|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES All Classes | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectde.jstacs.data.sequences.annotation.SplitSequenceAnnotationParser
de.jstacs.data.sequences.annotation.MotifAnnotationParser
public class MotifAnnotationParser
Annotation parser for MotifAnnotation
s.
Field Summary |
---|
Fields inherited from class de.jstacs.data.sequences.annotation.SplitSequenceAnnotationParser |
---|
annot, annotationDelimiter, keyValueDelimiter |
Constructor Summary | |
---|---|
MotifAnnotationParser()
Creates a new MotifAnnotationParser with default delimiters. |
|
MotifAnnotationParser(String keyValueDelimiter,
String annotationDelimiter)
Creates a new MotifAnnotationParser with the supplied delimiters |
Method Summary | |
---|---|
protected void |
add(String identifier,
int position,
int length,
StrandedLocatedSequenceAnnotationWithLength.Strand strandedness)
Adds the motif with identifier identifier at position position
with length length and StrandedLocatedSequenceAnnotationWithLength.Strand strandedness |
void |
addToAnnotation(String unparsed)
This method adds the unparsed String in some way to
the SequenceAnnotation . |
String |
parseAnnotationToComment(char commentChar,
SequenceAnnotation... annotations)
This method returns a String representation of the given
SequenceAnnotation s that can be used as comment line in a file. |
Methods inherited from class de.jstacs.data.sequences.annotation.SplitSequenceAnnotationParser |
---|
add, clearAnnotation, getCurrentAnnotation |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
---|
public MotifAnnotationParser()
MotifAnnotationParser
with default delimiters.
SplitSequenceAnnotationParser.SplitSequenceAnnotationParser()
public MotifAnnotationParser(String keyValueDelimiter, String annotationDelimiter)
MotifAnnotationParser
with the supplied delimiters
keyValueDelimiter
- the delimiter between key and valueannotationDelimiter
- the delimiter between different annotationsMethod Detail |
---|
public void addToAnnotation(String unparsed)
SequenceAnnotationParser
unparsed
String
in some way to
the SequenceAnnotation
.
addToAnnotation
in interface SequenceAnnotationParser
addToAnnotation
in class SplitSequenceAnnotationParser
unparsed
- the String containing the annotationprotected void add(String identifier, int position, int length, StrandedLocatedSequenceAnnotationWithLength.Strand strandedness)
identifier
at position position
with length length
and StrandedLocatedSequenceAnnotationWithLength.Strand
strandedness
identifier
- the identifier of the motifposition
- the position of the motiflength
- the length of the motifstrandedness
- the strand of the motifpublic String parseAnnotationToComment(char commentChar, SequenceAnnotation... annotations)
SequenceAnnotationParser
String
representation of the given
SequenceAnnotation
s that can be used as comment line in a file.
SequenceAnnotationParser.addToAnnotation(String)
.
parseAnnotationToComment
in interface SequenceAnnotationParser
parseAnnotationToComment
in class SplitSequenceAnnotationParser
commentChar
- the char at the beginning of comment linesannotations
- the SequenceAnnotation
s to be parsed
SequenceAnnotation
sDataSet.save(java.io.OutputStream, char, SequenceAnnotationParser)
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES All Classes | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |