Uses of Class
com.hfg.bio.seq.NucleicAcid

Packages that use NucleicAcid

Package	Description
com.hfg.bio.seq
com.hfg.bio.seq.alignment
com.hfg.bio.seq.alignment.assembler
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.translation

Uses of NucleicAcid in com.hfg.bio.seq

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

Modifier and Type	Method and Description
NucleicAcid	NucleicAcid.clone()
NucleicAcid	NucleicAcidFactory.createSeqObj()
NucleicAcid	NucleicAcid.setDescription(CharSequence inValue)
NucleicAcid	NucleicAcid.setID(String inValue)
NucleicAcid	NucleicAcid.setNCBITaxon(NCBITaxon inValue)
NucleicAcid	NucleicAcid.setSeqQualityScores(SeqQualityScores inValue)
NucleicAcid	NucleicAcid.setSequence(CharSequence inValue)
NucleicAcid	NucleicAcidTrimmer.trim(NucleicAcid inSeq)

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

Modifier and Type	Method and Description
SeqLocation	NucleicAcidTrimmer.calculateTrimRange(NucleicAcid inSeq)
NucleicAcid	NucleicAcidTrimmer.trim(NucleicAcid inSeq)

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

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

Modifier and Type	Method and Description
List<PairwiseSeqAlignment>	PairwiseSeqAligner.align(NucleicAcid inQuery, NucleicAcid inSubject)

Uses of NucleicAcid in com.hfg.bio.seq.alignment.assembler

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

Modifier and Type	Method and Description
ContigAssemblerResults	ContigAssembler.assemble(Collection<NucleicAcid> inReads)

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

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

Modifier and Type	Class and Description
class	FASTQ<T extends NucleicAcid> FASTQ sequence format encompassing sequences and their per-base sequencing quality scores.
class	IlluminaFASTQ<T extends NucleicAcid> FASTQ sequence format from Illumina.

Uses of NucleicAcid in com.hfg.bio.seq.format.abi

Methods in com.hfg.bio.seq.format.abi that return NucleicAcid

Modifier and Type	Method and Description
NucleicAcid	ABIF.toNucleicAcid()

Uses of NucleicAcid in com.hfg.bio.seq.format.feature.genbank

Methods in com.hfg.bio.seq.format.feature.genbank with parameters of type NucleicAcid

Modifier and Type	Method and Description
String	GenBankFeatureLocation.eval(NucleicAcid inNucleicAcid)

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

Subclasses of NucleicAcid in com.hfg.bio.seq.genomic

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

Uses of NucleicAcid in com.hfg.bio.seq.translation

Methods in com.hfg.bio.seq.translation with parameters of type NucleicAcid

Modifier and Type	Method and Description
Protein	NucleicAcidTranslator.translate(NucleicAcid inSeq, TranslationFrame inFrame)