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         String newtitle = new String("Copied sequences");\r
 277         if( getTitle().startsWith("Copied sequences"))\r
 278          newtitle = getTitle();\r
 279        else\r
 280          newtitle = newtitle.concat("- from "+getTitle());\r
 281         jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
 282       }\r
 283       else\r
 284       {\r
 285         viewport.setEndSeq(viewport.alignment.getHeight());\r
 286         viewport.alignment.getWidth();\r
 287         viewport.updateConservation();\r
 288         viewport.updateConsensus();\r
 289         alignPanel.repaint();\r
 290       }\r
 291 \r
 292     }catch(Exception ex){}// could be anything being pasted in here\r
 293 \r
 294   }\r
 295 \r
 296 \r
 297   protected void cut_actionPerformed(ActionEvent e)\r
 298   {\r
 299     copy_actionPerformed(null);\r
 300     delete_actionPerformed(null);\r
 301   }\r
 302 \r
 303   protected void delete_actionPerformed(ActionEvent e)\r
 304   {\r
 305     addHistoryItem("Delete");\r
 306     if (viewport.getSelectionGroup() == null)\r
 307       return;\r
 308 \r
 309      SequenceGroup sg = viewport.getSelectionGroup();\r
 310      for (int i=0;i < sg.sequences.size(); i++)\r
 311      {\r
 312        SequenceI seq = sg.getSequenceAt(i);\r
 313        int index = viewport.getAlignment().findIndex(seq);\r
 314        seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);\r
 315 \r
 316        if(seq.getSequence().length()<1)\r
 317           viewport.getAlignment().deleteSequence(seq);\r
 318       else\r
 319           viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 320      }\r
 321 \r
 322      viewport.setSelectionGroup(null);\r
 323      viewport.alignment.deleteGroup(sg);\r
 324      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getSize().height);\r
 325      if(viewport.getAlignment().getHeight()<1)\r
 326      try\r
 327      {\r
 328        this.setVisible(false);\r
 329      }catch(Exception ex){}\r
 330    viewport.updateConservation();\r
 331    viewport.updateConsensus();\r
 332      alignPanel.repaint();\r
 333 \r
 334   }\r
 335 \r
 336 \r
 337 \r
 338   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 339   {\r
 340      Object [] history = (Object[])redoList.pop();\r
 341      SequenceI[] seq = (SequenceI[]) history[1];\r
 342 \r
 343      AlignmentAnnotation[] old = viewport.alignment.getAlignmentAnnotation();\r
 344      viewport.setAlignment(new Alignment(seq));\r
 345      for (int i = 0; i < old.length; i++)\r
 346        viewport.alignment.addAnnotation(old[i]);\r
 347 \r
 348      viewport.updateConservation();\r
 349      viewport.updateConsensus();\r
 350      updateEditMenuBar();\r
 351      alignPanel.repaint();\r
 352   }\r
 353 \r
 354 \r
 355   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 356   {\r
 357     viewport.alignment.deleteAllGroups();\r
 358     viewport.setSelectionGroup(null);\r
 359 \r
 360     alignPanel.repaint();\r
 361   }\r
 362 \r
 363 \r
 364 \r
 365   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 366   {\r
 367     SequenceGroup sg = new SequenceGroup();\r
 368     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 369       sg.addSequence( viewport.getAlignment().getSequenceAt(i));\r
 370     sg.setEndRes(viewport.alignment.getWidth());\r
 371     viewport.setSelectionGroup(sg);\r
 372     alignPanel.repaint();\r
 373     PaintRefresher.Refresh(null);\r
 374   }\r
 375 \r
 376   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 377   {\r
 378     viewport.setSelectionGroup(null);\r
 379     viewport.getColumnSelection().clear();\r
 380     viewport.setSelectionGroup(null);\r
 381     PaintRefresher.Refresh(null);\r
 382   }\r
 383 \r
 384   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 385   {\r
 386     SequenceGroup sg = viewport.getSelectionGroup();\r
 387     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 388       sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));\r
 389 \r
 390     PaintRefresher.Refresh(null);\r
 391   }\r
 392 \r
 393   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 394   {\r
 395     addHistoryItem("delete columns");\r
 396     ColumnSelection colSel = viewport.getColumnSelection();\r
 397     if (colSel.size() > 0)\r
 398     {\r
 399       int min = colSel.getMin();\r
 400       viewport.getAlignment().trimLeft(min);\r
 401       colSel.compensateForEdit(0,min);\r
 402 \r
 403       if(viewport.getSelectionGroup()!=null)\r
 404         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 405 \r
 406       Vector groups = viewport.alignment.getGroups();\r
 407       for(int i=0; i<groups.size(); i++)\r
 408       {\r
 409         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 410         if(!sg.adjustForRemoveLeft(min))\r
 411           viewport.alignment.deleteGroup(sg);\r
 412       }\r
 413 \r
 414       alignPanel.repaint();\r
 415     }\r
 416   }\r
 417 \r
 418   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 419   {\r
 420     addHistoryItem("delete columns");\r
 421     ColumnSelection colSel = viewport.getColumnSelection();\r
 422     if (colSel.size() > 0)\r
 423     {\r
 424       int max = colSel.getMax();\r
 425       viewport.getAlignment().trimRight(max);\r
 426       if(viewport.getSelectionGroup()!=null)\r
 427         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 428 \r
 429       Vector groups = viewport.alignment.getGroups();\r
 430       for(int i=0; i<groups.size(); i++)\r
 431       {\r
 432         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 433         if(!sg.adjustForRemoveRight(max))\r
 434           viewport.alignment.deleteGroup(sg);\r
 435       }\r
 436 \r
 437 \r
 438 \r
 439       alignPanel.repaint();\r
 440     }\r
 441 \r
 442   }\r
 443 \r
 444   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 445   {\r
 446     addHistoryItem("delete gapped columns");\r
 447     viewport.getAlignment().removeGaps();\r
 448     viewport.updateConservation();\r
 449     viewport.updateConsensus();\r
 450     alignPanel.repaint();\r
 451   }\r
 452 \r
 453   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 454   {\r
 455     addHistoryItem("delete all gaps");\r
 456     SequenceI current;\r
 457     int jSize;\r
 458     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 459     {\r
 460       current = viewport.getAlignment().getSequenceAt(i);\r
 461       jSize = current.getLength();\r
 462       for (int j=0; j < jSize; j++)\r
 463         if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 464         {\r
 465           current.deleteCharAt(j);\r
 466           j--;\r
 467           jSize--;\r
 468         }\r
 469     }\r
 470     viewport.updateConservation();\r
 471     viewport.updateConsensus();\r
 472     alignPanel.repaint();\r
 473   }\r
 474 \r
 475 \r
 476   public void findMenuItem_actionPerformed(ActionEvent e)\r
 477   {\r
 478     Finder finder = new Finder(alignPanel);\r
 479   }\r
 480 \r
 481 \r
 482   public void font_actionPerformed(ActionEvent e)\r
 483   {\r
 484     Frame frame = new Frame();\r
 485     FontChooser fc = new FontChooser( alignPanel, frame);\r
 486     frame.add(fc);\r
 487     jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440,100);\r
 488 \r
 489   }\r
 490 \r
 491   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 492   {\r
 493     viewport.setShowFullId( fullSeqId.getState() );\r
 494     alignPanel.idPanel.idCanvas.setSize( alignPanel.calculateIdWidth() );\r
 495     alignPanel.repaint();\r
 496   }\r
 497 \r
 498   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 499   {\r
 500       viewport.setColourText( colourTextMenuItem.getState() );\r
 501       alignPanel.repaint();\r
 502   }\r
 503 \r
 504   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 505   {\r
 506     viewport.setWrapAlignment( wrapMenuItem.getState() );\r
 507     alignPanel.setWrapAlignment( wrapMenuItem.getState() );\r
 508     scaleAbove.setEnabled( wrapMenuItem.getState() );\r
 509     scaleLeft.setEnabled( wrapMenuItem.getState());\r
 510     scaleRight.setEnabled( wrapMenuItem.getState());\r
 511     alignPanel.repaint();\r
 512   }\r
 513 \r
 514   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 515   {\r
 516     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
 517     alignPanel.repaint();\r
 518   }\r
 519 \r
 520   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 521   {\r
 522     viewport.setScaleLeftWrapped(scaleLeft.getState());\r
 523     alignPanel.repaint();\r
 524   }\r
 525 \r
 526   protected void scaleRight_actionPerformed(ActionEvent e)\r
 527   {\r
 528     viewport.setScaleRightWrapped(scaleRight.getState());\r
 529     alignPanel.repaint();\r
 530   }\r
 531 \r
 532 \r
 533 \r
 534   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 535   {\r
 536     viewport.setShowBoxes( viewBoxesMenuItem.getState() );\r
 537     alignPanel.repaint();\r
 538   }\r
 539 \r
 540   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 541   {\r
 542     viewport.setShowText( viewTextMenuItem.getState() );\r
 543     alignPanel.repaint();\r
 544   }\r
 545 \r
 546 \r
 547   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 548   {\r
 549     viewport.setRenderGaps(renderGapsMenuItem.getState());\r
 550     alignPanel.repaint();\r
 551   }\r
 552 \r
 553 \r
 554   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 555   {\r
 556     if(annotationPanelMenuItem.getState() && viewport.getWrapAlignment())\r
 557     {\r
 558       annotationPanelMenuItem.setState(false);\r
 559       return;\r
 560     }\r
 561     viewport.setShowAnnotation( annotationPanelMenuItem.getState() );\r
 562     alignPanel.setAnnotationVisible( annotationPanelMenuItem.getState() );\r
 563   }\r
 564 \r
 565   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 566   {\r
 567    if (alignPanel.overviewPanel != null)\r
 568       return;\r
 569 \r
 570     Frame frame = new Frame();\r
 571     OverviewPanel overview = new OverviewPanel(alignPanel);\r
 572     frame.add(overview);\r
 573     // +50 must allow for applet frame window\r
 574     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
 575                              overview.preferredSize().width, overview.preferredSize().height+50);\r
 576 \r
 577     frame.pack();\r
 578     frame.addWindowListener(new WindowAdapter()\r
 579     { public void windowClosing(WindowEvent e)\r
 580       {\r
 581             alignPanel.setOverviewPanel(null);\r
 582       };\r
 583     });\r
 584 \r
 585     alignPanel.setOverviewPanel( overview );\r
 586 \r
 587 \r
 588   }\r
 589 \r
 590   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 591   {\r
 592     changeColour( null );\r
 593   }\r
 594 \r
 595 \r
 596   public void clustalColour_actionPerformed(ActionEvent e)\r
 597   {\r
 598     abovePIDThreshold.setState(false);\r
 599     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 600   }\r
 601 \r
 602   public void zappoColour_actionPerformed(ActionEvent e)\r
 603   {\r
 604     changeColour(new ZappoColourScheme());\r
 605   }\r
 606 \r
 607   public void taylorColour_actionPerformed(ActionEvent e)\r
 608   {\r
 609     changeColour(new TaylorColourScheme());\r
 610   }\r
 611 \r
 612 \r
 613   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 614   {\r
 615     changeColour( new HydrophobicColourScheme() );\r
 616   }\r
 617 \r
 618   public void helixColour_actionPerformed(ActionEvent e)\r
 619   {\r
 620     changeColour(new HelixColourScheme() );\r
 621   }\r
 622 \r
 623 \r
 624   public void strandColour_actionPerformed(ActionEvent e)\r
 625   {\r
 626     changeColour(new StrandColourScheme());\r
 627   }\r
 628 \r
 629 \r
 630   public void turnColour_actionPerformed(ActionEvent e)\r
 631   {\r
 632     changeColour(new TurnColourScheme());\r
 633   }\r
 634 \r
 635 \r
 636   public void buriedColour_actionPerformed(ActionEvent e)\r
 637   {\r
 638     changeColour(new BuriedColourScheme() );\r
 639   }\r
 640 \r
 641   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 642   {\r
 643     changeColour(new NucleotideColourScheme());\r
 644   }\r
 645 \r
 646 \r
 647   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 648   {\r
 649     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
 650   }\r
 651 \r
 652 \r
 653 \r
 654   void changeColour(ColourSchemeI cs)\r
 655   {\r
 656     int threshold = 0;\r
 657 \r
 658     if ( viewport.getAbovePIDThreshold() )\r
 659     {\r
 660       threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
 661 \r
 662       if (cs instanceof ResidueColourScheme)\r
 663         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
 664       else if (cs instanceof ScoreColourScheme)\r
 665         ( (ScoreColourScheme) cs).setThreshold(threshold);\r
 666 \r
 667       viewport.setGlobalColourScheme(cs);\r
 668     }\r
 669     else if (cs instanceof ResidueColourScheme)\r
 670       ( (ResidueColourScheme) cs).setThreshold(0);\r
 671     else if (cs instanceof ScoreColourScheme)\r
 672       ( (ScoreColourScheme) cs).setThreshold(0);\r
 673 \r
 674 \r
 675 \r
 676     if (viewport.getConservationSelected())\r
 677     {\r
 678       ConservationColourScheme ccs = null;\r
 679 \r
 680       Alignment al = (Alignment) viewport.alignment;\r
 681       Conservation c = new Conservation("All",\r
 682                                         ResidueProperties.propHash, 3,\r
 683                                         al.getSequences(), 0,\r
 684                                         al.getWidth() - 1);\r
 685 \r
 686       c.calculate();\r
 687       c.verdict(false, viewport.ConsPercGaps);\r
 688 \r
 689       ccs = new ConservationColourScheme(c, cs);\r
 690 \r
 691       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 692       ccs.setConsensus( viewport.vconsensus );\r
 693       viewport.setGlobalColourScheme(ccs);\r
 694 \r
 695       SliderPanel.setConservationSlider(alignPanel, ccs, "Background");\r
 696 \r
 697     }\r
 698     else\r
 699     {\r
 700         // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 701         if (cs != null)\r
 702           cs.setConsensus(viewport.vconsensus);\r
 703         viewport.setGlobalColourScheme(cs);\r
 704     }\r
 705 \r
 706 \r
 707     if(viewport.getColourAppliesToAllGroups())\r
 708     {\r
 709       Vector groups = viewport.alignment.getGroups();\r
 710       for(int i=0; i<groups.size(); i++)\r
 711       {\r
 712         SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
 713 \r
 714         if (cs instanceof ClustalxColourScheme)\r
 715         {\r
 716           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
 717         }\r
 718         else\r
 719           try\r
 720           {\r
 721             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
 722           }\r
 723           catch (Exception ex)\r
 724           {\r
 725             ex.printStackTrace();\r
 726             sg.cs = cs;\r
 727           }\r
 728 \r
 729         if(viewport.getAbovePIDThreshold())\r
 730         {\r
 731           if (sg.cs instanceof ResidueColourScheme)\r
 732             ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
 733           else if (sg.cs instanceof ScoreColourScheme)\r
 734             ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
 735 \r
 736            sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );\r
 737         }\r
 738 \r
 739         if( viewport.getConservationSelected() )\r
 740         {\r
 741           Conservation c = new Conservation("Group",\r
 742                                             ResidueProperties.propHash, 3,\r
 743                                             sg.sequences, 0, viewport.alignment.getWidth()-1);\r
 744           c.calculate();\r
 745           c.verdict(false, viewport.ConsPercGaps);\r
 746           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 747 \r
 748           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 749           ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 750           sg.cs = ccs;\r
 751         }\r
 752         else\r
 753         {\r
 754           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 755           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 756         }\r
 757 \r
 758       }\r
 759     }\r
 760 \r
 761     if(alignPanel.getOverviewPanel()!=null)\r
 762       alignPanel.getOverviewPanel().updateOverviewImage();\r
 763 \r
 764     alignPanel.repaint();\r
 765   }\r
 766 \r
 767   protected void modifyPID_actionPerformed(ActionEvent e)\r
 768   {\r
 769       if(viewport.getAbovePIDThreshold())\r
 770       {\r
 771         SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
 772                                    "Background");\r
 773         SliderPanel.showPIDSlider();\r
 774       }\r
 775   }\r
 776 \r
 777   protected void modifyConservation_actionPerformed(ActionEvent e)\r
 778   {\r
 779     if(viewport.getConservationSelected())\r
 780     {\r
 781       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
 782                                         "Background");\r
 783       SliderPanel.showConservationSlider();\r
 784     }\r
 785   }\r
 786 \r
 787 \r
 788   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 789   {\r
 790     viewport.setConservationSelected(conservationMenuItem.getState());\r
 791 \r
 792     viewport.setAbovePIDThreshold(false);\r
 793     abovePIDThreshold.setState(false);\r
 794 \r
 795    ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 796    if(cs instanceof ConservationColourScheme )\r
 797      changeColour( ((ConservationColourScheme)cs).cs );\r
 798     else\r
 799       changeColour( cs );\r
 800 \r
 801     modifyConservation_actionPerformed(null);\r
 802   }\r
 803 \r
 804   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 805   {\r
 806     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
 807 \r
 808     conservationMenuItem.setState(false);\r
 809     viewport.setConservationSelected(false);\r
 810 \r
 811     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 812 \r
 813     if(cs instanceof ConservationColourScheme )\r
 814         changeColour( ((ConservationColourScheme)cs).cs );\r
 815     else\r
 816         changeColour( cs );\r
 817 \r
 818     modifyPID_actionPerformed(null);\r
 819   }\r
 820 \r
 821 \r
 822 \r
 823   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 824   {\r
 825     UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);\r
 826   }\r
 827 \r
 828   public void PIDColour_actionPerformed(ActionEvent e)\r
 829   {\r
 830     changeColour( new PIDColourScheme() );\r
 831   }\r
 832 \r
 833 \r
 834   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 835   {\r
 836     changeColour(new Blosum62ColourScheme() );\r
 837   }\r
 838 \r
 839 \r
 840 \r
 841   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 842   {\r
 843     addHistoryItem("sort");\r
 844     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 845     alignPanel.repaint();\r
 846   }\r
 847 \r
 848   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 849   {\r
 850     addHistoryItem("sort");\r
 851     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 852     alignPanel.repaint();\r
 853   }\r
 854 \r
 855   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 856   {\r
 857     addHistoryItem("sort");\r
 858     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 859     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 860     alignPanel.repaint();\r
 861   }\r
 862 \r
 863   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 864   {\r
 865     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 866     Frame frame = new Frame();\r
 867     frame.add(sp);\r
 868     jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection", 400, 120);\r
 869 \r
 870   }\r
 871 \r
 872   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 873   {\r
 874     if(viewport.getSelectionGroup().getSize()>1)\r
 875     {\r
 876       Frame frame = new Frame();\r
 877       frame.add(new PairwiseAlignPanel(viewport));\r
 878       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
 879     }\r
 880   }\r
 881 \r
 882   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 883   {\r
 884 \r
 885     if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)\r
 886        || viewport.getAlignment().getHeight()<4)\r
 887     {\r
 888       return;\r
 889     }\r
 890 \r
 891     try{\r
 892       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 893       Frame frame = new Frame();\r
 894       frame.add(pcaPanel);\r
 895       jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis", 400, 400);\r
 896    }catch(java.lang.OutOfMemoryError ex)\r
 897    {\r
 898    }\r
 899 \r
 900 \r
 901   }\r
 902 \r
 903   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 904   {\r
 905     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
 906   }\r
 907 \r
 908   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 909   {\r
 910     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
 911   }\r
 912 \r
 913 \r
 914   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 915   {\r
 916     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
 917   }\r
 918 \r
 919   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 920   {\r
 921     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
 922   }\r
 923 \r
 924   void NewTreePanel(String type, String pwType, String title)\r
 925   {\r
 926     //are the sequences aligned?\r
 927     if(!viewport.alignment.isAligned())\r
 928     {\r
 929       return;\r
 930     }\r
 931 \r
 932     final TreePanel tp;\r
 933     if (viewport.getSelectionGroup() != null &&\r
 934         viewport.getSelectionGroup().getSize() > 3)\r
 935     {\r
 936       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
 937                          pwType,\r
 938                          0, viewport.alignment.getWidth());\r
 939     }\r
 940     else\r
 941     {\r
 942       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
 943                          type, pwType, 0, viewport.alignment.getWidth());\r
 944     }\r
 945 \r
 946    addTreeMenuItem(tp, title);\r
 947 \r
 948    jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
 949   }\r
 950 \r
 951   void addTreeMenuItem(final TreePanel treePanel, String title)\r
 952   {\r
 953     final MenuItem item = new MenuItem(title);\r
 954     sortByTreeMenu.add(item);\r
 955     item.addActionListener(new java.awt.event.ActionListener()\r
 956     {\r
 957       public void actionPerformed(ActionEvent e)\r
 958       {\r
 959         addHistoryItem("sort");\r
 960         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
 961         alignPanel.repaint();\r
 962       }\r
 963     });\r
 964 \r
 965     treePanel.addWindowListener(new WindowAdapter()\r
 966     {\r
 967       public void windowClosing(WindowEvent e)\r
 968       {\r
 969         sortByTreeMenu.remove(item);\r
 970       };\r
 971     });\r
 972   }\r
 973 \r
 974   protected void documentation_actionPerformed(ActionEvent e) {\r
 975 \r
 976     jalview.bin.JalviewLite.showURL("http://www.jalview.org");\r
 977 \r
 978   }\r
 979 \r
 980   protected void about_actionPerformed(ActionEvent e)\r
 981   {\r
 982     class AboutPanel extends Canvas\r
 983     {\r
 984       public void paint(Graphics g)\r
 985       {\r
 986         g.setColor(Color.white);\r
 987         g.fillRect(0,0,getSize().width, getSize().height);\r
 988         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
 989         FontMetrics fm = g.getFontMetrics();\r
 990         int fh = fm.getHeight();\r
 991         int y=20, x=7;\r
 992         g.setColor(Color.black);\r
 993         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
 994         g.drawString("JalView - Release 2.0", 200,y+=fh);\r
 995         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
 996         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",x,y+=fh*2);\r
 997         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",x,y+=fh);\r
 998         g.drawString("If  you use JalView, please cite:",x,y+=fh+8);\r
 999         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",x,y+=fh);\r
1000         g.drawString("Bioinformatics,  2004 12;426-7.",x,y+=fh);\r
1001       }\r
1002     }\r
1003     Frame frame = new Frame();\r
1004     frame.add(new AboutPanel());\r
1005     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580,200);\r
1006 \r
1007 \r
1008 \r
1009   }\r
1010 }\r