Uses of Class
org.biojava.utils.lsid.LifeScienceIdentifier
Packages that use LifeScienceIdentifier
Package
Description
Experimental parsers using the tagvalue framework.
A flat-file ascii index of ascii flat files as per the OBDA specification.
Classes and interfaces for processing and producing flat-file representations
of sequences.
Representation of the Symbols that make up a sequence, and locations within
them.
Life Science Identifier (LSID) package.
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Uses of LifeScienceIdentifier in org.biojava.bio.program.formats
Methods in org.biojava.bio.program.formats that return LifeScienceIdentifier -
Uses of LifeScienceIdentifier in org.biojava.bio.program.indexdb
Methods in org.biojava.bio.program.indexdb that return LifeScienceIdentifierModifier and TypeMethodDescriptionBioStoreFactory.getSequenceFormat()
getSequenceFormat
returns the current sequence format name.Methods in org.biojava.bio.program.indexdb with parameters of type LifeScienceIdentifierModifier and TypeMethodDescriptionvoid
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 LifeScienceIdentifierModifier and TypeFieldDescriptionstatic final LifeScienceIdentifier
SeqIOConstants.LSID_EMBL_AA
LSID_EMBL_AA
sequence format LSID for EMBL AA.static final LifeScienceIdentifier
SeqIOConstants.LSID_EMBL_DNA
LSID_EMBL_DNA
sequence format LSID for EMBL DNA.static final LifeScienceIdentifier
SeqIOConstants.LSID_EMBL_RNA
LSID_EMBL_RNA
sequence format LSID for EMBL RNA.static final LifeScienceIdentifier
SeqIOConstants.LSID_FASTA_AA
LSID_FASTA_AA
sequence format LSID for Fasta AA.static final LifeScienceIdentifier
SeqIOConstants.LSID_FASTA_DNA
LSID_FASTA_DNA
sequence format LSID for Fasta DNA.static final LifeScienceIdentifier
SeqIOConstants.LSID_FASTA_RNA
LSID_FASTA_RNA
sequence format LSID for Fasta RNA.static final LifeScienceIdentifier
SeqIOConstants.LSID_GENBANK_AA
LSID_GENBANK_AA
sequence format LSID for Genbank AA.static final LifeScienceIdentifier
SeqIOConstants.LSID_GENBANK_DNA
LSID_GENBANK_DNA
sequence format LSID for Genbank DNA.static final LifeScienceIdentifier
SeqIOConstants.LSID_GENBANK_RNA
LSID_GENBANK_RNA
sequence format LSID for Genbank RNA.static final 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 LifeScienceIdentifierModifier and TypeMethodDescriptionstatic 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 LifeScienceIdentifierModifier and TypeMethodDescriptionIdentifiable.getIdentifier()
Return the identifier of this object.static LifeScienceIdentifier
Create a new LifeScienceIdentifier parsed from the properly formatted stringlsid
.static LifeScienceIdentifier
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.