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