Uses of Package
com.hfg.bio.seq

Packages that use com.hfg.bio.seq

Package	Description
com.hfg.bio
com.hfg.bio.molbio
com.hfg.bio.phylogeny
com.hfg.bio.proteinproperty	Classes for calculating physical properties of proteins.
com.hfg.bio.seq
com.hfg.bio.seq.alignment
com.hfg.bio.seq.alignment.assembler
com.hfg.bio.seq.alignment.blast
com.hfg.bio.seq.alignment.matrix
com.hfg.bio.seq.alignment.muscle
com.hfg.bio.seq.format
com.hfg.bio.seq.format.abi
com.hfg.bio.seq.format.feature.genbank
com.hfg.bio.seq.genomic
com.hfg.bio.seq.graphics
com.hfg.bio.seq.pattern
com.hfg.bio.seq.translation
com.hfg.graphics

Classes in com.hfg.bio.seq used by com.hfg.bio

Class and Description
BioSequence Interface for a biological Protein, DNA, or RNA sequence.
BioSequenceImpl Biological Protein, DNA, or RNA sequence.
BioSequencePlus Interface for an exetended biological protein, DNA, or RNA sequence with support for features, citations, db xrefs, etc.
BioSequencePlusImpl Exetended biological protein, DNA, or RNA sequence with support for features, citations, db xrefs, etc.
Protein Biological protein sequence.
SeqLocation 1-based biological sequence location object.

Classes in com.hfg.bio.seq used by com.hfg.bio.molbio

Class and Description
SeqLocation 1-based biological sequence location object.

Classes in com.hfg.bio.seq used by com.hfg.bio.phylogeny

Class and Description
BioSequence Interface for a biological Protein, DNA, or RNA sequence.

Classes in com.hfg.bio.seq used by com.hfg.bio.proteinproperty

Class and Description
Protein Biological protein sequence.

Classes in com.hfg.bio.seq used by com.hfg.bio.seq

Class and Description
AminoAcidComposition
BioSequence Interface for a biological Protein, DNA, or RNA sequence.
BioSequenceFactory
BioSequenceImpl Biological Protein, DNA, or RNA sequence.
BioSequencePlus Interface for an exetended biological protein, DNA, or RNA sequence with support for features, citations, db xrefs, etc.
BioSequencePlusImpl Exetended biological protein, DNA, or RNA sequence with support for features, citations, db xrefs, etc.
BioSequenceType Enumeration of biological sequence types.
Clone Sequence clone name container.
Exon An exon in a gene.
Gene A gene representation.
GenomicLocation Genomic location.
NucleicAcid Biological DNA or RNA sequence.
NucleicAcidFactory Factory for creating NucleicAcid sequence objects.
NucleicAcidTrimmer Nucleotide quality trimmer based on Phred's modified-Mott trimming algorithm.
NucleotideEnd Enumeration of nucleotide end (terminus) values.
PositionalFrequencyMatrix Positional frequency matrix.
PositionalFrequencyMatrix.Flag
Protein Biological protein sequence.
ProteinXLink Biological protein sequence crosslink.
ProteinXLinkChainLinkage Enumeration of protein cross-link linkage types.
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.
SeqQualityScoreScheme
SeqTopology Enumeration of sequence topology types

Classes in com.hfg.bio.seq used by com.hfg.bio.seq.alignment

Class and Description
BioSequence Interface for a biological Protein, DNA, or RNA sequence.
BioSequenceType Enumeration of biological sequence types.
NucleicAcid Biological DNA or RNA sequence.
PositionalFrequencyMatrix Positional frequency matrix.
PositionalFrequencyMatrix.Flag
Protein Biological protein sequence.
SeqLocation 1-based biological sequence location object.

Classes in com.hfg.bio.seq used by com.hfg.bio.seq.alignment.assembler

Class and Description
NucleicAcid Biological DNA or RNA sequence.

Classes in com.hfg.bio.seq used by com.hfg.bio.seq.alignment.blast

Class and Description
BioSequence Interface for a biological Protein, DNA, or RNA sequence.
BioSequenceType Enumeration of biological sequence types.

Classes in com.hfg.bio.seq used by com.hfg.bio.seq.alignment.matrix

Class and Description
BioSequence Interface for a biological Protein, DNA, or RNA sequence.

Classes in com.hfg.bio.seq used by com.hfg.bio.seq.alignment.muscle

Class and Description
BioSequence Interface for a biological Protein, DNA, or RNA sequence.

Classes in com.hfg.bio.seq used by com.hfg.bio.seq.format

Class and Description
BioSequence Interface for a biological Protein, DNA, or RNA sequence.
BioSequenceFactory
NucleicAcid Biological DNA or RNA sequence.
SeqLocation 1-based biological sequence location object.
SeqQualityScoreScheme

Classes in com.hfg.bio.seq used by com.hfg.bio.seq.format.abi

Class and Description
NucleicAcid Biological DNA or RNA sequence.

Classes in com.hfg.bio.seq used by com.hfg.bio.seq.format.feature.genbank

Class and Description
NucleicAcid Biological DNA or RNA sequence.
SeqLocation 1-based biological sequence location object.

Classes in com.hfg.bio.seq used by com.hfg.bio.seq.genomic

Class and Description
BioSequence Interface for a biological Protein, DNA, or RNA sequence.
BioSequenceImpl Biological Protein, DNA, or RNA sequence.
BioSequencePlus Interface for an exetended biological protein, DNA, or RNA sequence with support for features, citations, db xrefs, etc.
BioSequencePlusImpl Exetended biological protein, DNA, or RNA sequence with support for features, citations, db xrefs, etc.
GenomicLocation Genomic location.
NucleicAcid Biological DNA or RNA sequence.

Classes in com.hfg.bio.seq used by com.hfg.bio.seq.graphics

Class and Description
Gene A gene representation.

Classes in com.hfg.bio.seq used by com.hfg.bio.seq.pattern

Class and Description
BioSequence Interface for a biological Protein, DNA, or RNA sequence.
BioSequenceType Enumeration of biological sequence types.
Protein Biological protein sequence.
SeqLocation 1-based biological sequence location object.

Classes in com.hfg.bio.seq used by com.hfg.bio.seq.translation

Class and Description
NucleicAcid Biological DNA or RNA sequence.
Protein Biological protein sequence.
ProteinFactory Factory for creating Protein sequence objects.

Classes in com.hfg.bio.seq used by com.hfg.graphics

Class and Description
Exon An exon in a gene.
SeqMappingCoverage Simple container for sequence mapping stats.