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                              seq.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         && viewport.getSelectionGroup().sequences != null\r
 572         && viewport.getSelectionGroup().sequences.size()>0)\r
 573     {\r
 574       seqs = viewport.getSelectionGroup().sequences;\r
 575       start = viewport.getSelectionGroup().getStartRes();\r
 576       end = viewport.getSelectionGroup().getEndRes();\r
 577     }\r
 578     else\r
 579       seqs = viewport.alignment.getSequences();\r
 580 \r
 581     for (int i = 0; i <seqs.size(); i++)\r
 582     {\r
 583       current = (SequenceI)seqs.elementAt(i);\r
 584       jSize = current.getLength();\r
 585 \r
 586       int j = start;\r
 587       do\r
 588       {\r
 589         if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 590         {\r
 591           current.deleteCharAt(j);\r
 592           j--;\r
 593           jSize--;\r
 594         }\r
 595         j++;\r
 596       }\r
 597       while(j < end && j < jSize) ;\r
 598     }\r
 599 \r
 600     viewport.updateConservation();\r
 601     viewport.updateConsensus();\r
 602     alignPanel.repaint();\r
 603   }\r
 604 \r
 605 \r
 606   public void findMenuItem_actionPerformed(ActionEvent e)\r
 607   {\r
 608     Finder finder = new Finder(alignPanel);\r
 609   }\r
 610 \r
 611   public void font_actionPerformed(ActionEvent e)\r
 612   {\r
 613     Frame frame = new Frame();\r
 614     FontChooser fc = new FontChooser(alignPanel, frame);\r
 615     frame.add(fc);\r
 616     jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);\r
 617 \r
 618   }\r
 619 \r
 620   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 621   {\r
 622     viewport.setShowFullId(fullSeqId.getState());\r
 623     alignPanel.fontChanged();\r
 624     alignPanel.repaint();\r
 625   }\r
 626 \r
 627   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 628   {\r
 629     viewport.setColourText(colourTextMenuItem.getState());\r
 630     alignPanel.repaint();\r
 631   }\r
 632 \r
 633   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 634   {\r
 635     viewport.setWrapAlignment(wrapMenuItem.getState());\r
 636     alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
 637     scaleAbove.setEnabled(wrapMenuItem.getState());\r
 638     scaleLeft.setEnabled(wrapMenuItem.getState());\r
 639     scaleRight.setEnabled(wrapMenuItem.getState());\r
 640     alignPanel.repaint();\r
 641   }\r
 642 \r
 643   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 644   {\r
 645     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
 646     alignPanel.repaint();\r
 647   }\r
 648 \r
 649   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 650   {\r
 651     viewport.setScaleLeftWrapped(scaleLeft.getState());\r
 652     alignPanel.repaint();\r
 653   }\r
 654 \r
 655   protected void scaleRight_actionPerformed(ActionEvent e)\r
 656   {\r
 657     viewport.setScaleRightWrapped(scaleRight.getState());\r
 658     alignPanel.repaint();\r
 659   }\r
 660 \r
 661   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 662   {\r
 663     viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
 664     alignPanel.repaint();\r
 665   }\r
 666 \r
 667   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 668   {\r
 669     viewport.setShowText(viewTextMenuItem.getState());\r
 670     alignPanel.repaint();\r
 671   }\r
 672 \r
 673   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 674   {\r
 675     viewport.setRenderGaps(renderGapsMenuItem.getState());\r
 676     alignPanel.repaint();\r
 677   }\r
 678 \r
 679   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 680   {\r
 681     if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment())\r
 682     {\r
 683       annotationPanelMenuItem.setState(false);\r
 684       return;\r
 685     }\r
 686     viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
 687     alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
 688   }\r
 689 \r
 690   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 691   {\r
 692     if (alignPanel.overviewPanel != null)\r
 693     {\r
 694       return;\r
 695     }\r
 696 \r
 697     Frame frame = new Frame();\r
 698     OverviewPanel overview = new OverviewPanel(alignPanel);\r
 699     frame.add(overview);\r
 700     // +50 must allow for applet frame window\r
 701     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
 702                                      overview.preferredSize().width,\r
 703                                      overview.preferredSize().height + 50);\r
 704 \r
 705     frame.pack();\r
 706     frame.addWindowListener(new WindowAdapter()\r
 707     {\r
 708       public void windowClosing(WindowEvent e)\r
 709       {\r
 710         alignPanel.setOverviewPanel(null);\r
 711       };\r
 712     });\r
 713 \r
 714     alignPanel.setOverviewPanel(overview);\r
 715 \r
 716   }\r
 717 \r
 718   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 719   {\r
 720     changeColour(null);\r
 721   }\r
 722 \r
 723   public void clustalColour_actionPerformed(ActionEvent e)\r
 724   {\r
 725     abovePIDThreshold.setState(false);\r
 726     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
 727                                           viewport.alignment.getWidth()));\r
 728   }\r
 729 \r
 730   public void zappoColour_actionPerformed(ActionEvent e)\r
 731   {\r
 732     changeColour(new ZappoColourScheme());\r
 733   }\r
 734 \r
 735   public void taylorColour_actionPerformed(ActionEvent e)\r
 736   {\r
 737     changeColour(new TaylorColourScheme());\r
 738   }\r
 739 \r
 740   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 741   {\r
 742     changeColour(new HydrophobicColourScheme());\r
 743   }\r
 744 \r
 745   public void helixColour_actionPerformed(ActionEvent e)\r
 746   {\r
 747     changeColour(new HelixColourScheme());\r
 748   }\r
 749 \r
 750   public void strandColour_actionPerformed(ActionEvent e)\r
 751   {\r
 752     changeColour(new StrandColourScheme());\r
 753   }\r
 754 \r
 755   public void turnColour_actionPerformed(ActionEvent e)\r
 756   {\r
 757     changeColour(new TurnColourScheme());\r
 758   }\r
 759 \r
 760   public void buriedColour_actionPerformed(ActionEvent e)\r
 761   {\r
 762     changeColour(new BuriedColourScheme());\r
 763   }\r
 764 \r
 765   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 766   {\r
 767     changeColour(new NucleotideColourScheme());\r
 768   }\r
 769 \r
 770   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 771   {\r
 772     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
 773   }\r
 774 \r
 775   void changeColour(ColourSchemeI cs)\r
 776   {\r
 777     int threshold = 0;\r
 778 \r
 779     if (viewport.getAbovePIDThreshold())\r
 780     {\r
 781       threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
 782 \r
 783       if (cs instanceof ResidueColourScheme)\r
 784       {\r
 785         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
 786       }\r
 787 \r
 788       viewport.setGlobalColourScheme(cs);\r
 789     }\r
 790     else if (cs instanceof ResidueColourScheme)\r
 791     {\r
 792       ( (ResidueColourScheme) cs).setThreshold(0);\r
 793     }\r
 794 \r
 795     if (viewport.getConservationSelected())\r
 796     {\r
 797       ConservationColourScheme ccs = null;\r
 798 \r
 799       Alignment al = (Alignment) viewport.alignment;\r
 800       Conservation c = new Conservation("All",\r
 801                                         ResidueProperties.propHash, 3,\r
 802                                         al.getSequences(), 0,\r
 803                                         al.getWidth() - 1);\r
 804 \r
 805       c.calculate();\r
 806       c.verdict(false, viewport.ConsPercGaps);\r
 807 \r
 808       ccs = new ConservationColourScheme(c, cs);\r
 809 \r
 810       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 811       ccs.setConsensus(viewport.vconsensus);\r
 812       viewport.setGlobalColourScheme(ccs);\r
 813 \r
 814       SliderPanel.setConservationSlider(alignPanel, ccs, "Background");\r
 815 \r
 816     }\r
 817     else\r
 818     {\r
 819       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 820       if (cs != null)\r
 821       {\r
 822         cs.setConsensus(viewport.vconsensus);\r
 823       }\r
 824       viewport.setGlobalColourScheme(cs);\r
 825     }\r
 826 \r
 827     if (viewport.getColourAppliesToAllGroups())\r
 828     {\r
 829       Vector groups = viewport.alignment.getGroups();\r
 830       for (int i = 0; i < groups.size(); i++)\r
 831       {\r
 832         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 833 \r
 834         if(cs==null)\r
 835         {\r
 836           sg.cs = null;\r
 837           continue;\r
 838         }\r
 839         if (cs instanceof ClustalxColourScheme)\r
 840         {\r
 841           ClustalxColourScheme cxs = (ClustalxColourScheme) cs;\r
 842           cxs.resetClustalX(viewport.alignment.getSequences(), viewport.alignment.getWidth());\r
 843           sg.cs = cxs;\r
 844         }\r
 845         else\r
 846         {\r
 847           try\r
 848           {\r
 849             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
 850           }\r
 851           catch (Exception ex)\r
 852           {\r
 853             ex.printStackTrace();\r
 854             sg.cs = cs;\r
 855           }\r
 856         }\r
 857 \r
 858         if (viewport.getAbovePIDThreshold())\r
 859         {\r
 860           if (sg.cs instanceof ResidueColourScheme)\r
 861           {\r
 862             ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
 863           }\r
 864 \r
 865           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 866         }\r
 867 \r
 868         if (viewport.getConservationSelected())\r
 869         {\r
 870           Conservation c = new Conservation("Group",\r
 871                                             ResidueProperties.propHash, 3,\r
 872                                             sg.sequences, 0,\r
 873                                             viewport.alignment.getWidth() - 1);\r
 874           c.calculate();\r
 875           c.verdict(false, viewport.ConsPercGaps);\r
 876           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 877 \r
 878           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 879           ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 880           sg.cs = ccs;\r
 881         }\r
 882         else\r
 883         {\r
 884           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 885           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 886         }\r
 887 \r
 888       }\r
 889     }\r
 890 \r
 891     if (alignPanel.getOverviewPanel() != null)\r
 892     {\r
 893       alignPanel.getOverviewPanel().updateOverviewImage();\r
 894     }\r
 895 \r
 896     alignPanel.repaint();\r
 897   }\r
 898 \r
 899   protected void modifyPID_actionPerformed(ActionEvent e)\r
 900   {\r
 901     if (viewport.getAbovePIDThreshold())\r
 902     {\r
 903       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
 904                                      "Background");\r
 905       SliderPanel.showPIDSlider();\r
 906     }\r
 907   }\r
 908 \r
 909   protected void modifyConservation_actionPerformed(ActionEvent e)\r
 910   {\r
 911     if (viewport.getConservationSelected())\r
 912     {\r
 913       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
 914                                         "Background");\r
 915       SliderPanel.showConservationSlider();\r
 916     }\r
 917   }\r
 918 \r
 919   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
 920   {\r
 921     viewport.setConservationSelected(conservationMenuItem.getState());\r
 922 \r
 923     viewport.setAbovePIDThreshold(false);\r
 924     abovePIDThreshold.setState(false);\r
 925 \r
 926     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 927     if (cs instanceof ConservationColourScheme)\r
 928     {\r
 929       changeColour( ( (ConservationColourScheme) cs).cs);\r
 930     }\r
 931     else\r
 932     {\r
 933       changeColour(cs);\r
 934     }\r
 935 \r
 936     modifyConservation_actionPerformed(null);\r
 937   }\r
 938 \r
 939   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 940   {\r
 941     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
 942 \r
 943     conservationMenuItem.setState(false);\r
 944     viewport.setConservationSelected(false);\r
 945 \r
 946     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 947 \r
 948     if (cs instanceof ConservationColourScheme)\r
 949     {\r
 950       changeColour( ( (ConservationColourScheme) cs).cs);\r
 951     }\r
 952     else\r
 953     {\r
 954       changeColour(cs);\r
 955     }\r
 956 \r
 957     modifyPID_actionPerformed(null);\r
 958   }\r
 959 \r
 960   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 961   {\r
 962     UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);\r
 963   }\r
 964 \r
 965   public void PIDColour_actionPerformed(ActionEvent e)\r
 966   {\r
 967     changeColour(new PIDColourScheme());\r
 968   }\r
 969 \r
 970   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 971   {\r
 972     changeColour(new Blosum62ColourScheme());\r
 973   }\r
 974 \r
 975   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 976   {\r
 977     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
 978                                    HistoryItem.SORT));\r
 979     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
 980                               viewport.getAlignment().getSequenceAt(0));\r
 981     alignPanel.repaint();\r
 982   }\r
 983 \r
 984   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 985   {\r
 986     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
 987                                    HistoryItem.SORT));\r
 988     AlignmentSorter.sortByID(viewport.getAlignment());\r
 989     alignPanel.repaint();\r
 990   }\r
 991 \r
 992   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 993   {\r
 994     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
 995                                    HistoryItem.SORT));\r
 996     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 997     alignPanel.repaint();\r
 998 \r
 999   }\r
1000 \r
1001   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1002   {\r
1003     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
1004     Frame frame = new Frame();\r
1005     frame.add(sp);\r
1006     jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",\r
1007                                      400, 120);\r
1008 \r
1009   }\r
1010 \r
1011   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1012   {\r
1013     if (viewport.getSelectionGroup().getSize() > 1)\r
1014     {\r
1015       Frame frame = new Frame();\r
1016       frame.add(new PairwiseAlignPanel(viewport));\r
1017       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
1018     }\r
1019   }\r
1020 \r
1021   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
1022   {\r
1023 \r
1024     if ( (viewport.getSelectionGroup() != null &&\r
1025           viewport.getSelectionGroup().getSize() < 4 &&\r
1026           viewport.getSelectionGroup().getSize() > 0)\r
1027         || viewport.getAlignment().getHeight() < 4)\r
1028     {\r
1029       return;\r
1030     }\r
1031 \r
1032     try\r
1033     {\r
1034       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
1035       Frame frame = new Frame();\r
1036       frame.add(pcaPanel);\r
1037       jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",\r
1038                                        400, 400);\r
1039     }\r
1040     catch (java.lang.OutOfMemoryError ex)\r
1041     {\r
1042     }\r
1043 \r
1044   }\r
1045 \r
1046   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1047   {\r
1048     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1049   }\r
1050 \r
1051   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1052   {\r
1053     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1054   }\r
1055 \r
1056   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1057   {\r
1058     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1059   }\r
1060 \r
1061   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1062   {\r
1063     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1064   }\r
1065 \r
1066   void NewTreePanel(String type, String pwType, String title)\r
1067   {\r
1068     //are the sequences aligned?\r
1069     if (!viewport.alignment.isAligned())\r
1070     {\r
1071       return;\r
1072     }\r
1073 \r
1074     final TreePanel tp;\r
1075     if (viewport.getSelectionGroup() != null &&\r
1076         viewport.getSelectionGroup().getSize() > 3)\r
1077     {\r
1078       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
1079                          pwType,\r
1080                          0, viewport.alignment.getWidth());\r
1081     }\r
1082     else\r
1083     {\r
1084       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1085                          type, pwType, 0, viewport.alignment.getWidth());\r
1086     }\r
1087 \r
1088     addTreeMenuItem(tp, title);\r
1089 \r
1090     jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
1091   }\r
1092 \r
1093   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1094   {\r
1095     final MenuItem item = new MenuItem(title);\r
1096     sortByTreeMenu.add(item);\r
1097     item.addActionListener(new java.awt.event.ActionListener()\r
1098     {\r
1099       public void actionPerformed(ActionEvent e)\r
1100       {\r
1101         addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1102                                        HistoryItem.SORT));\r
1103         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1104         alignPanel.repaint();\r
1105       }\r
1106     });\r
1107 \r
1108     treePanel.addWindowListener(new WindowAdapter()\r
1109     {\r
1110       public void windowClosing(WindowEvent e)\r
1111       {\r
1112         sortByTreeMenu.remove(item);\r
1113       };\r
1114     });\r
1115   }\r
1116 \r
1117   protected void documentation_actionPerformed(ActionEvent e)\r
1118   {\r
1119     jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");\r
1120   }\r
1121 \r
1122   protected void about_actionPerformed(ActionEvent e)\r
1123   {\r
1124     class AboutPanel\r
1125         extends Canvas\r
1126     {\r
1127       public void paint(Graphics g)\r
1128       {\r
1129         g.setColor(Color.white);\r
1130         g.fillRect(0, 0, getSize().width, getSize().height);\r
1131         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1132         FontMetrics fm = g.getFontMetrics();\r
1133         int fh = fm.getHeight();\r
1134         int y = 5, x = 7;\r
1135         g.setColor(Color.black);\r
1136         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1137         g.drawString("JalView - Release 2.01", 200, y += fh);\r
1138         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1139         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
1140                      x, y += fh * 2);\r
1141         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
1142                      x, y += fh);\r
1143         g.drawString(\r
1144             "For any issues relating to Jalview, email help@jalview.org", x,\r
1145             y += fh);\r
1146         g.drawString("If  you use JalView, please cite:", x, y += fh + 8);\r
1147         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
1148                      x, y += fh);\r
1149         g.drawString("Bioinformatics,  2004 12;426-7.", x, y += fh);\r
1150       }\r
1151     }\r
1152 \r
1153     Frame frame = new Frame();\r
1154     frame.add(new AboutPanel());\r
1155     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
1156 \r
1157   }\r
1158 }\r