/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.bio.seq.io;
/**
* 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:
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.
* UNKNOWN
indicates that the alignment format is
* unknown.
*/
public static final int UNKNOWN = 100;
/**
* RAW
indicates that the alignment format is raw
* (symbols only).
*/
public static final int RAW = 101;
/**
* FASTA
indicates that the alignment format is
* Fasta.
*/
public static final int FASTA = 102;
/**
* CLUSTAL
indicates that the alignment format is
* Clustal.
*/
public static final int CLUSTAL = 103;
/**
* MSF
indicates that the alignment format is MSF.
*/
public static final int MSF = 104;
/**
* RAW_DNA
premade RAW | DNA.
*/
public static final int RAW_DNA = RAW | SeqIOConstants.DNA;
/**
* RAW_RNA
premade RAW | RNA.
*/
public static final int RAW_RNA = RAW | SeqIOConstants.RNA;
/**
* RAW_AA
premade RAW | AA.
*/
public static final int RAW_AA = RAW | SeqIOConstants.AA;
/**
* FASTA_DNA
premade FASTA | DNA;
*/
public static final int FASTA_DNA = FASTA | SeqIOConstants.DNA;
/**
* FASTA_RNA
premade FASTA | RNA;
*/
public static final int FASTA_RNA = FASTA | SeqIOConstants.RNA;
/**
* FASTA_AA
premade FASTA | AA;
*/
public static final int FASTA_AA = FASTA | SeqIOConstants.AA;
/**
* CLUSTAL_DNA
premade CLUSTAL | DNA;
*/
public static final int CLUSTAL_DNA = CLUSTAL | SeqIOConstants.DNA;
/**
* CLUSTAL_RNA
premade CLUSTAL | RNA;
*/
public static final int CLUSTAL_RNA = CLUSTAL | SeqIOConstants.RNA;
/**
* CLUSTAL_AA
premade CLUSTAL | AA;
*/
public static final int CLUSTAL_AA = CLUSTAL | SeqIOConstants.AA;
/**
* MSF_DNA
premade MSF | DNA;
*/
public static final int MSF_DNA = MSF | SeqIOConstants.DNA;
/**
* MSF_DNA
premade MSF | RNA;
*/
public static final int MSF_RNA = MSF | SeqIOConstants.RNA;
/**
* MSF_AA
premade MSF | AA;
*/
public static final int MSF_AA = MSF | SeqIOConstants.AA;
}