-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 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 java.util.*;\r
-\r
-import jalview.datamodel.*;\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\r
- 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[]\r
- {\r
- new Edit(command, seqs, position, number, al)};\r
- }\r
-\r
- performEdit(0);\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
- 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
- {\r
- edits = new Edit[]\r
- {\r
- edit};\r
- }\r
-\r
- if (performEdit)\r
- {\r
- performEdit(edits.length - 1);\r
- }\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,\r
- 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;\r
- 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
- {\r
- command.al.getSequences().insertElementAt(command.seqs[i],\r
- command.alIndex[i]);\r
- }\r
- else\r
- {\r
- command.al.addSequence(command.seqs[i]);\r
- }\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]] !=\r
- 23)\r
- {\r
- newDSNeeded = true;\r
- start = command.seqs[i].findPosition(command.position);\r
- end = command.seqs[i].findPosition(command.position +\r
- command.number);\r
- break;\r
- }\r
- }\r
- command.string[i] = null;\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
- adjustAnnotations(command, true);\r
-\r
- command.string = null;\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
- {\r
- continue;\r
- }\r
-\r
- if (aSize == 0)\r
- {\r
- annotations = command.seqs[s].getAnnotation();\r
- }\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,\r
- command.seqs[s].getAnnotation().length);\r
-\r
- annotations = tmp;\r
- }\r
-\r
- aSize = annotations.length;\r
- }\r
- }\r
-\r
- if (annotations == null)\r
- {\r
- return;\r
- }\r
-\r
- if (!insert)\r
- {\r
- command.deletedAnnotations = new Hashtable();\r
- }\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
- {\r
- temp = new Annotation[aSize + command.number];\r
- }\r
- else\r
- {\r
- if (command.position < aSize)\r
- {\r
- if (command.position + command.number > aSize)\r
- {\r
- tSize = aSize;\r
- }\r
- else\r
- {\r
- tSize = aSize - command.number + command.position;\r
- }\r
- }\r
- else\r
- {\r
- tSize = aSize;\r
- }\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].\r
- 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].\r
- 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,\r
- annotations[a].annotations.length, restore.length);\r
- }\r
- else\r
- {\r
- temp = annotations[a].annotations;\r
- }\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,\r
- command.position);\r
- temp = new Annotation[tSize];\r
- System.arraycopy(annotations[a].annotations,\r
- 0, temp, 0, tSize);\r
- }\r
- else\r
- {\r
- temp = annotations[a].annotations;\r
- }\r
- }\r
- }\r
-\r
- annotations[a].annotations = temp;\r
- }\r
- }\r
-\r
- final void adjustFeatures(Edit command, int index, int i, int j,\r
- boolean insert)\r
- {\r
- SequenceI seq = command.seqs[index];\r
- SequenceI sequence = seq.getDatasetSequence();\r
- if (sequence == null)\r
- {\r
- sequence = seq;\r
- }\r
-\r
- if (insert)\r
- {\r
- if (command.editedFeatures != null\r
- && command.editedFeatures.containsKey(seq))\r
- {\r
- sequence.setSequenceFeatures(\r
- (SequenceFeature[]) command.editedFeatures.get(seq)\r
- );\r
- }\r
-\r
- return;\r
- }\r
-\r
- SequenceFeature[] sf = sequence.getSequenceFeatures();\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
- {\r
- continue;\r
- }\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
- {\r
- sf[s].setBegin(i);\r
- }\r
-\r
- if (sf[s].getEnd() < j)\r
- {\r
- sf[s].setEnd(j - 1);\r
- }\r
-\r
- sf[s].setEnd(sf[s].getEnd() - (cSize));\r
-\r
- if (sf[s].getBegin() > sf[s].getEnd())\r
- {\r
- sequence.deleteFeature(sf[s]);\r
- }\r
- }\r
-\r
- if (command.editedFeatures == null)\r
- {\r
- command.editedFeatures = new Hashtable();\r
- }\r
-\r
- command.editedFeatures.put(seq, oldsf);\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
- 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
+ * 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
+ * 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 java.util.*;
+
+import jalview.datamodel.*;
+
+/**
+ *
+ * <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 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; 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;
+ }
+
+ 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<tmp.length; aa++)
+ {
+ command.al.deleteAnnotation(tmp[aa]);
+ }
+ command.seqs[s].setAlignmentAnnotation(null);
+ }
+ } else {
+ // recover rows
+ if (command.deletedAnnotationRows!=null && command.deletedAnnotationRows.containsKey(command.seqs[s]))
+ {
+ AlignmentAnnotation[] revealed = (AlignmentAnnotation[]) command.deletedAnnotationRows.get(command.seqs[s]);
+ command.seqs[s].setAlignmentAnnotation(revealed);
+ if (revealed!=null) {
+ for (int aa =0; aa<revealed.length; aa++)
+ {
+ command.al.addAnnotation(revealed[aa]);
+ }
+ for (int aa =0; aa<revealed.length; aa++)
+ {
+ command.al.setAnnotationIndex(revealed[aa], aa);
+ }
+ }
+ }
+ }
+ 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();
+ }
+
+ int aSize;
+ Annotation[] temp;
+ for (int a = 0; a < annotations.length; a++)
+ {
+ if (annotations[a].autoCalculated)
+ {
+ continue;
+ }
+
+ int tSize = 0;
+
+ aSize = annotations[a].annotations.length;
+ if (insert)
+ {
+ temp = new Annotation[aSize + command.number];
+ }
+ else
+ {
+ if (command.position < aSize)
+ {
+ if (command.position + command.number > 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);
+ }
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff