Uses of Class
org.episteme.natural.biology.genetics.BioSequence

Packages that use BioSequence

Package	Description
org.episteme.natural.biology
org.episteme.natural.biology.genetics	Biological modeling, genetics, and life science simulations.
org.episteme.natural.biology.loaders

Uses of BioSequence in org.episteme.natural.biology

Methods in org.episteme.natural.biology that return BioSequence

Modifier and Type	Method	Description
BioSequence	Virus.getGenome()

Constructors in org.episteme.natural.biology with parameters of type BioSequence

Modifier	Constructor	Description
	Virus(String name, String family, VirusGenomeType genomeType, VirusMorphology morphology, BioSequence genome, double capsidDiameterNm)
	Virus(String name, String family, VirusGenomeType genomeType, VirusMorphology morphology, BioSequence genome, Quantity<Length> capsidDiameter)

Uses of BioSequence in org.episteme.natural.biology.genetics

Methods in org.episteme.natural.biology.genetics that return BioSequence

Modifier and Type	Method	Description
BioSequence	BioSequence.complement()	Returns the complement sequence (DNA only). 5'-ATGC-3' -> 5'-TACG-3' (Note: usually reverse complement is more useful)
BioSequence	BioSequence.reverseComplement()	Returns the reverse complement sequence. 5'-ATGC-3' -> 5'-GCAT-3'
BioSequence	BioSequence.reverseTranscribe()	Reverse transcribes RNA to DNA.
BioSequence	BioSequence.transcribe()	Transcribes DNA to RNA.
BioSequence	BioSequence.translate()	Translates RNA/DNA to Protein.

Uses of BioSequence in org.episteme.natural.biology.loaders

Subclasses with type arguments of type BioSequence in org.episteme.natural.biology.loaders

Modifier and Type	Class	Description
class	FASTABioSequenceReader	Parser for FASTA format files.
class	FASTQReader	Parser for FASTQ format files (includes quality scores).

Methods in org.episteme.natural.biology.loaders that return types with arguments of type BioSequence

Modifier and Type	Method	Description
Class<List<BioSequence>>	FASTABioSequenceReader.getResourceType()
Class<List<BioSequence>>	FASTQReader.getResourceType()
protected List<BioSequence>	FASTABioSequenceReader.loadFromSource(String resourceId)
protected List<BioSequence>	FASTQReader.loadFromSource(String resourceId)
List<BioSequence>	FASTABioSequenceReader.parse(InputStream inputStream)	Parses a FASTA input stream.
List<BioSequence>	FASTQReader.parse(InputStream inputStream)	Parses a FASTQ input stream.