Package com.milaboratory.core.sequence

Interface Summary

Interface	Description
MultiNSequenceWithQuality
NSeq<S extends NSeq<S>>
Seq<S extends Seq<S>>	Common interface for all objects representing sequence-like objects like (parent of all subtypes of Sequence; SequenceQuality; SequenceWithQuality)
SeqBuilder<S extends Seq<S>>	Interface for classes that build seq objects.
SequenceBuilder<S extends Sequence<S>>	Interface for factory class for a certain type of sequence.

Class Summary

Class	Description
AbstractSeq<S extends AbstractSeq<S>>
Alphabet<S extends Sequence<S>>	Interface for sequence letters alphabet (amino acid, nucleotide, etc.).
Alphabet.AlphabetSerialization
Alphabets	Registry of all alphabets.
Alphabets.Deserializer
Alphabets.Serializer
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<S extends AbstractSeq<S>,B extends ArraySeqBuilder<S,B>>
GeneticCode	Defines standard genetic code.
MultiNSequenceWithQualityImpl
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.
Sequence<S extends Sequence<S>>	Parent class for all types of sequences.
SequenceQuality	Representation of nucleotide sequence quality based on phred quality scores.
SequenceQualityBuilder	Created by poslavsky on 09/07/14.
SequencesUtils	Utility methods for sequences.
SequenceWithQuality<S extends Sequence<S>>	A container of sequence and its quality.
TranslationParameters
UnsafeFactory	Don't use this class.
Wildcard	Representation of a wildcard symbol.