\r
import jalview.datamodel.*;\r
\r
+import java.util.Hashtable;\r
+\r
/**\r
*\r
* <p>Title: EditCommmand</p>\r
*/\r
public class EditCommand implements CommandI\r
{\r
- public static String INSERT_GAP = "InsertGap";\r
- public static String DELETE_GAP = "DeleteGap";\r
- public static String CUT = "Cut";\r
- public static String PASTE = "Paste";\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
this.description = description;\r
}\r
\r
- public EditCommand(String description,\r
- String command,\r
- SequenceI[] seqs,\r
- int position,\r
- int number,\r
- char gapChar)\r
- {\r
- this.description = description;\r
-\r
- if (command.equalsIgnoreCase(INSERT_GAP)\r
- || command.equalsIgnoreCase(DELETE_GAP))\r
- {\r
- edits = new Edit[] { new Edit(command, seqs, position, number, gapChar)};\r
- }\r
-\r
- performEdit(0);\r
- }\r
-\r
public EditCommand( String description,\r
- String command,\r
+ int command,\r
SequenceI[] seqs,\r
int position,\r
int number,\r
AlignmentI al)\r
{\r
this.description = description;\r
- if ( command.equalsIgnoreCase(CUT) || command.equalsIgnoreCase(PASTE))\r
+ if ( command==CUT || command==PASTE)\r
{\r
edits = new Edit[]{new Edit(command, seqs, position, number, al)};\r
}\r
}\r
\r
\r
- public String getDescription()\r
+ final public String getDescription()\r
{\r
return description;\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
- public void appendEdit(String command,\r
+ final public void appendEdit(int command,\r
SequenceI[] seqs,\r
int position,\r
int number,\r
- char gapChar,\r
+ AlignmentI al,\r
boolean performEdit)\r
{\r
- Edit edit = new Edit(command, seqs, position, number, gapChar);\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
performEdit(edits.length - 1);\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.equals(INSERT_GAP))\r
+ if (edits[e].command==INSERT_GAP)\r
{\r
insertGap(edits[e]);\r
}\r
- else if (edits[e].command.equals(DELETE_GAP))\r
+ else if (edits[e].command==DELETE_GAP)\r
{\r
deleteGap(edits[e]);\r
}\r
- else if(edits[e].command.equals(CUT))\r
+ else if(edits[e].command==CUT)\r
{\r
cut(edits[e]);\r
}\r
- else if(edits[e].command.equals(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
{\r
- if (edits[e].command.equals(INSERT_GAP))\r
+ if (edits[e].command==INSERT_GAP)\r
{\r
deleteGap(edits[e]);\r
}\r
- else if (edits[e].command.equals(DELETE_GAP))\r
+ else if (edits[e].command==DELETE_GAP)\r
{\r
insertGap(edits[e]);\r
}\r
- else if (edits[e].command.equals(CUT))\r
+ else if (edits[e].command==CUT)\r
{\r
paste(edits[e]);\r
}\r
- else if (edits[e].command.equals(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
{\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
}\r
+\r
+ adjustAnnotations(command, false);\r
}\r
\r
void cut(Edit command)\r
{\r
- command.string = new String [command.seqs.length];\r
+ command.string = new char [command.seqs.length][];\r
\r
for(int i=0; i<command.seqs.length; i++)\r
{\r
- command.string[i] = command.seqs[i].getSequence(command.position,\r
- command.position + command.number);\r
-\r
- command.seqs[i].deleteChars(command.position,\r
- command.position+command.number);\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
else\r
command.al.addSequence(command.seqs[i]);\r
}\r
- tmp = new StringBuffer(command.seqs[i].getSequence());\r
- if(command.string!=null)\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
+ 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 (aSize - command.number + command.position > 0)\r
+ temp = new Annotation[aSize - command.number + command.position];\r
+ else\r
+ temp = new Annotation[aSize];\r
+ }\r
+ else\r
+ temp = new Annotation[aSize];\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
+ temp = annotations[a].annotations;\r
+ }\r
+ else\r
+ {\r
+ if(command.position < aSize && aSize - command.number+command.position>0)\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
+ temp = annotations[a].annotations;\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
- String command;\r
- String [] string;\r
+ int command;\r
+ char [][] string;\r
SequenceI[] seqs;\r
int [] alIndex;\r
int position, number;\r
char gapChar;\r
\r
- Edit(String command,\r
+ Edit(int command,\r
SequenceI[] seqs,\r
int position,\r
int number,\r
}\r
\r
\r
- Edit(String command,\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
\r
+ fullAlignmentHeight = (al.getHeight()==seqs.length);\r
+ }\r
}\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff