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 public class AlignFrame\r
  32     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.\r
  65             getCodeBase() + treeFile, "URL");\r
  66         fin.parse();\r
  67 \r
  68         if (fin.getTree() != null)\r
  69         {\r
  70           TreePanel tp = null;\r
  71           tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
  72                              fin, "FromFile", applet.getCodeBase() + treeFile);\r
  73           jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
  74           addTreeMenuItem(tp, treeFile);\r
  75         }\r
  76       }\r
  77       catch (Exception ex)\r
  78       {\r
  79         ex.printStackTrace();\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   protected void outputText_actionPerformed(ActionEvent e)\r
  94   {\r
  95     CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
  96     Frame frame = new Frame();\r
  97     frame.add(cap);\r
  98     jalview.bin.JalviewLite.addFrame(frame,\r
  99                                      "Alignment output - " + e.getActionCommand(),\r
 100                                      600, 500);\r
 101     cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),\r
 102                                               viewport.getAlignment().\r
 103                                               getSequences()));\r
 104   }\r
 105 \r
 106   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 107   {\r
 108     dispose();\r
 109   }\r
 110 \r
 111   Stack historyList = new Stack();\r
 112   Stack redoList = new Stack();\r
 113 \r
 114   void updateEditMenuBar()\r
 115   {\r
 116     if (historyList.size() > 0)\r
 117     {\r
 118       undoMenuItem.setEnabled(true);\r
 119       HistoryItem hi = (HistoryItem) historyList.peek();\r
 120       undoMenuItem.setLabel("Undo " + hi.getDescription());\r
 121     }\r
 122     else\r
 123     {\r
 124       undoMenuItem.setEnabled(false);\r
 125       undoMenuItem.setLabel("Undo");\r
 126     }\r
 127 \r
 128     if (redoList.size() > 0)\r
 129     {\r
 130       redoMenuItem.setEnabled(true);\r
 131       HistoryItem hi = (HistoryItem) redoList.peek();\r
 132       redoMenuItem.setLabel("Redo " + hi.getDescription());\r
 133     }\r
 134     else\r
 135     {\r
 136       redoMenuItem.setEnabled(false);\r
 137       redoMenuItem.setLabel("Redo");\r
 138     }\r
 139   }\r
 140 \r
 141   public void addHistoryItem(HistoryItem hi)\r
 142   {\r
 143     historyList.push(hi);\r
 144     updateEditMenuBar();\r
 145   }\r
 146 \r
 147   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 148   {\r
 149     HistoryItem hi = (HistoryItem) historyList.pop();\r
 150     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
 151                                   HistoryItem.HIDE));\r
 152     restoreHistoryItem(hi);\r
 153   }\r
 154 \r
 155   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 156   {\r
 157     HistoryItem hi = (HistoryItem) redoList.pop();\r
 158     restoreHistoryItem(hi);\r
 159     updateEditMenuBar();\r
 160     viewport.updateConsensus();\r
 161     alignPanel.repaint();\r
 162     alignPanel.repaint();\r
 163   }\r
 164 \r
 165   // used by undo and redo\r
 166   void restoreHistoryItem(HistoryItem hi)\r
 167   {\r
 168     if (hi.getType() == HistoryItem.SORT)\r
 169     {\r
 170       for (int i = 0; i < hi.getSequences().size(); i++)\r
 171       {\r
 172         viewport.alignment.getSequences().setElementAt(hi.getSequences().\r
 173             elementAt(i), i);\r
 174       }\r
 175     }\r
 176     else\r
 177     {\r
 178       for (int i = 0; i < hi.getSequences().size(); i++)\r
 179       {\r
 180         SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
 181         if (restore.getLength() == 0)\r
 182         {\r
 183           // log.System.out.println(hi.getHidden().elementAt(i));\r
 184           restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 185           viewport.alignment.getSequences().insertElementAt(\r
 186               restore,\r
 187               hi.getAlignIndex(i));\r
 188         }\r
 189         else\r
 190         {\r
 191           restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 192         }\r
 193       }\r
 194       if (hi.getType() == HistoryItem.PASTE)\r
 195       {\r
 196         for (int i = viewport.alignment.getHeight() - 1;\r
 197              i > hi.getSequences().size() - 1; i--)\r
 198         {\r
 199           viewport.alignment.deleteSequence(i);\r
 200         }\r
 201       }\r
 202     }\r
 203 \r
 204     updateEditMenuBar();\r
 205 \r
 206     viewport.updateConsensus();\r
 207     viewport.updateConservation();\r
 208     alignPanel.repaint();\r
 209   }\r
 210 \r
 211   public void moveSelectedSequences(boolean up)\r
 212   {\r
 213     SequenceGroup sg = viewport.getSelectionGroup();\r
 214     if (sg == null)\r
 215     {\r
 216       return;\r
 217     }\r
 218 \r
 219     if (up)\r
 220     {\r
 221       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 222       {\r
 223         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 224         if (!sg.sequences.contains(seq))\r
 225         {\r
 226           continue;\r
 227         }\r
 228 \r
 229         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 230         if (sg.sequences.contains(temp))\r
 231         {\r
 232           continue;\r
 233         }\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     else\r
 240     {\r
 241       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 242       {\r
 243         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 244         if (!sg.sequences.contains(seq))\r
 245         {\r
 246           continue;\r
 247         }\r
 248 \r
 249         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 250         if (sg.sequences.contains(temp))\r
 251         {\r
 252           continue;\r
 253         }\r
 254 \r
 255         viewport.alignment.getSequences().setElementAt(temp, i);\r
 256         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 257       }\r
 258     }\r
 259 \r
 260     alignPanel.repaint();\r
 261   }\r
 262 \r
 263   StringBuffer copiedSequences;\r
 264   protected void copy_actionPerformed(ActionEvent e)\r
 265   {\r
 266     if (viewport.getSelectionGroup() == null)\r
 267     {\r
 268       return;\r
 269     }\r
 270 \r
 271     SequenceGroup sg = viewport.getSelectionGroup();\r
 272     copiedSequences = new StringBuffer();\r
 273     Hashtable orderedSeqs = new Hashtable();\r
 274     for (int i = 0; i < sg.getSize(); i++)\r
 275     {\r
 276       SequenceI seq = sg.getSequenceAt(i);\r
 277       int index = viewport.alignment.findIndex(seq);\r
 278       orderedSeqs.put(index + "", seq);\r
 279     }\r
 280 \r
 281     int index = 0;\r
 282     for (int i = 0; i < sg.getSize(); i++)\r
 283     {\r
 284       SequenceI seq = null;\r
 285       while (seq == null)\r
 286       {\r
 287         if (orderedSeqs.containsKey(index + ""))\r
 288         {\r
 289           seq = (SequenceI) orderedSeqs.get(index + "");\r
 290           index++;\r
 291           break;\r
 292         }\r
 293         else\r
 294         {\r
 295           index++;\r
 296         }\r
 297       }\r
 298 \r
 299       copiedSequences.append(seq.getName() + "\t" +\r
 300                              seq.findPosition(sg.getStartRes()) + "\t"\r
 301                              + seq.findPosition(sg.getEndRes()) + "\t"\r
 302                              +\r
 303                              sg.getSequenceAt(i).getSequence(sg.getStartRes(),\r
 304           sg.getEndRes() + 1) + "\n");\r
 305     }\r
 306 \r
 307   }\r
 308 \r
 309   protected void pasteNew_actionPerformed(ActionEvent e)\r
 310   {\r
 311     paste(true);\r
 312   }\r
 313 \r
 314   protected void pasteThis_actionPerformed(ActionEvent e)\r
 315   {\r
 316     addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
 317                                    HistoryItem.PASTE));\r
 318     paste(false);\r
 319   }\r
 320 \r
 321   void paste(boolean newAlignment)\r
 322   {\r
 323     try\r
 324     {\r
 325       if (copiedSequences == null)\r
 326       {\r
 327         return;\r
 328       }\r
 329 \r
 330       StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
 331       Vector seqs = new Vector();\r
 332       while (st.hasMoreElements())\r
 333       {\r
 334         String name = st.nextToken();\r
 335         int start = Integer.parseInt(st.nextToken());\r
 336         int end = Integer.parseInt(st.nextToken());\r
 337         Sequence sequence = new Sequence(name, st.nextToken(), start, end);\r
 338 \r
 339         if (!newAlignment)\r
 340         {\r
 341           viewport.alignment.addSequence(sequence);\r
 342         }\r
 343         else\r
 344         {\r
 345           seqs.addElement(sequence);\r
 346         }\r
 347       }\r
 348 \r
 349       if (newAlignment)\r
 350       {\r
 351         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 352         for (int i = 0; i < seqs.size(); i++)\r
 353         {\r
 354           newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
 355         }\r
 356 \r
 357         AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);\r
 358         String newtitle = new String("Copied sequences");\r
 359         if (getTitle().startsWith("Copied sequences"))\r
 360         {\r
 361           newtitle = getTitle();\r
 362         }\r
 363         else\r
 364         {\r
 365           newtitle = newtitle.concat("- from " + getTitle());\r
 366         }\r
 367         jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
 368                                          NEW_WINDOW_HEIGHT);\r
 369       }\r
 370       else\r
 371       {\r
 372         viewport.setEndSeq(viewport.alignment.getHeight());\r
 373         viewport.alignment.getWidth();\r
 374         viewport.updateConservation();\r
 375         viewport.updateConsensus();\r
 376         alignPanel.repaint();\r
 377       }\r
 378 \r
 379     }\r
 380     catch (Exception ex)\r
 381     {} // could be anything being pasted in here\r
 382 \r
 383   }\r
 384 \r
 385   protected void cut_actionPerformed(ActionEvent e)\r
 386   {\r
 387     copy_actionPerformed(null);\r
 388     delete_actionPerformed(null);\r
 389   }\r
 390 \r
 391   protected void delete_actionPerformed(ActionEvent e)\r
 392   {\r
 393     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
 394                                    HistoryItem.HIDE));\r
 395     if (viewport.getSelectionGroup() == null)\r
 396     {\r
 397       return;\r
 398     }\r
 399 \r
 400     SequenceGroup sg = viewport.getSelectionGroup();\r
 401     for (int i = 0; i < sg.sequences.size(); i++)\r
 402     {\r
 403       SequenceI seq = sg.getSequenceAt(i);\r
 404       int index = viewport.getAlignment().findIndex(seq);\r
 405       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
 406 \r
 407       if (seq.getSequence().length() < 1)\r
 408       {\r
 409         viewport.getAlignment().deleteSequence(seq);\r
 410       }\r
 411       else\r
 412       {\r
 413         viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 414       }\r
 415     }\r
 416 \r
 417     viewport.setSelectionGroup(null);\r
 418     viewport.alignment.deleteGroup(sg);\r
 419     viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);\r
 420     if (viewport.getAlignment().getHeight() < 1)\r
 421     {\r
 422       try\r
 423       {\r
 424         this.setVisible(false);\r
 425       }\r
 426       catch (Exception ex)\r
 427       {}\r
 428     }\r
 429     viewport.updateConservation();\r
 430     viewport.updateConsensus();\r
 431     alignPanel.repaint();\r
 432 \r
 433   }\r
 434 \r
 435   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 436   {\r
 437     viewport.alignment.deleteAllGroups();\r
 438     viewport.setSelectionGroup(null);\r
 439 \r
 440     alignPanel.repaint();\r
 441   }\r
 442 \r
 443   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 444   {\r
 445     SequenceGroup sg = new SequenceGroup();\r
 446     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 447     {\r
 448       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
 449     }\r
 450     sg.setEndRes(viewport.alignment.getWidth());\r
 451     viewport.setSelectionGroup(sg);\r
 452     alignPanel.repaint();\r
 453     PaintRefresher.Refresh(null);\r
 454   }\r
 455 \r
 456   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 457   {\r
 458     viewport.setSelectionGroup(null);\r
 459     viewport.getColumnSelection().clear();\r
 460     viewport.setSelectionGroup(null);\r
 461     PaintRefresher.Refresh(null);\r
 462   }\r
 463 \r
 464   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 465   {\r
 466     SequenceGroup sg = viewport.getSelectionGroup();\r
 467     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 468     {\r
 469       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
 470     }\r
 471 \r
 472     PaintRefresher.Refresh(null);\r
 473   }\r
 474 \r
 475   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 476   {\r
 477     ColumnSelection colSel = viewport.getColumnSelection();\r
 478     if (colSel.size() > 0)\r
 479     {\r
 480       addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
 481                                      HistoryItem.HIDE));\r
 482       int min = colSel.getMin();\r
 483       viewport.getAlignment().trimLeft(min);\r
 484       colSel.compensateForEdit(0, min);\r
 485 \r
 486       if (viewport.getSelectionGroup() != null)\r
 487       {\r
 488         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 489       }\r
 490 \r
 491       Vector groups = viewport.alignment.getGroups();\r
 492       for (int i = 0; i < groups.size(); i++)\r
 493       {\r
 494         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 495         if (!sg.adjustForRemoveLeft(min))\r
 496         {\r
 497           viewport.alignment.deleteGroup(sg);\r
 498         }\r
 499       }\r
 500 \r
 501       alignPanel.repaint();\r
 502     }\r
 503   }\r
 504 \r
 505   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 506   {\r
 507     ColumnSelection colSel = viewport.getColumnSelection();\r
 508     if (colSel.size() > 0)\r
 509     {\r
 510       addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
 511                                      HistoryItem.HIDE));\r
 512       int max = colSel.getMax();\r
 513       viewport.getAlignment().trimRight(max);\r
 514       if (viewport.getSelectionGroup() != null)\r
 515       {\r
 516         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 517       }\r
 518 \r
 519       Vector groups = viewport.alignment.getGroups();\r
 520       for (int i = 0; i < groups.size(); i++)\r
 521       {\r
 522         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 523         if (!sg.adjustForRemoveRight(max))\r
 524         {\r
 525           viewport.alignment.deleteGroup(sg);\r
 526         }\r
 527       }\r
 528 \r
 529       alignPanel.repaint();\r
 530     }\r
 531 \r
 532   }\r
 533 \r
 534   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 535   {\r
 536     addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
 537                                    viewport.alignment,\r
 538                                    HistoryItem.HIDE));\r
 539     viewport.getAlignment().removeGaps();\r
 540     viewport.updateConservation();\r
 541     viewport.updateConsensus();\r
 542     alignPanel.repaint();\r
 543   }\r
 544 \r
 545   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 546   {\r
 547     addHistoryItem(new HistoryItem("Remove Gaps",\r
 548                                    viewport.alignment,\r
 549                                    HistoryItem.HIDE));\r
 550     SequenceI current;\r
 551     int jSize;\r
 552     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 553     {\r
 554       current = viewport.getAlignment().getSequenceAt(i);\r
 555       jSize = current.getLength();\r
 556       for (int j = 0; j < jSize; j++)\r
 557       {\r
 558         if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 559         {\r
 560           current.deleteCharAt(j);\r
 561           j--;\r
 562           jSize--;\r
 563         }\r
 564       }\r
 565     }\r
 566     viewport.updateConservation();\r
 567     viewport.updateConsensus();\r
 568     alignPanel.repaint();\r
 569   }\r
 570 \r
 571   public void findMenuItem_actionPerformed(ActionEvent e)\r
 572   {\r
 573     Finder finder = new Finder(alignPanel);\r
 574   }\r
 575 \r
 576   public void font_actionPerformed(ActionEvent e)\r
 577   {\r
 578     Frame frame = new Frame();\r
 579     FontChooser fc = new FontChooser(alignPanel, frame);\r
 580     frame.add(fc);\r
 581     jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);\r
 582 \r
 583   }\r
 584 \r
 585   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 586   {\r
 587     viewport.setShowFullId(fullSeqId.getState());\r
 588     alignPanel.fontChanged();\r
 589     alignPanel.repaint();\r
 590   }\r
 591 \r
 592   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 593   {\r
 594     viewport.setColourText(colourTextMenuItem.getState());\r
 595     alignPanel.repaint();\r
 596   }\r
 597 \r
 598   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 599   {\r
 600     viewport.setWrapAlignment(wrapMenuItem.getState());\r
 601     alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
 602     scaleAbove.setEnabled(wrapMenuItem.getState());\r
 603     scaleLeft.setEnabled(wrapMenuItem.getState());\r
 604     scaleRight.setEnabled(wrapMenuItem.getState());\r
 605     alignPanel.repaint();\r
 606   }\r
 607 \r
 608   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 609   {\r
 610     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
 611     alignPanel.repaint();\r
 612   }\r
 613 \r
 614   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 615   {\r
 616     viewport.setScaleLeftWrapped(scaleLeft.getState());\r
 617     alignPanel.repaint();\r
 618   }\r
 619 \r
 620   protected void scaleRight_actionPerformed(ActionEvent e)\r
 621   {\r
 622     viewport.setScaleRightWrapped(scaleRight.getState());\r
 623     alignPanel.repaint();\r
 624   }\r
 625 \r
 626   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 627   {\r
 628     viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
 629     alignPanel.repaint();\r
 630   }\r
 631 \r
 632   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 633   {\r
 634     viewport.setShowText(viewTextMenuItem.getState());\r
 635     alignPanel.repaint();\r
 636   }\r
 637 \r
 638   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 639   {\r
 640     viewport.setRenderGaps(renderGapsMenuItem.getState());\r
 641     alignPanel.repaint();\r
 642   }\r
 643 \r
 644   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 645   {\r
 646     if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment())\r
 647     {\r
 648       annotationPanelMenuItem.setState(false);\r
 649       return;\r
 650     }\r
 651     viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
 652     alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
 653   }\r
 654 \r
 655   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 656   {\r
 657     if (alignPanel.overviewPanel != null)\r
 658     {\r
 659       return;\r
 660     }\r
 661 \r
 662     Frame frame = new Frame();\r
 663     OverviewPanel overview = new OverviewPanel(alignPanel);\r
 664     frame.add(overview);\r
 665     // +50 must allow for applet frame window\r
 666     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
 667                                      overview.preferredSize().width,\r
 668                                      overview.preferredSize().height + 50);\r
 669 \r
 670     frame.pack();\r
 671     frame.addWindowListener(new WindowAdapter()\r
 672     {\r
 673       public void windowClosing(WindowEvent e)\r
 674       {\r
 675         alignPanel.setOverviewPanel(null);\r
 676       };\r
 677     });\r
 678 \r
 679     alignPanel.setOverviewPanel(overview);\r
 680 \r
 681   }\r
 682 \r
 683   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 684   {\r
 685     changeColour(null);\r
 686   }\r
 687 \r
 688   public void clustalColour_actionPerformed(ActionEvent e)\r
 689   {\r
 690     abovePIDThreshold.setState(false);\r
 691     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
 692                                           viewport.alignment.getWidth()));\r
 693   }\r
 694 \r
 695   public void zappoColour_actionPerformed(ActionEvent e)\r
 696   {\r
 697     changeColour(new ZappoColourScheme());\r
 698   }\r
 699 \r
 700   public void taylorColour_actionPerformed(ActionEvent e)\r
 701   {\r
 702     changeColour(new TaylorColourScheme());\r
 703   }\r
 704 \r
 705   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 706   {\r
 707     changeColour(new HydrophobicColourScheme());\r
 708   }\r
 709 \r
 710   public void helixColour_actionPerformed(ActionEvent e)\r
 711   {\r
 712     changeColour(new HelixColourScheme());\r
 713   }\r
 714 \r
 715   public void strandColour_actionPerformed(ActionEvent e)\r
 716   {\r
 717     changeColour(new StrandColourScheme());\r
 718   }\r
 719 \r
 720   public void turnColour_actionPerformed(ActionEvent e)\r
 721   {\r
 722     changeColour(new TurnColourScheme());\r
 723   }\r
 724 \r
 725   public void buriedColour_actionPerformed(ActionEvent e)\r
 726   {\r
 727     changeColour(new BuriedColourScheme());\r
 728   }\r
 729 \r
 730   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 731   {\r
 732     changeColour(new NucleotideColourScheme());\r
 733   }\r
 734 \r
 735   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 736   {\r
 737     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
 738   }\r
 739 \r
 740   void changeColour(ColourSchemeI cs)\r
 741   {\r
 742     int threshold = 0;\r
 743 \r
 744     if (viewport.getAbovePIDThreshold())\r
 745     {\r
 746       threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
 747 \r
 748       if (cs instanceof ResidueColourScheme)\r
 749       {\r
 750         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
 751       }\r
 752       else if (cs instanceof ScoreColourScheme)\r
 753       {\r
 754         ( (ScoreColourScheme) cs).setThreshold(threshold);\r
 755       }\r
 756 \r
 757       viewport.setGlobalColourScheme(cs);\r
 758     }\r
 759     else if (cs instanceof ResidueColourScheme)\r
 760     {\r
 761       ( (ResidueColourScheme) cs).setThreshold(0);\r
 762     }\r
 763     else if (cs instanceof ScoreColourScheme)\r
 764     {\r
 765       ( (ScoreColourScheme) cs).setThreshold(0);\r
 766     }\r
 767 \r
 768     if (viewport.getConservationSelected())\r
 769     {\r
 770       ConservationColourScheme ccs = null;\r
 771 \r
 772       Alignment al = (Alignment) viewport.alignment;\r
 773       Conservation c = new Conservation("All",\r
 774                                         ResidueProperties.propHash, 3,\r
 775                                         al.getSequences(), 0,\r
 776                                         al.getWidth() - 1);\r
 777 \r
 778       c.calculate();\r
 779       c.verdict(false, viewport.ConsPercGaps);\r
 780 \r
 781       ccs = new ConservationColourScheme(c, cs);\r
 782 \r
 783       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 784       ccs.setConsensus(viewport.vconsensus);\r
 785       viewport.setGlobalColourScheme(ccs);\r
 786 \r
 787       SliderPanel.setConservationSlider(alignPanel, ccs, "Background");\r
 788 \r
 789     }\r
 790     else\r
 791     {\r
 792       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 793       if (cs != null)\r
 794       {\r
 795         cs.setConsensus(viewport.vconsensus);\r
 796       }\r
 797       viewport.setGlobalColourScheme(cs);\r
 798     }\r
 799 \r
 800     if (viewport.getColourAppliesToAllGroups())\r
 801     {\r
 802       Vector groups = viewport.alignment.getGroups();\r
 803       for (int i = 0; i < groups.size(); i++)\r
 804       {\r
 805         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 806 \r
 807         if (cs instanceof ClustalxColourScheme)\r
 808         {\r
 809           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
 810         }\r
 811         else\r
 812         {\r
 813           try\r
 814           {\r
 815             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
 816           }\r
 817           catch (Exception ex)\r
 818           {\r
 819             ex.printStackTrace();\r
 820             sg.cs = cs;\r
 821           }\r
 822         }\r
 823 \r
 824         if (viewport.getAbovePIDThreshold())\r
 825         {\r
 826           if (sg.cs instanceof ResidueColourScheme)\r
 827           {\r
 828             ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
 829           }\r
 830           else if (sg.cs instanceof ScoreColourScheme)\r
 831           {\r
 832             ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
 833           }\r
 834 \r
 835           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 836         }\r
 837 \r
 838         if (viewport.getConservationSelected())\r
 839         {\r
 840           Conservation c = new Conservation("Group",\r
 841                                             ResidueProperties.propHash, 3,\r
 842                                             sg.sequences, 0,\r
 843                                             viewport.alignment.getWidth() - 1);\r
 844           c.calculate();\r
 845           c.verdict(false, viewport.ConsPercGaps);\r
 846           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 847 \r
 848           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 849           ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 850           sg.cs = ccs;\r
 851         }\r
 852         else\r
 853         {\r
 854           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 855           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 856         }\r
 857 \r
 858       }\r
 859     }\r
 860 \r
 861     if (alignPanel.getOverviewPanel() != null)\r
 862     {\r
 863       alignPanel.getOverviewPanel().updateOverviewImage();\r
 864     }\r
 865 \r
 866     alignPanel.repaint();\r
 867   }\r
 868 \r
 869   protected void modifyPID_actionPerformed(ActionEvent e)\r
 870   {\r
 871     if (viewport.getAbovePIDThreshold())\r
 872     {\r
 873       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
 874                                      "Background");\r
 875       SliderPanel.showPIDSlider();\r
 876     }\r
 877   }\r
 878 \r
 879   protected void modifyConservation_actionPerformed(ActionEvent e)\r
 880   {\r
 881     if (viewport.getConservationSelected())\r
 882     {\r
 883       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
 884                                         "Background");\r
 885       SliderPanel.showConservationSlider();\r
 886     }\r
 887   }\r
 888 \r
 889   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
 890   {\r
 891     viewport.setConservationSelected(conservationMenuItem.getState());\r
 892 \r
 893     viewport.setAbovePIDThreshold(false);\r
 894     abovePIDThreshold.setState(false);\r
 895 \r
 896     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 897     if (cs instanceof ConservationColourScheme)\r
 898     {\r
 899       changeColour( ( (ConservationColourScheme) cs).cs);\r
 900     }\r
 901     else\r
 902     {\r
 903       changeColour(cs);\r
 904     }\r
 905 \r
 906     modifyConservation_actionPerformed(null);\r
 907   }\r
 908 \r
 909   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 910   {\r
 911     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
 912 \r
 913     conservationMenuItem.setState(false);\r
 914     viewport.setConservationSelected(false);\r
 915 \r
 916     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 917 \r
 918     if (cs instanceof ConservationColourScheme)\r
 919     {\r
 920       changeColour( ( (ConservationColourScheme) cs).cs);\r
 921     }\r
 922     else\r
 923     {\r
 924       changeColour(cs);\r
 925     }\r
 926 \r
 927     modifyPID_actionPerformed(null);\r
 928   }\r
 929 \r
 930   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 931   {\r
 932     UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);\r
 933   }\r
 934 \r
 935   public void PIDColour_actionPerformed(ActionEvent e)\r
 936   {\r
 937     changeColour(new PIDColourScheme());\r
 938   }\r
 939 \r
 940   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 941   {\r
 942     changeColour(new Blosum62ColourScheme());\r
 943   }\r
 944 \r
 945   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 946   {\r
 947     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
 948                                    HistoryItem.SORT));\r
 949     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
 950                               viewport.getAlignment().getSequenceAt(0));\r
 951     alignPanel.repaint();\r
 952   }\r
 953 \r
 954   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 955   {\r
 956     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
 957                                    HistoryItem.SORT));\r
 958     AlignmentSorter.sortByID(viewport.getAlignment());\r
 959     alignPanel.repaint();\r
 960   }\r
 961 \r
 962   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 963   {\r
 964     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
 965                                    HistoryItem.SORT));\r
 966     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 967     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 968     alignPanel.repaint();\r
 969   }\r
 970 \r
 971   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 972   {\r
 973     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 974     Frame frame = new Frame();\r
 975     frame.add(sp);\r
 976     jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",\r
 977                                      400, 120);\r
 978 \r
 979   }\r
 980 \r
 981   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 982   {\r
 983     if (viewport.getSelectionGroup().getSize() > 1)\r
 984     {\r
 985       Frame frame = new Frame();\r
 986       frame.add(new PairwiseAlignPanel(viewport));\r
 987       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
 988     }\r
 989   }\r
 990 \r
 991   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 992   {\r
 993 \r
 994     if ( (viewport.getSelectionGroup() != null &&\r
 995           viewport.getSelectionGroup().getSize() < 4 &&\r
 996           viewport.getSelectionGroup().getSize() > 0)\r
 997         || viewport.getAlignment().getHeight() < 4)\r
 998     {\r
 999       return;\r
1000     }\r
1001 \r
1002     try\r
1003     {\r
1004       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
1005       Frame frame = new Frame();\r
1006       frame.add(pcaPanel);\r
1007       jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",\r
1008                                        400, 400);\r
1009     }\r
1010     catch (java.lang.OutOfMemoryError ex)\r
1011     {\r
1012     }\r
1013 \r
1014   }\r
1015 \r
1016   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1017   {\r
1018     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1019   }\r
1020 \r
1021   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1022   {\r
1023     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1024   }\r
1025 \r
1026   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1027   {\r
1028     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1029   }\r
1030 \r
1031   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1032   {\r
1033     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1034   }\r
1035 \r
1036   void NewTreePanel(String type, String pwType, String title)\r
1037   {\r
1038     //are the sequences aligned?\r
1039     if (!viewport.alignment.isAligned())\r
1040     {\r
1041       return;\r
1042     }\r
1043 \r
1044     final TreePanel tp;\r
1045     if (viewport.getSelectionGroup() != null &&\r
1046         viewport.getSelectionGroup().getSize() > 3)\r
1047     {\r
1048       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
1049                          pwType,\r
1050                          0, viewport.alignment.getWidth());\r
1051     }\r
1052     else\r
1053     {\r
1054       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1055                          type, pwType, 0, viewport.alignment.getWidth());\r
1056     }\r
1057 \r
1058     addTreeMenuItem(tp, title);\r
1059 \r
1060     jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
1061   }\r
1062 \r
1063   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1064   {\r
1065     final MenuItem item = new MenuItem(title);\r
1066     sortByTreeMenu.add(item);\r
1067     item.addActionListener(new java.awt.event.ActionListener()\r
1068     {\r
1069       public void actionPerformed(ActionEvent e)\r
1070       {\r
1071         addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1072                                        HistoryItem.SORT));\r
1073         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1074         alignPanel.repaint();\r
1075       }\r
1076     });\r
1077 \r
1078     treePanel.addWindowListener(new WindowAdapter()\r
1079     {\r
1080       public void windowClosing(WindowEvent e)\r
1081       {\r
1082         sortByTreeMenu.remove(item);\r
1083       };\r
1084     });\r
1085   }\r
1086 \r
1087   protected void documentation_actionPerformed(ActionEvent e)\r
1088   {\r
1089 \r
1090     jalview.bin.JalviewLite.showURL("http://www.jalview.org");\r
1091 \r
1092   }\r
1093 \r
1094   protected void about_actionPerformed(ActionEvent e)\r
1095   {\r
1096     class AboutPanel\r
1097         extends Canvas\r
1098     {\r
1099       public void paint(Graphics g)\r
1100       {\r
1101         g.setColor(Color.white);\r
1102         g.fillRect(0, 0, getSize().width, getSize().height);\r
1103         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1104         FontMetrics fm = g.getFontMetrics();\r
1105         int fh = fm.getHeight();\r
1106         int y = 5, x = 7;\r
1107         g.setColor(Color.black);\r
1108         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1109         g.drawString("JalView - Release 2.0", 200, y += fh);\r
1110         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1111         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
1112                      x, y += fh * 2);\r
1113         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
1114                      x, y += fh);\r
1115         g.drawString(\r
1116             "For any issues relating to Jalview, email help@jalview.org", x,\r
1117             y += fh);\r
1118         g.drawString("If  you use JalView, please cite:", x, y += fh + 8);\r
1119         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
1120                      x, y += fh);\r
1121         g.drawString("Bioinformatics,  2004 12;426-7.", x, y += fh);\r
1122       }\r
1123     }\r
1124 \r
1125     Frame frame = new Frame();\r
1126     frame.add(new AboutPanel());\r
1127     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
1128 \r
1129   }\r
1130 }\r