src/jalview/appletgui/APopupMenu.java

   1 /*\r
   2 * Jalview - A Sequence Alignment Editor and Viewer\r
   3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4 *\r
   5 * This program is free software; you can redistribute it and/or\r
   6 * modify it under the terms of the GNU General Public License\r
   7 * as published by the Free Software Foundation; either version 2\r
   8 * of the License, or (at your option) any later version.\r
   9 *\r
  10 * This program is distributed in the hope that it will be useful,\r
  11 * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13 * GNU General Public License for more details.\r
  14 *\r
  15 * You should have received a copy of the GNU General Public License\r
  16 * along with this program; if not, write to the Free Software\r
  17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18 */\r
  19 \r
  20 package jalview.appletgui;\r
  21 \r
  22 import jalview.datamodel.*;\r
  23 import jalview.analysis.*;\r
  24 import jalview.schemes.*;\r
  25 import java.awt.*;\r
  26 import java.awt.event.*;\r
  27 \r
  28 public class APopupMenu extends java.awt.PopupMenu\r
  29 {\r
  30   Menu groupMenu = new Menu();\r
  31   protected MenuItem clustalColour = new MenuItem();\r
  32   protected MenuItem zappoColour = new MenuItem();\r
  33   protected MenuItem taylorColour = new MenuItem();\r
  34   protected MenuItem hydrophobicityColour = new MenuItem();\r
  35   protected MenuItem helixColour = new MenuItem();\r
  36   protected MenuItem strandColour = new MenuItem();\r
  37   protected MenuItem turnColour = new MenuItem();\r
  38   protected MenuItem buriedColour = new MenuItem();\r
  39   protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();\r
  40   protected MenuItem userDefinedColour = new MenuItem();\r
  41   protected MenuItem PIDColour = new MenuItem();\r
  42   protected MenuItem BLOSUM62Colour = new MenuItem();\r
  43   MenuItem noColourmenuItem = new MenuItem();\r
  44   protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
  45 \r
  46 \r
  47   AlignmentPanel ap;\r
  48   Menu sequenceMenu = new Menu();\r
  49   MenuItem sequenceName = new MenuItem();\r
  50   Sequence sequence;\r
  51   MenuItem unGroupMenuItem = new MenuItem();\r
  52   MenuItem nucleotideMenuItem = new MenuItem();\r
  53   Menu colourMenu = new Menu();\r
  54   CheckboxMenuItem showBoxes = new CheckboxMenuItem();\r
  55   CheckboxMenuItem showText = new CheckboxMenuItem();\r
  56   CheckboxMenuItem showColourText = new CheckboxMenuItem();\r
  57 \r
  58   public APopupMenu(AlignmentPanel ap, Sequence seq)\r
  59   {\r
  60     ///////////////////////////////////////////////////////////\r
  61     // If this is activated from the sequence panel, the user may want to\r
  62     // edit or annotate a particular residue. Therefore display the residue menu\r
  63     //\r
  64     // If from the IDPanel, we must display the sequence menu\r
  65     //////////////////////////////////////////////////////////\r
  66 \r
  67     this.ap = ap;\r
  68     sequence = seq;\r
  69 \r
  70     try\r
  71     {     jbInit();   }\r
  72     catch(Exception e)\r
  73     {    e.printStackTrace();    }\r
  74 \r
  75 \r
  76     SequenceGroup sg = ap.av.getSelectionGroup();\r
  77     if(sg!=null)\r
  78     {\r
  79       showText.setState(sg.getDisplayText());\r
  80       showColourText.setState(sg.getColourText());\r
  81       showBoxes.setState(sg.getDisplayBoxes());\r
  82     }\r
  83 \r
  84     if( !ap.av.alignment.getGroups().contains(sg))\r
  85         groupMenu.remove(unGroupMenuItem);\r
  86 \r
  87     if(seq==null)\r
  88        remove(sequenceMenu);\r
  89 \r
  90 \r
  91   }\r
  92   private void jbInit() throws Exception\r
  93   {\r
  94     groupMenu.setLabel("Group");\r
  95     groupMenu.setLabel("Define");\r
  96 \r
  97     sequenceMenu.setLabel("Sequence");\r
  98     sequenceName.setLabel("Edit name");\r
  99     unGroupMenuItem.setLabel("Remove Group");\r
 100     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 101     {\r
 102       public void actionPerformed(ActionEvent e)\r
 103       {\r
 104         unGroupMenuItem_actionPerformed(e);\r
 105       }\r
 106     });\r
 107 \r
 108 \r
 109     nucleotideMenuItem.setLabel("Nucleotide");\r
 110     nucleotideMenuItem.addActionListener(new ActionListener()\r
 111     {\r
 112       public void actionPerformed(ActionEvent e)\r
 113       {\r
 114         nucleotideMenuItem_actionPerformed(e);\r
 115       }\r
 116     });\r
 117     conservationMenuItem.addItemListener(new ItemListener()\r
 118     {\r
 119       public void itemStateChanged(ItemEvent itemEvent)\r
 120       {\r
 121         conservationMenuItem_itemStateChanged(itemEvent);\r
 122       }\r
 123     });\r
 124     abovePIDColour.addItemListener(new ItemListener()\r
 125     {\r
 126       public void itemStateChanged(ItemEvent itemEvent)\r
 127       {\r
 128         abovePIDColour_itemStateChanged(itemEvent);\r
 129       }\r
 130     });\r
 131     colourMenu.setLabel("Group Colour");\r
 132     showBoxes.setLabel("Boxes");\r
 133     showBoxes.setState(true);\r
 134     showBoxes.addItemListener(new ItemListener()\r
 135     {\r
 136       public void itemStateChanged(ItemEvent itemEvent)\r
 137       {\r
 138         showBoxes_itemStateChanged(itemEvent);\r
 139       }\r
 140     });\r
 141 \r
 142     showText.setLabel("Text");\r
 143     showText.addItemListener(new ItemListener()\r
 144     {\r
 145       public void itemStateChanged(ItemEvent itemEvent)\r
 146       {\r
 147         showText_itemStateChanged(itemEvent);\r
 148       }\r
 149     });\r
 150     showColourText.setLabel("Colour Text");\r
 151     showColourText.addItemListener(new ItemListener()\r
 152     {\r
 153       public void itemStateChanged(ItemEvent itemEvent)\r
 154       {\r
 155         showColourText_itemStateChanged(itemEvent);\r
 156       }\r
 157     });\r
 158 \r
 159     add(groupMenu);\r
 160     this.add(sequenceMenu);\r
 161     groupMenu.add(unGroupMenuItem);\r
 162     groupMenu.add(colourMenu);\r
 163     groupMenu.addSeparator();\r
 164     groupMenu.add(showBoxes);\r
 165     groupMenu.add(showText);\r
 166     groupMenu.add(showColourText);\r
 167     sequenceMenu.add(sequenceName);\r
 168     colourMenu.add(noColourmenuItem);\r
 169     colourMenu.add(clustalColour);\r
 170     colourMenu.add(BLOSUM62Colour);\r
 171     colourMenu.add(PIDColour);\r
 172     colourMenu.add(zappoColour);\r
 173     colourMenu.add(taylorColour);\r
 174     colourMenu.add(hydrophobicityColour);\r
 175     colourMenu.add(helixColour);\r
 176     colourMenu.add(strandColour);\r
 177     colourMenu.add(turnColour);\r
 178     colourMenu.add(buriedColour);\r
 179     colourMenu.add(nucleotideMenuItem);\r
 180     colourMenu.add(userDefinedColour);\r
 181     colourMenu.addSeparator();\r
 182     colourMenu.add(abovePIDColour);\r
 183     colourMenu.add(conservationMenuItem);\r
 184 \r
 185     noColourmenuItem.setLabel("None");\r
 186     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 187     {\r
 188       public void actionPerformed(ActionEvent e)\r
 189       {\r
 190         noColourmenuItem_actionPerformed(e);\r
 191       }\r
 192     });\r
 193 \r
 194     clustalColour.setLabel("Clustalx colours");\r
 195     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 196     {\r
 197       public void actionPerformed(ActionEvent e)\r
 198       {\r
 199         clustalColour_actionPerformed(e);\r
 200       }\r
 201     });\r
 202     zappoColour.setLabel("Zappo");\r
 203     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 204     {\r
 205       public void actionPerformed(ActionEvent e)\r
 206       {\r
 207         zappoColour_actionPerformed(e);\r
 208       }\r
 209     });\r
 210     taylorColour.setLabel("Taylor");\r
 211     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 212     {\r
 213       public void actionPerformed(ActionEvent e)\r
 214       {\r
 215         taylorColour_actionPerformed(e);\r
 216       }\r
 217     });\r
 218     hydrophobicityColour.setLabel("Hydrophobicity");\r
 219     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 220     {\r
 221       public void actionPerformed(ActionEvent e)\r
 222       {\r
 223         hydrophobicityColour_actionPerformed(e);\r
 224       }\r
 225     });\r
 226     helixColour.setLabel("Helix propensity");\r
 227     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 228     {\r
 229       public void actionPerformed(ActionEvent e)\r
 230       {\r
 231         helixColour_actionPerformed(e);\r
 232       }\r
 233     });\r
 234     strandColour.setLabel("Strand propensity");\r
 235     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 236     {\r
 237       public void actionPerformed(ActionEvent e)\r
 238       {\r
 239         strandColour_actionPerformed(e);\r
 240       }\r
 241     });\r
 242     turnColour.setLabel("Turn propensity");\r
 243     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 244     {\r
 245       public void actionPerformed(ActionEvent e)\r
 246       {\r
 247         turnColour_actionPerformed(e);\r
 248       }\r
 249     });\r
 250     buriedColour.setLabel("Buried Index");\r
 251     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 252     {\r
 253       public void actionPerformed(ActionEvent e)\r
 254       {\r
 255         buriedColour_actionPerformed(e);\r
 256       }\r
 257     });\r
 258     abovePIDColour.setLabel("Above % Identity");\r
 259 \r
 260     userDefinedColour.setLabel("User Defined");\r
 261     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 262     {\r
 263       public void actionPerformed(ActionEvent e)\r
 264       {\r
 265         userDefinedColour_actionPerformed(e);\r
 266       }\r
 267     });\r
 268     PIDColour.setLabel("Percentage Identity");\r
 269     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 270     {\r
 271       public void actionPerformed(ActionEvent e)\r
 272       {\r
 273         PIDColour_actionPerformed(e);\r
 274       }\r
 275     });\r
 276     BLOSUM62Colour.setLabel("BLOSUM62");\r
 277     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 278     {\r
 279       public void actionPerformed(ActionEvent e)\r
 280       {\r
 281         BLOSUM62Colour_actionPerformed(e);\r
 282       }\r
 283     });\r
 284     conservationMenuItem.setLabel("Conservation");\r
 285 \r
 286 \r
 287   }\r
 288 \r
 289   void refresh()\r
 290   {\r
 291     SequenceGroup sg = getGroup();\r
 292     SuperGroup superG = ap.av.alignment.getSuperGroup( sg );\r
 293     if( superG !=null)\r
 294       superG.setSuperGroupProperties( sg );\r
 295 \r
 296     ap.seqPanel.seqCanvas.repaint();\r
 297   }\r
 298 \r
 299   protected void clustalColour_actionPerformed(ActionEvent e)\r
 300   {\r
 301     SequenceGroup sg = getGroup();\r
 302     sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());\r
 303     refresh();\r
 304   }\r
 305 \r
 306   protected void zappoColour_actionPerformed(ActionEvent e)\r
 307   {\r
 308     getGroup().cs = new ZappoColourScheme();\r
 309     refresh();\r
 310   }\r
 311 \r
 312   protected void taylorColour_actionPerformed(ActionEvent e)\r
 313   {\r
 314     getGroup().cs = new TaylorColourScheme();\r
 315     refresh();\r
 316   }\r
 317 \r
 318 \r
 319   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 320   {\r
 321     getGroup().cs = new HydrophobicColourScheme();\r
 322     refresh();\r
 323   }\r
 324 \r
 325   protected void helixColour_actionPerformed(ActionEvent e)\r
 326   {\r
 327     getGroup().cs = new HelixColourScheme();\r
 328     refresh();\r
 329   }\r
 330 \r
 331   protected void strandColour_actionPerformed(ActionEvent e)\r
 332   {\r
 333     getGroup().cs = new StrandColourScheme();\r
 334     refresh();\r
 335   }\r
 336 \r
 337   protected void turnColour_actionPerformed(ActionEvent e)\r
 338   {\r
 339     getGroup().cs = new TurnColourScheme();\r
 340     refresh();\r
 341   }\r
 342 \r
 343   protected void buriedColour_actionPerformed(ActionEvent e)\r
 344   {\r
 345     getGroup().cs = new BuriedColourScheme();\r
 346     refresh();\r
 347   }\r
 348 \r
 349   public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
 350   {\r
 351     getGroup().cs = new NucleotideColourScheme();\r
 352     refresh();\r
 353   }\r
 354 \r
 355 \r
 356 \r
 357   protected void abovePIDColour_itemStateChanged(ItemEvent ie)\r
 358   {\r
 359     SequenceGroup sg = getGroup();\r
 360     if (abovePIDColour.getState())\r
 361     {\r
 362       sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 363                                                ap.av.alignment.getWidth()));\r
 364       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());\r
 365       if (sg.cs instanceof ResidueColourScheme)\r
 366         ( (ResidueColourScheme)sg. cs).setThreshold(threshold);\r
 367       else if (sg.cs instanceof ScoreColourScheme)\r
 368         ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
 369 \r
 370       SliderPanel.showPIDSlider();\r
 371 \r
 372 \r
 373     }\r
 374     else // remove PIDColouring\r
 375     {\r
 376       ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;\r
 377       rcs.setThreshold(0);\r
 378       sg.cs = rcs;\r
 379     }\r
 380 \r
 381     refresh();\r
 382 \r
 383   }\r
 384 \r
 385 \r
 386   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 387   {\r
 388     new UserDefinedColours( ap, getGroup());\r
 389   }\r
 390 \r
 391   protected void PIDColour_actionPerformed(ActionEvent e)\r
 392   {\r
 393     SequenceGroup sg = getGroup();\r
 394     sg.cs = new PIDColourScheme();\r
 395     sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 396                                                ap.av.alignment.getWidth()));\r
 397     refresh();\r
 398   }\r
 399 \r
 400   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 401   {\r
 402     SequenceGroup sg = getGroup();\r
 403 \r
 404     sg.cs = new Blosum62ColourScheme();\r
 405 \r
 406     sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 407                                                ap.av.alignment.getWidth()));\r
 408 \r
 409     refresh();\r
 410   }\r
 411 \r
 412 \r
 413   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 414   {\r
 415     getGroup().cs = null;\r
 416     refresh();\r
 417   }\r
 418 \r
 419   protected  void conservationMenuItem_itemStateChanged(ItemEvent ie)\r
 420   {\r
 421     SequenceGroup sg = getGroup();\r
 422 \r
 423     if(conservationMenuItem.getState())\r
 424     {\r
 425 \r
 426         Conservation c = new Conservation("Group",\r
 427                                           ResidueProperties.propHash, 3,\r
 428                                           sg.sequences, 0,\r
 429                                           ap.av.alignment.getWidth());\r
 430 \r
 431         c.calculate();\r
 432         c.verdict(false, ap.av.ConsPercGaps);\r
 433         ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 434 \r
 435 \r
 436       sg.cs = ccs;\r
 437 \r
 438       SliderPanel.setConservationSlider(ap, ccs, sg.getName());\r
 439       SliderPanel.showConservationSlider();\r
 440     }\r
 441     else // remove ConservationColouring\r
 442     {\r
 443         ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
 444         sg.cs = ccs.cs;\r
 445     }\r
 446 \r
 447      refresh();\r
 448   }\r
 449 \r
 450 \r
 451   protected void analyze_actionPerformed(ActionEvent e)\r
 452   {\r
 453      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
 454      Frame frame = new Frame();\r
 455      frame.add(cap);\r
 456      jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300);\r
 457      SequenceGroup sg = getGroup();\r
 458      StringBuffer sb = new StringBuffer();\r
 459 \r
 460      for(int i=0; i<sg.sequences.size(); i++)\r
 461      {\r
 462        Sequence tmp = (Sequence)sg.sequences.elementAt(i);\r
 463        sb.append(  tmp.getSequence(sg.getStartRes(), sg.getEndRes()+1));\r
 464        sb.append("\n");\r
 465      }\r
 466 \r
 467      sb.append("Something amazing will happen soon");\r
 468      cap.setText( sb.toString() );\r
 469 \r
 470   }\r
 471 \r
 472   SequenceGroup getGroup()\r
 473   {\r
 474     SequenceGroup sg = ap.av.getSelectionGroup();\r
 475 \r
 476     // this method won't add a new group if it already exists\r
 477     ap.av.alignment.addGroup(sg);\r
 478 \r
 479     return sg;\r
 480   }\r
 481 \r
 482   void unGroupMenuItem_actionPerformed(ActionEvent e)\r
 483   {\r
 484      SequenceGroup sg = ap.av.getSelectionGroup();\r
 485      ap.av.alignment.deleteGroup(sg);\r
 486      ap.av.setSelectionGroup(null);\r
 487      ap.repaint();\r
 488   }\r
 489 \r
 490 \r
 491   public void showColourText_itemStateChanged(ItemEvent itemEvent)\r
 492   {\r
 493     getGroup().setColourText(showColourText.getState());\r
 494     refresh();\r
 495   }\r
 496 \r
 497   public void showText_itemStateChanged(ItemEvent itemEvent)\r
 498   {\r
 499     getGroup().setDisplayText(showText.getState());\r
 500     refresh();\r
 501   }\r
 502 \r
 503   public void showBoxes_itemStateChanged(ItemEvent itemEvent)\r
 504   {\r
 505     getGroup().setDisplayBoxes(showBoxes.getState());\r
 506     refresh();\r
 507   }\r
 508 \r
 509 }\r