src/jalview/gui/PopupMenu.java

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