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

Packages that use AminoAcidSequence

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

Uses of AminoAcidSequence in com.milaboratory.core.alignment

Methods in com.milaboratory.core.alignment that return types with arguments of type AminoAcidSequence

Modifier and Type	Method and Description
static LinearGapAlignmentScoring<AminoAcidSequence>	LinearGapAlignmentScoring.getAminoAcidBLASTScoring(BLASTMatrix matrix) Returns standard amino acid BLAST scoring with #gapPenalty=5
static AffineGapAlignmentScoring<AminoAcidSequence>	AffineGapAlignmentScoring.getAminoAcidBLASTScoring(BLASTMatrix matrix) Returns standard AminoAcid BLAST scoring (#gapOpenPenalty=-10, #gapExtensionPenalty=-1)
static LinearGapAlignmentScoring<AminoAcidSequence>	LinearGapAlignmentScoring.getAminoAcidBLASTScoring(BLASTMatrix matrix, int gapPenalty) Returns standard amino acid BLAST scoring
static AffineGapAlignmentScoring<AminoAcidSequence>	AffineGapAlignmentScoring.getAminoAcidBLASTScoring(BLASTMatrix matrix, int gapOpenPenalty, int gapExtensionPenalty) Returns AminoAcid BLAST scoring

Uses of AminoAcidSequence in com.milaboratory.core.alignment.blast

Method parameters in com.milaboratory.core.alignment.blast with type arguments of type AminoAcidSequence

Modifier and Type	Method and Description
protected AABlastHitExt	AABlastAlignerExt.createHit(Alignment<AminoAcidSequence> alignment, double score, double bitScore, double eValue, Range subjectRange, String subjectId, String subjectTitle)
protected AABlastHit<P>	AABlastAligner.createHit(Alignment<AminoAcidSequence> alignment, P recordPayload, BlastHit<AminoAcidSequence,?> hit)
protected AABlastHit<P>	AABlastAligner.createHit(Alignment<AminoAcidSequence> alignment, P recordPayload, BlastHit<AminoAcidSequence,?> hit)

Constructor parameters in com.milaboratory.core.alignment.blast with type arguments of type AminoAcidSequence

Constructor and Description
AABlastHit(Alignment<AminoAcidSequence> alignment, P recordPayload, BlastHit<AminoAcidSequence,?> hit)
AABlastHit(Alignment<AminoAcidSequence> alignment, P recordPayload, BlastHit<AminoAcidSequence,?> hit)
AABlastHit(Alignment<AminoAcidSequence> alignment, P recordPayload, double score, double bitScore, double eValue, Range subjectRange, String subjectId, String subjectTitle)
AABlastHitExt(Alignment<AminoAcidSequence> alignment, double score, double bitScore, double eValue, Range subjectRange, String subjectId, String subjectTitle)

Uses of AminoAcidSequence in com.milaboratory.core.mutations

Fields in com.milaboratory.core.mutations with type parameters of type AminoAcidSequence

Modifier and Type	Field and Description
static Mutations<AminoAcidSequence>	Mutations.EMPTY_AMINO_ACID_MUTATIONS Identity mutations object for amino acid sequences.
Mutations<AminoAcidSequence>	MutationsUtil.MutationsWitMapping.mutations

Methods in com.milaboratory.core.mutations that return types with arguments of type AminoAcidSequence

Modifier and Type	Method and Description
static Mutations<AminoAcidSequence>	Mutations.decodeAA(String string)
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)

Constructor parameters in com.milaboratory.core.mutations with type arguments of type AminoAcidSequence

Constructor and Description
MutationsUtil.MutationsWitMapping(Mutations<AminoAcidSequence> mutations, int[] mapping)

Uses of AminoAcidSequence in com.milaboratory.core.sequence

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

Modifier and Type	Field and Description
static AminoAcidSequence	AminoAcidSequence.EMPTY Empty sequence

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

Modifier and Type	Method and Description
static AminoAcidSequence	AminoAcidSequence.translate(NucleotideSequence sequence) Translates sequence having length divisible by 3, starting from first nucleotide.
static AminoAcidSequence	AminoAcidSequence.translate(NucleotideSequence sequence, int frame) Translate sequence in one of frames (-1, -2, -3 frames are not implemented, use NucleotideSequence.getReverseComplement()) discarding all incomplete codons on both boundaries.
static AminoAcidSequence	AminoAcidSequence.translate(NucleotideSequence ns, TranslationParameters translationParameters) Use one of specialized method instead: translateFromLeft(NucleotideSequence) translateFromRight(NucleotideSequence) translateFromCenter(NucleotideSequence)
static AminoAcidSequence	AminoAcidSequence.translateFromCenter(NucleotideSequence ns) Translates sequence from both sides, so the first nucleotide of the first triplet matches first nucleotide of the sequence, and last (3rd) nucleotide of last triplet matches last nucleotide of the sequence.
static AminoAcidSequence	AminoAcidSequence.translateFromLeft(NucleotideSequence ns) Translates sequence from the left side, so the first nucleotide of the first triplet matches first nucleotide of the sequence.
static AminoAcidSequence	AminoAcidSequence.translateFromRight(NucleotideSequence ns) Translates sequence from the right side, so the last (3rd) nucleotide of last triplet matches last nucleotide of the sequence.