Package org.biojava.bio.seq.io

Class AlignIOConstants

java.lang.Object

org.biojava.bio.seq.io.AlignIOConstants

public final class AlignIOConstants
extends Object

AlignIOConstants contains constants used to identify sequence formats, alphabets etc, in the context of reading and writing alignments.

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 MSF, CLUSTAL 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	CLUSTAL	CLUSTAL indicates that the alignment format is Clustal.
static int	CLUSTAL_AA	CLUSTAL_AA premade CLUSTAL | AA;
static int	CLUSTAL_DNA	CLUSTAL_DNA premade CLUSTAL | DNA;
static int	CLUSTAL_RNA	CLUSTAL_RNA premade CLUSTAL | RNA;
static int	FASTA	FASTA indicates that the alignment 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	MSF	MSF indicates that the alignment format is MSF.
static int	MSF_AA	MSF_AA premade MSF | AA;
static int	MSF_DNA	MSF_DNA premade MSF | DNA;
static int	MSF_RNA	MSF_DNA premade MSF | RNA;
static int	RAW	RAW indicates that the alignment format is raw (symbols only).
static int	RAW_AA	RAW_AA premade RAW | AA.
static int	RAW_DNA	RAW_DNA premade RAW | DNA.
static int	RAW_RNA	RAW_RNA premade RAW | RNA.
static int	UNKNOWN	UNKNOWN indicates that the alignment format is unknown.

Constructor Summary

Constructors

Constructor	Description
AlignIOConstants()

Method Summary

Methods inherited from class java.lang.Object

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

Field Detail

UNKNOWN

public static final int UNKNOWN

UNKNOWN indicates that the alignment format is unknown.

See Also:

Constant Field Values

RAW

public static final int RAW

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

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Constant Field Values

FASTA

public static final int FASTA

FASTA indicates that the alignment format is Fasta.

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Constant Field Values

CLUSTAL

public static final int CLUSTAL

CLUSTAL indicates that the alignment format is Clustal.

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Constant Field Values

MSF

public static final int MSF

MSF indicates that the alignment format is MSF.

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Constant Field Values

RAW_DNA

public static final int RAW_DNA

RAW_DNA premade RAW | DNA.

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Constant Field Values

RAW_RNA

public static final int RAW_RNA

RAW_RNA premade RAW | RNA.

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Constant Field Values

RAW_AA

public static final int RAW_AA

RAW_AA premade RAW | 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

CLUSTAL_DNA

public static final int CLUSTAL_DNA

CLUSTAL_DNA premade CLUSTAL | DNA;

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Constant Field Values

CLUSTAL_RNA

public static final int CLUSTAL_RNA

CLUSTAL_RNA premade CLUSTAL | RNA;

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Constant Field Values

CLUSTAL_AA

public static final int CLUSTAL_AA

CLUSTAL_AA premade CLUSTAL | AA;

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Constant Field Values

MSF_DNA

public static final int MSF_DNA

MSF_DNA premade MSF | DNA;

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Constant Field Values

MSF_RNA

public static final int MSF_RNA

MSF_DNA premade MSF | RNA;

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Constant Field Values

MSF_AA

public static final int MSF_AA

MSF_AA premade MSF | AA;

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Constant Field Values

Constructor Detail

AlignIOConstants

public AlignIOConstants()