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

Class TranscriptionEngine.Builder

java.lang.Object

org.biojava.nbio.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

Constructors

Constructor	Description
Builder()

Method Summary

Modifier and Type	Method	Description
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	stopAtStopCodons(boolean stopAtStopCodons)	If set, then the last codon translated in the resulting peptide sequence will be the stop codon
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)
TranscriptionEngine.Builder	waitForStartCodon(boolean waitForStartCodon)	If set, then translation will not start until a start codon is encountered

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Builder

public 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)

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.