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   JMenuItem toggle = new JMenuItem();\r
  77 \r
  78   /**\r
  79      * Creates a new PopupMenu object.\r
  80      *\r
  81      * @param ap DOCUMENT ME!\r
  82      * @param seq DOCUMENT ME!\r
  83      */\r
  84     public PopupMenu(final AlignmentPanel ap, Sequence seq)\r
  85     {\r
  86         ///////////////////////////////////////////////////////////\r
  87         // If this is activated from the sequence panel, the user may want to\r
  88         // edit or annotate a particular residue. Therefore display the residue menu\r
  89         //\r
  90         // If from the IDPanel, we must display the sequence menu\r
  91         //////////////////////////////////////////////////////////\r
  92         this.ap = ap;\r
  93         sequence = seq;\r
  94 \r
  95         ButtonGroup colours = new ButtonGroup();\r
  96         colours.add(noColourmenuItem);\r
  97         colours.add(clustalColour);\r
  98         colours.add(zappoColour);\r
  99         colours.add(taylorColour);\r
 100         colours.add(hydrophobicityColour);\r
 101         colours.add(helixColour);\r
 102         colours.add(strandColour);\r
 103         colours.add(turnColour);\r
 104         colours.add(buriedColour);\r
 105         colours.add(abovePIDColour);\r
 106         colours.add(userDefinedColour);\r
 107         colours.add(PIDColour);\r
 108         colours.add(BLOSUM62Colour);\r
 109 \r
 110         try\r
 111         {\r
 112             jbInit();\r
 113         }\r
 114         catch (Exception e)\r
 115         {\r
 116             e.printStackTrace();\r
 117         }\r
 118 \r
 119 \r
 120         if (seq != null)\r
 121         {\r
 122           JMenuItem menuItem;\r
 123           if( seq.getDatasetSequence().getPDBId() != null)\r
 124           {\r
 125             java.util.Enumeration e = seq.getDatasetSequence().getPDBId().\r
 126                 elements();\r
 127             while (e.hasMoreElements())\r
 128             {\r
 129               final PDBEntry pdb = (PDBEntry) e.nextElement();\r
 130 \r
 131               menuItem = new JMenuItem();\r
 132               menuItem.setText("View PDB entry: " + pdb.getId());\r
 133               menuItem.addActionListener(new java.awt.event.ActionListener()\r
 134               {\r
 135                 public void actionPerformed(ActionEvent e)\r
 136                 {\r
 137                   new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);\r
 138                 }\r
 139               });\r
 140               sequenceMenu.add(menuItem);\r
 141             }\r
 142           }\r
 143 \r
 144        /*   menuItem = new JMenuItem("Hide Sequences");\r
 145           menuItem.addActionListener(new java.awt.event.ActionListener()\r
 146               {\r
 147                 public void actionPerformed(ActionEvent e)\r
 148                 {\r
 149                   hideSequences(false);\r
 150                 }\r
 151               });\r
 152           sequenceMenu.add(menuItem);\r
 153 \r
 154           if(ap.av.getSelectionGroup() !=null && ap.av.getSelectionGroup().getSize()>1)\r
 155           {\r
 156             menuItem = new JMenuItem("Represent Group with " + seq.getName());\r
 157             menuItem.addActionListener(new java.awt.event.ActionListener()\r
 158             {\r
 159               public void actionPerformed(ActionEvent e)\r
 160               {\r
 161                 hideSequences(true);\r
 162               }\r
 163             });\r
 164             sequenceMenu.add(menuItem);\r
 165           }*/\r
 166 \r
 167 \r
 168         }\r
 169 \r
 170 \r
 171 \r
 172         SequenceGroup sg = ap.av.getSelectionGroup();\r
 173 \r
 174         if (sg != null)\r
 175         {\r
 176             groupName.setText(sg.getName());\r
 177 \r
 178             if (sg.cs instanceof ZappoColourScheme)\r
 179             {\r
 180                 zappoColour.setSelected(true);\r
 181             }\r
 182             else if (sg.cs instanceof TaylorColourScheme)\r
 183             {\r
 184                 taylorColour.setSelected(true);\r
 185             }\r
 186             else if (sg.cs instanceof PIDColourScheme)\r
 187             {\r
 188                 PIDColour.setSelected(true);\r
 189             }\r
 190             else if (sg.cs instanceof Blosum62ColourScheme)\r
 191             {\r
 192                 BLOSUM62Colour.setSelected(true);\r
 193             }\r
 194             else if (sg.cs instanceof UserColourScheme)\r
 195             {\r
 196                 userDefinedColour.setSelected(true);\r
 197             }\r
 198             else if (sg.cs instanceof HydrophobicColourScheme)\r
 199             {\r
 200                 hydrophobicityColour.setSelected(true);\r
 201             }\r
 202             else if (sg.cs instanceof HelixColourScheme)\r
 203             {\r
 204                 helixColour.setSelected(true);\r
 205             }\r
 206             else if (sg.cs instanceof StrandColourScheme)\r
 207             {\r
 208                 strandColour.setSelected(true);\r
 209             }\r
 210             else if (sg.cs instanceof TurnColourScheme)\r
 211             {\r
 212                 turnColour.setSelected(true);\r
 213             }\r
 214             else if (sg.cs instanceof BuriedColourScheme)\r
 215             {\r
 216                 buriedColour.setSelected(true);\r
 217             }\r
 218             else if (sg.cs instanceof ClustalxColourScheme)\r
 219             {\r
 220                 clustalColour.setSelected(true);\r
 221             }\r
 222             else\r
 223             {\r
 224                 noColourmenuItem.setSelected(true);\r
 225             }\r
 226 \r
 227             if (sg.cs!=null && sg.cs.conservationApplied())\r
 228             {\r
 229                 conservationMenuItem.setSelected(true);\r
 230             }\r
 231 \r
 232             showText.setSelected(sg.getDisplayText());\r
 233             showColourText.setSelected(sg.getColourText());\r
 234             showBoxes.setSelected(sg.getDisplayBoxes());\r
 235         }\r
 236         else\r
 237         {\r
 238           groupMenu.setVisible(false);\r
 239           editMenu.setVisible(false);\r
 240         }\r
 241 \r
 242         if (!ap.av.alignment.getGroups().contains(sg))\r
 243         {\r
 244             unGroupMenuItem.setVisible(false);\r
 245         }\r
 246         else\r
 247         {\r
 248             groupMenu.insertSeparator(3);\r
 249         }\r
 250 \r
 251         if (seq == null)\r
 252         {\r
 253             sequenceMenu.setVisible(false);\r
 254         }\r
 255         else\r
 256         {\r
 257           java.util.Vector links = Preferences.sequenceURLLinks;\r
 258 \r
 259           JMenu linkMenu = new JMenu("Link");\r
 260           JMenuItem item;\r
 261           for(int i=0; i<links.size(); i++)\r
 262           {\r
 263             String link = links.elementAt(i).toString();\r
 264 \r
 265             item = new JMenuItem(link.substring(0, link.indexOf("|")));\r
 266             String id = sequence.getName();\r
 267             if(id.indexOf("|")>-1)\r
 268               id = id.substring(id.lastIndexOf("|")+1);\r
 269 \r
 270             final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))\r
 271                 + id +\r
 272                 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
 273 \r
 274 \r
 275             item.addActionListener(new java.awt.event.ActionListener()\r
 276             {\r
 277                 public void actionPerformed(ActionEvent e)\r
 278                 {\r
 279                     showLink(url);\r
 280                 }\r
 281             });\r
 282 \r
 283             linkMenu.add(item);\r
 284           }\r
 285           add(linkMenu);\r
 286         }\r
 287     }\r
 288 \r
 289 \r
 290     /**\r
 291      * DOCUMENT ME!\r
 292      *\r
 293      * @throws Exception DOCUMENT ME!\r
 294      */\r
 295     private void jbInit() throws Exception\r
 296     {\r
 297         groupMenu.setText("Group");\r
 298         groupMenu.setText("Group");\r
 299         groupName.setText("Name");\r
 300         groupName.addActionListener(new java.awt.event.ActionListener()\r
 301             {\r
 302                 public void actionPerformed(ActionEvent e)\r
 303                 {\r
 304                     groupName_actionPerformed(e);\r
 305                 }\r
 306             });\r
 307         sequenceMenu.setText("Sequence");\r
 308         sequenceName.setText("Edit Name/Description");\r
 309         sequenceName.addActionListener(new java.awt.event.ActionListener()\r
 310             {\r
 311                 public void actionPerformed(ActionEvent e)\r
 312                 {\r
 313                     sequenceName_actionPerformed(e);\r
 314                 }\r
 315             });\r
 316         PIDColour.setFocusPainted(false);\r
 317         unGroupMenuItem.setText("Remove Group");\r
 318         unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 319             {\r
 320                 public void actionPerformed(ActionEvent e)\r
 321                 {\r
 322                     unGroupMenuItem_actionPerformed(e);\r
 323                 }\r
 324             });\r
 325 \r
 326         outline.setText("Border colour");\r
 327         outline.addActionListener(new java.awt.event.ActionListener()\r
 328             {\r
 329                 public void actionPerformed(ActionEvent e)\r
 330                 {\r
 331                     outline_actionPerformed(e);\r
 332                 }\r
 333             });\r
 334         nucleotideMenuItem.setText("Nucleotide");\r
 335         nucleotideMenuItem.addActionListener(new ActionListener()\r
 336             {\r
 337                 public void actionPerformed(ActionEvent e)\r
 338                 {\r
 339                     nucleotideMenuItem_actionPerformed(e);\r
 340                 }\r
 341             });\r
 342         colourMenu.setText("Group Colour");\r
 343         showBoxes.setText("Boxes");\r
 344         showBoxes.setState(true);\r
 345         showBoxes.addActionListener(new ActionListener()\r
 346             {\r
 347                 public void actionPerformed(ActionEvent e)\r
 348                 {\r
 349                     showBoxes_actionPerformed(e);\r
 350                 }\r
 351             });\r
 352         showText.setText("Text");\r
 353         showText.setState(true);\r
 354         showText.addActionListener(new ActionListener()\r
 355             {\r
 356                 public void actionPerformed(ActionEvent e)\r
 357                 {\r
 358                     showText_actionPerformed(e);\r
 359                 }\r
 360             });\r
 361         showColourText.setText("Colour Text");\r
 362         showColourText.addActionListener(new ActionListener()\r
 363             {\r
 364                 public void actionPerformed(ActionEvent e)\r
 365                 {\r
 366                     showColourText_actionPerformed(e);\r
 367                 }\r
 368             });\r
 369     editMenu.setText("Edit");\r
 370     cut.setText("Cut");\r
 371     cut.addActionListener(new ActionListener()\r
 372     {\r
 373       public void actionPerformed(ActionEvent e)\r
 374       {\r
 375         cut_actionPerformed(e);\r
 376       }\r
 377     });\r
 378     upperCase.setText("To Upper Case");\r
 379     upperCase.addActionListener(new ActionListener()\r
 380     {\r
 381       public void actionPerformed(ActionEvent e)\r
 382       {\r
 383         upperCase_actionPerformed(e);\r
 384       }\r
 385     });\r
 386     copy.setText("Copy");\r
 387     copy.addActionListener(new ActionListener()\r
 388     {\r
 389       public void actionPerformed(ActionEvent e)\r
 390       {\r
 391         copy_actionPerformed(e);\r
 392       }\r
 393     });\r
 394     lowerCase.setText("To Lower Case");\r
 395     lowerCase.addActionListener(new ActionListener()\r
 396     {\r
 397       public void actionPerformed(ActionEvent e)\r
 398       {\r
 399         lowerCase_actionPerformed(e);\r
 400       }\r
 401     });\r
 402     toggle.setText("Toggle Case");\r
 403     toggle.addActionListener(new ActionListener()\r
 404     {\r
 405       public void actionPerformed(ActionEvent e)\r
 406       {\r
 407         toggle_actionPerformed(e);\r
 408       }\r
 409     });\r
 410     add(groupMenu);\r
 411         add(sequenceMenu);\r
 412     this.add(editMenu);\r
 413     groupMenu.add(groupName);\r
 414         groupMenu.addSeparator();\r
 415         groupMenu.add(unGroupMenuItem);\r
 416         groupMenu.add(colourMenu);\r
 417         groupMenu.addSeparator();\r
 418         groupMenu.add(showBoxes);\r
 419         groupMenu.add(showText);\r
 420         groupMenu.add(showColourText);\r
 421         groupMenu.addSeparator();\r
 422         groupMenu.add(outline);\r
 423         sequenceMenu.add(sequenceName);\r
 424         colourMenu.add(noColourmenuItem);\r
 425         colourMenu.add(clustalColour);\r
 426         colourMenu.add(BLOSUM62Colour);\r
 427         colourMenu.add(PIDColour);\r
 428         colourMenu.add(zappoColour);\r
 429         colourMenu.add(taylorColour);\r
 430         colourMenu.add(hydrophobicityColour);\r
 431         colourMenu.add(helixColour);\r
 432         colourMenu.add(strandColour);\r
 433         colourMenu.add(turnColour);\r
 434         colourMenu.add(buriedColour);\r
 435         colourMenu.add(nucleotideMenuItem);\r
 436         colourMenu.add(userDefinedColour);\r
 437 \r
 438         if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
 439         {\r
 440           java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 441               getUserColourSchemes().keys();\r
 442 \r
 443           while (userColours.hasMoreElements())\r
 444           {\r
 445             JMenuItem item = new JMenuItem(userColours.\r
 446                 nextElement().toString());\r
 447             item.addActionListener(new ActionListener()\r
 448             {\r
 449               public void actionPerformed(ActionEvent evt)\r
 450               {\r
 451                 userDefinedColour_actionPerformed(evt);\r
 452               }\r
 453             });\r
 454             colourMenu.add(item);\r
 455           }\r
 456         }\r
 457 \r
 458 \r
 459         colourMenu.addSeparator();\r
 460         colourMenu.add(abovePIDColour);\r
 461         colourMenu.add(conservationMenuItem);\r
 462     editMenu.add(copy);\r
 463     editMenu.add(cut);\r
 464     editMenu.add(upperCase);\r
 465     editMenu.add(lowerCase);\r
 466     editMenu.add(toggle);\r
 467     noColourmenuItem.setText("None");\r
 468         noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 469             {\r
 470                 public void actionPerformed(ActionEvent e)\r
 471                 {\r
 472                     noColourmenuItem_actionPerformed(e);\r
 473                 }\r
 474             });\r
 475 \r
 476         clustalColour.setText("Clustalx colours");\r
 477         clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 478             {\r
 479                 public void actionPerformed(ActionEvent e)\r
 480                 {\r
 481                     clustalColour_actionPerformed(e);\r
 482                 }\r
 483             });\r
 484         zappoColour.setText("Zappo");\r
 485         zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 486             {\r
 487                 public void actionPerformed(ActionEvent e)\r
 488                 {\r
 489                     zappoColour_actionPerformed(e);\r
 490                 }\r
 491             });\r
 492         taylorColour.setText("Taylor");\r
 493         taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 494             {\r
 495                 public void actionPerformed(ActionEvent e)\r
 496                 {\r
 497                     taylorColour_actionPerformed(e);\r
 498                 }\r
 499             });\r
 500         hydrophobicityColour.setText("Hydrophobicity");\r
 501         hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 502             {\r
 503                 public void actionPerformed(ActionEvent e)\r
 504                 {\r
 505                     hydrophobicityColour_actionPerformed(e);\r
 506                 }\r
 507             });\r
 508         helixColour.setText("Helix propensity");\r
 509         helixColour.addActionListener(new java.awt.event.ActionListener()\r
 510             {\r
 511                 public void actionPerformed(ActionEvent e)\r
 512                 {\r
 513                     helixColour_actionPerformed(e);\r
 514                 }\r
 515             });\r
 516         strandColour.setText("Strand propensity");\r
 517         strandColour.addActionListener(new java.awt.event.ActionListener()\r
 518             {\r
 519                 public void actionPerformed(ActionEvent e)\r
 520                 {\r
 521                     strandColour_actionPerformed(e);\r
 522                 }\r
 523             });\r
 524         turnColour.setText("Turn propensity");\r
 525         turnColour.addActionListener(new java.awt.event.ActionListener()\r
 526             {\r
 527                 public void actionPerformed(ActionEvent e)\r
 528                 {\r
 529                     turnColour_actionPerformed(e);\r
 530                 }\r
 531             });\r
 532         buriedColour.setText("Buried Index");\r
 533         buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 534             {\r
 535                 public void actionPerformed(ActionEvent e)\r
 536                 {\r
 537                     buriedColour_actionPerformed(e);\r
 538                 }\r
 539             });\r
 540         abovePIDColour.setText("Above % Identity");\r
 541         abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
 542             {\r
 543                 public void actionPerformed(ActionEvent e)\r
 544                 {\r
 545                     abovePIDColour_actionPerformed(e);\r
 546                 }\r
 547             });\r
 548         userDefinedColour.setText("User Defined...");\r
 549         userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 550             {\r
 551                 public void actionPerformed(ActionEvent e)\r
 552                 {\r
 553                     userDefinedColour_actionPerformed(e);\r
 554                 }\r
 555             });\r
 556         PIDColour.setText("Percentage Identity");\r
 557         PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 558             {\r
 559                 public void actionPerformed(ActionEvent e)\r
 560                 {\r
 561                     PIDColour_actionPerformed(e);\r
 562                 }\r
 563             });\r
 564         BLOSUM62Colour.setText("BLOSUM62");\r
 565         BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 566             {\r
 567                 public void actionPerformed(ActionEvent e)\r
 568                 {\r
 569                     BLOSUM62Colour_actionPerformed(e);\r
 570                 }\r
 571             });\r
 572         conservationMenuItem.setText("Conservation");\r
 573         conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 574             {\r
 575                 public void actionPerformed(ActionEvent e)\r
 576                 {\r
 577                     conservationMenuItem_actionPerformed(e);\r
 578                 }\r
 579             });\r
 580     }\r
 581 \r
 582     /**\r
 583      * DOCUMENT ME!\r
 584      */\r
 585     void refresh()\r
 586     {\r
 587         if (ap.overviewPanel != null)\r
 588           ap.overviewPanel.updateOverviewImage();\r
 589 \r
 590         ap.seqPanel.repaint();\r
 591     }\r
 592 \r
 593     /**\r
 594      * DOCUMENT ME!\r
 595      *\r
 596      * @param e DOCUMENT ME!\r
 597      */\r
 598     protected void clustalColour_actionPerformed(ActionEvent e)\r
 599     {\r
 600         SequenceGroup sg = getGroup();\r
 601         sg.cs = new ClustalxColourScheme(sg.sequences,\r
 602                 ap.av.alignment.getWidth());\r
 603         refresh();\r
 604     }\r
 605 \r
 606     /**\r
 607      * DOCUMENT ME!\r
 608      *\r
 609      * @param e DOCUMENT ME!\r
 610      */\r
 611     protected void zappoColour_actionPerformed(ActionEvent e)\r
 612     {\r
 613         getGroup().cs = new ZappoColourScheme();\r
 614         refresh();\r
 615     }\r
 616 \r
 617     /**\r
 618      * DOCUMENT ME!\r
 619      *\r
 620      * @param e DOCUMENT ME!\r
 621      */\r
 622     protected void taylorColour_actionPerformed(ActionEvent e)\r
 623     {\r
 624         getGroup().cs = new TaylorColourScheme();\r
 625         refresh();\r
 626     }\r
 627 \r
 628     /**\r
 629      * DOCUMENT ME!\r
 630      *\r
 631      * @param e DOCUMENT ME!\r
 632      */\r
 633     protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 634     {\r
 635         getGroup().cs = new HydrophobicColourScheme();\r
 636         refresh();\r
 637     }\r
 638 \r
 639     /**\r
 640      * DOCUMENT ME!\r
 641      *\r
 642      * @param e DOCUMENT ME!\r
 643      */\r
 644     protected void helixColour_actionPerformed(ActionEvent e)\r
 645     {\r
 646         getGroup().cs = new HelixColourScheme();\r
 647         refresh();\r
 648     }\r
 649 \r
 650     /**\r
 651      * DOCUMENT ME!\r
 652      *\r
 653      * @param e DOCUMENT ME!\r
 654      */\r
 655     protected void strandColour_actionPerformed(ActionEvent e)\r
 656     {\r
 657         getGroup().cs = new StrandColourScheme();\r
 658         refresh();\r
 659     }\r
 660 \r
 661     /**\r
 662      * DOCUMENT ME!\r
 663      *\r
 664      * @param e DOCUMENT ME!\r
 665      */\r
 666     protected void turnColour_actionPerformed(ActionEvent e)\r
 667     {\r
 668         getGroup().cs = new TurnColourScheme();\r
 669         refresh();\r
 670     }\r
 671 \r
 672     /**\r
 673      * DOCUMENT ME!\r
 674      *\r
 675      * @param e DOCUMENT ME!\r
 676      */\r
 677     protected void buriedColour_actionPerformed(ActionEvent e)\r
 678     {\r
 679         getGroup().cs = new BuriedColourScheme();\r
 680         refresh();\r
 681     }\r
 682 \r
 683     /**\r
 684      * DOCUMENT ME!\r
 685      *\r
 686      * @param e DOCUMENT ME!\r
 687      */\r
 688     public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
 689     {\r
 690         getGroup().cs = new NucleotideColourScheme();\r
 691         refresh();\r
 692     }\r
 693 \r
 694     /**\r
 695      * DOCUMENT ME!\r
 696      *\r
 697      * @param e DOCUMENT ME!\r
 698      */\r
 699     protected void abovePIDColour_actionPerformed(ActionEvent e)\r
 700     {\r
 701         SequenceGroup sg = getGroup();\r
 702         if(sg.cs==null)\r
 703           return;\r
 704 \r
 705         if (abovePIDColour.isSelected())\r
 706         {\r
 707             sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 708                     ap.av.alignment.getWidth()));\r
 709 \r
 710             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
 711                     getGroup().getName());\r
 712 \r
 713            sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
 714 \r
 715             SliderPanel.showPIDSlider();\r
 716         }\r
 717         else // remove PIDColouring\r
 718         {\r
 719             sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
 720         }\r
 721 \r
 722         refresh();\r
 723     }\r
 724 \r
 725     /**\r
 726      * DOCUMENT ME!\r
 727      *\r
 728      * @param e DOCUMENT ME!\r
 729      */\r
 730     protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 731     {\r
 732        SequenceGroup sg = getGroup();\r
 733 \r
 734        if (e.getActionCommand().equals("User Defined..."))\r
 735          new UserDefinedColours(ap, sg);\r
 736        else\r
 737        {\r
 738          UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
 739              getUserColourSchemes().get(e.getActionCommand());\r
 740 \r
 741          sg.cs = udc;\r
 742        }\r
 743      }\r
 744     /**\r
 745      * DOCUMENT ME!\r
 746      *\r
 747      * @param e DOCUMENT ME!\r
 748      */\r
 749     protected void PIDColour_actionPerformed(ActionEvent e)\r
 750     {\r
 751         SequenceGroup sg = getGroup();\r
 752         sg.cs = new PIDColourScheme();\r
 753         sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 754                 ap.av.alignment.getWidth()));\r
 755         refresh();\r
 756     }\r
 757 \r
 758     /**\r
 759      * DOCUMENT ME!\r
 760      *\r
 761      * @param e DOCUMENT ME!\r
 762      */\r
 763     protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 764     {\r
 765         SequenceGroup sg = getGroup();\r
 766 \r
 767         sg.cs = new Blosum62ColourScheme();\r
 768 \r
 769         sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 770                 ap.av.alignment.getWidth()));\r
 771 \r
 772         refresh();\r
 773     }\r
 774 \r
 775     /**\r
 776      * DOCUMENT ME!\r
 777      *\r
 778      * @param e DOCUMENT ME!\r
 779      */\r
 780     protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 781     {\r
 782         getGroup().cs = null;\r
 783         refresh();\r
 784     }\r
 785 \r
 786     /**\r
 787      * DOCUMENT ME!\r
 788      *\r
 789      * @param e DOCUMENT ME!\r
 790      */\r
 791     protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
 792     {\r
 793         SequenceGroup sg = getGroup();\r
 794         if(sg.cs==null)\r
 795           return;\r
 796 \r
 797         if (conservationMenuItem.isSelected())\r
 798         {\r
 799             Conservation c = new Conservation("Group",\r
 800                     ResidueProperties.propHash, 3, sg.sequences, 0,\r
 801                     ap.av.alignment.getWidth());\r
 802 \r
 803             c.calculate();\r
 804             c.verdict(false, ap.av.ConsPercGaps);\r
 805 \r
 806             sg.cs.setConservation(c);\r
 807 \r
 808             SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
 809             SliderPanel.showConservationSlider();\r
 810         }\r
 811         else // remove ConservationColouring\r
 812         {\r
 813             sg.cs.setConservation(null);\r
 814         }\r
 815 \r
 816         refresh();\r
 817     }\r
 818 \r
 819     /**\r
 820      * DOCUMENT ME!\r
 821      *\r
 822      * @param e DOCUMENT ME!\r
 823      */\r
 824     protected void groupName_actionPerformed(ActionEvent e)\r
 825     {\r
 826         SequenceGroup sg = getGroup();\r
 827         String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
 828                 "Enter new group name", "Edit group name",\r
 829                 JOptionPane.QUESTION_MESSAGE);\r
 830 \r
 831         if (reply == null)\r
 832         {\r
 833             return;\r
 834         }\r
 835 \r
 836         sg.setName(reply);\r
 837         groupName.setText(reply);\r
 838     }\r
 839 \r
 840     /**\r
 841      * DOCUMENT ME!\r
 842      *\r
 843      * @param e DOCUMENT ME!\r
 844      */\r
 845     protected void analyze_actionPerformed(ActionEvent e)\r
 846     {\r
 847         CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
 848         JInternalFrame frame = new JInternalFrame();\r
 849         frame.setContentPane(cap);\r
 850         Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
 851 \r
 852         SequenceGroup sg = getGroup();\r
 853         StringBuffer sb = new StringBuffer();\r
 854 \r
 855         for (int i = 0; i < sg.sequences.size(); i++)\r
 856         {\r
 857             Sequence tmp = (Sequence) sg.sequences.get(i);\r
 858             sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
 859             sb.append("\n");\r
 860         }\r
 861 \r
 862         sb.append("Something amazing will happen soon");\r
 863         cap.setText(sb.toString());\r
 864     }\r
 865 \r
 866     /**\r
 867      * DOCUMENT ME!\r
 868      *\r
 869      * @return DOCUMENT ME!\r
 870      */\r
 871     SequenceGroup getGroup()\r
 872     {\r
 873         SequenceGroup sg = ap.av.getSelectionGroup();\r
 874       // this method won't add a new group if it already exists\r
 875         if(sg!=null)\r
 876           ap.av.alignment.addGroup(sg);\r
 877 \r
 878         return sg;\r
 879     }\r
 880 \r
 881     /**\r
 882      * DOCUMENT ME!\r
 883      *\r
 884      * @param e DOCUMENT ME!\r
 885      */\r
 886     void sequenceName_actionPerformed(ActionEvent e)\r
 887     {\r
 888       JLabel idlabel = new JLabel(  "       Sequence Name ");\r
 889       JLabel desclabel = new JLabel("Sequence Description ");\r
 890       idlabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
 891       desclabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
 892       JTextField id = new JTextField(sequence.getName(), 40);\r
 893       JTextField description = new JTextField(sequence.getDescription(), 40);\r
 894       JPanel panel = new JPanel(new BorderLayout());\r
 895       JPanel panel2 = new JPanel(new BorderLayout());\r
 896       panel2.add(idlabel, BorderLayout.WEST);\r
 897       panel2.add(id, BorderLayout.CENTER);\r
 898       panel.add(panel2, BorderLayout.NORTH);\r
 899       panel2 = new JPanel(new BorderLayout());\r
 900       panel2.add(desclabel, BorderLayout.WEST);\r
 901       panel2.add(description, BorderLayout.CENTER);\r
 902       panel.add(panel2, BorderLayout.SOUTH);\r
 903 \r
 904 \r
 905        int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
 906           panel, "Edit Sequence Name/Description",\r
 907           JOptionPane.OK_CANCEL_OPTION );\r
 908 \r
 909 \r
 910         if (reply != JOptionPane.OK_OPTION )\r
 911         {\r
 912             return;\r
 913         }\r
 914 \r
 915         String s = id.getText();\r
 916 \r
 917         if (s != null)\r
 918         {\r
 919             if (s.indexOf(" ") > -1)\r
 920             {\r
 921                 JOptionPane.showMessageDialog(ap,\r
 922                     "Spaces have been converted to \"_\"",\r
 923                     "No spaces allowed in Sequence Name",\r
 924                     JOptionPane.WARNING_MESSAGE);\r
 925             }\r
 926 \r
 927             s = s.replace(' ', '_');\r
 928             sequence.getDatasetSequence().setName(s);\r
 929             sequence.setName(s);\r
 930             ap.repaint();\r
 931         }\r
 932 \r
 933         sequence.getDatasetSequence().setDescription(description.getText());\r
 934         sequence.setDescription(description.getText());\r
 935     }\r
 936 \r
 937     /**\r
 938      * DOCUMENT ME!\r
 939      *\r
 940      * @param e DOCUMENT ME!\r
 941      */\r
 942     void unGroupMenuItem_actionPerformed(ActionEvent e)\r
 943     {\r
 944         SequenceGroup sg = ap.av.getSelectionGroup();\r
 945         ap.av.alignment.deleteGroup(sg);\r
 946         ap.av.setSelectionGroup(null);\r
 947         refresh();\r
 948     }\r
 949 \r
 950 \r
 951     /**\r
 952      * DOCUMENT ME!\r
 953      *\r
 954      * @param e DOCUMENT ME!\r
 955      */\r
 956     protected void outline_actionPerformed(ActionEvent e)\r
 957     {\r
 958         SequenceGroup sg = getGroup();\r
 959         Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
 960                 Color.BLUE);\r
 961 \r
 962         if (col != null)\r
 963         {\r
 964             sg.setOutlineColour(col);\r
 965         }\r
 966 \r
 967         refresh();\r
 968     }\r
 969 \r
 970     /**\r
 971      * DOCUMENT ME!\r
 972      *\r
 973      * @param e DOCUMENT ME!\r
 974      */\r
 975     public void showBoxes_actionPerformed(ActionEvent e)\r
 976     {\r
 977         getGroup().setDisplayBoxes(showBoxes.isSelected());\r
 978         refresh();\r
 979     }\r
 980 \r
 981     /**\r
 982      * DOCUMENT ME!\r
 983      *\r
 984      * @param e DOCUMENT ME!\r
 985      */\r
 986     public void showText_actionPerformed(ActionEvent e)\r
 987     {\r
 988         getGroup().setDisplayText(showText.isSelected());\r
 989         refresh();\r
 990     }\r
 991 \r
 992     /**\r
 993      * DOCUMENT ME!\r
 994      *\r
 995      * @param e DOCUMENT ME!\r
 996      */\r
 997     public void showColourText_actionPerformed(ActionEvent e)\r
 998     {\r
 999         getGroup().setColourText(showColourText.isSelected());\r
1000         refresh();\r
1001     }\r
1002 \r
1003     public void showLink(String url)\r
1004     {\r
1005       try\r
1006       {\r
1007         jalview.util.BrowserLauncher.openURL(url);\r
1008       }\r
1009       catch (Exception ex)\r
1010       {\r
1011         JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
1012             "Unixers: Couldn't find default web browser."\r
1013            +"\nAdd the full path to your browser in Preferences.",\r
1014            "Web browser not found", JOptionPane.WARNING_MESSAGE );\r
1015 \r
1016 \r
1017         ex.printStackTrace();\r
1018       }\r
1019     }\r
1020 \r
1021     void hideSequences(boolean representGroup)\r
1022     {\r
1023       SequenceGroup sg = ap.av.getSelectionGroup();\r
1024       if(sg==null || sg.getSize()<1)\r
1025       {\r
1026         ap.av.hideSequence(sequence);\r
1027         return;\r
1028       }\r
1029 \r
1030         int index = 0;\r
1031         while(index < sg.sequences.size())\r
1032         {\r
1033           if(representGroup && sg.getSequenceAt(index)!=sequence)\r
1034           {\r
1035             sequence.addHiddenSequence(sg.getSequenceAt(index));\r
1036             ap.av.hideSequence(sg.getSequenceAt(index));\r
1037           }\r
1038           else if(!representGroup)\r
1039           {\r
1040             ap.av.hideSequence(sg.getSequenceAt(index));\r
1041           }\r
1042           index ++;\r
1043         }\r
1044 \r
1045         ap.av.setSelectionGroup(null);\r
1046         refresh();\r
1047     }\r
1048 \r
1049   public void copy_actionPerformed(ActionEvent e)\r
1050   {\r
1051     ap.alignFrame.copy_actionPerformed(null);\r
1052   }\r
1053 \r
1054   public void cut_actionPerformed(ActionEvent e)\r
1055   {\r
1056     ap.alignFrame.cut_actionPerformed(null);\r
1057   }\r
1058 \r
1059   public void upperCase_actionPerformed(ActionEvent e)\r
1060   {\r
1061     SequenceGroup sg = ap.av.getSelectionGroup();\r
1062     if(sg==null)\r
1063       return;\r
1064 \r
1065     for(int g=0; g<sg.getSize(); g++)\r
1066     {\r
1067       sg.getSequenceAt(g).changeCase(true, sg.getStartRes(), sg.getEndRes()+1);\r
1068     }\r
1069     ap.repaint();\r
1070   }\r
1071 \r
1072   public void lowerCase_actionPerformed(ActionEvent e)\r
1073   {\r
1074     SequenceGroup sg = ap.av.getSelectionGroup();\r
1075     if(sg==null)\r
1076       return;\r
1077 \r
1078     for(int g=0; g<sg.getSize(); g++)\r
1079     {\r
1080       sg.getSequenceAt(g).changeCase(false, sg.getStartRes(), sg.getEndRes()+1);\r
1081     }\r
1082     ap.repaint();\r
1083   }\r
1084 \r
1085   public void toggle_actionPerformed(ActionEvent e)\r
1086   {\r
1087     SequenceGroup sg = ap.av.getSelectionGroup();\r
1088     if (sg == null)\r
1089       return;\r
1090 \r
1091     for (int g = 0; g < sg.getSize(); g++)\r
1092     {\r
1093       sg.getSequenceAt(g).toggleCase(sg.getStartRes(), sg.getEndRes() + 1);\r
1094     }\r
1095 \r
1096     ap.repaint();\r
1097   }\r
1098 \r
1099 }\r