Uses of Class
org.biojava.utils.lsid.LifeScienceIdentifier

Packages that use LifeScienceIdentifier

Package	Description
org.biojava.bio.program.formats	Experimental parsers using the tagvalue framework.
org.biojava.bio.program.indexdb	A flat-file ascii index of ascii flat files as per the OBDA specification.
org.biojava.bio.seq.io	Classes and interfaces for processing and producing flat-file representations of sequences.
org.biojava.bio.symbol	Representation of the Symbols that make up a sequence, and locations within them.
org.biojava.utils.lsid	Life Science Identifier (LSID) package.

Uses of LifeScienceIdentifier in org.biojava.bio.program.formats

Methods in org.biojava.bio.program.formats that return LifeScienceIdentifier

Modifier and Type	Method and Description
LifeScienceIdentifier	Swissprot.getLSID()
LifeScienceIdentifier	Ligand.Enzyme.getLSID()
LifeScienceIdentifier	Ligand.Reaction.getLSID()
LifeScienceIdentifier	Ligand.Compound.getLSID()
LifeScienceIdentifier	Format.getLSID() Retrieve the LSID associated with this format.
LifeScienceIdentifier	Enzyme.getLSID()
LifeScienceIdentifier	Embl.getLSID()

Uses of LifeScienceIdentifier in org.biojava.bio.program.indexdb

Methods in org.biojava.bio.program.indexdb that return LifeScienceIdentifier

Modifier and Type	Method and Description
LifeScienceIdentifier	BioStoreFactory.getSequenceFormat() getSequenceFormat returns the current sequence format name.

Methods in org.biojava.bio.program.indexdb with parameters of type LifeScienceIdentifier

Modifier and Type	Method and Description
void	BioStoreFactory.setSequenceFormat(LifeScienceIdentifier format) setSequenceFormat sets the sequence format name which will be indicated in the index.

Uses of LifeScienceIdentifier in org.biojava.bio.seq.io

Fields in org.biojava.bio.seq.io declared as LifeScienceIdentifier

Modifier and Type	Field and Description
static LifeScienceIdentifier	SeqIOConstants.LSID_EMBL_AA LSID_EMBL_AA sequence format LSID for EMBL AA.
static LifeScienceIdentifier	SeqIOConstants.LSID_EMBL_DNA LSID_EMBL_DNA sequence format LSID for EMBL DNA.
static LifeScienceIdentifier	SeqIOConstants.LSID_EMBL_RNA LSID_EMBL_RNA sequence format LSID for EMBL RNA.
static LifeScienceIdentifier	SeqIOConstants.LSID_FASTA_AA LSID_FASTA_AA sequence format LSID for Fasta AA.
static LifeScienceIdentifier	SeqIOConstants.LSID_FASTA_DNA LSID_FASTA_DNA sequence format LSID for Fasta DNA.
static LifeScienceIdentifier	SeqIOConstants.LSID_FASTA_RNA LSID_FASTA_RNA sequence format LSID for Fasta RNA.
static LifeScienceIdentifier	SeqIOConstants.LSID_GENBANK_AA LSID_GENBANK_AA sequence format LSID for Genbank AA.
static LifeScienceIdentifier	SeqIOConstants.LSID_GENBANK_DNA LSID_GENBANK_DNA sequence format LSID for Genbank DNA.
static LifeScienceIdentifier	SeqIOConstants.LSID_GENBANK_RNA LSID_GENBANK_RNA sequence format LSID for Genbank RNA.
static LifeScienceIdentifier	SeqIOConstants.LSID_SWISSPROT LSID_SWISSPROT sequence format LSID for Swissprot.

Uses of LifeScienceIdentifier in org.biojava.bio.symbol

Methods in org.biojava.bio.symbol with parameters of type LifeScienceIdentifier

Modifier and Type	Method and Description
static Symbol	AlphabetManager.symbolForLifeScienceID(LifeScienceIdentifier lsid) Retreives the Symbol for the LSID

Uses of LifeScienceIdentifier in org.biojava.utils.lsid

Methods in org.biojava.utils.lsid that return LifeScienceIdentifier

Modifier and Type	Method and Description
LifeScienceIdentifier	Identifiable.getIdentifier() Return the identifier of this object.
static LifeScienceIdentifier	LifeScienceIdentifier.valueOf(String lsid) Create a new LifeScienceIdentifier parsed from the properly formatted string lsid.
static LifeScienceIdentifier	LifeScienceIdentifier.valueOf(String authorityId, String namespaceId, String objectId) Create a new LifeScienceIdentifier from the specified parameters.
static LifeScienceIdentifier	LifeScienceIdentifier.valueOf(String authorityId, String namespaceId, String objectId, String revisionId) Create a new LifeScienceIdentifier from the specified parameters.