Uses of Interface
org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface
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Packages that use SequenceCreatorInterface Package Description org.biojava.nbio.core.sequence.io org.biojava.nbio.core.sequence.template org.biojava.nbio.core.sequence.transcription org.biojava.nbio.structure.io Input and Output of Structures -
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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 sequenceConstructors 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 useFileProxyProteinSequenceCreator
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)
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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)
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Uses of SequenceCreatorInterface in org.biojava.nbio.structure.io
Constructors in org.biojava.nbio.structure.io with parameters of type SequenceCreatorInterface Constructor Description FastaStructureParser(File file, SequenceHeaderParserInterface<ProteinSequence,AminoAcidCompound> headerParser, SequenceCreatorInterface<AminoAcidCompound> sequenceCreator, AtomCache cache)
FastaStructureParser(InputStream is, SequenceHeaderParserInterface<ProteinSequence,AminoAcidCompound> headerParser, SequenceCreatorInterface<AminoAcidCompound> sequenceCreator, AtomCache cache)
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