src/jalview/appletgui/AlignFrame.java

   1 /********************\r
   2  * 2004 Jalview Reengineered\r
   3  * Barton Group\r
   4  * Dundee University\r
   5  *\r
   6  * AM Waterhouse\r
   7  *******************/\r
   8 \r
   9 \r
  10 \r
  11 \r
  12 package jalview.appletgui;\r
  13 \r
  14 import jalview.jbappletgui.GAlignFrame;\r
  15 import jalview.schemes.*;\r
  16 import jalview.datamodel.*;\r
  17 import jalview.analysis.*;\r
  18 import jalview.io.*;\r
  19 import java.awt.*;\r
  20 import java.awt.event.*;\r
  21 import java.util.*;\r
  22 \r
  23 \r
  24 public class AlignFrame extends GAlignFrame\r
  25 {\r
  26   final AlignmentPanel alignPanel;\r
  27   final AlignViewport  viewport;\r
  28   public static final int NEW_WINDOW_WIDTH = 700;\r
  29   public static final int NEW_WINDOW_HEIGHT = 500;\r
  30   jalview.bin.JalviewLite applet;\r
  31 \r
  32   public AlignFrame(AlignmentI al)\r
  33   {\r
  34     this.applet = null;\r
  35     viewport = new AlignViewport(al, null);\r
  36     alignPanel = new AlignmentPanel(this, viewport);\r
  37     add(alignPanel);\r
  38     alignPanel.validate();\r
  39   }\r
  40 \r
  41   public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet)\r
  42   {\r
  43     this.applet = applet;\r
  44     viewport = new AlignViewport(al, applet);\r
  45     alignPanel = new AlignmentPanel(this, viewport);\r
  46     add(alignPanel);\r
  47     alignPanel.validate();\r
  48 \r
  49     String treeFile = applet.getParameter("treeFile");\r
  50     TreePanel treepanel = null;\r
  51     if (treeFile != null)\r
  52     {\r
  53       try\r
  54       {\r
  55         treeFile = treeFile;\r
  56         jalview.io.NewickFile fin = new jalview.io.NewickFile( applet.getCodeBase()+treeFile, "URL");\r
  57         fin.parse();\r
  58 \r
  59         if (fin.getTree() != null)\r
  60         {\r
  61           TreePanel tp = null;\r
  62           tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
  63                              fin, "FromFile", applet.getCodeBase()+treeFile);\r
  64           jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
  65           addTreeMenuItem(tp, treeFile);\r
  66         }\r
  67       }\r
  68       catch (Exception ex)\r
  69       {\r
  70         ex.printStackTrace();\r
  71       }\r
  72     }\r
  73 \r
  74 \r
  75   }\r
  76 \r
  77   public void inputText_actionPerformed(ActionEvent e)\r
  78   {\r
  79      CutAndPasteTransfer cap = new CutAndPasteTransfer(true);\r
  80      Frame frame = new Frame();\r
  81      frame.add(cap);\r
  82      jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500,500);\r
  83   }\r
  84 \r
  85 \r
  86   protected void outputText_actionPerformed(ActionEvent e)\r
  87   {\r
  88      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
  89      Frame frame = new Frame();\r
  90      frame.add(cap);\r
  91      jalview.bin.JalviewLite.addFrame(frame,"Alignment output - "+e.getActionCommand(),600, 500);\r
  92      cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
  93   }\r
  94 \r
  95   public void closeMenuItem_actionPerformed(ActionEvent e)\r
  96   {\r
  97     dispose();\r
  98   }\r
  99 \r
 100   Stack historyList = new Stack();\r
 101   Stack redoList = new Stack();\r
 102 \r
 103   void updateEditMenuBar()\r
 104   {\r
 105     if(historyList.size()>0)\r
 106      {\r
 107        undoMenuItem.setEnabled(true);\r
 108        Object [] history = (Object[])historyList.elementAt(0);\r
 109        undoMenuItem.setLabel("Undo "+history[0]);\r
 110      }\r
 111     else\r
 112     {\r
 113       undoMenuItem.setEnabled(false);\r
 114       undoMenuItem.setLabel("Undo");\r
 115     }\r
 116 \r
 117     if(redoList.size()>0)\r
 118      {\r
 119        redoMenuItem.setEnabled(true);\r
 120        Object [] history = (Object[])redoList.elementAt(0);\r
 121        redoMenuItem.setLabel("Redo "+history[0]);\r
 122      }\r
 123     else\r
 124     {\r
 125       redoMenuItem.setEnabled(false);\r
 126       redoMenuItem.setLabel("Redo");\r
 127     }\r
 128   }\r
 129 \r
 130   public void addHistoryItem(String type)\r
 131   {\r
 132     // must make sure we add new sequence objects her, not refs to the existing sequences\r
 133     redoList.removeAllElements();\r
 134     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 135     for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
 136     {\r
 137       seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
 138                              viewport.getAlignment().getSequenceAt(i).getSequence());\r
 139     }\r
 140 \r
 141     historyList.addElement(new Object[]{type,  seq} );\r
 142     updateEditMenuBar();\r
 143   }\r
 144 \r
 145   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 146   {\r
 147     Object [] history = (Object[])historyList.elementAt(0);\r
 148     historyList.removeElementAt(0);\r
 149     // add the redo state before continuing!!\r
 150     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 151     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
 152     {\r
 153       seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
 154                             viewport.getAlignment().getSequenceAt(i).\r
 155                             getSequence());\r
 156     }\r
 157     /////////\r
 158 \r
 159     redoList.addElement(new Object[] {history[0], seq});\r
 160 \r
 161       seq = (SequenceI[]) history[1];\r
 162 \r
 163       AlignmentAnnotation[] old = viewport.alignment.getAlignmentAnnotation();\r
 164       viewport.setAlignment(new Alignment(seq));\r
 165       updateEditMenuBar();\r
 166       for (int i = 0; i < old.length; i++)\r
 167         viewport.alignment.addAnnotation(old[i]);\r
 168 \r
 169       viewport.updateConservation();\r
 170       viewport.updateConsensus();\r
 171       alignPanel.repaint();\r
 172   }\r
 173 \r
 174   public void moveSelectedSequences(boolean up)\r
 175   {\r
 176     SequenceGroup sg = viewport.getSelectionGroup();\r
 177     if (sg == null)\r
 178       return;\r
 179 \r
 180     if (up)\r
 181     {\r
 182       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 183       {\r
 184         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 185         if (!sg.sequences.contains(seq))\r
 186           continue;\r
 187 \r
 188         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 189         if (sg.sequences.contains(temp))\r
 190           continue;\r
 191 \r
 192         viewport.alignment.getSequences().setElementAt(temp, i);\r
 193         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 194       }\r
 195     }\r
 196     else\r
 197     {\r
 198       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 199       {\r
 200         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 201         if (!sg.sequences.contains(seq))\r
 202           continue;\r
 203 \r
 204         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 205         if (sg.sequences.contains(temp))\r
 206           continue;\r
 207 \r
 208         viewport.alignment.getSequences().setElementAt(temp, i);\r
 209         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 210       }\r
 211     }\r
 212 \r
 213     alignPanel.repaint();\r
 214   }\r
 215 \r
 216 \r
 217   StringBuffer copiedSequences;\r
 218   protected void copy_actionPerformed(ActionEvent e)\r
 219   {\r
 220    if(viewport.getSelectionGroup()==null)\r
 221      return;\r
 222 \r
 223    SequenceGroup sg = viewport.getSelectionGroup();\r
 224    copiedSequences = new StringBuffer();\r
 225 \r
 226        for(int i=0; i<sg.getSize(); i++)\r
 227        {\r
 228          SequenceI seq = sg.getSequenceAt(i);\r
 229          copiedSequences.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"\r
 230                         +seq.findPosition( sg.getEndRes() )+ "\t"\r
 231                         +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");\r
 232        }\r
 233 \r
 234   }\r
 235 \r
 236 \r
 237   protected void pasteNew_actionPerformed(ActionEvent e)\r
 238   {\r
 239     paste(true);\r
 240   }\r
 241 \r
 242   protected void pasteThis_actionPerformed(ActionEvent e)\r
 243   {\r
 244     addHistoryItem("Paste");\r
 245     paste(false);\r
 246   }\r
 247 \r
 248   void paste(boolean newAlignment)\r
 249   {\r
 250     try{\r
 251       if (copiedSequences == null)\r
 252         return;\r
 253 \r
 254       StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
 255       Vector seqs = new Vector();\r
 256       while (st.hasMoreElements())\r
 257       {\r
 258         String name = st.nextToken();\r
 259         int start = Integer.parseInt(st.nextToken());\r
 260         int end = Integer.parseInt(st.nextToken());\r
 261         Sequence sequence = new Sequence(name,st.nextToken(), start, end);\r
 262 \r
 263         if(!newAlignment)\r
 264           viewport.alignment.addSequence(sequence);\r
 265         else\r
 266           seqs.addElement(sequence);\r
 267       }\r
 268 \r
 269       if(newAlignment)\r
 270       {\r
 271         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 272         for(int i=0; i<seqs.size(); i++)\r
 273          newSeqs[i] = (SequenceI)seqs.elementAt(i);\r
 274 \r
 275         AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);\r
 276         jalview.bin.JalviewLite.addFrame(af, "Copied sequences", NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
 277       }\r
 278       else\r
 279       {\r
 280         viewport.setEndSeq(viewport.alignment.getHeight());\r
 281         viewport.alignment.getWidth();\r
 282         viewport.updateConservation();\r
 283         viewport.updateConsensus();\r
 284         alignPanel.repaint();\r
 285       }\r
 286 \r
 287     }catch(Exception ex){}// could be anything being pasted in here\r
 288 \r
 289   }\r
 290 \r
 291 \r
 292   protected void cut_actionPerformed(ActionEvent e)\r
 293   {\r
 294     copy_actionPerformed(null);\r
 295     delete_actionPerformed(null);\r
 296   }\r
 297 \r
 298   protected void delete_actionPerformed(ActionEvent e)\r
 299   {\r
 300     addHistoryItem("Delete");\r
 301     if (viewport.getSelectionGroup() == null)\r
 302       return;\r
 303 \r
 304      SequenceGroup sg = viewport.getSelectionGroup();\r
 305      for (int i=0;i < sg.sequences.size(); i++)\r
 306      {\r
 307        SequenceI seq = sg.getSequenceAt(i);\r
 308        int index = viewport.getAlignment().findIndex(seq);\r
 309        seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);\r
 310 \r
 311        if(seq.getSequence().length()<1)\r
 312           viewport.getAlignment().deleteSequence(seq);\r
 313       else\r
 314           viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 315      }\r
 316 \r
 317      viewport.setSelectionGroup(null);\r
 318      viewport.alignment.deleteGroup(sg);\r
 319      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getSize().height);\r
 320      if(viewport.getAlignment().getHeight()<1)\r
 321      try\r
 322      {\r
 323        this.setVisible(false);\r
 324      }catch(Exception ex){}\r
 325    viewport.updateConservation();\r
 326    viewport.updateConsensus();\r
 327      alignPanel.repaint();\r
 328 \r
 329   }\r
 330 \r
 331 \r
 332 \r
 333   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 334   {\r
 335      Object [] history = (Object[])redoList.pop();\r
 336      SequenceI[] seq = (SequenceI[]) history[1];\r
 337 \r
 338      AlignmentAnnotation[] old = viewport.alignment.getAlignmentAnnotation();\r
 339      viewport.setAlignment(new Alignment(seq));\r
 340      for (int i = 0; i < old.length; i++)\r
 341        viewport.alignment.addAnnotation(old[i]);\r
 342 \r
 343      viewport.updateConservation();\r
 344      viewport.updateConsensus();\r
 345      updateEditMenuBar();\r
 346      alignPanel.repaint();\r
 347   }\r
 348 \r
 349 \r
 350   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 351   {\r
 352     viewport.alignment.deleteAllGroups();\r
 353     viewport.setSelectionGroup(null);\r
 354 \r
 355     alignPanel.repaint();\r
 356   }\r
 357 \r
 358 \r
 359 \r
 360   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 361   {\r
 362     SequenceGroup sg = new SequenceGroup();\r
 363     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 364       sg.addSequence( viewport.getAlignment().getSequenceAt(i));\r
 365     sg.setEndRes(viewport.alignment.getWidth());\r
 366     viewport.setSelectionGroup(sg);\r
 367     alignPanel.repaint();\r
 368     PaintRefresher.Refresh(null);\r
 369   }\r
 370 \r
 371   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 372   {\r
 373     viewport.setSelectionGroup(null);\r
 374     viewport.getColumnSelection().clear();\r
 375     viewport.setSelectionGroup(null);\r
 376     PaintRefresher.Refresh(null);\r
 377   }\r
 378 \r
 379   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 380   {\r
 381     SequenceGroup sg = viewport.getSelectionGroup();\r
 382     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 383       sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));\r
 384 \r
 385     PaintRefresher.Refresh(null);\r
 386   }\r
 387 \r
 388   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 389   {\r
 390     addHistoryItem("delete columns");\r
 391     ColumnSelection colSel = viewport.getColumnSelection();\r
 392     if (colSel.size() > 0)\r
 393     {\r
 394       int min = colSel.getMin();\r
 395       viewport.getAlignment().trimLeft(min);\r
 396       colSel.compensateForEdit(0,min);\r
 397 \r
 398       if(viewport.getSelectionGroup()!=null)\r
 399         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 400 \r
 401       Vector groups = viewport.alignment.getGroups();\r
 402       for(int i=0; i<groups.size(); i++)\r
 403       {\r
 404         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 405         if(!sg.adjustForRemoveLeft(min))\r
 406           viewport.alignment.deleteGroup(sg);\r
 407       }\r
 408 \r
 409       alignPanel.repaint();\r
 410     }\r
 411   }\r
 412 \r
 413   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 414   {\r
 415     addHistoryItem("delete columns");\r
 416     ColumnSelection colSel = viewport.getColumnSelection();\r
 417     if (colSel.size() > 0)\r
 418     {\r
 419       int max = colSel.getMax();\r
 420       viewport.getAlignment().trimRight(max);\r
 421       if(viewport.getSelectionGroup()!=null)\r
 422         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 423 \r
 424       Vector groups = viewport.alignment.getGroups();\r
 425       for(int i=0; i<groups.size(); i++)\r
 426       {\r
 427         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 428         if(!sg.adjustForRemoveRight(max))\r
 429           viewport.alignment.deleteGroup(sg);\r
 430       }\r
 431 \r
 432 \r
 433 \r
 434       alignPanel.repaint();\r
 435     }\r
 436 \r
 437   }\r
 438 \r
 439   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 440   {\r
 441     addHistoryItem("delete gapped columns");\r
 442     viewport.getAlignment().removeGaps();\r
 443     viewport.updateConservation();\r
 444     viewport.updateConsensus();\r
 445     alignPanel.repaint();\r
 446   }\r
 447 \r
 448   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 449   {\r
 450     addHistoryItem("delete all gaps");\r
 451     SequenceI current;\r
 452     int jSize;\r
 453     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 454     {\r
 455       current = viewport.getAlignment().getSequenceAt(i);\r
 456       jSize = current.getLength();\r
 457       for (int j=0; j < jSize; j++)\r
 458         if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 459         {\r
 460           current.deleteCharAt(j);\r
 461           j--;\r
 462           jSize--;\r
 463         }\r
 464     }\r
 465     viewport.updateConservation();\r
 466     viewport.updateConsensus();\r
 467     alignPanel.repaint();\r
 468   }\r
 469 \r
 470 \r
 471   public void findMenuItem_actionPerformed(ActionEvent e)\r
 472   {\r
 473     Finder finder = new Finder(alignPanel);\r
 474   }\r
 475 \r
 476 \r
 477   public void font_actionPerformed(ActionEvent e)\r
 478   {\r
 479     Frame frame = new Frame();\r
 480     FontChooser fc = new FontChooser( alignPanel, frame);\r
 481     frame.add(fc);\r
 482     jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440,100);\r
 483 \r
 484   }\r
 485 \r
 486   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 487   {\r
 488     viewport.setShowFullId( fullSeqId.getState() );\r
 489     alignPanel.idPanel.idCanvas.setSize( alignPanel.calculateIdWidth() );\r
 490     alignPanel.repaint();\r
 491   }\r
 492 \r
 493   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 494   {\r
 495       viewport.setColourText( colourTextMenuItem.getState() );\r
 496       alignPanel.repaint();\r
 497   }\r
 498 \r
 499   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 500   {\r
 501     viewport.setWrapAlignment( wrapMenuItem.getState() );\r
 502     alignPanel.setWrapAlignment( wrapMenuItem.getState() );\r
 503     scaleAbove.setEnabled( wrapMenuItem.getState() );\r
 504     scaleLeft.setEnabled( wrapMenuItem.getState());\r
 505     scaleRight.setEnabled( wrapMenuItem.getState());\r
 506     alignPanel.repaint();\r
 507   }\r
 508 \r
 509   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 510   {\r
 511     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
 512     alignPanel.repaint();\r
 513   }\r
 514 \r
 515   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 516   {\r
 517     viewport.setScaleLeftWrapped(scaleLeft.getState());\r
 518     alignPanel.repaint();\r
 519   }\r
 520 \r
 521   protected void scaleRight_actionPerformed(ActionEvent e)\r
 522   {\r
 523     viewport.setScaleRightWrapped(scaleRight.getState());\r
 524     alignPanel.repaint();\r
 525   }\r
 526 \r
 527 \r
 528 \r
 529   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 530   {\r
 531     viewport.setShowBoxes( viewBoxesMenuItem.getState() );\r
 532     alignPanel.repaint();\r
 533   }\r
 534 \r
 535   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 536   {\r
 537     viewport.setShowText( viewTextMenuItem.getState() );\r
 538     alignPanel.repaint();\r
 539   }\r
 540 \r
 541 \r
 542   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 543   {\r
 544     viewport.setRenderGaps(renderGapsMenuItem.getState());\r
 545     alignPanel.repaint();\r
 546   }\r
 547 \r
 548 \r
 549   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 550   {\r
 551     if(annotationPanelMenuItem.getState() && viewport.getWrapAlignment())\r
 552     {\r
 553       annotationPanelMenuItem.setState(false);\r
 554       return;\r
 555     }\r
 556     viewport.setShowAnnotation( annotationPanelMenuItem.getState() );\r
 557     alignPanel.setAnnotationVisible( annotationPanelMenuItem.getState() );\r
 558   }\r
 559 \r
 560   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 561   {\r
 562    if (alignPanel.overviewPanel != null)\r
 563       return;\r
 564 \r
 565     Frame frame = new Frame();\r
 566     OverviewPanel overview = new OverviewPanel(alignPanel);\r
 567     frame.add(overview);\r
 568     // +50 must allow for applet frame window\r
 569     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
 570                              overview.preferredSize().width, overview.preferredSize().height+50);\r
 571 \r
 572     frame.pack();\r
 573     frame.addWindowListener(new WindowAdapter()\r
 574     { public void windowClosing(WindowEvent e)\r
 575       {\r
 576             alignPanel.setOverviewPanel(null);\r
 577       };\r
 578     });\r
 579 \r
 580     alignPanel.setOverviewPanel( overview );\r
 581 \r
 582 \r
 583   }\r
 584 \r
 585   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 586   {\r
 587     changeColour( null );\r
 588   }\r
 589 \r
 590 \r
 591   public void clustalColour_actionPerformed(ActionEvent e)\r
 592   {\r
 593     abovePIDThreshold.setState(false);\r
 594     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 595   }\r
 596 \r
 597   public void zappoColour_actionPerformed(ActionEvent e)\r
 598   {\r
 599     changeColour(new ZappoColourScheme());\r
 600   }\r
 601 \r
 602   public void taylorColour_actionPerformed(ActionEvent e)\r
 603   {\r
 604     changeColour(new TaylorColourScheme());\r
 605   }\r
 606 \r
 607 \r
 608   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 609   {\r
 610     changeColour( new HydrophobicColourScheme() );\r
 611   }\r
 612 \r
 613   public void helixColour_actionPerformed(ActionEvent e)\r
 614   {\r
 615     changeColour(new HelixColourScheme() );\r
 616   }\r
 617 \r
 618 \r
 619   public void strandColour_actionPerformed(ActionEvent e)\r
 620   {\r
 621     changeColour(new StrandColourScheme());\r
 622   }\r
 623 \r
 624 \r
 625   public void turnColour_actionPerformed(ActionEvent e)\r
 626   {\r
 627     changeColour(new TurnColourScheme());\r
 628   }\r
 629 \r
 630 \r
 631   public void buriedColour_actionPerformed(ActionEvent e)\r
 632   {\r
 633     changeColour(new BuriedColourScheme() );\r
 634   }\r
 635 \r
 636   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 637   {\r
 638     changeColour(new NucleotideColourScheme());\r
 639   }\r
 640 \r
 641 \r
 642   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 643   {\r
 644     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
 645   }\r
 646 \r
 647 \r
 648 \r
 649   void changeColour(ColourSchemeI cs)\r
 650   {\r
 651     int threshold = 0;\r
 652 \r
 653     if ( viewport.getAbovePIDThreshold() )\r
 654     {\r
 655       threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
 656 \r
 657       if (cs instanceof ResidueColourScheme)\r
 658         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
 659       else if (cs instanceof ScoreColourScheme)\r
 660         ( (ScoreColourScheme) cs).setThreshold(threshold);\r
 661 \r
 662       viewport.setGlobalColourScheme(cs);\r
 663     }\r
 664     else if (cs instanceof ResidueColourScheme)\r
 665       ( (ResidueColourScheme) cs).setThreshold(0);\r
 666     else if (cs instanceof ScoreColourScheme)\r
 667       ( (ScoreColourScheme) cs).setThreshold(0);\r
 668 \r
 669 \r
 670 \r
 671     if (viewport.getConservationSelected())\r
 672     {\r
 673       ConservationColourScheme ccs = null;\r
 674 \r
 675       Alignment al = (Alignment) viewport.alignment;\r
 676       Conservation c = new Conservation("All",\r
 677                                         ResidueProperties.propHash, 3,\r
 678                                         al.getSequences(), 0,\r
 679                                         al.getWidth() - 1);\r
 680 \r
 681       c.calculate();\r
 682       c.verdict(false, viewport.ConsPercGaps);\r
 683 \r
 684       ccs = new ConservationColourScheme(c, cs);\r
 685 \r
 686       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 687       ccs.setConsensus( viewport.vconsensus );\r
 688       viewport.setGlobalColourScheme(ccs);\r
 689 \r
 690       SliderPanel.setConservationSlider(alignPanel, ccs, "Background");\r
 691 \r
 692     }\r
 693     else\r
 694     {\r
 695         // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 696         if (cs != null)\r
 697           cs.setConsensus(viewport.vconsensus);\r
 698         viewport.setGlobalColourScheme(cs);\r
 699     }\r
 700 \r
 701 \r
 702     if(viewport.getColourAppliesToAllGroups())\r
 703     {\r
 704       Vector groups = viewport.alignment.getGroups();\r
 705       for(int i=0; i<groups.size(); i++)\r
 706       {\r
 707         SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
 708 \r
 709         if (cs instanceof ClustalxColourScheme)\r
 710         {\r
 711           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
 712         }\r
 713         else\r
 714           try\r
 715           {\r
 716             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
 717           }\r
 718           catch (Exception ex)\r
 719           {\r
 720             ex.printStackTrace();\r
 721             sg.cs = cs;\r
 722           }\r
 723 \r
 724         if(viewport.getAbovePIDThreshold())\r
 725         {\r
 726           if (sg.cs instanceof ResidueColourScheme)\r
 727             ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
 728           else if (sg.cs instanceof ScoreColourScheme)\r
 729             ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
 730 \r
 731            sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );\r
 732         }\r
 733 \r
 734         if( viewport.getConservationSelected() )\r
 735         {\r
 736           Conservation c = new Conservation("Group",\r
 737                                             ResidueProperties.propHash, 3,\r
 738                                             sg.sequences, 0, viewport.alignment.getWidth()-1);\r
 739           c.calculate();\r
 740           c.verdict(false, viewport.ConsPercGaps);\r
 741           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 742 \r
 743           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 744           ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 745           sg.cs = ccs;\r
 746         }\r
 747         else\r
 748         {\r
 749           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 750           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 751         }\r
 752 \r
 753       }\r
 754     }\r
 755 \r
 756     if(alignPanel.getOverviewPanel()!=null)\r
 757       alignPanel.getOverviewPanel().updateOverviewImage();\r
 758 \r
 759     alignPanel.repaint();\r
 760   }\r
 761 \r
 762   protected void modifyPID_actionPerformed(ActionEvent e)\r
 763   {\r
 764       if(viewport.getAbovePIDThreshold())\r
 765       {\r
 766         SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
 767                                    "Background");\r
 768         SliderPanel.showPIDSlider();\r
 769       }\r
 770   }\r
 771 \r
 772   protected void modifyConservation_actionPerformed(ActionEvent e)\r
 773   {\r
 774     if(viewport.getConservationSelected())\r
 775     {\r
 776       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
 777                                         "Background");\r
 778       SliderPanel.showConservationSlider();\r
 779     }\r
 780   }\r
 781 \r
 782 \r
 783   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 784   {\r
 785     viewport.setConservationSelected(conservationMenuItem.getState());\r
 786 \r
 787     viewport.setAbovePIDThreshold(false);\r
 788     abovePIDThreshold.setState(false);\r
 789 \r
 790    ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 791    if(cs instanceof ConservationColourScheme )\r
 792      changeColour( ((ConservationColourScheme)cs).cs );\r
 793     else\r
 794       changeColour( cs );\r
 795 \r
 796     modifyConservation_actionPerformed(null);\r
 797   }\r
 798 \r
 799   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 800   {\r
 801     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
 802 \r
 803     conservationMenuItem.setState(false);\r
 804     viewport.setConservationSelected(false);\r
 805 \r
 806     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 807 \r
 808     if(cs instanceof ConservationColourScheme )\r
 809         changeColour( ((ConservationColourScheme)cs).cs );\r
 810     else\r
 811         changeColour( cs );\r
 812 \r
 813     modifyPID_actionPerformed(null);\r
 814   }\r
 815 \r
 816 \r
 817 \r
 818   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 819   {\r
 820     UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);\r
 821   }\r
 822 \r
 823   public void PIDColour_actionPerformed(ActionEvent e)\r
 824   {\r
 825     changeColour( new PIDColourScheme() );\r
 826   }\r
 827 \r
 828 \r
 829   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 830   {\r
 831     changeColour(new Blosum62ColourScheme() );\r
 832   }\r
 833 \r
 834 \r
 835 \r
 836   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 837   {\r
 838     addHistoryItem("sort");\r
 839     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 840     alignPanel.repaint();\r
 841   }\r
 842 \r
 843   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 844   {\r
 845     addHistoryItem("sort");\r
 846     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 847     alignPanel.repaint();\r
 848   }\r
 849 \r
 850   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 851   {\r
 852     addHistoryItem("sort");\r
 853     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 854     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 855     alignPanel.repaint();\r
 856   }\r
 857 \r
 858   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 859   {\r
 860     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 861     Frame frame = new Frame();\r
 862     frame.add(sp);\r
 863     jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection", 400, 120);\r
 864 \r
 865   }\r
 866 \r
 867   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 868   {\r
 869     if(viewport.getSelectionGroup().getSize()>1)\r
 870     {\r
 871       Frame frame = new Frame();\r
 872       frame.add(new PairwiseAlignPanel(viewport));\r
 873       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
 874     }\r
 875   }\r
 876 \r
 877   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 878   {\r
 879 \r
 880     if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)\r
 881        || viewport.getAlignment().getHeight()<4)\r
 882     {\r
 883       return;\r
 884     }\r
 885 \r
 886     try{\r
 887       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 888       Frame frame = new Frame();\r
 889       frame.add(pcaPanel);\r
 890       jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis", 400, 400);\r
 891    }catch(java.lang.OutOfMemoryError ex)\r
 892    {\r
 893    }\r
 894 \r
 895 \r
 896   }\r
 897 \r
 898   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 899   {\r
 900     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
 901   }\r
 902 \r
 903   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 904   {\r
 905     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
 906   }\r
 907 \r
 908 \r
 909   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 910   {\r
 911     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
 912   }\r
 913 \r
 914   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 915   {\r
 916     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
 917   }\r
 918 \r
 919   void NewTreePanel(String type, String pwType, String title)\r
 920   {\r
 921     //are the sequences aligned?\r
 922     if(!viewport.alignment.isAligned())\r
 923     {\r
 924       return;\r
 925     }\r
 926 \r
 927     final TreePanel tp;\r
 928     if (viewport.getSelectionGroup() != null &&\r
 929         viewport.getSelectionGroup().getSize() > 3)\r
 930     {\r
 931       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
 932                          pwType,\r
 933                          0, viewport.alignment.getWidth());\r
 934     }\r
 935     else\r
 936     {\r
 937       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
 938                          type, pwType, 0, viewport.alignment.getWidth());\r
 939     }\r
 940 \r
 941    addTreeMenuItem(tp, title);\r
 942 \r
 943    jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
 944   }\r
 945 \r
 946   void addTreeMenuItem(final TreePanel treePanel, String title)\r
 947   {\r
 948     final MenuItem item = new MenuItem(title);\r
 949     sortByTreeMenu.add(item);\r
 950     item.addActionListener(new java.awt.event.ActionListener()\r
 951     {\r
 952       public void actionPerformed(ActionEvent e)\r
 953       {\r
 954         addHistoryItem("sort");\r
 955         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
 956         alignPanel.repaint();\r
 957       }\r
 958     });\r
 959 \r
 960     treePanel.addWindowListener(new WindowAdapter()\r
 961     {\r
 962       public void windowClosing(WindowEvent e)\r
 963       {\r
 964         sortByTreeMenu.remove(item);\r
 965       };\r
 966     });\r
 967   }\r
 968 \r
 969   protected void documentation_actionPerformed(ActionEvent e) {\r
 970 \r
 971     jalview.bin.JalviewLite.showURL("http://www.jalview.org");\r
 972 \r
 973   }\r
 974 \r
 975   protected void about_actionPerformed(ActionEvent e)\r
 976   {\r
 977     class AboutPanel extends Canvas\r
 978     {\r
 979       public void paint(Graphics g)\r
 980       {\r
 981         g.setColor(Color.white);\r
 982         g.fillRect(0,0,getSize().width, getSize().height);\r
 983         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
 984         FontMetrics fm = g.getFontMetrics();\r
 985         int fh = fm.getHeight();\r
 986         int y=20, x=7;\r
 987         g.setColor(Color.black);\r
 988         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
 989         g.drawString("JalView 2005", 200,y+=fh);\r
 990         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
 991         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",x,y+=fh*2);\r
 992         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",x,y+=fh);\r
 993         g.drawString("If  you use JalView, please cite:",x,y+=fh+8);\r
 994         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",x,y+=fh);\r
 995         g.drawString("Bioinformatics,  2004 12;426-7.",x,y+=fh);\r
 996       }\r
 997     }\r
 998     Frame frame = new Frame();\r
 999     frame.add(new AboutPanel());\r
1000     jalview.bin.JalviewLite.addFrame(frame, "Jalview 2005", 580,200);\r
1001 \r
1002 \r
1003 \r
1004   }\r
1005 }\r