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