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 \r
 401     SequenceGroup sg = viewport.getSelectionGroup();\r
 402     boolean allSequences = false;\r
 403     if(sg.sequences.size()==viewport.alignment.getHeight())\r
 404           allSequences = true;\r
 405 \r
 406     for (int i = 0; i < sg.sequences.size(); i++)\r
 407     {\r
 408       SequenceI seq = sg.getSequenceAt(i);\r
 409       int index = viewport.getAlignment().findIndex(seq);\r
 410       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
 411 \r
 412       // If the cut affects all sequences, remove highlighted columns\r
 413       if (allSequences)\r
 414       {\r
 415         viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
 416                                                      sg.getEndRes() + 1);\r
 417       }\r
 418 \r
 419 \r
 420       if (seq.getSequence().length() < 1)\r
 421       {\r
 422         viewport.getAlignment().deleteSequence(seq);\r
 423       }\r
 424       else\r
 425       {\r
 426         viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 427       }\r
 428     }\r
 429 \r
 430     viewport.setSelectionGroup(null);\r
 431     viewport.alignment.deleteGroup(sg);\r
 432     viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);\r
 433     if (viewport.getAlignment().getHeight() < 1)\r
 434     {\r
 435       try\r
 436       {\r
 437         this.setVisible(false);\r
 438       }\r
 439       catch (Exception ex)\r
 440       {}\r
 441     }\r
 442     viewport.updateConservation();\r
 443     viewport.updateConsensus();\r
 444     alignPanel.repaint();\r
 445 \r
 446   }\r
 447 \r
 448   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 449   {\r
 450     viewport.alignment.deleteAllGroups();\r
 451     viewport.setSelectionGroup(null);\r
 452 \r
 453     alignPanel.repaint();\r
 454   }\r
 455 \r
 456   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 457   {\r
 458     SequenceGroup sg = new SequenceGroup();\r
 459     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 460     {\r
 461       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
 462     }\r
 463     sg.setEndRes(viewport.alignment.getWidth());\r
 464     viewport.setSelectionGroup(sg);\r
 465     alignPanel.repaint();\r
 466     PaintRefresher.Refresh(null);\r
 467   }\r
 468 \r
 469   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 470   {\r
 471     viewport.setSelectionGroup(null);\r
 472     viewport.getColumnSelection().clear();\r
 473     viewport.setSelectionGroup(null);\r
 474     PaintRefresher.Refresh(null);\r
 475   }\r
 476 \r
 477   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 478   {\r
 479     SequenceGroup sg = viewport.getSelectionGroup();\r
 480     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 481     {\r
 482       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
 483     }\r
 484 \r
 485     PaintRefresher.Refresh(null);\r
 486   }\r
 487 \r
 488   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 489   {\r
 490     ColumnSelection colSel = viewport.getColumnSelection();\r
 491     if (colSel.size() > 0)\r
 492     {\r
 493       addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
 494                                      HistoryItem.HIDE));\r
 495       int min = colSel.getMin();\r
 496       viewport.getAlignment().trimLeft(min);\r
 497       colSel.compensateForEdit(0, min);\r
 498 \r
 499       if (viewport.getSelectionGroup() != null)\r
 500       {\r
 501         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 502       }\r
 503 \r
 504       Vector groups = viewport.alignment.getGroups();\r
 505       for (int i = 0; i < groups.size(); i++)\r
 506       {\r
 507         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 508         if (!sg.adjustForRemoveLeft(min))\r
 509         {\r
 510           viewport.alignment.deleteGroup(sg);\r
 511         }\r
 512       }\r
 513 \r
 514       alignPanel.repaint();\r
 515     }\r
 516   }\r
 517 \r
 518   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 519   {\r
 520     ColumnSelection colSel = viewport.getColumnSelection();\r
 521     if (colSel.size() > 0)\r
 522     {\r
 523       addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
 524                                      HistoryItem.HIDE));\r
 525       int max = colSel.getMax();\r
 526       viewport.getAlignment().trimRight(max);\r
 527       if (viewport.getSelectionGroup() != null)\r
 528       {\r
 529         viewport.getSelectionGroup().adjustForRemoveRight(max);\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.adjustForRemoveRight(max))\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 \r
 547   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 548   {\r
 549     addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
 550                                    viewport.alignment,\r
 551                                    HistoryItem.HIDE));\r
 552     viewport.getAlignment().removeGaps();\r
 553     viewport.updateConservation();\r
 554     viewport.updateConsensus();\r
 555     alignPanel.repaint();\r
 556   }\r
 557 \r
 558   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 559   {\r
 560     addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
 561                                    HistoryItem.HIDE));\r
 562 \r
 563     SequenceI current;\r
 564     int jSize;\r
 565 \r
 566     Vector seqs=null;\r
 567 \r
 568     int start=0, end = viewport.alignment.getWidth();\r
 569 \r
 570     if(viewport.getSelectionGroup()!=null)\r
 571     {\r
 572       seqs = viewport.getSelectionGroup().sequences;\r
 573       start = viewport.getSelectionGroup().getStartRes();\r
 574       end = viewport.getSelectionGroup().getEndRes();\r
 575     }\r
 576     else\r
 577       seqs = viewport.alignment.getSequences();\r
 578 \r
 579     for (int i = 0; i <seqs.size(); i++)\r
 580     {\r
 581       current = (SequenceI)seqs.elementAt(i);\r
 582       jSize = current.getLength();\r
 583 \r
 584       int j = start;\r
 585       do\r
 586       {\r
 587         if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 588         {\r
 589           current.deleteCharAt(j);\r
 590           j--;\r
 591           jSize--;\r
 592         }\r
 593         j++;\r
 594       }\r
 595       while(j < end && j < jSize) ;\r
 596     }\r
 597 \r
 598     viewport.updateConservation();\r
 599     viewport.updateConsensus();\r
 600     alignPanel.repaint();\r
 601   }\r
 602 \r
 603 \r
 604   public void findMenuItem_actionPerformed(ActionEvent e)\r
 605   {\r
 606     Finder finder = new Finder(alignPanel);\r
 607   }\r
 608 \r
 609   public void font_actionPerformed(ActionEvent e)\r
 610   {\r
 611     Frame frame = new Frame();\r
 612     FontChooser fc = new FontChooser(alignPanel, frame);\r
 613     frame.add(fc);\r
 614     jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);\r
 615 \r
 616   }\r
 617 \r
 618   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 619   {\r
 620     viewport.setShowFullId(fullSeqId.getState());\r
 621     alignPanel.fontChanged();\r
 622     alignPanel.repaint();\r
 623   }\r
 624 \r
 625   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 626   {\r
 627     viewport.setColourText(colourTextMenuItem.getState());\r
 628     alignPanel.repaint();\r
 629   }\r
 630 \r
 631   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 632   {\r
 633     viewport.setWrapAlignment(wrapMenuItem.getState());\r
 634     alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
 635     scaleAbove.setEnabled(wrapMenuItem.getState());\r
 636     scaleLeft.setEnabled(wrapMenuItem.getState());\r
 637     scaleRight.setEnabled(wrapMenuItem.getState());\r
 638     alignPanel.repaint();\r
 639   }\r
 640 \r
 641   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 642   {\r
 643     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
 644     alignPanel.repaint();\r
 645   }\r
 646 \r
 647   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 648   {\r
 649     viewport.setScaleLeftWrapped(scaleLeft.getState());\r
 650     alignPanel.repaint();\r
 651   }\r
 652 \r
 653   protected void scaleRight_actionPerformed(ActionEvent e)\r
 654   {\r
 655     viewport.setScaleRightWrapped(scaleRight.getState());\r
 656     alignPanel.repaint();\r
 657   }\r
 658 \r
 659   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 660   {\r
 661     viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
 662     alignPanel.repaint();\r
 663   }\r
 664 \r
 665   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 666   {\r
 667     viewport.setShowText(viewTextMenuItem.getState());\r
 668     alignPanel.repaint();\r
 669   }\r
 670 \r
 671   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 672   {\r
 673     viewport.setRenderGaps(renderGapsMenuItem.getState());\r
 674     alignPanel.repaint();\r
 675   }\r
 676 \r
 677   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 678   {\r
 679     if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment())\r
 680     {\r
 681       annotationPanelMenuItem.setState(false);\r
 682       return;\r
 683     }\r
 684     viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
 685     alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
 686   }\r
 687 \r
 688   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 689   {\r
 690     if (alignPanel.overviewPanel != null)\r
 691     {\r
 692       return;\r
 693     }\r
 694 \r
 695     Frame frame = new Frame();\r
 696     OverviewPanel overview = new OverviewPanel(alignPanel);\r
 697     frame.add(overview);\r
 698     // +50 must allow for applet frame window\r
 699     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
 700                                      overview.preferredSize().width,\r
 701                                      overview.preferredSize().height + 50);\r
 702 \r
 703     frame.pack();\r
 704     frame.addWindowListener(new WindowAdapter()\r
 705     {\r
 706       public void windowClosing(WindowEvent e)\r
 707       {\r
 708         alignPanel.setOverviewPanel(null);\r
 709       };\r
 710     });\r
 711 \r
 712     alignPanel.setOverviewPanel(overview);\r
 713 \r
 714   }\r
 715 \r
 716   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 717   {\r
 718     changeColour(null);\r
 719   }\r
 720 \r
 721   public void clustalColour_actionPerformed(ActionEvent e)\r
 722   {\r
 723     abovePIDThreshold.setState(false);\r
 724     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
 725                                           viewport.alignment.getWidth()));\r
 726   }\r
 727 \r
 728   public void zappoColour_actionPerformed(ActionEvent e)\r
 729   {\r
 730     changeColour(new ZappoColourScheme());\r
 731   }\r
 732 \r
 733   public void taylorColour_actionPerformed(ActionEvent e)\r
 734   {\r
 735     changeColour(new TaylorColourScheme());\r
 736   }\r
 737 \r
 738   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 739   {\r
 740     changeColour(new HydrophobicColourScheme());\r
 741   }\r
 742 \r
 743   public void helixColour_actionPerformed(ActionEvent e)\r
 744   {\r
 745     changeColour(new HelixColourScheme());\r
 746   }\r
 747 \r
 748   public void strandColour_actionPerformed(ActionEvent e)\r
 749   {\r
 750     changeColour(new StrandColourScheme());\r
 751   }\r
 752 \r
 753   public void turnColour_actionPerformed(ActionEvent e)\r
 754   {\r
 755     changeColour(new TurnColourScheme());\r
 756   }\r
 757 \r
 758   public void buriedColour_actionPerformed(ActionEvent e)\r
 759   {\r
 760     changeColour(new BuriedColourScheme());\r
 761   }\r
 762 \r
 763   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 764   {\r
 765     changeColour(new NucleotideColourScheme());\r
 766   }\r
 767 \r
 768   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 769   {\r
 770     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
 771   }\r
 772 \r
 773   void changeColour(ColourSchemeI cs)\r
 774   {\r
 775     int threshold = 0;\r
 776 \r
 777     if (viewport.getAbovePIDThreshold())\r
 778     {\r
 779       threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
 780 \r
 781       if (cs instanceof ResidueColourScheme)\r
 782       {\r
 783         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
 784       }\r
 785 \r
 786       viewport.setGlobalColourScheme(cs);\r
 787     }\r
 788     else if (cs instanceof ResidueColourScheme)\r
 789     {\r
 790       ( (ResidueColourScheme) cs).setThreshold(0);\r
 791     }\r
 792 \r
 793     if (viewport.getConservationSelected())\r
 794     {\r
 795       ConservationColourScheme ccs = null;\r
 796 \r
 797       Alignment al = (Alignment) viewport.alignment;\r
 798       Conservation c = new Conservation("All",\r
 799                                         ResidueProperties.propHash, 3,\r
 800                                         al.getSequences(), 0,\r
 801                                         al.getWidth() - 1);\r
 802 \r
 803       c.calculate();\r
 804       c.verdict(false, viewport.ConsPercGaps);\r
 805 \r
 806       ccs = new ConservationColourScheme(c, cs);\r
 807 \r
 808       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 809       ccs.setConsensus(viewport.vconsensus);\r
 810       viewport.setGlobalColourScheme(ccs);\r
 811 \r
 812       SliderPanel.setConservationSlider(alignPanel, ccs, "Background");\r
 813 \r
 814     }\r
 815     else\r
 816     {\r
 817       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 818       if (cs != null)\r
 819       {\r
 820         cs.setConsensus(viewport.vconsensus);\r
 821       }\r
 822       viewport.setGlobalColourScheme(cs);\r
 823     }\r
 824 \r
 825     if (viewport.getColourAppliesToAllGroups())\r
 826     {\r
 827       Vector groups = viewport.alignment.getGroups();\r
 828       for (int i = 0; i < groups.size(); i++)\r
 829       {\r
 830         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 831 \r
 832         if(cs==null)\r
 833         {\r
 834           sg.cs = null;\r
 835           continue;\r
 836         }\r
 837         if (cs instanceof ClustalxColourScheme)\r
 838         {\r
 839           ClustalxColourScheme cxs = (ClustalxColourScheme) cs;\r
 840           cxs.resetClustalX(viewport.alignment.getSequences(), viewport.alignment.getWidth());\r
 841           sg.cs = cxs;\r
 842         }\r
 843         else\r
 844         {\r
 845           try\r
 846           {\r
 847             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
 848           }\r
 849           catch (Exception ex)\r
 850           {\r
 851             ex.printStackTrace();\r
 852             sg.cs = cs;\r
 853           }\r
 854         }\r
 855 \r
 856         if (viewport.getAbovePIDThreshold())\r
 857         {\r
 858           if (sg.cs instanceof ResidueColourScheme)\r
 859           {\r
 860             ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
 861           }\r
 862 \r
 863           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 864         }\r
 865 \r
 866         if (viewport.getConservationSelected())\r
 867         {\r
 868           Conservation c = new Conservation("Group",\r
 869                                             ResidueProperties.propHash, 3,\r
 870                                             sg.sequences, 0,\r
 871                                             viewport.alignment.getWidth() - 1);\r
 872           c.calculate();\r
 873           c.verdict(false, viewport.ConsPercGaps);\r
 874           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 875 \r
 876           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 877           ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 878           sg.cs = ccs;\r
 879         }\r
 880         else\r
 881         {\r
 882           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 883           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 884         }\r
 885 \r
 886       }\r
 887     }\r
 888 \r
 889     if (alignPanel.getOverviewPanel() != null)\r
 890     {\r
 891       alignPanel.getOverviewPanel().updateOverviewImage();\r
 892     }\r
 893 \r
 894     alignPanel.repaint();\r
 895   }\r
 896 \r
 897   protected void modifyPID_actionPerformed(ActionEvent e)\r
 898   {\r
 899     if (viewport.getAbovePIDThreshold())\r
 900     {\r
 901       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
 902                                      "Background");\r
 903       SliderPanel.showPIDSlider();\r
 904     }\r
 905   }\r
 906 \r
 907   protected void modifyConservation_actionPerformed(ActionEvent e)\r
 908   {\r
 909     if (viewport.getConservationSelected())\r
 910     {\r
 911       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
 912                                         "Background");\r
 913       SliderPanel.showConservationSlider();\r
 914     }\r
 915   }\r
 916 \r
 917   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
 918   {\r
 919     viewport.setConservationSelected(conservationMenuItem.getState());\r
 920 \r
 921     viewport.setAbovePIDThreshold(false);\r
 922     abovePIDThreshold.setState(false);\r
 923 \r
 924     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 925     if (cs instanceof ConservationColourScheme)\r
 926     {\r
 927       changeColour( ( (ConservationColourScheme) cs).cs);\r
 928     }\r
 929     else\r
 930     {\r
 931       changeColour(cs);\r
 932     }\r
 933 \r
 934     modifyConservation_actionPerformed(null);\r
 935   }\r
 936 \r
 937   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 938   {\r
 939     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
 940 \r
 941     conservationMenuItem.setState(false);\r
 942     viewport.setConservationSelected(false);\r
 943 \r
 944     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 945 \r
 946     if (cs instanceof ConservationColourScheme)\r
 947     {\r
 948       changeColour( ( (ConservationColourScheme) cs).cs);\r
 949     }\r
 950     else\r
 951     {\r
 952       changeColour(cs);\r
 953     }\r
 954 \r
 955     modifyPID_actionPerformed(null);\r
 956   }\r
 957 \r
 958   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 959   {\r
 960     UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);\r
 961   }\r
 962 \r
 963   public void PIDColour_actionPerformed(ActionEvent e)\r
 964   {\r
 965     changeColour(new PIDColourScheme());\r
 966   }\r
 967 \r
 968   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 969   {\r
 970     changeColour(new Blosum62ColourScheme());\r
 971   }\r
 972 \r
 973   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 974   {\r
 975     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
 976                                    HistoryItem.SORT));\r
 977     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
 978                               viewport.getAlignment().getSequenceAt(0));\r
 979     alignPanel.repaint();\r
 980   }\r
 981 \r
 982   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 983   {\r
 984     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
 985                                    HistoryItem.SORT));\r
 986     AlignmentSorter.sortByID(viewport.getAlignment());\r
 987     alignPanel.repaint();\r
 988   }\r
 989 \r
 990   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 991   {\r
 992     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
 993                                    HistoryItem.SORT));\r
 994     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 995     alignPanel.repaint();\r
 996 \r
 997   }\r
 998 \r
 999   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1000   {\r
1001     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
1002     Frame frame = new Frame();\r
1003     frame.add(sp);\r
1004     jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",\r
1005                                      400, 120);\r
1006 \r
1007   }\r
1008 \r
1009   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1010   {\r
1011     if (viewport.getSelectionGroup().getSize() > 1)\r
1012     {\r
1013       Frame frame = new Frame();\r
1014       frame.add(new PairwiseAlignPanel(viewport));\r
1015       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
1016     }\r
1017   }\r
1018 \r
1019   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
1020   {\r
1021 \r
1022     if ( (viewport.getSelectionGroup() != null &&\r
1023           viewport.getSelectionGroup().getSize() < 4 &&\r
1024           viewport.getSelectionGroup().getSize() > 0)\r
1025         || viewport.getAlignment().getHeight() < 4)\r
1026     {\r
1027       return;\r
1028     }\r
1029 \r
1030     try\r
1031     {\r
1032       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
1033       Frame frame = new Frame();\r
1034       frame.add(pcaPanel);\r
1035       jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",\r
1036                                        400, 400);\r
1037     }\r
1038     catch (java.lang.OutOfMemoryError ex)\r
1039     {\r
1040     }\r
1041 \r
1042   }\r
1043 \r
1044   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1045   {\r
1046     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1047   }\r
1048 \r
1049   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1050   {\r
1051     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1052   }\r
1053 \r
1054   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1055   {\r
1056     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1057   }\r
1058 \r
1059   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1060   {\r
1061     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1062   }\r
1063 \r
1064   void NewTreePanel(String type, String pwType, String title)\r
1065   {\r
1066     //are the sequences aligned?\r
1067     if (!viewport.alignment.isAligned())\r
1068     {\r
1069       return;\r
1070     }\r
1071 \r
1072     final TreePanel tp;\r
1073     if (viewport.getSelectionGroup() != null &&\r
1074         viewport.getSelectionGroup().getSize() > 3)\r
1075     {\r
1076       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
1077                          pwType,\r
1078                          0, viewport.alignment.getWidth());\r
1079     }\r
1080     else\r
1081     {\r
1082       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1083                          type, pwType, 0, viewport.alignment.getWidth());\r
1084     }\r
1085 \r
1086     addTreeMenuItem(tp, title);\r
1087 \r
1088     jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
1089   }\r
1090 \r
1091   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1092   {\r
1093     final MenuItem item = new MenuItem(title);\r
1094     sortByTreeMenu.add(item);\r
1095     item.addActionListener(new java.awt.event.ActionListener()\r
1096     {\r
1097       public void actionPerformed(ActionEvent e)\r
1098       {\r
1099         addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1100                                        HistoryItem.SORT));\r
1101         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1102         alignPanel.repaint();\r
1103       }\r
1104     });\r
1105 \r
1106     treePanel.addWindowListener(new WindowAdapter()\r
1107     {\r
1108       public void windowClosing(WindowEvent e)\r
1109       {\r
1110         sortByTreeMenu.remove(item);\r
1111       };\r
1112     });\r
1113   }\r
1114 \r
1115   protected void documentation_actionPerformed(ActionEvent e)\r
1116   {\r
1117     jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");\r
1118   }\r
1119 \r
1120   protected void about_actionPerformed(ActionEvent e)\r
1121   {\r
1122     class AboutPanel\r
1123         extends Canvas\r
1124     {\r
1125       public void paint(Graphics g)\r
1126       {\r
1127         g.setColor(Color.white);\r
1128         g.fillRect(0, 0, getSize().width, getSize().height);\r
1129         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1130         FontMetrics fm = g.getFontMetrics();\r
1131         int fh = fm.getHeight();\r
1132         int y = 5, x = 7;\r
1133         g.setColor(Color.black);\r
1134         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1135         g.drawString("JalView - Release 2.01", 200, y += fh);\r
1136         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1137         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
1138                      x, y += fh * 2);\r
1139         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
1140                      x, y += fh);\r
1141         g.drawString(\r
1142             "For any issues relating to Jalview, email help@jalview.org", x,\r
1143             y += fh);\r
1144         g.drawString("If  you use JalView, please cite:", x, y += fh + 8);\r
1145         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
1146                      x, y += fh);\r
1147         g.drawString("Bioinformatics,  2004 12;426-7.", x, y += fh);\r
1148       }\r
1149     }\r
1150 \r
1151     Frame frame = new Frame();\r
1152     frame.add(new AboutPanel());\r
1153     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
1154 \r
1155   }\r
1156 }\r