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