/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\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
*/\r
package jalview.commands;\r
\r
-import jalview.datamodel.*;\r
+import java.util.*;\r
\r
-import java.util.Hashtable;\r
+import jalview.datamodel.*;\r
\r
/**\r
*\r
* @author not attributable\r
* @version 1.0\r
*/\r
-public class EditCommand implements CommandI\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
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
+ 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
- public String getDescription()\r
+ final public String getDescription()\r
{\r
return description;\r
}\r
\r
public int getSize()\r
{\r
- return edits==null?0:edits.length;\r
+ return edits == null ? 0 : edits.length;\r
}\r
\r
- public AlignmentI getAlignment()\r
+ final public AlignmentI getAlignment()\r
{\r
return edits[0].al;\r
}\r
\r
-\r
- public void appendEdit(int command,\r
- SequenceI[] seqs,\r
- int position,\r
- int number,\r
- AlignmentI al,\r
- boolean performEdit)\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
+ if (al.getHeight() == seqs.length)\r
{\r
edit.al = al;\r
edit.fullAlignmentHeight = true;\r
edits[edits.length - 1] = edit;\r
}\r
else\r
- edits = new Edit[] { edit };\r
+ {\r
+ edits = new Edit[]\r
+ {\r
+ edit};\r
+ }\r
\r
if (performEdit)\r
+ {\r
performEdit(edits.length - 1);\r
+ }\r
}\r
\r
- void performEdit(int commandIndex)\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
+ if (edits[e].command == INSERT_GAP)\r
{\r
insertGap(edits[e]);\r
}\r
- else if (edits[e].command==DELETE_GAP)\r
+ else if (edits[e].command == DELETE_GAP)\r
{\r
deleteGap(edits[e]);\r
}\r
- else if(edits[e].command==CUT)\r
+ else if (edits[e].command == CUT)\r
{\r
cut(edits[e]);\r
}\r
- else if(edits[e].command==PASTE)\r
+ else if (edits[e].command == PASTE)\r
{\r
paste(edits[e]);\r
}\r
}\r
}\r
\r
- public void doCommand()\r
+ final public void doCommand()\r
{\r
performEdit(0);\r
}\r
\r
- public void undoCommand()\r
+ final public void undoCommand()\r
{\r
int e = 0, eSize = edits.length;\r
- for (e = eSize-1; e > -1; e--)\r
+ for (e = eSize - 1; e > -1; e--)\r
{\r
- if (edits[e].command==INSERT_GAP)\r
+ if (edits[e].command == INSERT_GAP)\r
{\r
deleteGap(edits[e]);\r
}\r
- else if (edits[e].command==DELETE_GAP)\r
+ else if (edits[e].command == DELETE_GAP)\r
{\r
insertGap(edits[e]);\r
}\r
- else if (edits[e].command==CUT)\r
+ else if (edits[e].command == CUT)\r
{\r
paste(edits[e]);\r
}\r
- else if (edits[e].command==PASTE)\r
+ else if (edits[e].command == PASTE)\r
{\r
cut(edits[e]);\r
}\r
}\r
}\r
\r
- void insertGap(Edit command)\r
+ final void insertGap(Edit command)\r
{\r
- for(int s=0; s<command.seqs.length; s++)\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
+ command.seqs[s].insertCharAt(command.position,\r
+ command.number,\r
+ command.gapChar);\r
}\r
\r
adjustAnnotations(command, true);\r
}\r
\r
- void deleteGap(Edit command)\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
+ command.seqs[s].deleteChars(command.position,\r
+ command.position + command.number);\r
}\r
\r
adjustAnnotations(command, false);\r
\r
void cut(Edit command)\r
{\r
- command.string = new char [command.seqs.length][];\r
+ command.string = new char[command.seqs.length][];\r
\r
- for(int i=0; i<command.seqs.length; i++)\r
+ for (int i = 0; i < command.seqs.length; i++)\r
{\r
- if(command.seqs[i].getLength()>command.position)\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
+ if (command.seqs[i].getLength() < 1)\r
{\r
command.al.deleteSequence(command.seqs[i]);\r
}\r
void paste(Edit command)\r
{\r
StringBuffer tmp;\r
- for(int i=0; i<command.seqs.length; i++)\r
+ boolean newDSNeeded;\r
+ int start = 0, end = 0;\r
+\r
+ for (int i = 0; i < command.seqs.length; i++)\r
{\r
- if(command.seqs[i].getLength()<1)\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
+ if (command.string != null && command.string[i] != null)\r
{\r
- if(command.position>=tmp.length())\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
+ int length = command.position - tmp.length();\r
while (length > 0)\r
{\r
tmp.append(command.gapChar);\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
\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
-\r
- void adjustAnnotations(Edit command, boolean insert)\r
+ final void adjustAnnotations(Edit command, boolean insert)\r
{\r
\r
- AlignmentAnnotation [] annotations = null;\r
+ AlignmentAnnotation[] annotations = null;\r
\r
if (command.fullAlignmentHeight)\r
{\r
else\r
{\r
int aSize = 0;\r
- AlignmentAnnotation [] tmp;\r
- for(int s=0; s<command.seqs.length; s++)\r
+ AlignmentAnnotation[] tmp;\r
+ for (int s = 0; s < command.seqs.length; s++)\r
{\r
- if(command.seqs[s].getAnnotation()==null)\r
+ if (command.seqs[s].getAnnotation() == null)\r
+ {\r
continue;\r
+ }\r
\r
if (aSize == 0)\r
- annotations = command.seqs[s].getAnnotation();\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
+ 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
+ 0, tmp, aSize,\r
+ command.seqs[s].getAnnotation().length);\r
\r
annotations = tmp;\r
}\r
\r
-\r
aSize = annotations.length;\r
}\r
}\r
\r
- if(annotations==null)\r
+ if (annotations == null)\r
+ {\r
return;\r
+ }\r
\r
+ if (!insert)\r
+ {\r
+ command.deletedAnnotations = new Hashtable();\r
+ }\r
\r
- if(!insert)\r
- command.deletedAnnotations = new Hashtable();\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
- int aSize, tSize;\r
- Annotation [] temp;\r
- for (int a = 0; a < annotations.length; a++)\r
+ aSize = annotations[a].annotations.length;\r
+ if (insert)\r
{\r
- if(annotations[a].autoCalculated)\r
+ temp = new Annotation[aSize + command.number];\r
+ }\r
+ else\r
+ {\r
+ if (command.position < aSize)\r
{\r
- continue;\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
-\r
- aSize = annotations[a].annotations.length;\r
- if(insert)\r
- tSize = aSize + command.number;\r
else\r
- tSize = aSize - command.number;\r
+ {\r
+ tSize = aSize;\r
+ }\r
\r
+ if (tSize < 0)\r
+ {\r
+ tSize = aSize;\r
+ }\r
temp = new Annotation[tSize];\r
\r
- if(insert)\r
+ }\r
+\r
+ if (insert)\r
+ {\r
+ if (command.position < annotations[a].annotations.length)\r
{\r
- if(command.position < annotations[a].annotations.length)\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
- System.arraycopy(annotations[a].annotations,\r
- 0, temp, 0, command.position);\r
+ Annotation[] restore = (Annotation[])\r
+ command.deletedAnnotations.get(annotations[a].annotationId);\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
+ System.arraycopy(restore,\r
+ 0,\r
+ temp,\r
+ command.position,\r
+ command.number);\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
- command.position, temp,\r
- command.position + command.number,\r
- aSize - command.position);\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
- if(command.position < annotations[a].annotations.length)\r
- {\r
- System.arraycopy(annotations[a].annotations,\r
- 0, temp, 0, command.position);\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, command.number);\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
- command.position + command.number,\r
- temp, command.position,\r
- aSize - command.position - command.number);\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
+ 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
+ char[][] string;\r
SequenceI[] seqs;\r
- int [] alIndex;\r
+ int[] alIndex;\r
int position, number;\r
char gapChar;\r
\r
this.gapChar = gapChar;\r
}\r
\r
-\r
Edit(int command,\r
SequenceI[] seqs,\r
int position,\r
this.al = al;\r
\r
alIndex = new int[seqs.length];\r
- for(int i=0; i<seqs.length; i++)\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
+ fullAlignmentHeight = (al.getHeight() == seqs.length);\r
}\r
}\r
\r
git://source.jalview.org / jalview.git / blobdiff