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         HistoryItem hi = (HistoryItem)historyList.peek();\r
 109         undoMenuItem.setLabel("Undo "+hi.getDescription());\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         HistoryItem hi = (HistoryItem)redoList.peek();\r
 121         redoMenuItem.setLabel("Redo "+hi.getDescription());\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(HistoryItem hi)\r
 131    {\r
 132      historyList.push(hi);\r
 133      updateEditMenuBar();\r
 134    }\r
 135 \r
 136    protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 137    {\r
 138        HistoryItem hi = (HistoryItem)historyList.pop();\r
 139        redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment, HistoryItem.HIDE));\r
 140        restoreHistoryItem(hi);\r
 141    }\r
 142 \r
 143    protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 144    {\r
 145       HistoryItem hi = (HistoryItem)redoList.pop();\r
 146       restoreHistoryItem(hi);\r
 147       updateEditMenuBar();\r
 148       viewport.updateConsensus();\r
 149       alignPanel.repaint();\r
 150       alignPanel.repaint();\r
 151    }\r
 152 \r
 153 \r
 154    // used by undo and redo\r
 155    void restoreHistoryItem(HistoryItem hi)\r
 156    {\r
 157       if(hi.getType()== HistoryItem.SORT)\r
 158       {\r
 159            for(int i=0; i<hi.getSequences().size(); i++)\r
 160              viewport.alignment.getSequences().setElementAt(hi.getSequences().elementAt(i), i);\r
 161       }\r
 162       else\r
 163       {\r
 164         for (int i = 0; i < hi.getSequences().size(); i++)\r
 165         {\r
 166           SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
 167           if(restore.getLength()==0)\r
 168           {\r
 169             // log.System.out.println(hi.getHidden().elementAt(i));\r
 170             restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 171             viewport.alignment.getSequences().insertElementAt(\r
 172                restore,\r
 173                hi.getAlignIndex(i));\r
 174           }\r
 175           else\r
 176             restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 177         }\r
 178         if(hi.getType()==HistoryItem.PASTE)\r
 179         {\r
 180           for(int i=viewport.alignment.getHeight()-1;i>hi.getSequences().size()-1; i--)\r
 181             viewport.alignment.deleteSequence(i);\r
 182         }\r
 183       }\r
 184 \r
 185        updateEditMenuBar();\r
 186 \r
 187        viewport.updateConsensus();\r
 188        viewport.updateConservation();\r
 189        alignPanel.repaint();\r
 190    }\r
 191 \r
 192 \r
 193   public void moveSelectedSequences(boolean up)\r
 194   {\r
 195     SequenceGroup sg = viewport.getSelectionGroup();\r
 196     if (sg == null)\r
 197       return;\r
 198 \r
 199     if (up)\r
 200     {\r
 201       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 202       {\r
 203         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 204         if (!sg.sequences.contains(seq))\r
 205           continue;\r
 206 \r
 207         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 208         if (sg.sequences.contains(temp))\r
 209           continue;\r
 210 \r
 211         viewport.alignment.getSequences().setElementAt(temp, i);\r
 212         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 213       }\r
 214     }\r
 215     else\r
 216     {\r
 217       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 218       {\r
 219         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 220         if (!sg.sequences.contains(seq))\r
 221           continue;\r
 222 \r
 223         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 224         if (sg.sequences.contains(temp))\r
 225           continue;\r
 226 \r
 227         viewport.alignment.getSequences().setElementAt(temp, i);\r
 228         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 229       }\r
 230     }\r
 231 \r
 232     alignPanel.repaint();\r
 233   }\r
 234 \r
 235 \r
 236   StringBuffer copiedSequences;\r
 237   protected void copy_actionPerformed(ActionEvent e)\r
 238   {\r
 239    if(viewport.getSelectionGroup()==null)\r
 240      return;\r
 241 \r
 242    SequenceGroup sg = viewport.getSelectionGroup();\r
 243    copiedSequences = new StringBuffer();\r
 244    Hashtable orderedSeqs = new Hashtable();\r
 245    for(int i=0; i<sg.getSize(); i++)\r
 246    {\r
 247       SequenceI seq = sg.getSequenceAt(i);\r
 248       int index = viewport.alignment.findIndex(seq);\r
 249       orderedSeqs.put(index+"", seq);\r
 250    }\r
 251 \r
 252    int index=0;\r
 253    for(int i=0; i<sg.getSize(); i++)\r
 254    {\r
 255      SequenceI seq = null;\r
 256      while( seq == null )\r
 257      {\r
 258        if(orderedSeqs.containsKey(index+""))\r
 259        {\r
 260          seq = (SequenceI) orderedSeqs.get(index + "");\r
 261          index++;\r
 262          break;\r
 263        }\r
 264        else\r
 265          index++;\r
 266      }\r
 267 \r
 268          copiedSequences.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"\r
 269                         +seq.findPosition( sg.getEndRes() )+ "\t"\r
 270                         +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");\r
 271        }\r
 272 \r
 273   }\r
 274 \r
 275 \r
 276   protected void pasteNew_actionPerformed(ActionEvent e)\r
 277   {\r
 278     paste(true);\r
 279   }\r
 280 \r
 281   protected void pasteThis_actionPerformed(ActionEvent e)\r
 282   {\r
 283     addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, HistoryItem.PASTE));\r
 284     paste(false);\r
 285   }\r
 286 \r
 287   void paste(boolean newAlignment)\r
 288   {\r
 289     try{\r
 290       if (copiedSequences == null)\r
 291         return;\r
 292 \r
 293       StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
 294       Vector seqs = new Vector();\r
 295       while (st.hasMoreElements())\r
 296       {\r
 297         String name = st.nextToken();\r
 298         int start = Integer.parseInt(st.nextToken());\r
 299         int end = Integer.parseInt(st.nextToken());\r
 300         Sequence sequence = new Sequence(name,st.nextToken(), start, end);\r
 301 \r
 302         if(!newAlignment)\r
 303           viewport.alignment.addSequence(sequence);\r
 304         else\r
 305           seqs.addElement(sequence);\r
 306       }\r
 307 \r
 308       if(newAlignment)\r
 309       {\r
 310         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 311         for(int i=0; i<seqs.size(); i++)\r
 312          newSeqs[i] = (SequenceI)seqs.elementAt(i);\r
 313 \r
 314         AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);\r
 315         String newtitle = new String("Copied sequences");\r
 316         if( getTitle().startsWith("Copied sequences"))\r
 317          newtitle = getTitle();\r
 318        else\r
 319          newtitle = newtitle.concat("- from "+getTitle());\r
 320         jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
 321       }\r
 322       else\r
 323       {\r
 324         viewport.setEndSeq(viewport.alignment.getHeight());\r
 325         viewport.alignment.getWidth();\r
 326         viewport.updateConservation();\r
 327         viewport.updateConsensus();\r
 328         alignPanel.repaint();\r
 329       }\r
 330 \r
 331     }catch(Exception ex){}// could be anything being pasted in here\r
 332 \r
 333   }\r
 334 \r
 335 \r
 336   protected void cut_actionPerformed(ActionEvent e)\r
 337   {\r
 338     copy_actionPerformed(null);\r
 339     delete_actionPerformed(null);\r
 340   }\r
 341 \r
 342   protected void delete_actionPerformed(ActionEvent e)\r
 343   {\r
 344     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, HistoryItem.HIDE));\r
 345     if (viewport.getSelectionGroup() == null)\r
 346       return;\r
 347 \r
 348      SequenceGroup sg = viewport.getSelectionGroup();\r
 349      for (int i=0;i < sg.sequences.size(); i++)\r
 350      {\r
 351        SequenceI seq = sg.getSequenceAt(i);\r
 352        int index = viewport.getAlignment().findIndex(seq);\r
 353        seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);\r
 354 \r
 355        if(seq.getSequence().length()<1)\r
 356           viewport.getAlignment().deleteSequence(seq);\r
 357       else\r
 358           viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 359      }\r
 360 \r
 361      viewport.setSelectionGroup(null);\r
 362      viewport.alignment.deleteGroup(sg);\r
 363      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getSize().height);\r
 364      if(viewport.getAlignment().getHeight()<1)\r
 365      try\r
 366      {\r
 367        this.setVisible(false);\r
 368      }catch(Exception ex){}\r
 369    viewport.updateConservation();\r
 370    viewport.updateConsensus();\r
 371      alignPanel.repaint();\r
 372 \r
 373   }\r
 374 \r
 375 \r
 376 \r
 377   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 378   {\r
 379     viewport.alignment.deleteAllGroups();\r
 380     viewport.setSelectionGroup(null);\r
 381 \r
 382     alignPanel.repaint();\r
 383   }\r
 384 \r
 385 \r
 386 \r
 387   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 388   {\r
 389     SequenceGroup sg = new SequenceGroup();\r
 390     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 391       sg.addSequence( viewport.getAlignment().getSequenceAt(i));\r
 392     sg.setEndRes(viewport.alignment.getWidth());\r
 393     viewport.setSelectionGroup(sg);\r
 394     alignPanel.repaint();\r
 395     PaintRefresher.Refresh(null);\r
 396   }\r
 397 \r
 398   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 399   {\r
 400     viewport.setSelectionGroup(null);\r
 401     viewport.getColumnSelection().clear();\r
 402     viewport.setSelectionGroup(null);\r
 403     PaintRefresher.Refresh(null);\r
 404   }\r
 405 \r
 406   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 407   {\r
 408     SequenceGroup sg = viewport.getSelectionGroup();\r
 409     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 410       sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));\r
 411 \r
 412     PaintRefresher.Refresh(null);\r
 413   }\r
 414 \r
 415   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 416   {\r
 417     ColumnSelection colSel = viewport.getColumnSelection();\r
 418     if (colSel.size() > 0)\r
 419     {\r
 420       addHistoryItem(new HistoryItem("Remove Left",viewport.alignment,\r
 421                                      HistoryItem.HIDE));\r
 422       int min = colSel.getMin();\r
 423       viewport.getAlignment().trimLeft(min);\r
 424       colSel.compensateForEdit(0,min);\r
 425 \r
 426       if(viewport.getSelectionGroup()!=null)\r
 427         viewport.getSelectionGroup().adjustForRemoveLeft(min);\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.adjustForRemoveLeft(min))\r
 434           viewport.alignment.deleteGroup(sg);\r
 435       }\r
 436 \r
 437       alignPanel.repaint();\r
 438     }\r
 439   }\r
 440 \r
 441   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 442   {\r
 443     ColumnSelection colSel = viewport.getColumnSelection();\r
 444     if (colSel.size() > 0)\r
 445     {\r
 446       addHistoryItem(new HistoryItem("Remove Right",viewport.alignment,\r
 447                                      HistoryItem.HIDE));\r
 448       int max = colSel.getMax();\r
 449       viewport.getAlignment().trimRight(max);\r
 450       if(viewport.getSelectionGroup()!=null)\r
 451         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 452 \r
 453       Vector groups = viewport.alignment.getGroups();\r
 454       for(int i=0; i<groups.size(); i++)\r
 455       {\r
 456         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 457         if(!sg.adjustForRemoveRight(max))\r
 458           viewport.alignment.deleteGroup(sg);\r
 459       }\r
 460 \r
 461 \r
 462 \r
 463       alignPanel.repaint();\r
 464     }\r
 465 \r
 466   }\r
 467 \r
 468   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 469   {\r
 470     addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
 471                                    viewport.alignment,\r
 472                                    HistoryItem.HIDE));\r
 473     viewport.getAlignment().removeGaps();\r
 474     viewport.updateConservation();\r
 475     viewport.updateConsensus();\r
 476     alignPanel.repaint();\r
 477   }\r
 478 \r
 479   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 480   {\r
 481     addHistoryItem(new HistoryItem("Remove Gaps",\r
 482                                    viewport.alignment,\r
 483                                    HistoryItem.HIDE));\r
 484     SequenceI current;\r
 485     int jSize;\r
 486     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 487     {\r
 488       current = viewport.getAlignment().getSequenceAt(i);\r
 489       jSize = current.getLength();\r
 490       for (int j=0; j < jSize; j++)\r
 491         if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 492         {\r
 493           current.deleteCharAt(j);\r
 494           j--;\r
 495           jSize--;\r
 496         }\r
 497     }\r
 498     viewport.updateConservation();\r
 499     viewport.updateConsensus();\r
 500     alignPanel.repaint();\r
 501   }\r
 502 \r
 503 \r
 504   public void findMenuItem_actionPerformed(ActionEvent e)\r
 505   {\r
 506     Finder finder = new Finder(alignPanel);\r
 507   }\r
 508 \r
 509 \r
 510   public void font_actionPerformed(ActionEvent e)\r
 511   {\r
 512     Frame frame = new Frame();\r
 513     FontChooser fc = new FontChooser( alignPanel, frame);\r
 514     frame.add(fc);\r
 515     jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440,100);\r
 516 \r
 517   }\r
 518 \r
 519   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 520   {\r
 521     viewport.setShowFullId( fullSeqId.getState() );\r
 522     alignPanel.fontChanged();\r
 523     alignPanel.repaint();\r
 524   }\r
 525 \r
 526   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 527   {\r
 528       viewport.setColourText( colourTextMenuItem.getState() );\r
 529       alignPanel.repaint();\r
 530   }\r
 531 \r
 532   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 533   {\r
 534     viewport.setWrapAlignment( wrapMenuItem.getState() );\r
 535     alignPanel.setWrapAlignment( wrapMenuItem.getState() );\r
 536     scaleAbove.setEnabled( wrapMenuItem.getState() );\r
 537     scaleLeft.setEnabled( wrapMenuItem.getState());\r
 538     scaleRight.setEnabled( wrapMenuItem.getState());\r
 539     alignPanel.repaint();\r
 540   }\r
 541 \r
 542   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 543   {\r
 544     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
 545     alignPanel.repaint();\r
 546   }\r
 547 \r
 548   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 549   {\r
 550     viewport.setScaleLeftWrapped(scaleLeft.getState());\r
 551     alignPanel.repaint();\r
 552   }\r
 553 \r
 554   protected void scaleRight_actionPerformed(ActionEvent e)\r
 555   {\r
 556     viewport.setScaleRightWrapped(scaleRight.getState());\r
 557     alignPanel.repaint();\r
 558   }\r
 559 \r
 560 \r
 561 \r
 562   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 563   {\r
 564     viewport.setShowBoxes( viewBoxesMenuItem.getState() );\r
 565     alignPanel.repaint();\r
 566   }\r
 567 \r
 568   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 569   {\r
 570     viewport.setShowText( viewTextMenuItem.getState() );\r
 571     alignPanel.repaint();\r
 572   }\r
 573 \r
 574 \r
 575   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 576   {\r
 577     viewport.setRenderGaps(renderGapsMenuItem.getState());\r
 578     alignPanel.repaint();\r
 579   }\r
 580 \r
 581 \r
 582   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 583   {\r
 584     if(annotationPanelMenuItem.getState() && viewport.getWrapAlignment())\r
 585     {\r
 586       annotationPanelMenuItem.setState(false);\r
 587       return;\r
 588     }\r
 589     viewport.setShowAnnotation( annotationPanelMenuItem.getState() );\r
 590     alignPanel.setAnnotationVisible( annotationPanelMenuItem.getState() );\r
 591   }\r
 592 \r
 593   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 594   {\r
 595    if (alignPanel.overviewPanel != null)\r
 596       return;\r
 597 \r
 598     Frame frame = new Frame();\r
 599     OverviewPanel overview = new OverviewPanel(alignPanel);\r
 600     frame.add(overview);\r
 601     // +50 must allow for applet frame window\r
 602     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
 603                              overview.preferredSize().width, overview.preferredSize().height+50);\r
 604 \r
 605     frame.pack();\r
 606     frame.addWindowListener(new WindowAdapter()\r
 607     { public void windowClosing(WindowEvent e)\r
 608       {\r
 609             alignPanel.setOverviewPanel(null);\r
 610       };\r
 611     });\r
 612 \r
 613     alignPanel.setOverviewPanel( overview );\r
 614 \r
 615 \r
 616   }\r
 617 \r
 618   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 619   {\r
 620     changeColour( null );\r
 621   }\r
 622 \r
 623 \r
 624   public void clustalColour_actionPerformed(ActionEvent e)\r
 625   {\r
 626     abovePIDThreshold.setState(false);\r
 627     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 628   }\r
 629 \r
 630   public void zappoColour_actionPerformed(ActionEvent e)\r
 631   {\r
 632     changeColour(new ZappoColourScheme());\r
 633   }\r
 634 \r
 635   public void taylorColour_actionPerformed(ActionEvent e)\r
 636   {\r
 637     changeColour(new TaylorColourScheme());\r
 638   }\r
 639 \r
 640 \r
 641   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 642   {\r
 643     changeColour( new HydrophobicColourScheme() );\r
 644   }\r
 645 \r
 646   public void helixColour_actionPerformed(ActionEvent e)\r
 647   {\r
 648     changeColour(new HelixColourScheme() );\r
 649   }\r
 650 \r
 651 \r
 652   public void strandColour_actionPerformed(ActionEvent e)\r
 653   {\r
 654     changeColour(new StrandColourScheme());\r
 655   }\r
 656 \r
 657 \r
 658   public void turnColour_actionPerformed(ActionEvent e)\r
 659   {\r
 660     changeColour(new TurnColourScheme());\r
 661   }\r
 662 \r
 663 \r
 664   public void buriedColour_actionPerformed(ActionEvent e)\r
 665   {\r
 666     changeColour(new BuriedColourScheme() );\r
 667   }\r
 668 \r
 669   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 670   {\r
 671     changeColour(new NucleotideColourScheme());\r
 672   }\r
 673 \r
 674 \r
 675   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 676   {\r
 677     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
 678   }\r
 679 \r
 680 \r
 681 \r
 682   void changeColour(ColourSchemeI cs)\r
 683   {\r
 684     int threshold = 0;\r
 685 \r
 686     if ( viewport.getAbovePIDThreshold() )\r
 687     {\r
 688       threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
 689 \r
 690       if (cs instanceof ResidueColourScheme)\r
 691         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
 692       else if (cs instanceof ScoreColourScheme)\r
 693         ( (ScoreColourScheme) cs).setThreshold(threshold);\r
 694 \r
 695       viewport.setGlobalColourScheme(cs);\r
 696     }\r
 697     else if (cs instanceof ResidueColourScheme)\r
 698       ( (ResidueColourScheme) cs).setThreshold(0);\r
 699     else if (cs instanceof ScoreColourScheme)\r
 700       ( (ScoreColourScheme) cs).setThreshold(0);\r
 701 \r
 702 \r
 703 \r
 704     if (viewport.getConservationSelected())\r
 705     {\r
 706       ConservationColourScheme ccs = null;\r
 707 \r
 708       Alignment al = (Alignment) viewport.alignment;\r
 709       Conservation c = new Conservation("All",\r
 710                                         ResidueProperties.propHash, 3,\r
 711                                         al.getSequences(), 0,\r
 712                                         al.getWidth() - 1);\r
 713 \r
 714       c.calculate();\r
 715       c.verdict(false, viewport.ConsPercGaps);\r
 716 \r
 717       ccs = new ConservationColourScheme(c, cs);\r
 718 \r
 719       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 720       ccs.setConsensus( viewport.vconsensus );\r
 721       viewport.setGlobalColourScheme(ccs);\r
 722 \r
 723       SliderPanel.setConservationSlider(alignPanel, ccs, "Background");\r
 724 \r
 725     }\r
 726     else\r
 727     {\r
 728         // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 729         if (cs != null)\r
 730           cs.setConsensus(viewport.vconsensus);\r
 731         viewport.setGlobalColourScheme(cs);\r
 732     }\r
 733 \r
 734 \r
 735     if(viewport.getColourAppliesToAllGroups())\r
 736     {\r
 737       Vector groups = viewport.alignment.getGroups();\r
 738       for(int i=0; i<groups.size(); i++)\r
 739       {\r
 740         SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
 741 \r
 742         if (cs instanceof ClustalxColourScheme)\r
 743         {\r
 744           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
 745         }\r
 746         else\r
 747           try\r
 748           {\r
 749             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
 750           }\r
 751           catch (Exception ex)\r
 752           {\r
 753             ex.printStackTrace();\r
 754             sg.cs = cs;\r
 755           }\r
 756 \r
 757         if(viewport.getAbovePIDThreshold())\r
 758         {\r
 759           if (sg.cs instanceof ResidueColourScheme)\r
 760             ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
 761           else if (sg.cs instanceof ScoreColourScheme)\r
 762             ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
 763 \r
 764            sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );\r
 765         }\r
 766 \r
 767         if( viewport.getConservationSelected() )\r
 768         {\r
 769           Conservation c = new Conservation("Group",\r
 770                                             ResidueProperties.propHash, 3,\r
 771                                             sg.sequences, 0, viewport.alignment.getWidth()-1);\r
 772           c.calculate();\r
 773           c.verdict(false, viewport.ConsPercGaps);\r
 774           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 775 \r
 776           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 777           ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 778           sg.cs = ccs;\r
 779         }\r
 780         else\r
 781         {\r
 782           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 783           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 784         }\r
 785 \r
 786       }\r
 787     }\r
 788 \r
 789     if(alignPanel.getOverviewPanel()!=null)\r
 790       alignPanel.getOverviewPanel().updateOverviewImage();\r
 791 \r
 792     alignPanel.repaint();\r
 793   }\r
 794 \r
 795   protected void modifyPID_actionPerformed(ActionEvent e)\r
 796   {\r
 797       if(viewport.getAbovePIDThreshold())\r
 798       {\r
 799         SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
 800                                    "Background");\r
 801         SliderPanel.showPIDSlider();\r
 802       }\r
 803   }\r
 804 \r
 805   protected void modifyConservation_actionPerformed(ActionEvent e)\r
 806   {\r
 807     if(viewport.getConservationSelected())\r
 808     {\r
 809       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
 810                                         "Background");\r
 811       SliderPanel.showConservationSlider();\r
 812     }\r
 813   }\r
 814 \r
 815 \r
 816   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 817   {\r
 818     viewport.setConservationSelected(conservationMenuItem.getState());\r
 819 \r
 820     viewport.setAbovePIDThreshold(false);\r
 821     abovePIDThreshold.setState(false);\r
 822 \r
 823    ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 824    if(cs instanceof ConservationColourScheme )\r
 825      changeColour( ((ConservationColourScheme)cs).cs );\r
 826     else\r
 827       changeColour( cs );\r
 828 \r
 829     modifyConservation_actionPerformed(null);\r
 830   }\r
 831 \r
 832   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 833   {\r
 834     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
 835 \r
 836     conservationMenuItem.setState(false);\r
 837     viewport.setConservationSelected(false);\r
 838 \r
 839     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 840 \r
 841     if(cs instanceof ConservationColourScheme )\r
 842         changeColour( ((ConservationColourScheme)cs).cs );\r
 843     else\r
 844         changeColour( cs );\r
 845 \r
 846     modifyPID_actionPerformed(null);\r
 847   }\r
 848 \r
 849 \r
 850 \r
 851   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 852   {\r
 853     UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);\r
 854   }\r
 855 \r
 856   public void PIDColour_actionPerformed(ActionEvent e)\r
 857   {\r
 858     changeColour( new PIDColourScheme() );\r
 859   }\r
 860 \r
 861 \r
 862   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 863   {\r
 864     changeColour(new Blosum62ColourScheme() );\r
 865   }\r
 866 \r
 867 \r
 868 \r
 869   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 870   {\r
 871     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment, HistoryItem.SORT));\r
 872     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 873     alignPanel.repaint();\r
 874   }\r
 875 \r
 876   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 877   {\r
 878     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, HistoryItem.SORT));\r
 879     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 880     alignPanel.repaint();\r
 881   }\r
 882 \r
 883   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 884   {\r
 885     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, HistoryItem.SORT));\r
 886     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 887     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 888     alignPanel.repaint();\r
 889   }\r
 890 \r
 891   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 892   {\r
 893     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 894     Frame frame = new Frame();\r
 895     frame.add(sp);\r
 896     jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection", 400, 120);\r
 897 \r
 898   }\r
 899 \r
 900   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 901   {\r
 902     if(viewport.getSelectionGroup().getSize()>1)\r
 903     {\r
 904       Frame frame = new Frame();\r
 905       frame.add(new PairwiseAlignPanel(viewport));\r
 906       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
 907     }\r
 908   }\r
 909 \r
 910   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 911   {\r
 912 \r
 913     if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)\r
 914        || viewport.getAlignment().getHeight()<4)\r
 915     {\r
 916       return;\r
 917     }\r
 918 \r
 919     try{\r
 920       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 921       Frame frame = new Frame();\r
 922       frame.add(pcaPanel);\r
 923       jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis", 400, 400);\r
 924    }catch(java.lang.OutOfMemoryError ex)\r
 925    {\r
 926    }\r
 927 \r
 928 \r
 929   }\r
 930 \r
 931   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 932   {\r
 933     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
 934   }\r
 935 \r
 936   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 937   {\r
 938     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
 939   }\r
 940 \r
 941 \r
 942   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 943   {\r
 944     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
 945   }\r
 946 \r
 947   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 948   {\r
 949     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
 950   }\r
 951 \r
 952   void NewTreePanel(String type, String pwType, String title)\r
 953   {\r
 954     //are the sequences aligned?\r
 955     if(!viewport.alignment.isAligned())\r
 956     {\r
 957       return;\r
 958     }\r
 959 \r
 960     final TreePanel tp;\r
 961     if (viewport.getSelectionGroup() != null &&\r
 962         viewport.getSelectionGroup().getSize() > 3)\r
 963     {\r
 964       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
 965                          pwType,\r
 966                          0, viewport.alignment.getWidth());\r
 967     }\r
 968     else\r
 969     {\r
 970       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
 971                          type, pwType, 0, viewport.alignment.getWidth());\r
 972     }\r
 973 \r
 974    addTreeMenuItem(tp, title);\r
 975 \r
 976    jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
 977   }\r
 978 \r
 979   void addTreeMenuItem(final TreePanel treePanel, String title)\r
 980   {\r
 981     final MenuItem item = new MenuItem(title);\r
 982     sortByTreeMenu.add(item);\r
 983     item.addActionListener(new java.awt.event.ActionListener()\r
 984     {\r
 985       public void actionPerformed(ActionEvent e)\r
 986       {\r
 987         addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
 988                                        HistoryItem.SORT));\r
 989         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
 990         alignPanel.repaint();\r
 991       }\r
 992     });\r
 993 \r
 994     treePanel.addWindowListener(new WindowAdapter()\r
 995     {\r
 996       public void windowClosing(WindowEvent e)\r
 997       {\r
 998         sortByTreeMenu.remove(item);\r
 999       };\r
1000     });\r
1001   }\r
1002 \r
1003   protected void documentation_actionPerformed(ActionEvent e) {\r
1004 \r
1005     jalview.bin.JalviewLite.showURL("http://www.jalview.org");\r
1006 \r
1007   }\r
1008 \r
1009   protected void about_actionPerformed(ActionEvent e)\r
1010   {\r
1011     class AboutPanel extends Canvas\r
1012     {\r
1013       public void paint(Graphics g)\r
1014       {\r
1015         g.setColor(Color.white);\r
1016         g.fillRect(0,0,getSize().width, getSize().height);\r
1017         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1018         FontMetrics fm = g.getFontMetrics();\r
1019         int fh = fm.getHeight();\r
1020         int y=20, x=7;\r
1021         g.setColor(Color.black);\r
1022         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1023         g.drawString("JalView - Release 2.0", 200,y+=fh);\r
1024         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1025         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",x,y+=fh*2);\r
1026         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",x,y+=fh);\r
1027         g.drawString("If  you use JalView, please cite:",x,y+=fh+8);\r
1028         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",x,y+=fh);\r
1029         g.drawString("Bioinformatics,  2004 12;426-7.",x,y+=fh);\r
1030       }\r
1031     }\r
1032     Frame frame = new Frame();\r
1033     frame.add(new AboutPanel());\r
1034     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580,200);\r
1035 \r
1036 \r
1037 \r
1038   }\r
1039 }\r