Package org.biojava.bio.seq.io
Class AlignIOConstants
java.lang.Object
org.biojava.bio.seq.io.AlignIOConstants
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 anint
identifier for DNA with ambiguity codes in Fasta format, bitwise OR the AMBIGUOUS, DNA and FASTA values.
- Author:
- Keith James
-
Field Summary
FieldsModifier and TypeFieldDescriptionstatic final int
CLUSTAL
indicates that the alignment format is Clustal.static final int
CLUSTAL_AA
premade CLUSTAL | AA;static final int
CLUSTAL_DNA
premade CLUSTAL | DNA;static final int
CLUSTAL_RNA
premade CLUSTAL | RNA;static final int
FASTA
indicates that the alignment format is Fasta.static final int
FASTA_AA
premade FASTA | AA;static final int
FASTA_DNA
premade FASTA | DNA;static final int
FASTA_RNA
premade FASTA | RNA;static final int
MSF
indicates that the alignment format is MSF.static final int
MSF_AA
premade MSF | AA;static final int
MSF_DNA
premade MSF | DNA;static final int
MSF_DNA
premade MSF | RNA;static final int
RAW
indicates that the alignment format is raw (symbols only).static final int
RAW_AA
premade RAW | AA.static final int
RAW_DNA
premade RAW | DNA.static final int
RAW_RNA
premade RAW | RNA.static final int
UNKNOWN
indicates that the alignment format is unknown. -
Constructor Summary
Constructors -
Method Summary
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Field Details
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UNKNOWN
UNKNOWN
indicates that the alignment format is unknown.- See Also:
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RAW
RAW
indicates that the alignment format is raw (symbols only).- See Also:
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FASTA
FASTA
indicates that the alignment format is Fasta.- See Also:
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CLUSTAL
CLUSTAL
indicates that the alignment format is Clustal.- See Also:
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MSF
MSF
indicates that the alignment format is MSF.- See Also:
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RAW_DNA
RAW_DNA
premade RAW | DNA.- See Also:
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RAW_RNA
RAW_RNA
premade RAW | RNA.- See Also:
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RAW_AA
RAW_AA
premade RAW | AA.- See Also:
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FASTA_DNA
FASTA_DNA
premade FASTA | DNA;- See Also:
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FASTA_RNA
FASTA_RNA
premade FASTA | RNA;- See Also:
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FASTA_AA
FASTA_AA
premade FASTA | AA;- See Also:
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CLUSTAL_DNA
CLUSTAL_DNA
premade CLUSTAL | DNA;- See Also:
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CLUSTAL_RNA
CLUSTAL_RNA
premade CLUSTAL | RNA;- See Also:
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CLUSTAL_AA
CLUSTAL_AA
premade CLUSTAL | AA;- See Also:
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MSF_DNA
MSF_DNA
premade MSF | DNA;- See Also:
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MSF_RNA
MSF_DNA
premade MSF | RNA;- See Also:
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MSF_AA
MSF_AA
premade MSF | AA;- See Also:
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Constructor Details
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AlignIOConstants
public AlignIOConstants()
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