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