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

Packages that use LifeScienceIdentifier
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
 LifeScienceIdentifier Swissprot.getLSID()
           
 LifeScienceIdentifier Enzyme.getLSID()
           
 LifeScienceIdentifier Format.getLSID()
          Retrieve the LSID associated with this format.
 LifeScienceIdentifier Embl.getLSID()
           
 LifeScienceIdentifier Ligand.Enzyme.getLSID()
           
 LifeScienceIdentifier Ligand.Reaction.getLSID()
           
 LifeScienceIdentifier Ligand.Compound.getLSID()
           
 

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

Methods in org.biojava.bio.program.indexdb that return LifeScienceIdentifier
 LifeScienceIdentifier BioStoreFactory.getSequenceFormat()
          getSequenceFormat returns the current sequence format name.
 

Methods in org.biojava.bio.program.indexdb with parameters of type LifeScienceIdentifier
 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
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
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
 LifeScienceIdentifier Identifiable.getIdentifier()
          Return the identifier of this object.
static LifeScienceIdentifier LifeScienceIdentifier.valueOf(java.lang.String lsid)
          Create a new LifeScienceIdentifier parsed from the properly formatted string lsid.
static LifeScienceIdentifier LifeScienceIdentifier.valueOf(java.lang.String authorityId, java.lang.String namespaceId, java.lang.String objectId)
          Create a new LifeScienceIdentifier from the specified parameters.
static LifeScienceIdentifier LifeScienceIdentifier.valueOf(java.lang.String authorityId, java.lang.String namespaceId, java.lang.String objectId, java.lang.String revisionId)
          Create a new LifeScienceIdentifier from the specified parameters.