Class TranscriptionEngine.Builder

Method Details

• build

  public TranscriptionEngine build()

  The method to finish any calls to the builder with which returns a transcription engine. The engine is designed to provide everything required for transcription to those classes which will do the transcription.

• table

  public TranscriptionEngine.Builder table(Integer id)

  Uses the static instance of IUPACParser to find instances of IUPACParser.IUPACTables by ID.

• table

  public TranscriptionEngine.Builder table(String name)

  Uses the static instance of IUPACParser to find instances of IUPACParser.IUPACTables by its String name

• table

  public TranscriptionEngine.Builder table(Table table)

• dnaCompounds

  public TranscriptionEngine.Builder dnaCompounds(CompoundSet<NucleotideCompound> compounds)

• rnaCompounds

  public TranscriptionEngine.Builder rnaCompounds(CompoundSet<NucleotideCompound> compounds)

• aminoAcidsCompounds

  public TranscriptionEngine.Builder aminoAcidsCompounds(CompoundSet<AminoAcidCompound> compounds)

• dnaRnaTranslator

  public TranscriptionEngine.Builder dnaRnaTranslator(DNAToRNATranslator translator)

• rnaAminoAcidTranslator

  public TranscriptionEngine.Builder rnaAminoAcidTranslator(RNAToAminoAcidTranslator translator)

• proteinCreator

  public TranscriptionEngine.Builder proteinCreator(SequenceCreatorInterface<AminoAcidCompound> creator)

• rnaCreator

  public TranscriptionEngine.Builder rnaCreator(SequenceCreatorInterface<NucleotideCompound> creator)

• initMet

  public TranscriptionEngine.Builder initMet(boolean initMet)

• trimStop

  public TranscriptionEngine.Builder trimStop(boolean trimStop)

• translateNCodons

  public TranscriptionEngine.Builder translateNCodons(boolean translateNCodons)

• stopAtStopCodons

  public TranscriptionEngine.Builder stopAtStopCodons(boolean stopAtStopCodons)

  If set, then the last codon translated in the resulting peptide sequence will be the stop codon

• waitForStartCodon

  public TranscriptionEngine.Builder waitForStartCodon(boolean waitForStartCodon)

  If set, then translation will not start until a start codon is encountered

• decorateRna

  public 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.