X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FEditCommand.java;h=2d3a8d807f0319d5119287c0307e5e3dbf6758c1;hb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;hp=ccc6a813692e1f32113b6ed01af246b1b591b758;hpb=04c49245650f804b89b88b6818fd8add2ef9343e;p=jalview.git
diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index ccc6a81..2d3a8d8 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -1,306 +1,636 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
- *
- * 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * 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;
/**
- *
- *
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
- *
+ *
+ *
+ * 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 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 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 edits = new ArrayList();
String description;
public EditCommand()
- {}
+ {
+ }
public EditCommand(String description)
{
this.description = description;
}
- public EditCommand(String description,
- int command,
- SequenceI[] seqs,
- int position,
- int number,
- AlignmentI al)
+ 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);
+ performEdit(0, null);
}
- public EditCommand(String description,
- int command,
- String replace,
- SequenceI[] seqs,
- int position,
- int number,
- AlignmentI al)
+ 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);
+ 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 == 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);
}
- final public void appendEdit(int command,
- SequenceI[] seqs,
- int position,
- int number,
- AlignmentI al,
- boolean performEdit)
+ /**
+ * 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)
{
- Edit edit = new Edit(command, seqs, position, number, al.getGapCharacter());
+ 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.getGapCharacter());
if (al.getHeight() == seqs.length)
{
edit.al = al;
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);
+ performEdit(edit, views);
}
}
- final void performEdit(int commandIndex)
+ /**
+ * 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 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]);
- break;
- case PASTE:
- paste(edits[e]);
- break;
- case REPLACE:
- replace(edits[e]);
- break;
- }
+ Edit edit = iterator.next();
+ performEdit(edit, views);
}
}
- final public void doCommand()
+ /**
+ * Execute one edit command in all the specified alignment views
+ *
+ * @param edit
+ * @param views
+ */
+ protected static void performEdit(Edit edit, AlignmentI[] views)
{
- performEdit(0);
+ 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;
+ }
}
- final public void undoCommand()
+ @Override
+ final public void doCommand(AlignmentI[] views)
{
- int e = 0, eSize = edits.length;
- for (e = eSize - 1; e > -1; e--)
+ 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())
{
- switch (edits[e].command)
+ Edit e = iterator.previous();
+ switch (e.command)
{
- case INSERT_GAP:
- deleteGap(edits[e]);
- break;
- case DELETE_GAP:
- insertGap(edits[e]);
- break;
- case CUT:
- paste(edits[e]);
- break;
- case PASTE:
- cut(edits[e]);
- break;
- case REPLACE:
- replace(edits[e]);
- break;
+ 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;
}
}
}
- 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);
+ command.number, command.gapChar);
+ // System.out.println("pos: "+command.position+" number: "+command.number);
}
- adjustAnnotations(command, true, false);
+ 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++)
{
- command.seqs[s].deleteChars(command.position,
- command.position + command.number);
+ command.seqs[s].deleteChars(command.position, command.position
+ + command.number);
}
- adjustAnnotations(command, false, false);
+ adjustAnnotations(command, false, false, null);
}
- void cut(Edit command)
+ /**
+ * 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;
+ 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.position + command.number);
-
- if (command.seqs[i].getDatasetSequence() != null
- || command.seqs[i].getSequenceFeatures() != null)
+ command.string[i] = sequence.getSequence(command.position,
+ command.position + command.number);
+ SequenceI oldds = sequence.getDatasetSequence();
+ if (command.oldds != null && command.oldds[i] != null)
{
- for (int s = command.position; s < command.position + command.number;
- s++)
+ // we are redoing an undone cut.
+ sequence.setDatasetSequence(null);
+ }
+ sequence.deleteChars(command.position, command.position
+ + command.number);
+ if (command.oldds != null && command.oldds[i] != null)
+ {
+ // oldds entry contains the cut dataset sequence.
+ sequence.setDatasetSequence(command.oldds[i]);
+ command.oldds[i] = oldds;
+ }
+ else
+ {
+ // modify the oldds if necessary
+ if (oldds != sequence.getDatasetSequence()
+ || sequence.getSequenceFeatures() != null)
{
- if (jalview.schemes.ResidueProperties
- .aaIndex[command.seqs[i].getCharAt(s)] != 23)
+ if (command.oldds == null)
{
- adjustFeatures(command, i,
- command.seqs[i].findPosition(command.position),
- command.seqs[i].findPosition(command.position +
- command.number),
- false);
- break;
+ command.oldds = new SequenceI[command.seqs.length];
}
+ command.oldds[i] = oldds;
+ adjustFeatures(
+ command,
+ i,
+ sequence.findPosition(command.position),
+ sequence.findPosition(command.position
+ + command.number), false);
}
}
- command.seqs[i].deleteChars(command.position,
- command.position + command.number);
}
- if (command.seqs[i].getLength() < 1)
+ if (sequence.getLength() < 1)
{
- command.al.deleteSequence(command.seqs[i]);
- seqDeleted=true;
+ command.al.deleteSequence(sequence);
+ seqDeleted = true;
}
}
- adjustAnnotations(command, false, seqDeleted);
+ adjustAnnotations(command, false, seqDeleted, views);
}
- void paste(Edit command)
+ /**
+ * 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;
- boolean seqWasDeleted=false;
+ boolean newDSWasNeeded;
+ int newstart, newend;
+ boolean seqWasDeleted = false;
int start = 0, end = 0;
for (int i = 0; i < command.seqs.length; i++)
{
newDSNeeded = false;
+ newDSWasNeeded = command.oldds != null && command.oldds[i] != null;
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())
{
- command.al.getSequences().insertElementAt(command.seqs[i],
- command.alIndex[i]);
+ List sequences;
+ synchronized (sequences = command.al.getSequences())
+ {
+ if (!(command.alIndex[i] < 0))
+ {
+ sequences.add(command.alIndex[i], command.seqs[i]);
+ }
+ }
}
else
{
command.al.addSequence(command.seqs[i]);
}
- seqWasDeleted=true;
+ seqWasDeleted = true;
}
+ newstart = command.seqs[i].getStart();
+ newend = command.seqs[i].getEnd();
+
tmp = new StringBuffer();
tmp.append(command.seqs[i].getSequence());
+ // Undo of a delete does not replace original dataset sequence on to
+ // alignment sequence.
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
+ // This occurs if padding is on, and residues
+ // are removed from end of alignment
int length = command.position - tmp.length();
while (length > 0)
{
@@ -309,76 +639,154 @@ public class EditCommand
}
}
tmp.insert(command.position, command.string[i]);
-
for (int s = 0; s < command.string[i].length; s++)
{
- if (jalview.schemes.ResidueProperties.aaIndex[command.string[i][s]] !=
- 23)
+ if (jalview.schemes.ResidueProperties.aaIndex[command.string[i][s]] != 23)
{
- newDSNeeded = true;
- start = command.seqs[i].findPosition(command.position);
- end = command.seqs[i].findPosition(command.position +
- command.number);
- break;
+ if (!newDSNeeded)
+ {
+ newDSNeeded = true;
+ start = command.seqs[i].findPosition(command.position);
+ end = command.seqs[i].findPosition(command.position
+ + command.number);
+ }
+ if (command.seqs[i].getStart() == start)
+ {
+ newstart--;
+ }
+ else
+ {
+ newend++;
+ }
}
}
command.string[i] = null;
}
command.seqs[i].setSequence(tmp.toString());
-
+ command.seqs[i].setStart(newstart);
+ command.seqs[i].setEnd(newend);
if (newDSNeeded)
{
if (command.seqs[i].getDatasetSequence() != null)
- { // use new ds mechanism here
- Sequence ds = new Sequence(command.seqs[i].getName(),
- jalview.analysis.AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars,
- command.seqs[i].getSequenceAsString()
- ),
- command.seqs[i].getStart(),
- command.seqs[i].getEnd());
- ds.setDescription(command.seqs[i].getDescription());
+ {
+ SequenceI ds;
+ if (newDSWasNeeded)
+ {
+ ds = command.oldds[i];
+ }
+ else
+ {
+ // make a new DS sequence
+ // use new ds mechanism here
+ ds = new Sequence(command.seqs[i].getName(),
+ jalview.analysis.AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars,
+ command.seqs[i].getSequenceAsString()),
+ command.seqs[i].getStart(), command.seqs[i].getEnd());
+ ds.setDescription(command.seqs[i].getDescription());
+ }
+ if (command.oldds == null)
+ {
+ command.oldds = new SequenceI[command.seqs.length];
+ }
+ command.oldds[i] = command.seqs[i].getDatasetSequence();
command.seqs[i].setDatasetSequence(ds);
}
-
adjustFeatures(command, i, start, end, true);
}
}
- adjustAnnotations(command, true, seqWasDeleted);
+ adjustAnnotations(command, true, seqWasDeleted, views);
command.string = null;
}
- void replace(Edit command)
+ static void replace(Edit command)
{
StringBuffer 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;
+
+ /**
+ * 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));
tmp.append(command.string[i]);
+ String nogaprep = jalview.analysis.AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars, new String(
+ command.string[i]));
+ int ipos = command.seqs[i].findPosition(start)
+ - command.seqs[i].getStart();
tmp.append(oldstring.substring(end));
command.seqs[i].setSequence(tmp.toString());
command.string[i] = oldstring.substring(start, end).toCharArray();
+ String nogapold = jalview.analysis.AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars, new String(
+ command.string[i]));
+ if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase()))
+ {
+ if (newDSWasNeeded)
+ {
+ SequenceI oldds = command.seqs[i].getDatasetSequence();
+ command.seqs[i].setDatasetSequence(command.oldds[i]);
+ command.oldds[i] = oldds;
+ }
+ else
+ {
+ if (command.oldds == null)
+ {
+ command.oldds = new SequenceI[command.seqs.length];
+ }
+ command.oldds[i] = command.seqs[i].getDatasetSequence();
+ SequenceI newds = new Sequence(
+ command.seqs[i].getDatasetSequence());
+ String fullseq, osp = newds.getSequenceAsString();
+ fullseq = osp.substring(0, ipos) + nogaprep
+ + osp.substring(ipos + nogaprep.length());
+ newds.setSequence(fullseq.toUpperCase());
+ // 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);
+
+ }
+ }
tmp = null;
oldstring = null;
}
}
- final void adjustAnnotations(Edit command, boolean insert, boolean modifyVisibility)
+ 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();
}
if (command.fullAlignmentHeight)
{
@@ -393,32 +801,108 @@ public class EditCommand
if (modifyVisibility)
{
// Rows are only removed or added to sequence object.
- if (!insert) {
+ if (!insert)
+ {
// remove rows
tmp = command.seqs[s].getAnnotation();
- if (tmp!=null) {
- command.deletedAnnotationRows.put(command.seqs[s], tmp);
- for (int aa =0; aa();
}
int aSize;
Annotation[] temp;
for (int a = 0; a < annotations.length; a++)
{
- if (annotations[a].autoCalculated)
+ if (annotations[a].autoCalculated
+ || annotations[a].annotations == null)
{
continue;
}
@@ -476,25 +960,25 @@ public class EditCommand
if (insert)
{
temp = new Annotation[aSize + command.number];
- if(annotations[a].padGaps)
+ if (annotations[a].padGaps)
+ {
for (int aa = 0; aa < temp.length; aa++)
{
- temp[aa] = new Annotation(
- command.al.getGapCharacter()+"",
- null, ' ', 0);
+ temp[aa] = new Annotation(command.gapChar + "", null, ' ', 0);
}
+ }
}
else
{
if (command.position < aSize)
{
- if (command.position + command.number > aSize)
+ if (command.position + command.number >= aSize)
{
tSize = aSize;
}
else
{
- tSize = aSize - command.number + command.position;
+ tSize = aSize - command.number;
}
}
else
@@ -507,54 +991,46 @@ public class EditCommand
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);
+ System.arraycopy(annotations[a].annotations, 0, temp, 0,
+ command.position);
if (command.deletedAnnotations != null
- &&
- command.deletedAnnotations.containsKey(annotations[a].
- annotationId))
+ && command.deletedAnnotations
+ .containsKey(annotations[a].annotationId))
{
- Annotation[] restore = (Annotation[])
- command.deletedAnnotations.get(annotations[a].annotationId);
+ Annotation[] restore = command.deletedAnnotations
+ .get(annotations[a].annotationId);
- System.arraycopy(restore,
- 0,
- temp,
- command.position,
- command.number);
+ System.arraycopy(restore, 0, temp, command.position,
+ command.number);
}
- System.arraycopy(annotations[a].annotations,
- command.position, temp,
- command.position + command.number,
- aSize - command.position);
+ 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))
+ && command.deletedAnnotations
+ .containsKey(annotations[a].annotationId))
{
- Annotation[] restore = (Annotation[])
- 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);
+ 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);
+ annotations[a].annotations.length, restore.length);
}
else
{
@@ -566,15 +1042,20 @@ public class EditCommand
{
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);
+ 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)
+ 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);
@@ -582,12 +1063,14 @@ public class EditCommand
}
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
+ 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
@@ -597,17 +1080,16 @@ public class EditCommand
if (dSize > 0)
{
Annotation[] deleted = new Annotation[command.number];
- System.arraycopy(annotations[a].annotations,
- command.position, deleted, 0, dSize);
+ System.arraycopy(annotations[a].annotations, command.position,
+ deleted, 0, dSize);
command.deletedAnnotations.put(annotations[a].annotationId,
- deleted);
+ deleted);
tSize = Math.min(annotations[a].annotations.length,
- command.position);
+ command.position);
temp = new Annotation[tSize];
- System.arraycopy(annotations[a].annotations,
- 0, temp, 0, tSize);
+ System.arraycopy(annotations[a].annotations, 0, temp, 0, tSize);
}
else
{
@@ -620,8 +1102,8 @@ public class EditCommand
}
}
- final void adjustFeatures(Edit command, int index, int i, int j,
- boolean insert)
+ final static void adjustFeatures(Edit command, int index, int i, int j,
+ boolean insert)
{
SequenceI seq = command.seqs[index];
SequenceI sequence = seq.getDatasetSequence();
@@ -633,11 +1115,10 @@ public class EditCommand
if (insert)
{
if (command.editedFeatures != null
- && command.editedFeatures.containsKey(seq))
+ && command.editedFeatures.containsKey(seq))
{
- sequence.setSequenceFeatures(
- (SequenceFeature[]) command.editedFeatures.get(seq)
- );
+ sequence.setSequenceFeatures(command.editedFeatures
+ .get(seq));
}
return;
@@ -692,32 +1173,146 @@ public class EditCommand
if (command.editedFeatures == null)
{
- command.editedFeatures = new Hashtable();
+ command.editedFeatures = new Hashtable();
}
command.editedFeatures.put(seq, oldsf);
}
- class Edit
+ /**
+ * 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 (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 edits = new ReverseListIterator(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 deletedAnnotations;
- Hashtable editedFeatures;
+
+ Hashtable deletedAnnotationRows;
+
+ Hashtable deletedAnnotations;
+
+ Hashtable editedFeatures;
+
AlignmentI al;
- int command;
+
+ Action command;
+
char[][] string;
+
SequenceI[] seqs;
+
int[] alIndex;
+
int position, number;
+
char gapChar;
- Edit(int command,
- SequenceI[] seqs,
- int position,
- int number,
- char gapChar)
+ public Edit(Action command, SequenceI[] seqs, int position, int number,
+ char gapChar)
{
this.command = command;
this.seqs = seqs;
@@ -726,11 +1321,8 @@ public class EditCommand
this.gapChar = gapChar;
}
- Edit(int command,
- SequenceI[] seqs,
- int position,
- int number,
- AlignmentI al)
+ Edit(Action command, SequenceI[] seqs, int position, int number,
+ AlignmentI al)
{
this.gapChar = al.getGapCharacter();
this.command = command;
@@ -748,18 +1340,15 @@ public class EditCommand
fullAlignmentHeight = (al.getHeight() == seqs.length);
}
- Edit(int command,
- SequenceI[] seqs,
- int position,
- int number,
- AlignmentI al,
- String replace)
+ Edit(Action command, SequenceI[] seqs, int position, int number,
+ AlignmentI al, String replace)
{
this.command = command;
this.seqs = seqs;
this.position = position;
this.number = number;
this.al = al;
+ this.gapChar = al.getGapCharacter();
string = new char[seqs.length][];
for (int i = 0; i < seqs.length; i++)
{
@@ -768,6 +1357,49 @@ public class EditCommand
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 getEditIterator(boolean forwards)
+ {
+ if (forwards)
+ {
+ return getEdits().iterator();
+ }
+ else
+ {
+ return new ReverseListIterator(getEdits());
+ }
+ }
}