src/jalview/appletgui/APopupMenu.java

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