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