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 javax.swing.*;\r
   7 import java.awt.event.*;\r
   8 \r
   9 \r
  10 public class PopupMenu extends JPopupMenu\r
  11 {\r
  12   JMenu groupMenu = new JMenu();\r
  13   JMenuItem copyGroup = new JMenuItem();\r
  14   JMenuItem moveGroup = new JMenuItem();\r
  15   JMenuItem deleteSequences = new JMenuItem();\r
  16   JMenuItem analyze = new JMenuItem();\r
  17   JMenu defineMenu = new JMenu();\r
  18   JMenuItem groupName = new JMenuItem();\r
  19   JMenuItem groupAnnotation = new JMenuItem();\r
  20   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  21   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  22   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  23   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
  24   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  25   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  26   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  27   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  28   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();\r
  29   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  30   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  31   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  32   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  33   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  34 \r
  35 \r
  36   AlignmentPanel ap;\r
  37   JMenu sequenceMenu = new JMenu();\r
  38   JMenuItem sequenceName = new JMenuItem();\r
  39   JMenu residueMenu = new JMenu();\r
  40   JMenuItem annotateResidue = new JMenuItem();\r
  41 \r
  42   SequenceI sequence;\r
  43 \r
  44   public PopupMenu(AlignmentPanel ap, SequenceI seq)\r
  45   {\r
  46     ///////////////////////////////////////////////////////////\r
  47     // If this is activated from the sequence panel, the user may want to\r
  48     // edit or annotate a particular residue. Therefore display the residue menu\r
  49     //\r
  50     // If from the IDPanel, we must display the sequence menu\r
  51     //////////////////////////////////////////////////////////\r
  52 \r
  53     this.ap = ap;\r
  54     sequence = seq;\r
  55 \r
  56     ButtonGroup colours = new ButtonGroup();\r
  57     colours.add(noColourmenuItem);\r
  58     colours.add(clustalColour);\r
  59     colours.add(zappoColour);\r
  60     colours.add(taylorColour);\r
  61     colours.add(hydrophobicityColour);\r
  62     colours.add(helixColour);\r
  63     colours.add(strandColour);\r
  64     colours.add(turnColour);\r
  65     colours.add(buriedColour);\r
  66     colours.add(abovePIDColour);\r
  67     colours.add(userDefinedColour);\r
  68     colours.add(PIDColour);\r
  69     colours.add(BLOSUM62Colour);\r
  70 \r
  71     try\r
  72     {     jbInit();   }\r
  73     catch(Exception e)\r
  74     {    e.printStackTrace();    }\r
  75 \r
  76     SequenceGroup sg = ap.av.getRubberbandGroup();\r
  77     if(sg!=null)\r
  78     {\r
  79       groupName.setText(sg.getName());\r
  80       if(sg.cs instanceof ZappoColourScheme)\r
  81         zappoColour.setSelected(true);\r
  82       else if(sg.cs instanceof TaylorColourScheme)\r
  83         taylorColour.setSelected(true);\r
  84       else if (sg.cs instanceof PIDColourScheme)\r
  85         PIDColour.setSelected(true);\r
  86       else if (sg.cs instanceof Blosum62ColourScheme)\r
  87         BLOSUM62Colour.setSelected(true);\r
  88       else if (sg.cs instanceof UserColourScheme)\r
  89         userDefinedColour.setSelected(true);\r
  90       else if (sg.cs instanceof HydrophobicColourScheme)\r
  91         hydrophobicityColour.setSelected(true);\r
  92       else if (sg.cs instanceof HelixColourScheme)\r
  93         helixColour.setSelected(true);\r
  94       else if (sg.cs instanceof StrandColourScheme)\r
  95         strandColour.setSelected(true);\r
  96       else if (sg.cs instanceof TurnColourScheme)\r
  97         turnColour.setSelected(true);\r
  98       else if (sg.cs instanceof BuriedColourScheme)\r
  99         buriedColour.setSelected(true);\r
 100       else if (sg.cs instanceof ClustalxColourScheme)\r
 101         clustalColour.setSelected(true);\r
 102       else\r
 103         noColourmenuItem.setSelected(true);\r
 104 \r
 105       if (sg.cs instanceof ConservationColourScheme)\r
 106         conservationMenuItem.setSelected(true);\r
 107 \r
 108     }\r
 109 \r
 110     if(seq!=null)\r
 111     {\r
 112       residueMenu.setVisible(false);\r
 113       sequenceName.setText( sequence.getName() );\r
 114     }\r
 115     else\r
 116       sequenceMenu.setVisible(false);\r
 117 \r
 118   }\r
 119   private void jbInit() throws Exception\r
 120   {\r
 121     groupMenu.setText("Group");\r
 122     copyGroup.setText("Copy region to new Alignment");\r
 123     copyGroup.addActionListener(new java.awt.event.ActionListener()\r
 124     {\r
 125       public void actionPerformed(ActionEvent e)\r
 126       {\r
 127         copyGroup_actionPerformed(e);\r
 128       }\r
 129     });\r
 130     moveGroup.setText("Move sequences to new Alignment");\r
 131     moveGroup.addActionListener(new java.awt.event.ActionListener()\r
 132     {\r
 133       public void actionPerformed(ActionEvent e)\r
 134       {\r
 135         moveGroup_actionPerformed(e);\r
 136       }\r
 137     });\r
 138     deleteSequences.setText("Delete sequences");\r
 139     deleteSequences.addActionListener(new java.awt.event.ActionListener()\r
 140     {\r
 141       public void actionPerformed(ActionEvent e)\r
 142       {\r
 143         deleteSequences_actionPerformed(e);\r
 144       }\r
 145     });\r
 146     analyze.setText("Analyze");\r
 147     analyze.addActionListener(new java.awt.event.ActionListener()\r
 148     {\r
 149       public void actionPerformed(ActionEvent e)\r
 150       {\r
 151         analyze_actionPerformed(e);\r
 152       }\r
 153     });\r
 154     defineMenu.setText("Define");\r
 155     groupName.setText("Name");\r
 156     groupName.addActionListener(new java.awt.event.ActionListener()\r
 157     {\r
 158       public void actionPerformed(ActionEvent e)\r
 159       {\r
 160         groupName_actionPerformed(e);\r
 161       }\r
 162     });\r
 163     groupAnnotation.setText("Annotation");\r
 164     groupAnnotation.addActionListener(new java.awt.event.ActionListener()\r
 165     {\r
 166       public void actionPerformed(ActionEvent e)\r
 167       {\r
 168         groupAnnotation_actionPerformed(e);\r
 169       }\r
 170     });\r
 171     sequenceMenu.setText("Sequence");\r
 172     sequenceName.setText("sequenceName");\r
 173     sequenceName.addActionListener(new java.awt.event.ActionListener()\r
 174     {\r
 175       public void actionPerformed(ActionEvent e)\r
 176       {\r
 177         sequenceName_actionPerformed(e);\r
 178       }\r
 179     });\r
 180     residueMenu.setText("Residue");\r
 181     annotateResidue.setText("annotate residue???");\r
 182     PIDColour.setFocusPainted(false);\r
 183     add(groupMenu);\r
 184     this.add(sequenceMenu);\r
 185     this.add(residueMenu);\r
 186     groupMenu.add(defineMenu);\r
 187     groupMenu.addSeparator();\r
 188     groupMenu.add(copyGroup);\r
 189     groupMenu.add(moveGroup);\r
 190     groupMenu.add(deleteSequences);\r
 191     groupMenu.addSeparator();\r
 192     groupMenu.add(analyze);\r
 193     defineMenu.add(groupName);\r
 194     defineMenu.add(groupAnnotation);\r
 195     defineMenu.addSeparator();\r
 196     defineMenu.add(noColourmenuItem);\r
 197     defineMenu.add(clustalColour);\r
 198     defineMenu.add(zappoColour);\r
 199     defineMenu.add(taylorColour);\r
 200     defineMenu.add(hydrophobicityColour);\r
 201     defineMenu.add(helixColour);\r
 202     defineMenu.add(strandColour);\r
 203     defineMenu.add(turnColour);\r
 204     defineMenu.add(buriedColour);\r
 205     defineMenu.add(userDefinedColour);\r
 206     defineMenu.add(PIDColour);\r
 207     defineMenu.add(BLOSUM62Colour);\r
 208     defineMenu.addSeparator();\r
 209     defineMenu.add(abovePIDColour);\r
 210     defineMenu.add(conservationMenuItem);\r
 211 \r
 212     sequenceMenu.add(sequenceName);\r
 213     residueMenu.add(annotateResidue);\r
 214 \r
 215     noColourmenuItem.setText("None");\r
 216     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 217     {\r
 218       public void actionPerformed(ActionEvent e)\r
 219       {\r
 220         noColourmenuItem_actionPerformed(e);\r
 221       }\r
 222     });\r
 223 \r
 224     clustalColour.setText("Clustalx colours");\r
 225     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 226     {\r
 227       public void actionPerformed(ActionEvent e)\r
 228       {\r
 229         clustalColour_actionPerformed(e);\r
 230       }\r
 231     });\r
 232     zappoColour.setText("Zappo colour scheme");\r
 233     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 234     {\r
 235       public void actionPerformed(ActionEvent e)\r
 236       {\r
 237         zappoColour_actionPerformed(e);\r
 238       }\r
 239     });\r
 240     taylorColour.setText("Taylor colour scheme");\r
 241     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 242     {\r
 243       public void actionPerformed(ActionEvent e)\r
 244       {\r
 245         taylorColour_actionPerformed(e);\r
 246       }\r
 247     });\r
 248     hydrophobicityColour.setText("By hydrophobicity");\r
 249     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 250     {\r
 251       public void actionPerformed(ActionEvent e)\r
 252       {\r
 253         hydrophobicityColour_actionPerformed(e);\r
 254       }\r
 255     });\r
 256     helixColour.setText("Helix propensity");\r
 257     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 258     {\r
 259       public void actionPerformed(ActionEvent e)\r
 260       {\r
 261         helixColour_actionPerformed(e);\r
 262       }\r
 263     });\r
 264     strandColour.setText("Strand propensity");\r
 265     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 266     {\r
 267       public void actionPerformed(ActionEvent e)\r
 268       {\r
 269         strandColour_actionPerformed(e);\r
 270       }\r
 271     });\r
 272     turnColour.setText("Turn propensity");\r
 273     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 274     {\r
 275       public void actionPerformed(ActionEvent e)\r
 276       {\r
 277         turnColour_actionPerformed(e);\r
 278       }\r
 279     });\r
 280     buriedColour.setText("Buried index");\r
 281     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 282     {\r
 283       public void actionPerformed(ActionEvent e)\r
 284       {\r
 285         buriedColour_actionPerformed(e);\r
 286       }\r
 287     });\r
 288     abovePIDColour.setText("Above PID threshold only");\r
 289     abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
 290     {\r
 291       public void actionPerformed(ActionEvent e)\r
 292       {\r
 293         abovePIDColour_actionPerformed(e);\r
 294       }\r
 295     });\r
 296     userDefinedColour.setText("User defined colours");\r
 297     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 298     {\r
 299       public void actionPerformed(ActionEvent e)\r
 300       {\r
 301         userDefinedColour_actionPerformed(e);\r
 302       }\r
 303     });\r
 304     PIDColour.setText("Percentage Identity");\r
 305     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 306     {\r
 307       public void actionPerformed(ActionEvent e)\r
 308       {\r
 309         PIDColour_actionPerformed(e);\r
 310       }\r
 311     });\r
 312     BLOSUM62Colour.setText("BLOSUM62 score");\r
 313     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 314     {\r
 315       public void actionPerformed(ActionEvent e)\r
 316       {\r
 317         BLOSUM62Colour_actionPerformed(e);\r
 318       }\r
 319     });\r
 320     conservationMenuItem.setText("By conservation");\r
 321    conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 322    {\r
 323      public void actionPerformed(ActionEvent e)\r
 324      {\r
 325        conservationMenuItem_actionPerformed(e);\r
 326      }\r
 327    });\r
 328 \r
 329 \r
 330 \r
 331   }\r
 332 \r
 333   void refresh()\r
 334   {\r
 335     SequenceGroup sg = getGroup();\r
 336     SuperGroup superG = ap.av.alignment.getSuperGroup( sg );\r
 337     if( superG !=null)\r
 338       superG.setSuperGroupProperties( sg );\r
 339 \r
 340     ap.seqPanel.seqCanvas.paintFlag=true;\r
 341     ap.seqPanel.repaint();\r
 342   }\r
 343 \r
 344   protected void clustalColour_actionPerformed(ActionEvent e)\r
 345   {\r
 346     getGroup().cs = new ClustalxColourScheme();\r
 347     refresh();\r
 348   }\r
 349 \r
 350   protected void zappoColour_actionPerformed(ActionEvent e)\r
 351   {\r
 352     getGroup().cs = new ZappoColourScheme();\r
 353     refresh();\r
 354   }\r
 355 \r
 356   protected void taylorColour_actionPerformed(ActionEvent e)\r
 357   {\r
 358     getGroup().cs = new TaylorColourScheme();\r
 359     refresh();\r
 360   }\r
 361 \r
 362 \r
 363   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 364   {\r
 365     getGroup().cs = new HydrophobicColourScheme();\r
 366     refresh();\r
 367   }\r
 368 \r
 369   protected void helixColour_actionPerformed(ActionEvent e)\r
 370   {\r
 371     getGroup().cs = new HelixColourScheme();\r
 372     refresh();\r
 373   }\r
 374 \r
 375   protected void strandColour_actionPerformed(ActionEvent e)\r
 376   {\r
 377     getGroup().cs = new StrandColourScheme();\r
 378     refresh();\r
 379   }\r
 380 \r
 381   protected void turnColour_actionPerformed(ActionEvent e)\r
 382   {\r
 383     getGroup().cs = new TurnColourScheme();\r
 384     refresh();\r
 385   }\r
 386 \r
 387   protected void buriedColour_actionPerformed(ActionEvent e)\r
 388   {\r
 389     getGroup().cs = new BuriedColourScheme();\r
 390     refresh();\r
 391   }\r
 392 \r
 393 \r
 394 /*\r
 395 public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)\r
 396 {\r
 397 ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel);\r
 398 JInternalFrame frame = new JInternalFrame();\r
 399 frame.setContentPane(cip);\r
 400 Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,90);\r
 401 frame.setMaximizable(false);\r
 402 \r
 403  }*/\r
 404 \r
 405 \r
 406   protected void abovePIDColour_actionPerformed(ActionEvent e)\r
 407   {\r
 408     SliderPanel sp = new SliderPanel(ap, 70, false, getGroup().cs );\r
 409     JInternalFrame frame = new JInternalFrame();\r
 410     frame.setContentPane(sp);\r
 411     Desktop.addInternalFrame(frame, "Percentage Identity Threshold ("+getGroup().getName()+")" , 400,90);\r
 412     frame.setMaximizable(false);\r
 413 \r
 414   }\r
 415 \r
 416 \r
 417   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 418   {\r
 419     JInternalFrame frame = new JInternalFrame();\r
 420     UserDefinedColours chooser = new UserDefinedColours( frame, ap, getGroup());\r
 421     frame.setContentPane(chooser);\r
 422     Desktop.addInternalFrame(frame,"User defined colours ("+getGroup().getName()+")", 450,540 );\r
 423     frame.setResizable(false);\r
 424     frame.setIconifiable(false);\r
 425     frame.setMaximizable(false);\r
 426 \r
 427   }\r
 428 \r
 429   protected void PIDColour_actionPerformed(ActionEvent e)\r
 430   {\r
 431 \r
 432   }\r
 433 \r
 434   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 435   {\r
 436     getGroup().cs = new Blosum62ColourScheme(ap.av);\r
 437     refresh();\r
 438   }\r
 439 \r
 440 \r
 441   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 442   {\r
 443     getGroup().cs = null;\r
 444     refresh();\r
 445   }\r
 446 \r
 447   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 448   {\r
 449     SequenceGroup sg = getGroup();\r
 450 \r
 451     Conservation c = new Conservation("Group",\r
 452                           ResidueProperties.propHash, 3, sg.sequences, sg.getStartRes(),\r
 453                           sg.getEndRes() );\r
 454 \r
 455      c.calculate();\r
 456      c.verdict(false, 100);\r
 457      ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 458 \r
 459      sg.cs = ccs;\r
 460 \r
 461      refresh();\r
 462   }\r
 463 \r
 464   protected void groupAnnotation_actionPerformed(ActionEvent e)\r
 465   {\r
 466 \r
 467   }\r
 468 \r
 469   protected void groupName_actionPerformed(ActionEvent e)\r
 470   {\r
 471     SequenceGroup sg = getGroup();\r
 472     String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE);\r
 473     if(reply==null)\r
 474       return;\r
 475 \r
 476     sg.setName(reply);\r
 477     groupName.setText(reply);\r
 478   }\r
 479 \r
 480   protected void copyGroup_actionPerformed(ActionEvent e)\r
 481   {\r
 482     SequenceGroup sg = ap.av.getRubberbandGroup();\r
 483 \r
 484     SequenceI[] s = new Sequence[sg.sequences.size()];\r
 485      for (int i=0; i < sg.sequences.size(); i++)\r
 486      {\r
 487        s[i] = new Sequence( sg.getSequenceAt(i));\r
 488        s[i].setSequence( s[i].getSequence(sg.getStartRes(), sg.getEndRes()+1) );\r
 489      }\r
 490      AlignFrame af = new AlignFrame(new Alignment(s));\r
 491      int newHeight = s.length * af.viewport.getCharHeight() + 200;\r
 492      if (newHeight > 500)\r
 493        newHeight = 500;\r
 494      Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);\r
 495    }\r
 496 \r
 497   protected  void moveGroup_actionPerformed(ActionEvent e)\r
 498   {\r
 499     SequenceGroup sg = ap.av.getRubberbandGroup();\r
 500 \r
 501     SequenceI[] s = new Sequence[sg.sequences.size()];\r
 502 \r
 503      for (int i=0; i < sg.sequences.size(); i++)\r
 504        s[i] = new Sequence( sg.getSequenceAt(i));\r
 505 \r
 506      AlignFrame af = new AlignFrame(new Alignment(s));\r
 507      int newHeight = s.length * af.viewport.getCharHeight() + 200;\r
 508      if(newHeight>500)\r
 509        newHeight=500;\r
 510      Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);\r
 511 \r
 512 \r
 513      for (int i=0; i < sg.sequences.size(); i++)\r
 514        ap.av.alignment.deleteSequence(sg.getSequenceAt(i));\r
 515 \r
 516 \r
 517      ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());\r
 518      ap.RefreshPanels();\r
 519 \r
 520 \r
 521   }\r
 522 \r
 523   protected void deleteSequences_actionPerformed(ActionEvent e)\r
 524   {\r
 525     SequenceGroup sg = ap.av.getRubberbandGroup();\r
 526     for (int i=0;i < sg.sequences.size(); i++)\r
 527             ap.av.getAlignment().deleteSequence(sg.getSequenceAt(i));\r
 528 \r
 529     ap.av.alignment.deleteGroup(sg);\r
 530     ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());\r
 531     ap.seqPanel.parent.RefreshPanels();\r
 532 \r
 533   }\r
 534 \r
 535   protected void analyze_actionPerformed(ActionEvent e)\r
 536   {\r
 537      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
 538      JInternalFrame frame = new JInternalFrame();\r
 539      cap.formatForOutput();\r
 540      frame.setContentPane(cap);\r
 541      Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
 542      SequenceGroup sg = getGroup();\r
 543      StringBuffer sb = new StringBuffer();\r
 544 \r
 545      for(int i=0; i<sg.sequences.size(); i++)\r
 546      {\r
 547        Sequence tmp = (Sequence)sg.sequences.get(i);\r
 548        sb.append(  tmp.getSequence(sg.getStartRes(), sg.getEndRes()+1));\r
 549        sb.append("\n");\r
 550      }\r
 551 \r
 552      sb.append("Something amazing will happen soon");\r
 553      cap.setText( sb.toString() );\r
 554 \r
 555   }\r
 556 \r
 557   SequenceGroup getGroup()\r
 558   {\r
 559     SequenceGroup sg = ap.av.getRubberbandGroup();\r
 560 \r
 561     // this method won't add a new group if it already exists\r
 562     ap.av.alignment.addGroup(sg);\r
 563     return sg;\r
 564   }\r
 565 \r
 566   void sequenceName_actionPerformed(ActionEvent e)\r
 567   {\r
 568     String id = sequence.getName();\r
 569     String s = (String)JOptionPane.showInternalInputDialog(\r
 570                 ap,\r
 571                 "Edit sequence name",\r
 572                 "Edit sequence name",\r
 573                 JOptionPane.PLAIN_MESSAGE,\r
 574                 null,\r
 575                 null,\r
 576                 id);\r
 577 \r
 578     if(s!=null)\r
 579     {\r
 580       sequence.setName(s);\r
 581       ap.RefreshPanels();\r
 582     }\r
 583 \r
 584   }\r
 585 }\r