X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FEditCommand.java;h=62ef66086e78bd53271b95ac642db2bacdcc7b12;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=97448e0c38f73ed2046895da678bed845825da74;hpb=4aad2f3624613cfc4d883f40c0470debd8f699b6;p=jalview.git
diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 97448e0..62ef660 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -1,294 +1,1750 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-package jalview.commands;
-
-import jalview.datamodel.*;
-
-/**
- *
- * Title: EditCommmand
- *
- * Description: Essential information for performing
- * undo and redo for cut/paste insert/delete gap
- * which can be stored in the HistoryList
- *
- * Copyright: Copyright (c) 2006
- *
- * Company: Dundee University
- *
- * @author not attributable
- * @version 1.0
- */
-public class EditCommand implements CommandI
-{
- public static String INSERT_GAP = "InsertGap";
- public static String DELETE_GAP = "DeleteGap";
- public static String CUT = "Cut";
- public static String PASTE = "Paste";
-
- Edit[] edits;
-
- String description;
-
- public EditCommand()
- {}
-
- public EditCommand(String description)
- {
- this.description = description;
- }
-
- public EditCommand(String description,
- String command,
- SequenceI[] seqs,
- int position,
- int number,
- char gapChar)
- {
- this.description = description;
-
- if (command.equalsIgnoreCase(INSERT_GAP)
- || command.equalsIgnoreCase(DELETE_GAP))
- {
- edits = new Edit[] { new Edit(command, seqs, position, number, gapChar)};
- }
-
- performEdit(0);
- }
-
- public EditCommand( String description,
- String command,
- SequenceI[] seqs,
- int position,
- int number,
- AlignmentI al)
- {
- this.description = description;
- if ( command.equalsIgnoreCase(CUT) || command.equalsIgnoreCase(PASTE))
- {
- edits = new Edit[]{new Edit(command, seqs, position, number, al)};
- }
-
- performEdit(0);
- }
-
-
- public String getDescription()
- {
- return description;
- }
-
- public int getSize()
- {
- return edits==null?0:edits.length;
- }
-
- public AlignmentI getAlignment()
- {
- return edits[0].al;
- }
-
-
- public void appendEdit(String command,
- SequenceI[] seqs,
- int position,
- int number,
- char gapChar,
- boolean performEdit)
- {
- Edit edit = new Edit(command, seqs, position, number, gapChar);
-
- if (edits != null)
- {
- Edit[] temp = new Edit[edits.length + 1];
- System.arraycopy(edits, 0, temp, 0, edits.length);
- edits = temp;
- edits[edits.length - 1] = edit;
- }
- else
- edits = new Edit[] { edit };
-
- if (performEdit)
- performEdit(edits.length - 1);
- }
-
- void performEdit(int commandIndex)
- {
- int eSize = edits.length;
- for (int e = commandIndex; e < eSize; e++)
- {
- if (edits[e].command.equals(INSERT_GAP))
- {
- insertGap(edits[e]);
- }
- else if (edits[e].command.equals(DELETE_GAP))
- {
- deleteGap(edits[e]);
- }
- else if(edits[e].command.equals(CUT))
- {
- cut(edits[e]);
- }
- else if(edits[e].command.equals(PASTE))
- {
- paste(edits[e]);
- }
- }
- }
-
- public void doCommand()
- {
- performEdit(0);
- }
-
- public void undoCommand()
- {
- int e = 0, eSize = edits.length;
- for (e = eSize-1; e > -1; e--)
- {
- if (edits[e].command.equals(INSERT_GAP))
- {
- deleteGap(edits[e]);
- }
- else if (edits[e].command.equals(DELETE_GAP))
- {
- insertGap(edits[e]);
- }
- else if (edits[e].command.equals(CUT))
- {
- paste(edits[e]);
- }
- else if (edits[e].command.equals(PASTE))
- {
- cut(edits[e]);
- }
- }
- }
-
- void insertGap(Edit command)
- {
- for(int s=0; scommand.position)
- {
- command.string[i] = command.seqs[i].getSequence(command.position,
- command.position + command.number);
-
- command.seqs[i].deleteChars(command.position,
- command.position + command.number);
- }
-
- if(command.seqs[i].getLength()<1)
- {
- command.al.deleteSequence(command.seqs[i]);
- }
- }
- }
-
- void paste(Edit command)
- {
- StringBuffer tmp;
- for(int i=0; i.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.commands;
+
+import java.util.Locale;
+
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.ContiguousI;
+import jalview.datamodel.Range;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeaturesI;
+import jalview.util.Comparison;
+import jalview.util.ReverseListIterator;
+import jalview.util.StringUtils;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.ListIterator;
+import java.util.Map;
+
+/**
+ *
+ *
+ * Title: EditCommmand
+ *
+ *
+ *
+ * Description: Essential information for performing undo and redo for cut/paste
+ * insert/delete gap which can be stored in the HistoryList
+ *
+ *
+ *
+ * Copyright: Copyright (c) 2006
+ *
+ *
+ *
+ * Company: Dundee University
+ *
+ *
+ * @author not attributable
+ * @version 1.0
+ */
+public class EditCommand implements CommandI
+{
+ public enum Action
+ {
+ INSERT_GAP
+ {
+ @Override
+ public Action getUndoAction()
+ {
+ return DELETE_GAP;
+ }
+ },
+ DELETE_GAP
+ {
+ @Override
+ public Action getUndoAction()
+ {
+ return INSERT_GAP;
+ }
+ },
+ CUT
+ {
+ @Override
+ public Action getUndoAction()
+ {
+ return PASTE;
+ }
+ },
+ PASTE
+ {
+ @Override
+ public Action getUndoAction()
+ {
+ return CUT;
+ }
+ },
+ REPLACE
+ {
+ @Override
+ public Action getUndoAction()
+ {
+ return REPLACE;
+ }
+ },
+ INSERT_NUC
+ {
+ @Override
+ public Action getUndoAction()
+ {
+ return null;
+ }
+ };
+
+ public abstract Action getUndoAction();
+ };
+
+ private List edits = new ArrayList<>();
+
+ String description;
+
+ public EditCommand()
+ {
+ }
+
+ public EditCommand(String desc)
+ {
+ this.description = desc;
+ }
+
+ public EditCommand(String desc, Action command, SequenceI[] seqs,
+ int position, int number, AlignmentI al)
+ {
+ this.description = desc;
+ if (command == Action.CUT || command == Action.PASTE)
+ {
+ setEdit(new Edit(command, seqs, position, number, al));
+ }
+
+ performEdit(0, null);
+ }
+
+ public EditCommand(String desc, Action command, String replace,
+ SequenceI[] seqs, int position, int number, AlignmentI al)
+ {
+ this.description = desc;
+ if (command == Action.REPLACE)
+ {
+ setEdit(new Edit(command, seqs, position, number, al, replace));
+ }
+
+ performEdit(0, null);
+ }
+
+ /**
+ * Set the list of edits to the specified item (only).
+ *
+ * @param e
+ */
+ protected void setEdit(Edit e)
+ {
+ edits.clear();
+ edits.add(e);
+ }
+
+ /**
+ * Add the given edit command to the stored list of commands. If simply
+ * expanding the range of the last command added, then modify it instead of
+ * adding a new command.
+ *
+ * @param e
+ */
+ public void addEdit(Edit e)
+ {
+ if (!expandEdit(edits, e))
+ {
+ edits.add(e);
+ }
+ }
+
+ /**
+ * Returns true if the new edit is incorporated by updating (expanding the
+ * range of) the last edit on the list, else false. We can 'expand' the last
+ * edit if the new one is the same action, on the same sequences, and acts on
+ * a contiguous range. This is the case where a mouse drag generates a series
+ * of contiguous gap insertions or deletions.
+ *
+ * @param edits
+ * @param e
+ * @return
+ */
+ protected static boolean expandEdit(List edits, Edit e)
+ {
+ if (edits == null || edits.isEmpty())
+ {
+ return false;
+ }
+ Edit lastEdit = edits.get(edits.size() - 1);
+ Action action = e.command;
+ if (lastEdit.command != action)
+ {
+ return false;
+ }
+
+ /*
+ * Both commands must act on the same sequences - compare the underlying
+ * dataset sequences, rather than the aligned sequences, which change as
+ * they are edited.
+ */
+ if (lastEdit.seqs.length != e.seqs.length)
+ {
+ return false;
+ }
+ for (int i = 0; i < e.seqs.length; i++)
+ {
+ if (lastEdit.seqs[i].getDatasetSequence() != e.seqs[i]
+ .getDatasetSequence())
+ {
+ return false;
+ }
+ }
+
+ /**
+ * Check a contiguous edit; either
+ *
+ * - a new Insert positions to the right of the last ,
+ * or
+ * - a new Delete gaps which is positions to the left of the last
+ * delete.
+ *
+ */
+ boolean contiguous = (action == Action.INSERT_GAP
+ && e.position == lastEdit.position + lastEdit.number)
+ || (action == Action.DELETE_GAP
+ && e.position + e.number == lastEdit.position);
+ if (contiguous)
+ {
+ /*
+ * We are just expanding the range of the last edit. For delete gap, also
+ * moving the start position left.
+ */
+ lastEdit.number += e.number;
+ lastEdit.seqs = e.seqs;
+ if (action == Action.DELETE_GAP)
+ {
+ lastEdit.position--;
+ }
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Clear the list of stored edit commands.
+ *
+ */
+ protected void clearEdits()
+ {
+ edits.clear();
+ }
+
+ /**
+ * Returns the i'th stored Edit command.
+ *
+ * @param i
+ * @return
+ */
+ protected Edit getEdit(int i)
+ {
+ if (i >= 0 && i < edits.size())
+ {
+ return edits.get(i);
+ }
+ return null;
+ }
+
+ @Override
+ final public String getDescription()
+ {
+ return description;
+ }
+
+ @Override
+ public int getSize()
+ {
+ return edits.size();
+ }
+
+ /**
+ * Return the alignment for the first edit (or null if no edit).
+ *
+ * @return
+ */
+ final public AlignmentI getAlignment()
+ {
+ return (edits.isEmpty() ? null : edits.get(0).al);
+ }
+
+ /**
+ * append a new editCommand Note. this shouldn't be called if the edit is an
+ * operation affects more alignment objects than the one referenced in al (for
+ * example, cut or pasting whole sequences). Use the form with an additional
+ * AlignmentI[] views parameter.
+ *
+ * @param command
+ * @param seqs
+ * @param position
+ * @param number
+ * @param al
+ * @param performEdit
+ */
+ final public void appendEdit(Action command, SequenceI[] seqs,
+ int position, int number, AlignmentI al, boolean performEdit)
+ {
+ appendEdit(command, seqs, position, number, al, performEdit, null);
+ }
+
+ /**
+ * append a new edit command with a set of alignment views that may be
+ * operated on
+ *
+ * @param command
+ * @param seqs
+ * @param position
+ * @param number
+ * @param al
+ * @param performEdit
+ * @param views
+ */
+ final public void appendEdit(Action command, SequenceI[] seqs,
+ int position, int number, AlignmentI al, boolean performEdit,
+ AlignmentI[] views)
+ {
+ Edit edit = new Edit(command, seqs, position, number, al);
+ appendEdit(edit, al, performEdit, views);
+ }
+
+ /**
+ * Overloaded method that accepts an Edit object with additional parameters.
+ *
+ * @param edit
+ * @param al
+ * @param performEdit
+ * @param views
+ */
+ final public void appendEdit(Edit edit, AlignmentI al,
+ boolean performEdit, AlignmentI[] views)
+ {
+ if (al.getHeight() == edit.seqs.length)
+ {
+ edit.al = al;
+ edit.fullAlignmentHeight = true;
+ }
+
+ addEdit(edit);
+
+ if (performEdit)
+ {
+ performEdit(edit, views);
+ }
+ }
+
+ /**
+ * Execute all the edit commands, starting at the given commandIndex
+ *
+ * @param commandIndex
+ * @param views
+ */
+ public final void performEdit(int commandIndex, AlignmentI[] views)
+ {
+ ListIterator iterator = edits.listIterator(commandIndex);
+ while (iterator.hasNext())
+ {
+ Edit edit = iterator.next();
+ performEdit(edit, views);
+ }
+ }
+
+ /**
+ * Execute one edit command in all the specified alignment views
+ *
+ * @param edit
+ * @param views
+ */
+ protected static void performEdit(Edit edit, AlignmentI[] views)
+ {
+ switch (edit.command)
+ {
+ case INSERT_GAP:
+ insertGap(edit);
+ break;
+ case DELETE_GAP:
+ deleteGap(edit);
+ break;
+ case CUT:
+ cut(edit, views);
+ break;
+ case PASTE:
+ paste(edit, views);
+ break;
+ case REPLACE:
+ replace(edit);
+ break;
+ case INSERT_NUC:
+ // TODO:add deleteNuc for UNDO
+ // case INSERT_NUC:
+ // insertNuc(edits[e]);
+ break;
+ default:
+ break;
+ }
+ }
+
+ @Override
+ final public void doCommand(AlignmentI[] views)
+ {
+ performEdit(0, views);
+ }
+
+ /**
+ * Undo the stored list of commands, in reverse order.
+ */
+ @Override
+ final public void undoCommand(AlignmentI[] views)
+ {
+ ListIterator iterator = edits.listIterator(edits.size());
+ while (iterator.hasPrevious())
+ {
+ Edit e = iterator.previous();
+ switch (e.command)
+ {
+ case INSERT_GAP:
+ deleteGap(e);
+ break;
+ case DELETE_GAP:
+ insertGap(e);
+ break;
+ case CUT:
+ paste(e, views);
+ break;
+ case PASTE:
+ cut(e, views);
+ break;
+ case REPLACE:
+ replace(e);
+ break;
+ case INSERT_NUC:
+ // not implemented
+ break;
+ default:
+ break;
+ }
+ }
+ }
+
+ /**
+ * Insert gap(s) in sequences as specified by the command, and adjust
+ * annotations.
+ *
+ * @param command
+ */
+ final private static void insertGap(Edit command)
+ {
+
+ for (int s = 0; s < command.seqs.length; s++)
+ {
+ command.seqs[s].insertCharAt(command.position, command.number,
+ command.gapChar);
+ // System.out.println("pos: "+command.position+" number:
+ // "+command.number);
+ }
+
+ adjustAnnotations(command, true, false, null);
+ }
+
+ //
+ // final void insertNuc(Edit command)
+ // {
+ //
+ // for (int s = 0; s < command.seqs.length; s++)
+ // {
+ // System.out.println("pos: "+command.position+" number: "+command.number);
+ // command.seqs[s].insertCharAt(command.position, command.number,'A');
+ // }
+ //
+ // adjustAnnotations(command, true, false, null);
+ // }
+
+ /**
+ * Delete gap(s) in sequences as specified by the command, and adjust
+ * annotations.
+ *
+ * @param command
+ */
+ final static private void deleteGap(Edit command)
+ {
+ for (int s = 0; s < command.seqs.length; s++)
+ {
+ command.seqs[s].deleteChars(command.position,
+ command.position + command.number);
+ }
+
+ adjustAnnotations(command, false, false, null);
+ }
+
+ /**
+ * Carry out a Cut action. The cut characters are saved in case Undo is
+ * requested.
+ *
+ * @param command
+ * @param views
+ */
+ static void cut(Edit command, AlignmentI[] views)
+ {
+ boolean seqDeleted = false;
+ command.string = new char[command.seqs.length][];
+
+ for (int i = 0; i < command.seqs.length; i++)
+ {
+ final SequenceI sequence = command.seqs[i];
+ if (sequence.getLength() > command.position)
+ {
+ command.string[i] = sequence.getSequence(command.position,
+ command.position + command.number);
+ SequenceI oldds = sequence.getDatasetSequence();
+ ContiguousI cutPositions = sequence.findPositions(
+ command.position + 1, command.position + command.number);
+ boolean cutIsInternal = cutPositions != null
+ && sequence.getStart() != cutPositions.getBegin()
+ && sequence.getEnd() != cutPositions.getEnd();
+
+ /*
+ * perform the cut; if this results in a new dataset sequence, add
+ * that to the alignment dataset
+ */
+ SequenceI ds = sequence.getDatasetSequence();
+ sequence.deleteChars(command.position,
+ command.position + command.number);
+
+ if (command.oldds != null && command.oldds[i] != null)
+ {
+ /*
+ * we are Redoing a Cut, or Undoing a Paste - so
+ * oldds entry contains the cut dataset sequence,
+ * with sequence features in expected place
+ */
+ sequence.setDatasetSequence(command.oldds[i]);
+ command.oldds[i] = oldds;
+ }
+ else
+ {
+ /*
+ * new cut operation: save the dataset sequence
+ * so it can be restored in an Undo
+ */
+ if (command.oldds == null)
+ {
+ command.oldds = new SequenceI[command.seqs.length];
+ }
+ command.oldds[i] = oldds;// todo not if !cutIsInternal?
+
+ // do we need to edit sequence features for new sequence ?
+ if (oldds != sequence.getDatasetSequence() || (cutIsInternal
+ && sequence.getFeatures().hasFeatures()))
+ // todo or just test cutIsInternal && cutPositions != null ?
+ {
+ if (cutPositions != null)
+ {
+ cutFeatures(command, sequence, cutPositions.getBegin(),
+ cutPositions.getEnd(), cutIsInternal);
+ }
+ }
+ }
+ SequenceI newDs = sequence.getDatasetSequence();
+ if (newDs != ds && command.al != null
+ && command.al.getDataset() != null
+ && !command.al.getDataset().getSequences().contains(newDs))
+ {
+ command.al.getDataset().addSequence(newDs);
+ }
+ }
+
+ if (sequence.getLength() < 1)
+ {
+ command.al.deleteSequence(sequence);
+ seqDeleted = true;
+ }
+ }
+
+ adjustAnnotations(command, false, seqDeleted, views);
+ }
+
+ /**
+ * Perform the given Paste command. This may be to add cut or copied sequences
+ * to an alignment, or to undo a 'Cut' action on a region of the alignment.
+ *
+ * @param command
+ * @param views
+ */
+ static void paste(Edit command, AlignmentI[] views)
+ {
+ boolean seqWasDeleted = false;
+
+ for (int i = 0; i < command.seqs.length; i++)
+ {
+ boolean newDSNeeded = false;
+ boolean newDSWasNeeded = command.oldds != null
+ && command.oldds[i] != null;
+ SequenceI sequence = command.seqs[i];
+ if (sequence.getLength() < 1)
+ {
+ /*
+ * sequence was deleted; re-add it to the alignment
+ */
+ if (command.alIndex[i] < command.al.getHeight())
+ {
+ List sequences = command.al.getSequences();
+ synchronized (sequences)
+ {
+ if (!(command.alIndex[i] < 0))
+ {
+ sequences.add(command.alIndex[i], sequence);
+ }
+ }
+ }
+ else
+ {
+ command.al.addSequence(sequence);
+ }
+ seqWasDeleted = true;
+ }
+ int newStart = sequence.getStart();
+ int newEnd = sequence.getEnd();
+
+ StringBuilder tmp = new StringBuilder();
+ tmp.append(sequence.getSequence());
+ // Undo of a delete does not replace original dataset sequence on to
+ // alignment sequence.
+
+ int start = 0;
+ int length = 0;
+
+ if (command.string != null && command.string[i] != null)
+ {
+ if (command.position >= tmp.length())
+ {
+ // This occurs if padding is on, and residues
+ // are removed from end of alignment
+ int len = command.position - tmp.length();
+ while (len > 0)
+ {
+ tmp.append(command.gapChar);
+ len--;
+ }
+ }
+ tmp.insert(command.position, command.string[i]);
+ for (int s = 0; s < command.string[i].length; s++)
+ {
+ if (!Comparison.isGap(command.string[i][s]))
+ {
+ length++;
+ if (!newDSNeeded)
+ {
+ newDSNeeded = true;
+ start = sequence.findPosition(command.position);
+ // end = sequence
+ // .findPosition(command.position + command.number);
+ }
+ if (sequence.getStart() == start)
+ {
+ newStart--;
+ }
+ else
+ {
+ newEnd++;
+ }
+ }
+ }
+ command.string[i] = null;
+ }
+
+ sequence.setSequence(tmp.toString());
+ sequence.setStart(newStart);
+ sequence.setEnd(newEnd);
+
+ /*
+ * command and Undo share the same dataset sequence if cut was
+ * at start or end of sequence
+ */
+ boolean sameDatasetSequence = false;
+ if (newDSNeeded)
+ {
+ if (sequence.getDatasetSequence() != null)
+ {
+ SequenceI ds;
+ if (newDSWasNeeded)
+ {
+ ds = command.oldds[i];
+ }
+ else
+ {
+ // make a new DS sequence
+ // use new ds mechanism here
+ String ungapped = AlignSeq.extractGaps(Comparison.GapChars,
+ sequence.getSequenceAsString());
+ ds = new Sequence(sequence.getName(), ungapped,
+ sequence.getStart(), sequence.getEnd());
+ ds.setDescription(sequence.getDescription());
+ }
+ if (command.oldds == null)
+ {
+ command.oldds = new SequenceI[command.seqs.length];
+ }
+ command.oldds[i] = sequence.getDatasetSequence();
+ sameDatasetSequence = ds == sequence.getDatasetSequence();
+ ds.setSequenceFeatures(sequence.getSequenceFeatures());
+ if (!sameDatasetSequence && command.al.getDataset() != null)
+ {
+ // delete 'undone' sequence from alignment dataset
+ command.al.getDataset()
+ .deleteSequence(sequence.getDatasetSequence());
+ }
+ sequence.setDatasetSequence(ds);
+ }
+ undoCutFeatures(command, command.seqs[i], start, length,
+ sameDatasetSequence);
+ }
+ }
+ adjustAnnotations(command, true, seqWasDeleted, views);
+
+ command.string = null;
+ }
+
+ static void replace(Edit command)
+ {
+ StringBuilder tmp;
+ String oldstring;
+ int start = command.position;
+ int end = command.number;
+ // TODO TUTORIAL - Fix for replacement with different length of sequence (or
+ // whole sequence)
+ // TODO Jalview 2.4 bugfix change to an aggregate command - original
+ // sequence string is cut, new string is pasted in.
+ command.number = start + command.string[0].length;
+ for (int i = 0; i < command.seqs.length; i++)
+ {
+ boolean newDSWasNeeded = command.oldds != null
+ && command.oldds[i] != null;
+ boolean newStartEndWasNeeded = command.oldStartEnd != null
+ && command.oldStartEnd[i] != null;
+
+ /**
+ * cut addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT,
+ * cut, sg.getStartRes(), sg.getEndRes()-sg.getStartRes()+1,
+ * viewport.alignment));
+ *
+ */
+ /**
+ * then addHistoryItem(new EditCommand( "Add sequences",
+ * EditCommand.PASTE, sequences, 0, alignment.getWidth(), alignment) );
+ *
+ */
+ ContiguousI beforeEditedPositions = command.seqs[i].findPositions(1,
+ start);
+ ContiguousI afterEditedPositions = command.seqs[i]
+ .findPositions(end + 1, command.seqs[i].getLength());
+
+ oldstring = command.seqs[i].getSequenceAsString();
+ tmp = new StringBuilder(oldstring.substring(0, start));
+ tmp.append(command.string[i]);
+ String nogaprep = AlignSeq.extractGaps(Comparison.GapChars,
+ new String(command.string[i]));
+ if (end < oldstring.length())
+ {
+ tmp.append(oldstring.substring(end));
+ }
+ // stash end prior to updating the sequence object so we can save it if
+ // need be.
+ Range oldstartend = new Range(command.seqs[i].getStart(),
+ command.seqs[i].getEnd());
+ command.seqs[i].setSequence(tmp.toString());
+ command.string[i] = oldstring
+ .substring(start, Math.min(end, oldstring.length()))
+ .toCharArray();
+ String nogapold = AlignSeq.extractGaps(Comparison.GapChars,
+ new String(command.string[i]));
+
+ if (!nogaprep.toLowerCase(Locale.ROOT)
+ .equals(nogapold.toLowerCase(Locale.ROOT)))
+ {
+ // we may already have dataset and limits stashed...
+ if (newDSWasNeeded || newStartEndWasNeeded)
+ {
+ if (newDSWasNeeded)
+ {
+ // then just switch the dataset sequence
+ SequenceI oldds = command.seqs[i].getDatasetSequence();
+ command.seqs[i].setDatasetSequence(command.oldds[i]);
+ command.oldds[i] = oldds;
+ }
+ if (newStartEndWasNeeded)
+ {
+ Range newStart = command.oldStartEnd[i];
+ command.oldStartEnd[i] = oldstartend;
+ command.seqs[i].setStart(newStart.getBegin());
+ command.seqs[i].setEnd(newStart.getEnd());
+ }
+ }
+ else
+ {
+ // decide if we need a new dataset sequence or modify start/end
+ // first edit the original dataset sequence string
+ SequenceI oldds = command.seqs[i].getDatasetSequence();
+ String osp = oldds.getSequenceAsString();
+ int beforeStartOfEdit = -oldds.getStart() + 1
+ + (beforeEditedPositions == null
+ ? ((afterEditedPositions != null)
+ ? afterEditedPositions.getBegin() - 1
+ : oldstartend.getBegin()
+ + nogapold.length())
+ : beforeEditedPositions.getEnd());
+ int afterEndOfEdit = -oldds.getStart() + 1
+ + ((afterEditedPositions == null) ? oldstartend.getEnd()
+ : afterEditedPositions.getBegin() - 1);
+ String fullseq = osp.substring(0, beforeStartOfEdit) + nogaprep
+ + osp.substring(afterEndOfEdit);
+
+ // and check if new sequence data is different..
+ if (!fullseq.equalsIgnoreCase(osp))
+ {
+ // old ds and edited ds are different, so
+ // create the new dataset sequence
+ SequenceI newds = new Sequence(oldds);
+ newds.setSequence(fullseq.toUpperCase(Locale.ROOT));
+
+ if (command.oldds == null)
+ {
+ command.oldds = new SequenceI[command.seqs.length];
+ }
+ command.oldds[i] = command.seqs[i].getDatasetSequence();
+
+ // And preserve start/end for good-measure
+
+ if (command.oldStartEnd == null)
+ {
+ command.oldStartEnd = new Range[command.seqs.length];
+ }
+ command.oldStartEnd[i] = oldstartend;
+ // TODO: JAL-1131 ensure newly created dataset sequence is added to
+ // the set of
+ // dataset sequences associated with the alignment.
+ // TODO: JAL-1131 fix up any annotation associated with new dataset
+ // sequence to ensure that original sequence/annotation
+ // relationships
+ // are preserved.
+ command.seqs[i].setDatasetSequence(newds);
+ }
+ else
+ {
+ if (command.oldStartEnd == null)
+ {
+ command.oldStartEnd = new Range[command.seqs.length];
+ }
+ command.oldStartEnd[i] = new Range(command.seqs[i].getStart(),
+ command.seqs[i].getEnd());
+ if (beforeEditedPositions != null
+ && afterEditedPositions == null)
+ {
+ // modification at end
+ command.seqs[i].setEnd(beforeEditedPositions.getEnd()
+ + nogaprep.length() - nogapold.length());
+ }
+ else if (afterEditedPositions != null
+ && beforeEditedPositions == null)
+ {
+ // modification at start
+ command.seqs[i].setStart(
+ afterEditedPositions.getBegin() - nogaprep.length());
+ }
+ else
+ {
+ // edit covered both start and end. Here we can only guess the
+ // new
+ // start/end
+ String nogapalseq = AlignSeq.extractGaps(Comparison.GapChars,
+ command.seqs[i].getSequenceAsString()
+ .toUpperCase(Locale.ROOT));
+ int newStart = command.seqs[i].getDatasetSequence()
+ .getSequenceAsString().indexOf(nogapalseq);
+ if (newStart == -1)
+ {
+ throw new Error(
+ "Implementation Error: could not locate start/end "
+ + "in dataset sequence after an edit of the sequence string");
+ }
+ int newEnd = newStart + nogapalseq.length() - 1;
+ command.seqs[i].setStart(newStart);
+ command.seqs[i].setEnd(newEnd);
+ }
+ }
+ }
+ }
+ tmp = null;
+ oldstring = null;
+ }
+ }
+
+ final static void adjustAnnotations(Edit command, boolean insert,
+ boolean modifyVisibility, AlignmentI[] views)
+ {
+ AlignmentAnnotation[] annotations = null;
+
+ if (modifyVisibility && !insert)
+ {
+ // only occurs if a sequence was added or deleted.
+ command.deletedAnnotationRows = new Hashtable<>();
+ }
+ if (command.fullAlignmentHeight)
+ {
+ annotations = command.al.getAlignmentAnnotation();
+ }
+ else
+ {
+ int aSize = 0;
+ AlignmentAnnotation[] tmp;
+ for (int s = 0; s < command.seqs.length; s++)
+ {
+ command.seqs[s].sequenceChanged();
+
+ if (modifyVisibility)
+ {
+ // Rows are only removed or added to sequence object.
+ if (!insert)
+ {
+ // remove rows
+ tmp = command.seqs[s].getAnnotation();
+ if (tmp != null)
+ {
+ int alen = tmp.length;
+ for (int aa = 0; aa < tmp.length; aa++)
+ {
+ if (!command.al.deleteAnnotation(tmp[aa]))
+ {
+ // strip out annotation not in the current al (will be put
+ // back on insert in all views)
+ tmp[aa] = null;
+ alen--;
+ }
+ }
+ command.seqs[s].setAlignmentAnnotation(null);
+ if (alen != tmp.length)
+ {
+ // save the non-null annotation references only
+ AlignmentAnnotation[] saved = new AlignmentAnnotation[alen];
+ for (int aa = 0, aapos = 0; aa < tmp.length; aa++)
+ {
+ if (tmp[aa] != null)
+ {
+ saved[aapos++] = tmp[aa];
+ tmp[aa] = null;
+ }
+ }
+ tmp = saved;
+ command.deletedAnnotationRows.put(command.seqs[s], saved);
+ // and then remove any annotation in the other views
+ for (int alview = 0; views != null
+ && alview < views.length; alview++)
+ {
+ if (views[alview] != command.al)
+ {
+ AlignmentAnnotation[] toremove = views[alview]
+ .getAlignmentAnnotation();
+ if (toremove == null || toremove.length == 0)
+ {
+ continue;
+ }
+ // remove any alignment annotation on this sequence that's
+ // on that alignment view.
+ for (int aa = 0; aa < toremove.length; aa++)
+ {
+ if (toremove[aa].sequenceRef == command.seqs[s])
+ {
+ views[alview].deleteAnnotation(toremove[aa]);
+ }
+ }
+ }
+ }
+ }
+ else
+ {
+ // save all the annotation
+ command.deletedAnnotationRows.put(command.seqs[s], tmp);
+ }
+ }
+ }
+ else
+ {
+ // recover rows
+ if (command.deletedAnnotationRows != null
+ && command.deletedAnnotationRows
+ .containsKey(command.seqs[s]))
+ {
+ AlignmentAnnotation[] revealed = command.deletedAnnotationRows
+ .get(command.seqs[s]);
+ command.seqs[s].setAlignmentAnnotation(revealed);
+ if (revealed != null)
+ {
+ for (int aa = 0; aa < revealed.length; aa++)
+ {
+ // iterate through al adding original annotation
+ command.al.addAnnotation(revealed[aa]);
+ }
+ for (int aa = 0; aa < revealed.length; aa++)
+ {
+ command.al.setAnnotationIndex(revealed[aa], aa);
+ }
+ // and then duplicate added annotation on every other alignment
+ // view
+ for (int vnum = 0; views != null
+ && vnum < views.length; vnum++)
+ {
+ if (views[vnum] != command.al)
+ {
+ int avwidth = views[vnum].getWidth() + 1;
+ // duplicate in this view
+ for (int a = 0; a < revealed.length; a++)
+ {
+ AlignmentAnnotation newann = new AlignmentAnnotation(
+ revealed[a]);
+ command.seqs[s].addAlignmentAnnotation(newann);
+ newann.padAnnotation(avwidth);
+ views[vnum].addAnnotation(newann);
+ views[vnum].setAnnotationIndex(newann, a);
+ }
+ }
+ }
+ }
+ }
+ }
+ continue;
+ }
+
+ if (command.seqs[s].getAnnotation() == null)
+ {
+ continue;
+ }
+
+ if (aSize == 0)
+ {
+ annotations = command.seqs[s].getAnnotation();
+ }
+ else
+ {
+ tmp = new AlignmentAnnotation[aSize
+ + command.seqs[s].getAnnotation().length];
+
+ System.arraycopy(annotations, 0, tmp, 0, aSize);
+
+ System.arraycopy(command.seqs[s].getAnnotation(), 0, tmp, aSize,
+ command.seqs[s].getAnnotation().length);
+
+ annotations = tmp;
+ }
+ aSize = annotations.length;
+ }
+ }
+
+ if (annotations == null)
+ {
+ return;
+ }
+
+ if (!insert)
+ {
+ command.deletedAnnotations = new Hashtable<>();
+ }
+
+ int aSize;
+ Annotation[] temp;
+ for (int a = 0; a < annotations.length; a++)
+ {
+ if (annotations[a].autoCalculated
+ || annotations[a].annotations == null)
+ {
+ continue;
+ }
+
+ int tSize = 0;
+
+ aSize = annotations[a].annotations.length;
+ if (insert)
+ {
+ temp = new Annotation[aSize + command.number];
+ if (annotations[a].padGaps)
+ {
+ for (int aa = 0; aa < temp.length; aa++)
+ {
+ temp[aa] = new Annotation(command.gapChar + "", null, ' ', 0);
+ }
+ }
+ }
+ else
+ {
+ if (command.position < aSize)
+ {
+ if (command.position + command.number >= aSize)
+ {
+ tSize = aSize;
+ }
+ else
+ {
+ tSize = aSize - command.number;
+ }
+ }
+ else
+ {
+ tSize = aSize;
+ }
+
+ if (tSize < 0)
+ {
+ tSize = aSize;
+ }
+ temp = new Annotation[tSize];
+ }
+
+ if (insert)
+ {
+ if (command.position < annotations[a].annotations.length)
+ {
+ System.arraycopy(annotations[a].annotations, 0, temp, 0,
+ command.position);
+
+ if (command.deletedAnnotations != null
+ && command.deletedAnnotations
+ .containsKey(annotations[a].annotationId))
+ {
+ Annotation[] restore = command.deletedAnnotations
+ .get(annotations[a].annotationId);
+
+ System.arraycopy(restore, 0, temp, command.position,
+ command.number);
+
+ }
+
+ System.arraycopy(annotations[a].annotations, command.position,
+ temp, command.position + command.number,
+ aSize - command.position);
+ }
+ else
+ {
+ if (command.deletedAnnotations != null
+ && command.deletedAnnotations
+ .containsKey(annotations[a].annotationId))
+ {
+ Annotation[] restore = command.deletedAnnotations
+ .get(annotations[a].annotationId);
+
+ temp = new Annotation[annotations[a].annotations.length
+ + restore.length];
+ System.arraycopy(annotations[a].annotations, 0, temp, 0,
+ annotations[a].annotations.length);
+ System.arraycopy(restore, 0, temp,
+ annotations[a].annotations.length, restore.length);
+ }
+ else
+ {
+ temp = annotations[a].annotations;
+ }
+ }
+ }
+ else
+ {
+ if (tSize != aSize || command.position < 2)
+ {
+ int copylen = Math.min(command.position,
+ annotations[a].annotations.length);
+ if (copylen > 0)
+ {
+ System.arraycopy(annotations[a].annotations, 0, temp, 0,
+ copylen); // command.position);
+ }
+
+ Annotation[] deleted = new Annotation[command.number];
+ if (copylen >= command.position)
+ {
+ copylen = Math.min(command.number,
+ annotations[a].annotations.length - command.position);
+ if (copylen > 0)
+ {
+ System.arraycopy(annotations[a].annotations, command.position,
+ deleted, 0, copylen); // command.number);
+ }
+ }
+
+ command.deletedAnnotations.put(annotations[a].annotationId,
+ deleted);
+ if (annotations[a].annotations.length > command.position
+ + command.number)
+ {
+ System.arraycopy(annotations[a].annotations,
+ command.position + command.number, temp,
+ command.position, annotations[a].annotations.length
+ - command.position - command.number); // aSize
+ }
+ }
+ else
+ {
+ int dSize = aSize - command.position;
+
+ if (dSize > 0)
+ {
+ Annotation[] deleted = new Annotation[command.number];
+ System.arraycopy(annotations[a].annotations, command.position,
+ deleted, 0, dSize);
+
+ command.deletedAnnotations.put(annotations[a].annotationId,
+ deleted);
+
+ tSize = Math.min(annotations[a].annotations.length,
+ command.position);
+ temp = new Annotation[tSize];
+ System.arraycopy(annotations[a].annotations, 0, temp, 0, tSize);
+ }
+ else
+ {
+ temp = annotations[a].annotations;
+ }
+ }
+ }
+
+ annotations[a].annotations = temp;
+ }
+ }
+
+ /**
+ * Restores features to the state before a Cut.
+ *
+ * - re-add any features deleted by the cut
+ * - remove any truncated features created by the cut
+ * - shift right any features to the right of the cut
+ *
+ *
+ * @param command
+ * the Cut command
+ * @param seq
+ * the sequence the Cut applied to
+ * @param start
+ * the start residue position of the cut
+ * @param length
+ * the number of residues cut
+ * @param sameDatasetSequence
+ * true if dataset sequence and frame of reference were left
+ * unchanged by the Cut
+ */
+ final static void undoCutFeatures(Edit command, SequenceI seq,
+ final int start, final int length, boolean sameDatasetSequence)
+ {
+ SequenceI sequence = seq.getDatasetSequence();
+ if (sequence == null)
+ {
+ sequence = seq;
+ }
+
+ /*
+ * shift right features that lie to the right of the restored cut (but not
+ * if dataset sequence unchanged - so coordinates were changed by Cut)
+ */
+ if (!sameDatasetSequence)
+ {
+ /*
+ * shift right all features right of and not
+ * contiguous with the cut position
+ */
+ seq.getFeatures().shiftFeatures(start + 1, length);
+
+ /*
+ * shift right any features that start at the cut position,
+ * unless they were truncated
+ */
+ List sfs = seq.getFeatures().findFeatures(start,
+ start);
+ for (SequenceFeature sf : sfs)
+ {
+ if (sf.getBegin() == start)
+ {
+ if (!command.truncatedFeatures.containsKey(seq)
+ || !command.truncatedFeatures.get(seq).contains(sf))
+ {
+ /*
+ * feature was shifted left to cut position (not truncated),
+ * so shift it back right
+ */
+ SequenceFeature shifted = new SequenceFeature(sf,
+ sf.getBegin() + length, sf.getEnd() + length,
+ sf.getFeatureGroup(), sf.getScore());
+ seq.addSequenceFeature(shifted);
+ seq.deleteFeature(sf);
+ }
+ }
+ }
+ }
+
+ /*
+ * restore any features that were deleted or truncated
+ */
+ if (command.deletedFeatures != null
+ && command.deletedFeatures.containsKey(seq))
+ {
+ for (SequenceFeature deleted : command.deletedFeatures.get(seq))
+ {
+ sequence.addSequenceFeature(deleted);
+ }
+ }
+
+ /*
+ * delete any truncated features
+ */
+ if (command.truncatedFeatures != null
+ && command.truncatedFeatures.containsKey(seq))
+ {
+ for (SequenceFeature amended : command.truncatedFeatures.get(seq))
+ {
+ sequence.deleteFeature(amended);
+ }
+ }
+ }
+
+ /**
+ * Returns the list of edit commands wrapped by this object.
+ *
+ * @return
+ */
+ public List getEdits()
+ {
+ return this.edits;
+ }
+
+ /**
+ * Returns a map whose keys are the dataset sequences, and values their
+ * aligned sequences before the command edit list was applied. The aligned
+ * sequences are copies, which may be updated without affecting the originals.
+ *
+ * The command holds references to the aligned sequences (after editing). If
+ * the command is an 'undo',then the prior state is simply the aligned state.
+ * Otherwise, we have to derive the prior state by working backwards through
+ * the edit list to infer the aligned sequences before editing.
+ *
+ * Note: an alternative solution would be to cache the 'before' state of each
+ * edit, but this would be expensive in space in the common case that the
+ * original is never needed (edits are not mirrored).
+ *
+ * @return
+ * @throws IllegalStateException
+ * on detecting an edit command of a type that can't be unwound
+ */
+ public Map priorState(boolean forUndo)
+ {
+ Map result = new HashMap<>();
+ if (getEdits() == null)
+ {
+ return result;
+ }
+ if (forUndo)
+ {
+ for (Edit e : getEdits())
+ {
+ for (SequenceI seq : e.getSequences())
+ {
+ SequenceI ds = seq.getDatasetSequence();
+ // SequenceI preEdit = result.get(ds);
+ if (!result.containsKey(ds))
+ {
+ /*
+ * copy sequence including start/end (but don't use copy constructor
+ * as we don't need annotations)
+ */
+ SequenceI preEdit = new Sequence("", seq.getSequenceAsString(),
+ seq.getStart(), seq.getEnd());
+ preEdit.setDatasetSequence(ds);
+ result.put(ds, preEdit);
+ }
+ }
+ }
+ return result;
+ }
+
+ /*
+ * Work backwards through the edit list, deriving the sequences before each
+ * was applied. The final result is the sequence set before any edits.
+ */
+ Iterator editList = new ReverseListIterator<>(getEdits());
+ while (editList.hasNext())
+ {
+ Edit oldEdit = editList.next();
+ Action action = oldEdit.getAction();
+ int position = oldEdit.getPosition();
+ int number = oldEdit.getNumber();
+ final char gap = oldEdit.getGapCharacter();
+ for (SequenceI seq : oldEdit.getSequences())
+ {
+ SequenceI ds = seq.getDatasetSequence();
+ SequenceI preEdit = result.get(ds);
+ if (preEdit == null)
+ {
+ preEdit = new Sequence("", seq.getSequenceAsString(),
+ seq.getStart(), seq.getEnd());
+ preEdit.setDatasetSequence(ds);
+ result.put(ds, preEdit);
+ }
+ /*
+ * 'Undo' this edit action on the sequence (updating the value in the
+ * map).
+ */
+ if (ds != null)
+ {
+ if (action == Action.DELETE_GAP)
+ {
+ preEdit.setSequence(new String(StringUtils.insertCharAt(
+ preEdit.getSequence(), position, number, gap)));
+ }
+ else if (action == Action.INSERT_GAP)
+ {
+ preEdit.setSequence(new String(StringUtils.deleteChars(
+ preEdit.getSequence(), position, position + number)));
+ }
+ else
+ {
+ System.err.println("Can't undo edit action " + action);
+ // throw new IllegalStateException("Can't undo edit action " +
+ // action);
+ }
+ }
+ }
+ }
+ return result;
+ }
+
+ public class Edit
+ {
+ SequenceI[] oldds;
+
+ /**
+ * start and end of sequence prior to edit
+ */
+ Range[] oldStartEnd;
+
+ boolean fullAlignmentHeight = false;
+
+ Map deletedAnnotationRows;
+
+ Map deletedAnnotations;
+
+ /*
+ * features deleted by the cut (re-add on Undo)
+ * (including the original of any shortened features)
+ */
+ Map> deletedFeatures;
+
+ /*
+ * shortened features added by the cut (delete on Undo)
+ */
+ Map> truncatedFeatures;
+
+ AlignmentI al;
+
+ final Action command;
+
+ char[][] string;
+
+ SequenceI[] seqs;
+
+ int[] alIndex;
+
+ int position;
+
+ int number;
+
+ char gapChar;
+
+ /*
+ * flag that identifies edits inserted to balance
+ * user edits in a 'locked editing' region
+ */
+ private boolean systemGenerated;
+
+ public Edit(Action cmd, SequenceI[] sqs, int pos, int count, char gap)
+ {
+ this.command = cmd;
+ this.seqs = sqs;
+ this.position = pos;
+ this.number = count;
+ this.gapChar = gap;
+ }
+
+ Edit(Action cmd, SequenceI[] sqs, int pos, int count, AlignmentI align)
+ {
+ this(cmd, sqs, pos, count, align.getGapCharacter());
+
+ this.al = align;
+
+ alIndex = new int[sqs.length];
+ for (int i = 0; i < sqs.length; i++)
+ {
+ alIndex[i] = align.findIndex(sqs[i]);
+ }
+
+ fullAlignmentHeight = (align.getHeight() == sqs.length);
+ }
+
+ /**
+ * Constructor given a REPLACE command and the replacement string
+ *
+ * @param cmd
+ * @param sqs
+ * @param pos
+ * @param count
+ * @param align
+ * @param replace
+ */
+ Edit(Action cmd, SequenceI[] sqs, int pos, int count, AlignmentI align,
+ String replace)
+ {
+ this(cmd, sqs, pos, count, align);
+
+ string = new char[sqs.length][];
+ for (int i = 0; i < sqs.length; i++)
+ {
+ string[i] = replace.toCharArray();
+ }
+ }
+
+ public SequenceI[] getSequences()
+ {
+ return seqs;
+ }
+
+ public int getPosition()
+ {
+ return position;
+ }
+
+ public Action getAction()
+ {
+ return command;
+ }
+
+ public int getNumber()
+ {
+ return number;
+ }
+
+ public char getGapCharacter()
+ {
+ return gapChar;
+ }
+
+ public void setSystemGenerated(boolean b)
+ {
+ systemGenerated = b;
+ }
+
+ public boolean isSystemGenerated()
+ {
+ return systemGenerated;
+ }
+ }
+
+ /**
+ * Returns an iterator over the list of edit commands which traverses the list
+ * either forwards or backwards.
+ *
+ * @param forwards
+ * @return
+ */
+ public Iterator getEditIterator(boolean forwards)
+ {
+ if (forwards)
+ {
+ return getEdits().iterator();
+ }
+ else
+ {
+ return new ReverseListIterator<>(getEdits());
+ }
+ }
+
+ /**
+ * Adjusts features for Cut, and saves details of changes made to allow Undo
+ *
+ * - features left of the cut are unchanged
+ * - features right of the cut are shifted left
+ * - features internal to the cut region are deleted
+ * - features that overlap or span the cut are shortened
+ * - the originals of any deleted or shortened features are saved, to re-add
+ * on Undo
+ * - any added (shortened) features are saved, to delete on Undo
+ *
+ *
+ * @param command
+ * @param seq
+ * @param fromPosition
+ * @param toPosition
+ * @param cutIsInternal
+ */
+ protected static void cutFeatures(Edit command, SequenceI seq,
+ int fromPosition, int toPosition, boolean cutIsInternal)
+ {
+ /*
+ * if the cut is at start or end of sequence
+ * then we don't modify the sequence feature store
+ */
+ if (!cutIsInternal)
+ {
+ return;
+ }
+ List added = new ArrayList<>();
+ List removed = new ArrayList<>();
+
+ SequenceFeaturesI featureStore = seq.getFeatures();
+ if (toPosition < fromPosition || featureStore == null)
+ {
+ return;
+ }
+
+ int cutStartPos = fromPosition;
+ int cutEndPos = toPosition;
+ int cutWidth = cutEndPos - cutStartPos + 1;
+
+ synchronized (featureStore)
+ {
+ /*
+ * get features that overlap the cut region
+ */
+ List toAmend = featureStore.findFeatures(cutStartPos,
+ cutEndPos);
+
+ /*
+ * add any contact features that span the cut region
+ * (not returned by findFeatures)
+ */
+ for (SequenceFeature contact : featureStore.getContactFeatures())
+ {
+ if (contact.getBegin() < cutStartPos
+ && contact.getEnd() > cutEndPos)
+ {
+ toAmend.add(contact);
+ }
+ }
+
+ /*
+ * adjust start-end of overlapping features;
+ * delete features enclosed by the cut;
+ * delete partially overlapping contact features
+ */
+ for (SequenceFeature sf : toAmend)
+ {
+ int sfBegin = sf.getBegin();
+ int sfEnd = sf.getEnd();
+ int newBegin = sfBegin;
+ int newEnd = sfEnd;
+ boolean toDelete = false;
+ boolean follows = false;
+
+ if (sfBegin >= cutStartPos && sfEnd <= cutEndPos)
+ {
+ /*
+ * feature lies within cut region - delete it
+ */
+ toDelete = true;
+ }
+ else if (sfBegin < cutStartPos && sfEnd > cutEndPos)
+ {
+ /*
+ * feature spans cut region - left-shift the end
+ */
+ newEnd -= cutWidth;
+ }
+ else if (sfEnd <= cutEndPos)
+ {
+ /*
+ * feature overlaps left of cut region - truncate right
+ */
+ newEnd = cutStartPos - 1;
+ if (sf.isContactFeature())
+ {
+ toDelete = true;
+ }
+ }
+ else if (sfBegin >= cutStartPos)
+ {
+ /*
+ * remaining case - feature overlaps right
+ * truncate left, adjust end of feature
+ */
+ newBegin = cutIsInternal ? cutStartPos : cutEndPos + 1;
+ newEnd = newBegin + sfEnd - cutEndPos - 1;
+ if (sf.isContactFeature())
+ {
+ toDelete = true;
+ }
+ }
+
+ seq.deleteFeature(sf);
+ if (!follows)
+ {
+ removed.add(sf);
+ }
+ if (!toDelete)
+ {
+ SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd,
+ sf.getFeatureGroup(), sf.getScore());
+ seq.addSequenceFeature(copy);
+ if (!follows)
+ {
+ added.add(copy);
+ }
+ }
+ }
+
+ /*
+ * and left shift any features lying to the right of the cut region
+ */
+
+ featureStore.shiftFeatures(cutEndPos + 1, -cutWidth);
+ }
+
+ /*
+ * save deleted and amended features, so that Undo can
+ * re-add or delete them respectively
+ */
+ if (command.deletedFeatures == null)
+ {
+ command.deletedFeatures = new HashMap<>();
+ }
+ if (command.truncatedFeatures == null)
+ {
+ command.truncatedFeatures = new HashMap<>();
+ }
+ command.deletedFeatures.put(seq, removed);
+ command.truncatedFeatures.put(seq, added);
+ }
+}