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