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