src/jalview/gui/PopupMenu.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 package jalview.gui;\r
  20 \r
  21 import MCview.*;\r
  22 \r
  23 import jalview.analysis.*;\r
  24 \r
  25 import jalview.datamodel.*;\r
  26 \r
  27 \r
  28 import jalview.schemes.*;\r
  29 \r
  30 import java.awt.*;\r
  31 import java.awt.event.*;\r
  32 \r
  33 import javax.swing.*;\r
  34 \r
  35 \r
  36 /**\r
  37  * DOCUMENT ME!\r
  38  *\r
  39  * @author $author$\r
  40  * @version $Revision$\r
  41  */\r
  42 public class PopupMenu extends JPopupMenu\r
  43 {\r
  44     JMenu groupMenu = new JMenu();\r
  45     JMenuItem groupName = new JMenuItem();\r
  46     protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  47     protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  48     protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  49     protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
  50     protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  51     protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  52     protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  53     protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  54     protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();\r
  55     protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  56     protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  57     protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  58     JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  59     protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  60     AlignmentPanel ap;\r
  61     JMenu sequenceMenu = new JMenu();\r
  62     JMenuItem sequenceName = new JMenuItem();\r
  63     Sequence sequence;\r
  64     JMenuItem unGroupMenuItem = new JMenuItem();\r
  65     JMenuItem outline = new JMenuItem();\r
  66     JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();\r
  67     JMenu colourMenu = new JMenu();\r
  68     JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();\r
  69     JCheckBoxMenuItem showText = new JCheckBoxMenuItem();\r
  70     JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();\r
  71 \r
  72     /**\r
  73      * Creates a new PopupMenu object.\r
  74      *\r
  75      * @param ap DOCUMENT ME!\r
  76      * @param seq DOCUMENT ME!\r
  77      */\r
  78     public PopupMenu(final AlignmentPanel ap, Sequence seq)\r
  79     {\r
  80         ///////////////////////////////////////////////////////////\r
  81         // If this is activated from the sequence panel, the user may want to\r
  82         // edit or annotate a particular residue. Therefore display the residue menu\r
  83         //\r
  84         // If from the IDPanel, we must display the sequence menu\r
  85         //////////////////////////////////////////////////////////\r
  86         this.ap = ap;\r
  87         sequence = seq;\r
  88 \r
  89         ButtonGroup colours = new ButtonGroup();\r
  90         colours.add(noColourmenuItem);\r
  91         colours.add(clustalColour);\r
  92         colours.add(zappoColour);\r
  93         colours.add(taylorColour);\r
  94         colours.add(hydrophobicityColour);\r
  95         colours.add(helixColour);\r
  96         colours.add(strandColour);\r
  97         colours.add(turnColour);\r
  98         colours.add(buriedColour);\r
  99         colours.add(abovePIDColour);\r
 100         colours.add(userDefinedColour);\r
 101         colours.add(PIDColour);\r
 102         colours.add(BLOSUM62Colour);\r
 103 \r
 104         try\r
 105         {\r
 106             jbInit();\r
 107         }\r
 108         catch (Exception e)\r
 109         {\r
 110             e.printStackTrace();\r
 111         }\r
 112 \r
 113 \r
 114         if ((seq != null)\r
 115             && seq.getDatasetSequence().getPDBId() != null)\r
 116         {\r
 117           java.util.Enumeration e = seq.getDatasetSequence().getPDBId().elements();\r
 118           while(e.hasMoreElements())\r
 119           {\r
 120             final PDBEntry pdb = (PDBEntry)e.nextElement();\r
 121 \r
 122             JMenuItem pdbMenuItem = new JMenuItem();\r
 123             pdbMenuItem.setText("View PDB entry: "+pdb.getId());\r
 124             pdbMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 125             {\r
 126                 public void actionPerformed(ActionEvent e)\r
 127                 {\r
 128                   new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);\r
 129                 }\r
 130             });\r
 131             sequenceMenu.add(pdbMenuItem);\r
 132           }\r
 133 \r
 134         }\r
 135 \r
 136         SequenceGroup sg = ap.av.getSelectionGroup();\r
 137 \r
 138         if (sg != null)\r
 139         {\r
 140             groupName.setText(sg.getName());\r
 141 \r
 142             if (sg.cs instanceof ZappoColourScheme)\r
 143             {\r
 144                 zappoColour.setSelected(true);\r
 145             }\r
 146             else if (sg.cs instanceof TaylorColourScheme)\r
 147             {\r
 148                 taylorColour.setSelected(true);\r
 149             }\r
 150             else if (sg.cs instanceof PIDColourScheme)\r
 151             {\r
 152                 PIDColour.setSelected(true);\r
 153             }\r
 154             else if (sg.cs instanceof Blosum62ColourScheme)\r
 155             {\r
 156                 BLOSUM62Colour.setSelected(true);\r
 157             }\r
 158             else if (sg.cs instanceof UserColourScheme)\r
 159             {\r
 160                 userDefinedColour.setSelected(true);\r
 161             }\r
 162             else if (sg.cs instanceof HydrophobicColourScheme)\r
 163             {\r
 164                 hydrophobicityColour.setSelected(true);\r
 165             }\r
 166             else if (sg.cs instanceof HelixColourScheme)\r
 167             {\r
 168                 helixColour.setSelected(true);\r
 169             }\r
 170             else if (sg.cs instanceof StrandColourScheme)\r
 171             {\r
 172                 strandColour.setSelected(true);\r
 173             }\r
 174             else if (sg.cs instanceof TurnColourScheme)\r
 175             {\r
 176                 turnColour.setSelected(true);\r
 177             }\r
 178             else if (sg.cs instanceof BuriedColourScheme)\r
 179             {\r
 180                 buriedColour.setSelected(true);\r
 181             }\r
 182             else if (sg.cs instanceof ClustalxColourScheme)\r
 183             {\r
 184                 clustalColour.setSelected(true);\r
 185             }\r
 186             else\r
 187             {\r
 188                 noColourmenuItem.setSelected(true);\r
 189             }\r
 190 \r
 191             if (sg.cs!=null && sg.cs.conservationApplied())\r
 192             {\r
 193                 conservationMenuItem.setSelected(true);\r
 194             }\r
 195 \r
 196             showText.setSelected(sg.getDisplayText());\r
 197             showColourText.setSelected(sg.getColourText());\r
 198             showBoxes.setSelected(sg.getDisplayBoxes());\r
 199         }\r
 200 \r
 201         if (!ap.av.alignment.getGroups().contains(sg))\r
 202         {\r
 203             unGroupMenuItem.setVisible(false);\r
 204         }\r
 205         else\r
 206         {\r
 207             groupMenu.insertSeparator(3);\r
 208         }\r
 209 \r
 210         if (seq == null)\r
 211         {\r
 212             sequenceMenu.setVisible(false);\r
 213         }\r
 214         else\r
 215         {\r
 216           java.util.Vector links = Preferences.sequenceURLLinks;\r
 217 \r
 218           JMenu linkMenu = new JMenu("Link");\r
 219           JMenuItem item;\r
 220           for(int i=0; i<links.size(); i++)\r
 221           {\r
 222             String link = links.elementAt(i).toString();\r
 223 \r
 224             item = new JMenuItem(link.substring(0, link.indexOf("|")));\r
 225 \r
 226             final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))\r
 227                 + sequence.getName() +\r
 228                 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
 229 \r
 230 \r
 231             item.addActionListener(new java.awt.event.ActionListener()\r
 232             {\r
 233                 public void actionPerformed(ActionEvent e)\r
 234                 {\r
 235                     showLink(url);\r
 236                 }\r
 237             });\r
 238 \r
 239             linkMenu.add(item);\r
 240           }\r
 241           add(linkMenu);\r
 242         }\r
 243     }\r
 244 \r
 245     /**\r
 246      * DOCUMENT ME!\r
 247      *\r
 248      * @throws Exception DOCUMENT ME!\r
 249      */\r
 250     private void jbInit() throws Exception\r
 251     {\r
 252         groupMenu.setText("Group");\r
 253         groupMenu.setText("Define");\r
 254         groupName.setText("Name");\r
 255         groupName.addActionListener(new java.awt.event.ActionListener()\r
 256             {\r
 257                 public void actionPerformed(ActionEvent e)\r
 258                 {\r
 259                     groupName_actionPerformed(e);\r
 260                 }\r
 261             });\r
 262         sequenceMenu.setText("Sequence");\r
 263         sequenceName.setText("Edit name");\r
 264         sequenceName.addActionListener(new java.awt.event.ActionListener()\r
 265             {\r
 266                 public void actionPerformed(ActionEvent e)\r
 267                 {\r
 268                     sequenceName_actionPerformed(e);\r
 269                 }\r
 270             });\r
 271         PIDColour.setFocusPainted(false);\r
 272         unGroupMenuItem.setText("Remove Group");\r
 273         unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 274             {\r
 275                 public void actionPerformed(ActionEvent e)\r
 276                 {\r
 277                     unGroupMenuItem_actionPerformed(e);\r
 278                 }\r
 279             });\r
 280 \r
 281         outline.setText("Border colour");\r
 282         outline.addActionListener(new java.awt.event.ActionListener()\r
 283             {\r
 284                 public void actionPerformed(ActionEvent e)\r
 285                 {\r
 286                     outline_actionPerformed(e);\r
 287                 }\r
 288             });\r
 289         nucleotideMenuItem.setText("Nucleotide");\r
 290         nucleotideMenuItem.addActionListener(new ActionListener()\r
 291             {\r
 292                 public void actionPerformed(ActionEvent e)\r
 293                 {\r
 294                     nucleotideMenuItem_actionPerformed(e);\r
 295                 }\r
 296             });\r
 297         colourMenu.setText("Group Colour");\r
 298         showBoxes.setText("Boxes");\r
 299         showBoxes.setState(true);\r
 300         showBoxes.addActionListener(new ActionListener()\r
 301             {\r
 302                 public void actionPerformed(ActionEvent e)\r
 303                 {\r
 304                     showBoxes_actionPerformed(e);\r
 305                 }\r
 306             });\r
 307         showText.setText("Text");\r
 308         showText.setState(true);\r
 309         showText.addActionListener(new ActionListener()\r
 310             {\r
 311                 public void actionPerformed(ActionEvent e)\r
 312                 {\r
 313                     showText_actionPerformed(e);\r
 314                 }\r
 315             });\r
 316         showColourText.setText("Colour Text");\r
 317         showColourText.addActionListener(new ActionListener()\r
 318             {\r
 319                 public void actionPerformed(ActionEvent e)\r
 320                 {\r
 321                     showColourText_actionPerformed(e);\r
 322                 }\r
 323             });\r
 324         add(groupMenu);\r
 325         add(sequenceMenu);\r
 326         groupMenu.add(groupName);\r
 327         groupMenu.addSeparator();\r
 328         groupMenu.add(unGroupMenuItem);\r
 329         groupMenu.add(colourMenu);\r
 330         groupMenu.addSeparator();\r
 331         groupMenu.add(showBoxes);\r
 332         groupMenu.add(showText);\r
 333         groupMenu.add(showColourText);\r
 334         groupMenu.addSeparator();\r
 335         groupMenu.add(outline);\r
 336         sequenceMenu.add(sequenceName);\r
 337         colourMenu.add(noColourmenuItem);\r
 338         colourMenu.add(clustalColour);\r
 339         colourMenu.add(BLOSUM62Colour);\r
 340         colourMenu.add(PIDColour);\r
 341         colourMenu.add(zappoColour);\r
 342         colourMenu.add(taylorColour);\r
 343         colourMenu.add(hydrophobicityColour);\r
 344         colourMenu.add(helixColour);\r
 345         colourMenu.add(strandColour);\r
 346         colourMenu.add(turnColour);\r
 347         colourMenu.add(buriedColour);\r
 348         colourMenu.add(nucleotideMenuItem);\r
 349         colourMenu.add(userDefinedColour);\r
 350 \r
 351         if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
 352         {\r
 353           java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 354               getUserColourSchemes().keys();\r
 355 \r
 356           while (userColours.hasMoreElements())\r
 357           {\r
 358             JMenuItem item = new JMenuItem(userColours.\r
 359                 nextElement().toString());\r
 360             item.addActionListener(new ActionListener()\r
 361             {\r
 362               public void actionPerformed(ActionEvent evt)\r
 363               {\r
 364                 userDefinedColour_actionPerformed(evt);\r
 365               }\r
 366             });\r
 367             colourMenu.add(item);\r
 368           }\r
 369         }\r
 370 \r
 371 \r
 372         colourMenu.addSeparator();\r
 373         colourMenu.add(abovePIDColour);\r
 374         colourMenu.add(conservationMenuItem);\r
 375         noColourmenuItem.setText("None");\r
 376         noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 377             {\r
 378                 public void actionPerformed(ActionEvent e)\r
 379                 {\r
 380                     noColourmenuItem_actionPerformed(e);\r
 381                 }\r
 382             });\r
 383 \r
 384         clustalColour.setText("Clustalx colours");\r
 385         clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 386             {\r
 387                 public void actionPerformed(ActionEvent e)\r
 388                 {\r
 389                     clustalColour_actionPerformed(e);\r
 390                 }\r
 391             });\r
 392         zappoColour.setText("Zappo");\r
 393         zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 394             {\r
 395                 public void actionPerformed(ActionEvent e)\r
 396                 {\r
 397                     zappoColour_actionPerformed(e);\r
 398                 }\r
 399             });\r
 400         taylorColour.setText("Taylor");\r
 401         taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 402             {\r
 403                 public void actionPerformed(ActionEvent e)\r
 404                 {\r
 405                     taylorColour_actionPerformed(e);\r
 406                 }\r
 407             });\r
 408         hydrophobicityColour.setText("Hydrophobicity");\r
 409         hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 410             {\r
 411                 public void actionPerformed(ActionEvent e)\r
 412                 {\r
 413                     hydrophobicityColour_actionPerformed(e);\r
 414                 }\r
 415             });\r
 416         helixColour.setText("Helix propensity");\r
 417         helixColour.addActionListener(new java.awt.event.ActionListener()\r
 418             {\r
 419                 public void actionPerformed(ActionEvent e)\r
 420                 {\r
 421                     helixColour_actionPerformed(e);\r
 422                 }\r
 423             });\r
 424         strandColour.setText("Strand propensity");\r
 425         strandColour.addActionListener(new java.awt.event.ActionListener()\r
 426             {\r
 427                 public void actionPerformed(ActionEvent e)\r
 428                 {\r
 429                     strandColour_actionPerformed(e);\r
 430                 }\r
 431             });\r
 432         turnColour.setText("Turn propensity");\r
 433         turnColour.addActionListener(new java.awt.event.ActionListener()\r
 434             {\r
 435                 public void actionPerformed(ActionEvent e)\r
 436                 {\r
 437                     turnColour_actionPerformed(e);\r
 438                 }\r
 439             });\r
 440         buriedColour.setText("Buried Index");\r
 441         buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 442             {\r
 443                 public void actionPerformed(ActionEvent e)\r
 444                 {\r
 445                     buriedColour_actionPerformed(e);\r
 446                 }\r
 447             });\r
 448         abovePIDColour.setText("Above % Identity");\r
 449         abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
 450             {\r
 451                 public void actionPerformed(ActionEvent e)\r
 452                 {\r
 453                     abovePIDColour_actionPerformed(e);\r
 454                 }\r
 455             });\r
 456         userDefinedColour.setText("User Defined...");\r
 457         userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 458             {\r
 459                 public void actionPerformed(ActionEvent e)\r
 460                 {\r
 461                     userDefinedColour_actionPerformed(e);\r
 462                 }\r
 463             });\r
 464         PIDColour.setText("Percentage Identity");\r
 465         PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 466             {\r
 467                 public void actionPerformed(ActionEvent e)\r
 468                 {\r
 469                     PIDColour_actionPerformed(e);\r
 470                 }\r
 471             });\r
 472         BLOSUM62Colour.setText("BLOSUM62");\r
 473         BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 474             {\r
 475                 public void actionPerformed(ActionEvent e)\r
 476                 {\r
 477                     BLOSUM62Colour_actionPerformed(e);\r
 478                 }\r
 479             });\r
 480         conservationMenuItem.setText("Conservation");\r
 481         conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 482             {\r
 483                 public void actionPerformed(ActionEvent e)\r
 484                 {\r
 485                     conservationMenuItem_actionPerformed(e);\r
 486                 }\r
 487             });\r
 488     }\r
 489 \r
 490     /**\r
 491      * DOCUMENT ME!\r
 492      */\r
 493     void refresh()\r
 494     {\r
 495         SequenceGroup sg = getGroup();\r
 496         if(sg!=null)\r
 497         {\r
 498           SuperGroup superG = ap.av.alignment.getSuperGroup(sg);\r
 499 \r
 500           if (superG != null)\r
 501           {\r
 502             superG.setSuperGroupProperties(sg);\r
 503           }\r
 504         }\r
 505         if (ap.overviewPanel != null)\r
 506           ap.overviewPanel.updateOverviewImage();\r
 507 \r
 508         ap.seqPanel.repaint();\r
 509     }\r
 510 \r
 511     /**\r
 512      * DOCUMENT ME!\r
 513      *\r
 514      * @param e DOCUMENT ME!\r
 515      */\r
 516     protected void clustalColour_actionPerformed(ActionEvent e)\r
 517     {\r
 518         SequenceGroup sg = getGroup();\r
 519         sg.cs = new ClustalxColourScheme(sg.sequences,\r
 520                 ap.av.alignment.getWidth());\r
 521         refresh();\r
 522     }\r
 523 \r
 524     /**\r
 525      * DOCUMENT ME!\r
 526      *\r
 527      * @param e DOCUMENT ME!\r
 528      */\r
 529     protected void zappoColour_actionPerformed(ActionEvent e)\r
 530     {\r
 531         getGroup().cs = new ZappoColourScheme();\r
 532         refresh();\r
 533     }\r
 534 \r
 535     /**\r
 536      * DOCUMENT ME!\r
 537      *\r
 538      * @param e DOCUMENT ME!\r
 539      */\r
 540     protected void taylorColour_actionPerformed(ActionEvent e)\r
 541     {\r
 542         getGroup().cs = new TaylorColourScheme();\r
 543         refresh();\r
 544     }\r
 545 \r
 546     /**\r
 547      * DOCUMENT ME!\r
 548      *\r
 549      * @param e DOCUMENT ME!\r
 550      */\r
 551     protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 552     {\r
 553         getGroup().cs = new HydrophobicColourScheme();\r
 554         refresh();\r
 555     }\r
 556 \r
 557     /**\r
 558      * DOCUMENT ME!\r
 559      *\r
 560      * @param e DOCUMENT ME!\r
 561      */\r
 562     protected void helixColour_actionPerformed(ActionEvent e)\r
 563     {\r
 564         getGroup().cs = new HelixColourScheme();\r
 565         refresh();\r
 566     }\r
 567 \r
 568     /**\r
 569      * DOCUMENT ME!\r
 570      *\r
 571      * @param e DOCUMENT ME!\r
 572      */\r
 573     protected void strandColour_actionPerformed(ActionEvent e)\r
 574     {\r
 575         getGroup().cs = new StrandColourScheme();\r
 576         refresh();\r
 577     }\r
 578 \r
 579     /**\r
 580      * DOCUMENT ME!\r
 581      *\r
 582      * @param e DOCUMENT ME!\r
 583      */\r
 584     protected void turnColour_actionPerformed(ActionEvent e)\r
 585     {\r
 586         getGroup().cs = new TurnColourScheme();\r
 587         refresh();\r
 588     }\r
 589 \r
 590     /**\r
 591      * DOCUMENT ME!\r
 592      *\r
 593      * @param e DOCUMENT ME!\r
 594      */\r
 595     protected void buriedColour_actionPerformed(ActionEvent e)\r
 596     {\r
 597         getGroup().cs = new BuriedColourScheme();\r
 598         refresh();\r
 599     }\r
 600 \r
 601     /**\r
 602      * DOCUMENT ME!\r
 603      *\r
 604      * @param e DOCUMENT ME!\r
 605      */\r
 606     public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
 607     {\r
 608         getGroup().cs = new NucleotideColourScheme();\r
 609         refresh();\r
 610     }\r
 611 \r
 612     /**\r
 613      * DOCUMENT ME!\r
 614      *\r
 615      * @param e DOCUMENT ME!\r
 616      */\r
 617     protected void abovePIDColour_actionPerformed(ActionEvent e)\r
 618     {\r
 619         SequenceGroup sg = getGroup();\r
 620         if(sg.cs==null)\r
 621           return;\r
 622 \r
 623         if (abovePIDColour.isSelected())\r
 624         {\r
 625             sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 626                     ap.av.alignment.getWidth()));\r
 627 \r
 628             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
 629                     getGroup().getName());\r
 630 \r
 631            sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
 632 \r
 633             SliderPanel.showPIDSlider();\r
 634         }\r
 635         else // remove PIDColouring\r
 636         {\r
 637             sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
 638         }\r
 639 \r
 640         refresh();\r
 641     }\r
 642 \r
 643     /**\r
 644      * DOCUMENT ME!\r
 645      *\r
 646      * @param e DOCUMENT ME!\r
 647      */\r
 648     protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 649     {\r
 650        SequenceGroup sg = getGroup();\r
 651 \r
 652        if (e.getActionCommand().equals("User Defined..."))\r
 653          new UserDefinedColours(ap, sg);\r
 654        else\r
 655        {\r
 656          UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
 657              getUserColourSchemes().get(e.getActionCommand());\r
 658 \r
 659          sg.cs = udc;\r
 660        }\r
 661      }\r
 662     /**\r
 663      * DOCUMENT ME!\r
 664      *\r
 665      * @param e DOCUMENT ME!\r
 666      */\r
 667     protected void PIDColour_actionPerformed(ActionEvent e)\r
 668     {\r
 669         SequenceGroup sg = getGroup();\r
 670         sg.cs = new PIDColourScheme();\r
 671         sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\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 BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 682     {\r
 683         SequenceGroup sg = getGroup();\r
 684 \r
 685         sg.cs = new Blosum62ColourScheme();\r
 686 \r
 687         sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 688                 ap.av.alignment.getWidth()));\r
 689 \r
 690         refresh();\r
 691     }\r
 692 \r
 693     /**\r
 694      * DOCUMENT ME!\r
 695      *\r
 696      * @param e DOCUMENT ME!\r
 697      */\r
 698     protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 699     {\r
 700         getGroup().cs = null;\r
 701         refresh();\r
 702     }\r
 703 \r
 704     /**\r
 705      * DOCUMENT ME!\r
 706      *\r
 707      * @param e DOCUMENT ME!\r
 708      */\r
 709     protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
 710     {\r
 711         SequenceGroup sg = getGroup();\r
 712         if(sg.cs==null)\r
 713           return;\r
 714 \r
 715         if (conservationMenuItem.isSelected())\r
 716         {\r
 717             Conservation c = new Conservation("Group",\r
 718                     ResidueProperties.propHash, 3, sg.sequences, 0,\r
 719                     ap.av.alignment.getWidth());\r
 720 \r
 721             c.calculate();\r
 722             c.verdict(false, ap.av.ConsPercGaps);\r
 723 \r
 724             sg.cs.setConservation(c);\r
 725 \r
 726             SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
 727             SliderPanel.showConservationSlider();\r
 728         }\r
 729         else // remove ConservationColouring\r
 730         {\r
 731             sg.cs.setConservation(null);\r
 732         }\r
 733 \r
 734         refresh();\r
 735     }\r
 736 \r
 737     /**\r
 738      * DOCUMENT ME!\r
 739      *\r
 740      * @param e DOCUMENT ME!\r
 741      */\r
 742     protected void groupName_actionPerformed(ActionEvent e)\r
 743     {\r
 744         SequenceGroup sg = getGroup();\r
 745         String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
 746                 "Enter new group name", "Edit group name",\r
 747                 JOptionPane.QUESTION_MESSAGE);\r
 748 \r
 749         if (reply == null)\r
 750         {\r
 751             return;\r
 752         }\r
 753 \r
 754         sg.setName(reply);\r
 755         groupName.setText(reply);\r
 756     }\r
 757 \r
 758     /**\r
 759      * DOCUMENT ME!\r
 760      *\r
 761      * @param e DOCUMENT ME!\r
 762      */\r
 763     protected void analyze_actionPerformed(ActionEvent e)\r
 764     {\r
 765         CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
 766         JInternalFrame frame = new JInternalFrame();\r
 767         frame.setContentPane(cap);\r
 768         Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
 769 \r
 770         SequenceGroup sg = getGroup();\r
 771         StringBuffer sb = new StringBuffer();\r
 772 \r
 773         for (int i = 0; i < sg.sequences.size(); i++)\r
 774         {\r
 775             Sequence tmp = (Sequence) sg.sequences.get(i);\r
 776             sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
 777             sb.append("\n");\r
 778         }\r
 779 \r
 780         sb.append("Something amazing will happen soon");\r
 781         cap.setText(sb.toString());\r
 782     }\r
 783 \r
 784     /**\r
 785      * DOCUMENT ME!\r
 786      *\r
 787      * @return DOCUMENT ME!\r
 788      */\r
 789     SequenceGroup getGroup()\r
 790     {\r
 791         SequenceGroup sg = ap.av.getSelectionGroup();\r
 792       // this method won't add a new group if it already exists\r
 793         if(sg!=null)\r
 794           ap.av.alignment.addGroup(sg);\r
 795 \r
 796         return sg;\r
 797     }\r
 798 \r
 799     /**\r
 800      * DOCUMENT ME!\r
 801      *\r
 802      * @param e DOCUMENT ME!\r
 803      */\r
 804     void sequenceName_actionPerformed(ActionEvent e)\r
 805     {\r
 806         String id = sequence.getName();\r
 807         String s = (String) JOptionPane.showInternalInputDialog(ap,\r
 808                 "Edit sequence name",\r
 809                 "Edit sequence name (" + sequence.getName() + ")",\r
 810                 JOptionPane.PLAIN_MESSAGE, null, null, id);\r
 811 \r
 812         if (s != null)\r
 813         {\r
 814             if (s.indexOf(" ") > -1)\r
 815             {\r
 816                 JOptionPane.showMessageDialog(ap,\r
 817                     "Spaces have been converted to \"_\"",\r
 818                     "No spaces allowed in Sequence Name",\r
 819                     JOptionPane.WARNING_MESSAGE);\r
 820             }\r
 821 \r
 822             s = s.replace(' ', '_');\r
 823             sequence.setName(s);\r
 824             ap.repaint();\r
 825         }\r
 826     }\r
 827 \r
 828     /**\r
 829      * DOCUMENT ME!\r
 830      *\r
 831      * @param e DOCUMENT ME!\r
 832      */\r
 833     void unGroupMenuItem_actionPerformed(ActionEvent e)\r
 834     {\r
 835         SequenceGroup sg = ap.av.getSelectionGroup();\r
 836         ap.av.alignment.deleteGroup(sg);\r
 837         ap.av.setSelectionGroup(null);\r
 838         refresh();\r
 839     }\r
 840 \r
 841 \r
 842     /**\r
 843      * DOCUMENT ME!\r
 844      *\r
 845      * @param e DOCUMENT ME!\r
 846      */\r
 847     protected void outline_actionPerformed(ActionEvent e)\r
 848     {\r
 849         SequenceGroup sg = getGroup();\r
 850         Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
 851                 Color.BLUE);\r
 852 \r
 853         if (col != null)\r
 854         {\r
 855             sg.setOutlineColour(col);\r
 856         }\r
 857 \r
 858         refresh();\r
 859     }\r
 860 \r
 861     /**\r
 862      * DOCUMENT ME!\r
 863      *\r
 864      * @param e DOCUMENT ME!\r
 865      */\r
 866     public void showBoxes_actionPerformed(ActionEvent e)\r
 867     {\r
 868         getGroup().setDisplayBoxes(showBoxes.isSelected());\r
 869         refresh();\r
 870     }\r
 871 \r
 872     /**\r
 873      * DOCUMENT ME!\r
 874      *\r
 875      * @param e DOCUMENT ME!\r
 876      */\r
 877     public void showText_actionPerformed(ActionEvent e)\r
 878     {\r
 879         getGroup().setDisplayText(showText.isSelected());\r
 880         refresh();\r
 881     }\r
 882 \r
 883     /**\r
 884      * DOCUMENT ME!\r
 885      *\r
 886      * @param e DOCUMENT ME!\r
 887      */\r
 888     public void showColourText_actionPerformed(ActionEvent e)\r
 889     {\r
 890         getGroup().setColourText(showColourText.isSelected());\r
 891         refresh();\r
 892     }\r
 893 \r
 894     public void showLink(String url)\r
 895     {\r
 896       try\r
 897       {\r
 898         jalview.util.BrowserLauncher.openURL(url);\r
 899       }\r
 900       catch (Exception ex)\r
 901       {\r
 902         JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 903             "Unixers: Couldn't find default web browser."\r
 904            +"\nAdd the full path to your browser in Preferences.",\r
 905            "Web browser not found", JOptionPane.WARNING_MESSAGE );\r
 906 \r
 907 \r
 908         ex.printStackTrace();\r
 909       }\r
 910     }\r
 911 }\r