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