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 java.awt.*;\r
  22 import java.awt.event.*;\r
  23 import javax.swing.*;\r
  24 \r
  25 import MCview.*;\r
  26 import jalview.analysis.*;\r
  27 import jalview.datamodel.*;\r
  28 import jalview.io.*;\r
  29 import jalview.schemes.*;\r
  30 \r
  31 public class PopupMenu\r
  32     extends JPopupMenu\r
  33 {\r
  34   JMenu groupMenu = new JMenu();\r
  35   JMenuItem groupName = new JMenuItem();\r
  36   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  37   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  38   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  39   protected JRadioButtonMenuItem hydrophobicityColour = new\r
  40       JRadioButtonMenuItem();\r
  41   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  42   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  43   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  44   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  45   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();\r
  46   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  47   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  48   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  49   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  50   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  51   AlignmentPanel ap;\r
  52   JMenu sequenceMenu = new JMenu();\r
  53   JMenuItem sequenceName = new JMenuItem();\r
  54   Sequence sequence;\r
  55   JMenuItem unGroupMenuItem = new JMenuItem();\r
  56   JMenuItem pdbMenuItem = new JMenuItem();\r
  57   JMenuItem outline = new JMenuItem();\r
  58   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();\r
  59   JMenu colourMenu = new JMenu();\r
  60   JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();\r
  61   JCheckBoxMenuItem showText = new JCheckBoxMenuItem();\r
  62   JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();\r
  63 \r
  64   public PopupMenu(AlignmentPanel ap, Sequence seq)\r
  65   {\r
  66     ///////////////////////////////////////////////////////////\r
  67     // If this is activated from the sequence panel, the user may want to\r
  68     // edit or annotate a particular residue. Therefore display the residue menu\r
  69     //\r
  70     // If from the IDPanel, we must display the sequence menu\r
  71     //////////////////////////////////////////////////////////\r
  72     this.ap = ap;\r
  73     sequence = seq;\r
  74 \r
  75     ButtonGroup colours = new ButtonGroup();\r
  76     colours.add(noColourmenuItem);\r
  77     colours.add(clustalColour);\r
  78     colours.add(zappoColour);\r
  79     colours.add(taylorColour);\r
  80     colours.add(hydrophobicityColour);\r
  81     colours.add(helixColour);\r
  82     colours.add(strandColour);\r
  83     colours.add(turnColour);\r
  84     colours.add(buriedColour);\r
  85     colours.add(abovePIDColour);\r
  86     colours.add(userDefinedColour);\r
  87     colours.add(PIDColour);\r
  88     colours.add(BLOSUM62Colour);\r
  89 \r
  90     try\r
  91     {\r
  92       jbInit();\r
  93     }\r
  94     catch (Exception e)\r
  95     {\r
  96       e.printStackTrace();\r
  97     }\r
  98 \r
  99     SequenceGroup sg = ap.av.getSelectionGroup();\r
 100 \r
 101     if (sg != null)\r
 102     {\r
 103       groupName.setText(sg.getName());\r
 104 \r
 105       if (sg.cs instanceof ZappoColourScheme)\r
 106       {\r
 107         zappoColour.setSelected(true);\r
 108       }\r
 109       else if (sg.cs instanceof TaylorColourScheme)\r
 110       {\r
 111         taylorColour.setSelected(true);\r
 112       }\r
 113       else if (sg.cs instanceof PIDColourScheme)\r
 114       {\r
 115         PIDColour.setSelected(true);\r
 116       }\r
 117       else if (sg.cs instanceof Blosum62ColourScheme)\r
 118       {\r
 119         BLOSUM62Colour.setSelected(true);\r
 120       }\r
 121       else if (sg.cs instanceof UserColourScheme)\r
 122       {\r
 123         userDefinedColour.setSelected(true);\r
 124       }\r
 125       else if (sg.cs instanceof HydrophobicColourScheme)\r
 126       {\r
 127         hydrophobicityColour.setSelected(true);\r
 128       }\r
 129       else if (sg.cs instanceof HelixColourScheme)\r
 130       {\r
 131         helixColour.setSelected(true);\r
 132       }\r
 133       else if (sg.cs instanceof StrandColourScheme)\r
 134       {\r
 135         strandColour.setSelected(true);\r
 136       }\r
 137       else if (sg.cs instanceof TurnColourScheme)\r
 138       {\r
 139         turnColour.setSelected(true);\r
 140       }\r
 141       else if (sg.cs instanceof BuriedColourScheme)\r
 142       {\r
 143         buriedColour.setSelected(true);\r
 144       }\r
 145       else if (sg.cs instanceof ClustalxColourScheme)\r
 146       {\r
 147         clustalColour.setSelected(true);\r
 148       }\r
 149       else\r
 150       {\r
 151         noColourmenuItem.setSelected(true);\r
 152       }\r
 153 \r
 154       if (sg.cs instanceof ConservationColourScheme)\r
 155       {\r
 156         conservationMenuItem.setSelected(true);\r
 157       }\r
 158 \r
 159       showText.setSelected(sg.getDisplayText());\r
 160       showColourText.setSelected(sg.getColourText());\r
 161       showBoxes.setSelected(sg.getDisplayBoxes());\r
 162     }\r
 163 \r
 164     if (!ap.av.alignment.getGroups().contains(sg))\r
 165     {\r
 166       unGroupMenuItem.setVisible(false);\r
 167     }\r
 168     else\r
 169     {\r
 170       groupMenu.insertSeparator(3);\r
 171     }\r
 172 \r
 173     if (seq == null)\r
 174     {\r
 175       sequenceMenu.setVisible(false);\r
 176     }\r
 177   }\r
 178 \r
 179   private void jbInit()\r
 180       throws Exception\r
 181   {\r
 182     groupMenu.setText("Group");\r
 183     groupMenu.setText("Define");\r
 184     groupName.setText("Name");\r
 185     groupName.addActionListener(new java.awt.event.ActionListener()\r
 186     {\r
 187       public void actionPerformed(ActionEvent e)\r
 188       {\r
 189         groupName_actionPerformed(e);\r
 190       }\r
 191     });\r
 192     sequenceMenu.setText("Sequence");\r
 193     sequenceName.setText("Edit name");\r
 194     sequenceName.addActionListener(new java.awt.event.ActionListener()\r
 195     {\r
 196       public void actionPerformed(ActionEvent e)\r
 197       {\r
 198         sequenceName_actionPerformed(e);\r
 199       }\r
 200     });\r
 201     PIDColour.setFocusPainted(false);\r
 202     unGroupMenuItem.setText("Remove Group");\r
 203     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 204     {\r
 205       public void actionPerformed(ActionEvent e)\r
 206       {\r
 207         unGroupMenuItem_actionPerformed(e);\r
 208       }\r
 209     });\r
 210     pdbMenuItem.setText("View PDB structure");\r
 211     pdbMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 212     {\r
 213       public void actionPerformed(ActionEvent e)\r
 214       {\r
 215         pdbMenuItem_actionPerformed(e);\r
 216       }\r
 217     });\r
 218     outline.setText("Border colour");\r
 219     outline.addActionListener(new java.awt.event.ActionListener()\r
 220     {\r
 221       public void actionPerformed(ActionEvent e)\r
 222       {\r
 223         outline_actionPerformed(e);\r
 224       }\r
 225     });\r
 226     nucleotideMenuItem.setText("Nucleotide");\r
 227     nucleotideMenuItem.addActionListener(new ActionListener()\r
 228     {\r
 229       public void actionPerformed(ActionEvent e)\r
 230       {\r
 231         nucleotideMenuItem_actionPerformed(e);\r
 232       }\r
 233     });\r
 234     colourMenu.setText("Group Colour");\r
 235     showBoxes.setText("Boxes");\r
 236     showBoxes.setState(true);\r
 237     showBoxes.addActionListener(new ActionListener()\r
 238     {\r
 239       public void actionPerformed(ActionEvent e)\r
 240       {\r
 241         showBoxes_actionPerformed(e);\r
 242       }\r
 243     });\r
 244     showText.setText("Text");\r
 245     showText.setState(true);\r
 246     showText.addActionListener(new ActionListener()\r
 247     {\r
 248       public void actionPerformed(ActionEvent e)\r
 249       {\r
 250         showText_actionPerformed(e);\r
 251       }\r
 252     });\r
 253     showColourText.setText("Colour Text");\r
 254     showColourText.addActionListener(new ActionListener()\r
 255     {\r
 256       public void actionPerformed(ActionEvent e)\r
 257       {\r
 258         showColourText_actionPerformed(e);\r
 259       }\r
 260     });\r
 261     add(groupMenu);\r
 262     add(sequenceMenu);\r
 263     groupMenu.add(groupName);\r
 264     groupMenu.addSeparator();\r
 265     groupMenu.add(unGroupMenuItem);\r
 266     groupMenu.add(colourMenu);\r
 267     groupMenu.addSeparator();\r
 268     groupMenu.add(showBoxes);\r
 269     groupMenu.add(showText);\r
 270     groupMenu.add(showColourText);\r
 271     groupMenu.addSeparator();\r
 272     groupMenu.add(outline);\r
 273     sequenceMenu.add(sequenceName);\r
 274     sequenceMenu.add(pdbMenuItem);\r
 275     colourMenu.add(noColourmenuItem);\r
 276     colourMenu.add(clustalColour);\r
 277     colourMenu.add(BLOSUM62Colour);\r
 278     colourMenu.add(PIDColour);\r
 279     colourMenu.add(zappoColour);\r
 280     colourMenu.add(taylorColour);\r
 281     colourMenu.add(hydrophobicityColour);\r
 282     colourMenu.add(helixColour);\r
 283     colourMenu.add(strandColour);\r
 284     colourMenu.add(turnColour);\r
 285     colourMenu.add(buriedColour);\r
 286     colourMenu.add(nucleotideMenuItem);\r
 287     colourMenu.add(userDefinedColour);\r
 288     colourMenu.addSeparator();\r
 289     colourMenu.add(abovePIDColour);\r
 290     colourMenu.add(conservationMenuItem);\r
 291     noColourmenuItem.setText("None");\r
 292     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 293     {\r
 294       public void actionPerformed(ActionEvent e)\r
 295       {\r
 296         noColourmenuItem_actionPerformed(e);\r
 297       }\r
 298     });\r
 299 \r
 300     clustalColour.setText("Clustalx colours");\r
 301     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 302     {\r
 303       public void actionPerformed(ActionEvent e)\r
 304       {\r
 305         clustalColour_actionPerformed(e);\r
 306       }\r
 307     });\r
 308     zappoColour.setText("Zappo");\r
 309     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 310     {\r
 311       public void actionPerformed(ActionEvent e)\r
 312       {\r
 313         zappoColour_actionPerformed(e);\r
 314       }\r
 315     });\r
 316     taylorColour.setText("Taylor");\r
 317     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 318     {\r
 319       public void actionPerformed(ActionEvent e)\r
 320       {\r
 321         taylorColour_actionPerformed(e);\r
 322       }\r
 323     });\r
 324     hydrophobicityColour.setText("Hydrophobicity");\r
 325     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 326     {\r
 327       public void actionPerformed(ActionEvent e)\r
 328       {\r
 329         hydrophobicityColour_actionPerformed(e);\r
 330       }\r
 331     });\r
 332     helixColour.setText("Helix propensity");\r
 333     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 334     {\r
 335       public void actionPerformed(ActionEvent e)\r
 336       {\r
 337         helixColour_actionPerformed(e);\r
 338       }\r
 339     });\r
 340     strandColour.setText("Strand propensity");\r
 341     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 342     {\r
 343       public void actionPerformed(ActionEvent e)\r
 344       {\r
 345         strandColour_actionPerformed(e);\r
 346       }\r
 347     });\r
 348     turnColour.setText("Turn propensity");\r
 349     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 350     {\r
 351       public void actionPerformed(ActionEvent e)\r
 352       {\r
 353         turnColour_actionPerformed(e);\r
 354       }\r
 355     });\r
 356     buriedColour.setText("Buried Index");\r
 357     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 358     {\r
 359       public void actionPerformed(ActionEvent e)\r
 360       {\r
 361         buriedColour_actionPerformed(e);\r
 362       }\r
 363     });\r
 364     abovePIDColour.setText("Above % Identity");\r
 365     abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
 366     {\r
 367       public void actionPerformed(ActionEvent e)\r
 368       {\r
 369         abovePIDColour_actionPerformed(e);\r
 370       }\r
 371     });\r
 372     userDefinedColour.setText("User Defined");\r
 373     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 374     {\r
 375       public void actionPerformed(ActionEvent e)\r
 376       {\r
 377         userDefinedColour_actionPerformed(e);\r
 378       }\r
 379     });\r
 380     PIDColour.setText("Percentage Identity");\r
 381     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 382     {\r
 383       public void actionPerformed(ActionEvent e)\r
 384       {\r
 385         PIDColour_actionPerformed(e);\r
 386       }\r
 387     });\r
 388     BLOSUM62Colour.setText("BLOSUM62");\r
 389     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 390     {\r
 391       public void actionPerformed(ActionEvent e)\r
 392       {\r
 393         BLOSUM62Colour_actionPerformed(e);\r
 394       }\r
 395     });\r
 396     conservationMenuItem.setText("Conservation");\r
 397     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 398     {\r
 399       public void actionPerformed(ActionEvent e)\r
 400       {\r
 401         conservationMenuItem_actionPerformed(e);\r
 402       }\r
 403     });\r
 404   }\r
 405 \r
 406   void refresh()\r
 407   {\r
 408     SequenceGroup sg = getGroup();\r
 409     SuperGroup superG = ap.av.alignment.getSuperGroup(sg);\r
 410 \r
 411     if (superG != null)\r
 412     {\r
 413       superG.setSuperGroupProperties(sg);\r
 414     }\r
 415 \r
 416     ap.seqPanel.repaint();\r
 417   }\r
 418 \r
 419   protected void clustalColour_actionPerformed(ActionEvent e)\r
 420   {\r
 421     SequenceGroup sg = getGroup();\r
 422     sg.cs = new ClustalxColourScheme(sg.sequences,\r
 423                                      ap.av.alignment.getWidth());\r
 424     refresh();\r
 425   }\r
 426 \r
 427   protected void zappoColour_actionPerformed(ActionEvent e)\r
 428   {\r
 429     getGroup().cs = new ZappoColourScheme();\r
 430     refresh();\r
 431   }\r
 432 \r
 433   protected void taylorColour_actionPerformed(ActionEvent e)\r
 434   {\r
 435     getGroup().cs = new TaylorColourScheme();\r
 436     refresh();\r
 437   }\r
 438 \r
 439   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 440   {\r
 441     getGroup().cs = new HydrophobicColourScheme();\r
 442     refresh();\r
 443   }\r
 444 \r
 445   protected void helixColour_actionPerformed(ActionEvent e)\r
 446   {\r
 447     getGroup().cs = new HelixColourScheme();\r
 448     refresh();\r
 449   }\r
 450 \r
 451   protected void strandColour_actionPerformed(ActionEvent e)\r
 452   {\r
 453     getGroup().cs = new StrandColourScheme();\r
 454     refresh();\r
 455   }\r
 456 \r
 457   protected void turnColour_actionPerformed(ActionEvent e)\r
 458   {\r
 459     getGroup().cs = new TurnColourScheme();\r
 460     refresh();\r
 461   }\r
 462 \r
 463   protected void buriedColour_actionPerformed(ActionEvent e)\r
 464   {\r
 465     getGroup().cs = new BuriedColourScheme();\r
 466     refresh();\r
 467   }\r
 468 \r
 469   public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
 470   {\r
 471     getGroup().cs = new NucleotideColourScheme();\r
 472     refresh();\r
 473   }\r
 474 \r
 475   protected void abovePIDColour_actionPerformed(ActionEvent e)\r
 476   {\r
 477     SequenceGroup sg = getGroup();\r
 478 \r
 479     if (abovePIDColour.isSelected())\r
 480     {\r
 481       sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 482                                                ap.av.alignment.getWidth()));\r
 483 \r
 484       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
 485           getGroup().getName());\r
 486 \r
 487       if (sg.cs instanceof ResidueColourScheme)\r
 488       {\r
 489         ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
 490       }\r
 491       else if (sg.cs instanceof ScoreColourScheme)\r
 492       {\r
 493         ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
 494       }\r
 495 \r
 496       SliderPanel.showPIDSlider();\r
 497     }\r
 498     else // remove PIDColouring\r
 499     {\r
 500       ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;\r
 501       rcs.setThreshold(0);\r
 502       sg.cs = rcs;\r
 503     }\r
 504 \r
 505     refresh();\r
 506   }\r
 507 \r
 508   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 509   {\r
 510     new UserDefinedColours(ap, getGroup());\r
 511   }\r
 512 \r
 513   protected void PIDColour_actionPerformed(ActionEvent e)\r
 514   {\r
 515     SequenceGroup sg = getGroup();\r
 516     sg.cs = new PIDColourScheme();\r
 517     sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 518                                              ap.av.alignment.getWidth()));\r
 519     refresh();\r
 520   }\r
 521 \r
 522   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 523   {\r
 524     SequenceGroup sg = getGroup();\r
 525 \r
 526     sg.cs = new Blosum62ColourScheme();\r
 527 \r
 528     sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 529                                              ap.av.alignment.getWidth()));\r
 530 \r
 531     refresh();\r
 532   }\r
 533 \r
 534   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 535   {\r
 536     getGroup().cs = null;\r
 537     refresh();\r
 538   }\r
 539 \r
 540   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
 541   {\r
 542     SequenceGroup sg = getGroup();\r
 543 \r
 544     if (conservationMenuItem.isSelected())\r
 545     {\r
 546       Conservation c = new Conservation("Group",\r
 547                                         ResidueProperties.propHash, 3,\r
 548                                         sg.sequences, 0,\r
 549                                         ap.av.alignment.getWidth());\r
 550 \r
 551       c.calculate();\r
 552       c.verdict(false, ap.av.ConsPercGaps);\r
 553 \r
 554       ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 555 \r
 556       sg.cs = ccs;\r
 557 \r
 558       SliderPanel.setConservationSlider(ap, ccs, sg.getName());\r
 559       SliderPanel.showConservationSlider();\r
 560     }\r
 561     else // remove ConservationColouring\r
 562     {\r
 563       ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;\r
 564       sg.cs = ccs.cs;\r
 565     }\r
 566 \r
 567     refresh();\r
 568   }\r
 569 \r
 570   protected void groupName_actionPerformed(ActionEvent e)\r
 571   {\r
 572     SequenceGroup sg = getGroup();\r
 573     String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
 574         "Enter new group name", "Edit group name",\r
 575         JOptionPane.QUESTION_MESSAGE);\r
 576 \r
 577     if (reply == null)\r
 578     {\r
 579       return;\r
 580     }\r
 581 \r
 582     sg.setName(reply);\r
 583     groupName.setText(reply);\r
 584   }\r
 585 \r
 586   protected void analyze_actionPerformed(ActionEvent e)\r
 587   {\r
 588     CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
 589     JInternalFrame frame = new JInternalFrame();\r
 590     frame.setContentPane(cap);\r
 591     Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
 592 \r
 593     SequenceGroup sg = getGroup();\r
 594     StringBuffer sb = new StringBuffer();\r
 595 \r
 596     for (int i = 0; i < sg.sequences.size(); i++)\r
 597     {\r
 598       Sequence tmp = (Sequence) sg.sequences.get(i);\r
 599       sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
 600       sb.append("\n");\r
 601     }\r
 602 \r
 603     sb.append("Something amazing will happen soon");\r
 604     cap.setText(sb.toString());\r
 605   }\r
 606 \r
 607   SequenceGroup getGroup()\r
 608   {\r
 609     SequenceGroup sg = ap.av.getSelectionGroup();\r
 610 \r
 611     // this method won't add a new group if it already exists\r
 612     ap.av.alignment.addGroup(sg);\r
 613 \r
 614     return sg;\r
 615   }\r
 616 \r
 617   void sequenceName_actionPerformed(ActionEvent e)\r
 618   {\r
 619     String id = sequence.getName();\r
 620     String s = (String) JOptionPane.showInternalInputDialog(ap,\r
 621         "Edit sequence name",\r
 622         "Edit sequence name (" + sequence.getName() + ")",\r
 623         JOptionPane.PLAIN_MESSAGE, null, null, id);\r
 624 \r
 625     if (s != null)\r
 626     {\r
 627       sequence.setName(s);\r
 628       ap.repaint();\r
 629     }\r
 630   }\r
 631 \r
 632   void unGroupMenuItem_actionPerformed(ActionEvent e)\r
 633   {\r
 634     SequenceGroup sg = ap.av.getSelectionGroup();\r
 635     ap.av.alignment.deleteGroup(sg);\r
 636     ap.av.setSelectionGroup(null);\r
 637     ap.repaint();\r
 638   }\r
 639 \r
 640   void pdbMenuItem_actionPerformed(ActionEvent e)\r
 641   {\r
 642     if (sequence.getPDBId() == null)\r
 643     {\r
 644       return;\r
 645     }\r
 646 \r
 647     try\r
 648     {\r
 649       EBIFetchClient ebi = new EBIFetchClient();\r
 650       String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null,\r
 651                                       null);\r
 652 \r
 653       PDBfile pdb = new PDBfile(result);\r
 654 \r
 655       rotCanvas rc = new rotCanvas(pdb, sequence, ap.av);\r
 656       JInternalFrame frame = new JInternalFrame();\r
 657       frame.setContentPane(rc);\r
 658       Desktop.addInternalFrame(frame,\r
 659                                sequence.getName() + " " + sequence.getPDBId(),\r
 660                                400, 400);\r
 661     }\r
 662     catch (Exception ex)\r
 663     {\r
 664       ex.printStackTrace();\r
 665     }\r
 666   }\r
 667 \r
 668   protected void outline_actionPerformed(ActionEvent e)\r
 669   {\r
 670     SequenceGroup sg = getGroup();\r
 671     Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
 672                                          Color.BLUE);\r
 673 \r
 674     if (col != null)\r
 675     {\r
 676       sg.setOutlineColour(col);\r
 677     }\r
 678 \r
 679     ap.repaint();\r
 680   }\r
 681 \r
 682   public void showBoxes_actionPerformed(ActionEvent e)\r
 683   {\r
 684     getGroup().setDisplayBoxes(showBoxes.isSelected());\r
 685     refresh();\r
 686   }\r
 687 \r
 688   public void showText_actionPerformed(ActionEvent e)\r
 689   {\r
 690     getGroup().setDisplayText(showText.isSelected());\r
 691     refresh();\r
 692   }\r
 693 \r
 694   public void showColourText_actionPerformed(ActionEvent e)\r
 695   {\r
 696     getGroup().setColourText(showColourText.isSelected());\r
 697     refresh();\r
 698   }\r
 699 }\r