Uses of Class
com.milaboratory.core.sequence.TranslationParameters

Packages that use TranslationParameters

Package	Description
com.milaboratory.core.mutations
com.milaboratory.core.sequence

Uses of TranslationParameters in com.milaboratory.core.mutations

Methods in com.milaboratory.core.mutations with parameters of type TranslationParameters

Modifier and Type	Method and Description
static Mutations<AminoAcidSequence>	MutationsUtil.nt2aa(NucleotideSequence seq1, Mutations<NucleotideSequence> mutations, TranslationParameters translationParameters)
static Mutations<AminoAcidSequence>	MutationsUtil.nt2aa(NucleotideSequence seq1, Mutations<NucleotideSequence> mutations, TranslationParameters translationParameters, int maxShiftedTriplets)
static MutationsUtil.MutationNt2AADescriptor[]	MutationsUtil.nt2aaDetailed(NucleotideSequence seq1, Mutations<NucleotideSequence> mutations, TranslationParameters translationParameters, int maxShiftedTriplets) Performs a comprehensive translation of mutations present in a nucleotide sequence to effective mutations in corresponding amino acid sequence.
static MutationsUtil.MutationsWitMapping	MutationsUtil.nt2aaWithMapping(NucleotideSequence seq1, Mutations<NucleotideSequence> mutations, TranslationParameters translationParameters, int maxShiftedTriplets)
static int[]	MutationsUtil.nt2IndividualAA(NucleotideSequence seq1, Mutations<NucleotideSequence> mutations, TranslationParameters translationParameters)

Uses of TranslationParameters in com.milaboratory.core.sequence

Fields in com.milaboratory.core.sequence declared as TranslationParameters

Modifier and Type	Field and Description
static TranslationParameters	TranslationParameters.FromCenter
static TranslationParameters	TranslationParameters.FromLeftWithIncompleteCodon
static TranslationParameters	TranslationParameters.FromLeftWithoutIncompleteCodon
static TranslationParameters	TranslationParameters.FromRightWithIncompleteCodon
static TranslationParameters	TranslationParameters.FromRightWithoutIncompleteCodon

Methods in com.milaboratory.core.sequence that return TranslationParameters

Modifier and Type	Method and Description
static TranslationParameters	TranslationParameters.withIncompleteCodon(int inFramePosition) E.g.
static TranslationParameters	TranslationParameters.withoutIncompleteCodon(int inFramePosition) E.g.

Methods in com.milaboratory.core.sequence that return types with arguments of type TranslationParameters

Modifier and Type	Method and Description
static Collection<TranslationParameters>	TranslationParameters.getPreDefinedParameters()

Methods in com.milaboratory.core.sequence with parameters of type TranslationParameters

Modifier and Type	Method and Description
static int	AminoAcidSequence.convertAAPositionToNt(int aaPosition, int ntSequenceLength, TranslationParameters translationParameters)
static AminoAcidSequence.AminoAcidSequencePosition	AminoAcidSequence.convertNtPositionToAA(int ntPosition, int ntSequenceLength, TranslationParameters translationParameters)
static AminoAcidSequence	AminoAcidSequence.translate(NucleotideSequence ns, TranslationParameters translationParameters) Use one of specialized method instead: AminoAcidSequence.translateFromLeft(NucleotideSequence) AminoAcidSequence.translateFromRight(NucleotideSequence) AminoAcidSequence.translateFromCenter(NucleotideSequence)