src/jalview/appletgui/AlignFrame.java

   1 /*\r
   2 * Jalview - A Sequence Alignment Editor and Viewer\r
   3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4 *\r
   5 * This program is free software; you can redistribute it and/or\r
   6 * modify it under the terms of the GNU General Public License\r
   7 * as published by the Free Software Foundation; either version 2\r
   8 * of the License, or (at your option) any later version.\r
   9 *\r
  10 * This program is distributed in the hope that it will be useful,\r
  11 * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13 * GNU General Public License for more details.\r
  14 *\r
  15 * You should have received a copy of the GNU General Public License\r
  16 * along with this program; if not, write to the Free Software\r
  17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18 */\r
  19 \r
  20 package jalview.appletgui;\r
  21 \r
  22 import jalview.jbappletgui.GAlignFrame;\r
  23 import jalview.schemes.*;\r
  24 import jalview.datamodel.*;\r
  25 import jalview.analysis.*;\r
  26 import jalview.io.*;\r
  27 import java.awt.*;\r
  28 import java.awt.event.*;\r
  29 import java.util.*;\r
  30 \r
  31 \r
  32 public class AlignFrame extends GAlignFrame\r
  33 {\r
  34   final AlignmentPanel alignPanel;\r
  35   final AlignViewport  viewport;\r
  36   public static final int NEW_WINDOW_WIDTH = 700;\r
  37   public static final int NEW_WINDOW_HEIGHT = 500;\r
  38   jalview.bin.JalviewLite applet;\r
  39 \r
  40   public AlignFrame(AlignmentI al)\r
  41   {\r
  42     this.applet = null;\r
  43     viewport = new AlignViewport(al, null);\r
  44     alignPanel = new AlignmentPanel(this, viewport);\r
  45     add(alignPanel);\r
  46     alignPanel.validate();\r
  47   }\r
  48 \r
  49   public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet)\r
  50   {\r
  51     this.applet = applet;\r
  52     viewport = new AlignViewport(al, applet);\r
  53     alignPanel = new AlignmentPanel(this, viewport);\r
  54     add(alignPanel);\r
  55     alignPanel.validate();\r
  56 \r
  57     String treeFile = applet.getParameter("treeFile");\r
  58     TreePanel treepanel = null;\r
  59     if (treeFile != null)\r
  60     {\r
  61       try\r
  62       {\r
  63         treeFile = treeFile;\r
  64         jalview.io.NewickFile fin = new jalview.io.NewickFile( applet.getCodeBase()+treeFile, "URL");\r
  65         fin.parse();\r
  66 \r
  67         if (fin.getTree() != null)\r
  68         {\r
  69           TreePanel tp = null;\r
  70           tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
  71                              fin, "FromFile", applet.getCodeBase()+treeFile);\r
  72           jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
  73           addTreeMenuItem(tp, treeFile);\r
  74         }\r
  75       }\r
  76       catch (Exception ex)\r
  77       {\r
  78         ex.printStackTrace();\r
  79       }\r
  80     }\r
  81 \r
  82 \r
  83   }\r
  84 \r
  85   public void inputText_actionPerformed(ActionEvent e)\r
  86   {\r
  87      CutAndPasteTransfer cap = new CutAndPasteTransfer(true);\r
  88      Frame frame = new Frame();\r
  89      frame.add(cap);\r
  90      jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500,500);\r
  91   }\r
  92 \r
  93 \r
  94   protected void outputText_actionPerformed(ActionEvent e)\r
  95   {\r
  96      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
  97      Frame frame = new Frame();\r
  98      frame.add(cap);\r
  99      jalview.bin.JalviewLite.addFrame(frame,"Alignment output - "+e.getActionCommand(),600, 500);\r
 100      cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
 101   }\r
 102 \r
 103   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 104   {\r
 105     dispose();\r
 106   }\r
 107 \r
 108   Stack historyList = new Stack();\r
 109   Stack redoList = new Stack();\r
 110 \r
 111   void updateEditMenuBar()\r
 112    {\r
 113      if(historyList.size()>0)\r
 114       {\r
 115         undoMenuItem.setEnabled(true);\r
 116         HistoryItem hi = (HistoryItem)historyList.peek();\r
 117         undoMenuItem.setLabel("Undo "+hi.getDescription());\r
 118       }\r
 119      else\r
 120      {\r
 121        undoMenuItem.setEnabled(false);\r
 122        undoMenuItem.setLabel("Undo");\r
 123      }\r
 124 \r
 125      if(redoList.size()>0)\r
 126       {\r
 127         redoMenuItem.setEnabled(true);\r
 128         HistoryItem hi = (HistoryItem)redoList.peek();\r
 129         redoMenuItem.setLabel("Redo "+hi.getDescription());\r
 130       }\r
 131      else\r
 132      {\r
 133        redoMenuItem.setEnabled(false);\r
 134        redoMenuItem.setLabel("Redo");\r
 135      }\r
 136    }\r
 137 \r
 138    public void addHistoryItem(HistoryItem hi)\r
 139    {\r
 140      historyList.push(hi);\r
 141      updateEditMenuBar();\r
 142    }\r
 143 \r
 144    protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 145    {\r
 146        HistoryItem hi = (HistoryItem)historyList.pop();\r
 147        redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment, HistoryItem.HIDE));\r
 148        restoreHistoryItem(hi);\r
 149    }\r
 150 \r
 151    protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 152    {\r
 153       HistoryItem hi = (HistoryItem)redoList.pop();\r
 154       restoreHistoryItem(hi);\r
 155       updateEditMenuBar();\r
 156       viewport.updateConsensus();\r
 157       alignPanel.repaint();\r
 158       alignPanel.repaint();\r
 159    }\r
 160 \r
 161 \r
 162    // used by undo and redo\r
 163    void restoreHistoryItem(HistoryItem hi)\r
 164    {\r
 165       if(hi.getType()== HistoryItem.SORT)\r
 166       {\r
 167            for(int i=0; i<hi.getSequences().size(); i++)\r
 168              viewport.alignment.getSequences().setElementAt(hi.getSequences().elementAt(i), i);\r
 169       }\r
 170       else\r
 171       {\r
 172         for (int i = 0; i < hi.getSequences().size(); i++)\r
 173         {\r
 174           SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
 175           if(restore.getLength()==0)\r
 176           {\r
 177             // log.System.out.println(hi.getHidden().elementAt(i));\r
 178             restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 179             viewport.alignment.getSequences().insertElementAt(\r
 180                restore,\r
 181                hi.getAlignIndex(i));\r
 182           }\r
 183           else\r
 184             restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 185         }\r
 186         if(hi.getType()==HistoryItem.PASTE)\r
 187         {\r
 188           for(int i=viewport.alignment.getHeight()-1;i>hi.getSequences().size()-1; i--)\r
 189             viewport.alignment.deleteSequence(i);\r
 190         }\r
 191       }\r
 192 \r
 193        updateEditMenuBar();\r
 194 \r
 195        viewport.updateConsensus();\r
 196        viewport.updateConservation();\r
 197        alignPanel.repaint();\r
 198    }\r
 199 \r
 200 \r
 201   public void moveSelectedSequences(boolean up)\r
 202   {\r
 203     SequenceGroup sg = viewport.getSelectionGroup();\r
 204     if (sg == null)\r
 205       return;\r
 206 \r
 207     if (up)\r
 208     {\r
 209       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 210       {\r
 211         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 212         if (!sg.sequences.contains(seq))\r
 213           continue;\r
 214 \r
 215         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 216         if (sg.sequences.contains(temp))\r
 217           continue;\r
 218 \r
 219         viewport.alignment.getSequences().setElementAt(temp, i);\r
 220         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 221       }\r
 222     }\r
 223     else\r
 224     {\r
 225       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 226       {\r
 227         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 228         if (!sg.sequences.contains(seq))\r
 229           continue;\r
 230 \r
 231         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 232         if (sg.sequences.contains(temp))\r
 233           continue;\r
 234 \r
 235         viewport.alignment.getSequences().setElementAt(temp, i);\r
 236         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 237       }\r
 238     }\r
 239 \r
 240     alignPanel.repaint();\r
 241   }\r
 242 \r
 243 \r
 244   StringBuffer copiedSequences;\r
 245   protected void copy_actionPerformed(ActionEvent e)\r
 246   {\r
 247    if(viewport.getSelectionGroup()==null)\r
 248      return;\r
 249 \r
 250    SequenceGroup sg = viewport.getSelectionGroup();\r
 251    copiedSequences = new StringBuffer();\r
 252    Hashtable orderedSeqs = new Hashtable();\r
 253    for(int i=0; i<sg.getSize(); i++)\r
 254    {\r
 255       SequenceI seq = sg.getSequenceAt(i);\r
 256       int index = viewport.alignment.findIndex(seq);\r
 257       orderedSeqs.put(index+"", seq);\r
 258    }\r
 259 \r
 260    int index=0;\r
 261    for(int i=0; i<sg.getSize(); i++)\r
 262    {\r
 263      SequenceI seq = null;\r
 264      while( seq == null )\r
 265      {\r
 266        if(orderedSeqs.containsKey(index+""))\r
 267        {\r
 268          seq = (SequenceI) orderedSeqs.get(index + "");\r
 269          index++;\r
 270          break;\r
 271        }\r
 272        else\r
 273          index++;\r
 274      }\r
 275 \r
 276          copiedSequences.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"\r
 277                         +seq.findPosition( sg.getEndRes() )+ "\t"\r
 278                         +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");\r
 279        }\r
 280 \r
 281   }\r
 282 \r
 283 \r
 284   protected void pasteNew_actionPerformed(ActionEvent e)\r
 285   {\r
 286     paste(true);\r
 287   }\r
 288 \r
 289   protected void pasteThis_actionPerformed(ActionEvent e)\r
 290   {\r
 291     addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, HistoryItem.PASTE));\r
 292     paste(false);\r
 293   }\r
 294 \r
 295   void paste(boolean newAlignment)\r
 296   {\r
 297     try{\r
 298       if (copiedSequences == null)\r
 299         return;\r
 300 \r
 301       StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
 302       Vector seqs = new Vector();\r
 303       while (st.hasMoreElements())\r
 304       {\r
 305         String name = st.nextToken();\r
 306         int start = Integer.parseInt(st.nextToken());\r
 307         int end = Integer.parseInt(st.nextToken());\r
 308         Sequence sequence = new Sequence(name,st.nextToken(), start, end);\r
 309 \r
 310         if(!newAlignment)\r
 311           viewport.alignment.addSequence(sequence);\r
 312         else\r
 313           seqs.addElement(sequence);\r
 314       }\r
 315 \r
 316       if(newAlignment)\r
 317       {\r
 318         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 319         for(int i=0; i<seqs.size(); i++)\r
 320          newSeqs[i] = (SequenceI)seqs.elementAt(i);\r
 321 \r
 322         AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);\r
 323         String newtitle = new String("Copied sequences");\r
 324         if( getTitle().startsWith("Copied sequences"))\r
 325          newtitle = getTitle();\r
 326        else\r
 327          newtitle = newtitle.concat("- from "+getTitle());\r
 328         jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
 329       }\r
 330       else\r
 331       {\r
 332         viewport.setEndSeq(viewport.alignment.getHeight());\r
 333         viewport.alignment.getWidth();\r
 334         viewport.updateConservation();\r
 335         viewport.updateConsensus();\r
 336         alignPanel.repaint();\r
 337       }\r
 338 \r
 339     }catch(Exception ex){}// could be anything being pasted in here\r
 340 \r
 341   }\r
 342 \r
 343 \r
 344   protected void cut_actionPerformed(ActionEvent e)\r
 345   {\r
 346     copy_actionPerformed(null);\r
 347     delete_actionPerformed(null);\r
 348   }\r
 349 \r
 350   protected void delete_actionPerformed(ActionEvent e)\r
 351   {\r
 352     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, HistoryItem.HIDE));\r
 353     if (viewport.getSelectionGroup() == null)\r
 354       return;\r
 355 \r
 356      SequenceGroup sg = viewport.getSelectionGroup();\r
 357      for (int i=0;i < sg.sequences.size(); i++)\r
 358      {\r
 359        SequenceI seq = sg.getSequenceAt(i);\r
 360        int index = viewport.getAlignment().findIndex(seq);\r
 361        seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);\r
 362 \r
 363        if(seq.getSequence().length()<1)\r
 364           viewport.getAlignment().deleteSequence(seq);\r
 365       else\r
 366           viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 367      }\r
 368 \r
 369      viewport.setSelectionGroup(null);\r
 370      viewport.alignment.deleteGroup(sg);\r
 371      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getSize().height);\r
 372      if(viewport.getAlignment().getHeight()<1)\r
 373      try\r
 374      {\r
 375        this.setVisible(false);\r
 376      }catch(Exception ex){}\r
 377    viewport.updateConservation();\r
 378    viewport.updateConsensus();\r
 379      alignPanel.repaint();\r
 380 \r
 381   }\r
 382 \r
 383 \r
 384 \r
 385   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 386   {\r
 387     viewport.alignment.deleteAllGroups();\r
 388     viewport.setSelectionGroup(null);\r
 389 \r
 390     alignPanel.repaint();\r
 391   }\r
 392 \r
 393 \r
 394 \r
 395   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 396   {\r
 397     SequenceGroup sg = new SequenceGroup();\r
 398     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 399       sg.addSequence( viewport.getAlignment().getSequenceAt(i));\r
 400     sg.setEndRes(viewport.alignment.getWidth());\r
 401     viewport.setSelectionGroup(sg);\r
 402     alignPanel.repaint();\r
 403     PaintRefresher.Refresh(null);\r
 404   }\r
 405 \r
 406   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 407   {\r
 408     viewport.setSelectionGroup(null);\r
 409     viewport.getColumnSelection().clear();\r
 410     viewport.setSelectionGroup(null);\r
 411     PaintRefresher.Refresh(null);\r
 412   }\r
 413 \r
 414   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 415   {\r
 416     SequenceGroup sg = viewport.getSelectionGroup();\r
 417     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 418       sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));\r
 419 \r
 420     PaintRefresher.Refresh(null);\r
 421   }\r
 422 \r
 423   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 424   {\r
 425     ColumnSelection colSel = viewport.getColumnSelection();\r
 426     if (colSel.size() > 0)\r
 427     {\r
 428       addHistoryItem(new HistoryItem("Remove Left",viewport.alignment,\r
 429                                      HistoryItem.HIDE));\r
 430       int min = colSel.getMin();\r
 431       viewport.getAlignment().trimLeft(min);\r
 432       colSel.compensateForEdit(0,min);\r
 433 \r
 434       if(viewport.getSelectionGroup()!=null)\r
 435         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 436 \r
 437       Vector groups = viewport.alignment.getGroups();\r
 438       for(int i=0; i<groups.size(); i++)\r
 439       {\r
 440         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 441         if(!sg.adjustForRemoveLeft(min))\r
 442           viewport.alignment.deleteGroup(sg);\r
 443       }\r
 444 \r
 445       alignPanel.repaint();\r
 446     }\r
 447   }\r
 448 \r
 449   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 450   {\r
 451     ColumnSelection colSel = viewport.getColumnSelection();\r
 452     if (colSel.size() > 0)\r
 453     {\r
 454       addHistoryItem(new HistoryItem("Remove Right",viewport.alignment,\r
 455                                      HistoryItem.HIDE));\r
 456       int max = colSel.getMax();\r
 457       viewport.getAlignment().trimRight(max);\r
 458       if(viewport.getSelectionGroup()!=null)\r
 459         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 460 \r
 461       Vector groups = viewport.alignment.getGroups();\r
 462       for(int i=0; i<groups.size(); i++)\r
 463       {\r
 464         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 465         if(!sg.adjustForRemoveRight(max))\r
 466           viewport.alignment.deleteGroup(sg);\r
 467       }\r
 468 \r
 469 \r
 470 \r
 471       alignPanel.repaint();\r
 472     }\r
 473 \r
 474   }\r
 475 \r
 476   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 477   {\r
 478     addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
 479                                    viewport.alignment,\r
 480                                    HistoryItem.HIDE));\r
 481     viewport.getAlignment().removeGaps();\r
 482     viewport.updateConservation();\r
 483     viewport.updateConsensus();\r
 484     alignPanel.repaint();\r
 485   }\r
 486 \r
 487   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 488   {\r
 489     addHistoryItem(new HistoryItem("Remove Gaps",\r
 490                                    viewport.alignment,\r
 491                                    HistoryItem.HIDE));\r
 492     SequenceI current;\r
 493     int jSize;\r
 494     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 495     {\r
 496       current = viewport.getAlignment().getSequenceAt(i);\r
 497       jSize = current.getLength();\r
 498       for (int j=0; j < jSize; j++)\r
 499         if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 500         {\r
 501           current.deleteCharAt(j);\r
 502           j--;\r
 503           jSize--;\r
 504         }\r
 505     }\r
 506     viewport.updateConservation();\r
 507     viewport.updateConsensus();\r
 508     alignPanel.repaint();\r
 509   }\r
 510 \r
 511 \r
 512   public void findMenuItem_actionPerformed(ActionEvent e)\r
 513   {\r
 514     Finder finder = new Finder(alignPanel);\r
 515   }\r
 516 \r
 517 \r
 518   public void font_actionPerformed(ActionEvent e)\r
 519   {\r
 520     Frame frame = new Frame();\r
 521     FontChooser fc = new FontChooser( alignPanel, frame);\r
 522     frame.add(fc);\r
 523     jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440,100);\r
 524 \r
 525   }\r
 526 \r
 527   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 528   {\r
 529     viewport.setShowFullId( fullSeqId.getState() );\r
 530     alignPanel.fontChanged();\r
 531     alignPanel.repaint();\r
 532   }\r
 533 \r
 534   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 535   {\r
 536       viewport.setColourText( colourTextMenuItem.getState() );\r
 537       alignPanel.repaint();\r
 538   }\r
 539 \r
 540   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 541   {\r
 542     viewport.setWrapAlignment( wrapMenuItem.getState() );\r
 543     alignPanel.setWrapAlignment( wrapMenuItem.getState() );\r
 544     scaleAbove.setEnabled( wrapMenuItem.getState() );\r
 545     scaleLeft.setEnabled( wrapMenuItem.getState());\r
 546     scaleRight.setEnabled( wrapMenuItem.getState());\r
 547     alignPanel.repaint();\r
 548   }\r
 549 \r
 550   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 551   {\r
 552     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
 553     alignPanel.repaint();\r
 554   }\r
 555 \r
 556   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 557   {\r
 558     viewport.setScaleLeftWrapped(scaleLeft.getState());\r
 559     alignPanel.repaint();\r
 560   }\r
 561 \r
 562   protected void scaleRight_actionPerformed(ActionEvent e)\r
 563   {\r
 564     viewport.setScaleRightWrapped(scaleRight.getState());\r
 565     alignPanel.repaint();\r
 566   }\r
 567 \r
 568 \r
 569 \r
 570   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 571   {\r
 572     viewport.setShowBoxes( viewBoxesMenuItem.getState() );\r
 573     alignPanel.repaint();\r
 574   }\r
 575 \r
 576   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 577   {\r
 578     viewport.setShowText( viewTextMenuItem.getState() );\r
 579     alignPanel.repaint();\r
 580   }\r
 581 \r
 582 \r
 583   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 584   {\r
 585     viewport.setRenderGaps(renderGapsMenuItem.getState());\r
 586     alignPanel.repaint();\r
 587   }\r
 588 \r
 589 \r
 590   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 591   {\r
 592     if(annotationPanelMenuItem.getState() && viewport.getWrapAlignment())\r
 593     {\r
 594       annotationPanelMenuItem.setState(false);\r
 595       return;\r
 596     }\r
 597     viewport.setShowAnnotation( annotationPanelMenuItem.getState() );\r
 598     alignPanel.setAnnotationVisible( annotationPanelMenuItem.getState() );\r
 599   }\r
 600 \r
 601   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 602   {\r
 603    if (alignPanel.overviewPanel != null)\r
 604       return;\r
 605 \r
 606     Frame frame = new Frame();\r
 607     OverviewPanel overview = new OverviewPanel(alignPanel);\r
 608     frame.add(overview);\r
 609     // +50 must allow for applet frame window\r
 610     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
 611                              overview.preferredSize().width, overview.preferredSize().height+50);\r
 612 \r
 613     frame.pack();\r
 614     frame.addWindowListener(new WindowAdapter()\r
 615     { public void windowClosing(WindowEvent e)\r
 616       {\r
 617             alignPanel.setOverviewPanel(null);\r
 618       };\r
 619     });\r
 620 \r
 621     alignPanel.setOverviewPanel( overview );\r
 622 \r
 623 \r
 624   }\r
 625 \r
 626   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 627   {\r
 628     changeColour( null );\r
 629   }\r
 630 \r
 631 \r
 632   public void clustalColour_actionPerformed(ActionEvent e)\r
 633   {\r
 634     abovePIDThreshold.setState(false);\r
 635     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 636   }\r
 637 \r
 638   public void zappoColour_actionPerformed(ActionEvent e)\r
 639   {\r
 640     changeColour(new ZappoColourScheme());\r
 641   }\r
 642 \r
 643   public void taylorColour_actionPerformed(ActionEvent e)\r
 644   {\r
 645     changeColour(new TaylorColourScheme());\r
 646   }\r
 647 \r
 648 \r
 649   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 650   {\r
 651     changeColour( new HydrophobicColourScheme() );\r
 652   }\r
 653 \r
 654   public void helixColour_actionPerformed(ActionEvent e)\r
 655   {\r
 656     changeColour(new HelixColourScheme() );\r
 657   }\r
 658 \r
 659 \r
 660   public void strandColour_actionPerformed(ActionEvent e)\r
 661   {\r
 662     changeColour(new StrandColourScheme());\r
 663   }\r
 664 \r
 665 \r
 666   public void turnColour_actionPerformed(ActionEvent e)\r
 667   {\r
 668     changeColour(new TurnColourScheme());\r
 669   }\r
 670 \r
 671 \r
 672   public void buriedColour_actionPerformed(ActionEvent e)\r
 673   {\r
 674     changeColour(new BuriedColourScheme() );\r
 675   }\r
 676 \r
 677   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 678   {\r
 679     changeColour(new NucleotideColourScheme());\r
 680   }\r
 681 \r
 682 \r
 683   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 684   {\r
 685     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
 686   }\r
 687 \r
 688 \r
 689 \r
 690   void changeColour(ColourSchemeI cs)\r
 691   {\r
 692     int threshold = 0;\r
 693 \r
 694     if ( viewport.getAbovePIDThreshold() )\r
 695     {\r
 696       threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
 697 \r
 698       if (cs instanceof ResidueColourScheme)\r
 699         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
 700       else if (cs instanceof ScoreColourScheme)\r
 701         ( (ScoreColourScheme) cs).setThreshold(threshold);\r
 702 \r
 703       viewport.setGlobalColourScheme(cs);\r
 704     }\r
 705     else if (cs instanceof ResidueColourScheme)\r
 706       ( (ResidueColourScheme) cs).setThreshold(0);\r
 707     else if (cs instanceof ScoreColourScheme)\r
 708       ( (ScoreColourScheme) cs).setThreshold(0);\r
 709 \r
 710 \r
 711 \r
 712     if (viewport.getConservationSelected())\r
 713     {\r
 714       ConservationColourScheme ccs = null;\r
 715 \r
 716       Alignment al = (Alignment) viewport.alignment;\r
 717       Conservation c = new Conservation("All",\r
 718                                         ResidueProperties.propHash, 3,\r
 719                                         al.getSequences(), 0,\r
 720                                         al.getWidth() - 1);\r
 721 \r
 722       c.calculate();\r
 723       c.verdict(false, viewport.ConsPercGaps);\r
 724 \r
 725       ccs = new ConservationColourScheme(c, cs);\r
 726 \r
 727       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 728       ccs.setConsensus( viewport.vconsensus );\r
 729       viewport.setGlobalColourScheme(ccs);\r
 730 \r
 731       SliderPanel.setConservationSlider(alignPanel, ccs, "Background");\r
 732 \r
 733     }\r
 734     else\r
 735     {\r
 736         // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 737         if (cs != null)\r
 738           cs.setConsensus(viewport.vconsensus);\r
 739         viewport.setGlobalColourScheme(cs);\r
 740     }\r
 741 \r
 742 \r
 743     if(viewport.getColourAppliesToAllGroups())\r
 744     {\r
 745       Vector groups = viewport.alignment.getGroups();\r
 746       for(int i=0; i<groups.size(); i++)\r
 747       {\r
 748         SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
 749 \r
 750         if (cs instanceof ClustalxColourScheme)\r
 751         {\r
 752           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
 753         }\r
 754         else\r
 755           try\r
 756           {\r
 757             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
 758           }\r
 759           catch (Exception ex)\r
 760           {\r
 761             ex.printStackTrace();\r
 762             sg.cs = cs;\r
 763           }\r
 764 \r
 765         if(viewport.getAbovePIDThreshold())\r
 766         {\r
 767           if (sg.cs instanceof ResidueColourScheme)\r
 768             ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
 769           else if (sg.cs instanceof ScoreColourScheme)\r
 770             ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
 771 \r
 772            sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );\r
 773         }\r
 774 \r
 775         if( viewport.getConservationSelected() )\r
 776         {\r
 777           Conservation c = new Conservation("Group",\r
 778                                             ResidueProperties.propHash, 3,\r
 779                                             sg.sequences, 0, viewport.alignment.getWidth()-1);\r
 780           c.calculate();\r
 781           c.verdict(false, viewport.ConsPercGaps);\r
 782           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 783 \r
 784           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 785           ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 786           sg.cs = ccs;\r
 787         }\r
 788         else\r
 789         {\r
 790           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 791           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 792         }\r
 793 \r
 794       }\r
 795     }\r
 796 \r
 797     if(alignPanel.getOverviewPanel()!=null)\r
 798       alignPanel.getOverviewPanel().updateOverviewImage();\r
 799 \r
 800     alignPanel.repaint();\r
 801   }\r
 802 \r
 803   protected void modifyPID_actionPerformed(ActionEvent e)\r
 804   {\r
 805       if(viewport.getAbovePIDThreshold())\r
 806       {\r
 807         SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
 808                                    "Background");\r
 809         SliderPanel.showPIDSlider();\r
 810       }\r
 811   }\r
 812 \r
 813   protected void modifyConservation_actionPerformed(ActionEvent e)\r
 814   {\r
 815     if(viewport.getConservationSelected())\r
 816     {\r
 817       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
 818                                         "Background");\r
 819       SliderPanel.showConservationSlider();\r
 820     }\r
 821   }\r
 822 \r
 823 \r
 824   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 825   {\r
 826     viewport.setConservationSelected(conservationMenuItem.getState());\r
 827 \r
 828     viewport.setAbovePIDThreshold(false);\r
 829     abovePIDThreshold.setState(false);\r
 830 \r
 831    ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 832    if(cs instanceof ConservationColourScheme )\r
 833      changeColour( ((ConservationColourScheme)cs).cs );\r
 834     else\r
 835       changeColour( cs );\r
 836 \r
 837     modifyConservation_actionPerformed(null);\r
 838   }\r
 839 \r
 840   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 841   {\r
 842     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
 843 \r
 844     conservationMenuItem.setState(false);\r
 845     viewport.setConservationSelected(false);\r
 846 \r
 847     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 848 \r
 849     if(cs instanceof ConservationColourScheme )\r
 850         changeColour( ((ConservationColourScheme)cs).cs );\r
 851     else\r
 852         changeColour( cs );\r
 853 \r
 854     modifyPID_actionPerformed(null);\r
 855   }\r
 856 \r
 857 \r
 858 \r
 859   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 860   {\r
 861     UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);\r
 862   }\r
 863 \r
 864   public void PIDColour_actionPerformed(ActionEvent e)\r
 865   {\r
 866     changeColour( new PIDColourScheme() );\r
 867   }\r
 868 \r
 869 \r
 870   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 871   {\r
 872     changeColour(new Blosum62ColourScheme() );\r
 873   }\r
 874 \r
 875 \r
 876 \r
 877   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 878   {\r
 879     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment, HistoryItem.SORT));\r
 880     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 881     alignPanel.repaint();\r
 882   }\r
 883 \r
 884   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 885   {\r
 886     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, HistoryItem.SORT));\r
 887     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 888     alignPanel.repaint();\r
 889   }\r
 890 \r
 891   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 892   {\r
 893     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, HistoryItem.SORT));\r
 894     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 895     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 896     alignPanel.repaint();\r
 897   }\r
 898 \r
 899   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 900   {\r
 901     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 902     Frame frame = new Frame();\r
 903     frame.add(sp);\r
 904     jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection", 400, 120);\r
 905 \r
 906   }\r
 907 \r
 908   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 909   {\r
 910     if(viewport.getSelectionGroup().getSize()>1)\r
 911     {\r
 912       Frame frame = new Frame();\r
 913       frame.add(new PairwiseAlignPanel(viewport));\r
 914       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
 915     }\r
 916   }\r
 917 \r
 918   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 919   {\r
 920 \r
 921     if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)\r
 922        || viewport.getAlignment().getHeight()<4)\r
 923     {\r
 924       return;\r
 925     }\r
 926 \r
 927     try{\r
 928       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 929       Frame frame = new Frame();\r
 930       frame.add(pcaPanel);\r
 931       jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis", 400, 400);\r
 932    }catch(java.lang.OutOfMemoryError ex)\r
 933    {\r
 934    }\r
 935 \r
 936 \r
 937   }\r
 938 \r
 939   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 940   {\r
 941     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
 942   }\r
 943 \r
 944   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 945   {\r
 946     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
 947   }\r
 948 \r
 949 \r
 950   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 951   {\r
 952     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
 953   }\r
 954 \r
 955   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 956   {\r
 957     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
 958   }\r
 959 \r
 960   void NewTreePanel(String type, String pwType, String title)\r
 961   {\r
 962     //are the sequences aligned?\r
 963     if(!viewport.alignment.isAligned())\r
 964     {\r
 965       return;\r
 966     }\r
 967 \r
 968     final TreePanel tp;\r
 969     if (viewport.getSelectionGroup() != null &&\r
 970         viewport.getSelectionGroup().getSize() > 3)\r
 971     {\r
 972       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
 973                          pwType,\r
 974                          0, viewport.alignment.getWidth());\r
 975     }\r
 976     else\r
 977     {\r
 978       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
 979                          type, pwType, 0, viewport.alignment.getWidth());\r
 980     }\r
 981 \r
 982    addTreeMenuItem(tp, title);\r
 983 \r
 984    jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
 985   }\r
 986 \r
 987   void addTreeMenuItem(final TreePanel treePanel, String title)\r
 988   {\r
 989     final MenuItem item = new MenuItem(title);\r
 990     sortByTreeMenu.add(item);\r
 991     item.addActionListener(new java.awt.event.ActionListener()\r
 992     {\r
 993       public void actionPerformed(ActionEvent e)\r
 994       {\r
 995         addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
 996                                        HistoryItem.SORT));\r
 997         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
 998         alignPanel.repaint();\r
 999       }\r
1000     });\r
1001 \r
1002     treePanel.addWindowListener(new WindowAdapter()\r
1003     {\r
1004       public void windowClosing(WindowEvent e)\r
1005       {\r
1006         sortByTreeMenu.remove(item);\r
1007       };\r
1008     });\r
1009   }\r
1010 \r
1011   protected void documentation_actionPerformed(ActionEvent e) {\r
1012 \r
1013     jalview.bin.JalviewLite.showURL("http://www.jalview.org");\r
1014 \r
1015   }\r
1016 \r
1017   protected void about_actionPerformed(ActionEvent e)\r
1018   {\r
1019     class AboutPanel extends Canvas\r
1020     {\r
1021       public void paint(Graphics g)\r
1022       {\r
1023         g.setColor(Color.white);\r
1024         g.fillRect(0,0,getSize().width, getSize().height);\r
1025         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1026         FontMetrics fm = g.getFontMetrics();\r
1027         int fh = fm.getHeight();\r
1028         int y=5, x=7;\r
1029         g.setColor(Color.black);\r
1030         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1031         g.drawString("JalView - Release 2.0", 200,y+=fh);\r
1032         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1033         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",x,y+=fh*2);\r
1034         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",x,y+=fh);\r
1035         g.drawString("For any issues relating to Jalview, email help@jalview.org", x,y+=fh);\r
1036         g.drawString("If  you use JalView, please cite:",x,y+=fh+8);\r
1037         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",x,y+=fh);\r
1038         g.drawString("Bioinformatics,  2004 12;426-7.",x,y+=fh);\r
1039       }\r
1040     }\r
1041     Frame frame = new Frame();\r
1042     frame.add(new AboutPanel());\r
1043     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580,200);\r
1044 \r
1045 \r
1046 \r
1047   }\r
1048 }\r