Package org.snpeff.codons
Class CodonTables
- java.lang.Object
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- org.snpeff.codons.CodonTables
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- All Implemented Interfaces:
java.lang.Iterable<CodonTable>
public class CodonTables extends java.lang.Object implements java.lang.Iterable<CodonTable>
All codon tables are stored here. Mapping for genome/chromosome to codon table are also stored here Note: This object is a singleton- Author:
- pcingola
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
STANDARD_TABLE
static java.lang.String
STANDARD_TABLE_NAME
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description java.lang.String
aa(java.lang.String codon, Genome genome, java.lang.String chromosome)
Translate a codon into an amino acid for a given genome+chromosomevoid
add(CodonTable codonTable)
Add a codon tablejava.util.List<java.lang.String>
codon(java.lang.String aa, Genome genome, java.lang.String chromosome)
Translate an amino acid into a codon for a given genome+chromosomestatic CodonTables
getInstance()
CodonTable
getTable(java.lang.String codonTableName)
Get a codon table by nameCodonTable
getTable(Genome genome)
Get default genome-wide codon tableCodonTable
getTable(Genome genome, java.lang.String chromosome)
Get a codon table WARNING: It will return the standard codon table if nothing if foundjava.util.Iterator<CodonTable>
iterator()
void
set(Genome genome, CodonTable codonTable)
Set a codon table for a all chromosomes in a genome I.e.: Default genome-wide chromosome tablevoid
set(Genome genome, Chromosome chr, CodonTable codonTable)
Set a codon table for a given genome & chromosome
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Field Detail
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STANDARD_TABLE
public static final java.lang.String STANDARD_TABLE
- See Also:
- Constant Field Values
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STANDARD_TABLE_NAME
public static final java.lang.String STANDARD_TABLE_NAME
- See Also:
- Constant Field Values
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Method Detail
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getInstance
public static CodonTables getInstance()
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aa
public java.lang.String aa(java.lang.String codon, Genome genome, java.lang.String chromosome)
Translate a codon into an amino acid for a given genome+chromosome
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add
public void add(CodonTable codonTable)
Add a codon table
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codon
public java.util.List<java.lang.String> codon(java.lang.String aa, Genome genome, java.lang.String chromosome)
Translate an amino acid into a codon for a given genome+chromosome
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getTable
public CodonTable getTable(Genome genome)
Get default genome-wide codon table
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getTable
public CodonTable getTable(Genome genome, java.lang.String chromosome)
Get a codon table WARNING: It will return the standard codon table if nothing if found
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getTable
public CodonTable getTable(java.lang.String codonTableName)
Get a codon table by name
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iterator
public java.util.Iterator<CodonTable> iterator()
- Specified by:
iterator
in interfacejava.lang.Iterable<CodonTable>
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set
public void set(Genome genome, Chromosome chr, CodonTable codonTable)
Set a codon table for a given genome & chromosome
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set
public void set(Genome genome, CodonTable codonTable)
Set a codon table for a all chromosomes in a genome I.e.: Default genome-wide chromosome table
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