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 instanceof ConservationColourScheme)\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     }\r
 199 \r
 200     /**\r
 201      * DOCUMENT ME!\r
 202      *\r
 203      * @throws Exception DOCUMENT ME!\r
 204      */\r
 205     private void jbInit() throws Exception\r
 206     {\r
 207         groupMenu.setText("Group");\r
 208         groupMenu.setText("Define");\r
 209         groupName.setText("Name");\r
 210         groupName.addActionListener(new java.awt.event.ActionListener()\r
 211             {\r
 212                 public void actionPerformed(ActionEvent e)\r
 213                 {\r
 214                     groupName_actionPerformed(e);\r
 215                 }\r
 216             });\r
 217         sequenceMenu.setText("Sequence");\r
 218         sequenceName.setText("Edit name");\r
 219         sequenceName.addActionListener(new java.awt.event.ActionListener()\r
 220             {\r
 221                 public void actionPerformed(ActionEvent e)\r
 222                 {\r
 223                     sequenceName_actionPerformed(e);\r
 224                 }\r
 225             });\r
 226         PIDColour.setFocusPainted(false);\r
 227         unGroupMenuItem.setText("Remove Group");\r
 228         unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 229             {\r
 230                 public void actionPerformed(ActionEvent e)\r
 231                 {\r
 232                     unGroupMenuItem_actionPerformed(e);\r
 233                 }\r
 234             });\r
 235         pdbMenuItem.setText("View PDB structure");\r
 236         pdbMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 237             {\r
 238                 public void actionPerformed(ActionEvent e)\r
 239                 {\r
 240                     pdbMenuItem_actionPerformed(e);\r
 241                 }\r
 242             });\r
 243         outline.setText("Border colour");\r
 244         outline.addActionListener(new java.awt.event.ActionListener()\r
 245             {\r
 246                 public void actionPerformed(ActionEvent e)\r
 247                 {\r
 248                     outline_actionPerformed(e);\r
 249                 }\r
 250             });\r
 251         nucleotideMenuItem.setText("Nucleotide");\r
 252         nucleotideMenuItem.addActionListener(new ActionListener()\r
 253             {\r
 254                 public void actionPerformed(ActionEvent e)\r
 255                 {\r
 256                     nucleotideMenuItem_actionPerformed(e);\r
 257                 }\r
 258             });\r
 259         colourMenu.setText("Group Colour");\r
 260         showBoxes.setText("Boxes");\r
 261         showBoxes.setState(true);\r
 262         showBoxes.addActionListener(new ActionListener()\r
 263             {\r
 264                 public void actionPerformed(ActionEvent e)\r
 265                 {\r
 266                     showBoxes_actionPerformed(e);\r
 267                 }\r
 268             });\r
 269         showText.setText("Text");\r
 270         showText.setState(true);\r
 271         showText.addActionListener(new ActionListener()\r
 272             {\r
 273                 public void actionPerformed(ActionEvent e)\r
 274                 {\r
 275                     showText_actionPerformed(e);\r
 276                 }\r
 277             });\r
 278         showColourText.setText("Colour Text");\r
 279         showColourText.addActionListener(new ActionListener()\r
 280             {\r
 281                 public void actionPerformed(ActionEvent e)\r
 282                 {\r
 283                     showColourText_actionPerformed(e);\r
 284                 }\r
 285             });\r
 286         add(groupMenu);\r
 287         add(sequenceMenu);\r
 288         groupMenu.add(groupName);\r
 289         groupMenu.addSeparator();\r
 290         groupMenu.add(unGroupMenuItem);\r
 291         groupMenu.add(colourMenu);\r
 292         groupMenu.addSeparator();\r
 293         groupMenu.add(showBoxes);\r
 294         groupMenu.add(showText);\r
 295         groupMenu.add(showColourText);\r
 296         groupMenu.addSeparator();\r
 297         groupMenu.add(outline);\r
 298         sequenceMenu.add(sequenceName);\r
 299         sequenceMenu.add(pdbMenuItem);\r
 300         colourMenu.add(noColourmenuItem);\r
 301         colourMenu.add(clustalColour);\r
 302         colourMenu.add(BLOSUM62Colour);\r
 303         colourMenu.add(PIDColour);\r
 304         colourMenu.add(zappoColour);\r
 305         colourMenu.add(taylorColour);\r
 306         colourMenu.add(hydrophobicityColour);\r
 307         colourMenu.add(helixColour);\r
 308         colourMenu.add(strandColour);\r
 309         colourMenu.add(turnColour);\r
 310         colourMenu.add(buriedColour);\r
 311         colourMenu.add(nucleotideMenuItem);\r
 312         colourMenu.add(userDefinedColour);\r
 313         colourMenu.addSeparator();\r
 314         colourMenu.add(abovePIDColour);\r
 315         colourMenu.add(conservationMenuItem);\r
 316         noColourmenuItem.setText("None");\r
 317         noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 318             {\r
 319                 public void actionPerformed(ActionEvent e)\r
 320                 {\r
 321                     noColourmenuItem_actionPerformed(e);\r
 322                 }\r
 323             });\r
 324 \r
 325         clustalColour.setText("Clustalx colours");\r
 326         clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 327             {\r
 328                 public void actionPerformed(ActionEvent e)\r
 329                 {\r
 330                     clustalColour_actionPerformed(e);\r
 331                 }\r
 332             });\r
 333         zappoColour.setText("Zappo");\r
 334         zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 335             {\r
 336                 public void actionPerformed(ActionEvent e)\r
 337                 {\r
 338                     zappoColour_actionPerformed(e);\r
 339                 }\r
 340             });\r
 341         taylorColour.setText("Taylor");\r
 342         taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 343             {\r
 344                 public void actionPerformed(ActionEvent e)\r
 345                 {\r
 346                     taylorColour_actionPerformed(e);\r
 347                 }\r
 348             });\r
 349         hydrophobicityColour.setText("Hydrophobicity");\r
 350         hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 351             {\r
 352                 public void actionPerformed(ActionEvent e)\r
 353                 {\r
 354                     hydrophobicityColour_actionPerformed(e);\r
 355                 }\r
 356             });\r
 357         helixColour.setText("Helix propensity");\r
 358         helixColour.addActionListener(new java.awt.event.ActionListener()\r
 359             {\r
 360                 public void actionPerformed(ActionEvent e)\r
 361                 {\r
 362                     helixColour_actionPerformed(e);\r
 363                 }\r
 364             });\r
 365         strandColour.setText("Strand propensity");\r
 366         strandColour.addActionListener(new java.awt.event.ActionListener()\r
 367             {\r
 368                 public void actionPerformed(ActionEvent e)\r
 369                 {\r
 370                     strandColour_actionPerformed(e);\r
 371                 }\r
 372             });\r
 373         turnColour.setText("Turn propensity");\r
 374         turnColour.addActionListener(new java.awt.event.ActionListener()\r
 375             {\r
 376                 public void actionPerformed(ActionEvent e)\r
 377                 {\r
 378                     turnColour_actionPerformed(e);\r
 379                 }\r
 380             });\r
 381         buriedColour.setText("Buried Index");\r
 382         buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 383             {\r
 384                 public void actionPerformed(ActionEvent e)\r
 385                 {\r
 386                     buriedColour_actionPerformed(e);\r
 387                 }\r
 388             });\r
 389         abovePIDColour.setText("Above % Identity");\r
 390         abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
 391             {\r
 392                 public void actionPerformed(ActionEvent e)\r
 393                 {\r
 394                     abovePIDColour_actionPerformed(e);\r
 395                 }\r
 396             });\r
 397         userDefinedColour.setText("User Defined");\r
 398         userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 399             {\r
 400                 public void actionPerformed(ActionEvent e)\r
 401                 {\r
 402                     userDefinedColour_actionPerformed(e);\r
 403                 }\r
 404             });\r
 405         PIDColour.setText("Percentage Identity");\r
 406         PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 407             {\r
 408                 public void actionPerformed(ActionEvent e)\r
 409                 {\r
 410                     PIDColour_actionPerformed(e);\r
 411                 }\r
 412             });\r
 413         BLOSUM62Colour.setText("BLOSUM62");\r
 414         BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 415             {\r
 416                 public void actionPerformed(ActionEvent e)\r
 417                 {\r
 418                     BLOSUM62Colour_actionPerformed(e);\r
 419                 }\r
 420             });\r
 421         conservationMenuItem.setText("Conservation");\r
 422         conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 423             {\r
 424                 public void actionPerformed(ActionEvent e)\r
 425                 {\r
 426                     conservationMenuItem_actionPerformed(e);\r
 427                 }\r
 428             });\r
 429     }\r
 430 \r
 431     /**\r
 432      * DOCUMENT ME!\r
 433      */\r
 434     void refresh()\r
 435     {\r
 436         SequenceGroup sg = getGroup();\r
 437         SuperGroup superG = ap.av.alignment.getSuperGroup(sg);\r
 438 \r
 439         if (superG != null)\r
 440         {\r
 441             superG.setSuperGroupProperties(sg);\r
 442         }\r
 443 \r
 444         ap.seqPanel.repaint();\r
 445     }\r
 446 \r
 447     /**\r
 448      * DOCUMENT ME!\r
 449      *\r
 450      * @param e DOCUMENT ME!\r
 451      */\r
 452     protected void clustalColour_actionPerformed(ActionEvent e)\r
 453     {\r
 454         SequenceGroup sg = getGroup();\r
 455         sg.cs = new ClustalxColourScheme(sg.sequences,\r
 456                 ap.av.alignment.getWidth());\r
 457         refresh();\r
 458     }\r
 459 \r
 460     /**\r
 461      * DOCUMENT ME!\r
 462      *\r
 463      * @param e DOCUMENT ME!\r
 464      */\r
 465     protected void zappoColour_actionPerformed(ActionEvent e)\r
 466     {\r
 467         getGroup().cs = new ZappoColourScheme();\r
 468         refresh();\r
 469     }\r
 470 \r
 471     /**\r
 472      * DOCUMENT ME!\r
 473      *\r
 474      * @param e DOCUMENT ME!\r
 475      */\r
 476     protected void taylorColour_actionPerformed(ActionEvent e)\r
 477     {\r
 478         getGroup().cs = new TaylorColourScheme();\r
 479         refresh();\r
 480     }\r
 481 \r
 482     /**\r
 483      * DOCUMENT ME!\r
 484      *\r
 485      * @param e DOCUMENT ME!\r
 486      */\r
 487     protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 488     {\r
 489         getGroup().cs = new HydrophobicColourScheme();\r
 490         refresh();\r
 491     }\r
 492 \r
 493     /**\r
 494      * DOCUMENT ME!\r
 495      *\r
 496      * @param e DOCUMENT ME!\r
 497      */\r
 498     protected void helixColour_actionPerformed(ActionEvent e)\r
 499     {\r
 500         getGroup().cs = new HelixColourScheme();\r
 501         refresh();\r
 502     }\r
 503 \r
 504     /**\r
 505      * DOCUMENT ME!\r
 506      *\r
 507      * @param e DOCUMENT ME!\r
 508      */\r
 509     protected void strandColour_actionPerformed(ActionEvent e)\r
 510     {\r
 511         getGroup().cs = new StrandColourScheme();\r
 512         refresh();\r
 513     }\r
 514 \r
 515     /**\r
 516      * DOCUMENT ME!\r
 517      *\r
 518      * @param e DOCUMENT ME!\r
 519      */\r
 520     protected void turnColour_actionPerformed(ActionEvent e)\r
 521     {\r
 522         getGroup().cs = new TurnColourScheme();\r
 523         refresh();\r
 524     }\r
 525 \r
 526     /**\r
 527      * DOCUMENT ME!\r
 528      *\r
 529      * @param e DOCUMENT ME!\r
 530      */\r
 531     protected void buriedColour_actionPerformed(ActionEvent e)\r
 532     {\r
 533         getGroup().cs = new BuriedColourScheme();\r
 534         refresh();\r
 535     }\r
 536 \r
 537     /**\r
 538      * DOCUMENT ME!\r
 539      *\r
 540      * @param e DOCUMENT ME!\r
 541      */\r
 542     public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
 543     {\r
 544         getGroup().cs = new NucleotideColourScheme();\r
 545         refresh();\r
 546     }\r
 547 \r
 548     /**\r
 549      * DOCUMENT ME!\r
 550      *\r
 551      * @param e DOCUMENT ME!\r
 552      */\r
 553     protected void abovePIDColour_actionPerformed(ActionEvent e)\r
 554     {\r
 555         SequenceGroup sg = getGroup();\r
 556 \r
 557         if (abovePIDColour.isSelected())\r
 558         {\r
 559             sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 560                     ap.av.alignment.getWidth()));\r
 561 \r
 562             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
 563                     getGroup().getName());\r
 564 \r
 565             if (sg.cs instanceof ResidueColourScheme)\r
 566             {\r
 567                 ((ResidueColourScheme) sg.cs).setThreshold(threshold);\r
 568             }\r
 569             else if (sg.cs instanceof ScoreColourScheme)\r
 570             {\r
 571                 ((ScoreColourScheme) sg.cs).setThreshold(threshold);\r
 572             }\r
 573 \r
 574             SliderPanel.showPIDSlider();\r
 575         }\r
 576         else // remove PIDColouring\r
 577         {\r
 578             ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;\r
 579             rcs.setThreshold(0);\r
 580             sg.cs = rcs;\r
 581         }\r
 582 \r
 583         refresh();\r
 584     }\r
 585 \r
 586     /**\r
 587      * DOCUMENT ME!\r
 588      *\r
 589      * @param e DOCUMENT ME!\r
 590      */\r
 591     protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 592     {\r
 593         new UserDefinedColours(ap, getGroup());\r
 594     }\r
 595 \r
 596     /**\r
 597      * DOCUMENT ME!\r
 598      *\r
 599      * @param e DOCUMENT ME!\r
 600      */\r
 601     protected void PIDColour_actionPerformed(ActionEvent e)\r
 602     {\r
 603         SequenceGroup sg = getGroup();\r
 604         sg.cs = new PIDColourScheme();\r
 605         sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 606                 ap.av.alignment.getWidth()));\r
 607         refresh();\r
 608     }\r
 609 \r
 610     /**\r
 611      * DOCUMENT ME!\r
 612      *\r
 613      * @param e DOCUMENT ME!\r
 614      */\r
 615     protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 616     {\r
 617         SequenceGroup sg = getGroup();\r
 618 \r
 619         sg.cs = new Blosum62ColourScheme();\r
 620 \r
 621         sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 622                 ap.av.alignment.getWidth()));\r
 623 \r
 624         refresh();\r
 625     }\r
 626 \r
 627     /**\r
 628      * DOCUMENT ME!\r
 629      *\r
 630      * @param e DOCUMENT ME!\r
 631      */\r
 632     protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 633     {\r
 634         getGroup().cs = null;\r
 635         refresh();\r
 636     }\r
 637 \r
 638     /**\r
 639      * DOCUMENT ME!\r
 640      *\r
 641      * @param e DOCUMENT ME!\r
 642      */\r
 643     protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
 644     {\r
 645         SequenceGroup sg = getGroup();\r
 646 \r
 647         if (conservationMenuItem.isSelected())\r
 648         {\r
 649             Conservation c = new Conservation("Group",\r
 650                     ResidueProperties.propHash, 3, sg.sequences, 0,\r
 651                     ap.av.alignment.getWidth());\r
 652 \r
 653             c.calculate();\r
 654             c.verdict(false, ap.av.ConsPercGaps);\r
 655 \r
 656             ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 657 \r
 658             sg.cs = ccs;\r
 659 \r
 660             SliderPanel.setConservationSlider(ap, ccs, sg.getName());\r
 661             SliderPanel.showConservationSlider();\r
 662         }\r
 663         else // remove ConservationColouring\r
 664         {\r
 665             ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;\r
 666             sg.cs = ccs.cs;\r
 667         }\r
 668 \r
 669         refresh();\r
 670     }\r
 671 \r
 672     /**\r
 673      * DOCUMENT ME!\r
 674      *\r
 675      * @param e DOCUMENT ME!\r
 676      */\r
 677     protected void groupName_actionPerformed(ActionEvent e)\r
 678     {\r
 679         SequenceGroup sg = getGroup();\r
 680         String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
 681                 "Enter new group name", "Edit group name",\r
 682                 JOptionPane.QUESTION_MESSAGE);\r
 683 \r
 684         if (reply == null)\r
 685         {\r
 686             return;\r
 687         }\r
 688 \r
 689         sg.setName(reply);\r
 690         groupName.setText(reply);\r
 691     }\r
 692 \r
 693     /**\r
 694      * DOCUMENT ME!\r
 695      *\r
 696      * @param e DOCUMENT ME!\r
 697      */\r
 698     protected void analyze_actionPerformed(ActionEvent e)\r
 699     {\r
 700         CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
 701         JInternalFrame frame = new JInternalFrame();\r
 702         frame.setContentPane(cap);\r
 703         Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
 704 \r
 705         SequenceGroup sg = getGroup();\r
 706         StringBuffer sb = new StringBuffer();\r
 707 \r
 708         for (int i = 0; i < sg.sequences.size(); i++)\r
 709         {\r
 710             Sequence tmp = (Sequence) sg.sequences.get(i);\r
 711             sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
 712             sb.append("\n");\r
 713         }\r
 714 \r
 715         sb.append("Something amazing will happen soon");\r
 716         cap.setText(sb.toString());\r
 717     }\r
 718 \r
 719     /**\r
 720      * DOCUMENT ME!\r
 721      *\r
 722      * @return DOCUMENT ME!\r
 723      */\r
 724     SequenceGroup getGroup()\r
 725     {\r
 726         SequenceGroup sg = ap.av.getSelectionGroup();\r
 727 \r
 728         // this method won't add a new group if it already exists\r
 729         ap.av.alignment.addGroup(sg);\r
 730 \r
 731         return sg;\r
 732     }\r
 733 \r
 734     /**\r
 735      * DOCUMENT ME!\r
 736      *\r
 737      * @param e DOCUMENT ME!\r
 738      */\r
 739     void sequenceName_actionPerformed(ActionEvent e)\r
 740     {\r
 741         String id = sequence.getName();\r
 742         String s = (String) JOptionPane.showInternalInputDialog(ap,\r
 743                 "Edit sequence name",\r
 744                 "Edit sequence name (" + sequence.getName() + ")",\r
 745                 JOptionPane.PLAIN_MESSAGE, null, null, id);\r
 746 \r
 747         if (s != null)\r
 748         {\r
 749             if (s.indexOf(" ") > -1)\r
 750             {\r
 751                 JOptionPane.showMessageDialog(ap,\r
 752                     "Spaces have been converted to \"_\"",\r
 753                     "No spaces allowed in Sequence Name",\r
 754                     JOptionPane.WARNING_MESSAGE);\r
 755             }\r
 756 \r
 757             s = s.replace(' ', '_');\r
 758             sequence.setName(s);\r
 759             ap.repaint();\r
 760         }\r
 761     }\r
 762 \r
 763     /**\r
 764      * DOCUMENT ME!\r
 765      *\r
 766      * @param e DOCUMENT ME!\r
 767      */\r
 768     void unGroupMenuItem_actionPerformed(ActionEvent e)\r
 769     {\r
 770         SequenceGroup sg = ap.av.getSelectionGroup();\r
 771         ap.av.alignment.deleteGroup(sg);\r
 772         ap.av.setSelectionGroup(null);\r
 773         refresh();\r
 774     }\r
 775 \r
 776     /**\r
 777      * DOCUMENT ME!\r
 778      *\r
 779      * @param e DOCUMENT ME!\r
 780      */\r
 781     void pdbMenuItem_actionPerformed(ActionEvent e)\r
 782     {\r
 783         if (sequence.getPDBId() == null)\r
 784         {\r
 785             return;\r
 786         }\r
 787 \r
 788         try\r
 789         {\r
 790             EBIFetchClient ebi = new EBIFetchClient();\r
 791             String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null,\r
 792                     null);\r
 793 \r
 794             PDBfile pdb = new PDBfile(result);\r
 795 \r
 796             rotCanvas rc = new rotCanvas(pdb, sequence, ap.av);\r
 797             JInternalFrame frame = new JInternalFrame();\r
 798             frame.setContentPane(rc);\r
 799             Desktop.addInternalFrame(frame,\r
 800                 sequence.getName() + " " + sequence.getPDBId(), 400, 400);\r
 801         }\r
 802         catch (Exception ex)\r
 803         {\r
 804             ex.printStackTrace();\r
 805         }\r
 806     }\r
 807 \r
 808     /**\r
 809      * DOCUMENT ME!\r
 810      *\r
 811      * @param e DOCUMENT ME!\r
 812      */\r
 813     protected void outline_actionPerformed(ActionEvent e)\r
 814     {\r
 815         SequenceGroup sg = getGroup();\r
 816         Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
 817                 Color.BLUE);\r
 818 \r
 819         if (col != null)\r
 820         {\r
 821             sg.setOutlineColour(col);\r
 822         }\r
 823 \r
 824         refresh();\r
 825     }\r
 826 \r
 827     /**\r
 828      * DOCUMENT ME!\r
 829      *\r
 830      * @param e DOCUMENT ME!\r
 831      */\r
 832     public void showBoxes_actionPerformed(ActionEvent e)\r
 833     {\r
 834         getGroup().setDisplayBoxes(showBoxes.isSelected());\r
 835         refresh();\r
 836     }\r
 837 \r
 838     /**\r
 839      * DOCUMENT ME!\r
 840      *\r
 841      * @param e DOCUMENT ME!\r
 842      */\r
 843     public void showText_actionPerformed(ActionEvent e)\r
 844     {\r
 845         getGroup().setDisplayText(showText.isSelected());\r
 846         refresh();\r
 847     }\r
 848 \r
 849     /**\r
 850      * DOCUMENT ME!\r
 851      *\r
 852      * @param e DOCUMENT ME!\r
 853      */\r
 854     public void showColourText_actionPerformed(ActionEvent e)\r
 855     {\r
 856         getGroup().setColourText(showColourText.isSelected());\r
 857         refresh();\r
 858     }\r
 859 }\r