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java.lang.Objectde.jstacs.data.sequences.annotation.SplitSequenceAnnotationParser
public class SplitSequenceAnnotationParser
This class implements a simple SequenceAnnotationParser
which simply splits the comments by specific delimiters.
Field Summary | |
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protected LinkedList<SequenceAnnotation> |
annot
The internal list of current SequenceAnnotation s. |
protected String |
annotationDelimiter
The delimiter between different annotations |
protected String |
keyValueDelimiter
The delimiter between key and value |
Constructor Summary | |
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SplitSequenceAnnotationParser()
Creates a new SplitSequenceAnnotationParser with specific delimiters, i.e., key value
delimiter "=" and annotation delimiter ";". |
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SplitSequenceAnnotationParser(String keyValueDelimiter,
String annotationDelimiter)
Creates a new SplitSequenceAnnotationParser with user-specified delimiters. |
Method Summary | |
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protected void |
add(String type,
String identifier)
This method actually adds a SequenceAnnotation to the internal list. |
void |
addToAnnotation(String unparsed)
This method adds the unparsed String in some way to
the SequenceAnnotation . |
void |
clearAnnotation()
This method reset the current SequenceAnnotation . |
SequenceAnnotation[] |
getCurrentAnnotation()
This method returns the current 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 java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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protected String keyValueDelimiter
protected String annotationDelimiter
protected LinkedList<SequenceAnnotation> annot
SequenceAnnotation
s.
Constructor Detail |
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public SplitSequenceAnnotationParser()
SplitSequenceAnnotationParser
with specific delimiters, i.e., key value
delimiter "=" and annotation delimiter ";".
SplitSequenceAnnotationParser(String, String)
public SplitSequenceAnnotationParser(String keyValueDelimiter, String annotationDelimiter)
SplitSequenceAnnotationParser
with user-specified delimiters.
keyValueDelimiter
- the delimiter between key and corresponding valueannotationDelimiter
- the delimiter between different SequenceAnnotation
s
IllegalArgumentException
- if the delimiters are identicalMethod Detail |
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public void addToAnnotation(String unparsed)
SequenceAnnotationParser
unparsed
String
in some way to
the SequenceAnnotation
.
addToAnnotation
in interface SequenceAnnotationParser
unparsed
- the String containing the annotationprotected void add(String type, String identifier)
SequenceAnnotation
to the internal list.
type
- the type of the SequenceAnnotation
identifier
- the identifier of the SequenceAnnotation
public void clearAnnotation()
SequenceAnnotationParser
SequenceAnnotation
.
clearAnnotation
in interface SequenceAnnotationParser
public SequenceAnnotation[] getCurrentAnnotation()
SequenceAnnotationParser
SequenceAnnotation
.
getCurrentAnnotation
in interface SequenceAnnotationParser
SequenceAnnotation
public 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
commentChar
- the char at the beginning of comment linesannotations
- the SequenceAnnotation
s to be parsed
SequenceAnnotation
sDataSet.save(java.io.OutputStream, char, SequenceAnnotationParser)
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