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