621      * @param e DOCUMENT ME!\r
 622      */\r
 623     protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 624     {\r
 625         getGroup().cs = new HydrophobicColourScheme();\r
 626         refresh();\r
 627     }\r
 628 \r
 629     /**\r
 630      * DOCUMENT ME!\r
 631      *\r
 632      * @param e DOCUMENT ME!\r
 633      */\r
 634     protected void helixColour_actionPerformed(ActionEvent e)\r
 635     {\r
 636         getGroup().cs = new HelixColourScheme();\r
 637         refresh();\r
 638     }\r
 639 \r
 640     /**\r
 641      * DOCUMENT ME!\r
 642      *\r
 643      * @param e DOCUMENT ME!\r
 644      */\r
 645     protected void strandColour_actionPerformed(ActionEvent e)\r
 646     {\r
 647         getGroup().cs = new StrandColourScheme();\r
 648         refresh();\r
 649     }\r
 650 \r
 651     /**\r
 652      * DOCUMENT ME!\r
 653      *\r
 654      * @param e DOCUMENT ME!\r
 655      */\r
 656     protected void turnColour_actionPerformed(ActionEvent e)\r
 657     {\r
 658         getGroup().cs = new TurnColourScheme();\r
 659         refresh();\r
 660     }\r
 661 \r
 662     /**\r
 663      * DOCUMENT ME!\r
 664      *\r
 665      * @param e DOCUMENT ME!\r
 666      */\r
 667     protected void buriedColour_actionPerformed(ActionEvent e)\r
 668     {\r
 669         getGroup().cs = new BuriedColourScheme();\r
 670         refresh();\r
 671     }\r
 672 \r
 673     /**\r
 674      * DOCUMENT ME!\r
 675      *\r
 676      * @param e DOCUMENT ME!\r
 677      */\r
 678     public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
 679     {\r
 680         getGroup().cs = new NucleotideColourScheme();\r
 681         refresh();\r
 682     }\r
 683 \r
 684     /**\r
 685      * DOCUMENT ME!\r
 686      *\r
 687      * @param e DOCUMENT ME!\r
 688      */\r
 689     protected void abovePIDColour_actionPerformed(ActionEvent e)\r
 690     {\r
 691         SequenceGroup sg = getGroup();\r
 692         if(sg.cs==null)\r
 693           return;\r
 694 \r
 695         if (abovePIDColour.isSelected())\r
 696         {\r
 697             sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 698                     ap.av.alignment.getWidth()));\r
 699 \r
 700             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
 701                     getGroup().getName());\r
 702 \r
 703            sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
 704 \r
 705             SliderPanel.showPIDSlider();\r
 706         }\r
 707         else // remove PIDColouring\r
 708         {\r
 709             sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
 710         }\r
 711 \r
 712         refresh();\r
 713     }\r
 714 \r
 715     /**\r
 716      * DOCUMENT ME!\r
 717      *\r
 718      * @param e DOCUMENT ME!\r
 719      */\r
 720     protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 721     {\r
 722        SequenceGroup sg = getGroup();\r
 723 \r
 724        if (e.getActionCommand().equals("User Defined..."))\r
 725          new UserDefinedColours(ap, sg);\r
 726        else\r
 727        {\r
 728          UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
 729              getUserColourSchemes().get(e.getActionCommand());\r
 730 \r
 731          sg.cs = udc;\r
 732        }\r
 733      }\r
 734     /**\r
 735      * DOCUMENT ME!\r
 736      *\r
 737      * @param e DOCUMENT ME!\r
 738      */\r
 739     protected void PIDColour_actionPerformed(ActionEvent e)\r
 740     {\r
 741         SequenceGroup sg = getGroup();\r
 742         sg.cs = new PIDColourScheme();\r
 743         sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 744                 ap.av.alignment.getWidth()));\r
 745         refresh();\r
 746     }\r
 747 \r
 748     /**\r
 749      * DOCUMENT ME!\r
 750      *\r
 751      * @param e DOCUMENT ME!\r
 752      */\r
 753     protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 754     {\r
 755         SequenceGroup sg = getGroup();\r
 756 \r
 757         sg.cs = new Blosum62ColourScheme();\r
 758 \r
 759         sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 760                 ap.av.alignment.getWidth()));\r
 761 \r
 762         refresh();\r
 763     }\r
 764 \r
 765     /**\r
 766      * DOCUMENT ME!\r
 767      *\r
 768      * @param e DOCUMENT ME!\r
 769      */\r
 770     protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 771     {\r
 772         getGroup().cs = null;\r
 773         refresh();\r
 774     }\r
 775 \r
 776     /**\r
 777      * DOCUMENT ME!\r
 778      *\r
 779      * @param e DOCUMENT ME!\r
 780      */\r
 781     protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
 782     {\r
 783         SequenceGroup sg = getGroup();\r
 784         if(sg.cs==null)\r
 785           return;\r
 786 \r
 787         if (conservationMenuItem.isSelected())\r
 788         {\r
 789             Conservation c = new Conservation("Group",\r
 790                     ResidueProperties.propHash, 3, sg.sequences, 0,\r
 791                     ap.av.alignment.getWidth());\r
 792 \r
 793             c.calculate();\r
 794             c.verdict(false, ap.av.ConsPercGaps);\r
 795 \r
 796             sg.cs.setConservation(c);\r
 797 \r
 798             SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
 799             SliderPanel.showConservationSlider();\r
 800         }\r
 801         else // remove ConservationColouring\r
 802         {\r
 803             sg.cs.setConservation(null);\r
 804         }\r
 805 \r
 806         refresh();\r
 807     }\r
 808 \r
 809     /**\r
 810      * DOCUMENT ME!\r
 811      *\r
 812      * @param e DOCUMENT ME!\r
 813      */\r
 814     protected void groupName_actionPerformed(ActionEvent e)\r
 815     {\r
 816         SequenceGroup sg = getGroup();\r
 817         String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
 818                 "Enter new group name", "Edit group name",\r
 819                 JOptionPane.QUESTION_MESSAGE);\r
 820 \r
 821         if (reply == null)\r
 822         {\r
 823             return;\r
 824         }\r
 825 \r
 826         sg.setName(reply);\r
 827         groupName.setText(reply);\r
 828     }\r
 829 \r
 830     /**\r
 831      * DOCUMENT ME!\r
 832      *\r
 833      * @param e DOCUMENT ME!\r
 834      */\r
 835     protected void analyze_actionPerformed(ActionEvent e)\r
 836     {\r
 837         CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
 838         JInternalFrame frame = new JInternalFrame();\r
 839         frame.setContentPane(cap);\r
 840         Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
 841 \r
 842         SequenceGroup sg = getGroup();\r
 843         StringBuffer sb = new StringBuffer();\r
 844 \r
 845         for (int i = 0; i < sg.sequences.size(); i++)\r
 846         {\r
 847             Sequence tmp = (Sequence) sg.sequences.get(i);\r
 848             sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
 849             sb.append("\n");\r
 850         }\r
 851 \r
 852         sb.append("Something amazing will happen soon");\r
 853         cap.setText(sb.toString());\r
 854     }\r
 855 \r
 856     /**\r
 857      * DOCUMENT ME!\r
 858      *\r
 859      * @return DOCUMENT ME!\r
 860      */\r
 861     SequenceGroup getGroup()\r
 862     {\r
 863         SequenceGroup sg = ap.av.getSelectionGroup();\r
 864       // this method won't add a new group if it already exists\r
 865         if(sg!=null)\r
 866           ap.av.alignment.addGroup(sg);\r
 867 \r
 868         return sg;\r
 869     }\r
 870 \r
 871     /**\r
 872      * DOCUMENT ME!\r
 873      *\r
 874      * @param e DOCUMENT ME!\r
 875      */\r
 876     void sequenceName_actionPerformed(ActionEvent e)\r
 877     {\r
 878       JLabel idlabel = new JLabel(  "       Sequence Name ");\r
 879       JLabel desclabel = new JLabel("Sequence Description ");\r
 880       idlabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
 881       desclabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
 882       JTextField id = new JTextField(sequence.getName(), 40);\r
 883       JTextField description = new JTextField(sequence.getDescription(), 40);\r
 884       JPanel panel = new JPanel(new BorderLayout());\r
 885       JPanel panel2 = new JPanel(new BorderLayout());\r
 886       panel2.add(idlabel, BorderLayout.WEST);\r
 887       panel2.add(id, BorderLayout.CENTER);\r
 888       panel.add(panel2, BorderLayout.NORTH);\r
 889       panel2 = new JPanel(new BorderLayout());\r
 890       panel2.add(desclabel, BorderLayout.WEST);\r
 891       panel2.add(description, BorderLayout.CENTER);\r
 892       panel.add(panel2, BorderLayout.SOUTH);\r
 893 \r
 894 \r
 895        int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
 896           panel, "Edit Sequence Name/Description",\r
 897           JOptionPane.OK_CANCEL_OPTION );\r
 898 \r
 899 \r
 900         if (reply != JOptionPane.OK_OPTION )\r
 901         {\r
 902             return;\r
 903         }\r
 904 \r
 905         String s = id.getText();\r
 906 \r
 907         if (s != null)\r
 908         {\r
 909             if (s.indexOf(" ") > -1)\r
 910             {\r
 911                 JOptionPane.showMessageDialog(ap,\r
 912                     "Spaces have been converted to \"_\"",\r
 913                     "No spaces allowed in Sequence Name",\r
 914                     JOptionPane.WARNING_MESSAGE);\r
 915             }\r
 916 \r
 917             s = s.replace(' ', '_');\r
 918             sequence.getDatasetSequence().setName(s);\r
 919             sequence.setName(s);\r
 920             ap.repaint();\r
 921         }\r
 922 \r
 923         sequence.getDatasetSequence().setDescription(description.getText());\r
 924         sequence.setDescription(description.getText());\r
 925     }\r
 926 \r
 927     /**\r
 928      * DOCUMENT ME!\r
 929      *\r
 930      * @param e DOCUMENT ME!\r
 931      */\r
 932     void unGroupMenuItem_actionPerformed(ActionEvent e)\r
 933     {\r
 934         SequenceGroup sg = ap.av.getSelectionGroup();\r
 935         ap.av.alignment.deleteGroup(sg);\r
 936         ap.av.setSelectionGroup(null);\r
 937         refresh();\r
 938     }\r
 939 \r
 940 \r
 941     /**\r
 942      * DOCUMENT ME!\r
 943      *\r
 944      * @param e DOCUMENT ME!\r
 945      */\r
 946     protected void outline_actionPerformed(ActionEvent e)\r
 947     {\r
 948         SequenceGroup sg = getGroup();\r
 949         Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
 950                 Color.BLUE);\r
 951 \r
 952         if (col != null)\r
 953         {\r
 954             sg.setOutlineColour(col);\r
 955         }\r
 956 \r
 957         refresh();\r
 958     }\r
 959 \r
 960     /**\r
 961      * DOCUMENT ME!\r
 962      *\r
 963      * @param e DOCUMENT ME!\r
 964      */\r
 965     public void showBoxes_actionPerformed(ActionEvent e)\r
 966     {\r
 967         getGroup().setDisplayBoxes(showBoxes.isSelected());\r
 968         refresh();\r
 969     }\r
 970 \r
 971     /**\r
 972      * DOCUMENT ME!\r
 973      *\r
 974      * @param e DOCUMENT ME!\r
 975      */\r
 976     public void showText_actionPerformed(ActionEvent e)\r
 977     {\r
 978         getGroup().setDisplayText(showText.isSelected());\r
 979         refresh();\r
 980     }\r
 981 \r
 982     /**\r
 983      * DOCUMENT ME!\r
 984      *\r
 985      * @param e DOCUMENT ME!\r
 986      */\r
 987     public void showColourText_actionPerformed(ActionEvent e)\r
 988     {\r
 989         getGroup().setColourText(showColourText.isSelected());\r
 990         refresh();\r
 991     }\r
 992 \r
 993     public void showLink(String url)\r
 994     {\r
 995       try\r
 996       {\r
 997         jalview.util.BrowserLauncher.openURL(url);\r
 998       }\r
 999       catch (Exception ex)\r
1000       {\r
1001         JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
1002             "Unixers: Couldn't find default web browser."\r
1003            +"\nAdd the full path to your browser in Preferences.",\r
1004            "Web browser not found", JOptionPane.WARNING_MESSAGE );\r
1005 \r
1006 \r
1007         ex.printStackTrace();\r
1008       }\r
1009     }\r
1010 \r
1011     void hideSequences(boolean representGroup)\r
1012     {\r
1013       SequenceGroup sg = ap.av.getSelectionGroup();\r
1014       if(sg==null || sg.getSize()<1)\r
1015       {\r
1016         ap.av.hideSequence(sequence);\r
1017         return;\r
1018       }\r
1019 \r
1020         int index = 0;\r
1021         while(index < sg.sequences.size())\r
1022         {\r
1023           if(representGroup && sg.getSequenceAt(index)!=sequence)\r
1024           {\r
1025             sequence.addHiddenSequence(sg.getSequenceAt(index));\r
1026             ap.av.hideSequence(sg.getSequenceAt(index));\r
1027           }\r
1028           else if(!representGroup)\r
1029           {\r
1030             ap.av.hideSequence(sg.getSequenceAt(index));\r
1031           }\r
1032           index ++;\r
1033         }\r
1034 \r
1035         ap.av.setSelectionGroup(null);\r
1036         refresh();\r
1037     }\r
1038 \r
1039   public void copy_actionPerformed(ActionEvent e)\r
1040   {\r
1041     ap.alignFrame.copy_actionPerformed(null);\r
1042   }\r
1043 \r
1044   public void cut_actionPerformed(ActionEvent e)\r
1045   {\r
1046     ap.alignFrame.cut_actionPerformed(null);\r
1047   }\r
1048 \r
1049   public void upperCase_actionPerformed(ActionEvent e)\r
1050   {\r
1051     SequenceGroup sg = ap.av.getSelectionGroup();\r
1052     if(sg==null)\r
1053       return;\r
1054 \r
1055     for(int g=0; g<sg.getSize(); g++)\r
1056     {\r
1057       sg.getSequenceAt(g).changeCase(true, sg.getStartRes(), sg.getEndRes()+1);\r
1058     }\r
1059     ap.repaint();\r
1060   }\r
1061 \r
1062   public void lowerCase_actionPerformed(ActionEvent e)\r
1063   {\r
1064     SequenceGroup sg = ap.av.getSelectionGroup();\r
1065     if(sg==null)\r
1066       return;\r
1067 \r
1068     for(int g=0; g<sg.getSize(); g++)\r
1069     {\r
1070       sg.getSequenceAt(g).changeCase(false, sg.getStartRes(), sg.getEndRes()+1);\r
1071     }\r
1072     ap.repaint();\r
1073   }\r
1074 \r
1075 }\r