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    Hashtable orderedSeqs = new Hashtable();\r
 226    for(int i=0; i<sg.getSize(); i++)\r
 227    {\r
 228       SequenceI seq = sg.getSequenceAt(i);\r
 229       int index = viewport.alignment.findIndex(seq);\r
 230       orderedSeqs.put(index+"", seq);\r
 231    }\r
 232 \r
 233    int index=0;\r
 234    for(int i=0; i<sg.getSize(); i++)\r
 235    {\r
 236      SequenceI seq = null;\r
 237      while( seq == null )\r
 238      {\r
 239        if(orderedSeqs.containsKey(index+""))\r
 240        {\r
 241          seq = (SequenceI) orderedSeqs.get(index + "");\r
 242          index++;\r
 243          break;\r
 244        }\r
 245        else\r
 246          index++;\r
 247      }\r
 248 \r
 249          copiedSequences.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"\r
 250                         +seq.findPosition( sg.getEndRes() )+ "\t"\r
 251                         +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");\r
 252        }\r
 253 \r
 254   }\r
 255 \r
 256 \r
 257   protected void pasteNew_actionPerformed(ActionEvent e)\r
 258   {\r
 259     paste(true);\r
 260   }\r
 261 \r
 262   protected void pasteThis_actionPerformed(ActionEvent e)\r
 263   {\r
 264     addHistoryItem("Paste");\r
 265     paste(false);\r
 266   }\r
 267 \r
 268   void paste(boolean newAlignment)\r
 269   {\r
 270     try{\r
 271       if (copiedSequences == null)\r
 272         return;\r
 273 \r
 274       StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
 275       Vector seqs = new Vector();\r
 276       while (st.hasMoreElements())\r
 277       {\r
 278         String name = st.nextToken();\r
 279         int start = Integer.parseInt(st.nextToken());\r
 280         int end = Integer.parseInt(st.nextToken());\r
 281         Sequence sequence = new Sequence(name,st.nextToken(), start, end);\r
 282 \r
 283         if(!newAlignment)\r
 284           viewport.alignment.addSequence(sequence);\r
 285         else\r
 286           seqs.addElement(sequence);\r
 287       }\r
 288 \r
 289       if(newAlignment)\r
 290       {\r
 291         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 292         for(int i=0; i<seqs.size(); i++)\r
 293          newSeqs[i] = (SequenceI)seqs.elementAt(i);\r
 294 \r
 295         AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);\r
 296         String newtitle = new String("Copied sequences");\r
 297         if( getTitle().startsWith("Copied sequences"))\r
 298          newtitle = getTitle();\r
 299        else\r
 300          newtitle = newtitle.concat("- from "+getTitle());\r
 301         jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
 302       }\r
 303       else\r
 304       {\r
 305         viewport.setEndSeq(viewport.alignment.getHeight());\r
 306         viewport.alignment.getWidth();\r
 307         viewport.updateConservation();\r
 308         viewport.updateConsensus();\r
 309         alignPanel.repaint();\r
 310       }\r
 311 \r
 312     }catch(Exception ex){}// could be anything being pasted in here\r
 313 \r
 314   }\r
 315 \r
 316 \r
 317   protected void cut_actionPerformed(ActionEvent e)\r
 318   {\r
 319     copy_actionPerformed(null);\r
 320     delete_actionPerformed(null);\r
 321   }\r
 322 \r
 323   protected void delete_actionPerformed(ActionEvent e)\r
 324   {\r
 325     addHistoryItem("Delete");\r
 326     if (viewport.getSelectionGroup() == null)\r
 327       return;\r
 328 \r
 329      SequenceGroup sg = viewport.getSelectionGroup();\r
 330      for (int i=0;i < sg.sequences.size(); i++)\r
 331      {\r
 332        SequenceI seq = sg.getSequenceAt(i);\r
 333        int index = viewport.getAlignment().findIndex(seq);\r
 334        seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);\r
 335 \r
 336        if(seq.getSequence().length()<1)\r
 337           viewport.getAlignment().deleteSequence(seq);\r
 338       else\r
 339           viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 340      }\r
 341 \r
 342      viewport.setSelectionGroup(null);\r
 343      viewport.alignment.deleteGroup(sg);\r
 344      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getSize().height);\r
 345      if(viewport.getAlignment().getHeight()<1)\r
 346      try\r
 347      {\r
 348        this.setVisible(false);\r
 349      }catch(Exception ex){}\r
 350    viewport.updateConservation();\r
 351    viewport.updateConsensus();\r
 352      alignPanel.repaint();\r
 353 \r
 354   }\r
 355 \r
 356 \r
 357 \r
 358   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 359   {\r
 360      Object [] history = (Object[])redoList.pop();\r
 361      SequenceI[] seq = (SequenceI[]) history[1];\r
 362 \r
 363      AlignmentAnnotation[] old = viewport.alignment.getAlignmentAnnotation();\r
 364      viewport.setAlignment(new Alignment(seq));\r
 365      for (int i = 0; i < old.length; i++)\r
 366        viewport.alignment.addAnnotation(old[i]);\r
 367 \r
 368      viewport.updateConservation();\r
 369      viewport.updateConsensus();\r
 370      updateEditMenuBar();\r
 371      alignPanel.repaint();\r
 372   }\r
 373 \r
 374 \r
 375   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 376   {\r
 377     viewport.alignment.deleteAllGroups();\r
 378     viewport.setSelectionGroup(null);\r
 379 \r
 380     alignPanel.repaint();\r
 381   }\r
 382 \r
 383 \r
 384 \r
 385   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 386   {\r
 387     SequenceGroup sg = new SequenceGroup();\r
 388     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 389       sg.addSequence( viewport.getAlignment().getSequenceAt(i));\r
 390     sg.setEndRes(viewport.alignment.getWidth());\r
 391     viewport.setSelectionGroup(sg);\r
 392     alignPanel.repaint();\r
 393     PaintRefresher.Refresh(null);\r
 394   }\r
 395 \r
 396   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 397   {\r
 398     viewport.setSelectionGroup(null);\r
 399     viewport.getColumnSelection().clear();\r
 400     viewport.setSelectionGroup(null);\r
 401     PaintRefresher.Refresh(null);\r
 402   }\r
 403 \r
 404   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 405   {\r
 406     SequenceGroup sg = viewport.getSelectionGroup();\r
 407     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 408       sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));\r
 409 \r
 410     PaintRefresher.Refresh(null);\r
 411   }\r
 412 \r
 413   public void remove2LeftMenuItem_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 min = colSel.getMin();\r
 420       viewport.getAlignment().trimLeft(min);\r
 421       colSel.compensateForEdit(0,min);\r
 422 \r
 423       if(viewport.getSelectionGroup()!=null)\r
 424         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 425 \r
 426       Vector groups = viewport.alignment.getGroups();\r
 427       for(int i=0; i<groups.size(); i++)\r
 428       {\r
 429         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 430         if(!sg.adjustForRemoveLeft(min))\r
 431           viewport.alignment.deleteGroup(sg);\r
 432       }\r
 433 \r
 434       alignPanel.repaint();\r
 435     }\r
 436   }\r
 437 \r
 438   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 439   {\r
 440     addHistoryItem("delete columns");\r
 441     ColumnSelection colSel = viewport.getColumnSelection();\r
 442     if (colSel.size() > 0)\r
 443     {\r
 444       int max = colSel.getMax();\r
 445       viewport.getAlignment().trimRight(max);\r
 446       if(viewport.getSelectionGroup()!=null)\r
 447         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 448 \r
 449       Vector groups = viewport.alignment.getGroups();\r
 450       for(int i=0; i<groups.size(); i++)\r
 451       {\r
 452         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 453         if(!sg.adjustForRemoveRight(max))\r
 454           viewport.alignment.deleteGroup(sg);\r
 455       }\r
 456 \r
 457 \r
 458 \r
 459       alignPanel.repaint();\r
 460     }\r
 461 \r
 462   }\r
 463 \r
 464   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 465   {\r
 466     addHistoryItem("delete gapped columns");\r
 467     viewport.getAlignment().removeGaps();\r
 468     viewport.updateConservation();\r
 469     viewport.updateConsensus();\r
 470     alignPanel.repaint();\r
 471   }\r
 472 \r
 473   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 474   {\r
 475     addHistoryItem("delete all gaps");\r
 476     SequenceI current;\r
 477     int jSize;\r
 478     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 479     {\r
 480       current = viewport.getAlignment().getSequenceAt(i);\r
 481       jSize = current.getLength();\r
 482       for (int j=0; j < jSize; j++)\r
 483         if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 484         {\r
 485           current.deleteCharAt(j);\r
 486           j--;\r
 487           jSize--;\r
 488         }\r
 489     }\r
 490     viewport.updateConservation();\r
 491     viewport.updateConsensus();\r
 492     alignPanel.repaint();\r
 493   }\r
 494 \r
 495 \r
 496   public void findMenuItem_actionPerformed(ActionEvent e)\r
 497   {\r
 498     Finder finder = new Finder(alignPanel);\r
 499   }\r
 500 \r
 501 \r
 502   public void font_actionPerformed(ActionEvent e)\r
 503   {\r
 504     Frame frame = new Frame();\r
 505     FontChooser fc = new FontChooser( alignPanel, frame);\r
 506     frame.add(fc);\r
 507     jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440,100);\r
 508 \r
 509   }\r
 510 \r
 511   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 512   {\r
 513     viewport.setShowFullId( fullSeqId.getState() );\r
 514     alignPanel.idPanel.idCanvas.setSize( alignPanel.calculateIdWidth() );\r
 515     alignPanel.repaint();\r
 516   }\r
 517 \r
 518   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 519   {\r
 520       viewport.setColourText( colourTextMenuItem.getState() );\r
 521       alignPanel.repaint();\r
 522   }\r
 523 \r
 524   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 525   {\r
 526     viewport.setWrapAlignment( wrapMenuItem.getState() );\r
 527     alignPanel.setWrapAlignment( wrapMenuItem.getState() );\r
 528     scaleAbove.setEnabled( wrapMenuItem.getState() );\r
 529     scaleLeft.setEnabled( wrapMenuItem.getState());\r
 530     scaleRight.setEnabled( wrapMenuItem.getState());\r
 531     alignPanel.repaint();\r
 532   }\r
 533 \r
 534   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 535   {\r
 536     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
 537     alignPanel.repaint();\r
 538   }\r
 539 \r
 540   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 541   {\r
 542     viewport.setScaleLeftWrapped(scaleLeft.getState());\r
 543     alignPanel.repaint();\r
 544   }\r
 545 \r
 546   protected void scaleRight_actionPerformed(ActionEvent e)\r
 547   {\r
 548     viewport.setScaleRightWrapped(scaleRight.getState());\r
 549     alignPanel.repaint();\r
 550   }\r
 551 \r
 552 \r
 553 \r
 554   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 555   {\r
 556     viewport.setShowBoxes( viewBoxesMenuItem.getState() );\r
 557     alignPanel.repaint();\r
 558   }\r
 559 \r
 560   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 561   {\r
 562     viewport.setShowText( viewTextMenuItem.getState() );\r
 563     alignPanel.repaint();\r
 564   }\r
 565 \r
 566 \r
 567   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 568   {\r
 569     viewport.setRenderGaps(renderGapsMenuItem.getState());\r
 570     alignPanel.repaint();\r
 571   }\r
 572 \r
 573 \r
 574   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 575   {\r
 576     if(annotationPanelMenuItem.getState() && viewport.getWrapAlignment())\r
 577     {\r
 578       annotationPanelMenuItem.setState(false);\r
 579       return;\r
 580     }\r
 581     viewport.setShowAnnotation( annotationPanelMenuItem.getState() );\r
 582     alignPanel.setAnnotationVisible( annotationPanelMenuItem.getState() );\r
 583   }\r
 584 \r
 585   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 586   {\r
 587    if (alignPanel.overviewPanel != null)\r
 588       return;\r
 589 \r
 590     Frame frame = new Frame();\r
 591     OverviewPanel overview = new OverviewPanel(alignPanel);\r
 592     frame.add(overview);\r
 593     // +50 must allow for applet frame window\r
 594     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
 595                              overview.preferredSize().width, overview.preferredSize().height+50);\r
 596 \r
 597     frame.pack();\r
 598     frame.addWindowListener(new WindowAdapter()\r
 599     { public void windowClosing(WindowEvent e)\r
 600       {\r
 601             alignPanel.setOverviewPanel(null);\r
 602       };\r
 603     });\r
 604 \r
 605     alignPanel.setOverviewPanel( overview );\r
 606 \r
 607 \r
 608   }\r
 609 \r
 610   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 611   {\r
 612     changeColour( null );\r
 613   }\r
 614 \r
 615 \r
 616   public void clustalColour_actionPerformed(ActionEvent e)\r
 617   {\r
 618     abovePIDThreshold.setState(false);\r
 619     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 620   }\r
 621 \r
 622   public void zappoColour_actionPerformed(ActionEvent e)\r
 623   {\r
 624     changeColour(new ZappoColourScheme());\r
 625   }\r
 626 \r
 627   public void taylorColour_actionPerformed(ActionEvent e)\r
 628   {\r
 629     changeColour(new TaylorColourScheme());\r
 630   }\r
 631 \r
 632 \r
 633   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 634   {\r
 635     changeColour( new HydrophobicColourScheme() );\r
 636   }\r
 637 \r
 638   public void helixColour_actionPerformed(ActionEvent e)\r
 639   {\r
 640     changeColour(new HelixColourScheme() );\r
 641   }\r
 642 \r
 643 \r
 644   public void strandColour_actionPerformed(ActionEvent e)\r
 645   {\r
 646     changeColour(new StrandColourScheme());\r
 647   }\r
 648 \r
 649 \r
 650   public void turnColour_actionPerformed(ActionEvent e)\r
 651   {\r
 652     changeColour(new TurnColourScheme());\r
 653   }\r
 654 \r
 655 \r
 656   public void buriedColour_actionPerformed(ActionEvent e)\r
 657   {\r
 658     changeColour(new BuriedColourScheme() );\r
 659   }\r
 660 \r
 661   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 662   {\r
 663     changeColour(new NucleotideColourScheme());\r
 664   }\r
 665 \r
 666 \r
 667   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 668   {\r
 669     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
 670   }\r
 671 \r
 672 \r
 673 \r
 674   void changeColour(ColourSchemeI cs)\r
 675   {\r
 676     int threshold = 0;\r
 677 \r
 678     if ( viewport.getAbovePIDThreshold() )\r
 679     {\r
 680       threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
 681 \r
 682       if (cs instanceof ResidueColourScheme)\r
 683         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
 684       else if (cs instanceof ScoreColourScheme)\r
 685         ( (ScoreColourScheme) cs).setThreshold(threshold);\r
 686 \r
 687       viewport.setGlobalColourScheme(cs);\r
 688     }\r
 689     else if (cs instanceof ResidueColourScheme)\r
 690       ( (ResidueColourScheme) cs).setThreshold(0);\r
 691     else if (cs instanceof ScoreColourScheme)\r
 692       ( (ScoreColourScheme) cs).setThreshold(0);\r
 693 \r
 694 \r
 695 \r
 696     if (viewport.getConservationSelected())\r
 697     {\r
 698       ConservationColourScheme ccs = null;\r
 699 \r
 700       Alignment al = (Alignment) viewport.alignment;\r
 701       Conservation c = new Conservation("All",\r
 702                                         ResidueProperties.propHash, 3,\r
 703                                         al.getSequences(), 0,\r
 704                                         al.getWidth() - 1);\r
 705 \r
 706       c.calculate();\r
 707       c.verdict(false, viewport.ConsPercGaps);\r
 708 \r
 709       ccs = new ConservationColourScheme(c, cs);\r
 710 \r
 711       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 712       ccs.setConsensus( viewport.vconsensus );\r
 713       viewport.setGlobalColourScheme(ccs);\r
 714 \r
 715       SliderPanel.setConservationSlider(alignPanel, ccs, "Background");\r
 716 \r
 717     }\r
 718     else\r
 719     {\r
 720         // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 721         if (cs != null)\r
 722           cs.setConsensus(viewport.vconsensus);\r
 723         viewport.setGlobalColourScheme(cs);\r
 724     }\r
 725 \r
 726 \r
 727     if(viewport.getColourAppliesToAllGroups())\r
 728     {\r
 729       Vector groups = viewport.alignment.getGroups();\r
 730       for(int i=0; i<groups.size(); i++)\r
 731       {\r
 732         SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
 733 \r
 734         if (cs instanceof ClustalxColourScheme)\r
 735         {\r
 736           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
 737         }\r
 738         else\r
 739           try\r
 740           {\r
 741             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
 742           }\r
 743           catch (Exception ex)\r
 744           {\r
 745             ex.printStackTrace();\r
 746             sg.cs = cs;\r
 747           }\r
 748 \r
 749         if(viewport.getAbovePIDThreshold())\r
 750         {\r
 751           if (sg.cs instanceof ResidueColourScheme)\r
 752             ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
 753           else if (sg.cs instanceof ScoreColourScheme)\r
 754             ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
 755 \r
 756            sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );\r
 757         }\r
 758 \r
 759         if( viewport.getConservationSelected() )\r
 760         {\r
 761           Conservation c = new Conservation("Group",\r
 762                                             ResidueProperties.propHash, 3,\r
 763                                             sg.sequences, 0, viewport.alignment.getWidth()-1);\r
 764           c.calculate();\r
 765           c.verdict(false, viewport.ConsPercGaps);\r
 766           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 767 \r
 768           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 769           ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 770           sg.cs = ccs;\r
 771         }\r
 772         else\r
 773         {\r
 774           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 775           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 776         }\r
 777 \r
 778       }\r
 779     }\r
 780 \r
 781     if(alignPanel.getOverviewPanel()!=null)\r
 782       alignPanel.getOverviewPanel().updateOverviewImage();\r
 783 \r
 784     alignPanel.repaint();\r
 785   }\r
 786 \r
 787   protected void modifyPID_actionPerformed(ActionEvent e)\r
 788   {\r
 789       if(viewport.getAbovePIDThreshold())\r
 790       {\r
 791         SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
 792                                    "Background");\r
 793         SliderPanel.showPIDSlider();\r
 794       }\r
 795   }\r
 796 \r
 797   protected void modifyConservation_actionPerformed(ActionEvent e)\r
 798   {\r
 799     if(viewport.getConservationSelected())\r
 800     {\r
 801       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
 802                                         "Background");\r
 803       SliderPanel.showConservationSlider();\r
 804     }\r
 805   }\r
 806 \r
 807 \r
 808   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 809   {\r
 810     viewport.setConservationSelected(conservationMenuItem.getState());\r
 811 \r
 812     viewport.setAbovePIDThreshold(false);\r
 813     abovePIDThreshold.setState(false);\r
 814 \r
 815    ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 816    if(cs instanceof ConservationColourScheme )\r
 817      changeColour( ((ConservationColourScheme)cs).cs );\r
 818     else\r
 819       changeColour( cs );\r
 820 \r
 821     modifyConservation_actionPerformed(null);\r
 822   }\r
 823 \r
 824   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 825   {\r
 826     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
 827 \r
 828     conservationMenuItem.setState(false);\r
 829     viewport.setConservationSelected(false);\r
 830 \r
 831     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 832 \r
 833     if(cs instanceof ConservationColourScheme )\r
 834         changeColour( ((ConservationColourScheme)cs).cs );\r
 835     else\r
 836         changeColour( cs );\r
 837 \r
 838     modifyPID_actionPerformed(null);\r
 839   }\r
 840 \r
 841 \r
 842 \r
 843   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 844   {\r
 845     UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);\r
 846   }\r
 847 \r
 848   public void PIDColour_actionPerformed(ActionEvent e)\r
 849   {\r
 850     changeColour( new PIDColourScheme() );\r
 851   }\r
 852 \r
 853 \r
 854   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 855   {\r
 856     changeColour(new Blosum62ColourScheme() );\r
 857   }\r
 858 \r
 859 \r
 860 \r
 861   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 862   {\r
 863     addHistoryItem("sort");\r
 864     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 865     alignPanel.repaint();\r
 866   }\r
 867 \r
 868   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 869   {\r
 870     addHistoryItem("sort");\r
 871     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 872     alignPanel.repaint();\r
 873   }\r
 874 \r
 875   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 876   {\r
 877     addHistoryItem("sort");\r
 878     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 879     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 880     alignPanel.repaint();\r
 881   }\r
 882 \r
 883   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 884   {\r
 885     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 886     Frame frame = new Frame();\r
 887     frame.add(sp);\r
 888     jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection", 400, 120);\r
 889 \r
 890   }\r
 891 \r
 892   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 893   {\r
 894     if(viewport.getSelectionGroup().getSize()>1)\r
 895     {\r
 896       Frame frame = new Frame();\r
 897       frame.add(new PairwiseAlignPanel(viewport));\r
 898       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
 899     }\r
 900   }\r
 901 \r
 902   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 903   {\r
 904 \r
 905     if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)\r
 906        || viewport.getAlignment().getHeight()<4)\r
 907     {\r
 908       return;\r
 909     }\r
 910 \r
 911     try{\r
 912       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 913       Frame frame = new Frame();\r
 914       frame.add(pcaPanel);\r
 915       jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis", 400, 400);\r
 916    }catch(java.lang.OutOfMemoryError ex)\r
 917    {\r
 918    }\r
 919 \r
 920 \r
 921   }\r
 922 \r
 923   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 924   {\r
 925     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
 926   }\r
 927 \r
 928   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 929   {\r
 930     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
 931   }\r
 932 \r
 933 \r
 934   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 935   {\r
 936     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
 937   }\r
 938 \r
 939   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 940   {\r
 941     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
 942   }\r
 943 \r
 944   void NewTreePanel(String type, String pwType, String title)\r
 945   {\r
 946     //are the sequences aligned?\r
 947     if(!viewport.alignment.isAligned())\r
 948     {\r
 949       return;\r
 950     }\r
 951 \r
 952     final TreePanel tp;\r
 953     if (viewport.getSelectionGroup() != null &&\r
 954         viewport.getSelectionGroup().getSize() > 3)\r
 955     {\r
 956       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
 957                          pwType,\r
 958                          0, viewport.alignment.getWidth());\r
 959     }\r
 960     else\r
 961     {\r
 962       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
 963                          type, pwType, 0, viewport.alignment.getWidth());\r
 964     }\r
 965 \r
 966    addTreeMenuItem(tp, title);\r
 967 \r
 968    jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
 969   }\r
 970 \r
 971   void addTreeMenuItem(final TreePanel treePanel, String title)\r
 972   {\r
 973     final MenuItem item = new MenuItem(title);\r
 974     sortByTreeMenu.add(item);\r
 975     item.addActionListener(new java.awt.event.ActionListener()\r
 976     {\r
 977       public void actionPerformed(ActionEvent e)\r
 978       {\r
 979         addHistoryItem("sort");\r
 980         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
 981         alignPanel.repaint();\r
 982       }\r
 983     });\r
 984 \r
 985     treePanel.addWindowListener(new WindowAdapter()\r
 986     {\r
 987       public void windowClosing(WindowEvent e)\r
 988       {\r
 989         sortByTreeMenu.remove(item);\r
 990       };\r
 991     });\r
 992   }\r
 993 \r
 994   protected void documentation_actionPerformed(ActionEvent e) {\r
 995 \r
 996     jalview.bin.JalviewLite.showURL("http://www.jalview.org");\r
 997 \r
 998   }\r
 999 \r
1000   protected void about_actionPerformed(ActionEvent e)\r
1001   {\r
1002     class AboutPanel extends Canvas\r
1003     {\r
1004       public void paint(Graphics g)\r
1005       {\r
1006         g.setColor(Color.white);\r
1007         g.fillRect(0,0,getSize().width, getSize().height);\r
1008         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1009         FontMetrics fm = g.getFontMetrics();\r
1010         int fh = fm.getHeight();\r
1011         int y=20, x=7;\r
1012         g.setColor(Color.black);\r
1013         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1014         g.drawString("JalView - Release 2.0", 200,y+=fh);\r
1015         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1016         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",x,y+=fh*2);\r
1017         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",x,y+=fh);\r
1018         g.drawString("If  you use JalView, please cite:",x,y+=fh+8);\r
1019         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",x,y+=fh);\r
1020         g.drawString("Bioinformatics,  2004 12;426-7.",x,y+=fh);\r
1021       }\r
1022     }\r
1023     Frame frame = new Frame();\r
1024     frame.add(new AboutPanel());\r
1025     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580,200);\r
1026 \r
1027 \r
1028 \r
1029   }\r
1030 }\r