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(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       if (end < oldstring.length())
 774       {
 775         tmp.append(oldstring.substring(end));
 776       }
 777       // stash end prior to updating the sequence object so we can save it if
 778       // need be.
 779       Range oldstartend = new Range(command.seqs[i].getStart(),
 780               command.seqs[i].getEnd());
 781       command.seqs[i].setSequence(tmp.toString());
 782       command.string[i] = oldstring
 783               .substring(start, Math.min(end, oldstring.length()))
 784               .toCharArray();
 785       String nogapold = AlignSeq.extractGaps(Comparison.GapChars,
 786               new String(command.string[i]));
 787
 788       if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase()))
 789       {
 790         // we may already have dataset and limits stashed...
 791         if (newDSWasNeeded || newStartEndWasNeeded)
 792         {
 793           if (newDSWasNeeded)
 794           {
 795           // then just switch the dataset sequence
 796           SequenceI oldds = command.seqs[i].getDatasetSequence();
 797           command.seqs[i].setDatasetSequence(command.oldds[i]);
 798           command.oldds[i] = oldds;
 799           }
 800           if (newStartEndWasNeeded)
 801           {
 802             Range newStart = command.oldStartEnd[i];
 803             command.oldStartEnd[i] = oldstartend;
 804             command.seqs[i].setStart(newStart.getBegin());
 805             command.seqs[i].setEnd(newStart.getEnd());
 806           }
 807         }
 808         else
 809         {
 810           // decide if we need a new dataset sequence or modify start/end
 811           // first edit the original dataset sequence string
 812           SequenceI oldds = command.seqs[i].getDatasetSequence();
 813           String osp = oldds.getSequenceAsString();
 814           int beforeStartOfEdit = -oldds.getStart() + 1
 815                   + (beforeEditedPositions == null
 816                           ? ((afterEditedPositions != null)
 817                                   ? afterEditedPositions.getBegin() - 1
 818                                   : oldstartend.getBegin()
 819                                           + nogapold.length())
 820                           : beforeEditedPositions.getEnd()
 821                   );
 822           int afterEndOfEdit = -oldds.getStart() + 1
 823                   + ((afterEditedPositions == null)
 824                   ? oldstartend.getEnd()
 825                           : afterEditedPositions.getBegin() - 1);
 826           String fullseq = osp.substring(0,
 827                   beforeStartOfEdit)
 828                   + nogaprep
 829                   + osp.substring(afterEndOfEdit);
 830
 831           // and check if new sequence data is different..
 832           if (!fullseq.equalsIgnoreCase(osp))
 833           {
 834             // old ds and edited ds are different, so
 835             // create the new dataset sequence
 836             SequenceI newds = new Sequence(oldds);
 837             newds.setSequence(fullseq.toUpperCase());
 838
 839             if (command.oldds == null)
 840             {
 841               command.oldds = new SequenceI[command.seqs.length];
 842             }
 843             command.oldds[i] = command.seqs[i].getDatasetSequence();
 844
 845             // And preserve start/end for good-measure
 846
 847             if (command.oldStartEnd == null)
 848             {
 849               command.oldStartEnd = new Range[command.seqs.length];
 850             }
 851             command.oldStartEnd[i] = oldstartend;
 852             // TODO: JAL-1131 ensure newly created dataset sequence is added to
 853             // the set of
 854             // dataset sequences associated with the alignment.
 855             // TODO: JAL-1131 fix up any annotation associated with new dataset
 856             // sequence to ensure that original sequence/annotation
 857             // relationships
 858             // are preserved.
 859             command.seqs[i].setDatasetSequence(newds);
 860           }
 861           else
 862           {
 863             if (command.oldStartEnd == null)
 864             {
 865               command.oldStartEnd = new Range[command.seqs.length];
 866             }
 867             command.oldStartEnd[i] = new Range(command.seqs[i].getStart(),
 868                     command.seqs[i].getEnd());
 869             if (beforeEditedPositions != null
 870                     && afterEditedPositions == null)
 871             {
 872               // modification at end
 873               command.seqs[i].setEnd(
 874                       beforeEditedPositions.getEnd() + nogaprep.length()
 875                               - nogapold.length());
 876             }
 877             else if (afterEditedPositions != null
 878                     && beforeEditedPositions == null)
 879             {
 880               // modification at start
 881               command.seqs[i].setStart(
 882                       afterEditedPositions.getBegin() - nogaprep.length());
 883             }
 884             else
 885             {
 886               // edit covered both start and end. Here we can only guess the
 887               // new
 888               // start/end
 889               String nogapalseq = jalview.analysis.AlignSeq.extractGaps(
 890                       jalview.util.Comparison.GapChars,
 891                       command.seqs[i].getSequenceAsString().toUpperCase());
 892               int newStart = command.seqs[i].getDatasetSequence()
 893                       .getSequenceAsString().indexOf(nogapalseq);
 894               if (newStart == -1)
 895               {
 896                 throw new Error(
 897                         "Implementation Error: could not locate start/end "
 898                                 + "in dataset sequence after an edit of the sequence string");
 899               }
 900               int newEnd = newStart + nogapalseq.length() - 1;
 901               command.seqs[i].setStart(newStart);
 902               command.seqs[i].setEnd(newEnd);
 903             }
 904           }
 905         }
 906       }
 907       tmp = null;
 908       oldstring = null;
 909     }
 910   }
 911
 912   final static void adjustAnnotations(Edit command, boolean insert,
 913           boolean modifyVisibility, AlignmentI[] views)
 914   {
 915     AlignmentAnnotation[] annotations = null;
 916
 917     if (modifyVisibility && !insert)
 918     {
 919       // only occurs if a sequence was added or deleted.
 920       command.deletedAnnotationRows = new Hashtable<SequenceI, AlignmentAnnotation[]>();
 921     }
 922     if (command.fullAlignmentHeight)
 923     {
 924       annotations = command.al.getAlignmentAnnotation();
 925     }
 926     else
 927     {
 928       int aSize = 0;
 929       AlignmentAnnotation[] tmp;
 930       for (int s = 0; s < command.seqs.length; s++)
 931       {
 932         command.seqs[s].sequenceChanged();
 933
 934         if (modifyVisibility)
 935         {
 936           // Rows are only removed or added to sequence object.
 937           if (!insert)
 938           {
 939             // remove rows
 940             tmp = command.seqs[s].getAnnotation();
 941             if (tmp != null)
 942             {
 943               int alen = tmp.length;
 944               for (int aa = 0; aa < tmp.length; aa++)
 945               {
 946                 if (!command.al.deleteAnnotation(tmp[aa]))
 947                 {
 948                   // strip out annotation not in the current al (will be put
 949                   // back on insert in all views)
 950                   tmp[aa] = null;
 951                   alen--;
 952                 }
 953               }
 954               command.seqs[s].setAlignmentAnnotation(null);
 955               if (alen != tmp.length)
 956               {
 957                 // save the non-null annotation references only
 958                 AlignmentAnnotation[] saved = new AlignmentAnnotation[alen];
 959                 for (int aa = 0, aapos = 0; aa < tmp.length; aa++)
 960                 {
 961                   if (tmp[aa] != null)
 962                   {
 963                     saved[aapos++] = tmp[aa];
 964                     tmp[aa] = null;
 965                   }
 966                 }
 967                 tmp = saved;
 968                 command.deletedAnnotationRows.put(command.seqs[s], saved);
 969                 // and then remove any annotation in the other views
 970                 for (int alview = 0; views != null
 971                         && alview < views.length; alview++)
 972                 {
 973                   if (views[alview] != command.al)
 974                   {
 975                     AlignmentAnnotation[] toremove = views[alview]
 976                             .getAlignmentAnnotation();
 977                     if (toremove == null || toremove.length == 0)
 978                     {
 979                       continue;
 980                     }
 981                     // remove any alignment annotation on this sequence that's
 982                     // on that alignment view.
 983                     for (int aa = 0; aa < toremove.length; aa++)
 984                     {
 985                       if (toremove[aa].sequenceRef == command.seqs[s])
 986                       {
 987                         views[alview].deleteAnnotation(toremove[aa]);
 988                       }
 989                     }
 990                   }
 991                 }
 992               }
 993               else
 994               {
 995                 // save all the annotation
 996                 command.deletedAnnotationRows.put(command.seqs[s], tmp);
 997               }
 998             }
 999           }
1000           else
1001           {
1002             // recover rows
1003             if (command.deletedAnnotationRows != null
1004                     && command.deletedAnnotationRows
1005                             .containsKey(command.seqs[s]))
1006             {
1007               AlignmentAnnotation[] revealed = command.deletedAnnotationRows
1008                       .get(command.seqs[s]);
1009               command.seqs[s].setAlignmentAnnotation(revealed);
1010               if (revealed != null)
1011               {
1012                 for (int aa = 0; aa < revealed.length; aa++)
1013                 {
1014                   // iterate through al adding original annotation
1015                   command.al.addAnnotation(revealed[aa]);
1016                 }
1017                 for (int aa = 0; aa < revealed.length; aa++)
1018                 {
1019                   command.al.setAnnotationIndex(revealed[aa], aa);
1020                 }
1021                 // and then duplicate added annotation on every other alignment
1022                 // view
1023                 for (int vnum = 0; views != null && vnum < views.length; vnum++)
1024                 {
1025                   if (views[vnum] != command.al)
1026                   {
1027                     int avwidth = views[vnum].getWidth() + 1;
1028                     // duplicate in this view
1029                     for (int a = 0; a < revealed.length; a++)
1030                     {
1031                       AlignmentAnnotation newann = new AlignmentAnnotation(
1032                               revealed[a]);
1033                       command.seqs[s].addAlignmentAnnotation(newann);
1034                       newann.padAnnotation(avwidth);
1035                       views[vnum].addAnnotation(newann);
1036                       views[vnum].setAnnotationIndex(newann, a);
1037                     }
1038                   }
1039                 }
1040               }
1041             }
1042           }
1043           continue;
1044         }
1045
1046         if (command.seqs[s].getAnnotation() == null)
1047         {
1048           continue;
1049         }
1050
1051         if (aSize == 0)
1052         {
1053           annotations = command.seqs[s].getAnnotation();
1054         }
1055         else
1056         {
1057           tmp = new AlignmentAnnotation[aSize
1058                   + command.seqs[s].getAnnotation().length];
1059
1060           System.arraycopy(annotations, 0, tmp, 0, aSize);
1061
1062           System.arraycopy(command.seqs[s].getAnnotation(), 0, tmp, aSize,
1063                   command.seqs[s].getAnnotation().length);
1064
1065           annotations = tmp;
1066         }
1067         aSize = annotations.length;
1068       }
1069     }
1070
1071     if (annotations == null)
1072     {
1073       return;
1074     }
1075
1076     if (!insert)
1077     {
1078       command.deletedAnnotations = new Hashtable<String, Annotation[]>();
1079     }
1080
1081     int aSize;
1082     Annotation[] temp;
1083     for (int a = 0; a < annotations.length; a++)
1084     {
1085       if (annotations[a].autoCalculated
1086               || annotations[a].annotations == null)
1087       {
1088         continue;
1089       }
1090
1091       int tSize = 0;
1092
1093       aSize = annotations[a].annotations.length;
1094       if (insert)
1095       {
1096         temp = new Annotation[aSize + command.number];
1097         if (annotations[a].padGaps)
1098         {
1099           for (int aa = 0; aa < temp.length; aa++)
1100           {
1101             temp[aa] = new Annotation(command.gapChar + "", null, ' ', 0);
1102           }
1103         }
1104       }
1105       else
1106       {
1107         if (command.position < aSize)
1108         {
1109           if (command.position + command.number >= aSize)
1110           {
1111             tSize = aSize;
1112           }
1113           else
1114           {
1115             tSize = aSize - command.number;
1116           }
1117         }
1118         else
1119         {
1120           tSize = aSize;
1121         }
1122
1123         if (tSize < 0)
1124         {
1125           tSize = aSize;
1126         }
1127         temp = new Annotation[tSize];
1128       }
1129
1130       if (insert)
1131       {
1132         if (command.position < annotations[a].annotations.length)
1133         {
1134           System.arraycopy(annotations[a].annotations, 0, temp, 0,
1135                   command.position);
1136
1137           if (command.deletedAnnotations != null
1138                   && command.deletedAnnotations
1139                           .containsKey(annotations[a].annotationId))
1140           {
1141             Annotation[] restore = command.deletedAnnotations
1142                     .get(annotations[a].annotationId);
1143
1144             System.arraycopy(restore, 0, temp, command.position,
1145                     command.number);
1146
1147           }
1148
1149           System.arraycopy(annotations[a].annotations, command.position,
1150                   temp, command.position + command.number,
1151                   aSize - command.position);
1152         }
1153         else
1154         {
1155           if (command.deletedAnnotations != null
1156                   && command.deletedAnnotations
1157                           .containsKey(annotations[a].annotationId))
1158           {
1159             Annotation[] restore = command.deletedAnnotations
1160                     .get(annotations[a].annotationId);
1161
1162             temp = new Annotation[annotations[a].annotations.length
1163                     + restore.length];
1164             System.arraycopy(annotations[a].annotations, 0, temp, 0,
1165                     annotations[a].annotations.length);
1166             System.arraycopy(restore, 0, temp,
1167                     annotations[a].annotations.length, restore.length);
1168           }
1169           else
1170           {
1171             temp = annotations[a].annotations;
1172           }
1173         }
1174       }
1175       else
1176       {
1177         if (tSize != aSize || command.position < 2)
1178         {
1179           int copylen = Math.min(command.position,
1180                   annotations[a].annotations.length);
1181           if (copylen > 0)
1182           {
1183             System.arraycopy(annotations[a].annotations, 0, temp, 0,
1184                     copylen); // command.position);
1185           }
1186
1187           Annotation[] deleted = new Annotation[command.number];
1188           if (copylen >= command.position)
1189           {
1190             copylen = Math.min(command.number,
1191                     annotations[a].annotations.length - command.position);
1192             if (copylen > 0)
1193             {
1194               System.arraycopy(annotations[a].annotations, command.position,
1195                       deleted, 0, copylen); // command.number);
1196             }
1197           }
1198
1199           command.deletedAnnotations.put(annotations[a].annotationId,
1200                   deleted);
1201           if (annotations[a].annotations.length > command.position
1202                   + command.number)
1203           {
1204             System.arraycopy(annotations[a].annotations,
1205                     command.position + command.number, temp,
1206                     command.position, annotations[a].annotations.length
1207                             - command.position - command.number); // aSize
1208           }
1209         }
1210         else
1211         {
1212           int dSize = aSize - command.position;
1213
1214           if (dSize > 0)
1215           {
1216             Annotation[] deleted = new Annotation[command.number];
1217             System.arraycopy(annotations[a].annotations, command.position,
1218                     deleted, 0, dSize);
1219
1220             command.deletedAnnotations.put(annotations[a].annotationId,
1221                     deleted);
1222
1223             tSize = Math.min(annotations[a].annotations.length,
1224                     command.position);
1225             temp = new Annotation[tSize];
1226             System.arraycopy(annotations[a].annotations, 0, temp, 0, tSize);
1227           }
1228           else
1229           {
1230             temp = annotations[a].annotations;
1231           }
1232         }
1233       }
1234
1235       annotations[a].annotations = temp;
1236     }
1237   }
1238
1239   /**
1240    * Restores features to the state before a Cut.
1241    * <ul>
1242    * <li>re-add any features deleted by the cut</li>
1243    * <li>remove any truncated features created by the cut</li>
1244    * <li>shift right any features to the right of the cut</li>
1245    * </ul>
1246    *
1247    * @param command
1248    *          the Cut command
1249    * @param seq
1250    *          the sequence the Cut applied to
1251    * @param start
1252    *          the start residue position of the cut
1253    * @param length
1254    *          the number of residues cut
1255    * @param sameDatasetSequence
1256    *          true if dataset sequence and frame of reference were left
1257    *          unchanged by the Cut
1258    */
1259   final static void undoCutFeatures(Edit command, SequenceI seq,
1260           final int start, final int length, boolean sameDatasetSequence)
1261   {
1262     SequenceI sequence = seq.getDatasetSequence();
1263     if (sequence == null)
1264     {
1265       sequence = seq;
1266     }
1267
1268     /*
1269      * shift right features that lie to the right of the restored cut (but not
1270      * if dataset sequence unchanged - so coordinates were changed by Cut)
1271      */
1272     if (!sameDatasetSequence)
1273     {
1274       /*
1275        * shift right all features right of and not
1276        * contiguous with the cut position
1277        */
1278       seq.getFeatures().shiftFeatures(start + 1, length);
1279
1280       /*
1281        * shift right any features that start at the cut position,
1282        * unless they were truncated
1283        */
1284       List<SequenceFeature> sfs = seq.getFeatures().findFeatures(start,
1285               start);
1286       for (SequenceFeature sf : sfs)
1287       {
1288         if (sf.getBegin() == start)
1289         {
1290           if (!command.truncatedFeatures.containsKey(seq)
1291                   || !command.truncatedFeatures.get(seq).contains(sf))
1292           {
1293             /*
1294              * feature was shifted left to cut position (not truncated),
1295              * so shift it back right
1296              */
1297             SequenceFeature shifted = new SequenceFeature(sf, sf.getBegin()
1298                     + length, sf.getEnd() + length, sf.getFeatureGroup(),
1299                     sf.getScore());
1300             seq.addSequenceFeature(shifted);
1301             seq.deleteFeature(sf);
1302           }
1303         }
1304       }
1305     }
1306
1307     /*
1308      * restore any features that were deleted or truncated
1309      */
1310     if (command.deletedFeatures != null
1311             && command.deletedFeatures.containsKey(seq))
1312     {
1313       for (SequenceFeature deleted : command.deletedFeatures.get(seq))
1314       {
1315         sequence.addSequenceFeature(deleted);
1316       }
1317     }
1318
1319     /*
1320      * delete any truncated features
1321      */
1322     if (command.truncatedFeatures != null
1323             && command.truncatedFeatures.containsKey(seq))
1324     {
1325       for (SequenceFeature amended : command.truncatedFeatures.get(seq))
1326       {
1327         sequence.deleteFeature(amended);
1328       }
1329     }
1330   }
1331
1332   /**
1333    * Returns the list of edit commands wrapped by this object.
1334    *
1335    * @return
1336    */
1337   public List<Edit> getEdits()
1338   {
1339     return this.edits;
1340   }
1341
1342   /**
1343    * Returns a map whose keys are the dataset sequences, and values their
1344    * aligned sequences before the command edit list was applied. The aligned
1345    * sequences are copies, which may be updated without affecting the originals.
1346    *
1347    * The command holds references to the aligned sequences (after editing). If
1348    * the command is an 'undo',then the prior state is simply the aligned state.
1349    * Otherwise, we have to derive the prior state by working backwards through
1350    * the edit list to infer the aligned sequences before editing.
1351    *
1352    * Note: an alternative solution would be to cache the 'before' state of each
1353    * edit, but this would be expensive in space in the common case that the
1354    * original is never needed (edits are not mirrored).
1355    *
1356    * @return
1357    * @throws IllegalStateException
1358    *           on detecting an edit command of a type that can't be unwound
1359    */
1360   public Map<SequenceI, SequenceI> priorState(boolean forUndo)
1361   {
1362     Map<SequenceI, SequenceI> result = new HashMap<SequenceI, SequenceI>();
1363     if (getEdits() == null)
1364     {
1365       return result;
1366     }
1367     if (forUndo)
1368     {
1369       for (Edit e : getEdits())
1370       {
1371         for (SequenceI seq : e.getSequences())
1372         {
1373           SequenceI ds = seq.getDatasetSequence();
1374           // SequenceI preEdit = result.get(ds);
1375           if (!result.containsKey(ds))
1376           {
1377             /*
1378              * copy sequence including start/end (but don't use copy constructor
1379              * as we don't need annotations)
1380              */
1381             SequenceI preEdit = new Sequence("", seq.getSequenceAsString(),
1382                     seq.getStart(), seq.getEnd());
1383             preEdit.setDatasetSequence(ds);
1384             result.put(ds, preEdit);
1385           }
1386         }
1387       }
1388       return result;
1389     }
1390
1391     /*
1392      * Work backwards through the edit list, deriving the sequences before each
1393      * was applied. The final result is the sequence set before any edits.
1394      */
1395     Iterator<Edit> editList = new ReverseListIterator<Edit>(getEdits());
1396     while (editList.hasNext())
1397     {
1398       Edit oldEdit = editList.next();
1399       Action action = oldEdit.getAction();
1400       int position = oldEdit.getPosition();
1401       int number = oldEdit.getNumber();
1402       final char gap = oldEdit.getGapCharacter();
1403       for (SequenceI seq : oldEdit.getSequences())
1404       {
1405         SequenceI ds = seq.getDatasetSequence();
1406         SequenceI preEdit = result.get(ds);
1407         if (preEdit == null)
1408         {
1409           preEdit = new Sequence("", seq.getSequenceAsString(),
1410                   seq.getStart(), seq.getEnd());
1411           preEdit.setDatasetSequence(ds);
1412           result.put(ds, preEdit);
1413         }
1414         /*
1415          * 'Undo' this edit action on the sequence (updating the value in the
1416          * map).
1417          */
1418         if (ds != null)
1419         {
1420           if (action == Action.DELETE_GAP)
1421           {
1422             preEdit.setSequence(new String(StringUtils.insertCharAt(
1423                     preEdit.getSequence(), position, number, gap)));
1424           }
1425           else if (action == Action.INSERT_GAP)
1426           {
1427             preEdit.setSequence(new String(StringUtils.deleteChars(
1428                     preEdit.getSequence(), position, position + number)));
1429           }
1430           else
1431           {
1432             System.err.println("Can't undo edit action " + action);
1433             // throw new IllegalStateException("Can't undo edit action " +
1434             // action);
1435           }
1436         }
1437       }
1438     }
1439     return result;
1440   }
1441
1442   public class Edit
1443   {
1444     private SequenceI[] oldds;
1445
1446     /**
1447      * start and end of sequence prior to edit
1448      */
1449     private Range[] oldStartEnd;
1450
1451     private boolean fullAlignmentHeight = false;
1452
1453     private Map<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
1454
1455     private Map<String, Annotation[]> deletedAnnotations;
1456
1457     /*
1458      * features deleted by the cut (re-add on Undo)
1459      * (including the original of any shortened features)
1460      */
1461     private Map<SequenceI, List<SequenceFeature>> deletedFeatures;
1462
1463     /*
1464      * shortened features added by the cut (delete on Undo)
1465      */
1466     private Map<SequenceI, List<SequenceFeature>> truncatedFeatures;
1467
1468     private AlignmentI al;
1469
1470     final private Action command;
1471
1472     char[][] string;
1473
1474     SequenceI[] seqs;
1475
1476     private int[] alIndex;
1477
1478     private int position;
1479
1480     private int number;
1481
1482     private char gapChar;
1483
1484     public Edit(Action cmd, SequenceI[] sqs, int pos, int count,
1485             char gap)
1486     {
1487       this.command = cmd;
1488       this.seqs = sqs;
1489       this.position = pos;
1490       this.number = count;
1491       this.gapChar = gap;
1492     }
1493
1494     Edit(Action cmd, SequenceI[] sqs, int pos, int count,
1495             AlignmentI align)
1496     {
1497       this(cmd, sqs, pos, count, align.getGapCharacter());
1498
1499       this.al = align;
1500
1501       alIndex = new int[sqs.length];
1502       for (int i = 0; i < sqs.length; i++)
1503       {
1504         alIndex[i] = align.findIndex(sqs[i]);
1505       }
1506
1507       fullAlignmentHeight = (align.getHeight() == sqs.length);
1508     }
1509
1510     /**
1511      * Constructor given a REPLACE command and the replacement string
1512      *
1513      * @param cmd
1514      * @param sqs
1515      * @param pos
1516      * @param count
1517      * @param align
1518      * @param replace
1519      */
1520     Edit(Action cmd, SequenceI[] sqs, int pos, int count,
1521             AlignmentI align, String replace)
1522     {
1523       this(cmd, sqs, pos, count, align);
1524
1525       string = new char[sqs.length][];
1526       for (int i = 0; i < sqs.length; i++)
1527       {
1528         string[i] = replace.toCharArray();
1529       }
1530     }
1531
1532     public SequenceI[] getSequences()
1533     {
1534       return seqs;
1535     }
1536
1537     public int getPosition()
1538     {
1539       return position;
1540     }
1541
1542     public Action getAction()
1543     {
1544       return command;
1545     }
1546
1547     public int getNumber()
1548     {
1549       return number;
1550     }
1551
1552     public char getGapCharacter()
1553     {
1554       return gapChar;
1555     }
1556   }
1557
1558   /**
1559    * Returns an iterator over the list of edit commands which traverses the list
1560    * either forwards or backwards.
1561    *
1562    * @param forwards
1563    * @return
1564    */
1565   public Iterator<Edit> getEditIterator(boolean forwards)
1566   {
1567     if (forwards)
1568     {
1569       return getEdits().iterator();
1570     }
1571     else
1572     {
1573       return new ReverseListIterator<Edit>(getEdits());
1574     }
1575   }
1576
1577   /**
1578    * Adjusts features for Cut, and saves details of changes made to allow Undo
1579    * <ul>
1580    * <li>features left of the cut are unchanged</li>
1581    * <li>features right of the cut are shifted left</li>
1582    * <li>features internal to the cut region are deleted</li>
1583    * <li>features that overlap or span the cut are shortened</li>
1584    * <li>the originals of any deleted or shortened features are saved, to re-add
1585    * on Undo</li>
1586    * <li>any added (shortened) features are saved, to delete on Undo</li>
1587    * </ul>
1588    *
1589    * @param command
1590    * @param seq
1591    * @param fromPosition
1592    * @param toPosition
1593    * @param cutIsInternal
1594    */
1595   protected static void cutFeatures(Edit command, SequenceI seq,
1596           int fromPosition, int toPosition, boolean cutIsInternal)
1597   {
1598     /*
1599      * if the cut is at start or end of sequence
1600      * then we don't modify the sequence feature store
1601      */
1602     if (!cutIsInternal)
1603     {
1604       return;
1605     }
1606     List<SequenceFeature> added = new ArrayList<>();
1607     List<SequenceFeature> removed = new ArrayList<>();
1608
1609     SequenceFeaturesI featureStore = seq.getFeatures();
1610     if (toPosition < fromPosition || featureStore == null)
1611     {
1612       return;
1613     }
1614
1615     int cutStartPos = fromPosition;
1616     int cutEndPos = toPosition;
1617     int cutWidth = cutEndPos - cutStartPos + 1;
1618
1619     synchronized (featureStore)
1620     {
1621       /*
1622        * get features that overlap the cut region
1623        */
1624       List<SequenceFeature> toAmend = featureStore.findFeatures(
1625               cutStartPos, cutEndPos);
1626
1627       /*
1628        * add any contact features that span the cut region
1629        * (not returned by findFeatures)
1630        */
1631       for (SequenceFeature contact : featureStore.getContactFeatures())
1632       {
1633         if (contact.getBegin() < cutStartPos
1634                 && contact.getEnd() > cutEndPos)
1635         {
1636           toAmend.add(contact);
1637         }
1638       }
1639
1640       /*
1641        * adjust start-end of overlapping features;
1642        * delete features enclosed by the cut;
1643        * delete partially overlapping contact features
1644        */
1645       for (SequenceFeature sf : toAmend)
1646       {
1647         int sfBegin = sf.getBegin();
1648         int sfEnd = sf.getEnd();
1649         int newBegin = sfBegin;
1650         int newEnd = sfEnd;
1651         boolean toDelete = false;
1652         boolean follows = false;
1653
1654         if (sfBegin >= cutStartPos && sfEnd <= cutEndPos)
1655         {
1656           /*
1657            * feature lies within cut region - delete it
1658            */
1659           toDelete = true;
1660         }
1661         else if (sfBegin < cutStartPos && sfEnd > cutEndPos)
1662         {
1663           /*
1664            * feature spans cut region - left-shift the end
1665            */
1666           newEnd -= cutWidth;
1667         }
1668         else if (sfEnd <= cutEndPos)
1669         {
1670           /*
1671            * feature overlaps left of cut region - truncate right
1672            */
1673           newEnd = cutStartPos - 1;
1674           if (sf.isContactFeature())
1675           {
1676             toDelete = true;
1677           }
1678         }
1679         else if (sfBegin >= cutStartPos)
1680         {
1681           /*
1682            * remaining case - feature overlaps right
1683            * truncate left, adjust end of feature
1684            */
1685           newBegin = cutIsInternal ? cutStartPos : cutEndPos + 1;
1686           newEnd = newBegin + sfEnd - cutEndPos - 1;
1687           if (sf.isContactFeature())
1688           {
1689             toDelete = true;
1690           }
1691         }
1692
1693         seq.deleteFeature(sf);
1694         if (!follows)
1695         {
1696           removed.add(sf);
1697         }
1698         if (!toDelete)
1699         {
1700           SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd,
1701                   sf.getFeatureGroup(), sf.getScore());
1702           seq.addSequenceFeature(copy);
1703           if (!follows)
1704           {
1705             added.add(copy);
1706           }
1707         }
1708       }
1709
1710       /*
1711        * and left shift any features lying to the right of the cut region
1712        */
1713
1714       featureStore.shiftFeatures(cutEndPos + 1, -cutWidth);
1715     }
1716
1717     /*
1718      * save deleted and amended features, so that Undo can
1719      * re-add or delete them respectively
1720      */
1721     if (command.deletedFeatures == null)
1722     {
1723       command.deletedFeatures = new HashMap<>();
1724     }
1725     if (command.truncatedFeatures == null)
1726     {
1727       command.truncatedFeatures = new HashMap<>();
1728     }
1729     command.deletedFeatures.put(seq, removed);
1730     command.truncatedFeatures.put(seq, added);
1731   }
1732 }