\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
return edits==null?0:edits.length;\r
}\r
\r
+ public AlignmentI getAlignment()\r
+ {\r
+ return edits[0].al;\r
+ }\r
+\r
\r
- public void appendEdit(String command,\r
+ 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
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
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
command.number,\r
command.gapChar);\r
}\r
+\r
+ if (command.fullAlignmentHeight)\r
+ {\r
+ adjustAnnotations(command, true);\r
+ }\r
}\r
\r
void deleteGap(Edit command)\r
{\r
command.seqs[s].deleteChars(command.position, command.position+command.number);\r
}\r
+\r
+ if (command.fullAlignmentHeight)\r
+ {\r
+ adjustAnnotations(command, false);\r
+ }\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.al.deleteSequence(command.seqs[i]);\r
}\r
}\r
+\r
+ if (command.fullAlignmentHeight)\r
+ {\r
+ adjustAnnotations(command, false);\r
+ }\r
+\r
}\r
\r
void paste(Edit command)\r
else\r
command.al.addSequence(command.seqs[i]);\r
}\r
- tmp = new StringBuffer(command.seqs[i].getSequence());\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
command.string[i] = null;\r
}\r
command.seqs[i].setSequence(tmp.toString());\r
}\r
\r
+ if (command.fullAlignmentHeight)\r
+ {\r
+ adjustAnnotations(command, true);\r
+ }\r
+\r
command.string = null;\r
}\r
\r
+\r
+ void adjustAnnotations(Edit command, boolean insert)\r
+ {\r
+ AlignmentAnnotation [] annotations = command.al.getAlignmentAnnotation();\r
+ if(annotations!=null)\r
+ {\r
+ if(!insert)\r
+ command.deletedAnnotations = new Hashtable();\r
+\r
+ int aSize, tSize;\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
+ tSize = aSize + command.number;\r
+ else\r
+ tSize = aSize - command.number;\r
+\r
+ temp = new Annotation[tSize];\r
+\r
+ if(insert)\r
+ {\r
+ System.arraycopy(annotations[a].annotations,\r
+ 0, temp, 0, command.position);\r
+\r
+ if(command.deletedAnnotations!=null\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.position < annotations[a].annotations.length)\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
+\r
+\r
class Edit\r
{\r
+ boolean fullAlignmentHeight = false;\r
+ Hashtable deletedAnnotations;\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
alIndex[i] = al.findIndex(seqs[i]);\r
+\r
+ fullAlignmentHeight = (al.getHeight()==seqs.length);\r
+\r
}\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff