org.biojavax.bio.seq.io
Class FastaHeader

java.lang.Object
  org.biojavax.bio.seq.io.FastaHeader

public class FastaHeader
extends Object

This class is used by FastaFormat to determine which fields are in the fasta header. By default they all are except for the sequence name. This is for compliance with fasta files that come from Genbank where the name is derived from the accession number so need not be repeated. The class can be used to customise what appears. Eg if you only want the accession set everything else false. Note that if fields in the RichSequence being parsed by the FastaFormat object then they may not be in the header even if they are specified in this class.

Since:

1.6

Author:

Mark Schreiber

Constructor Summary

FastaHeader()

Method Summary

boolean	isShowAccession()
boolean	isShowDescription()
boolean	isShowIdentifier()
boolean	isShowName()
boolean	isShowNamespace()
boolean	isShowVersion()
void	setShowAccession(boolean showAccession)
void	setShowDescription(boolean showDescription)
void	setShowIdentifier(boolean showIdentifier)
void	setShowName(boolean showName)
void	setShowNamespace(boolean showNamespace)
void	setShowVersion(boolean showVersion) Determines if the version number of a sequence should be displayed.

Methods inherited from class java.lang.Object

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

Constructor Detail

FastaHeader

public FastaHeader()

Method Detail

isShowIdentifier

public boolean isShowIdentifier()

setShowIdentifier

public void setShowIdentifier(boolean showIdentifier)

isShowNamespace

public boolean isShowNamespace()

setShowNamespace

public void setShowNamespace(boolean showNamespace)

isShowAccession

public boolean isShowAccession()

setShowAccession

public void setShowAccession(boolean showAccession)

isShowVersion

public boolean isShowVersion()

setShowVersion

public void setShowVersion(boolean showVersion)

Determines if the version number of a sequence should be displayed. If there is no accession this may not make much sense.

Parameters:

showVersion -

isShowName

public boolean isShowName()

setShowName

public void setShowName(boolean showName)

isShowDescription

public boolean isShowDescription()

setShowDescription

public void setShowDescription(boolean showDescription)