src/jalview/commands/EditCommand.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.commands;
  22
  23 import jalview.analysis.AlignSeq;
  24 import jalview.datamodel.AlignmentAnnotation;
  25 import jalview.datamodel.AlignmentI;
  26 import jalview.datamodel.Annotation;
  27 import jalview.datamodel.Range;
  28 import jalview.datamodel.Sequence;
  29 import jalview.datamodel.SequenceFeature;
  30 import jalview.datamodel.SequenceI;
  31 import jalview.datamodel.features.SequenceFeaturesI;
  32 import jalview.util.Comparison;
  33 import jalview.util.ReverseListIterator;
  34 import jalview.util.StringUtils;
  35
  36 import java.util.ArrayList;
  37 import java.util.HashMap;
  38 import java.util.Hashtable;
  39 import java.util.Iterator;
  40 import java.util.List;
  41 import java.util.ListIterator;
  42 import java.util.Map;
  43
  44 /**
  45  *
  46  * <p>
  47  * Title: EditCommmand
  48  * </p>
  49  *
  50  * <p>
  51  * Description: Essential information for performing undo and redo for cut/paste
  52  * insert/delete gap which can be stored in the HistoryList
  53  * </p>
  54  *
  55  * <p>
  56  * Copyright: Copyright (c) 2006
  57  * </p>
  58  *
  59  * <p>
  60  * Company: Dundee University
  61  * </p>
  62  *
  63  * @author not attributable
  64  * @version 1.0
  65  */
  66 public class EditCommand implements CommandI
  67 {
  68   public enum Action
  69   {
  70     INSERT_GAP
  71     {
  72       @Override
  73       public Action getUndoAction()
  74       {
  75         return DELETE_GAP;
  76       }
  77     },
  78     DELETE_GAP
  79     {
  80       @Override
  81       public Action getUndoAction()
  82       {
  83         return INSERT_GAP;
  84       }
  85     },
  86     CUT
  87     {
  88       @Override
  89       public Action getUndoAction()
  90       {
  91         return PASTE;
  92       }
  93     },
  94     PASTE
  95     {
  96       @Override
  97       public Action getUndoAction()
  98       {
  99         return CUT;
 100       }
 101     },
 102     REPLACE
 103     {
 104       @Override
 105       public Action getUndoAction()
 106       {
 107         return REPLACE;
 108       }
 109     },
 110     INSERT_NUC
 111     {
 112       @Override
 113       public Action getUndoAction()
 114       {
 115         return null;
 116       }
 117     };
 118     public abstract Action getUndoAction();
 119   };
 120
 121   private List<Edit> edits = new ArrayList<Edit>();
 122
 123   String description;
 124
 125   public EditCommand()
 126   {
 127   }
 128
 129   public EditCommand(String desc)
 130   {
 131     this.description = desc;
 132   }
 133
 134   public EditCommand(String desc, Action command, SequenceI[] seqs,
 135           int position, int number, AlignmentI al)
 136   {
 137     this.description = desc;
 138     if (command == Action.CUT || command == Action.PASTE)
 139     {
 140       setEdit(new Edit(command, seqs, position, number, al));
 141     }
 142
 143     performEdit(0, null);
 144   }
 145
 146   public EditCommand(String desc, Action command, String replace,
 147           SequenceI[] seqs, int position, int number, AlignmentI al)
 148   {
 149     this.description = desc;
 150     if (command == Action.REPLACE)
 151     {
 152       setEdit(new Edit(command, seqs, position, number, al, replace));
 153     }
 154
 155     performEdit(0, null);
 156   }
 157
 158   /**
 159    * Set the list of edits to the specified item (only).
 160    *
 161    * @param e
 162    */
 163   protected void setEdit(Edit e)
 164   {
 165     edits.clear();
 166     edits.add(e);
 167   }
 168
 169   /**
 170    * Add the given edit command to the stored list of commands. If simply
 171    * expanding the range of the last command added, then modify it instead of
 172    * adding a new command.
 173    *
 174    * @param e
 175    */
 176   public void addEdit(Edit e)
 177   {
 178     if (!expandEdit(edits, e))
 179     {
 180       edits.add(e);
 181     }
 182   }
 183
 184   /**
 185    * Returns true if the new edit is incorporated by updating (expanding the
 186    * range of) the last edit on the list, else false. We can 'expand' the last
 187    * edit if the new one is the same action, on the same sequences, and acts on
 188    * a contiguous range. This is the case where a mouse drag generates a series
 189    * of contiguous gap insertions or deletions.
 190    *
 191    * @param edits
 192    * @param e
 193    * @return
 194    */
 195   protected static boolean expandEdit(List<Edit> edits, Edit e)
 196   {
 197     if (edits == null || edits.isEmpty())
 198     {
 199       return false;
 200     }
 201     Edit lastEdit = edits.get(edits.size() - 1);
 202     Action action = e.command;
 203     if (lastEdit.command != action)
 204     {
 205       return false;
 206     }
 207
 208     /*
 209      * Both commands must act on the same sequences - compare the underlying
 210      * dataset sequences, rather than the aligned sequences, which change as
 211      * they are edited.
 212      */
 213     if (lastEdit.seqs.length != e.seqs.length)
 214     {
 215       return false;
 216     }
 217     for (int i = 0; i < e.seqs.length; i++)
 218     {
 219       if (lastEdit.seqs[i].getDatasetSequence() != e.seqs[i]
 220               .getDatasetSequence())
 221       {
 222         return false;
 223       }
 224     }
 225
 226     /**
 227      * Check a contiguous edit; either
 228      * <ul>
 229      * <li>a new Insert <n> positions to the right of the last <insert n>,
 230      * or</li>
 231      * <li>a new Delete <n> gaps which is <n> positions to the left of the last
 232      * delete.</li>
 233      * </ul>
 234      */
 235     boolean contiguous = (action == Action.INSERT_GAP
 236             && e.position == lastEdit.position + lastEdit.number)
 237             || (action == Action.DELETE_GAP
 238                     && e.position + e.number == lastEdit.position);
 239     if (contiguous)
 240     {
 241       /*
 242        * We are just expanding the range of the last edit. For delete gap, also
 243        * moving the start position left.
 244        */
 245       lastEdit.number += e.number;
 246       lastEdit.seqs = e.seqs;
 247       if (action == Action.DELETE_GAP)
 248       {
 249         lastEdit.position--;
 250       }
 251       return true;
 252     }
 253     return false;
 254   }
 255
 256   /**
 257    * Clear the list of stored edit commands.
 258    *
 259    */
 260   protected void clearEdits()
 261   {
 262     edits.clear();
 263   }
 264
 265   /**
 266    * Returns the i'th stored Edit command.
 267    *
 268    * @param i
 269    * @return
 270    */
 271   protected Edit getEdit(int i)
 272   {
 273     if (i >= 0 && i < edits.size())
 274     {
 275       return edits.get(i);
 276     }
 277     return null;
 278   }
 279
 280   @Override
 281   final public String getDescription()
 282   {
 283     return description;
 284   }
 285
 286   @Override
 287   public int getSize()
 288   {
 289     return edits.size();
 290   }
 291
 292   /**
 293    * Return the alignment for the first edit (or null if no edit).
 294    *
 295    * @return
 296    */
 297   final public AlignmentI getAlignment()
 298   {
 299     return (edits.isEmpty() ? null : edits.get(0).al);
 300   }
 301
 302   /**
 303    * append a new editCommand Note. this shouldn't be called if the edit is an
 304    * operation affects more alignment objects than the one referenced in al (for
 305    * example, cut or pasting whole sequences). Use the form with an additional
 306    * AlignmentI[] views parameter.
 307    *
 308    * @param command
 309    * @param seqs
 310    * @param position
 311    * @param number
 312    * @param al
 313    * @param performEdit
 314    */
 315   final public void appendEdit(Action command, SequenceI[] seqs,
 316           int position, int number, AlignmentI al, boolean performEdit)
 317   {
 318     appendEdit(command, seqs, position, number, al, performEdit, null);
 319   }
 320
 321   /**
 322    * append a new edit command with a set of alignment views that may be
 323    * operated on
 324    *
 325    * @param command
 326    * @param seqs
 327    * @param position
 328    * @param number
 329    * @param al
 330    * @param performEdit
 331    * @param views
 332    */
 333   final public void appendEdit(Action command, SequenceI[] seqs,
 334           int position, int number, AlignmentI al, boolean performEdit,
 335           AlignmentI[] views)
 336   {
 337     Edit edit = new Edit(command, seqs, position, number, al);
 338     appendEdit(edit, al, performEdit, views);
 339   }
 340
 341   /**
 342    * Overloaded method that accepts an Edit object with additional parameters.
 343    *
 344    * @param edit
 345    * @param al
 346    * @param performEdit
 347    * @param views
 348    */
 349   final public void appendEdit(Edit edit, AlignmentI al,
 350           boolean performEdit, AlignmentI[] views)
 351   {
 352     if (al.getHeight() == edit.seqs.length)
 353     {
 354       edit.al = al;
 355       edit.fullAlignmentHeight = true;
 356     }
 357
 358     addEdit(edit);
 359
 360     if (performEdit)
 361     {
 362       performEdit(edit, views);
 363     }
 364   }
 365
 366   /**
 367    * Execute all the edit commands, starting at the given commandIndex
 368    *
 369    * @param commandIndex
 370    * @param views
 371    */
 372   public final void performEdit(int commandIndex, AlignmentI[] views)
 373   {
 374     ListIterator<Edit> iterator = edits.listIterator(commandIndex);
 375     while (iterator.hasNext())
 376     {
 377       Edit edit = iterator.next();
 378       performEdit(edit, views);
 379     }
 380   }
 381
 382   /**
 383    * Execute one edit command in all the specified alignment views
 384    *
 385    * @param edit
 386    * @param views
 387    */
 388   protected static void performEdit(Edit edit, AlignmentI[] views)
 389   {
 390     switch (edit.command)
 391     {
 392     case INSERT_GAP:
 393       insertGap(edit);
 394       break;
 395     case DELETE_GAP:
 396       deleteGap(edit);
 397       break;
 398     case CUT:
 399       cut(edit, views);
 400       break;
 401     case PASTE:
 402       paste(edit, views);
 403       break;
 404     case REPLACE:
 405       replace(edit);
 406       break;
 407     case INSERT_NUC:
 408       // TODO:add deleteNuc for UNDO
 409       // case INSERT_NUC:
 410       // insertNuc(edits[e]);
 411       break;
 412     default:
 413       break;
 414     }
 415   }
 416
 417   @Override
 418   final public void doCommand(AlignmentI[] views)
 419   {
 420     performEdit(0, views);
 421   }
 422
 423   /**
 424    * Undo the stored list of commands, in reverse order.
 425    */
 426   @Override
 427   final public void undoCommand(AlignmentI[] views)
 428   {
 429     ListIterator<Edit> iterator = edits.listIterator(edits.size());
 430     while (iterator.hasPrevious())
 431     {
 432       Edit e = iterator.previous();
 433       switch (e.command)
 434       {
 435       case INSERT_GAP:
 436         deleteGap(e);
 437         break;
 438       case DELETE_GAP:
 439         insertGap(e);
 440         break;
 441       case CUT:
 442         paste(e, views);
 443         break;
 444       case PASTE:
 445         cut(e, views);
 446         break;
 447       case REPLACE:
 448         replace(e);
 449         break;
 450       case INSERT_NUC:
 451         // not implemented
 452         break;
 453       default:
 454         break;
 455       }
 456     }
 457   }
 458
 459   /**
 460    * Insert gap(s) in sequences as specified by the command, and adjust
 461    * annotations.
 462    *
 463    * @param command
 464    */
 465   final private static void insertGap(Edit command)
 466   {
 467
 468     for (int s = 0; s < command.seqs.length; s++)
 469     {
 470       command.seqs[s].insertCharAt(command.position, command.number,
 471               command.gapChar);
 472       // System.out.println("pos: "+command.position+" number:
 473       // "+command.number);
 474     }
 475
 476     adjustAnnotations(command, true, false, null);
 477   }
 478
 479   //
 480   // final void insertNuc(Edit command)
 481   // {
 482   //
 483   // for (int s = 0; s < command.seqs.length; s++)
 484   // {
 485   // System.out.println("pos: "+command.position+" number: "+command.number);
 486   // command.seqs[s].insertCharAt(command.position, command.number,'A');
 487   // }
 488   //
 489   // adjustAnnotations(command, true, false, null);
 490   // }
 491
 492   /**
 493    * Delete gap(s) in sequences as specified by the command, and adjust
 494    * annotations.
 495    *
 496    * @param command
 497    */
 498   final static private void deleteGap(Edit command)
 499   {
 500     for (int s = 0; s < command.seqs.length; s++)
 501     {
 502       command.seqs[s].deleteChars(command.position,
 503               command.position + command.number);
 504     }
 505
 506     adjustAnnotations(command, false, false, null);
 507   }
 508
 509   /**
 510    * Carry out a Cut action. The cut characters are saved in case Undo is
 511    * requested.
 512    *
 513    * @param command
 514    * @param views
 515    */
 516   static void cut(Edit command, AlignmentI[] views)
 517   {
 518     boolean seqDeleted = false;
 519     command.string = new char[command.seqs.length][];
 520
 521     for (int i = 0; i < command.seqs.length; i++)
 522     {
 523       final SequenceI sequence = command.seqs[i];
 524       if (sequence.getLength() > command.position)
 525       {
 526         command.string[i] = sequence.getSequence(command.position,
 527                 command.position + command.number);
 528         SequenceI oldds = sequence.getDatasetSequence();
 529         if (command.oldds != null && command.oldds[i] != null)
 530         {
 531           // we are redoing an undone cut.
 532           sequence.setDatasetSequence(null);
 533         }
 534         Range cutPositions = sequence.findPositions(command.position + 1,
 535                 command.position + command.number);
 536         boolean cutIsInternal = cutPositions != null
 537                 && sequence.getStart() != cutPositions
 538                 .getBegin() && sequence.getEnd() != cutPositions.getEnd();
 539
 540         /*
 541          * perform the cut; if this results in a new dataset sequence, add
 542          * that to the alignment dataset
 543          */
 544         SequenceI ds = sequence.getDatasetSequence();
 545         sequence.deleteChars(command.position, command.position
 546                 + command.number);
 547         SequenceI newDs = sequence.getDatasetSequence();
 548         if (newDs != ds && command.al != null
 549                 && command.al.getDataset() != null
 550                 && !command.al.getDataset().getSequences().contains(newDs))
 551         {
 552           command.al.getDataset().addSequence(newDs);
 553         }
 554
 555         if (command.oldds != null && command.oldds[i] != null)
 556         {
 557           // Undoing previous Paste - so
 558           // oldds entry contains the cut dataset sequence,
 559           // with sequence features in expected place.
 560           sequence.setDatasetSequence(command.oldds[i]);
 561           command.oldds[i] = oldds;
 562         }
 563         else
 564         {
 565           // New cut operation
 566           // We always keep track of the dataset sequence so we can safely
 567           // restore it during the Undo
 568           if (command.oldds == null)
 569           {
 570             command.oldds = new SequenceI[command.seqs.length];
 571           }
 572           command.oldds[i] = oldds;// todo not if !cutIsInternal?
 573
 574           // do we need to edit sequence features for new sequence ?
 575           if (oldds != sequence.getDatasetSequence()
 576                   || (cutIsInternal
 577                           && sequence.getFeatures().hasFeatures()))
 578           // todo or just test cutIsInternal && cutPositions != null ?
 579           {
 580             if (cutPositions != null)
 581             {
 582               cutFeatures(command, sequence, cutPositions.getBegin(),
 583                               cutPositions.getEnd(), cutIsInternal);
 584             }
 585           }
 586         }
 587       }
 588
 589       if (sequence.getLength() < 1)
 590       {
 591         command.al.deleteSequence(sequence);
 592         seqDeleted = true;
 593       }
 594     }
 595
 596     adjustAnnotations(command, false, seqDeleted, views);
 597   }
 598
 599   /**
 600    * Perform the given Paste command. This may be to add cut or copied sequences
 601    * to an alignment, or to undo a 'Cut' action on a region of the alignment.
 602    *
 603    * @param command
 604    * @param views
 605    */
 606   static void paste(Edit command, AlignmentI[] views)
 607   {
 608     boolean seqWasDeleted = false;
 609
 610     for (int i = 0; i < command.seqs.length; i++)
 611     {
 612       boolean newDSNeeded = false;
 613       boolean newDSWasNeeded = command.oldds != null
 614               && command.oldds[i] != null;
 615       SequenceI sequence = command.seqs[i];
 616       if (sequence.getLength() < 1)
 617       {
 618         /*
 619          * sequence was deleted; re-add it to the alignment
 620          */
 621         if (command.alIndex[i] < command.al.getHeight())
 622         {
 623           List<SequenceI> sequences;
 624           synchronized (sequences = command.al.getSequences())
 625           {
 626             if (!(command.alIndex[i] < 0))
 627             {
 628               sequences.add(command.alIndex[i], sequence);
 629             }
 630           }
 631         }
 632         else
 633         {
 634           command.al.addSequence(sequence);
 635         }
 636         seqWasDeleted = true;
 637       }
 638       int newStart = sequence.getStart();
 639       int newEnd = sequence.getEnd();
 640
 641       StringBuilder tmp = new StringBuilder();
 642       tmp.append(sequence.getSequence());
 643       // Undo of a delete does not replace original dataset sequence on to
 644       // alignment sequence.
 645
 646       int start = 0;
 647       int length = 0;
 648
 649       if (command.string != null && command.string[i] != null)
 650       {
 651         if (command.position >= tmp.length())
 652         {
 653           // This occurs if padding is on, and residues
 654           // are removed from end of alignment
 655           int len = command.position - tmp.length();
 656           while (len > 0)
 657           {
 658             tmp.append(command.gapChar);
 659             len--;
 660           }
 661         }
 662         tmp.insert(command.position, command.string[i]);
 663         for (int s = 0; s < command.string[i].length; s++)
 664         {
 665           if (!Comparison.isGap(command.string[i][s]))
 666           {
 667             length++;
 668             if (!newDSNeeded)
 669             {
 670               newDSNeeded = true;
 671               start = sequence.findPosition(command.position);
 672               // end = sequence
 673               // .findPosition(command.position + command.number);
 674             }
 675             if (sequence.getStart() == start)
 676             {
 677               newStart--;
 678             }
 679             else
 680             {
 681               newEnd++;
 682             }
 683           }
 684         }
 685         command.string[i] = null;
 686       }
 687
 688       sequence.setSequence(tmp.toString());
 689       sequence.setStart(newStart);
 690       sequence.setEnd(newEnd);
 691
 692       /*
 693        * command and Undo share the same dataset sequence if cut was
 694        * at start or end of sequence
 695        */
 696       boolean sameDatasetSequence = false;
 697       if (newDSNeeded)
 698       {
 699         if (sequence.getDatasetSequence() != null)
 700         {
 701           SequenceI ds;
 702           if (newDSWasNeeded)
 703           {
 704             ds = command.oldds[i];
 705           }
 706           else
 707           {
 708             // make a new DS sequence
 709             // use new ds mechanism here
 710             String ungapped = AlignSeq.extractGaps(Comparison.GapChars,
 711                     sequence.getSequenceAsString());
 712             ds = new Sequence(sequence.getName(), ungapped,
 713                     sequence.getStart(), sequence.getEnd());
 714             ds.setDescription(sequence.getDescription());
 715           }
 716           if (command.oldds == null)
 717           {
 718             command.oldds = new SequenceI[command.seqs.length];
 719           }
 720           command.oldds[i] = sequence.getDatasetSequence();
 721           sameDatasetSequence = ds == sequence.getDatasetSequence();
 722           ds.setSequenceFeatures(sequence.getSequenceFeatures());
 723           sequence.setDatasetSequence(ds);
 724         }
 725         undoCutFeatures(command, command.seqs[i], start, length,
 726                 sameDatasetSequence);
 727       }
 728     }
 729     adjustAnnotations(command, true, seqWasDeleted, views);
 730
 731     command.string = null;
 732   }
 733
 734   static void replace(Edit command)
 735   {
 736     StringBuffer tmp;
 737     String oldstring;
 738     int start = command.position;
 739     int end = command.number;
 740     // TODO TUTORIAL - Fix for replacement with different length of sequence (or
 741     // whole sequence)
 742     // TODO Jalview 2.4 bugfix change to an aggregate command - original
 743     // sequence string is cut, new string is pasted in.
 744     command.number = start + command.string[0].length;
 745     for (int i = 0; i < command.seqs.length; i++)
 746     {
 747       boolean newDSWasNeeded = command.oldds != null
 748               && command.oldds[i] != null;
 749       boolean newStartEndWasNeeded = command.oldStartEnd!=null && command.oldStartEnd[i]!=null;
 750
 751       /**
 752        * cut addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT,
 753        * cut, sg.getStartRes(), sg.getEndRes()-sg.getStartRes()+1,
 754        * viewport.alignment));
 755        *
 756        */
 757       /**
 758        * then addHistoryItem(new EditCommand( "Add sequences",
 759        * EditCommand.PASTE, sequences, 0, alignment.getWidth(), alignment) );
 760        *
 761        */
 762
 763       Range beforeEditedPositions = command.seqs[i].findPositions(1, start);
 764       Range afterEditedPositions = command.seqs[i]
 765               .findPositions(start + end + 1, command.seqs[i].getLength());
 766
 767       oldstring = command.seqs[i].getSequenceAsString();
 768       tmp = new StringBuffer(oldstring.substring(0, start));
 769       tmp.append(command.string[i]);
 770       String nogaprep = jalview.analysis.AlignSeq.extractGaps(
 771               jalview.util.Comparison.GapChars,
 772               new String(command.string[i]));
 773       int ipos = command.seqs[i].findPosition(start)
 774               - command.seqs[i].getStart();
 775       if (end < oldstring.length())
 776       {
 777         tmp.append(oldstring.substring(end));
 778       }
 779       command.seqs[i].setSequence(tmp.toString());
 780       command.string[i] = oldstring
 781               .substring(start, Math.min(end, oldstring.length()))
 782               .toCharArray();
 783       String nogapold = AlignSeq.extractGaps(Comparison.GapChars,
 784               new String(command.string[i]));
 785
 786       if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase()))
 787       {
 788         // probably need a new dataset sequence
 789         if (newDSWasNeeded)
 790         {
 791           // then just switch the dataset sequence
 792           SequenceI oldds = command.seqs[i].getDatasetSequence();
 793           command.seqs[i].setDatasetSequence(command.oldds[i]);
 794           command.oldds[i] = oldds;
 795         }
 796         else
 797         if (newStartEndWasNeeded)
 798         {
 799           Range newStart = command.oldStartEnd[i];
 800           command.oldStartEnd[i] = new Range(command.seqs[i].getStart(),
 801                   command.seqs[i].getEnd());
 802           command.seqs[i].setStart(newStart.getBegin());
 803           command.seqs[i].setEnd(newStart.getEnd());
 804         }
 805         else
 806         {
 807           // first edit the original dataset sequence string
 808           SequenceI oldds = command.seqs[i].getDatasetSequence();
 809           String osp = oldds.getSequenceAsString();
 810
 811           String fullseq = osp.substring(0, ipos) + nogaprep
 812                   + osp.substring(ipos + nogaprep.length());
 813
 814           // and check if new sequence data is different..
 815           if (!fullseq.equalsIgnoreCase(osp))
 816           {
 817             // old ds and edited ds are different, so
 818             // create the new dataset sequence
 819             SequenceI newds = new Sequence(oldds);
 820             newds.setSequence(fullseq.toUpperCase());
 821
 822             if (command.oldds == null)
 823             {
 824               command.oldds = new SequenceI[command.seqs.length];
 825             }
 826             command.oldds[i] = command.seqs[i].getDatasetSequence();
 827             // TODO: JAL-1131 ensure newly created dataset sequence is added to
 828             // the set of
 829             // dataset sequences associated with the alignment.
 830             // TODO: JAL-1131 fix up any annotation associated with new dataset
 831             // sequence to ensure that original sequence/annotation
 832             // relationships
 833             // are preserved.
 834             command.seqs[i].setDatasetSequence(newds);
 835           }
 836           else
 837           {
 838             if (command.oldStartEnd == null)
 839             {
 840               command.oldStartEnd = new Range[command.seqs.length];
 841             }
 842             command.oldStartEnd[i] = new Range(command.seqs[i].getStart(),
 843                     command.seqs[i].getEnd());
 844             if (beforeEditedPositions != null
 845                     && afterEditedPositions == null)
 846             {
 847               // modification at end
 848               command.seqs[i].setEnd(
 849                       beforeEditedPositions.getEnd() + nogaprep.length());
 850             }
 851             else if (afterEditedPositions != null
 852                     && beforeEditedPositions == null)
 853             {
 854               // modification at start
 855               command.seqs[i].setStart(
 856                       afterEditedPositions.getBegin() - nogaprep.length());
 857             }
 858             else
 859             {
 860               // edit covered both start and end. Here we can only guess the
 861               // new
 862               // start/end
 863               String nogapalseq = jalview.analysis.AlignSeq.extractGaps(
 864                       jalview.util.Comparison.GapChars,
 865                       command.seqs[i].getSequenceAsString().toUpperCase());
 866               int newStart = command.seqs[i].getDatasetSequence()
 867                       .getSequenceAsString().indexOf(nogapalseq);
 868               if (newStart == -1)
 869               {
 870                 throw new Error(
 871                         "Implementation Error: could not locate start/end "
 872                                 + "in dataset sequence after an edit of the sequence string");
 873               }
 874               int newEnd = newStart + nogapalseq.length() - 1;
 875               command.seqs[i].setStart(newStart);
 876               command.seqs[i].setEnd(newEnd);
 877             }
 878           }
 879         }
 880       }
 881       tmp = null;
 882       oldstring = null;
 883     }
 884   }
 885
 886   final static void adjustAnnotations(Edit command, boolean insert,
 887           boolean modifyVisibility, AlignmentI[] views)
 888   {
 889     AlignmentAnnotation[] annotations = null;
 890
 891     if (modifyVisibility && !insert)
 892     {
 893       // only occurs if a sequence was added or deleted.
 894       command.deletedAnnotationRows = new Hashtable<SequenceI, AlignmentAnnotation[]>();
 895     }
 896     if (command.fullAlignmentHeight)
 897     {
 898       annotations = command.al.getAlignmentAnnotation();
 899     }
 900     else
 901     {
 902       int aSize = 0;
 903       AlignmentAnnotation[] tmp;
 904       for (int s = 0; s < command.seqs.length; s++)
 905       {
 906         command.seqs[s].sequenceChanged();
 907
 908         if (modifyVisibility)
 909         {
 910           // Rows are only removed or added to sequence object.
 911           if (!insert)
 912           {
 913             // remove rows
 914             tmp = command.seqs[s].getAnnotation();
 915             if (tmp != null)
 916             {
 917               int alen = tmp.length;
 918               for (int aa = 0; aa < tmp.length; aa++)
 919               {
 920                 if (!command.al.deleteAnnotation(tmp[aa]))
 921                 {
 922                   // strip out annotation not in the current al (will be put
 923                   // back on insert in all views)
 924                   tmp[aa] = null;
 925                   alen--;
 926                 }
 927               }
 928               command.seqs[s].setAlignmentAnnotation(null);
 929               if (alen != tmp.length)
 930               {
 931                 // save the non-null annotation references only
 932                 AlignmentAnnotation[] saved = new AlignmentAnnotation[alen];
 933                 for (int aa = 0, aapos = 0; aa < tmp.length; aa++)
 934                 {
 935                   if (tmp[aa] != null)
 936                   {
 937                     saved[aapos++] = tmp[aa];
 938                     tmp[aa] = null;
 939                   }
 940                 }
 941                 tmp = saved;
 942                 command.deletedAnnotationRows.put(command.seqs[s], saved);
 943                 // and then remove any annotation in the other views
 944                 for (int alview = 0; views != null
 945                         && alview < views.length; alview++)
 946                 {
 947                   if (views[alview] != command.al)
 948                   {
 949                     AlignmentAnnotation[] toremove = views[alview]
 950                             .getAlignmentAnnotation();
 951                     if (toremove == null || toremove.length == 0)
 952                     {
 953                       continue;
 954                     }
 955                     // remove any alignment annotation on this sequence that's
 956                     // on that alignment view.
 957                     for (int aa = 0; aa < toremove.length; aa++)
 958                     {
 959                       if (toremove[aa].sequenceRef == command.seqs[s])
 960                       {
 961                         views[alview].deleteAnnotation(toremove[aa]);
 962                       }
 963                     }
 964                   }
 965                 }
 966               }
 967               else
 968               {
 969                 // save all the annotation
 970                 command.deletedAnnotationRows.put(command.seqs[s], tmp);
 971               }
 972             }
 973           }
 974           else
 975           {
 976             // recover rows
 977             if (command.deletedAnnotationRows != null
 978                     && command.deletedAnnotationRows
 979                             .containsKey(command.seqs[s]))
 980             {
 981               AlignmentAnnotation[] revealed = command.deletedAnnotationRows
 982                       .get(command.seqs[s]);
 983               command.seqs[s].setAlignmentAnnotation(revealed);
 984               if (revealed != null)
 985               {
 986                 for (int aa = 0; aa < revealed.length; aa++)
 987                 {
 988                   // iterate through al adding original annotation
 989                   command.al.addAnnotation(revealed[aa]);
 990                 }
 991                 for (int aa = 0; aa < revealed.length; aa++)
 992                 {
 993                   command.al.setAnnotationIndex(revealed[aa], aa);
 994                 }
 995                 // and then duplicate added annotation on every other alignment
 996                 // view
 997                 for (int vnum = 0; views != null && vnum < views.length; vnum++)
 998                 {
 999                   if (views[vnum] != command.al)
1000                   {
1001                     int avwidth = views[vnum].getWidth() + 1;
1002                     // duplicate in this view
1003                     for (int a = 0; a < revealed.length; a++)
1004                     {
1005                       AlignmentAnnotation newann = new AlignmentAnnotation(
1006                               revealed[a]);
1007                       command.seqs[s].addAlignmentAnnotation(newann);
1008                       newann.padAnnotation(avwidth);
1009                       views[vnum].addAnnotation(newann);
1010                       views[vnum].setAnnotationIndex(newann, a);
1011                     }
1012                   }
1013                 }
1014               }
1015             }
1016           }
1017           continue;
1018         }
1019
1020         if (command.seqs[s].getAnnotation() == null)
1021         {
1022           continue;
1023         }
1024
1025         if (aSize == 0)
1026         {
1027           annotations = command.seqs[s].getAnnotation();
1028         }
1029         else
1030         {
1031           tmp = new AlignmentAnnotation[aSize
1032                   + command.seqs[s].getAnnotation().length];
1033
1034           System.arraycopy(annotations, 0, tmp, 0, aSize);
1035
1036           System.arraycopy(command.seqs[s].getAnnotation(), 0, tmp, aSize,
1037                   command.seqs[s].getAnnotation().length);
1038
1039           annotations = tmp;
1040         }
1041         aSize = annotations.length;
1042       }
1043     }
1044
1045     if (annotations == null)
1046     {
1047       return;
1048     }
1049
1050     if (!insert)
1051     {
1052       command.deletedAnnotations = new Hashtable<String, Annotation[]>();
1053     }
1054
1055     int aSize;
1056     Annotation[] temp;
1057     for (int a = 0; a < annotations.length; a++)
1058     {
1059       if (annotations[a].autoCalculated
1060               || annotations[a].annotations == null)
1061       {
1062         continue;
1063       }
1064
1065       int tSize = 0;
1066
1067       aSize = annotations[a].annotations.length;
1068       if (insert)
1069       {
1070         temp = new Annotation[aSize + command.number];
1071         if (annotations[a].padGaps)
1072         {
1073           for (int aa = 0; aa < temp.length; aa++)
1074           {
1075             temp[aa] = new Annotation(command.gapChar + "", null, ' ', 0);
1076           }
1077         }
1078       }
1079       else
1080       {
1081         if (command.position < aSize)
1082         {
1083           if (command.position + command.number >= aSize)
1084           {
1085             tSize = aSize;
1086           }
1087           else
1088           {
1089             tSize = aSize - command.number;
1090           }
1091         }
1092         else
1093         {
1094           tSize = aSize;
1095         }
1096
1097         if (tSize < 0)
1098         {
1099           tSize = aSize;
1100         }
1101         temp = new Annotation[tSize];
1102       }
1103
1104       if (insert)
1105       {
1106         if (command.position < annotations[a].annotations.length)
1107         {
1108           System.arraycopy(annotations[a].annotations, 0, temp, 0,
1109                   command.position);
1110
1111           if (command.deletedAnnotations != null
1112                   && command.deletedAnnotations
1113                           .containsKey(annotations[a].annotationId))
1114           {
1115             Annotation[] restore = command.deletedAnnotations
1116                     .get(annotations[a].annotationId);
1117
1118             System.arraycopy(restore, 0, temp, command.position,
1119                     command.number);
1120
1121           }
1122
1123           System.arraycopy(annotations[a].annotations, command.position,
1124                   temp, command.position + command.number,
1125                   aSize - command.position);
1126         }
1127         else
1128         {
1129           if (command.deletedAnnotations != null
1130                   && command.deletedAnnotations
1131                           .containsKey(annotations[a].annotationId))
1132           {
1133             Annotation[] restore = command.deletedAnnotations
1134                     .get(annotations[a].annotationId);
1135
1136             temp = new Annotation[annotations[a].annotations.length
1137                     + restore.length];
1138             System.arraycopy(annotations[a].annotations, 0, temp, 0,
1139                     annotations[a].annotations.length);
1140             System.arraycopy(restore, 0, temp,
1141                     annotations[a].annotations.length, restore.length);
1142           }
1143           else
1144           {
1145             temp = annotations[a].annotations;
1146           }
1147         }
1148       }
1149       else
1150       {
1151         if (tSize != aSize || command.position < 2)
1152         {
1153           int copylen = Math.min(command.position,
1154                   annotations[a].annotations.length);
1155           if (copylen > 0)
1156           {
1157             System.arraycopy(annotations[a].annotations, 0, temp, 0,
1158                     copylen); // command.position);
1159           }
1160
1161           Annotation[] deleted = new Annotation[command.number];
1162           if (copylen >= command.position)
1163           {
1164             copylen = Math.min(command.number,
1165                     annotations[a].annotations.length - command.position);
1166             if (copylen > 0)
1167             {
1168               System.arraycopy(annotations[a].annotations, command.position,
1169                       deleted, 0, copylen); // command.number);
1170             }
1171           }
1172
1173           command.deletedAnnotations.put(annotations[a].annotationId,
1174                   deleted);
1175           if (annotations[a].annotations.length > command.position
1176                   + command.number)
1177           {
1178             System.arraycopy(annotations[a].annotations,
1179                     command.position + command.number, temp,
1180                     command.position, annotations[a].annotations.length
1181                             - command.position - command.number); // aSize
1182           }
1183         }
1184         else
1185         {
1186           int dSize = aSize - command.position;
1187
1188           if (dSize > 0)
1189           {
1190             Annotation[] deleted = new Annotation[command.number];
1191             System.arraycopy(annotations[a].annotations, command.position,
1192                     deleted, 0, dSize);
1193
1194             command.deletedAnnotations.put(annotations[a].annotationId,
1195                     deleted);
1196
1197             tSize = Math.min(annotations[a].annotations.length,
1198                     command.position);
1199             temp = new Annotation[tSize];
1200             System.arraycopy(annotations[a].annotations, 0, temp, 0, tSize);
1201           }
1202           else
1203           {
1204             temp = annotations[a].annotations;
1205           }
1206         }
1207       }
1208
1209       annotations[a].annotations = temp;
1210     }
1211   }
1212
1213   /**
1214    * Restores features to the state before a Cut.
1215    * <ul>
1216    * <li>re-add any features deleted by the cut</li>
1217    * <li>remove any truncated features created by the cut</li>
1218    * <li>shift right any features to the right of the cut</li>
1219    * </ul>
1220    *
1221    * @param command
1222    *          the Cut command
1223    * @param seq
1224    *          the sequence the Cut applied to
1225    * @param start
1226    *          the start residue position of the cut
1227    * @param length
1228    *          the number of residues cut
1229    * @param sameDatasetSequence
1230    *          true if dataset sequence and frame of reference were left
1231    *          unchanged by the Cut
1232    */
1233   final static void undoCutFeatures(Edit command, SequenceI seq,
1234           final int start, final int length, boolean sameDatasetSequence)
1235   {
1236     SequenceI sequence = seq.getDatasetSequence();
1237     if (sequence == null)
1238     {
1239       sequence = seq;
1240     }
1241
1242     /*
1243      * shift right features that lie to the right of the restored cut (but not
1244      * if dataset sequence unchanged - so coordinates were changed by Cut)
1245      */
1246     if (!sameDatasetSequence)
1247     {
1248       /*
1249        * shift right all features right of and not
1250        * contiguous with the cut position
1251        */
1252       seq.getFeatures().shiftFeatures(start + 1, length);
1253
1254       /*
1255        * shift right any features that start at the cut position,
1256        * unless they were truncated
1257        */
1258       List<SequenceFeature> sfs = seq.getFeatures().findFeatures(start,
1259               start);
1260       for (SequenceFeature sf : sfs)
1261       {
1262         if (sf.getBegin() == start)
1263         {
1264           if (!command.truncatedFeatures.containsKey(seq)
1265                   || !command.truncatedFeatures.get(seq).contains(sf))
1266           {
1267             /*
1268              * feature was shifted left to cut position (not truncated),
1269              * so shift it back right
1270              */
1271             SequenceFeature shifted = new SequenceFeature(sf, sf.getBegin()
1272                     + length, sf.getEnd() + length, sf.getFeatureGroup(),
1273                     sf.getScore());
1274             seq.addSequenceFeature(shifted);
1275             seq.deleteFeature(sf);
1276           }
1277         }
1278       }
1279     }
1280
1281     /*
1282      * restore any features that were deleted or truncated
1283      */
1284     if (command.deletedFeatures != null
1285             && command.deletedFeatures.containsKey(seq))
1286     {
1287       for (SequenceFeature deleted : command.deletedFeatures.get(seq))
1288       {
1289         sequence.addSequenceFeature(deleted);
1290       }
1291     }
1292
1293     /*
1294      * delete any truncated features
1295      */
1296     if (command.truncatedFeatures != null
1297             && command.truncatedFeatures.containsKey(seq))
1298     {
1299       for (SequenceFeature amended : command.truncatedFeatures.get(seq))
1300       {
1301         sequence.deleteFeature(amended);
1302       }
1303     }
1304   }
1305
1306   /**
1307    * Returns the list of edit commands wrapped by this object.
1308    *
1309    * @return
1310    */
1311   public List<Edit> getEdits()
1312   {
1313     return this.edits;
1314   }
1315
1316   /**
1317    * Returns a map whose keys are the dataset sequences, and values their
1318    * aligned sequences before the command edit list was applied. The aligned
1319    * sequences are copies, which may be updated without affecting the originals.
1320    *
1321    * The command holds references to the aligned sequences (after editing). If
1322    * the command is an 'undo',then the prior state is simply the aligned state.
1323    * Otherwise, we have to derive the prior state by working backwards through
1324    * the edit list to infer the aligned sequences before editing.
1325    *
1326    * Note: an alternative solution would be to cache the 'before' state of each
1327    * edit, but this would be expensive in space in the common case that the
1328    * original is never needed (edits are not mirrored).
1329    *
1330    * @return
1331    * @throws IllegalStateException
1332    *           on detecting an edit command of a type that can't be unwound
1333    */
1334   public Map<SequenceI, SequenceI> priorState(boolean forUndo)
1335   {
1336     Map<SequenceI, SequenceI> result = new HashMap<SequenceI, SequenceI>();
1337     if (getEdits() == null)
1338     {
1339       return result;
1340     }
1341     if (forUndo)
1342     {
1343       for (Edit e : getEdits())
1344       {
1345         for (SequenceI seq : e.getSequences())
1346         {
1347           SequenceI ds = seq.getDatasetSequence();
1348           // SequenceI preEdit = result.get(ds);
1349           if (!result.containsKey(ds))
1350           {
1351             /*
1352              * copy sequence including start/end (but don't use copy constructor
1353              * as we don't need annotations)
1354              */
1355             SequenceI preEdit = new Sequence("", seq.getSequenceAsString(),
1356                     seq.getStart(), seq.getEnd());
1357             preEdit.setDatasetSequence(ds);
1358             result.put(ds, preEdit);
1359           }
1360         }
1361       }
1362       return result;
1363     }
1364
1365     /*
1366      * Work backwards through the edit list, deriving the sequences before each
1367      * was applied. The final result is the sequence set before any edits.
1368      */
1369     Iterator<Edit> editList = new ReverseListIterator<Edit>(getEdits());
1370     while (editList.hasNext())
1371     {
1372       Edit oldEdit = editList.next();
1373       Action action = oldEdit.getAction();
1374       int position = oldEdit.getPosition();
1375       int number = oldEdit.getNumber();
1376       final char gap = oldEdit.getGapCharacter();
1377       for (SequenceI seq : oldEdit.getSequences())
1378       {
1379         SequenceI ds = seq.getDatasetSequence();
1380         SequenceI preEdit = result.get(ds);
1381         if (preEdit == null)
1382         {
1383           preEdit = new Sequence("", seq.getSequenceAsString(),
1384                   seq.getStart(), seq.getEnd());
1385           preEdit.setDatasetSequence(ds);
1386           result.put(ds, preEdit);
1387         }
1388         /*
1389          * 'Undo' this edit action on the sequence (updating the value in the
1390          * map).
1391          */
1392         if (ds != null)
1393         {
1394           if (action == Action.DELETE_GAP)
1395           {
1396             preEdit.setSequence(new String(StringUtils.insertCharAt(
1397                     preEdit.getSequence(), position, number, gap)));
1398           }
1399           else if (action == Action.INSERT_GAP)
1400           {
1401             preEdit.setSequence(new String(StringUtils.deleteChars(
1402                     preEdit.getSequence(), position, position + number)));
1403           }
1404           else
1405           {
1406             System.err.println("Can't undo edit action " + action);
1407             // throw new IllegalStateException("Can't undo edit action " +
1408             // action);
1409           }
1410         }
1411       }
1412     }
1413     return result;
1414   }
1415
1416   public class Edit
1417   {
1418     private SequenceI[] oldds;
1419
1420     /**
1421      * start and end of sequence prior to edit
1422      */
1423     private Range[] oldStartEnd;
1424
1425     private boolean fullAlignmentHeight = false;
1426
1427     private Map<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
1428
1429     private Map<String, Annotation[]> deletedAnnotations;
1430
1431     /*
1432      * features deleted by the cut (re-add on Undo)
1433      * (including the original of any shortened features)
1434      */
1435     private Map<SequenceI, List<SequenceFeature>> deletedFeatures;
1436
1437     /*
1438      * shortened features added by the cut (delete on Undo)
1439      */
1440     private Map<SequenceI, List<SequenceFeature>> truncatedFeatures;
1441
1442     private AlignmentI al;
1443
1444     final private Action command;
1445
1446     char[][] string;
1447
1448     SequenceI[] seqs;
1449
1450     private int[] alIndex;
1451
1452     private int position;
1453
1454     private int number;
1455
1456     private char gapChar;
1457
1458     public Edit(Action cmd, SequenceI[] sqs, int pos, int count,
1459             char gap)
1460     {
1461       this.command = cmd;
1462       this.seqs = sqs;
1463       this.position = pos;
1464       this.number = count;
1465       this.gapChar = gap;
1466     }
1467
1468     Edit(Action cmd, SequenceI[] sqs, int pos, int count,
1469             AlignmentI align)
1470     {
1471       this(cmd, sqs, pos, count, align.getGapCharacter());
1472
1473       this.al = align;
1474
1475       alIndex = new int[sqs.length];
1476       for (int i = 0; i < sqs.length; i++)
1477       {
1478         alIndex[i] = align.findIndex(sqs[i]);
1479       }
1480
1481       fullAlignmentHeight = (align.getHeight() == sqs.length);
1482     }
1483
1484     /**
1485      * Constructor given a REPLACE command and the replacement string
1486      *
1487      * @param cmd
1488      * @param sqs
1489      * @param pos
1490      * @param count
1491      * @param align
1492      * @param replace
1493      */
1494     Edit(Action cmd, SequenceI[] sqs, int pos, int count,
1495             AlignmentI align, String replace)
1496     {
1497       this(cmd, sqs, pos, count, align);
1498
1499       string = new char[sqs.length][];
1500       for (int i = 0; i < sqs.length; i++)
1501       {
1502         string[i] = replace.toCharArray();
1503       }
1504     }
1505
1506     public SequenceI[] getSequences()
1507     {
1508       return seqs;
1509     }
1510
1511     public int getPosition()
1512     {
1513       return position;
1514     }
1515
1516     public Action getAction()
1517     {
1518       return command;
1519     }
1520
1521     public int getNumber()
1522     {
1523       return number;
1524     }
1525
1526     public char getGapCharacter()
1527     {
1528       return gapChar;
1529     }
1530   }
1531
1532   /**
1533    * Returns an iterator over the list of edit commands which traverses the list
1534    * either forwards or backwards.
1535    *
1536    * @param forwards
1537    * @return
1538    */
1539   public Iterator<Edit> getEditIterator(boolean forwards)
1540   {
1541     if (forwards)
1542     {
1543       return getEdits().iterator();
1544     }
1545     else
1546     {
1547       return new ReverseListIterator<Edit>(getEdits());
1548     }
1549   }
1550
1551   /**
1552    * Adjusts features for Cut, and saves details of changes made to allow Undo
1553    * <ul>
1554    * <li>features left of the cut are unchanged</li>
1555    * <li>features right of the cut are shifted left</li>
1556    * <li>features internal to the cut region are deleted</li>
1557    * <li>features that overlap or span the cut are shortened</li>
1558    * <li>the originals of any deleted or shortened features are saved, to re-add
1559    * on Undo</li>
1560    * <li>any added (shortened) features are saved, to delete on Undo</li>
1561    * </ul>
1562    *
1563    * @param command
1564    * @param seq
1565    * @param fromPosition
1566    * @param toPosition
1567    * @param cutIsInternal
1568    */
1569   protected static void cutFeatures(Edit command, SequenceI seq,
1570           int fromPosition, int toPosition, boolean cutIsInternal)
1571   {
1572     /*
1573      * if the cut is at start or end of sequence
1574      * then we don't modify the sequence feature store
1575      */
1576     if (!cutIsInternal)
1577     {
1578       return;
1579     }
1580     List<SequenceFeature> added = new ArrayList<>();
1581     List<SequenceFeature> removed = new ArrayList<>();
1582
1583     SequenceFeaturesI featureStore = seq.getFeatures();
1584     if (toPosition < fromPosition || featureStore == null)
1585     {
1586       return;
1587     }
1588
1589     int cutStartPos = fromPosition;
1590     int cutEndPos = toPosition;
1591     int cutWidth = cutEndPos - cutStartPos + 1;
1592
1593     synchronized (featureStore)
1594     {
1595       /*
1596        * get features that overlap the cut region
1597        */
1598       List<SequenceFeature> toAmend = featureStore.findFeatures(
1599               cutStartPos, cutEndPos);
1600
1601       /*
1602        * add any contact features that span the cut region
1603        * (not returned by findFeatures)
1604        */
1605       for (SequenceFeature contact : featureStore.getContactFeatures())
1606       {
1607         if (contact.getBegin() < cutStartPos
1608                 && contact.getEnd() > cutEndPos)
1609         {
1610           toAmend.add(contact);
1611         }
1612       }
1613
1614       /*
1615        * adjust start-end of overlapping features;
1616        * delete features enclosed by the cut;
1617        * delete partially overlapping contact features
1618        */
1619       for (SequenceFeature sf : toAmend)
1620       {
1621         int sfBegin = sf.getBegin();
1622         int sfEnd = sf.getEnd();
1623         int newBegin = sfBegin;
1624         int newEnd = sfEnd;
1625         boolean toDelete = false;
1626         boolean follows = false;
1627
1628         if (sfBegin >= cutStartPos && sfEnd <= cutEndPos)
1629         {
1630           /*
1631            * feature lies within cut region - delete it
1632            */
1633           toDelete = true;
1634         }
1635         else if (sfBegin < cutStartPos && sfEnd > cutEndPos)
1636         {
1637           /*
1638            * feature spans cut region - left-shift the end
1639            */
1640           newEnd -= cutWidth;
1641         }
1642         else if (sfEnd <= cutEndPos)
1643         {
1644           /*
1645            * feature overlaps left of cut region - truncate right
1646            */
1647           newEnd = cutStartPos - 1;
1648           if (sf.isContactFeature())
1649           {
1650             toDelete = true;
1651           }
1652         }
1653         else if (sfBegin >= cutStartPos)
1654         {
1655           /*
1656            * remaining case - feature overlaps right
1657            * truncate left, adjust end of feature
1658            */
1659           newBegin = cutIsInternal ? cutStartPos : cutEndPos + 1;
1660           newEnd = newBegin + sfEnd - cutEndPos - 1;
1661           if (sf.isContactFeature())
1662           {
1663             toDelete = true;
1664           }
1665         }
1666
1667         seq.deleteFeature(sf);
1668         if (!follows)
1669         {
1670           removed.add(sf);
1671         }
1672         if (!toDelete)
1673         {
1674           SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd,
1675                   sf.getFeatureGroup(), sf.getScore());
1676           seq.addSequenceFeature(copy);
1677           if (!follows)
1678           {
1679             added.add(copy);
1680           }
1681         }
1682       }
1683
1684       /*
1685        * and left shift any features lying to the right of the cut region
1686        */
1687
1688       featureStore.shiftFeatures(cutEndPos + 1, -cutWidth);
1689     }
1690
1691     /*
1692      * save deleted and amended features, so that Undo can
1693      * re-add or delete them respectively
1694      */
1695     if (command.deletedFeatures == null)
1696     {
1697       command.deletedFeatures = new HashMap<>();
1698     }
1699     if (command.truncatedFeatures == null)
1700     {
1701       command.truncatedFeatures = new HashMap<>();
1702     }
1703     command.deletedFeatures.put(seq, removed);
1704     command.truncatedFeatures.put(seq, added);
1705   }
1706 }