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 import java.util.Vector;\r
  36 import jalview.io.FormatAdapter;\r
  37 \r
  38 \r
  39 /**\r
  40  * DOCUMENT ME!\r
  41  *\r
  42  * @author $author$\r
  43  * @version $Revision$\r
  44  */\r
  45 public class PopupMenu extends JPopupMenu\r
  46 {\r
  47     JMenu groupMenu = new JMenu();\r
  48     JMenuItem groupName = new JMenuItem();\r
  49     protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  50     protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  51     protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  52     protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
  53     protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  54     protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  55     protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  56     protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  57     protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();\r
  58     protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  59     protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  60     protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  61     JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  62     protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  63     AlignmentPanel ap;\r
  64     JMenu sequenceMenu = new JMenu();\r
  65     JMenuItem sequenceName = new JMenuItem();\r
  66     Sequence sequence;\r
  67     JMenuItem unGroupMenuItem = new JMenuItem();\r
  68     JMenuItem outline = new JMenuItem();\r
  69     JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();\r
  70     JMenu colourMenu = new JMenu();\r
  71     JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();\r
  72     JCheckBoxMenuItem showText = new JCheckBoxMenuItem();\r
  73     JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();\r
  74   JMenu editMenu = new JMenu();\r
  75   JMenuItem cut = new JMenuItem();\r
  76   JMenuItem copy = new JMenuItem();\r
  77   JMenuItem upperCase = new JMenuItem();\r
  78   JMenuItem lowerCase = new JMenuItem();\r
  79   JMenuItem toggle = new JMenuItem();\r
  80   JMenu outputMenu = new JMenu();\r
  81 \r
  82   /**\r
  83      * Creates a new PopupMenu object.\r
  84      *\r
  85      * @param ap DOCUMENT ME!\r
  86      * @param seq DOCUMENT ME!\r
  87      */\r
  88     public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)\r
  89     {\r
  90         ///////////////////////////////////////////////////////////\r
  91         // If this is activated from the sequence panel, the user may want to\r
  92         // edit or annotate a particular residue. Therefore display the residue menu\r
  93         //\r
  94         // If from the IDPanel, we must display the sequence menu\r
  95         //////////////////////////////////////////////////////////\r
  96         this.ap = ap;\r
  97         sequence = seq;\r
  98 \r
  99         ButtonGroup colours = new ButtonGroup();\r
 100         colours.add(noColourmenuItem);\r
 101         colours.add(clustalColour);\r
 102         colours.add(zappoColour);\r
 103         colours.add(taylorColour);\r
 104         colours.add(hydrophobicityColour);\r
 105         colours.add(helixColour);\r
 106         colours.add(strandColour);\r
 107         colours.add(turnColour);\r
 108         colours.add(buriedColour);\r
 109         colours.add(abovePIDColour);\r
 110         colours.add(userDefinedColour);\r
 111         colours.add(PIDColour);\r
 112         colours.add(BLOSUM62Colour);\r
 113 \r
 114         for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)\r
 115         {\r
 116           JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
 117                                          elementAt(\r
 118                                              i));\r
 119           item.addActionListener(new java.awt.event.ActionListener()\r
 120           {\r
 121             public void actionPerformed(ActionEvent e)\r
 122             {\r
 123               outputText_actionPerformed(e);\r
 124             }\r
 125           });\r
 126 \r
 127           outputMenu.add(item);\r
 128         }\r
 129 \r
 130 \r
 131         try\r
 132         {\r
 133             jbInit();\r
 134         }\r
 135         catch (Exception e)\r
 136         {\r
 137             e.printStackTrace();\r
 138         }\r
 139 \r
 140 \r
 141         if (seq != null)\r
 142         {\r
 143           JMenuItem menuItem;\r
 144           if( seq.getDatasetSequence().getPDBId() != null)\r
 145           {\r
 146             java.util.Enumeration e = seq.getDatasetSequence().getPDBId().\r
 147                 elements();\r
 148             while (e.hasMoreElements())\r
 149             {\r
 150               final PDBEntry pdb = (PDBEntry) e.nextElement();\r
 151 \r
 152               menuItem = new JMenuItem();\r
 153               menuItem.setText("View PDB entry: " + pdb.getId());\r
 154               menuItem.addActionListener(new java.awt.event.ActionListener()\r
 155               {\r
 156                 public void actionPerformed(ActionEvent e)\r
 157                 {\r
 158                   new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);\r
 159                 }\r
 160               });\r
 161               sequenceMenu.add(menuItem);\r
 162             }\r
 163           }\r
 164 \r
 165           menuItem = new JMenuItem("Hide Sequences");\r
 166           menuItem.addActionListener(new java.awt.event.ActionListener()\r
 167               {\r
 168                 public void actionPerformed(ActionEvent e)\r
 169                 {\r
 170                   hideSequences(false);\r
 171                 }\r
 172               });\r
 173           sequenceMenu.add(menuItem);\r
 174 \r
 175           if(ap.av.getSelectionGroup() !=null\r
 176              && ap.av.getSelectionGroup().getSize(false)>1)\r
 177           {\r
 178             menuItem = new JMenuItem("Represent Group with " + seq.getName());\r
 179             menuItem.addActionListener(new java.awt.event.ActionListener()\r
 180             {\r
 181               public void actionPerformed(ActionEvent e)\r
 182               {\r
 183                 hideSequences(true);\r
 184               }\r
 185             });\r
 186             sequenceMenu.add(menuItem);\r
 187           }\r
 188 \r
 189           if (ap.av.hasHiddenRows)\r
 190           {\r
 191             final int index = ap.av.alignment.findIndex(seq);\r
 192 \r
 193             if (ap.av.adjustForHiddenSeqs(index) -\r
 194                 ap.av.adjustForHiddenSeqs(index - 1) > 1)\r
 195             {\r
 196               menuItem = new JMenuItem("Reveal");\r
 197               menuItem.addActionListener(new ActionListener()\r
 198               {\r
 199                 public void actionPerformed(ActionEvent e)\r
 200                 {\r
 201                   ap.av.showSequence(index);\r
 202                   ap.repaint();\r
 203                   if (ap.overviewPanel != null)\r
 204                     ap.overviewPanel.updateOverviewImage();\r
 205                 }\r
 206               });\r
 207               sequenceMenu.add(menuItem);\r
 208             }\r
 209 \r
 210             menuItem = new JMenuItem("Reveal All");\r
 211             menuItem.addActionListener(new ActionListener()\r
 212                 {\r
 213                   public void actionPerformed(ActionEvent e)\r
 214                   {\r
 215                     ap.av.showAllHiddenSeqs();\r
 216                     ap.repaint();\r
 217                     if (ap.overviewPanel != null)\r
 218                       ap.overviewPanel.updateOverviewImage();\r
 219                       }\r
 220                 });\r
 221 \r
 222             sequenceMenu.add(menuItem);\r
 223 \r
 224 \r
 225 \r
 226           }\r
 227 \r
 228 \r
 229         }\r
 230 \r
 231 \r
 232 \r
 233         SequenceGroup sg = ap.av.getSelectionGroup();\r
 234 \r
 235         if (sg != null)\r
 236         {\r
 237             groupName.setText(sg.getName());\r
 238 \r
 239             if (sg.cs instanceof ZappoColourScheme)\r
 240             {\r
 241                 zappoColour.setSelected(true);\r
 242             }\r
 243             else if (sg.cs instanceof TaylorColourScheme)\r
 244             {\r
 245                 taylorColour.setSelected(true);\r
 246             }\r
 247             else if (sg.cs instanceof PIDColourScheme)\r
 248             {\r
 249                 PIDColour.setSelected(true);\r
 250             }\r
 251             else if (sg.cs instanceof Blosum62ColourScheme)\r
 252             {\r
 253                 BLOSUM62Colour.setSelected(true);\r
 254             }\r
 255             else if (sg.cs instanceof UserColourScheme)\r
 256             {\r
 257                 userDefinedColour.setSelected(true);\r
 258             }\r
 259             else if (sg.cs instanceof HydrophobicColourScheme)\r
 260             {\r
 261                 hydrophobicityColour.setSelected(true);\r
 262             }\r
 263             else if (sg.cs instanceof HelixColourScheme)\r
 264             {\r
 265                 helixColour.setSelected(true);\r
 266             }\r
 267             else if (sg.cs instanceof StrandColourScheme)\r
 268             {\r
 269                 strandColour.setSelected(true);\r
 270             }\r
 271             else if (sg.cs instanceof TurnColourScheme)\r
 272             {\r
 273                 turnColour.setSelected(true);\r
 274             }\r
 275             else if (sg.cs instanceof BuriedColourScheme)\r
 276             {\r
 277                 buriedColour.setSelected(true);\r
 278             }\r
 279             else if (sg.cs instanceof ClustalxColourScheme)\r
 280             {\r
 281                 clustalColour.setSelected(true);\r
 282             }\r
 283             else\r
 284             {\r
 285                 noColourmenuItem.setSelected(true);\r
 286             }\r
 287 \r
 288             if (sg.cs!=null && sg.cs.conservationApplied())\r
 289             {\r
 290                 conservationMenuItem.setSelected(true);\r
 291             }\r
 292 \r
 293             showText.setSelected(sg.getDisplayText());\r
 294             showColourText.setSelected(sg.getColourText());\r
 295             showBoxes.setSelected(sg.getDisplayBoxes());\r
 296         }\r
 297         else\r
 298         {\r
 299           groupMenu.setVisible(false);\r
 300           editMenu.setVisible(false);\r
 301         }\r
 302 \r
 303         if (!ap.av.alignment.getGroups().contains(sg))\r
 304         {\r
 305             unGroupMenuItem.setVisible(false);\r
 306         }\r
 307         else\r
 308         {\r
 309             groupMenu.insertSeparator(3);\r
 310         }\r
 311 \r
 312         if (seq == null)\r
 313         {\r
 314             sequenceMenu.setVisible(false);\r
 315         }\r
 316 \r
 317         if(links != null && links.size()>0)\r
 318         {\r
 319           JMenu linkMenu = new JMenu("Link");\r
 320           JMenuItem item;\r
 321           for(int i=0; i<links.size(); i++)\r
 322           {\r
 323             String link = links.elementAt(i).toString();\r
 324             final String label = link.substring(0, link.indexOf("|"));\r
 325             item = new JMenuItem(label);\r
 326             final String url;\r
 327 \r
 328             if (link.indexOf("$SEQUENCE_ID$") > -1)\r
 329             {\r
 330               String id = seq.getName();\r
 331               if (id.indexOf("|") > -1)\r
 332                 id = id.substring(id.lastIndexOf("|") + 1);\r
 333 \r
 334               url = link.substring(link.indexOf("|") + 1,\r
 335                                    link.indexOf("$SEQUENCE_ID$"))\r
 336                   + id +\r
 337                   link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
 338             }\r
 339             else\r
 340               url = link.substring(link.lastIndexOf("|")+1);\r
 341 \r
 342 \r
 343             item.addActionListener(new java.awt.event.ActionListener()\r
 344             {\r
 345                 public void actionPerformed(ActionEvent e)\r
 346                 {\r
 347                     showLink(url);\r
 348                 }\r
 349             });\r
 350 \r
 351             linkMenu.add(item);\r
 352           }\r
 353           add(linkMenu);\r
 354         }\r
 355     }\r
 356 \r
 357 \r
 358     /**\r
 359      * DOCUMENT ME!\r
 360      *\r
 361      * @throws Exception DOCUMENT ME!\r
 362      */\r
 363     private void jbInit() throws Exception\r
 364     {\r
 365         groupMenu.setText("Group");\r
 366         groupMenu.setText("Group");\r
 367         groupName.setText("Name");\r
 368         groupName.addActionListener(new java.awt.event.ActionListener()\r
 369             {\r
 370                 public void actionPerformed(ActionEvent e)\r
 371                 {\r
 372                     groupName_actionPerformed(e);\r
 373                 }\r
 374             });\r
 375         sequenceMenu.setText("Sequence");\r
 376         sequenceName.setText("Edit Name/Description");\r
 377         sequenceName.addActionListener(new java.awt.event.ActionListener()\r
 378             {\r
 379                 public void actionPerformed(ActionEvent e)\r
 380                 {\r
 381                     sequenceName_actionPerformed(e);\r
 382                 }\r
 383             });\r
 384         PIDColour.setFocusPainted(false);\r
 385         unGroupMenuItem.setText("Remove Group");\r
 386         unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 387             {\r
 388                 public void actionPerformed(ActionEvent e)\r
 389                 {\r
 390                     unGroupMenuItem_actionPerformed(e);\r
 391                 }\r
 392             });\r
 393 \r
 394         outline.setText("Border colour");\r
 395         outline.addActionListener(new java.awt.event.ActionListener()\r
 396             {\r
 397                 public void actionPerformed(ActionEvent e)\r
 398                 {\r
 399                     outline_actionPerformed(e);\r
 400                 }\r
 401             });\r
 402         nucleotideMenuItem.setText("Nucleotide");\r
 403         nucleotideMenuItem.addActionListener(new ActionListener()\r
 404             {\r
 405                 public void actionPerformed(ActionEvent e)\r
 406                 {\r
 407                     nucleotideMenuItem_actionPerformed(e);\r
 408                 }\r
 409             });\r
 410         colourMenu.setText("Group Colour");\r
 411         showBoxes.setText("Boxes");\r
 412         showBoxes.setState(true);\r
 413         showBoxes.addActionListener(new ActionListener()\r
 414             {\r
 415                 public void actionPerformed(ActionEvent e)\r
 416                 {\r
 417                     showBoxes_actionPerformed(e);\r
 418                 }\r
 419             });\r
 420         showText.setText("Text");\r
 421         showText.setState(true);\r
 422         showText.addActionListener(new ActionListener()\r
 423             {\r
 424                 public void actionPerformed(ActionEvent e)\r
 425                 {\r
 426                     showText_actionPerformed(e);\r
 427                 }\r
 428             });\r
 429         showColourText.setText("Colour Text");\r
 430         showColourText.addActionListener(new ActionListener()\r
 431             {\r
 432                 public void actionPerformed(ActionEvent e)\r
 433                 {\r
 434                     showColourText_actionPerformed(e);\r
 435                 }\r
 436             });\r
 437     editMenu.setText("Edit");\r
 438     cut.setText("Cut");\r
 439     cut.addActionListener(new ActionListener()\r
 440     {\r
 441       public void actionPerformed(ActionEvent e)\r
 442       {\r
 443         cut_actionPerformed(e);\r
 444       }\r
 445     });\r
 446     upperCase.setText("To Upper Case");\r
 447     upperCase.addActionListener(new ActionListener()\r
 448     {\r
 449       public void actionPerformed(ActionEvent e)\r
 450       {\r
 451         upperCase_actionPerformed(e);\r
 452       }\r
 453     });\r
 454     copy.setText("Copy");\r
 455     copy.addActionListener(new ActionListener()\r
 456     {\r
 457       public void actionPerformed(ActionEvent e)\r
 458       {\r
 459         copy_actionPerformed(e);\r
 460       }\r
 461     });\r
 462     lowerCase.setText("To Lower Case");\r
 463     lowerCase.addActionListener(new ActionListener()\r
 464     {\r
 465       public void actionPerformed(ActionEvent e)\r
 466       {\r
 467         lowerCase_actionPerformed(e);\r
 468       }\r
 469     });\r
 470     toggle.setText("Toggle Case");\r
 471     toggle.addActionListener(new ActionListener()\r
 472     {\r
 473       public void actionPerformed(ActionEvent e)\r
 474       {\r
 475         toggle_actionPerformed(e);\r
 476       }\r
 477     });\r
 478     outputMenu.setText("Output to Textbox...");\r
 479     add(groupMenu);\r
 480         add(sequenceMenu);\r
 481     this.add(editMenu);\r
 482     this.add(outputMenu);\r
 483     groupMenu.add(groupName);\r
 484         groupMenu.addSeparator();\r
 485         groupMenu.add(unGroupMenuItem);\r
 486         groupMenu.add(colourMenu);\r
 487         groupMenu.addSeparator();\r
 488         groupMenu.add(showBoxes);\r
 489         groupMenu.add(showText);\r
 490         groupMenu.add(showColourText);\r
 491         groupMenu.addSeparator();\r
 492         groupMenu.add(outline);\r
 493         sequenceMenu.add(sequenceName);\r
 494         colourMenu.add(noColourmenuItem);\r
 495         colourMenu.add(clustalColour);\r
 496         colourMenu.add(BLOSUM62Colour);\r
 497         colourMenu.add(PIDColour);\r
 498         colourMenu.add(zappoColour);\r
 499         colourMenu.add(taylorColour);\r
 500         colourMenu.add(hydrophobicityColour);\r
 501         colourMenu.add(helixColour);\r
 502         colourMenu.add(strandColour);\r
 503         colourMenu.add(turnColour);\r
 504         colourMenu.add(buriedColour);\r
 505         colourMenu.add(nucleotideMenuItem);\r
 506         colourMenu.add(userDefinedColour);\r
 507 \r
 508         if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
 509         {\r
 510           java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 511               getUserColourSchemes().keys();\r
 512 \r
 513           while (userColours.hasMoreElements())\r
 514           {\r
 515             JMenuItem item = new JMenuItem(userColours.\r
 516                 nextElement().toString());\r
 517             item.addActionListener(new ActionListener()\r
 518             {\r
 519               public void actionPerformed(ActionEvent evt)\r
 520               {\r
 521                 userDefinedColour_actionPerformed(evt);\r
 522               }\r
 523             });\r
 524             colourMenu.add(item);\r
 525           }\r
 526         }\r
 527 \r
 528 \r
 529         colourMenu.addSeparator();\r
 530         colourMenu.add(abovePIDColour);\r
 531         colourMenu.add(conservationMenuItem);\r
 532     editMenu.add(copy);\r
 533     editMenu.add(cut);\r
 534     editMenu.add(upperCase);\r
 535     editMenu.add(lowerCase);\r
 536     editMenu.add(toggle);\r
 537     noColourmenuItem.setText("None");\r
 538         noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 539             {\r
 540                 public void actionPerformed(ActionEvent e)\r
 541                 {\r
 542                     noColourmenuItem_actionPerformed(e);\r
 543                 }\r
 544             });\r
 545 \r
 546         clustalColour.setText("Clustalx colours");\r
 547         clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 548             {\r
 549                 public void actionPerformed(ActionEvent e)\r
 550                 {\r
 551                     clustalColour_actionPerformed(e);\r
 552                 }\r
 553             });\r
 554         zappoColour.setText("Zappo");\r
 555         zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 556             {\r
 557                 public void actionPerformed(ActionEvent e)\r
 558                 {\r
 559                     zappoColour_actionPerformed(e);\r
 560                 }\r
 561             });\r
 562         taylorColour.setText("Taylor");\r
 563         taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 564             {\r
 565                 public void actionPerformed(ActionEvent e)\r
 566                 {\r
 567                     taylorColour_actionPerformed(e);\r
 568                 }\r
 569             });\r
 570         hydrophobicityColour.setText("Hydrophobicity");\r
 571         hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 572             {\r
 573                 public void actionPerformed(ActionEvent e)\r
 574                 {\r
 575                     hydrophobicityColour_actionPerformed(e);\r
 576                 }\r
 577             });\r
 578         helixColour.setText("Helix propensity");\r
 579         helixColour.addActionListener(new java.awt.event.ActionListener()\r
 580             {\r
 581                 public void actionPerformed(ActionEvent e)\r
 582                 {\r
 583                     helixColour_actionPerformed(e);\r
 584                 }\r
 585             });\r
 586         strandColour.setText("Strand propensity");\r
 587         strandColour.addActionListener(new java.awt.event.ActionListener()\r
 588             {\r
 589                 public void actionPerformed(ActionEvent e)\r
 590                 {\r
 591                     strandColour_actionPerformed(e);\r
 592                 }\r
 593             });\r
 594         turnColour.setText("Turn propensity");\r
 595         turnColour.addActionListener(new java.awt.event.ActionListener()\r
 596             {\r
 597                 public void actionPerformed(ActionEvent e)\r
 598                 {\r
 599                     turnColour_actionPerformed(e);\r
 600                 }\r
 601             });\r
 602         buriedColour.setText("Buried Index");\r
 603         buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 604             {\r
 605                 public void actionPerformed(ActionEvent e)\r
 606                 {\r
 607                     buriedColour_actionPerformed(e);\r
 608                 }\r
 609             });\r
 610         abovePIDColour.setText("Above % Identity");\r
 611         abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
 612             {\r
 613                 public void actionPerformed(ActionEvent e)\r
 614                 {\r
 615                     abovePIDColour_actionPerformed(e);\r
 616                 }\r
 617             });\r
 618         userDefinedColour.setText("User Defined...");\r
 619         userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 620             {\r
 621                 public void actionPerformed(ActionEvent e)\r
 622                 {\r
 623                     userDefinedColour_actionPerformed(e);\r
 624                 }\r
 625             });\r
 626         PIDColour.setText("Percentage Identity");\r
 627         PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 628             {\r
 629                 public void actionPerformed(ActionEvent e)\r
 630                 {\r
 631                     PIDColour_actionPerformed(e);\r
 632                 }\r
 633             });\r
 634         BLOSUM62Colour.setText("BLOSUM62");\r
 635         BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 636             {\r
 637                 public void actionPerformed(ActionEvent e)\r
 638                 {\r
 639                     BLOSUM62Colour_actionPerformed(e);\r
 640                 }\r
 641             });\r
 642         conservationMenuItem.setText("Conservation");\r
 643         conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 644             {\r
 645                 public void actionPerformed(ActionEvent e)\r
 646                 {\r
 647                     conservationMenuItem_actionPerformed(e);\r
 648                 }\r
 649             });\r
 650     }\r
 651 \r
 652     /**\r
 653      * DOCUMENT ME!\r
 654      */\r
 655     void refresh()\r
 656     {\r
 657         if (ap.overviewPanel != null)\r
 658           ap.overviewPanel.updateOverviewImage();\r
 659 \r
 660         ap.seqPanel.repaint();\r
 661     }\r
 662 \r
 663     /**\r
 664      * DOCUMENT ME!\r
 665      *\r
 666      * @param e DOCUMENT ME!\r
 667      */\r
 668     protected void clustalColour_actionPerformed(ActionEvent e)\r
 669     {\r
 670         SequenceGroup sg = getGroup();\r
 671         sg.cs = new ClustalxColourScheme(sg.getSequences(true),\r
 672                 ap.av.alignment.getWidth());\r
 673         refresh();\r
 674     }\r
 675 \r
 676     /**\r
 677      * DOCUMENT ME!\r
 678      *\r
 679      * @param e DOCUMENT ME!\r
 680      */\r
 681     protected void zappoColour_actionPerformed(ActionEvent e)\r
 682     {\r
 683         getGroup().cs = new ZappoColourScheme();\r
 684         refresh();\r
 685     }\r
 686 \r
 687     /**\r
 688      * DOCUMENT ME!\r
 689      *\r
 690      * @param e DOCUMENT ME!\r
 691      */\r
 692     protected void taylorColour_actionPerformed(ActionEvent e)\r
 693     {\r
 694         getGroup().cs = new TaylorColourScheme();\r
 695         refresh();\r
 696     }\r
 697 \r
 698     /**\r
 699      * DOCUMENT ME!\r
 700      *\r
 701      * @param e DOCUMENT ME!\r
 702      */\r
 703     protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 704     {\r
 705         getGroup().cs = new HydrophobicColourScheme();\r
 706         refresh();\r
 707     }\r
 708 \r
 709     /**\r
 710      * DOCUMENT ME!\r
 711      *\r
 712      * @param e DOCUMENT ME!\r
 713      */\r
 714     protected void helixColour_actionPerformed(ActionEvent e)\r
 715     {\r
 716         getGroup().cs = new HelixColourScheme();\r
 717         refresh();\r
 718     }\r
 719 \r
 720     /**\r
 721      * DOCUMENT ME!\r
 722      *\r
 723      * @param e DOCUMENT ME!\r
 724      */\r
 725     protected void strandColour_actionPerformed(ActionEvent e)\r
 726     {\r
 727         getGroup().cs = new StrandColourScheme();\r
 728         refresh();\r
 729     }\r
 730 \r
 731     /**\r
 732      * DOCUMENT ME!\r
 733      *\r
 734      * @param e DOCUMENT ME!\r
 735      */\r
 736     protected void turnColour_actionPerformed(ActionEvent e)\r
 737     {\r
 738         getGroup().cs = new TurnColourScheme();\r
 739         refresh();\r
 740     }\r
 741 \r
 742     /**\r
 743      * DOCUMENT ME!\r
 744      *\r
 745      * @param e DOCUMENT ME!\r
 746      */\r
 747     protected void buriedColour_actionPerformed(ActionEvent e)\r
 748     {\r
 749         getGroup().cs = new BuriedColourScheme();\r
 750         refresh();\r
 751     }\r
 752 \r
 753     /**\r
 754      * DOCUMENT ME!\r
 755      *\r
 756      * @param e DOCUMENT ME!\r
 757      */\r
 758     public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
 759     {\r
 760         getGroup().cs = new NucleotideColourScheme();\r
 761         refresh();\r
 762     }\r
 763 \r
 764     /**\r
 765      * DOCUMENT ME!\r
 766      *\r
 767      * @param e DOCUMENT ME!\r
 768      */\r
 769     protected void abovePIDColour_actionPerformed(ActionEvent e)\r
 770     {\r
 771         SequenceGroup sg = getGroup();\r
 772         if(sg.cs==null)\r
 773           return;\r
 774 \r
 775         if (abovePIDColour.isSelected())\r
 776         {\r
 777             sg.cs.setConsensus(AAFrequency.calculate(\r
 778                     sg.getSequences(true), 0,\r
 779                     ap.av.alignment.getWidth()));\r
 780 \r
 781             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
 782                     getGroup().getName());\r
 783 \r
 784            sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
 785 \r
 786             SliderPanel.showPIDSlider();\r
 787         }\r
 788         else // remove PIDColouring\r
 789         {\r
 790             sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
 791         }\r
 792 \r
 793         refresh();\r
 794     }\r
 795 \r
 796     /**\r
 797      * DOCUMENT ME!\r
 798      *\r
 799      * @param e DOCUMENT ME!\r
 800      */\r
 801     protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 802     {\r
 803        SequenceGroup sg = getGroup();\r
 804 \r
 805        if (e.getActionCommand().equals("User Defined..."))\r
 806          new UserDefinedColours(ap, sg);\r
 807        else\r
 808        {\r
 809          UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
 810              getUserColourSchemes().get(e.getActionCommand());\r
 811 \r
 812          sg.cs = udc;\r
 813        }\r
 814      }\r
 815     /**\r
 816      * DOCUMENT ME!\r
 817      *\r
 818      * @param e DOCUMENT ME!\r
 819      */\r
 820     protected void PIDColour_actionPerformed(ActionEvent e)\r
 821     {\r
 822         SequenceGroup sg = getGroup();\r
 823         sg.cs = new PIDColourScheme();\r
 824         sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
 825                 ap.av.alignment.getWidth()));\r
 826         refresh();\r
 827     }\r
 828 \r
 829     /**\r
 830      * DOCUMENT ME!\r
 831      *\r
 832      * @param e DOCUMENT ME!\r
 833      */\r
 834     protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 835     {\r
 836         SequenceGroup sg = getGroup();\r
 837 \r
 838         sg.cs = new Blosum62ColourScheme();\r
 839 \r
 840         sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
 841                 ap.av.alignment.getWidth()));\r
 842 \r
 843         refresh();\r
 844     }\r
 845 \r
 846     /**\r
 847      * DOCUMENT ME!\r
 848      *\r
 849      * @param e DOCUMENT ME!\r
 850      */\r
 851     protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 852     {\r
 853         getGroup().cs = null;\r
 854         refresh();\r
 855     }\r
 856 \r
 857     /**\r
 858      * DOCUMENT ME!\r
 859      *\r
 860      * @param e DOCUMENT ME!\r
 861      */\r
 862     protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
 863     {\r
 864         SequenceGroup sg = getGroup();\r
 865         if(sg.cs==null)\r
 866           return;\r
 867 \r
 868         if (conservationMenuItem.isSelected())\r
 869         {\r
 870             Conservation c = new Conservation("Group",\r
 871                     ResidueProperties.propHash, 3,\r
 872                     sg.getSequences(true), 0,\r
 873                     ap.av.alignment.getWidth());\r
 874 \r
 875             c.calculate();\r
 876             c.verdict(false, ap.av.ConsPercGaps);\r
 877 \r
 878             sg.cs.setConservation(c);\r
 879 \r
 880             SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
 881             SliderPanel.showConservationSlider();\r
 882         }\r
 883         else // remove ConservationColouring\r
 884         {\r
 885             sg.cs.setConservation(null);\r
 886         }\r
 887 \r
 888         refresh();\r
 889     }\r
 890 \r
 891     /**\r
 892      * DOCUMENT ME!\r
 893      *\r
 894      * @param e DOCUMENT ME!\r
 895      */\r
 896     protected void groupName_actionPerformed(ActionEvent e)\r
 897     {\r
 898         SequenceGroup sg = getGroup();\r
 899         String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
 900                 "Enter new group name", "Edit group name",\r
 901                 JOptionPane.QUESTION_MESSAGE);\r
 902 \r
 903         if (reply == null)\r
 904         {\r
 905             return;\r
 906         }\r
 907 \r
 908         sg.setName(reply);\r
 909         groupName.setText(reply);\r
 910     }\r
 911 \r
 912     /**\r
 913      * DOCUMENT ME!\r
 914      *\r
 915      * @param e DOCUMENT ME!\r
 916      */\r
 917     protected void analyze_actionPerformed(ActionEvent e)\r
 918     {\r
 919         CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
 920         JInternalFrame frame = new JInternalFrame();\r
 921         frame.setContentPane(cap);\r
 922         Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
 923 \r
 924         SequenceGroup sg = getGroup();\r
 925         StringBuffer sb = new StringBuffer();\r
 926 \r
 927         for (int i = 0; i < sg.getSize(false); i++)\r
 928         {\r
 929             Sequence tmp = (Sequence) sg.getSequences(false).elementAt(i);\r
 930             sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
 931             sb.append("\n");\r
 932         }\r
 933 \r
 934         sb.append("Something amazing will happen soon");\r
 935         cap.setText(sb.toString());\r
 936     }\r
 937 \r
 938     /**\r
 939      * DOCUMENT ME!\r
 940      *\r
 941      * @return DOCUMENT ME!\r
 942      */\r
 943     SequenceGroup getGroup()\r
 944     {\r
 945         SequenceGroup sg = ap.av.getSelectionGroup();\r
 946       // this method won't add a new group if it already exists\r
 947         if(sg!=null)\r
 948           ap.av.alignment.addGroup(sg);\r
 949 \r
 950         return sg;\r
 951     }\r
 952 \r
 953     /**\r
 954      * DOCUMENT ME!\r
 955      *\r
 956      * @param e DOCUMENT ME!\r
 957      */\r
 958     void sequenceName_actionPerformed(ActionEvent e)\r
 959     {\r
 960       JLabel idlabel = new JLabel(  "       Sequence Name ");\r
 961       JLabel desclabel = new JLabel("Sequence Description ");\r
 962       idlabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
 963       desclabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
 964       JTextField id = new JTextField(sequence.getName(), 40);\r
 965       JTextField description = new JTextField(sequence.getDescription(), 40);\r
 966       JPanel panel = new JPanel(new BorderLayout());\r
 967       JPanel panel2 = new JPanel(new BorderLayout());\r
 968       panel2.add(idlabel, BorderLayout.WEST);\r
 969       panel2.add(id, BorderLayout.CENTER);\r
 970       panel.add(panel2, BorderLayout.NORTH);\r
 971       panel2 = new JPanel(new BorderLayout());\r
 972       panel2.add(desclabel, BorderLayout.WEST);\r
 973       panel2.add(description, BorderLayout.CENTER);\r
 974       panel.add(panel2, BorderLayout.SOUTH);\r
 975 \r
 976 \r
 977        int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
 978           panel, "Edit Sequence Name/Description",\r
 979           JOptionPane.OK_CANCEL_OPTION );\r
 980 \r
 981 \r
 982         if (reply != JOptionPane.OK_OPTION )\r
 983         {\r
 984             return;\r
 985         }\r
 986 \r
 987         String s = id.getText();\r
 988 \r
 989         if (s != null)\r
 990         {\r
 991             if (s.indexOf(" ") > -1)\r
 992             {\r
 993                 JOptionPane.showMessageDialog(ap,\r
 994                     "Spaces have been converted to \"_\"",\r
 995                     "No spaces allowed in Sequence Name",\r
 996                     JOptionPane.WARNING_MESSAGE);\r
 997             }\r
 998 \r
 999             s = s.replace(' ', '_');\r
1000             sequence.getDatasetSequence().setName(s);\r
1001             sequence.setName(s);\r
1002             ap.repaint();\r
1003         }\r
1004 \r
1005         sequence.getDatasetSequence().setDescription(description.getText());\r
1006         sequence.setDescription(description.getText());\r
1007     }\r
1008 \r
1009     /**\r
1010      * DOCUMENT ME!\r
1011      *\r
1012      * @param e DOCUMENT ME!\r
1013      */\r
1014     void unGroupMenuItem_actionPerformed(ActionEvent e)\r
1015     {\r
1016         SequenceGroup sg = ap.av.getSelectionGroup();\r
1017         ap.av.alignment.deleteGroup(sg);\r
1018         ap.av.setSelectionGroup(null);\r
1019         refresh();\r
1020     }\r
1021 \r
1022 \r
1023     /**\r
1024      * DOCUMENT ME!\r
1025      *\r
1026      * @param e DOCUMENT ME!\r
1027      */\r
1028     protected void outline_actionPerformed(ActionEvent e)\r
1029     {\r
1030         SequenceGroup sg = getGroup();\r
1031         Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
1032                 Color.BLUE);\r
1033 \r
1034         if (col != null)\r
1035         {\r
1036             sg.setOutlineColour(col);\r
1037         }\r
1038 \r
1039         refresh();\r
1040     }\r
1041 \r
1042     /**\r
1043      * DOCUMENT ME!\r
1044      *\r
1045      * @param e DOCUMENT ME!\r
1046      */\r
1047     public void showBoxes_actionPerformed(ActionEvent e)\r
1048     {\r
1049         getGroup().setDisplayBoxes(showBoxes.isSelected());\r
1050         refresh();\r
1051     }\r
1052 \r
1053     /**\r
1054      * DOCUMENT ME!\r
1055      *\r
1056      * @param e DOCUMENT ME!\r
1057      */\r
1058     public void showText_actionPerformed(ActionEvent e)\r
1059     {\r
1060         getGroup().setDisplayText(showText.isSelected());\r
1061         refresh();\r
1062     }\r
1063 \r
1064     /**\r
1065      * DOCUMENT ME!\r
1066      *\r
1067      * @param e DOCUMENT ME!\r
1068      */\r
1069     public void showColourText_actionPerformed(ActionEvent e)\r
1070     {\r
1071         getGroup().setColourText(showColourText.isSelected());\r
1072         refresh();\r
1073     }\r
1074 \r
1075     public void showLink(String url)\r
1076     {\r
1077       try\r
1078       {\r
1079         jalview.util.BrowserLauncher.openURL(url);\r
1080       }\r
1081       catch (Exception ex)\r
1082       {\r
1083         JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
1084             "Unixers: Couldn't find default web browser."\r
1085            +"\nAdd the full path to your browser in Preferences.",\r
1086            "Web browser not found", JOptionPane.WARNING_MESSAGE );\r
1087 \r
1088 \r
1089         ex.printStackTrace();\r
1090       }\r
1091     }\r
1092 \r
1093     void hideSequences(boolean representGroup)\r
1094     {\r
1095       SequenceGroup sg = ap.av.getSelectionGroup();\r
1096       if(sg==null || sg.getSize(false)<1)\r
1097       {\r
1098         ap.av.hideSequence(sequence);\r
1099         return;\r
1100       }\r
1101 \r
1102         int index = 0;\r
1103         while(index < sg.getSize(false))\r
1104         {\r
1105           if(representGroup && sg.getSequenceAt(index)!=sequence)\r
1106           {\r
1107             sequence.addHiddenSequence(sg.getSequenceAt(index));\r
1108             ap.av.hideSequence(sg.getSequenceAt(index));\r
1109           }\r
1110           else if(!representGroup)\r
1111           {\r
1112             ap.av.hideSequence(sg.getSequenceAt(index));\r
1113           }\r
1114           index ++;\r
1115         }\r
1116 \r
1117         ap.av.setSelectionGroup(null);\r
1118         refresh();\r
1119     }\r
1120 \r
1121   public void copy_actionPerformed(ActionEvent e)\r
1122   {\r
1123     ap.alignFrame.copy_actionPerformed(null);\r
1124   }\r
1125 \r
1126   public void cut_actionPerformed(ActionEvent e)\r
1127   {\r
1128     ap.alignFrame.cut_actionPerformed(null);\r
1129   }\r
1130 \r
1131   public void upperCase_actionPerformed(ActionEvent e)\r
1132   {\r
1133     SequenceGroup sg = ap.av.getSelectionGroup();\r
1134     if(sg==null)\r
1135       return;\r
1136 \r
1137     for(int g=0; g<sg.getSize(true); g++)\r
1138     {\r
1139     ( (SequenceI)sg.getSequences(true).elementAt(g))\r
1140         .changeCase(true, sg.getStartRes(), sg.getEndRes()+1);\r
1141     }\r
1142     ap.repaint();\r
1143   }\r
1144 \r
1145   public void lowerCase_actionPerformed(ActionEvent e)\r
1146   {\r
1147     SequenceGroup sg = ap.av.getSelectionGroup();\r
1148     if(sg==null)\r
1149       return;\r
1150 \r
1151     for(int g=0; g<sg.getSize(true); g++)\r
1152     {\r
1153        ( (SequenceI)sg.getSequences(true).elementAt(g))\r
1154            .changeCase(false, sg.getStartRes(), sg.getEndRes()+1);\r
1155     }\r
1156     ap.repaint();\r
1157   }\r
1158 \r
1159   public void toggle_actionPerformed(ActionEvent e)\r
1160   {\r
1161     SequenceGroup sg = ap.av.getSelectionGroup();\r
1162     if (sg == null)\r
1163       return;\r
1164 \r
1165     for (int g = 0; g < sg.getSize(true); g++)\r
1166     {\r
1167       ( (SequenceI)sg.getSequences(true).elementAt(g))\r
1168           .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);\r
1169     }\r
1170 \r
1171     ap.repaint();\r
1172   }\r
1173 \r
1174   public void outputText_actionPerformed(ActionEvent e)\r
1175   {\r
1176     CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
1177     Desktop.addInternalFrame(cap,\r
1178                              "Alignment output - " + e.getActionCommand(), 600,\r
1179                              500);\r
1180 \r
1181     String [] omitHidden = null;\r
1182 \r
1183     if(ap.av.hasHiddenColumns)\r
1184     {\r
1185       System.out.println("PROMPT USER HERE");\r
1186       omitHidden = ap.av.getViewAsString(true);\r
1187     }\r
1188 \r
1189     cap.setText(new FormatAdapter().formatSequences(\r
1190         e.getActionCommand(),\r
1191         ap.av.getSelectionAsNewSequence(),\r
1192         omitHidden));\r
1193   }\r
1194 }\r