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