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