src/jalview/appletgui/AlignFrame.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 \r
  20 package jalview.appletgui;\r
  21 \r
  22 import jalview.jbappletgui.GAlignFrame;\r
  23 import jalview.schemes.*;\r
  24 import jalview.datamodel.*;\r
  25 import jalview.analysis.*;\r
  26 import jalview.io.*;\r
  27 import java.awt.*;\r
  28 import java.awt.event.*;\r
  29 import java.util.*;\r
  30 import java.io.InputStreamReader;\r
  31 import java.io.BufferedReader;\r
  32 \r
  33 public class AlignFrame\r
  34     extends GAlignFrame\r
  35 {\r
  36   final AlignmentPanel alignPanel;\r
  37   final AlignViewport viewport;\r
  38   public static final int NEW_WINDOW_WIDTH = 700;\r
  39   public static final int NEW_WINDOW_HEIGHT = 500;\r
  40   jalview.bin.JalviewLite applet;\r
  41 \r
  42   public AlignFrame(AlignmentI al)\r
  43   {\r
  44     this.applet = null;\r
  45     viewport = new AlignViewport(al, null);\r
  46     alignPanel = new AlignmentPanel(this, viewport);\r
  47     add(alignPanel);\r
  48     alignPanel.validate();\r
  49 \r
  50     this.addWindowListener(new WindowAdapter()\r
  51     {\r
  52       public void windowClosing(WindowEvent e)\r
  53       {\r
  54         closeMenuItem_actionPerformed(null);\r
  55       }\r
  56     });\r
  57 \r
  58   }\r
  59 \r
  60 \r
  61   public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet)\r
  62   {\r
  63     this.applet = applet;\r
  64     viewport = new AlignViewport(al, applet);\r
  65     alignPanel = new AlignmentPanel(this, viewport);\r
  66     add(alignPanel);\r
  67     alignPanel.validate();\r
  68 \r
  69     String treeFile = applet.getParameter("treeFile");\r
  70     if (treeFile != null)\r
  71     {\r
  72       try\r
  73       {\r
  74         treeFile = treeFile;\r
  75         jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.\r
  76             getCodeBase() + treeFile, "URL");\r
  77         fin.parse();\r
  78 \r
  79         if (fin.getTree() != null)\r
  80         {\r
  81           TreePanel tp = null;\r
  82           tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
  83                              fin, "FromFile", applet.getCodeBase() + treeFile);\r
  84           jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
  85           addTreeMenuItem(tp, treeFile);\r
  86         }\r
  87       }\r
  88       catch (Exception ex)\r
  89       {\r
  90         ex.printStackTrace();\r
  91       }\r
  92     }\r
  93 \r
  94     this.addWindowListener(new WindowAdapter()\r
  95     {\r
  96       public void windowClosing(WindowEvent e)\r
  97           {\r
  98             closeMenuItem_actionPerformed(null);\r
  99           }\r
 100     });\r
 101 \r
 102 \r
 103 \r
 104   }\r
 105 \r
 106   public void inputText_actionPerformed(ActionEvent e)\r
 107   {\r
 108     CutAndPasteTransfer cap = new CutAndPasteTransfer(true);\r
 109     Frame frame = new Frame();\r
 110     frame.add(cap);\r
 111     jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
 112   }\r
 113 \r
 114   protected void outputText_actionPerformed(ActionEvent e)\r
 115   {\r
 116     CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
 117     Frame frame = new Frame();\r
 118     frame.add(cap);\r
 119     jalview.bin.JalviewLite.addFrame(frame,\r
 120                                      "Alignment output - " + e.getActionCommand(),\r
 121                                      600, 500);\r
 122     cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),\r
 123                                               viewport.getAlignment().\r
 124                                               getSequences()));\r
 125   }\r
 126 \r
 127   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 128   {\r
 129     PaintRefresher.components.remove(viewport.alignment);\r
 130     dispose();\r
 131   }\r
 132 \r
 133   Stack historyList = new Stack();\r
 134   Stack redoList = new Stack();\r
 135 \r
 136   void updateEditMenuBar()\r
 137   {\r
 138     if (historyList.size() > 0)\r
 139     {\r
 140       undoMenuItem.setEnabled(true);\r
 141       HistoryItem hi = (HistoryItem) historyList.peek();\r
 142       undoMenuItem.setLabel("Undo " + hi.getDescription());\r
 143     }\r
 144     else\r
 145     {\r
 146       undoMenuItem.setEnabled(false);\r
 147       undoMenuItem.setLabel("Undo");\r
 148     }\r
 149 \r
 150     if (redoList.size() > 0)\r
 151     {\r
 152       redoMenuItem.setEnabled(true);\r
 153       HistoryItem hi = (HistoryItem) redoList.peek();\r
 154       redoMenuItem.setLabel("Redo " + hi.getDescription());\r
 155     }\r
 156     else\r
 157     {\r
 158       redoMenuItem.setEnabled(false);\r
 159       redoMenuItem.setLabel("Redo");\r
 160     }\r
 161   }\r
 162 \r
 163   public void addHistoryItem(HistoryItem hi)\r
 164   {\r
 165     historyList.push(hi);\r
 166     updateEditMenuBar();\r
 167   }\r
 168 \r
 169   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 170   {\r
 171     HistoryItem hi = (HistoryItem) historyList.pop();\r
 172     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
 173                                   HistoryItem.HIDE));\r
 174     restoreHistoryItem(hi);\r
 175   }\r
 176 \r
 177   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 178   {\r
 179     HistoryItem hi = (HistoryItem) redoList.pop();\r
 180     restoreHistoryItem(hi);\r
 181     updateEditMenuBar();\r
 182     viewport.updateConsensus();\r
 183     alignPanel.repaint();\r
 184     alignPanel.repaint();\r
 185   }\r
 186 \r
 187   // used by undo and redo\r
 188   void restoreHistoryItem(HistoryItem hi)\r
 189   {\r
 190     if (hi.getType() == HistoryItem.SORT)\r
 191     {\r
 192       for (int i = 0; i < hi.getSequences().size(); i++)\r
 193       {\r
 194         viewport.alignment.getSequences().setElementAt(hi.getSequences().\r
 195             elementAt(i), i);\r
 196       }\r
 197     }\r
 198     else\r
 199     {\r
 200       for (int i = 0; i < hi.getSequences().size(); i++)\r
 201       {\r
 202         SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
 203         if (restore.getLength() == 0)\r
 204         {\r
 205           // log.System.out.println(hi.getHidden().elementAt(i));\r
 206           restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 207           viewport.alignment.getSequences().insertElementAt(\r
 208               restore,\r
 209               hi.getAlignIndex(i));\r
 210         }\r
 211         else\r
 212         {\r
 213           restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 214         }\r
 215       }\r
 216       if (hi.getType() == HistoryItem.PASTE)\r
 217       {\r
 218         for (int i = viewport.alignment.getHeight() - 1;\r
 219              i > hi.getSequences().size() - 1; i--)\r
 220         {\r
 221           viewport.alignment.deleteSequence(i);\r
 222         }\r
 223       }\r
 224     }\r
 225 \r
 226     updateEditMenuBar();\r
 227 \r
 228     viewport.updateConsensus();\r
 229     viewport.updateConservation();\r
 230     alignPanel.repaint();\r
 231   }\r
 232 \r
 233   public void moveSelectedSequences(boolean up)\r
 234   {\r
 235     SequenceGroup sg = viewport.getSelectionGroup();\r
 236     if (sg == null)\r
 237     {\r
 238       return;\r
 239     }\r
 240 \r
 241     if (up)\r
 242     {\r
 243       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 244       {\r
 245         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 246         if (!sg.sequences.contains(seq))\r
 247         {\r
 248           continue;\r
 249         }\r
 250 \r
 251         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 252         if (sg.sequences.contains(temp))\r
 253         {\r
 254           continue;\r
 255         }\r
 256 \r
 257         viewport.alignment.getSequences().setElementAt(temp, i);\r
 258         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 259       }\r
 260     }\r
 261     else\r
 262     {\r
 263       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 264       {\r
 265         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 266         if (!sg.sequences.contains(seq))\r
 267         {\r
 268           continue;\r
 269         }\r
 270 \r
 271         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 272         if (sg.sequences.contains(temp))\r
 273         {\r
 274           continue;\r
 275         }\r
 276 \r
 277         viewport.alignment.getSequences().setElementAt(temp, i);\r
 278         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 279       }\r
 280     }\r
 281 \r
 282     alignPanel.repaint();\r
 283   }\r
 284 \r
 285   StringBuffer copiedSequences;\r
 286   protected void copy_actionPerformed(ActionEvent e)\r
 287   {\r
 288     if (viewport.getSelectionGroup() == null)\r
 289     {\r
 290       return;\r
 291     }\r
 292 \r
 293     SequenceGroup sg = viewport.getSelectionGroup();\r
 294     copiedSequences = new StringBuffer();\r
 295     Hashtable orderedSeqs = new Hashtable();\r
 296     for (int i = 0; i < sg.getSize(); i++)\r
 297     {\r
 298       SequenceI seq = sg.getSequenceAt(i);\r
 299       int index = viewport.alignment.findIndex(seq);\r
 300       orderedSeqs.put(index + "", seq);\r
 301     }\r
 302 \r
 303     int index = 0, startRes, endRes;\r
 304     char ch;\r
 305 \r
 306     for (int i = 0; i < sg.getSize(); i++)\r
 307     {\r
 308         SequenceI seq = null;\r
 309 \r
 310         while (seq == null)\r
 311         {\r
 312             if (orderedSeqs.containsKey(index + ""))\r
 313             {\r
 314                 seq = (SequenceI) orderedSeqs.get(index + "");\r
 315                 index++;\r
 316 \r
 317                 break;\r
 318             }\r
 319             else\r
 320             {\r
 321                 index++;\r
 322             }\r
 323         }\r
 324 \r
 325         //FIND START RES\r
 326         //Returns residue following index if gap\r
 327         startRes = seq.findPosition(sg.getStartRes());\r
 328 \r
 329         //FIND END RES\r
 330         //Need to find the residue preceeding index if gap\r
 331         endRes = 0;\r
 332 \r
 333         for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
 334         {\r
 335           ch = seq.getCharAt(j);\r
 336           if (!jalview.util.Comparison.isGap( (ch)))\r
 337           {\r
 338             endRes++;\r
 339           }\r
 340         }\r
 341 \r
 342         if(endRes>0)\r
 343         {\r
 344           endRes += seq.getStart() -1;\r
 345         }\r
 346 \r
 347         copiedSequences.append(seq.getName() + "\t" +\r
 348             startRes + "\t" +\r
 349             endRes + "\t" +\r
 350             seq.getSequence(sg.getStartRes(),\r
 351                 sg.getEndRes() + 1) + "\n");\r
 352     }\r
 353 \r
 354   }\r
 355 \r
 356   protected void pasteNew_actionPerformed(ActionEvent e)\r
 357   {\r
 358     paste(true);\r
 359   }\r
 360 \r
 361   protected void pasteThis_actionPerformed(ActionEvent e)\r
 362   {\r
 363     addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
 364                                    HistoryItem.PASTE));\r
 365     paste(false);\r
 366   }\r
 367 \r
 368   void paste(boolean newAlignment)\r
 369   {\r
 370     try\r
 371     {\r
 372       if (copiedSequences == null)\r
 373       {\r
 374         return;\r
 375       }\r
 376 \r
 377       StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
 378       Vector seqs = new Vector();\r
 379       while (st.hasMoreElements())\r
 380       {\r
 381         String name = st.nextToken();\r
 382         int start = Integer.parseInt(st.nextToken());\r
 383         int end = Integer.parseInt(st.nextToken());\r
 384         Sequence sequence = new Sequence(name, st.nextToken(), start, end);\r
 385 \r
 386         if (!newAlignment)\r
 387         {\r
 388           viewport.alignment.addSequence(sequence);\r
 389         }\r
 390         else\r
 391         {\r
 392           seqs.addElement(sequence);\r
 393         }\r
 394       }\r
 395 \r
 396       if (newAlignment)\r
 397       {\r
 398         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 399         for (int i = 0; i < seqs.size(); i++)\r
 400         {\r
 401           newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
 402         }\r
 403 \r
 404         AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);\r
 405         String newtitle = new String("Copied sequences");\r
 406         if (getTitle().startsWith("Copied sequences"))\r
 407         {\r
 408           newtitle = getTitle();\r
 409         }\r
 410         else\r
 411         {\r
 412           newtitle = newtitle.concat("- from " + getTitle());\r
 413         }\r
 414         jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
 415                                          NEW_WINDOW_HEIGHT);\r
 416       }\r
 417       else\r
 418       {\r
 419         viewport.setEndSeq(viewport.alignment.getHeight());\r
 420         viewport.alignment.getWidth();\r
 421         viewport.updateConservation();\r
 422         viewport.updateConsensus();\r
 423         alignPanel.repaint();\r
 424       }\r
 425 \r
 426     }\r
 427     catch (Exception ex)\r
 428     {} // could be anything being pasted in here\r
 429 \r
 430   }\r
 431 \r
 432   protected void cut_actionPerformed(ActionEvent e)\r
 433   {\r
 434     copy_actionPerformed(null);\r
 435     delete_actionPerformed(null);\r
 436   }\r
 437 \r
 438   protected void delete_actionPerformed(ActionEvent e)\r
 439   {\r
 440     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
 441                                    HistoryItem.HIDE));\r
 442     if (viewport.getSelectionGroup() == null)\r
 443     {\r
 444       return;\r
 445     }\r
 446 \r
 447 \r
 448     SequenceGroup sg = viewport.getSelectionGroup();\r
 449     boolean allSequences = false;\r
 450     if(sg.sequences.size()==viewport.alignment.getHeight())\r
 451           allSequences = true;\r
 452 \r
 453     for (int i = 0; i < sg.sequences.size(); i++)\r
 454     {\r
 455       SequenceI seq = sg.getSequenceAt(i);\r
 456       int index = viewport.getAlignment().findIndex(seq);\r
 457       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
 458 \r
 459       // If the cut affects all sequences, remove highlighted columns\r
 460       if (allSequences)\r
 461       {\r
 462         viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
 463                                                      sg.getEndRes() + 1);\r
 464       }\r
 465 \r
 466 \r
 467       if (seq.getSequence().length() < 1)\r
 468       {\r
 469         viewport.getAlignment().deleteSequence(seq);\r
 470       }\r
 471       else\r
 472       {\r
 473         viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 474       }\r
 475     }\r
 476 \r
 477     viewport.setSelectionGroup(null);\r
 478     viewport.alignment.deleteGroup(sg);\r
 479     viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);\r
 480     if (viewport.getAlignment().getHeight() < 1)\r
 481     {\r
 482       try\r
 483       {\r
 484         this.setVisible(false);\r
 485       }\r
 486       catch (Exception ex)\r
 487       {}\r
 488     }\r
 489     viewport.updateConservation();\r
 490     viewport.updateConsensus();\r
 491     alignPanel.repaint();\r
 492 \r
 493   }\r
 494 \r
 495   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 496   {\r
 497     viewport.alignment.deleteAllGroups();\r
 498     viewport.setSelectionGroup(null);\r
 499 \r
 500     alignPanel.repaint();\r
 501   }\r
 502 \r
 503   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 504   {\r
 505     SequenceGroup sg = new SequenceGroup();\r
 506     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 507     {\r
 508       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
 509     }\r
 510     sg.setEndRes(viewport.alignment.getWidth()-1);\r
 511     viewport.setSelectionGroup(sg);\r
 512     alignPanel.repaint();\r
 513     PaintRefresher.Refresh(null, viewport.alignment);\r
 514   }\r
 515 \r
 516   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 517   {\r
 518     viewport.setSelectionGroup(null);\r
 519     viewport.getColumnSelection().clear();\r
 520     viewport.setSelectionGroup(null);\r
 521     PaintRefresher.Refresh(null, viewport.alignment);\r
 522   }\r
 523 \r
 524   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 525   {\r
 526     SequenceGroup sg = viewport.getSelectionGroup();\r
 527     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 528     {\r
 529       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
 530     }\r
 531 \r
 532     PaintRefresher.Refresh(null, viewport.alignment);\r
 533   }\r
 534 \r
 535   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 536   {\r
 537     ColumnSelection colSel = viewport.getColumnSelection();\r
 538     if (colSel.size() > 0)\r
 539     {\r
 540       addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
 541                                      HistoryItem.HIDE));\r
 542       int min = colSel.getMin();\r
 543       viewport.getAlignment().trimLeft(min);\r
 544       colSel.compensateForEdit(0, min);\r
 545 \r
 546       if (viewport.getSelectionGroup() != null)\r
 547       {\r
 548         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 549       }\r
 550 \r
 551       Vector groups = viewport.alignment.getGroups();\r
 552       for (int i = 0; i < groups.size(); i++)\r
 553       {\r
 554         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 555         if (!sg.adjustForRemoveLeft(min))\r
 556         {\r
 557           viewport.alignment.deleteGroup(sg);\r
 558         }\r
 559       }\r
 560 \r
 561       alignPanel.repaint();\r
 562     }\r
 563   }\r
 564 \r
 565   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 566   {\r
 567     ColumnSelection colSel = viewport.getColumnSelection();\r
 568     if (colSel.size() > 0)\r
 569     {\r
 570       addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
 571                                      HistoryItem.HIDE));\r
 572       int max = colSel.getMax();\r
 573       viewport.getAlignment().trimRight(max);\r
 574       if (viewport.getSelectionGroup() != null)\r
 575       {\r
 576         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 577       }\r
 578 \r
 579       Vector groups = viewport.alignment.getGroups();\r
 580       for (int i = 0; i < groups.size(); i++)\r
 581       {\r
 582         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 583         if (!sg.adjustForRemoveRight(max))\r
 584         {\r
 585           viewport.alignment.deleteGroup(sg);\r
 586         }\r
 587       }\r
 588 \r
 589       alignPanel.repaint();\r
 590     }\r
 591 \r
 592   }\r
 593 \r
 594   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 595   {\r
 596     addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
 597                                    viewport.alignment,\r
 598                                    HistoryItem.HIDE));\r
 599 \r
 600     //This is to maintain viewport position on first residue\r
 601     //of first sequence\r
 602     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
 603     int startRes = seq.findPosition(viewport.startRes);\r
 604 \r
 605     viewport.getAlignment().removeGaps();\r
 606 \r
 607     viewport.setStartRes(seq.findIndex(startRes)-1);\r
 608 \r
 609     viewport.updateConservation();\r
 610     viewport.updateConsensus();\r
 611     resetAllClustalSchemes();\r
 612     alignPanel.repaint();\r
 613   }\r
 614 \r
 615   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 616   {\r
 617     addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
 618                                    HistoryItem.HIDE));\r
 619 \r
 620     //This is to maintain viewport position on first residue\r
 621     //of first sequence\r
 622     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
 623     int startRes = seq.findPosition(viewport.startRes);\r
 624 \r
 625     SequenceI current;\r
 626     int jSize;\r
 627 \r
 628     Vector seqs=null;\r
 629 \r
 630     int start=0, end = viewport.alignment.getWidth();\r
 631 \r
 632     if (viewport.getSelectionGroup() != null\r
 633         && viewport.getSelectionGroup().sequences != null\r
 634         && viewport.getSelectionGroup().sequences.size()>0)\r
 635     {\r
 636       seqs = viewport.getSelectionGroup().sequences;\r
 637       start = viewport.getSelectionGroup().getStartRes();\r
 638       end = viewport.getSelectionGroup().getEndRes();\r
 639     }\r
 640     else\r
 641       seqs = viewport.alignment.getSequences();\r
 642 \r
 643     for (int i = 0; i <seqs.size(); i++)\r
 644     {\r
 645       current = (SequenceI)seqs.elementAt(i);\r
 646       jSize = current.getLength();\r
 647 \r
 648       int j = start;\r
 649       do\r
 650       {\r
 651         if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 652         {\r
 653           current.deleteCharAt(j);\r
 654           j--;\r
 655           jSize--;\r
 656         }\r
 657         j++;\r
 658       }\r
 659       while(j < end && j < jSize) ;\r
 660     }\r
 661 \r
 662     viewport.setStartRes(seq.findIndex(startRes)-1);\r
 663     resetAllClustalSchemes();\r
 664     viewport.updateConservation();\r
 665     viewport.updateConsensus();\r
 666     alignPanel.repaint();\r
 667   }\r
 668 \r
 669   void resetAllClustalSchemes()\r
 670   {\r
 671     if(viewport.getGlobalColourScheme()!=null\r
 672        && viewport.getGlobalColourScheme() instanceof ClustalxColourScheme)\r
 673     {\r
 674       ((ClustalxColourScheme)viewport.getGlobalColourScheme()).\r
 675           resetClustalX(viewport.alignment.getSequences(),\r
 676                         viewport.alignment.getWidth());\r
 677     }\r
 678 \r
 679     int s, sSize = viewport.alignment.getGroups().size();\r
 680     for(s=0; s<sSize; s++)\r
 681     {\r
 682       SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
 683       if(sg.cs instanceof ClustalxColourScheme)\r
 684       {\r
 685         ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());\r
 686       }\r
 687     }\r
 688   }\r
 689 \r
 690 \r
 691 \r
 692   public void findMenuItem_actionPerformed(ActionEvent e)\r
 693   {\r
 694     Finder finder = new Finder(alignPanel);\r
 695   }\r
 696 \r
 697   public void font_actionPerformed(ActionEvent e)\r
 698   {\r
 699     Frame frame = new Frame();\r
 700     FontChooser fc = new FontChooser(alignPanel, frame);\r
 701     frame.add(fc);\r
 702     jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);\r
 703 \r
 704   }\r
 705 \r
 706   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 707   {\r
 708     viewport.setShowFullId(fullSeqId.getState());\r
 709     alignPanel.fontChanged();\r
 710     alignPanel.repaint();\r
 711   }\r
 712 \r
 713   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 714   {\r
 715     viewport.setColourText(colourTextMenuItem.getState());\r
 716     alignPanel.repaint();\r
 717   }\r
 718 \r
 719   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 720   {\r
 721     viewport.setWrapAlignment(wrapMenuItem.getState());\r
 722     alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
 723     scaleAbove.setEnabled(wrapMenuItem.getState());\r
 724     scaleLeft.setEnabled(wrapMenuItem.getState());\r
 725     scaleRight.setEnabled(wrapMenuItem.getState());\r
 726     alignPanel.repaint();\r
 727   }\r
 728 \r
 729   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 730   {\r
 731     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
 732     alignPanel.repaint();\r
 733   }\r
 734 \r
 735   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 736   {\r
 737     viewport.setScaleLeftWrapped(scaleLeft.getState());\r
 738     alignPanel.repaint();\r
 739   }\r
 740 \r
 741   protected void scaleRight_actionPerformed(ActionEvent e)\r
 742   {\r
 743     viewport.setScaleRightWrapped(scaleRight.getState());\r
 744     alignPanel.repaint();\r
 745   }\r
 746 \r
 747   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 748   {\r
 749     viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
 750     alignPanel.repaint();\r
 751   }\r
 752 \r
 753   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 754   {\r
 755     viewport.setShowText(viewTextMenuItem.getState());\r
 756     alignPanel.repaint();\r
 757   }\r
 758 \r
 759   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 760   {\r
 761     viewport.setRenderGaps(renderGapsMenuItem.getState());\r
 762     alignPanel.repaint();\r
 763   }\r
 764 \r
 765   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 766   {\r
 767     if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment())\r
 768     {\r
 769       annotationPanelMenuItem.setState(false);\r
 770       return;\r
 771     }\r
 772     viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
 773     alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
 774   }\r
 775 \r
 776   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 777   {\r
 778     if (alignPanel.overviewPanel != null)\r
 779     {\r
 780       return;\r
 781     }\r
 782 \r
 783     Frame frame = new Frame();\r
 784     OverviewPanel overview = new OverviewPanel(alignPanel);\r
 785     frame.add(overview);\r
 786     // +50 must allow for applet frame window\r
 787     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
 788                                      overview.preferredSize().width,\r
 789                                      overview.preferredSize().height + 50);\r
 790 \r
 791     frame.pack();\r
 792     frame.addWindowListener(new WindowAdapter()\r
 793     {\r
 794       public void windowClosing(WindowEvent e)\r
 795       {\r
 796         alignPanel.setOverviewPanel(null);\r
 797       };\r
 798     });\r
 799 \r
 800     alignPanel.setOverviewPanel(overview);\r
 801 \r
 802   }\r
 803 \r
 804   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 805   {\r
 806     changeColour(null);\r
 807   }\r
 808 \r
 809   public void clustalColour_actionPerformed(ActionEvent e)\r
 810   {\r
 811     abovePIDThreshold.setState(false);\r
 812     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
 813                                           viewport.alignment.getWidth()));\r
 814   }\r
 815 \r
 816   public void zappoColour_actionPerformed(ActionEvent e)\r
 817   {\r
 818     changeColour(new ZappoColourScheme());\r
 819   }\r
 820 \r
 821   public void taylorColour_actionPerformed(ActionEvent e)\r
 822   {\r
 823     changeColour(new TaylorColourScheme());\r
 824   }\r
 825 \r
 826   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 827   {\r
 828     changeColour(new HydrophobicColourScheme());\r
 829   }\r
 830 \r
 831   public void helixColour_actionPerformed(ActionEvent e)\r
 832   {\r
 833     changeColour(new HelixColourScheme());\r
 834   }\r
 835 \r
 836   public void strandColour_actionPerformed(ActionEvent e)\r
 837   {\r
 838     changeColour(new StrandColourScheme());\r
 839   }\r
 840 \r
 841   public void turnColour_actionPerformed(ActionEvent e)\r
 842   {\r
 843     changeColour(new TurnColourScheme());\r
 844   }\r
 845 \r
 846   public void buriedColour_actionPerformed(ActionEvent e)\r
 847   {\r
 848     changeColour(new BuriedColourScheme());\r
 849   }\r
 850 \r
 851   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 852   {\r
 853     changeColour(new NucleotideColourScheme());\r
 854   }\r
 855 \r
 856   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 857   {\r
 858     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
 859   }\r
 860 \r
 861   void changeColour(ColourSchemeI cs)\r
 862   {\r
 863     int threshold = 0;\r
 864 \r
 865     if(cs!=null)\r
 866     {\r
 867       if (viewport.getAbovePIDThreshold())\r
 868       {\r
 869         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
 870 \r
 871         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
 872 \r
 873         viewport.setGlobalColourScheme(cs);\r
 874       }\r
 875       else\r
 876       {\r
 877         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
 878       }\r
 879 \r
 880       if (viewport.getConservationSelected())\r
 881       {\r
 882 \r
 883         Alignment al = (Alignment) viewport.alignment;\r
 884         Conservation c = new Conservation("All",\r
 885                                           ResidueProperties.propHash, 3,\r
 886                                           al.getSequences(), 0,\r
 887                                           al.getWidth() - 1);\r
 888 \r
 889         c.calculate();\r
 890         c.verdict(false, viewport.ConsPercGaps);\r
 891 \r
 892         cs.setConservation(c);\r
 893 \r
 894         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,\r
 895             "Background"));\r
 896 \r
 897       }\r
 898       else\r
 899       {\r
 900         cs.setConservation(null);\r
 901       }\r
 902 \r
 903       cs.setConsensus(viewport.vconsensus);\r
 904 \r
 905     }\r
 906     viewport.setGlobalColourScheme(cs);\r
 907 \r
 908     if (viewport.getColourAppliesToAllGroups())\r
 909     {\r
 910       Vector groups = viewport.alignment.getGroups();\r
 911       for (int i = 0; i < groups.size(); i++)\r
 912       {\r
 913         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 914 \r
 915         if(cs==null)\r
 916         {\r
 917           sg.cs = null;\r
 918           continue;\r
 919         }\r
 920         if (cs instanceof ClustalxColourScheme)\r
 921         {\r
 922           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
 923         }\r
 924         else\r
 925         {\r
 926           try\r
 927           {\r
 928             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
 929           }\r
 930           catch (Exception ex)\r
 931           {\r
 932             ex.printStackTrace();\r
 933             sg.cs = cs;\r
 934           }\r
 935         }\r
 936 \r
 937         if (viewport.getAbovePIDThreshold()\r
 938             || cs instanceof PIDColourScheme\r
 939             || cs instanceof Blosum62ColourScheme)\r
 940         {\r
 941           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
 942           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 943         }\r
 944         else\r
 945           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
 946 \r
 947         if (viewport.getConservationSelected())\r
 948         {\r
 949           Conservation c = new Conservation("Group",\r
 950                                             ResidueProperties.propHash, 3,\r
 951                                             sg.sequences, 0,\r
 952                                             viewport.alignment.getWidth() - 1);\r
 953           c.calculate();\r
 954           c.verdict(false, viewport.ConsPercGaps);\r
 955           sg.cs.setConservation(c);\r
 956         }\r
 957         else\r
 958         {\r
 959           sg.cs.setConservation(null);\r
 960           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
 961         }\r
 962 \r
 963       }\r
 964     }\r
 965 \r
 966 \r
 967     if (alignPanel.getOverviewPanel() != null)\r
 968     {\r
 969       alignPanel.getOverviewPanel().updateOverviewImage();\r
 970     }\r
 971 \r
 972     alignPanel.repaint();\r
 973   }\r
 974 \r
 975 \r
 976 \r
 977   protected void modifyPID_actionPerformed(ActionEvent e)\r
 978   {\r
 979     if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
 980     {\r
 981       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
 982                                      "Background");\r
 983       SliderPanel.showPIDSlider();\r
 984     }\r
 985   }\r
 986 \r
 987   protected void modifyConservation_actionPerformed(ActionEvent e)\r
 988   {\r
 989     if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
 990     {\r
 991       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
 992                                         "Background");\r
 993       SliderPanel.showConservationSlider();\r
 994     }\r
 995   }\r
 996 \r
 997   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
 998   {\r
 999     viewport.setConservationSelected(conservationMenuItem.getState());\r
1000 \r
1001     viewport.setAbovePIDThreshold(false);\r
1002     abovePIDThreshold.setState(false);\r
1003 \r
1004     changeColour(viewport.getGlobalColourScheme());\r
1005 \r
1006     modifyConservation_actionPerformed(null);\r
1007   }\r
1008 \r
1009   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1010   {\r
1011     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
1012 \r
1013     conservationMenuItem.setState(false);\r
1014     viewport.setConservationSelected(false);\r
1015 \r
1016     changeColour(viewport.getGlobalColourScheme());\r
1017 \r
1018     modifyPID_actionPerformed(null);\r
1019   }\r
1020 \r
1021   public void userDefinedColour_actionPerformed(ActionEvent e)\r
1022   {\r
1023     UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);\r
1024   }\r
1025 \r
1026   public void PIDColour_actionPerformed(ActionEvent e)\r
1027   {\r
1028     changeColour(new PIDColourScheme());\r
1029   }\r
1030 \r
1031   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1032   {\r
1033     changeColour(new Blosum62ColourScheme());\r
1034   }\r
1035 \r
1036   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1037   {\r
1038     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
1039                                    HistoryItem.SORT));\r
1040     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
1041                               viewport.getAlignment().getSequenceAt(0));\r
1042     alignPanel.repaint();\r
1043   }\r
1044 \r
1045   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1046   {\r
1047     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
1048                                    HistoryItem.SORT));\r
1049     AlignmentSorter.sortByID(viewport.getAlignment());\r
1050     alignPanel.repaint();\r
1051   }\r
1052 \r
1053   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1054   {\r
1055     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
1056                                    HistoryItem.SORT));\r
1057     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
1058     alignPanel.repaint();\r
1059 \r
1060   }\r
1061 \r
1062   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1063   {\r
1064     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
1065     Frame frame = new Frame();\r
1066     frame.add(sp);\r
1067     jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",\r
1068                                      400, 120);\r
1069 \r
1070   }\r
1071 \r
1072   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1073   {\r
1074     if (viewport.getSelectionGroup().getSize() > 1)\r
1075     {\r
1076       Frame frame = new Frame();\r
1077       frame.add(new PairwiseAlignPanel(viewport));\r
1078       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
1079     }\r
1080   }\r
1081 \r
1082   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
1083   {\r
1084 \r
1085     if ( (viewport.getSelectionGroup() != null &&\r
1086           viewport.getSelectionGroup().getSize() < 4 &&\r
1087           viewport.getSelectionGroup().getSize() > 0)\r
1088         || viewport.getAlignment().getHeight() < 4)\r
1089     {\r
1090       return;\r
1091     }\r
1092 \r
1093     try\r
1094     {\r
1095       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
1096       Frame frame = new Frame();\r
1097       frame.add(pcaPanel);\r
1098       jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",\r
1099                                        400, 400);\r
1100     }\r
1101     catch (java.lang.OutOfMemoryError ex)\r
1102     {\r
1103     }\r
1104 \r
1105   }\r
1106 \r
1107   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1108   {\r
1109     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1110   }\r
1111 \r
1112   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1113   {\r
1114     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1115   }\r
1116 \r
1117   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1118   {\r
1119     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1120   }\r
1121 \r
1122   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1123   {\r
1124     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1125   }\r
1126 \r
1127   void NewTreePanel(String type, String pwType, String title)\r
1128   {\r
1129     //are the sequences aligned?\r
1130     if (!viewport.alignment.isAligned())\r
1131     {\r
1132       SequenceI current;\r
1133       int Width = viewport.getAlignment().getWidth();\r
1134 \r
1135       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1136            i++)\r
1137       {\r
1138         current = viewport.getAlignment().getSequenceAt(i);\r
1139 \r
1140         if (current.getLength() < Width)\r
1141         {\r
1142           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1143         }\r
1144       }\r
1145       alignPanel.repaint();\r
1146 \r
1147     }\r
1148 \r
1149     final TreePanel tp;\r
1150     if (viewport.getSelectionGroup() != null &&\r
1151         viewport.getSelectionGroup().getSize() > 3)\r
1152     {\r
1153       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
1154                          pwType,\r
1155                          0, viewport.alignment.getWidth());\r
1156     }\r
1157     else\r
1158     {\r
1159       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1160                          type, pwType, 0, viewport.alignment.getWidth());\r
1161     }\r
1162 \r
1163     addTreeMenuItem(tp, title);\r
1164 \r
1165     jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
1166   }\r
1167 \r
1168   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1169   {\r
1170     final MenuItem item = new MenuItem(title);\r
1171     sortByTreeMenu.add(item);\r
1172     item.addActionListener(new java.awt.event.ActionListener()\r
1173     {\r
1174       public void actionPerformed(ActionEvent e)\r
1175       {\r
1176         addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1177                                        HistoryItem.SORT));\r
1178         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1179         alignPanel.repaint();\r
1180       }\r
1181     });\r
1182 \r
1183     treePanel.addWindowListener(new WindowAdapter()\r
1184     {\r
1185       public void windowClosing(WindowEvent e)\r
1186       {\r
1187         sortByTreeMenu.remove(item);\r
1188       };\r
1189     });\r
1190   }\r
1191 \r
1192   protected void documentation_actionPerformed(ActionEvent e)\r
1193   {\r
1194     jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");\r
1195   }\r
1196 \r
1197   protected void about_actionPerformed(ActionEvent e)\r
1198   {\r
1199 \r
1200     class AboutPanel extends Canvas\r
1201     {\r
1202       String version;\r
1203       public AboutPanel(String version)\r
1204       { this.version = version; }\r
1205 \r
1206       public void paint(Graphics g)\r
1207       {\r
1208         g.setColor(Color.white);\r
1209         g.fillRect(0, 0, getSize().width, getSize().height);\r
1210         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1211         FontMetrics fm = g.getFontMetrics();\r
1212         int fh = fm.getHeight();\r
1213         int y = 5, x = 7;\r
1214         g.setColor(Color.black);\r
1215         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1216         g.drawString("Jalview - Release "+version, 200, y += fh);\r
1217         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1218         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
1219                      x, y += fh * 2);\r
1220         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
1221                      x, y += fh);\r
1222         g.drawString(\r
1223             "For any issues relating to Jalview, email help@jalview.org", x,\r
1224             y += fh);\r
1225         g.drawString("If  you use JalView, please cite:", x, y += fh + 8);\r
1226         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
1227                      x, y += fh);\r
1228         g.drawString("Bioinformatics,  2004 12;426-7.", x, y += fh);\r
1229       }\r
1230     }\r
1231 \r
1232     String version = "test";\r
1233     java.net.URL url = getClass().getResource("/.build_properties");\r
1234     if (url != null)\r
1235     {\r
1236       try\r
1237       {\r
1238         BufferedReader reader = new BufferedReader(new InputStreamReader(\r
1239             url.openStream()));\r
1240         String line;\r
1241         while ( (line = reader.readLine()) != null)\r
1242         {\r
1243           if (line.indexOf("VERSION") > -1)\r
1244           {\r
1245             version = line.substring(line.indexOf("=") + 1);\r
1246           }\r
1247         }\r
1248       }\r
1249       catch (Exception ex)\r
1250       {\r
1251         ex.printStackTrace();\r
1252       }\r
1253     }\r
1254 \r
1255 \r
1256     Frame frame = new Frame();\r
1257     frame.add(new AboutPanel(version));\r
1258     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
1259 \r
1260   }\r
1261 }\r