org.biojava3.core.sequence.transcription
Class TranscriptionEngine.Builder

java.lang.Object
  extended by org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder
Enclosing class:
TranscriptionEngine

public static class TranscriptionEngine.Builder
extends Object

This class is the way to create a TranslationEngine.


Constructor Summary
TranscriptionEngine.Builder()
           
 
Method Summary
 TranscriptionEngine.Builder aminoAcidsCompounds(CompoundSet<AminoAcidCompound> compounds)
           
 TranscriptionEngine build()
          The method to finish any calls to the builder with which returns a transcription engine.
 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 dnaCompounds(CompoundSet<NucleotideCompound> compounds)
           
 TranscriptionEngine.Builder dnaRnaTranslator(DNAToRNATranslator translator)
           
 TranscriptionEngine.Builder initMet(boolean initMet)
           
 TranscriptionEngine.Builder proteinCreator(SequenceCreatorInterface<AminoAcidCompound> creator)
           
 TranscriptionEngine.Builder rnaAminoAcidTranslator(RNAToAminoAcidTranslator translator)
           
 TranscriptionEngine.Builder rnaCompounds(CompoundSet<NucleotideCompound> compounds)
           
 TranscriptionEngine.Builder rnaCreator(SequenceCreatorInterface<NucleotideCompound> creator)
           
 TranscriptionEngine.Builder table(Integer id)
          Uses the static instance of IUPACParser to find instances of IUPACParser.IUPACTables by ID.
 TranscriptionEngine.Builder table(String name)
          Uses the static instance of IUPACParser to find instances of IUPACParser.IUPACTables by its String name
 TranscriptionEngine.Builder table(Table table)
           
 TranscriptionEngine.Builder translateNCodons(boolean translateNCodons)
           
 TranscriptionEngine.Builder trimStop(boolean trimStop)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

TranscriptionEngine.Builder

public TranscriptionEngine.Builder()
Method Detail

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)

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.