Class AlignIOConstants


  • public final class AlignIOConstants
    extends java.lang.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.
    • 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
      • 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
      • 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;
        See Also:
        Constant Field Values
      • CLUSTAL_AA

        public static final int CLUSTAL_AA
        CLUSTAL_AA premade CLUSTAL | AA;
        See Also:
        Constant Field Values
    • Constructor Detail

      • AlignIOConstants

        public AlignIOConstants()