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