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