performs an optimisation where rnasequences are not translated into their own objects but are views onto the base dna sequence . concode_field_sep RNAToAminoAcidTranslator rnaAminoAcidTranslator concode_elem_sep boolean decorateRna concode_elem_sep DNAToRNATranslator dnaRnaTranslator concode_elem_sep SequenceCreatorInterface<AminoAcidCompound> proteinSequenceCreator concode_elem_sep SequenceCreatorInterface<NucleotideCompound> rnaSequenceCreator concode_elem_sep boolean initMet concode_elem_sep TranscriptionEngine INSTANCE concode_elem_sep boolean trimStop concode_elem_sep boolean waitForStartCodon concode_elem_sep CompoundSet<NucleotideCompound> dnaCompounds concode_elem_sep CompoundSet<AminoAcidCompound> aminoAcidCompounds concode_elem_sep boolean translateNCodons concode_elem_sep CompoundSet<NucleotideCompound> rnaCompounds concode_elem_sep boolean stopAtStopCodons concode_elem_sep Table table concode_field_sep Builder translateNCodons concode_elem_sep RNAToAminoAcidTranslator getRnaAminoAcidTranslator concode_elem_sep RNAToAminoAcidTranslator getRnaAminoAcidTranslator concode_elem_sep SequenceCreatorInterface<NucleotideCompound> getRnaCreator concode_elem_sep Builder aminoAcidsCompounds concode_elem_sep Map<Frame,Sequence<AminoAcidCompound>> multipleFrameTranslation concode_elem_sep Builder initMet concode_elem_sep Sequence<AminoAcidCompound> translate concode_elem_sep Builder dnaCompounds concode_elem_sep CompoundSet<NucleotideCompound> getRnaCompounds concode_elem_sep CompoundSet<NucleotideCompound> getRnaCompounds concode_elem_sep boolean isTrimStop concode_elem_sep Builder table concode_elem_sep Builder table concode_elem_sep Builder table concode_elem_sep Builder decorateRna concode_elem_sep CompoundSet<Codon> getCodons concode_elem_sep SequenceCreatorInterface<NucleotideCompound> getRnaSequenceCreator concode_elem_sep Builder rnaAminoAcidTranslator concode_elem_sep Builder waitForStartCodon concode_elem_sep SequenceCreatorInterface<AminoAcidCompound> getProteinSequenceCreator concode_elem_sep boolean isWaitForStartCodon concode_elem_sep Builder dnaRnaTranslator concode_elem_sep Builder trimStop concode_elem_sep Builder stopAtStopCodons concode_elem_sep TranscriptionEngine getDefault concode_elem_sep SequenceCreatorInterface<AminoAcidCompound> getProteinCreator concode_elem_sep boolean isTranslateNCodons concode_elem_sep boolean isInitMet concode_elem_sep Builder rnaCreator concode_elem_sep CompoundSet<NucleotideCompound> getDnaCompounds concode_elem_sep CompoundSet<NucleotideCompound> getDnaCompounds concode_elem_sep Table getTable concode_elem_sep Table getTable concode_elem_sep CompoundSet<AminoAcidCompound> getAminoAcidCompounds concode_elem_sep CompoundSet<AminoAcidCompound> getAminoAcidCompounds concode_elem_sep TranscriptionEngine build concode_elem_sep Builder proteinCreator concode_elem_sep boolean isDecorateRna concode_elem_sep DNAToRNATranslator getDnaRnaTranslator concode_elem_sep DNAToRNATranslator getDnaRnaTranslator concode_elem_sep Builder rnaCompounds concode_elem_sep boolean isStopAtStopCodons
Builder function ( boolean arg0 ) { this . decorateRna = arg0 ; return this ; }