Uses of Package
com.milaboratory.core.sequence

Packages that use com.milaboratory.core.sequence

Package	Description
com.milaboratory.core
com.milaboratory.core.alignment
com.milaboratory.core.alignment.batch
com.milaboratory.core.alignment.benchmark
com.milaboratory.core.alignment.blast
com.milaboratory.core.alignment.kaligner1
com.milaboratory.core.alignment.kaligner2
com.milaboratory.core.clustering
com.milaboratory.core.io.sequence
com.milaboratory.core.io.sequence.fasta
com.milaboratory.core.merger
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.sequence.quality
com.milaboratory.core.tree
com.milaboratory.util

Classes in com.milaboratory.core.sequence used by com.milaboratory.core

Class and Description
NSequenceWithQuality Container of nucleotide sequence with its quality.

Classes in com.milaboratory.core.sequence used by com.milaboratory.core.alignment

Class and Description
Alphabet Interface for sequence letters alphabet (amino acid, nucleotide, etc.).
AminoAcidSequence Representation of amino acid sequences.
NucleotideSequence Representation of nucleotide sequence.
Sequence Parent class for all types of sequences.
SequenceQuality Representation of nucleotide sequence quality based on phred quality scores.

Classes in com.milaboratory.core.sequence used by com.milaboratory.core.alignment.batch

Class and Description
NucleotideSequence Representation of nucleotide sequence.
Sequence Parent class for all types of sequences.

Classes in com.milaboratory.core.sequence used by com.milaboratory.core.alignment.benchmark

Class and Description
Alphabet Interface for sequence letters alphabet (amino acid, nucleotide, etc.).
NucleotideSequence Representation of nucleotide sequence.
Sequence Parent class for all types of sequences.

Classes in com.milaboratory.core.sequence used by com.milaboratory.core.alignment.blast

Class and Description
Alphabet Interface for sequence letters alphabet (amino acid, nucleotide, etc.).
AminoAcidSequence Representation of amino acid sequences.
NucleotideSequence Representation of nucleotide sequence.
Sequence Parent class for all types of sequences.

Classes in com.milaboratory.core.sequence used by com.milaboratory.core.alignment.kaligner1

Class and Description
NucleotideSequence Representation of nucleotide sequence.

Classes in com.milaboratory.core.sequence used by com.milaboratory.core.alignment.kaligner2

Class and Description
NucleotideSequence Representation of nucleotide sequence.

Classes in com.milaboratory.core.sequence used by com.milaboratory.core.clustering

Class and Description
Sequence Parent class for all types of sequences.

Classes in com.milaboratory.core.sequence used by com.milaboratory.core.io.sequence

Class and Description
NSequenceWithQuality Container of nucleotide sequence with its quality.

Classes in com.milaboratory.core.sequence used by com.milaboratory.core.io.sequence.fasta

Class and Description
Alphabet Interface for sequence letters alphabet (amino acid, nucleotide, etc.).
NucleotideSequence Representation of nucleotide sequence.
Sequence Parent class for all types of sequences.

Classes in com.milaboratory.core.sequence used by com.milaboratory.core.merger

Class and Description
NSequenceWithQuality Container of nucleotide sequence with its quality.

Classes in com.milaboratory.core.sequence used by com.milaboratory.core.motif

Class and Description
Alphabet Interface for sequence letters alphabet (amino acid, nucleotide, etc.).
Sequence Parent class for all types of sequences.

Classes in com.milaboratory.core.sequence used by com.milaboratory.core.mutations

Class and Description
Alphabet Interface for sequence letters alphabet (amino acid, nucleotide, etc.).
AminoAcidSequence Representation of amino acid sequences.
NSequenceWithQuality Container of nucleotide sequence with its quality.
NucleotideSequence Representation of nucleotide sequence.
Sequence Parent class for all types of sequences.
SequenceQuality Representation of nucleotide sequence quality based on phred quality scores.
TranslationParameters

Classes in com.milaboratory.core.sequence used by com.milaboratory.core.mutations.generator

Class and Description
Alphabet Interface for sequence letters alphabet (amino acid, nucleotide, etc.).
NucleotideSequence Representation of nucleotide sequence.
Sequence Parent class for all types of sequences.

Classes in com.milaboratory.core.sequence used by com.milaboratory.core.sequence

Class and Description
AbstractSeq
Alphabet Interface for sequence letters alphabet (amino acid, nucleotide, etc.).
AminoAcidAlphabet Amino acid alphabet with additional symbols.
AminoAcidSequence Representation of amino acid sequences.
AminoAcidSequence.AminoAcidSequencePosition This class represents mapping of nucleotide sequence position onto translated amino acid sequence.
ArraySeqBuilder
MultiNSequenceWithQuality
NSeq
NSequenceWithQuality Container of nucleotide sequence with its quality.
NSequenceWithQualityBuilder Created by poslavsky on 10/07/14.
NucleotideAlphabet An alphabet for nucleotide sequences.
NucleotideSequence Representation of nucleotide sequence.
Seq Common interface for all objects representing sequence-like objects like (parent of all subtypes of Sequence; SequenceQuality; SequenceWithQuality)
SeqBuilder Interface for classes that build seq objects.
Sequence Parent class for all types of sequences.
SequenceBuilder Interface for factory class for a certain type of sequence.
SequenceQuality Representation of nucleotide sequence quality based on phred quality scores.
SequenceQualityBuilder Created by poslavsky on 09/07/14.
SequenceWithQuality A container of sequence and its quality.
TranslationParameters
Wildcard Representation of a wildcard symbol.

Classes in com.milaboratory.core.sequence used by com.milaboratory.core.sequence.provider

Class and Description
Alphabet Interface for sequence letters alphabet (amino acid, nucleotide, etc.).
NucleotideSequence Representation of nucleotide sequence.
Sequence Parent class for all types of sequences.

Classes in com.milaboratory.core.sequence used by com.milaboratory.core.sequence.quality

Class and Description
SequenceQuality Representation of nucleotide sequence quality based on phred quality scores.

Classes in com.milaboratory.core.sequence used by com.milaboratory.core.tree

Class and Description
Alphabet Interface for sequence letters alphabet (amino acid, nucleotide, etc.).
Sequence Parent class for all types of sequences.

Classes in com.milaboratory.core.sequence used by com.milaboratory.util

Class and Description
NSequenceWithQuality Container of nucleotide sequence with its quality.