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

Packages that use Alphabet

Package	Description
com.milaboratory.core.alignment
com.milaboratory.core.alignment.benchmark
com.milaboratory.core.alignment.blast
com.milaboratory.core.io.sequence.fasta
com.milaboratory.core.motif
com.milaboratory.core.mutations
com.milaboratory.core.mutations.generator
com.milaboratory.core.sequence
com.milaboratory.core.sequence.provider
com.milaboratory.core.tree

Uses of Alphabet in com.milaboratory.core.alignment

Fields in com.milaboratory.core.alignment declared as Alphabet

Modifier and Type	Field and Description
protected Alphabet<S>	AbstractAlignmentScoring.alphabet Link to alphabet

Methods in com.milaboratory.core.alignment that return Alphabet

Modifier and Type	Method and Description
Alphabet<S>	AlignmentScoring.getAlphabet()
Alphabet<S>	AbstractAlignmentScoring.getAlphabet() Returns alphabet

Methods in com.milaboratory.core.alignment with parameters of type Alphabet

Modifier and Type	Method and Description
static <S extends Sequence<S>> Alignment<S>	AlignerCustom.alignAffineSemiLocalLeft0(AffineGapAlignmentScoring<S> scoring, S seq1, S seq2, int offset1, int length1, int offset2, int length2, boolean boundSeq1, boolean boundSeq2, Alphabet<S> alphabet, AlignerCustom.AffineMatrixCache cache)
static <S extends Sequence<S>> Alignment<S>	AlignerCustom.alignLinearSemiLocalLeft0(LinearGapAlignmentScoring<S> scoring, S seq1, S seq2, int offset1, int length1, int offset2, int length2, boolean boundSeq1, boolean boundSeq2, Alphabet<S> alphabet, AlignerCustom.LinearMatrixCache cache) Align two sequences from left to right; left edges of both sequences considered to be already aligned.
static <S extends Sequence<S>> Alignment<S>	AlignerCustom.alignLinearSemiLocalRight0(LinearGapAlignmentScoring<S> scoring, S seq1, S seq2, int offset1, int length1, int offset2, int length2, boolean boundSeq1, boolean boundSeq2, Alphabet<S> alphabet, AlignerCustom.LinearMatrixCache cache)
static int[]	ScoringUtils.fillWildcardScores(int[] matrix, Alphabet<?> alphabet, byte... exclude) Fills up scores for wildcards by averaging scores for all their matching scores combinations.
static int[]	ScoringUtils.getSymmetricMatrix(int match, int mismatch, Alphabet<?> alphabet) Returns simple substitution matrix
static int[]	ScoringUtils.setMatchScore(Alphabet<?> alphabet, int[] matrix, int match)
static int[]	ScoringUtils.setMismatchScore(Alphabet<?> alphabet, int[] matrix, int mismatch)

Constructors in com.milaboratory.core.alignment with parameters of type Alphabet

Constructor and Description
AbstractAlignmentScoring(Alphabet<S> alphabet, com.milaboratory.core.alignment.SubstitutionMatrix subsMatrix) Abstract class constructor.
AffineGapAlignmentScoring.SerializationObject(Alphabet alphabet, com.milaboratory.core.alignment.SubstitutionMatrix matrix, int gapOpenPenalty, int gapExtensionPenalty)
AffineGapAlignmentScoring(Alphabet<S> alphabet, int[] subsMatrix, int gapOpenPenalty, int gapExtensionPenalty) Creates new AffineGapScoring
AffineGapAlignmentScoring(Alphabet<S> alphabet, int match, int mismatch, int gapOpen, int gapExtension) Creates scoring with uniform match and mismatch scores
AffineGapAlignmentScoring(Alphabet<S> alphabet, com.milaboratory.core.alignment.SubstitutionMatrix subsMatrix, int gapOpenPenalty, int gapExtensionPenalty)
LinearGapAlignmentScoring.SerializationObject(Alphabet alphabet, com.milaboratory.core.alignment.SubstitutionMatrix matrix, int gapPenalty)
LinearGapAlignmentScoring(Alphabet<S> alphabet, int[] subsMatrix, int gapPenalty) Creates new LinearGapAlignmentScoring
LinearGapAlignmentScoring(Alphabet<S> alphabet, int match, int mismatch, int gap) Returns scoring with uniform match and mismatch scores
LinearGapAlignmentScoring(Alphabet<S> alphabet, com.milaboratory.core.alignment.SubstitutionMatrix subsMatrix, int gapPenalty)

Uses of Alphabet in com.milaboratory.core.alignment.benchmark

Methods in com.milaboratory.core.alignment.benchmark with parameters of type Alphabet

Modifier and Type	Method and Description
static <S extends Sequence<S>> S	ChallengeProvider.randomSequence(Alphabet<S> alphabet, org.apache.commons.math3.random.RandomDataGenerator r, int minLength, int maxLength, boolean basicLettersOnly)
static <S extends Sequence<S>> S	ChallengeProvider.randomSequence(Alphabet<S> alphabet, org.apache.commons.math3.random.RandomGenerator r, int minLength, int maxLength, boolean basicLettersOnly)

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

Methods in com.milaboratory.core.alignment.blast that return Alphabet

Modifier and Type	Method and Description
Alphabet<S>	BlastDB.getAlphabet()

Methods in com.milaboratory.core.alignment.blast with parameters of type Alphabet

Modifier and Type	Method and Description
void	BlastAlignerParameters.chechAlphabet(Alphabet<?> alphabet)

Constructors in com.milaboratory.core.alignment.blast with parameters of type Alphabet

Constructor and Description
BlastDB(String name, String title, long recordsCount, long lettersCount, Alphabet<S> alphabet, List<String> volumes, boolean temp)

Uses of Alphabet in com.milaboratory.core.io.sequence.fasta

Methods in com.milaboratory.core.io.sequence.fasta that return Alphabet

Modifier and Type	Method and Description
Alphabet<S>	RandomAccessFastaReader.getAlphabet()

Constructors in com.milaboratory.core.io.sequence.fasta with parameters of type Alphabet

Constructor and Description
FastaReader(File file, Alphabet<S> alphabet) Creates FASTA reader for file
FastaReader(InputStream inputStream, Alphabet<S> alphabet) Creates reader for stream with unknown size.
FastaReader(InputStream inputStream, Alphabet<S> alphabet, long size) Creates reader from the specified input stream.
FastaReader(String file, Alphabet<S> alphabet) Creates FASTA reader for file
RandomAccessFastaReader(Path file, Alphabet<S> alphabet)
RandomAccessFastaReader(Path file, Alphabet<S> alphabet, boolean saveIndexFile)
RandomAccessFastaReader(Path file, RandomAccessFastaIndex index, Alphabet<S> alphabet)
RandomAccessFastaReader(SeekableByteChannel channel, RandomAccessFastaIndex index, Alphabet<S> alphabet, int bufferSize)
RandomAccessFastaReader(String file, Alphabet<S> alphabet)
RandomAccessFastaReader(String file, Alphabet<S> alphabet, boolean saveIndexFile)

Uses of Alphabet in com.milaboratory.core.motif

Constructors in com.milaboratory.core.motif with parameters of type Alphabet

Constructor and Description
MotifBuilder(Alphabet<S> alphabet, int size)

Uses of Alphabet in com.milaboratory.core.mutations

Methods in com.milaboratory.core.mutations that return Alphabet

Modifier and Type	Method and Description
Alphabet<S>	Mutations.getAlphabet()

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

Modifier and Type	Method and Description
static int[]	MutationsUtil.btopDecode(String alignment, Alphabet alphabet) Decodes btop-encoded mutations.
<S extends Sequence<S>> Mutations<S>	MutationsCounter.build(Alphabet<S> alphabet, MutationsCounter.Filter filter)
static int[]	MutationsUtil.decode(String mutations, Alphabet alphabet) Decodes mutations encoded using format described in Mutation.encode(int, com.milaboratory.core.sequence.Alphabet).
static <S extends Sequence<S>> Mutations<S>	Mutations.decode(String string, Alphabet<S> alphabet)
static <S extends Sequence<S>> Mutations<S>	Mutations.empty(Alphabet<S> alphabet)
static String	MutationsUtil.encode(int[] mutations, Alphabet alphabet) Encodes mutations in compact human-readable string, that can be decoded by method MutationsUtil.decode(String, com.milaboratory.core.sequence.Alphabet).
static String	MutationsUtil.encode(int[] mutations, Alphabet alphabet, String separator) Encodes mutations in compact human-readable string, that can be decoded by method MutationsUtil.decode(String, com.milaboratory.core.sequence.Alphabet).
static String	Mutation.encode(int mutation, Alphabet alphabet) Encodes single mutation in compact human-readable string, that can be decoded by method MutationsUtil.decode(String, com.milaboratory.core.sequence.Alphabet).
static String	MutationsUtil.encodeFixed(int[] mutations, Alphabet alphabet)
static String	Mutation.encodeFixed(int mutation, Alphabet alphabet)
static char	Mutation.getFromSymbol(int code, Alphabet alphabet)
static char	Mutation.getToSymbol(int code, Alphabet alphabet)
static String	Mutation.toString(Alphabet alphabet, int mutation)

Constructors in com.milaboratory.core.mutations with parameters of type Alphabet

Constructor and Description
Mutations(Alphabet<S> alphabet, int... mutations)
Mutations(Alphabet<S> alphabet, IntArrayList mutations)
Mutations(Alphabet<S> alphabet, String encodedMutations)
MutationsBuilder(Alphabet<S> alphabet)
MutationsBuilder(Alphabet<S> alphabet, boolean reversed)
MutationsBuilder(Alphabet<S> alphabet, boolean reversed, int[] mutations, int size)

Uses of Alphabet in com.milaboratory.core.mutations.generator

Constructors in com.milaboratory.core.mutations.generator with parameters of type Alphabet

Constructor and Description
SubstitutionModelBuilder(Alphabet alphabet)

Uses of Alphabet in com.milaboratory.core.sequence

Subclasses of Alphabet in com.milaboratory.core.sequence

Modifier and Type	Class and Description
class	AminoAcidAlphabet Amino acid alphabet with additional symbols.
class	NucleotideAlphabet An alphabet for nucleotide sequences.

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

Modifier and Type	Method and Description
Alphabet	Alphabets.Deserializer.deserialize(com.fasterxml.jackson.core.JsonParser jp, com.fasterxml.jackson.databind.DeserializationContext ctxt)
abstract Alphabet<S>	Sequence.getAlphabet() Returns the alphabet corresponding to this type of sequence.
static Alphabet	Alphabets.getByFirstLetterOfName(char letter) Searches for instance of Alphabet using first letter of it's name
static Alphabet	Alphabets.getById(byte id) Returns instance of Alphabet from its byte id.
static Alphabet	Alphabets.getByName(String name) Returns instance of Alphabet from its string name.
Alphabet	Alphabets.Deserializer.getEmptyValue(com.fasterxml.jackson.databind.DeserializationContext context)
Alphabet	Alphabets.Deserializer.getNullValue(com.fasterxml.jackson.databind.DeserializationContext context)

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

Modifier and Type	Method and Description
static Collection<Alphabet>	Alphabets.getAll() Returns unmodifiable collection of all registered alphabets.
static Set<Alphabet<?>>	SequencesUtils.possibleAlphabets(String string) Returns a set of possible alphabets for a given string.

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

Modifier and Type	Method and Description
static boolean	SequencesUtils.belongsToAlphabet(Alphabet<?> alphabet, String string) Check if a sequence contains letters only from specified alphabet.
static void	Alphabets.register(Alphabet alphabet) Register new alphabet
void	Alphabets.Serializer.serialize(Alphabet value, com.fasterxml.jackson.core.JsonGenerator jgen, com.fasterxml.jackson.databind.SerializerProvider provider)

Uses of Alphabet in com.milaboratory.core.sequence.provider

Constructors in com.milaboratory.core.sequence.provider with parameters of type Alphabet

Constructor and Description
CachedSequenceProvider(Alphabet<S> alphabet) Cached sequence provider without underlying sequence provider, with automatically inferred provider size.
CachedSequenceProvider(Alphabet<S> alphabet, int size) Cached sequence provider without underlying sequence provider, with fixed provider size.
CachedSequenceProvider(Alphabet<S> alphabet, int size, String missingErrorMessage) Cached sequence provider without underlying sequence provider, with fixed provider size.
CachedSequenceProvider(Alphabet<S> alphabet, SequenceProvider<S> provider) Cached sequence provider wrapping specified sequence provider.
CachedSequenceProvider(Alphabet<S> alphabet, String missingErrorMessage) Cached sequence provider without underlying sequence provider, with automatically inferred provider size.

Uses of Alphabet in com.milaboratory.core.tree

Fields in com.milaboratory.core.tree declared as Alphabet

Modifier and Type	Field and Description
Alphabet<S>	SequenceTreeMap.alphabet

Constructors in com.milaboratory.core.tree with parameters of type Alphabet

Constructor and Description
SequenceTreeMap(Alphabet<S> alphabet) Creates a tree map for specified Alphabet.