org.biojava3.core.sequence.transcription
Class TranscriptionEngine.Builder
java.lang.Object
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
.
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
TranscriptionEngine.Builder
public TranscriptionEngine.Builder()
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.IUPACTable
s by ID.
table
public TranscriptionEngine.Builder table(String name)
- Uses the static instance of
IUPACParser
to find instances of
IUPACParser.IUPACTable
s 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.