X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FEditCommand.java;h=ce881273d13d79100884ba4e42ca30257a1b2707;hb=855f7a4bb3e8d5fcfa9059df64262fc73f0164be;hp=1d4880a189a55c85854000b5dfe828449c44b6de;hpb=1e968e44cb033e74e9f81d7140b5393f8ad6e305;p=jalview.git
diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 1d4880a..ce88127 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -1,603 +1,778 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-package jalview.commands;
-
-import jalview.datamodel.*;
-
-import java.util.Hashtable;
-
-/**
- *
- *
Title: EditCommmand
- *
- * Description: Essential information for performing
- * undo and redo for cut/paste insert/delete gap
- * which can be stored in the HistoryList
- *
- * Copyright: Copyright (c) 2006
- *
- * Company: Dundee University
- *
- * @author not attributable
- * @version 1.0
- */
-public class EditCommand implements CommandI
-{
- public static final int INSERT_GAP = 0;
- public static final int DELETE_GAP = 1;
- public static final int CUT = 2;
- public static final int PASTE = 3;
-
- 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)
- {
- this.description = description;
- if ( command==CUT || command==PASTE)
- {
- edits = new Edit[]{new Edit(command, seqs, position, number, al)};
- }
-
- performEdit(0);
- }
-
-
- final public String getDescription()
- {
- return description;
- }
-
- public int getSize()
- {
- return edits==null?0:edits.length;
- }
-
- final public AlignmentI getAlignment()
- {
- return edits[0].al;
- }
-
-
- 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());
- 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 };
-
- if (performEdit)
- performEdit(edits.length - 1);
- }
-
- final void performEdit(int commandIndex)
- {
- int eSize = edits.length;
- for (int e = commandIndex; e < eSize; e++)
- {
- if (edits[e].command==INSERT_GAP)
- {
- insertGap(edits[e]);
- }
- else if (edits[e].command==DELETE_GAP)
- {
- deleteGap(edits[e]);
- }
- else if(edits[e].command==CUT)
- {
- cut(edits[e]);
- }
- else if(edits[e].command==PASTE)
- {
- paste(edits[e]);
- }
- }
- }
-
- final public void doCommand()
- {
- performEdit(0);
- }
-
- final public void undoCommand()
- {
- int e = 0, eSize = edits.length;
- for (e = eSize-1; e > -1; e--)
- {
- if (edits[e].command==INSERT_GAP)
- {
- deleteGap(edits[e]);
- }
- else if (edits[e].command==DELETE_GAP)
- {
- insertGap(edits[e]);
- }
- else if (edits[e].command==CUT)
- {
- paste(edits[e]);
- }
- else if (edits[e].command==PASTE)
- {
- cut(edits[e]);
- }
- }
- }
-
- final void insertGap(Edit command)
- {
- for(int s=0; scommand.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)
- {
- for (int s = command.position; s < command.position + command.number; s++)
- {
- if (jalview.schemes.ResidueProperties
- .aaIndex[command.seqs[i].getCharAt(s)] != 23)
- {
- adjustFeatures(command, i,
- command.seqs[i].findPosition(command.position),
- command.seqs[i].findPosition(command.position +
- command.number),
- false);
- break;
- }
- }
- }
- command.seqs[i].deleteChars(command.position,
- command.position + command.number);
- }
-
- if(command.seqs[i].getLength()<1)
- {
- command.al.deleteSequence(command.seqs[i]);
- }
- }
-
- adjustAnnotations(command, false);
- }
-
- void paste(Edit command)
- {
- StringBuffer tmp;
- boolean newDSNeeded;
- int start=0, end=0;
-
- for(int i=0; i=tmp.length())
- {
- //This occurs if padding is on, and residues
- //are removed from end of alignment
- int length = command.position-tmp.length();
- while (length > 0)
- {
- tmp.append(command.gapChar);
- length--;
- }
- }
- 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)
- {
- newDSNeeded = true;
- start = command.seqs[i].findPosition(command.position);
- end = command.seqs[i].findPosition(command.position+command.number);
- break;
- }
- }
- command.string[i] = null;
- }
-
-
- command.seqs[i].setSequence(tmp.toString());
-
- if(newDSNeeded)
- {
- if (command.seqs[i].getDatasetSequence() != null)
- {
- 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());
- command.seqs[i].setDatasetSequence(ds);
- }
-
- adjustFeatures(command, i, start, end, true);
- }
- }
-
-
- adjustAnnotations(command, true);
-
- command.string = null;
- }
-
-
- final void adjustAnnotations(Edit command, boolean insert)
- {
-
- AlignmentAnnotation [] annotations = null;
-
- if (command.fullAlignmentHeight)
- {
- annotations = command.al.getAlignmentAnnotation();
- }
- else
- {
- int aSize = 0;
- AlignmentAnnotation [] tmp;
- for(int s=0; saSize)
- tSize = aSize;
- else
- tSize = aSize - command.number + command.position;
- }
- else
- tSize = aSize;
-
- if(tSize<0)
- tSize = aSize;
-
- temp = new Annotation[tSize];
-
- }
-
- if(insert)
- {
- if(command.position < annotations[a].annotations.length)
- {
- System.arraycopy(annotations[a].annotations,
- 0, temp, 0, command.position);
-
- if (command.deletedAnnotations != null
- &&
- command.deletedAnnotations.containsKey(annotations[a].annotationId))
- {
- Annotation[] restore = (Annotation[])
- command.deletedAnnotations.get(annotations[a].annotationId);
-
- System.arraycopy(restore,
- 0,
- temp,
- command.position,
- command.number);
-
- }
-
- System.arraycopy(annotations[a].annotations,
- command.position, temp,
- command.position + command.number,
- aSize - command.position);
- }
- else
- {
- if (command.deletedAnnotations != null
- &&
- command.deletedAnnotations.containsKey(annotations[a].annotationId))
- {
- Annotation[] restore = (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);
- }
- else
- temp = annotations[a].annotations;
- }
- }
- else
- {
- if(tSize!=aSize)
- {
- System.arraycopy(annotations[a].annotations,
- 0, temp, 0, command.position);
-
- Annotation[] deleted = new Annotation[command.number];
- System.arraycopy(annotations[a].annotations,
- command.position, deleted, 0, command.number);
-
- command.deletedAnnotations.put(annotations[a].annotationId,
- deleted);
-
- System.arraycopy(annotations[a].annotations,
- command.position + command.number,
- temp, command.position,
- aSize - command.position - command.number);
- }
- else
- {
- int dSize = aSize - command.position;
-
- if(dSize>0)
- {
- Annotation[] deleted = new Annotation[command.number];
- System.arraycopy(annotations[a].annotations,
- command.position, deleted, 0, dSize);
-
- command.deletedAnnotations.put(annotations[a].annotationId,
- deleted);
-
- tSize = Math.min(annotations[a].annotations.length, command.position);
- temp = new Annotation[tSize];
- System.arraycopy(annotations[a].annotations,
- 0, temp, 0, tSize);
- }
- else
- temp = annotations[a].annotations;
- }
- }
-
- annotations[a].annotations = temp;
- }
- }
-
- final void adjustFeatures(Edit command, int index, int i, int j, boolean insert)
- {
- SequenceI seq = command.seqs[index];
- SequenceI sequence = seq.getDatasetSequence();
- if(sequence==null)
- sequence = seq;
-
- if(insert)
- {
- if (command.editedFeatures != null
- && command.editedFeatures.containsKey(seq))
- sequence.setSequenceFeatures(
- (SequenceFeature[]) command.editedFeatures.get(seq)
- );
-
- return;
- }
-
-
- SequenceFeature [] sf = sequence.getSequenceFeatures();
-
-
- if(sf==null)
- {
- return;
- }
-
- SequenceFeature [] oldsf = new SequenceFeature[sf.length];
-
- int cSize = j - i;
-
- for (int s = 0; s < sf.length; s++)
- {
- SequenceFeature copy = new SequenceFeature(sf[s]);
-
- oldsf[s] = copy;
-
- if (sf[s].getEnd() < i)
- continue;
-
- if (sf[s].getBegin() > j)
- {
- sf[s].setBegin(copy.getBegin() - cSize);
- sf[s].setEnd(copy.getEnd() - cSize);
- continue;
- }
-
- if (sf[s].getBegin() >= i)
- sf[s].setBegin(i);
-
- if (sf[s].getEnd() < j)
- sf[s].setEnd(j - 1);
-
- sf[s].setEnd(sf[s].getEnd() - (cSize));
-
- if (sf[s].getBegin() > sf[s].getEnd())
- sequence.deleteFeature(sf[s]);
- }
-
- if (command.editedFeatures == null)
- command.editedFeatures = new Hashtable();
-
- command.editedFeatures.put(seq, oldsf);
-
- }
-
-
- class Edit
- {
- boolean fullAlignmentHeight = false;
- 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)
- {
- this.command = command;
- this.seqs = seqs;
- this.position = position;
- this.number = number;
- this.gapChar = gapChar;
- }
-
-
- Edit(int command,
- SequenceI[] seqs,
- int position,
- int number,
- AlignmentI al)
- {
- this.gapChar = al.getGapCharacter();
- this.command = command;
- this.seqs = seqs;
- this.position = position;
- this.number = number;
- this.al = al;
-
- alIndex = new int[seqs.length];
- for(int i=0; iTitle: EditCommmand
+ *
+ * Description: Essential information for performing
+ * undo and redo for cut/paste insert/delete gap
+ * which can be stored in the HistoryList
+ *
+ * Copyright: Copyright (c) 2006
+ *
+ * Company: Dundee University
+ *
+ * @author not attributable
+ * @version 1.0
+ */
+public class EditCommand
+ implements CommandI
+{
+ public static 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;
+
+ 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)
+ {
+ this.description = description;
+ if (command == CUT || command == PASTE)
+ {
+ edits = new Edit[]
+ {
+ new Edit(command, seqs, position, number, al)};
+ }
+
+ performEdit(0);
+ }
+
+ 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);
+ }
+
+ final public String getDescription()
+ {
+ return description;
+ }
+
+ public int getSize()
+ {
+ return edits == null ? 0 : edits.length;
+ }
+
+ final public AlignmentI getAlignment()
+ {
+ return edits[0].al;
+ }
+
+ 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());
+ 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};
+ }
+
+ if (performEdit)
+ {
+ performEdit(edits.length - 1);
+ }
+ }
+
+ final void performEdit(int commandIndex)
+ {
+ int eSize = edits.length;
+ for (int e = commandIndex; e < eSize; e++)
+ {
+ 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;
+ }
+ }
+ }
+
+ final public void doCommand()
+ {
+ performEdit(0);
+ }
+
+ final public void undoCommand()
+ {
+ int e = 0, eSize = edits.length;
+ for (e = eSize - 1; e > -1; e--)
+ {
+ switch (edits[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;
+ }
+ }
+ }
+
+ final void insertGap(Edit command)
+ {
+ for (int s = 0; s < command.seqs.length; s++)
+ {
+ command.seqs[s].insertCharAt(command.position,
+ command.number,
+ command.gapChar);
+ }
+
+ adjustAnnotations(command, true, false);
+ }
+
+ final void deleteGap(Edit command)
+ {
+ for (int s = 0; s < command.seqs.length; s++)
+ {
+ command.seqs[s].deleteChars(command.position,
+ command.position + command.number);
+ }
+
+ adjustAnnotations(command, false, false);
+ }
+
+ void cut(Edit command)
+ {
+ 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)
+ {
+ command.string[i] = command.seqs[i].getSequence(command.position,
+ command.position + command.number);
+
+ if (command.seqs[i].getDatasetSequence() != null
+ || command.seqs[i].getSequenceFeatures() != null)
+ {
+ for (int s = command.position; s < command.position + command.number;
+ s++)
+ {
+ if (jalview.schemes.ResidueProperties
+ .aaIndex[command.seqs[i].getCharAt(s)] != 23)
+ {
+ adjustFeatures(command, i,
+ command.seqs[i].findPosition(command.position),
+ command.seqs[i].findPosition(command.position +
+ command.number),
+ false);
+ break;
+ }
+ }
+ }
+ command.seqs[i].deleteChars(command.position,
+ command.position + command.number);
+ }
+
+ if (command.seqs[i].getLength() < 1)
+ {
+ command.al.deleteSequence(command.seqs[i]);
+ seqDeleted=true;
+ }
+ }
+
+ adjustAnnotations(command, false, seqDeleted);
+ }
+
+ void paste(Edit command)
+ {
+ StringBuffer tmp;
+ boolean newDSNeeded;
+ boolean seqWasDeleted=false;
+ int start = 0, end = 0;
+
+ for (int i = 0; i < command.seqs.length; i++)
+ {
+ newDSNeeded = false;
+ 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]);
+ }
+ else
+ {
+ command.al.addSequence(command.seqs[i]);
+ }
+ seqWasDeleted=true;
+ }
+ tmp = new StringBuffer();
+ tmp.append(command.seqs[i].getSequence());
+
+ if (command.string != null && command.string[i] != null)
+ {
+ if (command.position >= tmp.length())
+ {
+ //This occurs if padding is on, and residues
+ //are removed from end of alignment
+ int length = command.position - tmp.length();
+ while (length > 0)
+ {
+ tmp.append(command.gapChar);
+ length--;
+ }
+ }
+ 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)
+ {
+ newDSNeeded = true;
+ start = command.seqs[i].findPosition(command.position);
+ end = command.seqs[i].findPosition(command.position +
+ command.number);
+ break;
+ }
+ }
+ command.string[i] = null;
+ }
+
+ command.seqs[i].setSequence(tmp.toString());
+
+ 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());
+ command.seqs[i].setDatasetSequence(ds);
+ }
+
+ adjustFeatures(command, i, start, end, true);
+ }
+ }
+ adjustAnnotations(command, true, seqWasDeleted);
+
+ command.string = null;
+ }
+
+ void replace(Edit command)
+ {
+ StringBuffer tmp;
+ String oldstring;
+ int start = command.position;
+ int end = command.number;
+
+ command.number = start + command.string[0].length;
+ for (int i = 0; i < command.seqs.length; i++)
+ {
+ oldstring = command.seqs[i].getSequenceAsString();
+ tmp = new StringBuffer(oldstring.substring(0, start));
+ tmp.append(command.string[i]);
+ tmp.append(oldstring.substring(end));
+ command.seqs[i].setSequence(tmp.toString());
+ command.string[i] = oldstring.substring(start, end).toCharArray();
+ tmp = null;
+ oldstring = null;
+ }
+ }
+
+ final void adjustAnnotations(Edit command, boolean insert, boolean modifyVisibility)
+ {
+
+ AlignmentAnnotation[] annotations = null;
+
+ if (modifyVisibility && !insert)
+ {
+ // only occurs if a sequence was added or deleted.
+ command.deletedAnnotationRows = new Hashtable();
+ }
+ if (command.fullAlignmentHeight)
+ {
+ annotations = command.al.getAlignmentAnnotation();
+ }
+ else
+ {
+ int aSize = 0;
+ AlignmentAnnotation[] tmp;
+ for (int s = 0; s < command.seqs.length; s++)
+ {
+ if (modifyVisibility)
+ {
+ // Rows are only removed or added to sequence object.
+ 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)
+ {
+ tSize = aSize;
+ }
+ else
+ {
+ tSize = aSize - command.number + command.position;
+ }
+ }
+ else
+ {
+ tSize = aSize;
+ }
+
+ if (tSize < 0)
+ {
+ tSize = aSize;
+ }
+ temp = new Annotation[tSize];
+
+ }
+
+ if (insert)
+ {
+ if (command.position < annotations[a].annotations.length)
+ {
+ System.arraycopy(annotations[a].annotations,
+ 0, temp, 0, command.position);
+
+ if (command.deletedAnnotations != null
+ &&
+ command.deletedAnnotations.containsKey(annotations[a].
+ annotationId))
+ {
+ Annotation[] restore = (Annotation[])
+ command.deletedAnnotations.get(annotations[a].annotationId);
+
+ System.arraycopy(restore,
+ 0,
+ temp,
+ command.position,
+ command.number);
+
+ }
+
+ System.arraycopy(annotations[a].annotations,
+ command.position, temp,
+ command.position + command.number,
+ aSize - command.position);
+ }
+ else
+ {
+ if (command.deletedAnnotations != null
+ &&
+ command.deletedAnnotations.containsKey(annotations[a].
+ annotationId))
+ {
+ Annotation[] restore = (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);
+ }
+ else
+ {
+ temp = annotations[a].annotations;
+ }
+ }
+ }
+ else
+ {
+ if (tSize != aSize || command.position < 2)
+ {
+ int copylen = Math.min(command.position, annotations[a].annotations.length);
+ if (copylen>0)
+ System.arraycopy(annotations[a].annotations,
+ 0, temp, 0, copylen); //command.position);
+
+ Annotation[] deleted = new Annotation[command.number];
+ if (copylen>command.position) {
+ copylen = Math.min(command.number, annotations[a].annotations.length-command.position);
+ if (copylen>0)
+ {
+ System.arraycopy(annotations[a].annotations,
+ command.position, deleted, 0, copylen); // command.number);
+ }
+ }
+
+ command.deletedAnnotations.put(annotations[a].annotationId,
+ deleted);
+ if (annotations[a].annotations.length>command.position+command.number) {
+ System.arraycopy(annotations[a].annotations,
+ command.position + command.number,
+ temp, command.position,
+ annotations[a].annotations.length - command.position - command.number); // aSize
+ }
+ }
+ else
+ {
+ int dSize = aSize - command.position;
+
+ if (dSize > 0)
+ {
+ Annotation[] deleted = new Annotation[command.number];
+ System.arraycopy(annotations[a].annotations,
+ command.position, deleted, 0, dSize);
+
+ command.deletedAnnotations.put(annotations[a].annotationId,
+ deleted);
+
+ tSize = Math.min(annotations[a].annotations.length,
+ command.position);
+ temp = new Annotation[tSize];
+ System.arraycopy(annotations[a].annotations,
+ 0, temp, 0, tSize);
+ }
+ else
+ {
+ temp = annotations[a].annotations;
+ }
+ }
+ }
+
+ annotations[a].annotations = temp;
+ }
+ }
+
+ final void adjustFeatures(Edit command, int index, int i, int j,
+ boolean insert)
+ {
+ SequenceI seq = command.seqs[index];
+ SequenceI sequence = seq.getDatasetSequence();
+ if (sequence == null)
+ {
+ sequence = seq;
+ }
+
+ if (insert)
+ {
+ if (command.editedFeatures != null
+ && command.editedFeatures.containsKey(seq))
+ {
+ sequence.setSequenceFeatures(
+ (SequenceFeature[]) command.editedFeatures.get(seq)
+ );
+ }
+
+ return;
+ }
+
+ SequenceFeature[] sf = sequence.getSequenceFeatures();
+
+ if (sf == null)
+ {
+ return;
+ }
+
+ SequenceFeature[] oldsf = new SequenceFeature[sf.length];
+
+ int cSize = j - i;
+
+ for (int s = 0; s < sf.length; s++)
+ {
+ SequenceFeature copy = new SequenceFeature(sf[s]);
+
+ oldsf[s] = copy;
+
+ if (sf[s].getEnd() < i)
+ {
+ continue;
+ }
+
+ if (sf[s].getBegin() > j)
+ {
+ sf[s].setBegin(copy.getBegin() - cSize);
+ sf[s].setEnd(copy.getEnd() - cSize);
+ continue;
+ }
+
+ if (sf[s].getBegin() >= i)
+ {
+ sf[s].setBegin(i);
+ }
+
+ if (sf[s].getEnd() < j)
+ {
+ sf[s].setEnd(j - 1);
+ }
+
+ sf[s].setEnd(sf[s].getEnd() - (cSize));
+
+ if (sf[s].getBegin() > sf[s].getEnd())
+ {
+ sequence.deleteFeature(sf[s]);
+ }
+ }
+
+ if (command.editedFeatures == null)
+ {
+ command.editedFeatures = new Hashtable();
+ }
+
+ command.editedFeatures.put(seq, oldsf);
+
+ }
+
+ class Edit
+ {
+ 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)
+ {
+ this.command = command;
+ this.seqs = seqs;
+ this.position = position;
+ this.number = number;
+ this.gapChar = gapChar;
+ }
+
+ Edit(int command,
+ SequenceI[] seqs,
+ int position,
+ int number,
+ AlignmentI al)
+ {
+ this.gapChar = al.getGapCharacter();
+ this.command = command;
+ this.seqs = seqs;
+ this.position = position;
+ this.number = number;
+ this.al = al;
+
+ alIndex = new int[seqs.length];
+ for (int i = 0; i < seqs.length; i++)
+ {
+ alIndex[i] = al.findIndex(seqs[i]);
+ }
+
+ 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);
+ }
+ }
+}