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