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