X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fcommands%2FEditCommand.java;h=83ba5367cf3af0ae9d73c630944cd47898c2d4b6;hb=095d07c7765f6925736c41896b9bdff8df369f4e;hp=052b212fed256fcc2efffbc1ab9fcb7361c2c8c0;hpb=537bad6655186ae1c9daf2dbe6746c7c7168aeb0;p=jalview.git
diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 052b212..83ba536 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -1,20 +1,22 @@
/*
- * 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 2.8.2)
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.commands;
@@ -23,63 +25,87 @@ import java.util.*;
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
- *
+ *
+ *
+ * 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 static final int INSERT_NUC = 5;
+
Edit[] edits;
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, int command, SequenceI[] seqs,
+ int position, int number, AlignmentI al)
{
this.description = description;
if (command == CUT || command == PASTE)
{
edits = new Edit[]
- {
- new Edit(command, seqs, position, number, al)};
+ { new Edit(command, seqs, position, number, al) };
+ }
+
+ performEdit(0, null);
+ }
+
+ public EditCommand(String description, int command, String replace,
+ SequenceI[] seqs, int position, int number, AlignmentI al)
+ {
+ this.description = description;
+ if (command == REPLACE)
+ {
+ edits = new Edit[]
+ { new Edit(command, seqs, position, number, al, replace) };
}
- performEdit(0);
+ performEdit(0, null);
}
+ @Override
final public String getDescription()
{
return description;
}
+ @Override
public int getSize()
{
return edits == null ? 0 : edits.length;
@@ -90,14 +116,42 @@ public class EditCommand
return edits[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(int 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(int 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;
@@ -114,95 +168,118 @@ public class EditCommand
else
{
edits = new Edit[]
- {
- edit};
+ { edit };
}
if (performEdit)
{
- performEdit(edits.length - 1);
+ performEdit(edits.length - 1, views);
}
}
- final void performEdit(int commandIndex)
+ final void performEdit(int commandIndex, AlignmentI[] views)
{
int eSize = edits.length;
for (int e = commandIndex; e < eSize; e++)
{
- if (edits[e].command == INSERT_GAP)
+ switch (edits[e].command)
{
+ case INSERT_GAP:
insertGap(edits[e]);
- }
- else if (edits[e].command == DELETE_GAP)
- {
+ break;
+ case DELETE_GAP:
deleteGap(edits[e]);
- }
- else if (edits[e].command == CUT)
- {
- cut(edits[e]);
- }
- else if (edits[e].command == PASTE)
- {
- paste(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;
}
}
}
- final public void doCommand()
+ @Override
+ final public void doCommand(AlignmentI[] views)
{
- performEdit(0);
+ performEdit(0, views);
}
- final public void undoCommand()
+ @Override
+ final public void undoCommand(AlignmentI[] views)
{
int e = 0, eSize = edits.length;
for (e = eSize - 1; e > -1; e--)
{
- if (edits[e].command == INSERT_GAP)
+ switch (edits[e].command)
{
+ case INSERT_GAP:
deleteGap(edits[e]);
- }
- else if (edits[e].command == DELETE_GAP)
- {
+ break;
+ case DELETE_GAP:
insertGap(edits[e]);
- }
- else if (edits[e].command == CUT)
- {
- paste(edits[e]);
- }
- else if (edits[e].command == PASTE)
- {
- cut(edits[e]);
+ break;
+ case CUT:
+ paste(edits[e], views);
+ break;
+ case PASTE:
+ cut(edits[e], views);
+ break;
+ case REPLACE:
+ replace(edits[e]);
+ break;
}
}
}
final 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 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)
{
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)
+ 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++)
@@ -210,74 +287,97 @@ public class EditCommand
if (command.seqs[i].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.position + command.number);
+ SequenceI oldds = command.seqs[i].getDatasetSequence();
+ if (command.oldds != null && command.oldds[i] != null)
+ {
+ // we are redoing an undone cut.
+ command.seqs[i].setDatasetSequence(null);
+ }
+ command.seqs[i].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]);
+ command.oldds[i] = oldds;
+ }
+ else
{
- for (int s = command.position; s < command.position + command.number;
- s++)
+ // modify the oldds if necessary
+ if (oldds != command.seqs[i].getDatasetSequence()
+ || command.seqs[i].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,
+ command.seqs[i].findPosition(command.position),
+ command.seqs[i].findPosition(command.position
+ + command.number), false);
}
}
- command.seqs[i].deleteChars(command.position,
- command.position + command.number);
}
if (command.seqs[i].getLength() < 1)
{
command.al.deleteSequence(command.seqs[i]);
- seqDeleted=true;
+ seqDeleted = true;
}
}
- adjustAnnotations(command, false, seqDeleted);
+ adjustAnnotations(command, false, seqDeleted, views);
}
- void paste(Edit command)
+ 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 sequences;
+ synchronized (sequences = command.al.getSequences())
+ {
+ 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)
{
@@ -286,50 +386,144 @@ 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;
}
- final void adjustAnnotations(Edit command, boolean insert, boolean modifyVisibility)
+ 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, AlignmentI[] views)
+ {
AlignmentAnnotation[] annotations = null;
if (modifyVisibility && !insert)
@@ -347,35 +541,111 @@ public class EditCommand
AlignmentAnnotation[] tmp;
for (int s = 0; s < command.seqs.length; s++)
{
- if (modifyVisibility)
+ 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 aSize)
+ if (command.position + command.number >= aSize)
{
tSize = aSize;
}
else
{
- tSize = aSize - command.number + command.position;
+ tSize = aSize - command.number;
}
}
else
@@ -457,54 +732,46 @@ 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 = (Annotation[]) 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 = (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);
System.arraycopy(restore, 0, temp,
- annotations[a].annotations.length, restore.length);
+ annotations[a].annotations.length, restore.length);
}
else
{
@@ -516,15 +783,18 @@ 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);
@@ -532,12 +802,14 @@ 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
@@ -547,17 +819,16 @@ 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
{
@@ -571,7 +842,7 @@ public class EditCommand
}
final void adjustFeatures(Edit command, int index, int i, int j,
- boolean insert)
+ boolean insert)
{
SequenceI seq = command.seqs[index];
SequenceI sequence = seq.getDatasetSequence();
@@ -583,11 +854,10 @@ 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((SequenceFeature[]) command.editedFeatures
+ .get(seq));
}
return;
@@ -651,23 +921,32 @@ public class EditCommand
class Edit
{
+ public SequenceI[] oldds;
+
boolean fullAlignmentHeight = false;
+
Hashtable deletedAnnotationRows;
+
Hashtable deletedAnnotations;
+
Hashtable editedFeatures;
+
AlignmentI al;
+
int command;
+
char[][] string;
+
SequenceI[] seqs;
+
int[] alIndex;
+
int position, number;
+
char gapChar;
- Edit(int command,
- SequenceI[] seqs,
- int position,
- int number,
- char gapChar)
+ Edit(int command, SequenceI[] seqs, int position, int number,
+ char gapChar)
{
this.command = command;
this.seqs = seqs;
@@ -676,11 +955,8 @@ public class EditCommand
this.gapChar = gapChar;
}
- Edit(int command,
- SequenceI[] seqs,
- int position,
- int number,
- AlignmentI al)
+ Edit(int command, SequenceI[] seqs, int position, int number,
+ AlignmentI al)
{
this.gapChar = al.getGapCharacter();
this.command = command;
@@ -697,6 +973,23 @@ public class EditCommand
fullAlignmentHeight = (al.getHeight() == seqs.length);
}
- }
+ Edit(int 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++)
+ {
+ string[i] = replace.toCharArray();
+ }
+
+ fullAlignmentHeight = (al.getHeight() == seqs.length);
+ }
+ }
}