com.hfg.bio.taxonomy.ncbi

Class NCBIGeneticCode

java.lang.Object

com.hfg.bio.taxonomy.ncbi.NCBIGeneticCode

All Implemented Interfaces:

TranslationTable

public class NCBIGeneticCode
extends Object
implements TranslationTable

Reference genetic code information used by the NCBI.

Field Summary

Fields

Modifier and Type	Field and Description
static NCBIGeneticCode	ALT_FLATWORM_MITO
static NCBIGeneticCode	ALT_YEAST_NUCLEAR
static NCBIGeneticCode	ASCIDIAN_MITO
static NCBIGeneticCode	BACTERIAL
static NCBIGeneticCode	BALANOPHORACEAE_NUCLEAR
static NCBIGeneticCode	BLASTOCRITHIDIA_NUCLEAR
static NCBIGeneticCode	CANDIDATE_DIVISION_SR1_MITO
static NCBIGeneticCode	CEPHALODISCIDAE_MITO
static NCBIGeneticCode	CHLOROPHYCEAN_MITO
static NCBIGeneticCode	CILIATE_NUCLEAR
static NCBIGeneticCode	CONDYLOSTOMA_NUCLEAR
static NCBIGeneticCode	ECHINODERM_MITO
static NCBIGeneticCode	EUPLOTID_NUCLEAR
static NCBIGeneticCode	INVERTEBRATE_MITO
static NCBIGeneticCode	KARYORELICT_NUCLEAR
static NCBIGeneticCode	MESODINIUM_NUCLEAR
static NCBIGeneticCode	MOLD_MITO
static NCBIGeneticCode	PACHYSOLEN_TANNOPHILUS_NUCLEAR
static NCBIGeneticCode	PERITRICH_NUCLEAR
static NCBIGeneticCode	RHABDOPLEURIDAE_MITO
static NCBIGeneticCode	SCENEDESMUS_MITO
static NCBIGeneticCode	STANDARD
static NCBIGeneticCode	THRAUSTOCHYTRIUM_MITO
static NCBIGeneticCode	TREMATODE_MITO
static NCBIGeneticCode	UNSPECIFIED
static NCBIGeneticCode	VERTEBRATE_MITO
static NCBIGeneticCode	YEAST_MITO

Method Summary

Modifier and Type	Method and Description
static NCBIGeneticCode	getById(int inId)
int	getId()
String	name()
String	toString()
char	translateCodon(String inCodon) Converts the specified codon (3 nucleotides) into a character representing the corresponding amino acid.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface com.hfg.bio.seq.translation.TranslationTable

isStopCodon

Field Detail

UNSPECIFIED

public static final NCBIGeneticCode UNSPECIFIED

STANDARD

public static final NCBIGeneticCode STANDARD

VERTEBRATE_MITO

public static final NCBIGeneticCode VERTEBRATE_MITO

YEAST_MITO

public static final NCBIGeneticCode YEAST_MITO

MOLD_MITO

public static final NCBIGeneticCode MOLD_MITO

INVERTEBRATE_MITO

public static final NCBIGeneticCode INVERTEBRATE_MITO

CILIATE_NUCLEAR

public static final NCBIGeneticCode CILIATE_NUCLEAR

ECHINODERM_MITO

public static final NCBIGeneticCode ECHINODERM_MITO

EUPLOTID_NUCLEAR

public static final NCBIGeneticCode EUPLOTID_NUCLEAR

BACTERIAL

public static final NCBIGeneticCode BACTERIAL

ALT_YEAST_NUCLEAR

public static final NCBIGeneticCode ALT_YEAST_NUCLEAR

ASCIDIAN_MITO

public static final NCBIGeneticCode ASCIDIAN_MITO

ALT_FLATWORM_MITO

public static final NCBIGeneticCode ALT_FLATWORM_MITO

CHLOROPHYCEAN_MITO

public static final NCBIGeneticCode CHLOROPHYCEAN_MITO

TREMATODE_MITO

public static final NCBIGeneticCode TREMATODE_MITO

SCENEDESMUS_MITO

public static final NCBIGeneticCode SCENEDESMUS_MITO

THRAUSTOCHYTRIUM_MITO

public static final NCBIGeneticCode THRAUSTOCHYTRIUM_MITO

RHABDOPLEURIDAE_MITO

public static final NCBIGeneticCode RHABDOPLEURIDAE_MITO

CANDIDATE_DIVISION_SR1_MITO

public static final NCBIGeneticCode CANDIDATE_DIVISION_SR1_MITO

PACHYSOLEN_TANNOPHILUS_NUCLEAR

public static final NCBIGeneticCode PACHYSOLEN_TANNOPHILUS_NUCLEAR

KARYORELICT_NUCLEAR

public static final NCBIGeneticCode KARYORELICT_NUCLEAR

CONDYLOSTOMA_NUCLEAR

public static final NCBIGeneticCode CONDYLOSTOMA_NUCLEAR

MESODINIUM_NUCLEAR

public static final NCBIGeneticCode MESODINIUM_NUCLEAR

PERITRICH_NUCLEAR

public static final NCBIGeneticCode PERITRICH_NUCLEAR

BLASTOCRITHIDIA_NUCLEAR

public static final NCBIGeneticCode BLASTOCRITHIDIA_NUCLEAR

BALANOPHORACEAE_NUCLEAR

public static final NCBIGeneticCode BALANOPHORACEAE_NUCLEAR

CEPHALODISCIDAE_MITO

public static final NCBIGeneticCode CEPHALODISCIDAE_MITO

Method Detail

getById

public static NCBIGeneticCode getById(int inId)

toString

public String toString()

Overrides:

toString in class Object

name

public String name()

getId

public int getId()

translateCodon

public char translateCodon(String inCodon)

Converts the specified codon (3 nucleotides) into a character representing the corresponding amino acid.

Specified by:

translateCodon in interface TranslationTable

Parameters:

inCodon - 3-letter nucleotide (DNA or RNA) string to be translated

Returns:

single letter amino acid