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 \r
  86   public void inputText_actionPerformed(ActionEvent e)\r
  87   {\r
  88     CutAndPasteTransfer cap = new CutAndPasteTransfer(true);\r
  89     Frame frame = new Frame();\r
  90     frame.add(cap);\r
  91     jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\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,\r
 100                                      "Alignment output - " + e.getActionCommand(),\r
 101                                      600, 500);\r
 102     cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),\r
 103                                               viewport.getAlignment().\r
 104                                               getSequences()));\r
 105   }\r
 106 \r
 107   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 108   {\r
 109     dispose();\r
 110   }\r
 111 \r
 112   Stack historyList = new Stack();\r
 113   Stack redoList = new Stack();\r
 114 \r
 115   void updateEditMenuBar()\r
 116   {\r
 117     if (historyList.size() > 0)\r
 118     {\r
 119       undoMenuItem.setEnabled(true);\r
 120       HistoryItem hi = (HistoryItem) historyList.peek();\r
 121       undoMenuItem.setLabel("Undo " + hi.getDescription());\r
 122     }\r
 123     else\r
 124     {\r
 125       undoMenuItem.setEnabled(false);\r
 126       undoMenuItem.setLabel("Undo");\r
 127     }\r
 128 \r
 129     if (redoList.size() > 0)\r
 130     {\r
 131       redoMenuItem.setEnabled(true);\r
 132       HistoryItem hi = (HistoryItem) redoList.peek();\r
 133       redoMenuItem.setLabel("Redo " + hi.getDescription());\r
 134     }\r
 135     else\r
 136     {\r
 137       redoMenuItem.setEnabled(false);\r
 138       redoMenuItem.setLabel("Redo");\r
 139     }\r
 140   }\r
 141 \r
 142   public void addHistoryItem(HistoryItem hi)\r
 143   {\r
 144     historyList.push(hi);\r
 145     updateEditMenuBar();\r
 146   }\r
 147 \r
 148   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 149   {\r
 150     HistoryItem hi = (HistoryItem) historyList.pop();\r
 151     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
 152                                   HistoryItem.HIDE));\r
 153     restoreHistoryItem(hi);\r
 154   }\r
 155 \r
 156   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 157   {\r
 158     HistoryItem hi = (HistoryItem) redoList.pop();\r
 159     restoreHistoryItem(hi);\r
 160     updateEditMenuBar();\r
 161     viewport.updateConsensus();\r
 162     alignPanel.repaint();\r
 163     alignPanel.repaint();\r
 164   }\r
 165 \r
 166   // used by undo and redo\r
 167   void restoreHistoryItem(HistoryItem hi)\r
 168   {\r
 169     if (hi.getType() == HistoryItem.SORT)\r
 170     {\r
 171       for (int i = 0; i < hi.getSequences().size(); i++)\r
 172       {\r
 173         viewport.alignment.getSequences().setElementAt(hi.getSequences().\r
 174             elementAt(i), i);\r
 175       }\r
 176     }\r
 177     else\r
 178     {\r
 179       for (int i = 0; i < hi.getSequences().size(); i++)\r
 180       {\r
 181         SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
 182         if (restore.getLength() == 0)\r
 183         {\r
 184           // log.System.out.println(hi.getHidden().elementAt(i));\r
 185           restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 186           viewport.alignment.getSequences().insertElementAt(\r
 187               restore,\r
 188               hi.getAlignIndex(i));\r
 189         }\r
 190         else\r
 191         {\r
 192           restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 193         }\r
 194       }\r
 195       if (hi.getType() == HistoryItem.PASTE)\r
 196       {\r
 197         for (int i = viewport.alignment.getHeight() - 1;\r
 198              i > hi.getSequences().size() - 1; i--)\r
 199         {\r
 200           viewport.alignment.deleteSequence(i);\r
 201         }\r
 202       }\r
 203     }\r
 204 \r
 205     updateEditMenuBar();\r
 206 \r
 207     viewport.updateConsensus();\r
 208     viewport.updateConservation();\r
 209     alignPanel.repaint();\r
 210   }\r
 211 \r
 212   public void moveSelectedSequences(boolean up)\r
 213   {\r
 214     SequenceGroup sg = viewport.getSelectionGroup();\r
 215     if (sg == null)\r
 216     {\r
 217       return;\r
 218     }\r
 219 \r
 220     if (up)\r
 221     {\r
 222       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 223       {\r
 224         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 225         if (!sg.sequences.contains(seq))\r
 226         {\r
 227           continue;\r
 228         }\r
 229 \r
 230         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 231         if (sg.sequences.contains(temp))\r
 232         {\r
 233           continue;\r
 234         }\r
 235 \r
 236         viewport.alignment.getSequences().setElementAt(temp, i);\r
 237         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 238       }\r
 239     }\r
 240     else\r
 241     {\r
 242       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 243       {\r
 244         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 245         if (!sg.sequences.contains(seq))\r
 246         {\r
 247           continue;\r
 248         }\r
 249 \r
 250         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 251         if (sg.sequences.contains(temp))\r
 252         {\r
 253           continue;\r
 254         }\r
 255 \r
 256         viewport.alignment.getSequences().setElementAt(temp, i);\r
 257         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 258       }\r
 259     }\r
 260 \r
 261     alignPanel.repaint();\r
 262   }\r
 263 \r
 264   StringBuffer copiedSequences;\r
 265   protected void copy_actionPerformed(ActionEvent e)\r
 266   {\r
 267     if (viewport.getSelectionGroup() == null)\r
 268     {\r
 269       return;\r
 270     }\r
 271 \r
 272     SequenceGroup sg = viewport.getSelectionGroup();\r
 273     copiedSequences = new StringBuffer();\r
 274     Hashtable orderedSeqs = new Hashtable();\r
 275     for (int i = 0; i < sg.getSize(); i++)\r
 276     {\r
 277       SequenceI seq = sg.getSequenceAt(i);\r
 278       int index = viewport.alignment.findIndex(seq);\r
 279       orderedSeqs.put(index + "", seq);\r
 280     }\r
 281 \r
 282     int index = 0, startRes, endRes;\r
 283     char ch;\r
 284 \r
 285     for (int i = 0; i < sg.getSize(); i++)\r
 286     {\r
 287         SequenceI seq = null;\r
 288 \r
 289         while (seq == null)\r
 290         {\r
 291             if (orderedSeqs.containsKey(index + ""))\r
 292             {\r
 293                 seq = (SequenceI) orderedSeqs.get(index + "");\r
 294                 index++;\r
 295 \r
 296                 break;\r
 297             }\r
 298             else\r
 299             {\r
 300                 index++;\r
 301             }\r
 302         }\r
 303 \r
 304         //FIND START RES\r
 305         //Returns residue following index if gap\r
 306         startRes = seq.findPosition(sg.getStartRes());\r
 307 \r
 308         //FIND END RES\r
 309         //Need to find the residue preceeding index if gap\r
 310         endRes = 0;\r
 311 \r
 312         for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
 313         {\r
 314           ch = seq.getCharAt(j);\r
 315           if (!jalview.util.Comparison.isGap( (ch)))\r
 316           {\r
 317             endRes++;\r
 318           }\r
 319         }\r
 320 \r
 321         if(endRes>0)\r
 322         {\r
 323           endRes += seq.getStart() -1;\r
 324         }\r
 325 \r
 326         copiedSequences.append(seq.getName() + "\t" +\r
 327             startRes + "\t" +\r
 328             endRes + "\t" +\r
 329             seq.getSequence(sg.getStartRes(),\r
 330                 sg.getEndRes() + 1) + "\n");\r
 331     }\r
 332 \r
 333   }\r
 334 \r
 335   protected void pasteNew_actionPerformed(ActionEvent e)\r
 336   {\r
 337     paste(true);\r
 338   }\r
 339 \r
 340   protected void pasteThis_actionPerformed(ActionEvent e)\r
 341   {\r
 342     addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
 343                                    HistoryItem.PASTE));\r
 344     paste(false);\r
 345   }\r
 346 \r
 347   void paste(boolean newAlignment)\r
 348   {\r
 349     try\r
 350     {\r
 351       if (copiedSequences == null)\r
 352       {\r
 353         return;\r
 354       }\r
 355 \r
 356       StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
 357       Vector seqs = new Vector();\r
 358       while (st.hasMoreElements())\r
 359       {\r
 360         String name = st.nextToken();\r
 361         int start = Integer.parseInt(st.nextToken());\r
 362         int end = Integer.parseInt(st.nextToken());\r
 363         Sequence sequence = new Sequence(name, st.nextToken(), start, end);\r
 364 \r
 365         if (!newAlignment)\r
 366         {\r
 367           viewport.alignment.addSequence(sequence);\r
 368         }\r
 369         else\r
 370         {\r
 371           seqs.addElement(sequence);\r
 372         }\r
 373       }\r
 374 \r
 375       if (newAlignment)\r
 376       {\r
 377         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 378         for (int i = 0; i < seqs.size(); i++)\r
 379         {\r
 380           newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
 381         }\r
 382 \r
 383         AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);\r
 384         String newtitle = new String("Copied sequences");\r
 385         if (getTitle().startsWith("Copied sequences"))\r
 386         {\r
 387           newtitle = getTitle();\r
 388         }\r
 389         else\r
 390         {\r
 391           newtitle = newtitle.concat("- from " + getTitle());\r
 392         }\r
 393         jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
 394                                          NEW_WINDOW_HEIGHT);\r
 395       }\r
 396       else\r
 397       {\r
 398         viewport.setEndSeq(viewport.alignment.getHeight());\r
 399         viewport.alignment.getWidth();\r
 400         viewport.updateConservation();\r
 401         viewport.updateConsensus();\r
 402         alignPanel.repaint();\r
 403       }\r
 404 \r
 405     }\r
 406     catch (Exception ex)\r
 407     {} // could be anything being pasted in here\r
 408 \r
 409   }\r
 410 \r
 411   protected void cut_actionPerformed(ActionEvent e)\r
 412   {\r
 413     copy_actionPerformed(null);\r
 414     delete_actionPerformed(null);\r
 415   }\r
 416 \r
 417   protected void delete_actionPerformed(ActionEvent e)\r
 418   {\r
 419     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
 420                                    HistoryItem.HIDE));\r
 421     if (viewport.getSelectionGroup() == null)\r
 422     {\r
 423       return;\r
 424     }\r
 425 \r
 426 \r
 427     SequenceGroup sg = viewport.getSelectionGroup();\r
 428     boolean allSequences = false;\r
 429     if(sg.sequences.size()==viewport.alignment.getHeight())\r
 430           allSequences = true;\r
 431 \r
 432     for (int i = 0; i < sg.sequences.size(); i++)\r
 433     {\r
 434       SequenceI seq = sg.getSequenceAt(i);\r
 435       int index = viewport.getAlignment().findIndex(seq);\r
 436       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
 437 \r
 438       // If the cut affects all sequences, remove highlighted columns\r
 439       if (allSequences)\r
 440       {\r
 441         viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
 442                                                      sg.getEndRes() + 1);\r
 443       }\r
 444 \r
 445 \r
 446       if (seq.getSequence().length() < 1)\r
 447       {\r
 448         viewport.getAlignment().deleteSequence(seq);\r
 449       }\r
 450       else\r
 451       {\r
 452         viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 453       }\r
 454     }\r
 455 \r
 456     viewport.setSelectionGroup(null);\r
 457     viewport.alignment.deleteGroup(sg);\r
 458     viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);\r
 459     if (viewport.getAlignment().getHeight() < 1)\r
 460     {\r
 461       try\r
 462       {\r
 463         this.setVisible(false);\r
 464       }\r
 465       catch (Exception ex)\r
 466       {}\r
 467     }\r
 468     viewport.updateConservation();\r
 469     viewport.updateConsensus();\r
 470     alignPanel.repaint();\r
 471 \r
 472   }\r
 473 \r
 474   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 475   {\r
 476     viewport.alignment.deleteAllGroups();\r
 477     viewport.setSelectionGroup(null);\r
 478 \r
 479     alignPanel.repaint();\r
 480   }\r
 481 \r
 482   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 483   {\r
 484     SequenceGroup sg = new SequenceGroup();\r
 485     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 486     {\r
 487       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
 488     }\r
 489     sg.setEndRes(viewport.alignment.getWidth());\r
 490     viewport.setSelectionGroup(sg);\r
 491     alignPanel.repaint();\r
 492     PaintRefresher.Refresh(null);\r
 493   }\r
 494 \r
 495   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 496   {\r
 497     viewport.setSelectionGroup(null);\r
 498     viewport.getColumnSelection().clear();\r
 499     viewport.setSelectionGroup(null);\r
 500     PaintRefresher.Refresh(null);\r
 501   }\r
 502 \r
 503   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 504   {\r
 505     SequenceGroup sg = viewport.getSelectionGroup();\r
 506     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 507     {\r
 508       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
 509     }\r
 510 \r
 511     PaintRefresher.Refresh(null);\r
 512   }\r
 513 \r
 514   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 515   {\r
 516     ColumnSelection colSel = viewport.getColumnSelection();\r
 517     if (colSel.size() > 0)\r
 518     {\r
 519       addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
 520                                      HistoryItem.HIDE));\r
 521       int min = colSel.getMin();\r
 522       viewport.getAlignment().trimLeft(min);\r
 523       colSel.compensateForEdit(0, min);\r
 524 \r
 525       if (viewport.getSelectionGroup() != null)\r
 526       {\r
 527         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 528       }\r
 529 \r
 530       Vector groups = viewport.alignment.getGroups();\r
 531       for (int i = 0; i < groups.size(); i++)\r
 532       {\r
 533         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 534         if (!sg.adjustForRemoveLeft(min))\r
 535         {\r
 536           viewport.alignment.deleteGroup(sg);\r
 537         }\r
 538       }\r
 539 \r
 540       alignPanel.repaint();\r
 541     }\r
 542   }\r
 543 \r
 544   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 545   {\r
 546     ColumnSelection colSel = viewport.getColumnSelection();\r
 547     if (colSel.size() > 0)\r
 548     {\r
 549       addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
 550                                      HistoryItem.HIDE));\r
 551       int max = colSel.getMax();\r
 552       viewport.getAlignment().trimRight(max);\r
 553       if (viewport.getSelectionGroup() != null)\r
 554       {\r
 555         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 556       }\r
 557 \r
 558       Vector groups = viewport.alignment.getGroups();\r
 559       for (int i = 0; i < groups.size(); i++)\r
 560       {\r
 561         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 562         if (!sg.adjustForRemoveRight(max))\r
 563         {\r
 564           viewport.alignment.deleteGroup(sg);\r
 565         }\r
 566       }\r
 567 \r
 568       alignPanel.repaint();\r
 569     }\r
 570 \r
 571   }\r
 572 \r
 573   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 574   {\r
 575     addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
 576                                    viewport.alignment,\r
 577                                    HistoryItem.HIDE));\r
 578     viewport.getAlignment().removeGaps();\r
 579     viewport.updateConservation();\r
 580     viewport.updateConsensus();\r
 581     alignPanel.repaint();\r
 582   }\r
 583 \r
 584   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 585   {\r
 586     addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
 587                                    HistoryItem.HIDE));\r
 588 \r
 589     SequenceI current;\r
 590     int jSize;\r
 591 \r
 592     Vector seqs=null;\r
 593 \r
 594     int start=0, end = viewport.alignment.getWidth();\r
 595 \r
 596     if (viewport.getSelectionGroup() != null\r
 597         && viewport.getSelectionGroup().sequences != null\r
 598         && viewport.getSelectionGroup().sequences.size()>0)\r
 599     {\r
 600       seqs = viewport.getSelectionGroup().sequences;\r
 601       start = viewport.getSelectionGroup().getStartRes();\r
 602       end = viewport.getSelectionGroup().getEndRes();\r
 603     }\r
 604     else\r
 605       seqs = viewport.alignment.getSequences();\r
 606 \r
 607     for (int i = 0; i <seqs.size(); i++)\r
 608     {\r
 609       current = (SequenceI)seqs.elementAt(i);\r
 610       jSize = current.getLength();\r
 611 \r
 612       int j = start;\r
 613       do\r
 614       {\r
 615         if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 616         {\r
 617           current.deleteCharAt(j);\r
 618           j--;\r
 619           jSize--;\r
 620         }\r
 621         j++;\r
 622       }\r
 623       while(j < end && j < jSize) ;\r
 624     }\r
 625 \r
 626     viewport.updateConservation();\r
 627     viewport.updateConsensus();\r
 628     alignPanel.repaint();\r
 629   }\r
 630 \r
 631 \r
 632   public void findMenuItem_actionPerformed(ActionEvent e)\r
 633   {\r
 634     Finder finder = new Finder(alignPanel);\r
 635   }\r
 636 \r
 637   public void font_actionPerformed(ActionEvent e)\r
 638   {\r
 639     Frame frame = new Frame();\r
 640     FontChooser fc = new FontChooser(alignPanel, frame);\r
 641     frame.add(fc);\r
 642     jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);\r
 643 \r
 644   }\r
 645 \r
 646   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 647   {\r
 648     viewport.setShowFullId(fullSeqId.getState());\r
 649     alignPanel.fontChanged();\r
 650     alignPanel.repaint();\r
 651   }\r
 652 \r
 653   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 654   {\r
 655     viewport.setColourText(colourTextMenuItem.getState());\r
 656     alignPanel.repaint();\r
 657   }\r
 658 \r
 659   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 660   {\r
 661     viewport.setWrapAlignment(wrapMenuItem.getState());\r
 662     alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
 663     scaleAbove.setEnabled(wrapMenuItem.getState());\r
 664     scaleLeft.setEnabled(wrapMenuItem.getState());\r
 665     scaleRight.setEnabled(wrapMenuItem.getState());\r
 666     alignPanel.repaint();\r
 667   }\r
 668 \r
 669   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 670   {\r
 671     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
 672     alignPanel.repaint();\r
 673   }\r
 674 \r
 675   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 676   {\r
 677     viewport.setScaleLeftWrapped(scaleLeft.getState());\r
 678     alignPanel.repaint();\r
 679   }\r
 680 \r
 681   protected void scaleRight_actionPerformed(ActionEvent e)\r
 682   {\r
 683     viewport.setScaleRightWrapped(scaleRight.getState());\r
 684     alignPanel.repaint();\r
 685   }\r
 686 \r
 687   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 688   {\r
 689     viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
 690     alignPanel.repaint();\r
 691   }\r
 692 \r
 693   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 694   {\r
 695     viewport.setShowText(viewTextMenuItem.getState());\r
 696     alignPanel.repaint();\r
 697   }\r
 698 \r
 699   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 700   {\r
 701     viewport.setRenderGaps(renderGapsMenuItem.getState());\r
 702     alignPanel.repaint();\r
 703   }\r
 704 \r
 705   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 706   {\r
 707     if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment())\r
 708     {\r
 709       annotationPanelMenuItem.setState(false);\r
 710       return;\r
 711     }\r
 712     viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
 713     alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
 714   }\r
 715 \r
 716   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 717   {\r
 718     if (alignPanel.overviewPanel != null)\r
 719     {\r
 720       return;\r
 721     }\r
 722 \r
 723     Frame frame = new Frame();\r
 724     OverviewPanel overview = new OverviewPanel(alignPanel);\r
 725     frame.add(overview);\r
 726     // +50 must allow for applet frame window\r
 727     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
 728                                      overview.preferredSize().width,\r
 729                                      overview.preferredSize().height + 50);\r
 730 \r
 731     frame.pack();\r
 732     frame.addWindowListener(new WindowAdapter()\r
 733     {\r
 734       public void windowClosing(WindowEvent e)\r
 735       {\r
 736         alignPanel.setOverviewPanel(null);\r
 737       };\r
 738     });\r
 739 \r
 740     alignPanel.setOverviewPanel(overview);\r
 741 \r
 742   }\r
 743 \r
 744   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 745   {\r
 746     changeColour(null);\r
 747   }\r
 748 \r
 749   public void clustalColour_actionPerformed(ActionEvent e)\r
 750   {\r
 751     abovePIDThreshold.setState(false);\r
 752     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
 753                                           viewport.alignment.getWidth()));\r
 754   }\r
 755 \r
 756   public void zappoColour_actionPerformed(ActionEvent e)\r
 757   {\r
 758     changeColour(new ZappoColourScheme());\r
 759   }\r
 760 \r
 761   public void taylorColour_actionPerformed(ActionEvent e)\r
 762   {\r
 763     changeColour(new TaylorColourScheme());\r
 764   }\r
 765 \r
 766   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 767   {\r
 768     changeColour(new HydrophobicColourScheme());\r
 769   }\r
 770 \r
 771   public void helixColour_actionPerformed(ActionEvent e)\r
 772   {\r
 773     changeColour(new HelixColourScheme());\r
 774   }\r
 775 \r
 776   public void strandColour_actionPerformed(ActionEvent e)\r
 777   {\r
 778     changeColour(new StrandColourScheme());\r
 779   }\r
 780 \r
 781   public void turnColour_actionPerformed(ActionEvent e)\r
 782   {\r
 783     changeColour(new TurnColourScheme());\r
 784   }\r
 785 \r
 786   public void buriedColour_actionPerformed(ActionEvent e)\r
 787   {\r
 788     changeColour(new BuriedColourScheme());\r
 789   }\r
 790 \r
 791   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 792   {\r
 793     changeColour(new NucleotideColourScheme());\r
 794   }\r
 795 \r
 796   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 797   {\r
 798     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
 799   }\r
 800 \r
 801   void changeColour(ColourSchemeI cs)\r
 802   {\r
 803     int threshold = 0;\r
 804 \r
 805     if (viewport.getAbovePIDThreshold())\r
 806     {\r
 807       threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
 808 \r
 809       if (cs instanceof ResidueColourScheme)\r
 810       {\r
 811         ( (ResidueColourScheme) cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
 812       }\r
 813 \r
 814       viewport.setGlobalColourScheme(cs);\r
 815     }\r
 816     else if (cs instanceof ResidueColourScheme)\r
 817     {\r
 818       ( (ResidueColourScheme) cs).setThreshold(0, viewport.getIgnoreGapsConsensus());\r
 819     }\r
 820 \r
 821     if (viewport.getConservationSelected())\r
 822     {\r
 823       ConservationColourScheme ccs = null;\r
 824 \r
 825       Alignment al = (Alignment) viewport.alignment;\r
 826       Conservation c = new Conservation("All",\r
 827                                         ResidueProperties.propHash, 3,\r
 828                                         al.getSequences(), 0,\r
 829                                         al.getWidth() - 1);\r
 830 \r
 831       c.calculate();\r
 832       c.verdict(false, viewport.ConsPercGaps);\r
 833 \r
 834       ccs = new ConservationColourScheme(c, cs);\r
 835 \r
 836       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 837       ccs.setConsensus(viewport.vconsensus);\r
 838       viewport.setGlobalColourScheme(ccs);\r
 839 \r
 840       SliderPanel.setConservationSlider(alignPanel, ccs, "Background");\r
 841 \r
 842     }\r
 843     else\r
 844     {\r
 845       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 846       if (cs != null)\r
 847       {\r
 848         cs.setConsensus(viewport.vconsensus);\r
 849       }\r
 850       viewport.setGlobalColourScheme(cs);\r
 851     }\r
 852 \r
 853     if (viewport.getColourAppliesToAllGroups())\r
 854     {\r
 855       Vector groups = viewport.alignment.getGroups();\r
 856       for (int i = 0; i < groups.size(); i++)\r
 857       {\r
 858         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 859 \r
 860         if(cs==null)\r
 861         {\r
 862           sg.cs = null;\r
 863           continue;\r
 864         }\r
 865         if (cs instanceof ClustalxColourScheme)\r
 866         {\r
 867           ClustalxColourScheme cxs = (ClustalxColourScheme) cs;\r
 868           cxs.resetClustalX(viewport.alignment.getSequences(), viewport.alignment.getWidth());\r
 869           sg.cs = cxs;\r
 870         }\r
 871         else\r
 872         {\r
 873           try\r
 874           {\r
 875             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
 876           }\r
 877           catch (Exception ex)\r
 878           {\r
 879             ex.printStackTrace();\r
 880             sg.cs = cs;\r
 881           }\r
 882         }\r
 883 \r
 884         if (viewport.getAbovePIDThreshold())\r
 885         {\r
 886           if (sg.cs instanceof ResidueColourScheme)\r
 887           {\r
 888             ( (ResidueColourScheme) sg.cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
 889           }\r
 890 \r
 891           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 892         }\r
 893 \r
 894         if (viewport.getConservationSelected())\r
 895         {\r
 896           Conservation c = new Conservation("Group",\r
 897                                             ResidueProperties.propHash, 3,\r
 898                                             sg.sequences, 0,\r
 899                                             viewport.alignment.getWidth() - 1);\r
 900           c.calculate();\r
 901           c.verdict(false, viewport.ConsPercGaps);\r
 902           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 903 \r
 904           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 905           ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 906           sg.cs = ccs;\r
 907         }\r
 908         else\r
 909         {\r
 910           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 911           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 912         }\r
 913 \r
 914       }\r
 915     }\r
 916 \r
 917     updateCSConsensus();\r
 918 \r
 919     if (alignPanel.getOverviewPanel() != null)\r
 920     {\r
 921       alignPanel.getOverviewPanel().updateOverviewImage();\r
 922     }\r
 923 \r
 924     alignPanel.repaint();\r
 925   }\r
 926 \r
 927   public void updateCSConsensus()\r
 928   {\r
 929     //Colour schemes must have their consensus updated\r
 930 \r
 931   }\r
 932 \r
 933   protected void modifyPID_actionPerformed(ActionEvent e)\r
 934   {\r
 935     if (viewport.getAbovePIDThreshold())\r
 936     {\r
 937       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
 938                                      "Background");\r
 939       SliderPanel.showPIDSlider();\r
 940     }\r
 941   }\r
 942 \r
 943   protected void modifyConservation_actionPerformed(ActionEvent e)\r
 944   {\r
 945     if (viewport.getConservationSelected())\r
 946     {\r
 947       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
 948                                         "Background");\r
 949       SliderPanel.showConservationSlider();\r
 950     }\r
 951   }\r
 952 \r
 953   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
 954   {\r
 955     viewport.setConservationSelected(conservationMenuItem.getState());\r
 956 \r
 957     viewport.setAbovePIDThreshold(false);\r
 958     abovePIDThreshold.setState(false);\r
 959 \r
 960     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 961     if (cs instanceof ConservationColourScheme)\r
 962     {\r
 963       changeColour( ( (ConservationColourScheme) cs).cs);\r
 964     }\r
 965     else\r
 966     {\r
 967       changeColour(cs);\r
 968     }\r
 969 \r
 970     modifyConservation_actionPerformed(null);\r
 971   }\r
 972 \r
 973   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 974   {\r
 975     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
 976 \r
 977     conservationMenuItem.setState(false);\r
 978     viewport.setConservationSelected(false);\r
 979 \r
 980     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 981 \r
 982     if (cs instanceof ConservationColourScheme)\r
 983     {\r
 984       changeColour( ( (ConservationColourScheme) cs).cs);\r
 985     }\r
 986     else\r
 987     {\r
 988       changeColour(cs);\r
 989     }\r
 990 \r
 991     modifyPID_actionPerformed(null);\r
 992   }\r
 993 \r
 994   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 995   {\r
 996     UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);\r
 997   }\r
 998 \r
 999   public void PIDColour_actionPerformed(ActionEvent e)\r
1000   {\r
1001     changeColour(new PIDColourScheme());\r
1002   }\r
1003 \r
1004   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1005   {\r
1006     changeColour(new Blosum62ColourScheme());\r
1007   }\r
1008 \r
1009   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1010   {\r
1011     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
1012                                    HistoryItem.SORT));\r
1013     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
1014                               viewport.getAlignment().getSequenceAt(0));\r
1015     alignPanel.repaint();\r
1016   }\r
1017 \r
1018   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1019   {\r
1020     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
1021                                    HistoryItem.SORT));\r
1022     AlignmentSorter.sortByID(viewport.getAlignment());\r
1023     alignPanel.repaint();\r
1024   }\r
1025 \r
1026   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1027   {\r
1028     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
1029                                    HistoryItem.SORT));\r
1030     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
1031     alignPanel.repaint();\r
1032 \r
1033   }\r
1034 \r
1035   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1036   {\r
1037     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
1038     Frame frame = new Frame();\r
1039     frame.add(sp);\r
1040     jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",\r
1041                                      400, 120);\r
1042 \r
1043   }\r
1044 \r
1045   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1046   {\r
1047     if (viewport.getSelectionGroup().getSize() > 1)\r
1048     {\r
1049       Frame frame = new Frame();\r
1050       frame.add(new PairwiseAlignPanel(viewport));\r
1051       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
1052     }\r
1053   }\r
1054 \r
1055   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
1056   {\r
1057 \r
1058     if ( (viewport.getSelectionGroup() != null &&\r
1059           viewport.getSelectionGroup().getSize() < 4 &&\r
1060           viewport.getSelectionGroup().getSize() > 0)\r
1061         || viewport.getAlignment().getHeight() < 4)\r
1062     {\r
1063       return;\r
1064     }\r
1065 \r
1066     try\r
1067     {\r
1068       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
1069       Frame frame = new Frame();\r
1070       frame.add(pcaPanel);\r
1071       jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",\r
1072                                        400, 400);\r
1073     }\r
1074     catch (java.lang.OutOfMemoryError ex)\r
1075     {\r
1076     }\r
1077 \r
1078   }\r
1079 \r
1080   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1081   {\r
1082     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1083   }\r
1084 \r
1085   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1086   {\r
1087     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1088   }\r
1089 \r
1090   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1091   {\r
1092     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1093   }\r
1094 \r
1095   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1096   {\r
1097     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1098   }\r
1099 \r
1100   void NewTreePanel(String type, String pwType, String title)\r
1101   {\r
1102     //are the sequences aligned?\r
1103     if (!viewport.alignment.isAligned())\r
1104     {\r
1105       SequenceI current;\r
1106       int Width = viewport.getAlignment().getWidth();\r
1107 \r
1108       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1109            i++)\r
1110       {\r
1111         current = viewport.getAlignment().getSequenceAt(i);\r
1112 \r
1113         if (current.getLength() < Width)\r
1114         {\r
1115           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1116         }\r
1117       }\r
1118       alignPanel.repaint();\r
1119 \r
1120     }\r
1121 \r
1122     final TreePanel tp;\r
1123     if (viewport.getSelectionGroup() != null &&\r
1124         viewport.getSelectionGroup().getSize() > 3)\r
1125     {\r
1126       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
1127                          pwType,\r
1128                          0, viewport.alignment.getWidth());\r
1129     }\r
1130     else\r
1131     {\r
1132       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1133                          type, pwType, 0, viewport.alignment.getWidth());\r
1134     }\r
1135 \r
1136     addTreeMenuItem(tp, title);\r
1137 \r
1138     jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
1139   }\r
1140 \r
1141   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1142   {\r
1143     final MenuItem item = new MenuItem(title);\r
1144     sortByTreeMenu.add(item);\r
1145     item.addActionListener(new java.awt.event.ActionListener()\r
1146     {\r
1147       public void actionPerformed(ActionEvent e)\r
1148       {\r
1149         addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1150                                        HistoryItem.SORT));\r
1151         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1152         alignPanel.repaint();\r
1153       }\r
1154     });\r
1155 \r
1156     treePanel.addWindowListener(new WindowAdapter()\r
1157     {\r
1158       public void windowClosing(WindowEvent e)\r
1159       {\r
1160         sortByTreeMenu.remove(item);\r
1161       };\r
1162     });\r
1163   }\r
1164 \r
1165   protected void documentation_actionPerformed(ActionEvent e)\r
1166   {\r
1167     jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");\r
1168   }\r
1169 \r
1170   protected void about_actionPerformed(ActionEvent e)\r
1171   {\r
1172     class AboutPanel\r
1173         extends Canvas\r
1174     {\r
1175       public void paint(Graphics g)\r
1176       {\r
1177         g.setColor(Color.white);\r
1178         g.fillRect(0, 0, getSize().width, getSize().height);\r
1179         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1180         FontMetrics fm = g.getFontMetrics();\r
1181         int fh = fm.getHeight();\r
1182         int y = 5, x = 7;\r
1183         g.setColor(Color.black);\r
1184         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1185         g.drawString("JalView - Release 2.02", 200, y += fh);\r
1186         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1187         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
1188                      x, y += fh * 2);\r
1189         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
1190                      x, y += fh);\r
1191         g.drawString(\r
1192             "For any issues relating to Jalview, email help@jalview.org", x,\r
1193             y += fh);\r
1194         g.drawString("If  you use JalView, please cite:", x, y += fh + 8);\r
1195         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
1196                      x, y += fh);\r
1197         g.drawString("Bioinformatics,  2004 12;426-7.", x, y += fh);\r
1198       }\r
1199     }\r
1200 \r
1201     Frame frame = new Frame();\r
1202     frame.add(new AboutPanel());\r
1203     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
1204 \r
1205   }\r
1206 }\r