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 import java.io.InputStreamReader;\r
  31 import java.io.BufferedReader;\r
  32 \r
  33 public class AlignFrame\r
  34     extends GAlignFrame\r
  35 {\r
  36   final AlignmentPanel alignPanel;\r
  37   final AlignViewport viewport;\r
  38   public static final int NEW_WINDOW_WIDTH = 700;\r
  39   public static final int NEW_WINDOW_HEIGHT = 500;\r
  40   jalview.bin.JalviewLite applet;\r
  41 \r
  42   public AlignFrame(AlignmentI al)\r
  43   {\r
  44     this.applet = null;\r
  45     viewport = new AlignViewport(al, null);\r
  46     alignPanel = new AlignmentPanel(this, viewport);\r
  47     add(alignPanel);\r
  48     alignPanel.validate();\r
  49   }\r
  50 \r
  51   public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet)\r
  52   {\r
  53     this.applet = applet;\r
  54     viewport = new AlignViewport(al, applet);\r
  55     alignPanel = new AlignmentPanel(this, viewport);\r
  56     add(alignPanel);\r
  57     alignPanel.validate();\r
  58 \r
  59     String treeFile = applet.getParameter("treeFile");\r
  60     TreePanel treepanel = null;\r
  61     if (treeFile != null)\r
  62     {\r
  63       try\r
  64       {\r
  65         treeFile = treeFile;\r
  66         jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.\r
  67             getCodeBase() + treeFile, "URL");\r
  68         fin.parse();\r
  69 \r
  70         if (fin.getTree() != null)\r
  71         {\r
  72           TreePanel tp = null;\r
  73           tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
  74                              fin, "FromFile", applet.getCodeBase() + treeFile);\r
  75           jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
  76           addTreeMenuItem(tp, treeFile);\r
  77         }\r
  78       }\r
  79       catch (Exception ex)\r
  80       {\r
  81         ex.printStackTrace();\r
  82       }\r
  83     }\r
  84 \r
  85 \r
  86   }\r
  87 \r
  88   public void inputText_actionPerformed(ActionEvent e)\r
  89   {\r
  90     CutAndPasteTransfer cap = new CutAndPasteTransfer(true);\r
  91     Frame frame = new Frame();\r
  92     frame.add(cap);\r
  93     jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
  94   }\r
  95 \r
  96   protected void outputText_actionPerformed(ActionEvent e)\r
  97   {\r
  98     CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
  99     Frame frame = new Frame();\r
 100     frame.add(cap);\r
 101     jalview.bin.JalviewLite.addFrame(frame,\r
 102                                      "Alignment output - " + e.getActionCommand(),\r
 103                                      600, 500);\r
 104     cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),\r
 105                                               viewport.getAlignment().\r
 106                                               getSequences()));\r
 107   }\r
 108 \r
 109   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 110   {\r
 111     dispose();\r
 112   }\r
 113 \r
 114   Stack historyList = new Stack();\r
 115   Stack redoList = new Stack();\r
 116 \r
 117   void updateEditMenuBar()\r
 118   {\r
 119     if (historyList.size() > 0)\r
 120     {\r
 121       undoMenuItem.setEnabled(true);\r
 122       HistoryItem hi = (HistoryItem) historyList.peek();\r
 123       undoMenuItem.setLabel("Undo " + hi.getDescription());\r
 124     }\r
 125     else\r
 126     {\r
 127       undoMenuItem.setEnabled(false);\r
 128       undoMenuItem.setLabel("Undo");\r
 129     }\r
 130 \r
 131     if (redoList.size() > 0)\r
 132     {\r
 133       redoMenuItem.setEnabled(true);\r
 134       HistoryItem hi = (HistoryItem) redoList.peek();\r
 135       redoMenuItem.setLabel("Redo " + hi.getDescription());\r
 136     }\r
 137     else\r
 138     {\r
 139       redoMenuItem.setEnabled(false);\r
 140       redoMenuItem.setLabel("Redo");\r
 141     }\r
 142   }\r
 143 \r
 144   public void addHistoryItem(HistoryItem hi)\r
 145   {\r
 146     historyList.push(hi);\r
 147     updateEditMenuBar();\r
 148   }\r
 149 \r
 150   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 151   {\r
 152     HistoryItem hi = (HistoryItem) historyList.pop();\r
 153     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
 154                                   HistoryItem.HIDE));\r
 155     restoreHistoryItem(hi);\r
 156   }\r
 157 \r
 158   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 159   {\r
 160     HistoryItem hi = (HistoryItem) redoList.pop();\r
 161     restoreHistoryItem(hi);\r
 162     updateEditMenuBar();\r
 163     viewport.updateConsensus();\r
 164     alignPanel.repaint();\r
 165     alignPanel.repaint();\r
 166   }\r
 167 \r
 168   // used by undo and redo\r
 169   void restoreHistoryItem(HistoryItem hi)\r
 170   {\r
 171     if (hi.getType() == HistoryItem.SORT)\r
 172     {\r
 173       for (int i = 0; i < hi.getSequences().size(); i++)\r
 174       {\r
 175         viewport.alignment.getSequences().setElementAt(hi.getSequences().\r
 176             elementAt(i), i);\r
 177       }\r
 178     }\r
 179     else\r
 180     {\r
 181       for (int i = 0; i < hi.getSequences().size(); i++)\r
 182       {\r
 183         SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
 184         if (restore.getLength() == 0)\r
 185         {\r
 186           // log.System.out.println(hi.getHidden().elementAt(i));\r
 187           restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 188           viewport.alignment.getSequences().insertElementAt(\r
 189               restore,\r
 190               hi.getAlignIndex(i));\r
 191         }\r
 192         else\r
 193         {\r
 194           restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 195         }\r
 196       }\r
 197       if (hi.getType() == HistoryItem.PASTE)\r
 198       {\r
 199         for (int i = viewport.alignment.getHeight() - 1;\r
 200              i > hi.getSequences().size() - 1; i--)\r
 201         {\r
 202           viewport.alignment.deleteSequence(i);\r
 203         }\r
 204       }\r
 205     }\r
 206 \r
 207     updateEditMenuBar();\r
 208 \r
 209     viewport.updateConsensus();\r
 210     viewport.updateConservation();\r
 211     alignPanel.repaint();\r
 212   }\r
 213 \r
 214   public void moveSelectedSequences(boolean up)\r
 215   {\r
 216     SequenceGroup sg = viewport.getSelectionGroup();\r
 217     if (sg == null)\r
 218     {\r
 219       return;\r
 220     }\r
 221 \r
 222     if (up)\r
 223     {\r
 224       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 225       {\r
 226         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 227         if (!sg.sequences.contains(seq))\r
 228         {\r
 229           continue;\r
 230         }\r
 231 \r
 232         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 233         if (sg.sequences.contains(temp))\r
 234         {\r
 235           continue;\r
 236         }\r
 237 \r
 238         viewport.alignment.getSequences().setElementAt(temp, i);\r
 239         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 240       }\r
 241     }\r
 242     else\r
 243     {\r
 244       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 245       {\r
 246         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 247         if (!sg.sequences.contains(seq))\r
 248         {\r
 249           continue;\r
 250         }\r
 251 \r
 252         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 253         if (sg.sequences.contains(temp))\r
 254         {\r
 255           continue;\r
 256         }\r
 257 \r
 258         viewport.alignment.getSequences().setElementAt(temp, i);\r
 259         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 260       }\r
 261     }\r
 262 \r
 263     alignPanel.repaint();\r
 264   }\r
 265 \r
 266   StringBuffer copiedSequences;\r
 267   protected void copy_actionPerformed(ActionEvent e)\r
 268   {\r
 269     if (viewport.getSelectionGroup() == null)\r
 270     {\r
 271       return;\r
 272     }\r
 273 \r
 274     SequenceGroup sg = viewport.getSelectionGroup();\r
 275     copiedSequences = new StringBuffer();\r
 276     Hashtable orderedSeqs = new Hashtable();\r
 277     for (int i = 0; i < sg.getSize(); i++)\r
 278     {\r
 279       SequenceI seq = sg.getSequenceAt(i);\r
 280       int index = viewport.alignment.findIndex(seq);\r
 281       orderedSeqs.put(index + "", seq);\r
 282     }\r
 283 \r
 284     int index = 0, startRes, endRes;\r
 285     char ch;\r
 286 \r
 287     for (int i = 0; i < sg.getSize(); i++)\r
 288     {\r
 289         SequenceI seq = null;\r
 290 \r
 291         while (seq == null)\r
 292         {\r
 293             if (orderedSeqs.containsKey(index + ""))\r
 294             {\r
 295                 seq = (SequenceI) orderedSeqs.get(index + "");\r
 296                 index++;\r
 297 \r
 298                 break;\r
 299             }\r
 300             else\r
 301             {\r
 302                 index++;\r
 303             }\r
 304         }\r
 305 \r
 306         //FIND START RES\r
 307         //Returns residue following index if gap\r
 308         startRes = seq.findPosition(sg.getStartRes());\r
 309 \r
 310         //FIND END RES\r
 311         //Need to find the residue preceeding index if gap\r
 312         endRes = 0;\r
 313 \r
 314         for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
 315         {\r
 316           ch = seq.getCharAt(j);\r
 317           if (!jalview.util.Comparison.isGap( (ch)))\r
 318           {\r
 319             endRes++;\r
 320           }\r
 321         }\r
 322 \r
 323         if(endRes>0)\r
 324         {\r
 325           endRes += seq.getStart() -1;\r
 326         }\r
 327 \r
 328         copiedSequences.append(seq.getName() + "\t" +\r
 329             startRes + "\t" +\r
 330             endRes + "\t" +\r
 331             seq.getSequence(sg.getStartRes(),\r
 332                 sg.getEndRes() + 1) + "\n");\r
 333     }\r
 334 \r
 335   }\r
 336 \r
 337   protected void pasteNew_actionPerformed(ActionEvent e)\r
 338   {\r
 339     paste(true);\r
 340   }\r
 341 \r
 342   protected void pasteThis_actionPerformed(ActionEvent e)\r
 343   {\r
 344     addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
 345                                    HistoryItem.PASTE));\r
 346     paste(false);\r
 347   }\r
 348 \r
 349   void paste(boolean newAlignment)\r
 350   {\r
 351     try\r
 352     {\r
 353       if (copiedSequences == null)\r
 354       {\r
 355         return;\r
 356       }\r
 357 \r
 358       StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
 359       Vector seqs = new Vector();\r
 360       while (st.hasMoreElements())\r
 361       {\r
 362         String name = st.nextToken();\r
 363         int start = Integer.parseInt(st.nextToken());\r
 364         int end = Integer.parseInt(st.nextToken());\r
 365         Sequence sequence = new Sequence(name, st.nextToken(), start, end);\r
 366 \r
 367         if (!newAlignment)\r
 368         {\r
 369           viewport.alignment.addSequence(sequence);\r
 370         }\r
 371         else\r
 372         {\r
 373           seqs.addElement(sequence);\r
 374         }\r
 375       }\r
 376 \r
 377       if (newAlignment)\r
 378       {\r
 379         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 380         for (int i = 0; i < seqs.size(); i++)\r
 381         {\r
 382           newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
 383         }\r
 384 \r
 385         AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);\r
 386         String newtitle = new String("Copied sequences");\r
 387         if (getTitle().startsWith("Copied sequences"))\r
 388         {\r
 389           newtitle = getTitle();\r
 390         }\r
 391         else\r
 392         {\r
 393           newtitle = newtitle.concat("- from " + getTitle());\r
 394         }\r
 395         jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
 396                                          NEW_WINDOW_HEIGHT);\r
 397       }\r
 398       else\r
 399       {\r
 400         viewport.setEndSeq(viewport.alignment.getHeight());\r
 401         viewport.alignment.getWidth();\r
 402         viewport.updateConservation();\r
 403         viewport.updateConsensus();\r
 404         alignPanel.repaint();\r
 405       }\r
 406 \r
 407     }\r
 408     catch (Exception ex)\r
 409     {} // could be anything being pasted in here\r
 410 \r
 411   }\r
 412 \r
 413   protected void cut_actionPerformed(ActionEvent e)\r
 414   {\r
 415     copy_actionPerformed(null);\r
 416     delete_actionPerformed(null);\r
 417   }\r
 418 \r
 419   protected void delete_actionPerformed(ActionEvent e)\r
 420   {\r
 421     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
 422                                    HistoryItem.HIDE));\r
 423     if (viewport.getSelectionGroup() == null)\r
 424     {\r
 425       return;\r
 426     }\r
 427 \r
 428 \r
 429     SequenceGroup sg = viewport.getSelectionGroup();\r
 430     boolean allSequences = false;\r
 431     if(sg.sequences.size()==viewport.alignment.getHeight())\r
 432           allSequences = true;\r
 433 \r
 434     for (int i = 0; i < sg.sequences.size(); i++)\r
 435     {\r
 436       SequenceI seq = sg.getSequenceAt(i);\r
 437       int index = viewport.getAlignment().findIndex(seq);\r
 438       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
 439 \r
 440       // If the cut affects all sequences, remove highlighted columns\r
 441       if (allSequences)\r
 442       {\r
 443         viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
 444                                                      sg.getEndRes() + 1);\r
 445       }\r
 446 \r
 447 \r
 448       if (seq.getSequence().length() < 1)\r
 449       {\r
 450         viewport.getAlignment().deleteSequence(seq);\r
 451       }\r
 452       else\r
 453       {\r
 454         viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 455       }\r
 456     }\r
 457 \r
 458     viewport.setSelectionGroup(null);\r
 459     viewport.alignment.deleteGroup(sg);\r
 460     viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);\r
 461     if (viewport.getAlignment().getHeight() < 1)\r
 462     {\r
 463       try\r
 464       {\r
 465         this.setVisible(false);\r
 466       }\r
 467       catch (Exception ex)\r
 468       {}\r
 469     }\r
 470     viewport.updateConservation();\r
 471     viewport.updateConsensus();\r
 472     alignPanel.repaint();\r
 473 \r
 474   }\r
 475 \r
 476   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 477   {\r
 478     viewport.alignment.deleteAllGroups();\r
 479     viewport.setSelectionGroup(null);\r
 480 \r
 481     alignPanel.repaint();\r
 482   }\r
 483 \r
 484   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 485   {\r
 486     SequenceGroup sg = new SequenceGroup();\r
 487     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 488     {\r
 489       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
 490     }\r
 491     sg.setEndRes(viewport.alignment.getWidth());\r
 492     viewport.setSelectionGroup(sg);\r
 493     alignPanel.repaint();\r
 494     PaintRefresher.Refresh(null, viewport.alignment);\r
 495   }\r
 496 \r
 497   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 498   {\r
 499     viewport.setSelectionGroup(null);\r
 500     viewport.getColumnSelection().clear();\r
 501     viewport.setSelectionGroup(null);\r
 502     PaintRefresher.Refresh(null, viewport.alignment);\r
 503   }\r
 504 \r
 505   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 506   {\r
 507     SequenceGroup sg = viewport.getSelectionGroup();\r
 508     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 509     {\r
 510       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
 511     }\r
 512 \r
 513     PaintRefresher.Refresh(null, viewport.alignment);\r
 514   }\r
 515 \r
 516   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 517   {\r
 518     ColumnSelection colSel = viewport.getColumnSelection();\r
 519     if (colSel.size() > 0)\r
 520     {\r
 521       addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
 522                                      HistoryItem.HIDE));\r
 523       int min = colSel.getMin();\r
 524       viewport.getAlignment().trimLeft(min);\r
 525       colSel.compensateForEdit(0, min);\r
 526 \r
 527       if (viewport.getSelectionGroup() != null)\r
 528       {\r
 529         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 530       }\r
 531 \r
 532       Vector groups = viewport.alignment.getGroups();\r
 533       for (int i = 0; i < groups.size(); i++)\r
 534       {\r
 535         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 536         if (!sg.adjustForRemoveLeft(min))\r
 537         {\r
 538           viewport.alignment.deleteGroup(sg);\r
 539         }\r
 540       }\r
 541 \r
 542       alignPanel.repaint();\r
 543     }\r
 544   }\r
 545 \r
 546   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 547   {\r
 548     ColumnSelection colSel = viewport.getColumnSelection();\r
 549     if (colSel.size() > 0)\r
 550     {\r
 551       addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
 552                                      HistoryItem.HIDE));\r
 553       int max = colSel.getMax();\r
 554       viewport.getAlignment().trimRight(max);\r
 555       if (viewport.getSelectionGroup() != null)\r
 556       {\r
 557         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 558       }\r
 559 \r
 560       Vector groups = viewport.alignment.getGroups();\r
 561       for (int i = 0; i < groups.size(); i++)\r
 562       {\r
 563         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 564         if (!sg.adjustForRemoveRight(max))\r
 565         {\r
 566           viewport.alignment.deleteGroup(sg);\r
 567         }\r
 568       }\r
 569 \r
 570       alignPanel.repaint();\r
 571     }\r
 572 \r
 573   }\r
 574 \r
 575   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 576   {\r
 577     addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
 578                                    viewport.alignment,\r
 579                                    HistoryItem.HIDE));\r
 580     viewport.getAlignment().removeGaps();\r
 581     viewport.updateConservation();\r
 582     viewport.updateConsensus();\r
 583     alignPanel.repaint();\r
 584   }\r
 585 \r
 586   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 587   {\r
 588     addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
 589                                    HistoryItem.HIDE));\r
 590 \r
 591     SequenceI current;\r
 592     int jSize;\r
 593 \r
 594     Vector seqs=null;\r
 595 \r
 596     int start=0, end = viewport.alignment.getWidth();\r
 597 \r
 598     if (viewport.getSelectionGroup() != null\r
 599         && viewport.getSelectionGroup().sequences != null\r
 600         && viewport.getSelectionGroup().sequences.size()>0)\r
 601     {\r
 602       seqs = viewport.getSelectionGroup().sequences;\r
 603       start = viewport.getSelectionGroup().getStartRes();\r
 604       end = viewport.getSelectionGroup().getEndRes();\r
 605     }\r
 606     else\r
 607       seqs = viewport.alignment.getSequences();\r
 608 \r
 609     for (int i = 0; i <seqs.size(); i++)\r
 610     {\r
 611       current = (SequenceI)seqs.elementAt(i);\r
 612       jSize = current.getLength();\r
 613 \r
 614       int j = start;\r
 615       do\r
 616       {\r
 617         if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 618         {\r
 619           current.deleteCharAt(j);\r
 620           j--;\r
 621           jSize--;\r
 622         }\r
 623         j++;\r
 624       }\r
 625       while(j < end && j < jSize) ;\r
 626     }\r
 627 \r
 628     viewport.updateConservation();\r
 629     viewport.updateConsensus();\r
 630     alignPanel.repaint();\r
 631   }\r
 632 \r
 633 \r
 634   public void findMenuItem_actionPerformed(ActionEvent e)\r
 635   {\r
 636     Finder finder = new Finder(alignPanel);\r
 637   }\r
 638 \r
 639   public void font_actionPerformed(ActionEvent e)\r
 640   {\r
 641     Frame frame = new Frame();\r
 642     FontChooser fc = new FontChooser(alignPanel, frame);\r
 643     frame.add(fc);\r
 644     jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);\r
 645 \r
 646   }\r
 647 \r
 648   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 649   {\r
 650     viewport.setShowFullId(fullSeqId.getState());\r
 651     alignPanel.fontChanged();\r
 652     alignPanel.repaint();\r
 653   }\r
 654 \r
 655   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 656   {\r
 657     viewport.setColourText(colourTextMenuItem.getState());\r
 658     alignPanel.repaint();\r
 659   }\r
 660 \r
 661   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 662   {\r
 663     viewport.setWrapAlignment(wrapMenuItem.getState());\r
 664     alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
 665     scaleAbove.setEnabled(wrapMenuItem.getState());\r
 666     scaleLeft.setEnabled(wrapMenuItem.getState());\r
 667     scaleRight.setEnabled(wrapMenuItem.getState());\r
 668     alignPanel.repaint();\r
 669   }\r
 670 \r
 671   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 672   {\r
 673     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
 674     alignPanel.repaint();\r
 675   }\r
 676 \r
 677   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 678   {\r
 679     viewport.setScaleLeftWrapped(scaleLeft.getState());\r
 680     alignPanel.repaint();\r
 681   }\r
 682 \r
 683   protected void scaleRight_actionPerformed(ActionEvent e)\r
 684   {\r
 685     viewport.setScaleRightWrapped(scaleRight.getState());\r
 686     alignPanel.repaint();\r
 687   }\r
 688 \r
 689   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 690   {\r
 691     viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
 692     alignPanel.repaint();\r
 693   }\r
 694 \r
 695   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 696   {\r
 697     viewport.setShowText(viewTextMenuItem.getState());\r
 698     alignPanel.repaint();\r
 699   }\r
 700 \r
 701   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 702   {\r
 703     viewport.setRenderGaps(renderGapsMenuItem.getState());\r
 704     alignPanel.repaint();\r
 705   }\r
 706 \r
 707   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 708   {\r
 709     if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment())\r
 710     {\r
 711       annotationPanelMenuItem.setState(false);\r
 712       return;\r
 713     }\r
 714     viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
 715     alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
 716   }\r
 717 \r
 718   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 719   {\r
 720     if (alignPanel.overviewPanel != null)\r
 721     {\r
 722       return;\r
 723     }\r
 724 \r
 725     Frame frame = new Frame();\r
 726     OverviewPanel overview = new OverviewPanel(alignPanel);\r
 727     frame.add(overview);\r
 728     // +50 must allow for applet frame window\r
 729     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
 730                                      overview.preferredSize().width,\r
 731                                      overview.preferredSize().height + 50);\r
 732 \r
 733     frame.pack();\r
 734     frame.addWindowListener(new WindowAdapter()\r
 735     {\r
 736       public void windowClosing(WindowEvent e)\r
 737       {\r
 738         alignPanel.setOverviewPanel(null);\r
 739       };\r
 740     });\r
 741 \r
 742     alignPanel.setOverviewPanel(overview);\r
 743 \r
 744   }\r
 745 \r
 746   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 747   {\r
 748     changeColour(null);\r
 749   }\r
 750 \r
 751   public void clustalColour_actionPerformed(ActionEvent e)\r
 752   {\r
 753     abovePIDThreshold.setState(false);\r
 754     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
 755                                           viewport.alignment.getWidth()));\r
 756   }\r
 757 \r
 758   public void zappoColour_actionPerformed(ActionEvent e)\r
 759   {\r
 760     changeColour(new ZappoColourScheme());\r
 761   }\r
 762 \r
 763   public void taylorColour_actionPerformed(ActionEvent e)\r
 764   {\r
 765     changeColour(new TaylorColourScheme());\r
 766   }\r
 767 \r
 768   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 769   {\r
 770     changeColour(new HydrophobicColourScheme());\r
 771   }\r
 772 \r
 773   public void helixColour_actionPerformed(ActionEvent e)\r
 774   {\r
 775     changeColour(new HelixColourScheme());\r
 776   }\r
 777 \r
 778   public void strandColour_actionPerformed(ActionEvent e)\r
 779   {\r
 780     changeColour(new StrandColourScheme());\r
 781   }\r
 782 \r
 783   public void turnColour_actionPerformed(ActionEvent e)\r
 784   {\r
 785     changeColour(new TurnColourScheme());\r
 786   }\r
 787 \r
 788   public void buriedColour_actionPerformed(ActionEvent e)\r
 789   {\r
 790     changeColour(new BuriedColourScheme());\r
 791   }\r
 792 \r
 793   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 794   {\r
 795     changeColour(new NucleotideColourScheme());\r
 796   }\r
 797 \r
 798   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 799   {\r
 800     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
 801   }\r
 802 \r
 803   void changeColour(ColourSchemeI cs)\r
 804   {\r
 805     int threshold = 0;\r
 806 \r
 807     if (viewport.getAbovePIDThreshold())\r
 808     {\r
 809       threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
 810 \r
 811       cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
 812 \r
 813       viewport.setGlobalColourScheme(cs);\r
 814     }\r
 815     else\r
 816     {\r
 817       cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
 818     }\r
 819 \r
 820     if (viewport.getConservationSelected())\r
 821     {\r
 822 \r
 823       Alignment al = (Alignment) viewport.alignment;\r
 824       Conservation c = new Conservation("All",\r
 825                                         ResidueProperties.propHash, 3,\r
 826                                         al.getSequences(), 0,\r
 827                                         al.getWidth() - 1);\r
 828 \r
 829       c.calculate();\r
 830       c.verdict(false, viewport.ConsPercGaps);\r
 831 \r
 832       cs.setConservation(c);\r
 833 \r
 834       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 835       cs.setConsensus(viewport.vconsensus);\r
 836       viewport.setGlobalColourScheme(cs);\r
 837 \r
 838       SliderPanel.setConservationSlider(alignPanel, cs, "Background");\r
 839 \r
 840     }\r
 841     else\r
 842     {\r
 843       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 844       if (cs != null)\r
 845       {\r
 846         cs.setConsensus(viewport.vconsensus);\r
 847       }\r
 848       viewport.setGlobalColourScheme(cs);\r
 849     }\r
 850 \r
 851     if (viewport.getColourAppliesToAllGroups())\r
 852     {\r
 853       Vector groups = viewport.alignment.getGroups();\r
 854       for (int i = 0; i < groups.size(); i++)\r
 855       {\r
 856         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 857 \r
 858         if(cs==null)\r
 859         {\r
 860           sg.cs = null;\r
 861           continue;\r
 862         }\r
 863         if (cs instanceof ClustalxColourScheme)\r
 864         {\r
 865           ClustalxColourScheme cxs = (ClustalxColourScheme) cs;\r
 866           cxs.resetClustalX(viewport.alignment.getSequences(), viewport.alignment.getWidth());\r
 867           sg.cs = cxs;\r
 868         }\r
 869         else\r
 870         {\r
 871           try\r
 872           {\r
 873             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
 874           }\r
 875           catch (Exception ex)\r
 876           {\r
 877             ex.printStackTrace();\r
 878             sg.cs = cs;\r
 879           }\r
 880         }\r
 881 \r
 882         if (viewport.getAbovePIDThreshold())\r
 883         {\r
 884           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
 885 \r
 886           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 887         }\r
 888 \r
 889         if (viewport.getConservationSelected())\r
 890         {\r
 891           Conservation c = new Conservation("Group",\r
 892                                             ResidueProperties.propHash, 3,\r
 893                                             sg.sequences, 0,\r
 894                                             viewport.alignment.getWidth() - 1);\r
 895           c.calculate();\r
 896           c.verdict(false, viewport.ConsPercGaps);\r
 897 \r
 898           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 899           cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 900           sg.cs = cs;\r
 901         }\r
 902         else\r
 903         {\r
 904           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 905           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 906         }\r
 907 \r
 908       }\r
 909     }\r
 910 \r
 911     updateCSConsensus();\r
 912 \r
 913     if (alignPanel.getOverviewPanel() != null)\r
 914     {\r
 915       alignPanel.getOverviewPanel().updateOverviewImage();\r
 916     }\r
 917 \r
 918     alignPanel.repaint();\r
 919   }\r
 920 \r
 921   public void updateCSConsensus()\r
 922   {\r
 923     //Colour schemes must have their consensus updated\r
 924 \r
 925   }\r
 926 \r
 927   protected void modifyPID_actionPerformed(ActionEvent e)\r
 928   {\r
 929     if (viewport.getAbovePIDThreshold())\r
 930     {\r
 931       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
 932                                      "Background");\r
 933       SliderPanel.showPIDSlider();\r
 934     }\r
 935   }\r
 936 \r
 937   protected void modifyConservation_actionPerformed(ActionEvent e)\r
 938   {\r
 939     if (viewport.getConservationSelected())\r
 940     {\r
 941       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
 942                                         "Background");\r
 943       SliderPanel.showConservationSlider();\r
 944     }\r
 945   }\r
 946 \r
 947   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
 948   {\r
 949     viewport.setConservationSelected(conservationMenuItem.getState());\r
 950 \r
 951     viewport.setAbovePIDThreshold(false);\r
 952     abovePIDThreshold.setState(false);\r
 953 \r
 954     changeColour(viewport.getGlobalColourScheme());\r
 955 \r
 956     modifyConservation_actionPerformed(null);\r
 957   }\r
 958 \r
 959   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 960   {\r
 961     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
 962 \r
 963     conservationMenuItem.setState(false);\r
 964     viewport.setConservationSelected(false);\r
 965 \r
 966     changeColour(viewport.getGlobalColourScheme());\r
 967 \r
 968     modifyPID_actionPerformed(null);\r
 969   }\r
 970 \r
 971   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 972   {\r
 973     UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);\r
 974   }\r
 975 \r
 976   public void PIDColour_actionPerformed(ActionEvent e)\r
 977   {\r
 978     changeColour(new PIDColourScheme());\r
 979   }\r
 980 \r
 981   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 982   {\r
 983     changeColour(new Blosum62ColourScheme());\r
 984   }\r
 985 \r
 986   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 987   {\r
 988     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
 989                                    HistoryItem.SORT));\r
 990     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
 991                               viewport.getAlignment().getSequenceAt(0));\r
 992     alignPanel.repaint();\r
 993   }\r
 994 \r
 995   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 996   {\r
 997     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
 998                                    HistoryItem.SORT));\r
 999     AlignmentSorter.sortByID(viewport.getAlignment());\r
1000     alignPanel.repaint();\r
1001   }\r
1002 \r
1003   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1004   {\r
1005     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
1006                                    HistoryItem.SORT));\r
1007     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
1008     alignPanel.repaint();\r
1009 \r
1010   }\r
1011 \r
1012   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1013   {\r
1014     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
1015     Frame frame = new Frame();\r
1016     frame.add(sp);\r
1017     jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",\r
1018                                      400, 120);\r
1019 \r
1020   }\r
1021 \r
1022   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1023   {\r
1024     if (viewport.getSelectionGroup().getSize() > 1)\r
1025     {\r
1026       Frame frame = new Frame();\r
1027       frame.add(new PairwiseAlignPanel(viewport));\r
1028       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
1029     }\r
1030   }\r
1031 \r
1032   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
1033   {\r
1034 \r
1035     if ( (viewport.getSelectionGroup() != null &&\r
1036           viewport.getSelectionGroup().getSize() < 4 &&\r
1037           viewport.getSelectionGroup().getSize() > 0)\r
1038         || viewport.getAlignment().getHeight() < 4)\r
1039     {\r
1040       return;\r
1041     }\r
1042 \r
1043     try\r
1044     {\r
1045       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
1046       Frame frame = new Frame();\r
1047       frame.add(pcaPanel);\r
1048       jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",\r
1049                                        400, 400);\r
1050     }\r
1051     catch (java.lang.OutOfMemoryError ex)\r
1052     {\r
1053     }\r
1054 \r
1055   }\r
1056 \r
1057   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1058   {\r
1059     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1060   }\r
1061 \r
1062   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1063   {\r
1064     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1065   }\r
1066 \r
1067   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1068   {\r
1069     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1070   }\r
1071 \r
1072   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1073   {\r
1074     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1075   }\r
1076 \r
1077   void NewTreePanel(String type, String pwType, String title)\r
1078   {\r
1079     //are the sequences aligned?\r
1080     if (!viewport.alignment.isAligned())\r
1081     {\r
1082       SequenceI current;\r
1083       int Width = viewport.getAlignment().getWidth();\r
1084 \r
1085       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1086            i++)\r
1087       {\r
1088         current = viewport.getAlignment().getSequenceAt(i);\r
1089 \r
1090         if (current.getLength() < Width)\r
1091         {\r
1092           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1093         }\r
1094       }\r
1095       alignPanel.repaint();\r
1096 \r
1097     }\r
1098 \r
1099     final TreePanel tp;\r
1100     if (viewport.getSelectionGroup() != null &&\r
1101         viewport.getSelectionGroup().getSize() > 3)\r
1102     {\r
1103       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
1104                          pwType,\r
1105                          0, viewport.alignment.getWidth());\r
1106     }\r
1107     else\r
1108     {\r
1109       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1110                          type, pwType, 0, viewport.alignment.getWidth());\r
1111     }\r
1112 \r
1113     addTreeMenuItem(tp, title);\r
1114 \r
1115     jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
1116   }\r
1117 \r
1118   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1119   {\r
1120     final MenuItem item = new MenuItem(title);\r
1121     sortByTreeMenu.add(item);\r
1122     item.addActionListener(new java.awt.event.ActionListener()\r
1123     {\r
1124       public void actionPerformed(ActionEvent e)\r
1125       {\r
1126         addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1127                                        HistoryItem.SORT));\r
1128         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1129         alignPanel.repaint();\r
1130       }\r
1131     });\r
1132 \r
1133     treePanel.addWindowListener(new WindowAdapter()\r
1134     {\r
1135       public void windowClosing(WindowEvent e)\r
1136       {\r
1137         sortByTreeMenu.remove(item);\r
1138       };\r
1139     });\r
1140   }\r
1141 \r
1142   protected void documentation_actionPerformed(ActionEvent e)\r
1143   {\r
1144     jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");\r
1145   }\r
1146 \r
1147   protected void about_actionPerformed(ActionEvent e)\r
1148   {\r
1149 \r
1150     class AboutPanel extends Canvas\r
1151     {\r
1152       String version;\r
1153       public AboutPanel(String version)\r
1154       { this.version = version; }\r
1155 \r
1156       public void paint(Graphics g)\r
1157       {\r
1158         g.setColor(Color.white);\r
1159         g.fillRect(0, 0, getSize().width, getSize().height);\r
1160         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1161         FontMetrics fm = g.getFontMetrics();\r
1162         int fh = fm.getHeight();\r
1163         int y = 5, x = 7;\r
1164         g.setColor(Color.black);\r
1165         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1166         g.drawString("Jalview - Release "+version, 200, y += fh);\r
1167         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1168         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
1169                      x, y += fh * 2);\r
1170         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
1171                      x, y += fh);\r
1172         g.drawString(\r
1173             "For any issues relating to Jalview, email help@jalview.org", x,\r
1174             y += fh);\r
1175         g.drawString("If  you use JalView, please cite:", x, y += fh + 8);\r
1176         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
1177                      x, y += fh);\r
1178         g.drawString("Bioinformatics,  2004 12;426-7.", x, y += fh);\r
1179       }\r
1180     }\r
1181 \r
1182     String version = "test";\r
1183     java.net.URL url = getClass().getResource("/.build_properties");\r
1184     if (url != null)\r
1185     {\r
1186       try\r
1187       {\r
1188         BufferedReader reader = new BufferedReader(new InputStreamReader(\r
1189             url.openStream()));\r
1190         String line;\r
1191         while ( (line = reader.readLine()) != null)\r
1192         {\r
1193           if (line.indexOf("VERSION") > -1)\r
1194           {\r
1195             version = line.substring(line.indexOf("=") + 1);\r
1196           }\r
1197         }\r
1198       }\r
1199       catch (Exception ex)\r
1200       {\r
1201         ex.printStackTrace();\r
1202       }\r
1203     }\r
1204 \r
1205 \r
1206     Frame frame = new Frame();\r
1207     frame.add(new AboutPanel(version));\r
1208     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
1209 \r
1210   }\r
1211 }\r