Uses of Class
org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

Packages that use TranscriptionEngine.Builder

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

Uses of TranscriptionEngine.Builder in org.biojava.nbio.core.sequence.transcription

Methods in org.biojava.nbio.core.sequence.transcription that return TranscriptionEngine.Builder

Modifier and Type	Method and Description
TranscriptionEngine.Builder	TranscriptionEngine.Builder.aminoAcidsCompounds(CompoundSet<AminoAcidCompound> compounds)
TranscriptionEngine.Builder	TranscriptionEngine.Builder.decorateRna(boolean decorateRna) Performs an optimisation where RNASequences are not translated into their own objects but are views onto the base DNA sequence.
TranscriptionEngine.Builder	TranscriptionEngine.Builder.dnaCompounds(CompoundSet<NucleotideCompound> compounds)
TranscriptionEngine.Builder	TranscriptionEngine.Builder.dnaRnaTranslator(DNAToRNATranslator translator)
TranscriptionEngine.Builder	TranscriptionEngine.Builder.initMet(boolean initMet)
TranscriptionEngine.Builder	TranscriptionEngine.Builder.proteinCreator(SequenceCreatorInterface<AminoAcidCompound> creator)
TranscriptionEngine.Builder	TranscriptionEngine.Builder.rnaAminoAcidTranslator(RNAToAminoAcidTranslator translator)
TranscriptionEngine.Builder	TranscriptionEngine.Builder.rnaCompounds(CompoundSet<NucleotideCompound> compounds)
TranscriptionEngine.Builder	TranscriptionEngine.Builder.rnaCreator(SequenceCreatorInterface<NucleotideCompound> creator)
TranscriptionEngine.Builder	TranscriptionEngine.Builder.stopAtStopCodons(boolean stopAtStopCodons) If set, then the last codon translated in the resulting peptide sequence will be the stop codon
TranscriptionEngine.Builder	TranscriptionEngine.Builder.table(Integer id) Uses the static instance of IUPACParser to find instances of IUPACParser.IUPACTables by ID.
TranscriptionEngine.Builder	TranscriptionEngine.Builder.table(String name) Uses the static instance of IUPACParser to find instances of IUPACParser.IUPACTables by its String name
TranscriptionEngine.Builder	TranscriptionEngine.Builder.table(Table table)
TranscriptionEngine.Builder	TranscriptionEngine.Builder.translateNCodons(boolean translateNCodons)
TranscriptionEngine.Builder	TranscriptionEngine.Builder.trimStop(boolean trimStop)
TranscriptionEngine.Builder	TranscriptionEngine.Builder.waitForStartCodon(boolean waitForStartCodon) If set, then translation will not start until a start codon is encountered