Package org.biojava.bio.seq.io

Class SeqIOConstants

java.lang.Object
org.biojava.bio.seq.io.SeqIOConstants
public final class SeqIOConstants extends Object
SeqIOConstants contains constants used to identify sequence formats, alphabets etc, in the context of reading and writing sequences.

An int used to specify symbol alphabet and sequence format type is derived thus:

  • The two least significant bytes are reserved for format types such as RAW, FASTA, EMBL etc.
  • The two most significant bytes are reserved for alphabet and symbol information such as AMBIGUOUS, DNA, RNA, AA etc.
  • Bitwise OR combinations of each component int are used to specify combinations of format type and symbol information. To derive an int identifier for DNA with ambiguity codes in Fasta format, bitwise OR the AMBIGUOUS, DNA and FASTA values.
Author:
Keith James

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final int
    AA
    AA indicates that a sequence contains AA (amino acid) symbols.
    static final int
    AMBIGUOUS
    AMBIGUOUS indicates that a sequence contains ambiguity symbols.
    static final int
    DNA
    DNA indicates that a sequence contains DNA (deoxyribonucleic acid) symbols.
    static final int
    EMBL
    EMBL indicates that the sequence format is EMBL.
    static final int
    EMBL_AA
    EMBL_AA premade EMBL | AA.
    static final int
    EMBL_DNA
    EMBL_DNA premade EMBL | DNA.
    static final int
    EMBL_RNA
    EMBL_RNA premade EMBL | RNA.
    static final int
    FASTA
    FASTA indicates that the sequence format is Fasta.
    static final int
    FASTA_AA
    FASTA_AA premade FASTA | AA.
    static final int
    FASTA_DNA
    FASTA_DNA premade FASTA | DNA.
    static final int
    FASTA_RNA
    FASTA_RNA premade FASTA | RNA.
    static final int
    GCG
    GCG indicates that the sequence format is GCG.
    static final int
    GENBANK
    GENBANK indicates that the sequence format is GENBANK.
    static final int
    GENBANK_AA
    GENBANK_DNA premade GENBANK | AA.
    static final int
    GENBANK_DNA
    GENBANK_DNA premade GENBANK | DNA.
    static final int
    GENBANK_RNA
    GENBANK_DNA premade GENBANK | RNA.
    static final int
    GENPEPT
    GENPEPT indicates that the sequence format is GENPEPT.
    static final int
    GFF
    GFF indicates that the sequence format is GFF.
    static final int
    IG
    IG indicates that the sequence format is IG.
    static final int
    INTEGER
    INTEGER indicates that a sequence contains integer alphabet symbols, such as used to describe sequence quality data.
    static final LifeScienceIdentifier
    LSID_EMBL_AA
    LSID_EMBL_AA sequence format LSID for EMBL AA.
    static final LifeScienceIdentifier
    LSID_EMBL_DNA
    LSID_EMBL_DNA sequence format LSID for EMBL DNA.
    static final LifeScienceIdentifier
    LSID_EMBL_RNA
    LSID_EMBL_RNA sequence format LSID for EMBL RNA.
    static final LifeScienceIdentifier
    LSID_FASTA_AA
    LSID_FASTA_AA sequence format LSID for Fasta AA.
    static final LifeScienceIdentifier
    LSID_FASTA_DNA
    LSID_FASTA_DNA sequence format LSID for Fasta DNA.
    static final LifeScienceIdentifier
    LSID_FASTA_RNA
    LSID_FASTA_RNA sequence format LSID for Fasta RNA.
    static final LifeScienceIdentifier
    LSID_GENBANK_AA
    LSID_GENBANK_AA sequence format LSID for Genbank AA.
    static final LifeScienceIdentifier
    LSID_GENBANK_DNA
    LSID_GENBANK_DNA sequence format LSID for Genbank DNA.
    static final LifeScienceIdentifier
    LSID_GENBANK_RNA
    LSID_GENBANK_RNA sequence format LSID for Genbank RNA.
    static final LifeScienceIdentifier
    LSID_SWISSPROT
    LSID_SWISSPROT sequence format LSID for Swissprot.
    static final int
    NBRF
    NBRF indicates that the sequence format is NBRF.
    static final int
    PDB
    PDB indicates that the sequence format is PDB.
    static final int
    PHRED
    PHRED indicates that the sequence format is PHRED.
    static final int
    RAW
    RAW indicates that the sequence format is raw (symbols only).
    static final int
    REFSEQ
    REFSEQ indicates that the sequence format is REFSEQ.
    static final int
    REFSEQ_AA
    REFSEQ_AA premade REFSEQ | AA.
    static final int
    REFSEQ_DNA
    REFSEQ_DNA premade REFSEQ | DNA.
    static final int
    REFSEQ_RNA
    REFSEQ_RNA premade REFSEQ | RNA.
    static final int
    RNA
    RNA indicates that a sequence contains RNA (ribonucleic acid) symbols.
    static final int
    SWISSPROT
    SWISSPROT indicates that the sequence format is SWISSPROT.
    static final int
    UNKNOWN
    UNKNOWN indicates that the sequence format is unknown.

  • Constructor Summary

    Constructors
    Constructor
    Description
    SeqIOConstants()
     

  • Method Summary

    Methods inherited from class java.lang.Object

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