/*
- * 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 2.8.2b1)
+ * Copyright (C) 2014 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.commands;
-import java.util.*;
+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.datamodel.*;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.ListIterator;
/**
- *
- * <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>
- *
+ *
+ * <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 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, DELETE_GAP, CUT, PASTE, REPLACE, INSERT_NUC
+ };
- Edit[] edits;
+ private List<Edit> edits = new ArrayList<Edit>();
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.
+ *
+ * @param e
+ */
+ protected void addEdit(Edit e)
+ {
+ edits.add(e);
+ }
+
+ /**
+ * 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);
+ }
+
+ /**
+ * 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);
}
- final public void appendEdit(int command,
- SequenceI[] seqs,
- int position,
- int number,
- AlignmentI al,
- boolean performEdit)
+ /**
+ * 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());
+ Edit edit = new Edit(command, seqs, position, number,
+ al.getGapCharacter());
if (al.getHeight() == seqs.length)
{
edit.al = al;
edit.fullAlignmentHeight = true;
}
- 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};
- }
+ edits.add(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
+ */
+ 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]);
- 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 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<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]);
- 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 void insertGap(Edit command)
{
+
for (int s = 0; s < command.seqs.length; s++)
{
- command.seqs[s].insertCharAt(command.position,
- command.number,
- command.gapChar);
+ command.seqs[s].insertCharAt(command.position, 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 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
+ */
+ 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
+ */
+ 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
if (command.alIndex[i] < command.al.getHeight())
{
- command.al.getSequences().insertElementAt(command.seqs[i],
- command.alIndex[i]);
+ List<SequenceI> 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)
{
}
}
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;
}
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 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)
{
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<tmp.length; aa++)
+ if (tmp != null)
+ {
+ int alen = tmp.length;
+ for (int aa = 0; aa < tmp.length; aa++)
{
- command.al.deleteAnnotation(tmp[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 {
+ }
+ else
+ {
// recover rows
- if (command.deletedAnnotationRows!=null && command.deletedAnnotationRows.containsKey(command.seqs[s]))
+ if (command.deletedAnnotationRows != null
+ && command.deletedAnnotationRows
+ .containsKey(command.seqs[s]))
{
- AlignmentAnnotation[] revealed = (AlignmentAnnotation[]) command.deletedAnnotationRows.get(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++)
+ 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++)
+ 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);
+ }
+ }
+ }
}
}
}
}
else
{
- tmp = new AlignmentAnnotation
- [aSize + command.seqs[s].getAnnotation().length];
+ 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);
+ System.arraycopy(command.seqs[s].getAnnotation(), 0, tmp, aSize,
+ command.seqs[s].getAnnotation().length);
annotations = tmp;
}
if (!insert)
{
- command.deletedAnnotations = new Hashtable();
+ command.deletedAnnotations = new Hashtable<String, Annotation[]>();
}
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;
}
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
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
{
{
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);
}
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
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
{
}
final void adjustFeatures(Edit command, int index, int i, int j,
- boolean insert)
+ boolean insert)
{
SequenceI seq = command.seqs[index];
SequenceI sequence = seq.getDatasetSequence();
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;
if (command.editedFeatures == null)
{
- command.editedFeatures = new Hashtable();
+ command.editedFeatures = new Hashtable<SequenceI, SequenceFeature[]>();
}
command.editedFeatures.put(seq, oldsf);
class Edit
{
+ public SequenceI[] oldds;
+
boolean fullAlignmentHeight = false;
- Hashtable deletedAnnotationRows;
- Hashtable deletedAnnotations;
- Hashtable editedFeatures;
+
+ Hashtable<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
+
+ Hashtable<String, Annotation[]> deletedAnnotations;
+
+ Hashtable<SequenceI, SequenceFeature[]> 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)
+ Edit(Action command, SequenceI[] seqs, int position, int number,
+ char gapChar)
{
this.command = command;
this.seqs = seqs;
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;
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++)
{
fullAlignmentHeight = (al.getHeight() == seqs.length);
}
}
-
}
git://source.jalview.org / jalview.git / blobdiff