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

Field Detail

AMBIGUOUS

public static final int AMBIGUOUS

AMBIGUOUS indicates that a sequence contains ambiguity symbols. The first bit of the most significant word of the int is set.

See Also:

Constant Field Values

DNA

public static final int DNA

DNA indicates that a sequence contains DNA (deoxyribonucleic acid) symbols. The second bit of the most significant word of the int is set.

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Constant Field Values

RNA

public static final int RNA

RNA indicates that a sequence contains RNA (ribonucleic acid) symbols. The third bit of the most significant word of the int is set.

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Constant Field Values

AA

public static final int AA

AA indicates that a sequence contains AA (amino acid) symbols. The fourth bit of the most significant word of the int is set.

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Constant Field Values

INTEGER

public static final int INTEGER

INTEGER indicates that a sequence contains integer alphabet symbols, such as used to describe sequence quality data. The fifth bit of the most significant word of the int is set.

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Constant Field Values

UNKNOWN

public static final int UNKNOWN

UNKNOWN indicates that the sequence format is unknown.

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Constant Field Values

RAW

public static final int RAW

RAW indicates that the sequence format is raw (symbols only).

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Constant Field Values

FASTA

public static final int FASTA

FASTA indicates that the sequence format is Fasta.

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Constant Field Values

NBRF

public static final int NBRF

NBRF indicates that the sequence format is NBRF.

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Constant Field Values

IG

public static final int IG

IG indicates that the sequence format is IG.

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Constant Field Values

EMBL

public static final int EMBL

EMBL indicates that the sequence format is EMBL.

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Constant Field Values

SWISSPROT

public static final int SWISSPROT

SWISSPROT indicates that the sequence format is SWISSPROT. Always protein, so already had the AA bit set.

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Constant Field Values

GENBANK

public static final int GENBANK

GENBANK indicates that the sequence format is GENBANK.

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Constant Field Values

GENPEPT

public static final int GENPEPT

GENPEPT indicates that the sequence format is GENPEPT. Always protein, so already had the AA bit set.

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Constant Field Values

REFSEQ

public static final int REFSEQ

REFSEQ indicates that the sequence format is REFSEQ.

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Constant Field Values

GCG

public static final int GCG

GCG indicates that the sequence format is GCG.

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Constant Field Values

GFF

public static final int GFF

GFF indicates that the sequence format is GFF.

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Constant Field Values

PDB

public static final int PDB

PDB indicates that the sequence format is PDB. Always protein, so already had the AA bit set.

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Constant Field Values

PHRED

public static final int PHRED

PHRED indicates that the sequence format is PHRED. Always DNA, so already had the DNA bit set. Also has INTEGER bit set for quality data.

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Constant Field Values

EMBL_DNA

public static final int EMBL_DNA

EMBL_DNA premade EMBL | DNA.

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Constant Field Values

EMBL_RNA

public static final int EMBL_RNA

EMBL_RNA premade EMBL | RNA.

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Constant Field Values

EMBL_AA

public static final int EMBL_AA

EMBL_AA premade EMBL | AA.

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Constant Field Values

GENBANK_DNA

public static final int GENBANK_DNA

GENBANK_DNA premade GENBANK | DNA.

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Constant Field Values

GENBANK_RNA

public static final int GENBANK_RNA

GENBANK_DNA premade GENBANK | RNA.

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Constant Field Values

GENBANK_AA

public static final int GENBANK_AA

GENBANK_DNA premade GENBANK | AA.

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Constant Field Values

REFSEQ_DNA

public static final int REFSEQ_DNA

REFSEQ_DNA premade REFSEQ | DNA.

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Constant Field Values

REFSEQ_RNA

public static final int REFSEQ_RNA

REFSEQ_RNA premade REFSEQ | RNA.

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Constant Field Values

REFSEQ_AA

public static final int REFSEQ_AA

REFSEQ_AA premade REFSEQ | AA.

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Constant Field Values

FASTA_DNA

public static final int FASTA_DNA

FASTA_DNA premade FASTA | DNA.

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Constant Field Values

FASTA_RNA

public static final int FASTA_RNA

FASTA_RNA premade FASTA | RNA.

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Constant Field Values

FASTA_AA

public static final int FASTA_AA

FASTA_AA premade FASTA | AA.

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Constant Field Values

LSID_FASTA_DNA

public static final LifeScienceIdentifier LSID_FASTA_DNA

LSID_FASTA_DNA sequence format LSID for Fasta DNA.

LSID_FASTA_RNA

public static final LifeScienceIdentifier LSID_FASTA_RNA

LSID_FASTA_RNA sequence format LSID for Fasta RNA.

LSID_FASTA_AA

public static final LifeScienceIdentifier LSID_FASTA_AA

LSID_FASTA_AA sequence format LSID for Fasta AA.

LSID_EMBL_DNA

public static final LifeScienceIdentifier LSID_EMBL_DNA

LSID_EMBL_DNA sequence format LSID for EMBL DNA.

LSID_EMBL_RNA

public static final LifeScienceIdentifier LSID_EMBL_RNA

LSID_EMBL_RNA sequence format LSID for EMBL RNA.

LSID_EMBL_AA

public static final LifeScienceIdentifier LSID_EMBL_AA

LSID_EMBL_AA sequence format LSID for EMBL AA.

LSID_GENBANK_DNA

public static final LifeScienceIdentifier LSID_GENBANK_DNA

LSID_GENBANK_DNA sequence format LSID for Genbank DNA.

LSID_GENBANK_RNA

public static final LifeScienceIdentifier LSID_GENBANK_RNA

LSID_GENBANK_RNA sequence format LSID for Genbank RNA.

LSID_GENBANK_AA

public static final LifeScienceIdentifier LSID_GENBANK_AA

LSID_GENBANK_AA sequence format LSID for Genbank AA.

LSID_SWISSPROT

public static final LifeScienceIdentifier LSID_SWISSPROT

LSID_SWISSPROT sequence format LSID for Swissprot.

Constructor Detail

SeqIOConstants

public SeqIOConstants()