Uses of Interface
org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface

Packages that use SequenceCreatorInterface

Package	Description
org.biojava.nbio.core.sequence.io
org.biojava.nbio.core.sequence.template
org.biojava.nbio.core.sequence.transcription

Uses of SequenceCreatorInterface in org.biojava.nbio.core.sequence.io

Classes in org.biojava.nbio.core.sequence.io that implement SequenceCreatorInterface

Modifier and Type	Class	Description
class	CasePreservingProteinSequenceCreator	A sequence creator which preserves the case of its input string in the user collection of the returned ProteinSequence.
class	DNASequenceCreator	A helper class that allows different ways to read a string and create a DNA sequence.
class	FileProxyDNASequenceCreator	This class is a good example of using the SequenceCreatorInterface where during parsing of the stream the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily.
class	FileProxyProteinSequenceCreator	This class is a good example of using the SequenceCreatorInterface where during parsing of the stream the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily.
class	FileProxyRNASequenceCreator	This class is a good example of using the SequenceCreatorInterface where during parsing of the stream the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily.
class	ProteinSequenceCreator	Used to create a ProteinSequence from a String to allow for details about the location of the sequence etc.
class	RNASequenceCreator	Used to create a RNA sequence

Constructors in org.biojava.nbio.core.sequence.io with parameters of type SequenceCreatorInterface

Constructor	Description
FastaReader(File file, SequenceHeaderParserInterface<S,C> headerParser, SequenceCreatorInterface<C> sequenceCreator)	If you are going to use the FileProxyProteinSequenceCreator then you need to use this constructor because we need details about the location of the file.
FastaReader(InputStream is, SequenceHeaderParserInterface<S,C> headerParser, SequenceCreatorInterface<C> sequenceCreator)	If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about local file offsets for quick reads.
GenbankReader(File file, SequenceHeaderParserInterface<S,C> headerParser, SequenceCreatorInterface<C> sequenceCreator)	If you are going to use the FileProxyProteinSequenceCreator then you need to use this constructor because we need details about the location of the file.
GenbankReader(InputStream is, SequenceHeaderParserInterface<S,C> headerParser, SequenceCreatorInterface<C> sequenceCreator)	If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about local file offsets for quick reads.

Uses of SequenceCreatorInterface in org.biojava.nbio.core.sequence.template

Methods in org.biojava.nbio.core.sequence.template that return SequenceCreatorInterface

Modifier and Type	Method	Description
SequenceCreatorInterface<T>	AbstractCompoundTranslator.getCreator()

Constructors in org.biojava.nbio.core.sequence.template with parameters of type SequenceCreatorInterface

Constructor	Description
AbstractCompoundTranslator(SequenceCreatorInterface<T> creator, CompoundSet<F> fromCompoundSet, CompoundSet<T> toCompoundSet)

Uses of SequenceCreatorInterface in org.biojava.nbio.core.sequence.transcription

Methods in org.biojava.nbio.core.sequence.transcription that return SequenceCreatorInterface

Modifier and Type	Method	Description
SequenceCreatorInterface<AminoAcidCompound>	TranscriptionEngine.getProteinSequenceCreator()
SequenceCreatorInterface<NucleotideCompound>	TranscriptionEngine.getRnaSequenceCreator()

Methods in org.biojava.nbio.core.sequence.transcription with parameters of type SequenceCreatorInterface

Modifier and Type	Method	Description
TranscriptionEngine.Builder	TranscriptionEngine.Builder.proteinCreator(SequenceCreatorInterface<AminoAcidCompound> creator)
TranscriptionEngine.Builder	TranscriptionEngine.Builder.rnaCreator(SequenceCreatorInterface<NucleotideCompound> creator)

Constructors in org.biojava.nbio.core.sequence.transcription with parameters of type SequenceCreatorInterface

Constructor	Description
DNAToRNATranslator(SequenceCreatorInterface<NucleotideCompound> rnaCreator, CompoundSet<NucleotideCompound> dna, CompoundSet<NucleotideCompound> rna, boolean shortCutTranslation)
RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound> creator, CompoundSet<NucleotideCompound> nucleotides, CompoundSet<Table.Codon> codons, CompoundSet<AminoAcidCompound> aminoAcids, Table table, boolean trimStops, boolean initMetOnly, boolean translateNCodons, boolean stopAtStopCodons, boolean waitForStartCodon)