Uses of Interface
com.hfg.bio.seq.BioSequence

Packages that use BioSequence

Package	Description
com.hfg.bio
com.hfg.bio.phylogeny
com.hfg.bio.seq
com.hfg.bio.seq.alignment
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.genomic
com.hfg.bio.seq.pattern

Uses of BioSequence in com.hfg.bio

Classes in com.hfg.bio that implement BioSequence

Modifier and Type	Class and Description
class	DigestFragment Product of a proteolytic digest.

Uses of BioSequence in com.hfg.bio.phylogeny

Methods in com.hfg.bio.phylogeny with parameters of type BioSequence

Modifier and Type	Method and Description
float	DistanceMatrixModel.calculateDistance(BioSequence inSeq1, BioSequence inSeq2)
float	JukesCantorModel.calculateDistance(BioSequence inSeq1, BioSequence inSeq2) Calculates the Jukes-Cantor distance score for a pair of sequences.
float	UncorrectedModel.calculateDistance(BioSequence inSeq1, BioSequence inSeq2) Calculates the distance score for a pair of sequences.

Uses of BioSequence in com.hfg.bio.seq

Classes in com.hfg.bio.seq with type parameters of type BioSequence

Modifier and Type	Interface and Description
interface	BioSequenceFactory<T extends BioSequence>
class	PositionalFrequencyMatrix<T extends BioSequence> Positional frequency matrix.

Subinterfaces of BioSequence in com.hfg.bio.seq

Modifier and Type	Interface and Description
interface	BioSequencePlus Interface for an exetended biological protein, DNA, or RNA sequence with support for features, citations, db xrefs, etc.

Classes in com.hfg.bio.seq that implement BioSequence

Modifier and Type	Class and Description
class	BioSequenceImpl Biological Protein, DNA, or RNA sequence.
class	BioSequencePlusImpl Exetended biological protein, DNA, or RNA sequence with support for features, citations, db xrefs, etc.
class	NucleicAcid Biological DNA or RNA sequence.
class	Protein Biological protein sequence.

Methods in com.hfg.bio.seq with type parameters of type BioSequence

Modifier and Type	Method and Description
static <T extends BioSequence> Collection<T>	SeqUtil.unique(Collection<T> inSequences) Retains only a single copy of each distinct sequence.

Methods in com.hfg.bio.seq that return BioSequence

Modifier and Type	Method and Description
BioSequence	BioSequencePlus.addDbXref(DbXref inValue)
BioSequence	BioSequencePlus.addFeature(SeqFeature inValue)
BioSequence	BioSequencePlus.addKeyword(String inValue)
BioSequence	BioSequencePlus.addKeywords(Collection<String> inValues)
BioSequence	BioSequencePlus.addKeywords(String[] inValues)
BioSequence	BioSequencePlus.addReference(SeqCitation inValue)
BioSequence	BioSequence.clone()
static BioSequence	BioSequence.instantiate(XMLNode inXMLNode)
BioSequence	BioSequenceImpl.setCompressionThreshold(int inNumBytes)
BioSequence	BioSequence.setDescription(CharSequence inValue)
BioSequence	BioSequenceImpl.setDescription(CharSequence inValue)
BioSequence	BioSequence.setID(String inValue) Sets the id or name for the sequence.
BioSequence	BioSequenceImpl.setID(String inValue)
BioSequence	BioSequence.setSequence(CharSequence inValue)
BioSequence	BioSequenceImpl.setSequence(CharSequence inValue)
BioSequence	BioSequence.setSequence(Reader inReader)
BioSequence	BioSequenceImpl.setSequence(Reader inReader)

Uses of BioSequence in com.hfg.bio.seq.alignment

Classes in com.hfg.bio.seq.alignment with type parameters of type BioSequence

Modifier and Type	Class and Description
class	MultipleSequenceAligner<T extends BioSequence> A basic multiple sequence aligner that uses an initial 3-mer analysis to produce a draft guide tree and then performs progressive pairwise alignments.
class	MultipleSequenceAlignment<T extends BioSequence> Container for aligned sequences.

Methods in com.hfg.bio.seq.alignment that return BioSequence

Modifier and Type	Method and Description
BioSequence	AlignedSeq.getSeq()

Methods in com.hfg.bio.seq.alignment with parameters of type BioSequence

Modifier and Type	Method and Description
List<PairwiseSeqAlignment>	PairwiseSeqAligner.align(BioSequence inQuery, PSSM inSubject)
void	KMerBitSet.fill(BioSequence inSequence)
AlignedSeq	AlignedSeq.setSeq(BioSequence inValue)
String	PairwiseSeqAligner.showScoring(BioSequence inQuery, PSSM inSubject)

Method parameters in com.hfg.bio.seq.alignment with type arguments of type BioSequence

Modifier and Type	Method and Description
DistanceMatrix	KMerSimilarity.generateKMerDistanceMatrix(List<? extends BioSequence> inSequences, int inKMerSize)
String	PairwiseSeqAligner.showScoring(Collection<? extends BioSequence> inQueries, PSSM inSubject)

Constructors in com.hfg.bio.seq.alignment with parameters of type BioSequence

Constructor and Description
AlignedQuery(BioSequence inSeq, CharSequence inAlignedSeq, int inStart)
AlignedSeq(BioSequence inSeq, CharSequence inAlignedSeq, int inStart)
AlignedSubject(BioSequence inSeq, CharSequence inAlignedSeq, int inStart)

Uses of BioSequence in com.hfg.bio.seq.alignment.blast

Methods in com.hfg.bio.seq.alignment.blast with parameters of type BioSequence

Modifier and Type	Method and Description
BLAST_Output	BLAST.run(BioSequence inQuery)

Uses of BioSequence in com.hfg.bio.seq.alignment.matrix

Method parameters in com.hfg.bio.seq.alignment.matrix with type arguments of type BioSequence

Modifier and Type	Method and Description
String	PSSM.showScoring(Collection<BioSequence> inSeqs)

Uses of BioSequence in com.hfg.bio.seq.alignment.muscle

Method parameters in com.hfg.bio.seq.alignment.muscle with type arguments of type BioSequence

Modifier and Type	Method and Description
MuscleOutput	Muscle.run(List<? extends BioSequence> inQueries)

Uses of BioSequence in com.hfg.bio.seq.format

Classes in com.hfg.bio.seq.format with type parameters of type BioSequence

Modifier and Type	Class and Description
class	BufferedSeqReader<T extends BioSequence> Buffered sequence reader.
class	EMBL<T extends BioSequence> EMBL sequence format.
class	FASTA<T extends BioSequence> FASTA sequence format.
class	GenBank<T extends BioSequence> GenBank sequence format.
interface	ReadableSeqFormat<T extends BioSequence> Interface for readable sequence formats.
class	ReadableSeqFormatBase<T extends BioSequence> Base class for readable sequence formats.
class	WIPO_ST_25<T extends BioSequence> Sequence format based on WIPO Standard ST.25.
interface	WritableSeqFormat<T extends BioSequence> Interface for writable sequence formats.

Methods in com.hfg.bio.seq.format with type parameters of type BioSequence

Modifier and Type	Method and Description
static <T extends BioSequence> ReadableSeqFormat<T>	BufferedSeqReader.determineSeqFormat(BufferedReader inReader, Collection<ReadableSeqFormat<T>> inSeqFormatObjects)

Uses of BioSequence in com.hfg.bio.seq.genomic

Classes in com.hfg.bio.seq.genomic that implement BioSequence

Modifier and Type	Class and Description
class	Intron An intron in a gene.

Uses of BioSequence in com.hfg.bio.seq.pattern

Classes in com.hfg.bio.seq.pattern with type parameters of type BioSequence

Modifier and Type	Class and Description
class	SeqPattern<S extends BioSequence,T extends SeqPatternMatch> Abstract container for a sequence pattern (motif).
interface	SeqPatternMatcher<S extends BioSequence,T extends SeqPatternMatch>