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     ap.seqPanel.seqCanvas.paintFlag=true;\r
 336     ap.seqPanel.repaint();\r
 337   }\r
 338 \r
 339   protected void clustalColour_actionPerformed(ActionEvent e)\r
 340   {\r
 341     getGroup().cs = new ClustalxColourScheme();\r
 342     refresh();\r
 343   }\r
 344 \r
 345   protected void zappoColour_actionPerformed(ActionEvent e)\r
 346   {\r
 347     getGroup().cs = new ZappoColourScheme();\r
 348     refresh();\r
 349   }\r
 350 \r
 351   protected void taylorColour_actionPerformed(ActionEvent e)\r
 352   {\r
 353     getGroup().cs = new TaylorColourScheme();\r
 354     refresh();\r
 355   }\r
 356 \r
 357 \r
 358   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 359   {\r
 360     getGroup().cs = new HydrophobicColourScheme();\r
 361     refresh();\r
 362   }\r
 363 \r
 364   protected void helixColour_actionPerformed(ActionEvent e)\r
 365   {\r
 366     getGroup().cs = new HelixColourScheme();\r
 367     refresh();\r
 368   }\r
 369 \r
 370   protected void strandColour_actionPerformed(ActionEvent e)\r
 371   {\r
 372     getGroup().cs = new StrandColourScheme();\r
 373     refresh();\r
 374   }\r
 375 \r
 376   protected void turnColour_actionPerformed(ActionEvent e)\r
 377   {\r
 378     getGroup().cs = new TurnColourScheme();\r
 379     refresh();\r
 380   }\r
 381 \r
 382   protected void buriedColour_actionPerformed(ActionEvent e)\r
 383   {\r
 384     getGroup().cs = new BuriedColourScheme();\r
 385     refresh();\r
 386   }\r
 387 \r
 388 \r
 389 /*\r
 390 public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)\r
 391 {\r
 392 ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel);\r
 393 JInternalFrame frame = new JInternalFrame();\r
 394 frame.setContentPane(cip);\r
 395 Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,90);\r
 396 frame.setMaximizable(false);\r
 397 \r
 398  }*/\r
 399 \r
 400 \r
 401   protected void abovePIDColour_actionPerformed(ActionEvent e)\r
 402   {\r
 403     SliderPanel sp = new SliderPanel(ap, 70, false, getGroup().cs );\r
 404     JInternalFrame frame = new JInternalFrame();\r
 405     frame.setContentPane(sp);\r
 406     Desktop.addInternalFrame(frame, "Percentage Identity Threshold ("+getGroup().getName()+")" , 400,90);\r
 407     frame.setMaximizable(false);\r
 408 \r
 409   }\r
 410 \r
 411 \r
 412   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 413   {\r
 414     JInternalFrame frame = new JInternalFrame();\r
 415     UserDefinedColours chooser = new UserDefinedColours( frame, ap, getGroup());\r
 416     frame.setContentPane(chooser);\r
 417     Desktop.addInternalFrame(frame,"User defined colours ("+getGroup().getName()+")", 450,540 );\r
 418     frame.setResizable(false);\r
 419     frame.setIconifiable(false);\r
 420     frame.setMaximizable(false);\r
 421 \r
 422   }\r
 423 \r
 424   protected void PIDColour_actionPerformed(ActionEvent e)\r
 425   {\r
 426 \r
 427   }\r
 428 \r
 429   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 430   {\r
 431     getGroup().cs = new Blosum62ColourScheme(ap.av);\r
 432     refresh();\r
 433   }\r
 434 \r
 435 \r
 436   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 437   {\r
 438     getGroup().cs = null;\r
 439     refresh();\r
 440   }\r
 441 \r
 442   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 443   {\r
 444     SequenceGroup sg = getGroup();\r
 445 \r
 446     Conservation c = new Conservation("Group",\r
 447                           ResidueProperties.propHash, 3, sg.sequences, sg.getStartRes(),\r
 448                           sg.getEndRes() );\r
 449 \r
 450      c.calculate();\r
 451      c.verdict(false, 100);\r
 452      ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 453 \r
 454      sg.cs = ccs;\r
 455 \r
 456      refresh();\r
 457   }\r
 458 \r
 459 /*\r
 460   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 461   {\r
 462     viewport.setGlobalColourScheme( null );\r
 463     changeColour();\r
 464   }\r
 465 \r
 466 \r
 467   public void clustalColour_actionPerformed(ActionEvent e)\r
 468   {\r
 469     viewport.setGlobalColourScheme(new ClustalxColourScheme( ));\r
 470     conservationMenuItem.setSelected(false);\r
 471     abovePIDThreshold.setSelected(false);\r
 472     changeColour();\r
 473   }\r
 474 \r
 475   public void zappoColour_actionPerformed(ActionEvent e)\r
 476   {\r
 477     viewport.setGlobalColourScheme(new ZappoColourScheme() );\r
 478     changeColour();\r
 479   }\r
 480 \r
 481   public void taylorColour_actionPerformed(ActionEvent e)\r
 482   {\r
 483     viewport.setGlobalColourScheme(new TaylorColourScheme() );\r
 484     changeColour();\r
 485   }\r
 486 \r
 487 \r
 488   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 489   {\r
 490     viewport.setGlobalColourScheme( new HydrophobicColourScheme() );\r
 491     changeColour();\r
 492   }\r
 493 \r
 494   public void helixColour_actionPerformed(ActionEvent e)\r
 495   {\r
 496     viewport.setGlobalColourScheme( new HelixColourScheme()  );\r
 497     changeColour();\r
 498   }\r
 499 \r
 500 \r
 501   public void strandColour_actionPerformed(ActionEvent e)\r
 502   {\r
 503     viewport.setGlobalColourScheme(new StrandColourScheme() );\r
 504     changeColour();\r
 505   }\r
 506 \r
 507 \r
 508   public void turnColour_actionPerformed(ActionEvent e)\r
 509   {\r
 510     viewport.setGlobalColourScheme(new TurnColourScheme() );\r
 511     changeColour();\r
 512   }\r
 513 \r
 514 \r
 515   public void buriedColour_actionPerformed(ActionEvent e)\r
 516   {\r
 517     viewport.setGlobalColourScheme( new BuriedColourScheme() );\r
 518     changeColour();\r
 519   }\r
 520 \r
 521   void changeColour()\r
 522   {\r
 523     if(abovePIDThreshold.isSelected())\r
 524       abovePIDThreshold_actionPerformed(null);\r
 525     else if(conservationMenuItem.isSelected())\r
 526       conservationMenuItem_actionPerformed(null);\r
 527 \r
 528      alignPanel.seqPanel.seqCanvas.paintFlag = true;\r
 529      alignPanel.repaint();\r
 530   }\r
 531 \r
 532   void addConservationOrPIDColour()\r
 533   {\r
 534     int x=0, y=0, threshold = 70;\r
 535 \r
 536     if(sliderFrame!=null)\r
 537        try\r
 538        {\r
 539          x = sliderFrame.getX();\r
 540          y = sliderFrame.getY();\r
 541          SliderPanel sp = (SliderPanel) sliderFrame.getContentPane();\r
 542          threshold = sp.getValue();\r
 543          sliderFrame.setClosed(true);\r
 544        }\r
 545        catch (Exception ex)\r
 546        {    ex.printStackTrace();   }\r
 547 \r
 548      ColourSchemeI oldCs = viewport.getGlobalColourScheme();\r
 549 \r
 550      ConservationColourScheme ccs = null;\r
 551      if (oldCs instanceof ConservationColourScheme)\r
 552        ccs = (ConservationColourScheme) oldCs;\r
 553 \r
 554      if(conservationMenuItem.isSelected())\r
 555      {\r
 556        Alignment al = (Alignment)viewport.alignment;\r
 557        Conservation c = new Conservation("All",\r
 558                             ResidueProperties.propHash, 3, al.getSequences(), 0,\r
 559                             al.getWidth() );\r
 560 \r
 561        c.calculate();\r
 562        c.verdict(false, 100);\r
 563 \r
 564        if(ccs!=null)\r
 565          ccs = new ConservationColourScheme(c, ccs.cs);\r
 566        else\r
 567          ccs = new ConservationColourScheme(c, oldCs);\r
 568 \r
 569         viewport.setGlobalColourScheme( ccs );\r
 570 \r
 571      }\r
 572      else if(oldCs instanceof ConservationColourScheme)\r
 573      {\r
 574        oldCs = ccs.cs;\r
 575        viewport.setGlobalColourScheme( oldCs );\r
 576      }\r
 577 \r
 578 \r
 579      if( conservationMenuItem.isSelected() || abovePIDThreshold.isSelected() )\r
 580      {\r
 581        sliderFrame = new JInternalFrame();\r
 582        sliderFrame.setMaximizable(false);\r
 583        sliderFrame.setResizable(false);\r
 584 \r
 585        SliderPanel sp = null;\r
 586        if (conservationMenuItem.isSelected())\r
 587        {\r
 588         if(threshold > 50)\r
 589           threshold = 30;\r
 590         sp = new SliderPanel(alignPanel, threshold, true,ccs);\r
 591         Desktop.addInternalFrame(sliderFrame, "Conservation Colour Increment  (Global colour)", 400, 90);\r
 592         threshold = 0;\r
 593        }\r
 594        else if (abovePIDThreshold.isSelected())\r
 595        {\r
 596          sp = new SliderPanel(alignPanel, threshold, false, oldCs);\r
 597          sp.cs = oldCs;\r
 598          Desktop.addInternalFrame(sliderFrame, "Percentage Identity Threshold (Global colour)", 400, 90);\r
 599        }\r
 600 \r
 601        sliderFrame.setContentPane(sp);\r
 602        if(x!=0 && y!=0)\r
 603                sliderFrame.setLocation(x,y);\r
 604 \r
 605      }\r
 606      else\r
 607        threshold = 0;\r
 608 \r
 609 \r
 610      if (oldCs instanceof ResidueColourScheme)\r
 611      {\r
 612        ResidueColourScheme rcs = (ResidueColourScheme) oldCs;\r
 613        rcs.setThreshold(threshold);\r
 614      }\r
 615      else if (oldCs instanceof ScoreColourScheme)\r
 616      {\r
 617        ScoreColourScheme scs = (ScoreColourScheme) oldCs;\r
 618        scs.setThreshold(threshold);\r
 619      }\r
 620 \r
 621      alignPanel.seqPanel.seqCanvas.paintFlag = true;\r
 622      alignPanel.repaint();\r
 623 \r
 624   }\r
 625 \r
 626   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 627   {\r
 628    if(abovePIDThreshold.isSelected())\r
 629     abovePIDThreshold.setSelected(false);\r
 630 \r
 631    viewport.setConservationSelected(conservationMenuItem.isSelected());\r
 632 \r
 633    addConservationOrPIDColour();\r
 634   }\r
 635 \r
 636   JInternalFrame sliderFrame;\r
 637   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 638   {\r
 639       if(conservationMenuItem.isSelected())\r
 640         conservationMenuItem.setSelected(false);\r
 641 \r
 642       addConservationOrPIDColour();\r
 643   }\r
 644 \r
 645 \r
 646 \r
 647   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 648   {\r
 649     JInternalFrame frame = new JInternalFrame();\r
 650     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
 651     frame.setContentPane(chooser);\r
 652     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
 653     frame.setResizable(false);\r
 654     frame.setIconifiable(false);\r
 655     frame.setMaximizable(false);\r
 656   }\r
 657 \r
 658   public void PIDColour_actionPerformed(ActionEvent e)\r
 659   {\r
 660     viewport.setGlobalColourScheme( new PIDColourScheme() );\r
 661     alignPanel.setColourScheme( );\r
 662   }\r
 663 \r
 664 \r
 665   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 666   {\r
 667     viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport)  );\r
 668     alignPanel.setColourScheme();\r
 669   }\r
 670 */\r
 671 //////////////////////////////////////\r
 672   protected void groupAnnotation_actionPerformed(ActionEvent e)\r
 673   {\r
 674 \r
 675   }\r
 676 \r
 677   protected void groupName_actionPerformed(ActionEvent e)\r
 678   {\r
 679     SequenceGroup sg = getGroup();\r
 680     String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE);\r
 681     if(reply==null)\r
 682       return;\r
 683 \r
 684     sg.setName(reply);\r
 685     groupName.setText(reply);\r
 686   }\r
 687 \r
 688   protected void copyGroup_actionPerformed(ActionEvent e)\r
 689   {\r
 690     SequenceGroup sg = ap.av.getRubberbandGroup();\r
 691 \r
 692     SequenceI[] s = new Sequence[sg.sequences.size()];\r
 693      for (int i=0; i < sg.sequences.size(); i++)\r
 694      {\r
 695        s[i] = new Sequence( sg.getSequenceAt(i));\r
 696        s[i].setSequence( s[i].getSequence(sg.getStartRes(), sg.getEndRes()+1) );\r
 697      }\r
 698      AlignFrame af = new AlignFrame(new Alignment(s));\r
 699      int newHeight = s.length * af.viewport.getCharHeight() + 200;\r
 700      if (newHeight > 500)\r
 701        newHeight = 500;\r
 702      Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);\r
 703    }\r
 704 \r
 705   protected  void moveGroup_actionPerformed(ActionEvent e)\r
 706   {\r
 707     SequenceGroup sg = ap.av.getRubberbandGroup();\r
 708 \r
 709     SequenceI[] s = new Sequence[sg.sequences.size()];\r
 710 \r
 711      for (int i=0; i < sg.sequences.size(); i++)\r
 712        s[i] = new Sequence( sg.getSequenceAt(i));\r
 713 \r
 714      AlignFrame af = new AlignFrame(new Alignment(s));\r
 715      int newHeight = s.length * af.viewport.getCharHeight() + 200;\r
 716      if(newHeight>500)\r
 717        newHeight=500;\r
 718      Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);\r
 719 \r
 720 \r
 721      for (int i=0; i < sg.sequences.size(); i++)\r
 722        ap.av.alignment.deleteSequence(sg.getSequenceAt(i));\r
 723 \r
 724 \r
 725      ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());\r
 726      ap.RefreshPanels();\r
 727 \r
 728 \r
 729   }\r
 730 \r
 731   protected void deleteSequences_actionPerformed(ActionEvent e)\r
 732   {\r
 733     SequenceGroup sg = ap.av.getRubberbandGroup();\r
 734     for (int i=0;i < sg.sequences.size(); i++)\r
 735             ap.av.getAlignment().deleteSequence(sg.getSequenceAt(i));\r
 736 \r
 737     ap.av.alignment.deleteGroup(sg);\r
 738     ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());\r
 739     ap.seqPanel.parent.RefreshPanels();\r
 740 \r
 741   }\r
 742 \r
 743   protected void analyze_actionPerformed(ActionEvent e)\r
 744   {\r
 745      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
 746      JInternalFrame frame = new JInternalFrame();\r
 747      cap.formatForOutput();\r
 748      frame.setContentPane(cap);\r
 749      Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
 750      SequenceGroup sg = getGroup();\r
 751      StringBuffer sb = new StringBuffer();\r
 752 \r
 753      for(int i=0; i<sg.sequences.size(); i++)\r
 754      {\r
 755        Sequence tmp = (Sequence)sg.sequences.get(i);\r
 756        sb.append(  tmp.getSequence(sg.getStartRes(), sg.getEndRes()+1));\r
 757        sb.append("\n");\r
 758      }\r
 759 \r
 760      sb.append("Something amazing will happen soon");\r
 761      cap.setText( sb.toString() );\r
 762 \r
 763   }\r
 764 \r
 765   SequenceGroup getGroup()\r
 766   {\r
 767     SequenceGroup sg = ap.av.getRubberbandGroup();\r
 768 \r
 769     // this method won't add a new group if it already exists\r
 770     ap.av.alignment.addGroup(sg);\r
 771     return sg;\r
 772   }\r
 773 \r
 774   void sequenceName_actionPerformed(ActionEvent e)\r
 775   {\r
 776     String id = sequence.getName();\r
 777     String s = (String)JOptionPane.showInternalInputDialog(\r
 778                 ap,\r
 779                 "Edit sequence name",\r
 780                 "Edit sequence name",\r
 781                 JOptionPane.PLAIN_MESSAGE,\r
 782                 null,\r
 783                 null,\r
 784                 id);\r
 785 \r
 786     if(s!=null)\r
 787     {\r
 788       sequence.setName(s);\r
 789       ap.RefreshPanels();\r
 790     }\r
 791 \r
 792   }\r
 793 }\r