-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.commands;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import java.util.Hashtable;\r
-\r
-/**\r
- *\r
- * <p>Title: EditCommmand</p>\r
- *\r
- * <p>Description: Essential information for performing\r
- * undo and redo for cut/paste insert/delete gap\r
- * which can be stored in the HistoryList </p>\r
- *\r
- * <p>Copyright: Copyright (c) 2006</p>\r
- *\r
- * <p>Company: Dundee University</p>\r
- *\r
- * @author not attributable\r
- * @version 1.0\r
- */\r
-public class EditCommand implements CommandI\r
-{\r
- public static final int INSERT_GAP = 0;\r
- public static final int DELETE_GAP = 1;\r
- public static final int CUT = 2;\r
- public static final int PASTE = 3;\r
-\r
- Edit[] edits;\r
-\r
- String description;\r
-\r
- public EditCommand()\r
- {}\r
-\r
- public EditCommand(String description)\r
- {\r
- this.description = description;\r
- }\r
-\r
- public EditCommand( String description,\r
- int command,\r
- SequenceI[] seqs,\r
- int position,\r
- int number,\r
- AlignmentI al)\r
- {\r
- this.description = description;\r
- if ( command==CUT || command==PASTE)\r
- {\r
- edits = new Edit[]{new Edit(command, seqs, position, number, al)};\r
- }\r
-\r
- performEdit(0);\r
- }\r
-\r
-\r
- final public String getDescription()\r
- {\r
- return description;\r
- }\r
-\r
- public int getSize()\r
- {\r
- return edits==null?0:edits.length;\r
- }\r
-\r
- final public AlignmentI getAlignment()\r
- {\r
- return edits[0].al;\r
- }\r
-\r
-\r
- final public void appendEdit(int command,\r
- SequenceI[] seqs,\r
- int position,\r
- int number,\r
- AlignmentI al,\r
- boolean performEdit)\r
- {\r
- Edit edit = new Edit(command, seqs, position, number, al.getGapCharacter());\r
- if(al.getHeight()==seqs.length)\r
- {\r
- edit.al = al;\r
- edit.fullAlignmentHeight = true;\r
- }\r
-\r
- if (edits != null)\r
- {\r
- Edit[] temp = new Edit[edits.length + 1];\r
- System.arraycopy(edits, 0, temp, 0, edits.length);\r
- edits = temp;\r
- edits[edits.length - 1] = edit;\r
- }\r
- else\r
- edits = new Edit[] { edit };\r
-\r
- if (performEdit)\r
- performEdit(edits.length - 1);\r
- }\r
-\r
- final void performEdit(int commandIndex)\r
- {\r
- int eSize = edits.length;\r
- for (int e = commandIndex; e < eSize; e++)\r
- {\r
- if (edits[e].command==INSERT_GAP)\r
- {\r
- insertGap(edits[e]);\r
- }\r
- else if (edits[e].command==DELETE_GAP)\r
- {\r
- deleteGap(edits[e]);\r
- }\r
- else if(edits[e].command==CUT)\r
- {\r
- cut(edits[e]);\r
- }\r
- else if(edits[e].command==PASTE)\r
- {\r
- paste(edits[e]);\r
- }\r
- }\r
- }\r
-\r
- final public void doCommand()\r
- {\r
- performEdit(0);\r
- }\r
-\r
- final public void undoCommand()\r
- {\r
- int e = 0, eSize = edits.length;\r
- for (e = eSize-1; e > -1; e--)\r
- {\r
- if (edits[e].command==INSERT_GAP)\r
- {\r
- deleteGap(edits[e]);\r
- }\r
- else if (edits[e].command==DELETE_GAP)\r
- {\r
- insertGap(edits[e]);\r
- }\r
- else if (edits[e].command==CUT)\r
- {\r
- paste(edits[e]);\r
- }\r
- else if (edits[e].command==PASTE)\r
- {\r
- cut(edits[e]);\r
- }\r
- }\r
- }\r
-\r
- final void insertGap(Edit command)\r
- {\r
- for(int s=0; s<command.seqs.length; s++)\r
- {\r
- command.seqs[s].insertCharAt(command.position,\r
- command.number,\r
- command.gapChar);\r
- }\r
-\r
- adjustAnnotations(command, true);\r
- }\r
-\r
- final void deleteGap(Edit command)\r
- {\r
- for (int s = 0; s < command.seqs.length; s++)\r
- {\r
- command.seqs[s].deleteChars(command.position, command.position+command.number);\r
- }\r
-\r
- adjustAnnotations(command, false);\r
- }\r
-\r
- void cut(Edit command)\r
- {\r
- command.string = new char [command.seqs.length][];\r
-\r
- for(int i=0; i<command.seqs.length; i++)\r
- {\r
- if(command.seqs[i].getLength()>command.position)\r
- {\r
- command.string[i] = command.seqs[i].getSequence(command.position,\r
- command.position + command.number);\r
-\r
- if(command.seqs[i].getDatasetSequence()!=null\r
- || command.seqs[i].getSequenceFeatures()!=null)\r
- {\r
- for (int s = command.position; s < command.position + command.number; s++)\r
- {\r
- if (jalview.schemes.ResidueProperties\r
- .aaIndex[command.seqs[i].getCharAt(s)] != 23)\r
- {\r
- adjustFeatures(command, i,\r
- command.seqs[i].findPosition(command.position),\r
- command.seqs[i].findPosition(command.position +\r
- command.number),\r
- false);\r
- break;\r
- }\r
- }\r
- }\r
- command.seqs[i].deleteChars(command.position,\r
- command.position + command.number);\r
- }\r
-\r
- if(command.seqs[i].getLength()<1)\r
- {\r
- command.al.deleteSequence(command.seqs[i]);\r
- }\r
- }\r
-\r
- adjustAnnotations(command, false);\r
- }\r
-\r
- void paste(Edit command)\r
- {\r
- StringBuffer tmp;\r
- boolean newDSNeeded;\r
- int start=0, end=0;\r
-\r
- for(int i=0; i<command.seqs.length; i++)\r
- {\r
- newDSNeeded = false;\r
- if(command.seqs[i].getLength()<1)\r
- {\r
- // ie this sequence was deleted, we need to\r
- // read it to the alignment\r
- if (command.alIndex[i] < command.al.getHeight())\r
- command.al.getSequences().insertElementAt(command.seqs[i],\r
- command.alIndex[i]);\r
- else\r
- command.al.addSequence(command.seqs[i]);\r
- }\r
- tmp = new StringBuffer();\r
- tmp.append(command.seqs[i].getSequence());\r
-\r
- if(command.string!=null && command.string[i]!=null)\r
- {\r
- if(command.position>=tmp.length())\r
- {\r
- //This occurs if padding is on, and residues\r
- //are removed from end of alignment\r
- int length = command.position-tmp.length();\r
- while (length > 0)\r
- {\r
- tmp.append(command.gapChar);\r
- length--;\r
- }\r
- }\r
- tmp.insert(command.position, command.string[i]);\r
-\r
- for (int s = 0; s < command.string[i].length; s++)\r
- {\r
- if (jalview.schemes.ResidueProperties.aaIndex[command.string[i][s]] != 23)\r
- {\r
- newDSNeeded = true;\r
- start = command.seqs[i].findPosition(command.position);\r
- end = command.seqs[i].findPosition(command.position+command.number);\r
- break;\r
- }\r
- }\r
- command.string[i] = null;\r
- }\r
-\r
-\r
- command.seqs[i].setSequence(tmp.toString());\r
-\r
- if(newDSNeeded)\r
- {\r
- if (command.seqs[i].getDatasetSequence() != null)\r
- {\r
- Sequence ds = new Sequence(command.seqs[i].getName(),\r
- jalview.analysis.AlignSeq.extractGaps(\r
- jalview.util.Comparison.GapChars,\r
- command.seqs[i].getSequenceAsString()\r
- ),\r
- command.seqs[i].getStart(),\r
- command.seqs[i].getEnd());\r
- ds.setDescription(command.seqs[i].getDescription());\r
- command.seqs[i].setDatasetSequence(ds);\r
- }\r
-\r
- adjustFeatures(command, i, start, end, true);\r
- }\r
- }\r
-\r
-\r
- adjustAnnotations(command, true);\r
-\r
- command.string = null;\r
- }\r
-\r
-\r
- final void adjustAnnotations(Edit command, boolean insert)\r
- {\r
-\r
- AlignmentAnnotation [] annotations = null;\r
-\r
- if (command.fullAlignmentHeight)\r
- {\r
- annotations = command.al.getAlignmentAnnotation();\r
- }\r
- else\r
- {\r
- int aSize = 0;\r
- AlignmentAnnotation [] tmp;\r
- for(int s=0; s<command.seqs.length; s++)\r
- {\r
- if(command.seqs[s].getAnnotation()==null)\r
- continue;\r
-\r
- if (aSize == 0)\r
- annotations = command.seqs[s].getAnnotation();\r
- else\r
- {\r
- tmp = new AlignmentAnnotation\r
- [aSize + command.seqs[s].getAnnotation().length];\r
-\r
- System.arraycopy(annotations,0,tmp,0,aSize);\r
-\r
- System.arraycopy(command.seqs[s].getAnnotation(),\r
- 0,tmp,aSize,command.seqs[s].getAnnotation().length);\r
-\r
- annotations = tmp;\r
- }\r
-\r
-\r
- aSize = annotations.length;\r
- }\r
- }\r
-\r
- if(annotations==null)\r
- return;\r
-\r
-\r
- if(!insert)\r
- command.deletedAnnotations = new Hashtable();\r
-\r
- int aSize;\r
- Annotation [] temp;\r
- for (int a = 0; a < annotations.length; a++)\r
- {\r
- if(annotations[a].autoCalculated)\r
- {\r
- continue;\r
- }\r
-\r
- int tSize = 0;\r
-\r
- aSize = annotations[a].annotations.length;\r
- if(insert)\r
- temp = new Annotation[aSize + command.number];\r
- else\r
- {\r
- if(command.position<aSize)\r
- {\r
- if(command.position+command.number>aSize)\r
- tSize = aSize;\r
- else\r
- {\r
- tSize = aSize - command.number + command.position;\r
- }\r
- }\r
- else\r
- tSize = aSize;\r
-\r
- if(tSize<0)\r
- {\r
- tSize = aSize;\r
- }\r
- temp = new Annotation[tSize];\r
-\r
- }\r
-\r
- if(insert)\r
- {\r
- if(command.position < annotations[a].annotations.length)\r
- {\r
- System.arraycopy(annotations[a].annotations,\r
- 0, temp, 0, command.position);\r
-\r
- if (command.deletedAnnotations != null\r
- &&\r
- command.deletedAnnotations.containsKey(annotations[a].annotationId))\r
- {\r
- Annotation[] restore = (Annotation[])\r
- command.deletedAnnotations.get(annotations[a].annotationId);\r
-\r
- System.arraycopy(restore,\r
- 0,\r
- temp,\r
- command.position,\r
- command.number);\r
-\r
- }\r
-\r
- System.arraycopy(annotations[a].annotations,\r
- command.position, temp,\r
- command.position + command.number,\r
- aSize - command.position);\r
- }\r
- else\r
- {\r
- if (command.deletedAnnotations != null\r
- &&\r
- command.deletedAnnotations.containsKey(annotations[a].annotationId))\r
- {\r
- Annotation[] restore = (Annotation[])\r
- command.deletedAnnotations.get(annotations[a].annotationId);\r
-\r
- temp = new Annotation[annotations[a].annotations.length+\r
- restore.length];\r
- System.arraycopy(annotations[a].annotations,\r
- 0,temp,0,\r
- annotations[a].annotations.length);\r
- System.arraycopy(restore,0,temp,annotations[a].annotations.length,restore.length);\r
- }\r
- else\r
- temp = annotations[a].annotations;\r
- }\r
- }\r
- else\r
- {\r
- if(tSize!=aSize || command.position<2)\r
- {\r
- System.arraycopy(annotations[a].annotations,\r
- 0, temp, 0, command.position);\r
-\r
- Annotation[] deleted = new Annotation[command.number];\r
- System.arraycopy(annotations[a].annotations,\r
- command.position, deleted, 0, command.number);\r
-\r
- command.deletedAnnotations.put(annotations[a].annotationId,\r
- deleted);\r
-\r
- System.arraycopy(annotations[a].annotations,\r
- command.position + command.number,\r
- temp, command.position,\r
- aSize - command.position - command.number);\r
- }\r
- else\r
- {\r
- int dSize = aSize - command.position;\r
-\r
- if(dSize>0)\r
- {\r
- Annotation[] deleted = new Annotation[command.number];\r
- System.arraycopy(annotations[a].annotations,\r
- command.position, deleted, 0, dSize);\r
-\r
- command.deletedAnnotations.put(annotations[a].annotationId,\r
- deleted);\r
-\r
- tSize = Math.min(annotations[a].annotations.length, command.position);\r
- temp = new Annotation[tSize];\r
- System.arraycopy(annotations[a].annotations,\r
- 0, temp, 0, tSize);\r
- }\r
- else\r
- temp = annotations[a].annotations;\r
- }\r
- }\r
-\r
- annotations[a].annotations = temp;\r
- }\r
- }\r
-\r
- final void adjustFeatures(Edit command, int index, int i, int j, boolean insert)\r
- {\r
- SequenceI seq = command.seqs[index];\r
- SequenceI sequence = seq.getDatasetSequence();\r
- if(sequence==null)\r
- sequence = seq;\r
-\r
- if(insert)\r
- {\r
- if (command.editedFeatures != null\r
- && command.editedFeatures.containsKey(seq))\r
- sequence.setSequenceFeatures(\r
- (SequenceFeature[]) command.editedFeatures.get(seq)\r
- );\r
-\r
- return;\r
- }\r
-\r
-\r
- SequenceFeature [] sf = sequence.getSequenceFeatures();\r
-\r
-\r
- if(sf==null)\r
- {\r
- return;\r
- }\r
-\r
- SequenceFeature [] oldsf = new SequenceFeature[sf.length];\r
-\r
- int cSize = j - i;\r
-\r
- for (int s = 0; s < sf.length; s++)\r
- {\r
- SequenceFeature copy = new SequenceFeature(sf[s]);\r
-\r
- oldsf[s] = copy;\r
-\r
- if (sf[s].getEnd() < i)\r
- continue;\r
-\r
- if (sf[s].getBegin() > j)\r
- {\r
- sf[s].setBegin(copy.getBegin() - cSize);\r
- sf[s].setEnd(copy.getEnd() - cSize);\r
- continue;\r
- }\r
-\r
- if (sf[s].getBegin() >= i)\r
- sf[s].setBegin(i);\r
-\r
- if (sf[s].getEnd() < j)\r
- sf[s].setEnd(j - 1);\r
-\r
- sf[s].setEnd(sf[s].getEnd() - (cSize));\r
-\r
- if (sf[s].getBegin() > sf[s].getEnd())\r
- sequence.deleteFeature(sf[s]);\r
- }\r
-\r
- if (command.editedFeatures == null)\r
- command.editedFeatures = new Hashtable();\r
-\r
- command.editedFeatures.put(seq, oldsf);\r
-\r
- }\r
-\r
-\r
- class Edit\r
- {\r
- boolean fullAlignmentHeight = false;\r
- Hashtable deletedAnnotations;\r
- Hashtable editedFeatures;\r
- AlignmentI al;\r
- int command;\r
- char [][] string;\r
- SequenceI[] seqs;\r
- int [] alIndex;\r
- int position, number;\r
- char gapChar;\r
-\r
- Edit(int command,\r
- SequenceI[] seqs,\r
- int position,\r
- int number,\r
- char gapChar)\r
- {\r
- this.command = command;\r
- this.seqs = seqs;\r
- this.position = position;\r
- this.number = number;\r
- this.gapChar = gapChar;\r
- }\r
-\r
-\r
- Edit(int command,\r
- SequenceI[] seqs,\r
- int position,\r
- int number,\r
- AlignmentI al)\r
- {\r
- this.gapChar = al.getGapCharacter();\r
- this.command = command;\r
- this.seqs = seqs;\r
- this.position = position;\r
- this.number = number;\r
- this.al = al;\r
-\r
- alIndex = new int[seqs.length];\r
- for(int i=0; i<seqs.length; i++)\r
- {\r
- alIndex[i] = al.findIndex(seqs[i]);\r
- }\r
-\r
- fullAlignmentHeight = (al.getHeight()==seqs.length);\r
- }\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.commands;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.util.ReverseListIterator;
+import jalview.util.StringUtils;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.ListIterator;
+import java.util.Map;
+
+/**
+ *
+ * <p>
+ * Title: EditCommmand
+ * </p>
+ *
+ * <p>
+ * Description: Essential information for performing undo and redo for cut/paste
+ * insert/delete gap which can be stored in the HistoryList
+ * </p>
+ *
+ * <p>
+ * Copyright: Copyright (c) 2006
+ * </p>
+ *
+ * <p>
+ * Company: Dundee University
+ * </p>
+ *
+ * @author not attributable
+ * @version 1.0
+ */
+public class EditCommand implements CommandI
+{
+ public 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();
+ };
+
+ private List<Edit> edits = new ArrayList<Edit>();
+
+ String description;
+
+ public EditCommand()
+ {
+ }
+
+ public EditCommand(String description)
+ {
+ this.description = description;
+ }
+
+ public EditCommand(String description, Action command, SequenceI[] seqs,
+ int position, int number, AlignmentI al)
+ {
+ this.description = description;
+ if (command == Action.CUT || command == Action.PASTE)
+ {
+ setEdit(new Edit(command, seqs, position, number, al));
+ }
+
+ performEdit(0, null);
+ }
+
+ public EditCommand(String description, Action command, String replace,
+ SequenceI[] seqs, int position, int number, AlignmentI al)
+ {
+ this.description = description;
+ if (command == Action.REPLACE)
+ {
+ setEdit(new Edit(command, seqs, position, number, al, replace));
+ }
+
+ performEdit(0, null);
+ }
+
+ /**
+ * Set the list of edits to the specified item (only).
+ *
+ * @param e
+ */
+ protected void setEdit(Edit e)
+ {
+ edits.clear();
+ edits.add(e);
+ }
+
+ /**
+ * Add the given edit command to the stored list of commands. If simply
+ * expanding the range of the last command added, then modify it instead of
+ * adding a new command.
+ *
+ * @param e
+ */
+ public void addEdit(Edit e)
+ {
+ if (!expandEdit(edits, e))
+ {
+ edits.add(e);
+ }
+ }
+
+ /**
+ * Returns true if the new edit is incorporated by updating (expanding the
+ * range of) the last edit on the list, else false. We can 'expand' the last
+ * edit if the new one is the same action, on the same sequences, and acts on
+ * a contiguous range. This is the case where a mouse drag generates a series
+ * of contiguous gap insertions or deletions.
+ *
+ * @param edits
+ * @param e
+ * @return
+ */
+ protected static boolean expandEdit(List<Edit> edits, Edit e)
+ {
+ if (edits == null || edits.isEmpty())
+ {
+ return false;
+ }
+ Edit lastEdit = edits.get(edits.size() - 1);
+ Action action = e.command;
+ if (lastEdit.command != action)
+ {
+ return false;
+ }
+
+ /*
+ * Both commands must act on the same sequences - compare the underlying
+ * dataset sequences, rather than the aligned sequences, which change as
+ * they are edited.
+ */
+ if (lastEdit.seqs.length != e.seqs.length)
+ {
+ return false;
+ }
+ for (int i = 0; i < e.seqs.length; i++)
+ {
+ if (lastEdit.seqs[i].getDatasetSequence() != e.seqs[i]
+ .getDatasetSequence())
+ {
+ return false;
+ }
+ }
+
+ /**
+ * Check a contiguous edit; either
+ * <ul>
+ * <li>a new Insert <n> positions to the right of the last <insert n>, or</li>
+ * <li>a new Delete <n> gaps which is <n> positions to the left of the last
+ * delete.</li>
+ * </ul>
+ */
+ boolean contiguous = (action == Action.INSERT_GAP && e.position == lastEdit.position
+ + lastEdit.number)
+ || (action == Action.DELETE_GAP && e.position + e.number == lastEdit.position);
+ if (contiguous)
+ {
+ /*
+ * We are just expanding the range of the last edit. For delete gap, also
+ * moving the start position left.
+ */
+ lastEdit.number += e.number;
+ lastEdit.seqs = e.seqs;
+ if (action == Action.DELETE_GAP)
+ {
+ lastEdit.position--;
+ }
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Clear the list of stored edit commands.
+ *
+ */
+ protected void clearEdits()
+ {
+ edits.clear();
+ }
+
+ /**
+ * Returns the i'th stored Edit command.
+ *
+ * @param i
+ * @return
+ */
+ protected Edit getEdit(int i)
+ {
+ if (i >= 0 && i < edits.size())
+ {
+ return edits.get(i);
+ }
+ return null;
+ }
+
+ @Override
+ final public String getDescription()
+ {
+ return description;
+ }
+
+ @Override
+ public int getSize()
+ {
+ return edits.size();
+ }
+
+ /**
+ * Return the alignment for the first edit (or null if no edit).
+ *
+ * @return
+ */
+ final public AlignmentI getAlignment()
+ {
+ 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);
+ }
+
+ /**
+ * 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;
+ }
+
+ addEdit(edit);
+
+ if (performEdit)
+ {
+ performEdit(edit, views);
+ }
+ }
+
+ /**
+ * 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)
+ {
+ edit.al = al;
+ edit.fullAlignmentHeight = true;
+ }
+
+ addEdit(edit);
+
+ if (performEdit)
+ {
+ performEdit(edit, views);
+ }
+ }
+
+ /**
+ * Execute all the edit commands, starting at the given commandIndex
+ *
+ * @param commandIndex
+ * @param views
+ */
+ public final void performEdit(int commandIndex, AlignmentI[] views)
+ {
+ ListIterator<Edit> iterator = edits.listIterator(commandIndex);
+ while (iterator.hasNext())
+ {
+ Edit edit = iterator.next();
+ performEdit(edit, views);
+ }
+ }
+
+ /**
+ * Execute one edit command in all the specified alignment views
+ *
+ * @param edit
+ * @param views
+ */
+ protected static void performEdit(Edit edit, AlignmentI[] views)
+ {
+ switch (edit.command)
+ {
+ case INSERT_GAP:
+ insertGap(edit);
+ break;
+ case DELETE_GAP:
+ deleteGap(edit);
+ break;
+ case CUT:
+ cut(edit, views);
+ break;
+ case PASTE:
+ paste(edit, views);
+ break;
+ case REPLACE:
+ replace(edit);
+ break;
+ case INSERT_NUC:
+ // TODO:add deleteNuc for UNDO
+ // case INSERT_NUC:
+ // insertNuc(edits[e]);
+ break;
+ default:
+ break;
+ }
+ }
+
+ @Override
+ final public void doCommand(AlignmentI[] views)
+ {
+ 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())
+ {
+ Edit e = iterator.previous();
+ switch (e.command)
+ {
+ 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;
+ }
+ }
+ }
+
+ /**
+ * Insert gap(s) in sequences as specified by the command, and adjust
+ * annotations.
+ *
+ * @param command
+ */
+ final private static void insertGap(Edit command)
+ {
+
+ for (int s = 0; s < command.seqs.length; s++)
+ {
+ command.seqs[s].insertCharAt(command.position, command.number,
+ command.gapChar);
+ // System.out.println("pos: "+command.position+" number: "+command.number);
+ }
+
+ 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);
+ // }
+
+ /**
+ * 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);
+ }
+
+ adjustAnnotations(command, false, false, null);
+ }
+
+ /**
+ * Carry out a Cut action. The cut characters are saved in case Undo is
+ * requested.
+ *
+ * @param command
+ * @param views
+ */
+ static void cut(Edit command, AlignmentI[] views)
+ {
+ boolean seqDeleted = false;
+ command.string = new char[command.seqs.length][];
+
+ for (int i = 0; i < command.seqs.length; i++)
+ {
+ final SequenceI sequence = command.seqs[i];
+ if (sequence.getLength() > command.position)
+ {
+ command.string[i] = sequence.getSequence(command.position,
+ command.position + command.number);
+ SequenceI oldds = sequence.getDatasetSequence();
+ if (command.oldds != null && command.oldds[i] != null)
+ {
+ // 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 (command.oldds == null)
+ {
+ 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);
+ }
+ }
+ }
+
+ if (sequence.getLength() < 1)
+ {
+ command.al.deleteSequence(sequence);
+ seqDeleted = true;
+ }
+ }
+
+ adjustAnnotations(command, false, seqDeleted, views);
+ }
+
+ /**
+ * Perform the given Paste command. This may be to add cut or copied sequences
+ * to an alignment, or to undo a 'Cut' action on a region of the alignment.
+ *
+ * @param command
+ * @param views
+ */
+ static void paste(Edit command, AlignmentI[] views)
+ {
+ StringBuffer tmp;
+ boolean newDSNeeded;
+ 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
+ // readd it to the alignment
+ if (command.alIndex[i] < command.al.getHeight())
+ {
+ 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;
+ }
+ 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
+ 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)
+ {
+ 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)
+ {
+ 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, views);
+
+ command.string = null;
+ }
+
+ 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 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<SequenceI, AlignmentAnnotation[]>();
+ }
+ 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)
+ {
+ int alen = tmp.length;
+ for (int aa = 0; aa < tmp.length; 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
+ {
+ // recover rows
+ if (command.deletedAnnotationRows != null
+ && command.deletedAnnotationRows
+ .containsKey(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++)
+ {
+ // iterate through al adding original annotation
+ command.al.addAnnotation(revealed[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);
+ }
+ }
+ }
+ }
+ }
+ }
+ continue;
+ }
+
+ if (command.seqs[s].getAnnotation() == null)
+ {
+ continue;
+ }
+
+ if (aSize == 0)
+ {
+ annotations = command.seqs[s].getAnnotation();
+ }
+ else
+ {
+ 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);
+
+ annotations = tmp;
+ }
+ aSize = annotations.length;
+ }
+ }
+
+ if (annotations == null)
+ {
+ return;
+ }
+
+ if (!insert)
+ {
+ command.deletedAnnotations = new Hashtable<String, Annotation[]>();
+ }
+
+ int aSize;
+ Annotation[] temp;
+ for (int a = 0; a < annotations.length; a++)
+ {
+ if (annotations[a].autoCalculated
+ || annotations[a].annotations == null)
+ {
+ continue;
+ }
+
+ int tSize = 0;
+
+ aSize = annotations[a].annotations.length;
+ if (insert)
+ {
+ temp = new Annotation[aSize + command.number];
+ if (annotations[a].padGaps)
+ {
+ for (int aa = 0; aa < temp.length; aa++)
+ {
+ temp[aa] = new Annotation(command.gapChar + "", null, ' ', 0);
+ }
+ }
+ }
+ else
+ {
+ if (command.position < aSize)
+ {
+ if (command.position + command.number >= aSize)
+ {
+ tSize = aSize;
+ }
+ else
+ {
+ tSize = aSize - command.number;
+ }
+ }
+ 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 = 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 = 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 static 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(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<SequenceI, SequenceFeature[]>();
+ }
+
+ command.editedFeatures.put(seq, oldsf);
+
+ }
+
+ /**
+ * Returns the list of edit commands wrapped by this object.
+ *
+ * @return
+ */
+ public List<Edit> getEdits()
+ {
+ return this.edits;
+ }
+
+ /**
+ * Returns a map whose keys are the dataset sequences, and values their
+ * aligned sequences before the command edit list was applied. The aligned
+ * sequences are copies, which may be updated without affecting the originals.
+ *
+ * The command holds references to the aligned sequences (after editing). If
+ * the command is an 'undo',then the prior state is simply the aligned state.
+ * Otherwise, we have to derive the prior state by working backwards through
+ * the edit list to infer the aligned sequences before editing.
+ *
+ * Note: an alternative solution would be to cache the 'before' state of each
+ * edit, but this would be expensive in space in the common case that the
+ * original is never needed (edits are not mirrored).
+ *
+ * @return
+ * @throws IllegalStateException
+ * on detecting an edit command of a type that can't be unwound
+ */
+ public Map<SequenceI, SequenceI> priorState(boolean forUndo)
+ {
+ Map<SequenceI, SequenceI> result = new HashMap<SequenceI, SequenceI>();
+ if (getEdits() == null)
+ {
+ return result;
+ }
+ if (forUndo)
+ {
+ for (Edit e : getEdits())
+ {
+ for (SequenceI seq : e.getSequences())
+ {
+ SequenceI ds = seq.getDatasetSequence();
+ SequenceI preEdit = result.get(ds);
+ if (preEdit == null)
+ {
+ preEdit = new Sequence("", seq.getSequenceAsString());
+ preEdit.setDatasetSequence(ds);
+ result.put(ds, preEdit);
+ }
+ }
+ }
+ return result;
+ }
+
+ /*
+ * Work backwards through the edit list, deriving the sequences before each
+ * was applied. The final result is the sequence set before any edits.
+ */
+ Iterator<Edit> edits = new ReverseListIterator<Edit>(getEdits());
+ while (edits.hasNext())
+ {
+ Edit oldEdit = edits.next();
+ Action action = oldEdit.getAction();
+ int position = oldEdit.getPosition();
+ int number = oldEdit.getNumber();
+ final char gap = oldEdit.getGapCharacter();
+ for (SequenceI seq : oldEdit.getSequences())
+ {
+ SequenceI ds = seq.getDatasetSequence();
+ SequenceI preEdit = result.get(ds);
+ if (preEdit == null)
+ {
+ preEdit = new Sequence("", seq.getSequenceAsString());
+ preEdit.setDatasetSequence(ds);
+ result.put(ds, preEdit);
+ }
+ /*
+ * 'Undo' this edit action on the sequence (updating the value in the
+ * map).
+ */
+ if (ds != null)
+ {
+ if (action == Action.DELETE_GAP)
+ {
+ preEdit.setSequence(new String(StringUtils.insertCharAt(
+ preEdit.getSequence(), position, number, gap)));
+ }
+ else if (action == Action.INSERT_GAP)
+ {
+ preEdit.setSequence(new String(StringUtils.deleteChars(
+ preEdit.getSequence(), position, position + number)));
+ }
+ else
+ {
+ System.err.println("Can't undo edit action " + action);
+ // throw new IllegalStateException("Can't undo edit action " +
+ // action);
+ }
+ }
+ }
+ }
+ return result;
+ }
+
+ public class Edit
+ {
+ public SequenceI[] oldds;
+
+ boolean fullAlignmentHeight = false;
+
+ Hashtable<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
+
+ Hashtable<String, Annotation[]> deletedAnnotations;
+
+ Hashtable<SequenceI, SequenceFeature[]> editedFeatures;
+
+ AlignmentI al;
+
+ Action command;
+
+ char[][] string;
+
+ SequenceI[] seqs;
+
+ int[] alIndex;
+
+ int position, number;
+
+ char gapChar;
+
+ public Edit(Action 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(Action 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(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++)
+ {
+ string[i] = replace.toCharArray();
+ }
+
+ fullAlignmentHeight = (al.getHeight() == seqs.length);
+ }
+
+ public SequenceI[] getSequences()
+ {
+ return seqs;
+ }
+
+ public int getPosition()
+ {
+ return position;
+ }
+
+ public Action getAction()
+ {
+ return command;
+ }
+
+ public int getNumber()
+ {
+ return number;
+ }
+
+ public char getGapCharacter()
+ {
+ return gapChar;
+ }
+ }
+
+ /**
+ * Returns an iterator over the list of edit commands which traverses the list
+ * either forwards or backwards.
+ *
+ * @param forwards
+ * @return
+ */
+ public Iterator<Edit> getEditIterator(boolean forwards)
+ {
+ if (forwards)
+ {
+ return getEdits().iterator();
+ }
+ else
+ {
+ return new ReverseListIterator<Edit>(getEdits());
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff