/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
* This file is part of Jalview.
- *
+ *
* Jalview 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 3 of the License, or (at your option) any later version.
- *
- * Jalview 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
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.commands;
-import java.util.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+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;
/**
- *
+ *
* <p>
* Title: EditCommmand
* </p>
- *
+ *
* <p>
* Description: Essential information for performing undo and redo for cut/paste
* insert/delete gap which can be stored in the HistoryList
* </p>
- *
+ *
* <p>
* Copyright: Copyright (c) 2006
* </p>
- *
+ *
* <p>
* Company: Dundee University
* </p>
- *
+ *
* @author not attributable
* @version 1.0
*/
public class EditCommand implements CommandI
{
- public static final int INSERT_GAP = 0;
-
- public static final int DELETE_GAP = 1;
-
- public static final int CUT = 2;
-
- public static final int PASTE = 3;
-
- public static final int REPLACE = 4;
-
- public static final int INSERT_NUC=5;
+ 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();
+ };
- Edit[] edits;
+ private List<Edit> edits = new ArrayList<Edit>();
String description;
this.description = description;
}
- public EditCommand(String description, int command, SequenceI[] seqs,
+ public EditCommand(String description, Action command, SequenceI[] seqs,
int position, int number, AlignmentI al)
{
this.description = description;
- if (command == CUT || command == PASTE)
+ if (command == Action.CUT || command == Action.PASTE)
{
- edits = new Edit[]
- { new Edit(command, seqs, position, number, al) };
+ setEdit(new Edit(command, seqs, position, number, al));
}
performEdit(0, null);
}
- public EditCommand(String description, int command, String replace,
+ public EditCommand(String description, Action command, String replace,
SequenceI[] seqs, int position, int number, AlignmentI al)
{
this.description = description;
- if (command == REPLACE)
+ if (command == Action.REPLACE)
{
- edits = new Edit[]
- { new Edit(command, seqs, position, number, al, 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<Edit> 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
+ * <ul>
+ * <li>a new Insert <n> positions to the right of the last <insert n>, or</li>
+ * <li>a new Delete <n> gaps which is <n> positions to the left of the last
+ * delete.</li>
+ * </ul>
+ */
+ 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()
{
@Override
public int getSize()
{
- return edits == null ? 0 : edits.length;
+ return edits.size();
}
+ /**
+ * Return the alignment for the first edit (or null if no edit).
+ *
+ * @return
+ */
final public AlignmentI getAlignment()
{
- return edits[0].al;
+ return (edits.isEmpty() ? null : edits.get(0).al);
}
/**
* 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 al
* @param performEdit
*/
- final public void appendEdit(int command, SequenceI[] seqs, int position,
- int number, AlignmentI al, boolean 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 performEdit
* @param views
*/
- final public void appendEdit(int command, SequenceI[] seqs, int position,
- int number, AlignmentI al, boolean performEdit, AlignmentI[] 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.getGapCharacter());
edit.fullAlignmentHeight = true;
}
- if (edits != null)
+ addEdit(edit);
+
+ if (performEdit)
{
- Edit[] temp = new Edit[edits.length + 1];
- System.arraycopy(edits, 0, temp, 0, edits.length);
- edits = temp;
- edits[edits.length - 1] = edit;
+ performEdit(edit, views);
}
- else
+ }
+
+ /**
+ * 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)
{
- edits = new Edit[]
- { edit };
+ edit.al = al;
+ edit.fullAlignmentHeight = true;
}
+ addEdit(edit);
+
if (performEdit)
{
- performEdit(edits.length - 1, views);
+ performEdit(edit, views);
}
}
- final void performEdit(int commandIndex, AlignmentI[] views)
+ /**
+ * Execute all the edit commands, starting at the given commandIndex
+ *
+ * @param commandIndex
+ * @param views
+ */
+ public final void performEdit(int commandIndex, AlignmentI[] views)
{
- int eSize = edits.length;
- for (int e = commandIndex; e < eSize; e++)
+ ListIterator<Edit> iterator = edits.listIterator(commandIndex);
+ while (iterator.hasNext())
{
- switch (edits[e].command)
- {
- case INSERT_GAP:
- insertGap(edits[e]);
- break;
- case DELETE_GAP:
- deleteGap(edits[e]);
- break;
- case CUT:
- cut(edits[e], views);
- break;
- case PASTE:
- paste(edits[e], views);
- break;
- case REPLACE:
- replace(edits[e]);
- break;
- //TODO:add deleteNuc for UNDO
-// case INSERT_NUC:
-// insertNuc(edits[e]);
-// break;
- }
+ 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;
}
}
performEdit(0, views);
}
+ /**
+ * Undo the stored list of commands, in reverse order.
+ */
@Override
final public void undoCommand(AlignmentI[] views)
{
- int e = 0, eSize = edits.length;
- for (e = eSize - 1; e > -1; e--)
+ ListIterator<Edit> iterator = edits.listIterator(edits.size());
+ while (iterator.hasPrevious())
{
- switch (edits[e].command)
+ Edit e = iterator.previous();
+ switch (e.command)
{
case INSERT_GAP:
- deleteGap(edits[e]);
+ deleteGap(e);
break;
case DELETE_GAP:
- insertGap(edits[e]);
+ insertGap(e);
break;
case CUT:
- paste(edits[e], views);
+ paste(e, views);
break;
case PASTE:
- cut(edits[e], views);
+ cut(e, views);
break;
case REPLACE:
- replace(edits[e]);
+ replace(e);
+ break;
+ case INSERT_NUC:
+ // not implemented
break;
- }
+ default:
+ break;
+ }
}
}
- final void insertGap(Edit command)
+ /**
+ * 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);
+ // 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);
-// }
-
- final void deleteGap(Edit command)
+
+ //
+ // 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++)
{
adjustAnnotations(command, false, false, null);
}
- void cut(Edit command, AlignmentI[] views)
+ /**
+ * 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++)
{
- if (command.seqs[i].getLength() > command.position)
+ final SequenceI sequence = command.seqs[i];
+ if (sequence.getLength() > command.position)
{
- command.string[i] = command.seqs[i].getSequence(command.position,
+ command.string[i] = sequence.getSequence(command.position,
command.position + command.number);
- SequenceI oldds = command.seqs[i].getDatasetSequence();
+ SequenceI oldds = sequence.getDatasetSequence();
if (command.oldds != null && command.oldds[i] != null)
{
// we are redoing an undone cut.
- command.seqs[i].setDatasetSequence(null);
+ sequence.setDatasetSequence(null);
}
- command.seqs[i].deleteChars(command.position, command.position
+ sequence.deleteChars(command.position, command.position
+ command.number);
if (command.oldds != null && command.oldds[i] != null)
{
// oldds entry contains the cut dataset sequence.
- command.seqs[i].setDatasetSequence(command.oldds[i]);
+ sequence.setDatasetSequence(command.oldds[i]);
command.oldds[i] = oldds;
}
else
{
// modify the oldds if necessary
- if (oldds != command.seqs[i].getDatasetSequence()
- || command.seqs[i].getSequenceFeatures() != null)
+ if (oldds != sequence.getDatasetSequence()
+ || sequence.getSequenceFeatures() != null)
{
if (command.oldds == null)
{
adjustFeatures(
command,
i,
- command.seqs[i].findPosition(command.position),
- command.seqs[i].findPosition(command.position
- + command.number), false);
+ sequence.findPosition(command.position),
+ sequence.findPosition(command.position + command.number),
+ false);
}
}
}
- if (command.seqs[i].getLength() < 1)
+ if (sequence.getLength() < 1)
{
- command.al.deleteSequence(command.seqs[i]);
+ command.al.deleteSequence(sequence);
seqDeleted = true;
}
}
adjustAnnotations(command, false, seqDeleted, views);
}
- void paste(Edit command, AlignmentI[] 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)
{
StringBuffer tmp;
boolean newDSNeeded;
if (command.seqs[i].getLength() < 1)
{
// ie this sequence was deleted, we need to
- // read it to the alignment
+ // readd it to the alignment
if (command.alIndex[i] < command.al.getHeight())
{
List<SequenceI> sequences;
- synchronized (sequences=command.al.getSequences()) {
- sequences.add(command.alIndex[i], command.seqs[i]);
+ synchronized (sequences = command.al.getSequences())
+ {
+ if (!(command.alIndex[i] < 0))
+ {
+ sequences.add(command.alIndex[i], command.seqs[i]);
+ }
}
}
else
+ command.number);
}
if (command.seqs[i].getStart() == start)
+ {
newstart--;
+ }
else
+ {
newend++;
+ }
}
}
command.string[i] = null;
command.string = null;
}
- void replace(Edit command)
+ static void replace(Edit command)
{
StringBuffer tmp;
String oldstring;
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 newDSWasNeeded = command.oldds != null
+ && command.oldds[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) );
- *
+ *
*/
oldstring = command.seqs[i].getSequenceAsString();
tmp = new StringBuffer(oldstring.substring(0, start));
fullseq = osp.substring(0, ipos) + nogaprep
+ osp.substring(ipos + nogaprep.length());
newds.setSequence(fullseq.toUpperCase());
- // TODO: ensure newly created dataset sequence is added to the set of
+ // 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);
}
}
}
- final void adjustAnnotations(Edit command, boolean insert,
+ 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();
+ command.deletedAnnotationRows = new Hashtable<SequenceI, AlignmentAnnotation[]>();
}
if (command.fullAlignmentHeight)
{
&& command.deletedAnnotationRows
.containsKey(command.seqs[s]))
{
- AlignmentAnnotation[] revealed = (AlignmentAnnotation[]) command.deletedAnnotationRows
+ AlignmentAnnotation[] revealed = command.deletedAnnotationRows
.get(command.seqs[s]);
command.seqs[s].setAlignmentAnnotation(revealed);
if (revealed != null)
if (!insert)
{
- command.deletedAnnotations = new Hashtable();
+ command.deletedAnnotations = new Hashtable<String, Annotation[]>();
}
int aSize;
{
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
{
&& command.deletedAnnotations
.containsKey(annotations[a].annotationId))
{
- Annotation[] restore = (Annotation[]) command.deletedAnnotations
+ Annotation[] restore = command.deletedAnnotations
.get(annotations[a].annotationId);
System.arraycopy(restore, 0, temp, command.position,
&& command.deletedAnnotations
.containsKey(annotations[a].annotationId))
{
- Annotation[] restore = (Annotation[]) command.deletedAnnotations
+ Annotation[] restore = command.deletedAnnotations
.get(annotations[a].annotationId);
temp = new Annotation[annotations[a].annotations.length
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)
}
}
- final void adjustFeatures(Edit command, int index, int i, int j,
+ final static void adjustFeatures(Edit command, int index, int i, int j,
boolean insert)
{
SequenceI seq = command.seqs[index];
if (command.editedFeatures != null
&& command.editedFeatures.containsKey(seq))
{
- sequence.setSequenceFeatures((SequenceFeature[]) command.editedFeatures
- .get(seq));
+ sequence.setSequenceFeatures(command.editedFeatures.get(seq));
}
return;
if (command.editedFeatures == null)
{
- command.editedFeatures = new Hashtable();
+ command.editedFeatures = new Hashtable<SequenceI, SequenceFeature[]>();
}
command.editedFeatures.put(seq, oldsf);
}
- class Edit
+ /**
+ * Returns the list of edit commands wrapped by this object.
+ *
+ * @return
+ */
+ public List<Edit> 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<SequenceI, SequenceI> priorState(boolean forUndo)
+ {
+ Map<SequenceI, SequenceI> result = new HashMap<SequenceI, SequenceI>();
+ 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 (preEdit == null)
+ {
+ preEdit = new Sequence("", seq.getSequenceAsString());
+ 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<Edit> edits = new ReverseListIterator<Edit>(getEdits());
+ while (edits.hasNext())
+ {
+ Edit oldEdit = edits.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());
+ 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
{
public SequenceI[] oldds;
boolean fullAlignmentHeight = false;
- Hashtable deletedAnnotationRows;
+ Hashtable<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
- Hashtable deletedAnnotations;
+ Hashtable<String, Annotation[]> deletedAnnotations;
- Hashtable editedFeatures;
+ Hashtable<SequenceI, SequenceFeature[]> editedFeatures;
AlignmentI al;
- int command;
+ Action command;
char[][] string;
char gapChar;
- Edit(int command, SequenceI[] seqs, int position, int number,
+ public Edit(Action command, SequenceI[] seqs, int position, int number,
char gapChar)
{
this.command = command;
this.gapChar = gapChar;
}
- Edit(int command, SequenceI[] seqs, int position, int number,
+ Edit(Action command, SequenceI[] seqs, int position, int number,
AlignmentI al)
{
this.gapChar = al.getGapCharacter();
fullAlignmentHeight = (al.getHeight() == seqs.length);
}
- Edit(int command, SequenceI[] seqs, int position, int number,
+ Edit(Action command, SequenceI[] seqs, int position, int number,
AlignmentI al, String replace)
{
this.command = command;
fullAlignmentHeight = (al.getHeight() == seqs.length);
}
+
+ 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;
+ }
+ }
+
+ /**
+ * Returns an iterator over the list of edit commands which traverses the list
+ * either forwards or backwards.
+ *
+ * @param forwards
+ * @return
+ */
+ public Iterator<Edit> getEditIterator(boolean forwards)
+ {
+ if (forwards)
+ {
+ return getEdits().iterator();
+ }
+ else
+ {
+ return new ReverseListIterator<Edit>(getEdits());
+ }
}
}
git://source.jalview.org / jalview.git / blobdiff