Package com.hfg.bio.seq

Interface Summary

Interface	Description
BioSequence	Interface for a biological Protein, DNA, or RNA sequence.
BioSequenceFactory<T extends BioSequence>
BioSequencePlus	Interface for an exetended biological protein, DNA, or RNA sequence with support for features, citations, db xrefs, etc.

Class Summary

Class	Description
AminoAcidComposition
BioSequenceImpl	Biological Protein, DNA, or RNA sequence.
BioSequencePlusImpl	Exetended biological protein, DNA, or RNA sequence with support for features, citations, db xrefs, etc.
Clone	Sequence clone name container.
Exon	An exon in a gene.
Gene	A gene representation.
GenomicLocation	Genomic location.
NucleicAcid	Biological DNA or RNA sequence.
NucleicAcidComplementFilterInputStream	Replaces nucleotides with their complementary nucleotide.
NucleicAcidFactory	Factory for creating NucleicAcid sequence objects.
NucleicAcidTrimmer	Nucleotide quality trimmer based on Phred's modified-Mott trimming algorithm.
PositionalFrequencyMatrix<T extends BioSequence>	Positional frequency matrix.
Protein	Biological protein sequence.
ProteinDigest	Performs a digestion of a protein via protease(s).
ProteinFactory	Factory for creating Protein sequence objects.
ProteinXLink	Biological protein sequence crosslink.
ProteinXLinkType	Biological protein sequence cross-link types.
SeqLocation	1-based biological sequence location object.
SeqMappingCoverage	Simple container for sequence mapping stats.
SeqQualityScores	Container for sequence quality scores.
SeqTopology	Enumeration of sequence topology types
SeqUtil	Utility class of generic sequence functions.

Enum Summary

Enum	Description
BioSequenceType	Enumeration of biological sequence types.
NucleotideEnd	Enumeration of nucleotide end (terminus) values.
PositionalFrequencyMatrix.Flag
ProteinXLinkChainLinkage	Enumeration of protein cross-link linkage types.
SeqQualityScoreScheme