org.biojava.bio.seq.io
Class SeqIOConstants

java.lang.Object
  extended by 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:

Author:
Keith James

Field Summary
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
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.

See Also:
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.

See Also:
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.

See Also:
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.

See Also:
Constant Field Values

UNKNOWN

public static final int UNKNOWN
UNKNOWN indicates that the sequence format is unknown.

See Also:
Constant Field Values

RAW

public static final int RAW
RAW indicates that the sequence format is raw (symbols only).

See Also:
Constant Field Values

FASTA

public static final int FASTA
FASTA indicates that the sequence format is Fasta.

See Also:
Constant Field Values

NBRF

public static final int NBRF
NBRF indicates that the sequence format is NBRF.

See Also:
Constant Field Values

IG

public static final int IG
IG indicates that the sequence format is IG.

See Also:
Constant Field Values

EMBL

public static final int EMBL
EMBL indicates that the sequence format is EMBL.

See Also:
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.

See Also:
Constant Field Values

GENBANK

public static final int GENBANK
GENBANK indicates that the sequence format is GENBANK.

See Also:
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.

See Also:
Constant Field Values

REFSEQ

public static final int REFSEQ
REFSEQ indicates that the sequence format is REFSEQ.

See Also:
Constant Field Values

GCG

public static final int GCG
GCG indicates that the sequence format is GCG.

See Also:
Constant Field Values

GFF

public static final int GFF
GFF indicates that the sequence format is GFF.

See Also:
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.

See Also:
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.

See Also:
Constant Field Values

EMBL_DNA

public static final int EMBL_DNA
EMBL_DNA premade EMBL | DNA.

See Also:
Constant Field Values

EMBL_RNA

public static final int EMBL_RNA
EMBL_RNA premade EMBL | RNA.

See Also:
Constant Field Values

EMBL_AA

public static final int EMBL_AA
EMBL_AA premade EMBL | AA.

See Also:
Constant Field Values

GENBANK_DNA

public static final int GENBANK_DNA
GENBANK_DNA premade GENBANK | DNA.

See Also:
Constant Field Values

GENBANK_RNA

public static final int GENBANK_RNA
GENBANK_DNA premade GENBANK | RNA.

See Also:
Constant Field Values

GENBANK_AA

public static final int GENBANK_AA
GENBANK_DNA premade GENBANK | AA.

See Also:
Constant Field Values

REFSEQ_DNA

public static final int REFSEQ_DNA
REFSEQ_DNA premade REFSEQ | DNA.

See Also:
Constant Field Values

REFSEQ_RNA

public static final int REFSEQ_RNA
REFSEQ_RNA premade REFSEQ | RNA.

See Also:
Constant Field Values

REFSEQ_AA

public static final int REFSEQ_AA
REFSEQ_AA premade REFSEQ | AA.

See Also:
Constant Field Values

FASTA_DNA

public static final int FASTA_DNA
FASTA_DNA premade FASTA | DNA.

See Also:
Constant Field Values

FASTA_RNA

public static final int FASTA_RNA
FASTA_RNA premade FASTA | RNA.

See Also:
Constant Field Values

FASTA_AA

public static final int FASTA_AA
FASTA_AA premade FASTA | AA.

See Also:
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()