org.biojava.bio.seq.io
Class AlignIOConstants

java.lang.Object
  extended by 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:

Author:
Keith James

Field Summary
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
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).

See Also:
Constant Field Values

FASTA

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

See Also:
Constant Field Values

CLUSTAL

public static final int CLUSTAL
CLUSTAL indicates that the alignment format is Clustal.

See Also:
Constant Field Values

MSF

public static final int MSF
MSF indicates that the alignment format is MSF.

See Also:
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;

See Also:
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;

See Also:
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;

See Also:
Constant Field Values
Constructor Detail

AlignIOConstants

public AlignIOConstants()