Package org.biojava.nbio.core.sequence.io

Class GenericGenbankHeaderParser<S extends AbstractSequence<C>,C extends Compound>

java.lang.Object

org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser<S,C>

All Implemented Interfaces:

SequenceHeaderParserInterface<S,C>

public class GenericGenbankHeaderParser<S extends AbstractSequence<C>,C extends Compound>
extends Object
implements SequenceHeaderParserInterface<S,C>

Constructor Summary

Constructors

Constructor	Description
GenericGenbankHeaderParser()

Method Summary

Modifier and Type	Method	Description
void	addReference(AbstractReference abstractReference)
String	getAccession()
ArrayList<String>	getComments()
String	getDescription()
String	getIdentifier()
String	getName()
List<AbstractReference>	getReferences()
int	getVersion()
void	parseHeader(String header, S sequence)	Parse the header and set the values in the sequence
void	setAccession(String accession)	The last accession passed to this routine will always be the one used.
void	setComment(String comment)
void	setDescription(String description)
void	setIdentifier(String identifier)
void	setName(String name)
void	setVersion(int version)	The last accession passed to this routine will always be the one used.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GenericGenbankHeaderParser

public GenericGenbankHeaderParser()

Method Detail

parseHeader

public void parseHeader(String header,
                        S sequence)

Parse the header and set the values in the sequence

Specified by:

parseHeader in interface SequenceHeaderParserInterface<S extends AbstractSequence<C>,C extends Compound>

Parameters:

header -

sequence -

getAccession

public String getAccession()

getIdentifier

public String getIdentifier()

getName

public String getName()

getVersion

public int getVersion()

getComments

public ArrayList<String> getComments()

getReferences

public List<AbstractReference> getReferences()

getDescription

public String getDescription()

setVersion

public void setVersion(int version)
                throws ParserException

The last accession passed to this routine will always be the one used.

Throws:

ParserException

setAccession

public void setAccession(String accession)
                  throws ParserException

The last accession passed to this routine will always be the one used.

Throws:

ParserException

setDescription

public void setDescription(String description)
                    throws ParserException

Throws:

ParserException

setIdentifier

public void setIdentifier(String identifier)
                   throws ParserException

Throws:

ParserException

setName

public void setName(String name)
             throws ParserException

Throws:

ParserException

setComment

public void setComment(String comment)
                throws ParserException

Throws:

ParserException

addReference

public void addReference(AbstractReference abstractReference)