org.biojava.nbio.core.sequence.transcription

Class DNAToRNATranslator

java.lang.Object

org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator<NucleotideCompound,NucleotideCompound>

org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator

All Implemented Interfaces:

CompoundTranslator<NucleotideCompound,NucleotideCompound>

public class DNAToRNATranslator
extends AbstractCompoundTranslator<NucleotideCompound,NucleotideCompound>

Performs the first stage of transcription by going from DNA to RNA. This class will first delegate to Frame in order to be in the correctly specified translation frame and then translates T to U. The other translation carried out is to convert an equivalent compound in DNA to RNA i.e. for the base A in DNA fetching the equivalent A base in the RNA CompoundSet.

Author:

ayates

Constructor Summary

Constructors

Constructor and Description
DNAToRNATranslator(SequenceCreatorInterface<NucleotideCompound> rnaCreator, CompoundSet<NucleotideCompound> dna, CompoundSet<NucleotideCompound> rna, boolean shortCutTranslation)

Method Summary

Modifier and Type	Method and Description
Sequence<NucleotideCompound>	createSequence(Sequence<NucleotideCompound> originalSequence)
Sequence<NucleotideCompound>	createSequence(Sequence<NucleotideCompound> originalSequence, Frame frame)
List<Sequence<NucleotideCompound>>	createSequences(Sequence<NucleotideCompound> originalSequence) Overloaded local version which delegates to an optional translator when told to (specified during construction).
protected void	postProcessCompoundLists(List<List<NucleotideCompound>> compoundLists)
protected RNASequence	wrapToRna(Sequence<NucleotideCompound> dna) Takes in the given DNA Sequence and returns an instance of RNASequence which is using RnaSequenceView as a ProxySequenceReader.

Methods inherited from class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator

addCompounds, addCompoundsToList, addCompoundToLists, addStrings, getCreator, getFromCompoundSet, getToCompoundSet, translate, translateMany, workingListToSequences

Methods inherited from class java.lang.Object

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

Constructor Detail

DNAToRNATranslator

public DNAToRNATranslator(SequenceCreatorInterface<NucleotideCompound> rnaCreator,
                          CompoundSet<NucleotideCompound> dna,
                          CompoundSet<NucleotideCompound> rna,
                          boolean shortCutTranslation)

Method Detail

createSequences

public List<Sequence<NucleotideCompound>> createSequences(Sequence<NucleotideCompound> originalSequence)

Overloaded local version which delegates to an optional translator when told to (specified during construction).

Specified by:

createSequences in interface CompoundTranslator<NucleotideCompound,NucleotideCompound>

Overrides:

createSequences in class AbstractCompoundTranslator<NucleotideCompound,NucleotideCompound>

Parameters:

originalSequence - The DNA sequence to translate

Returns:

The translated single sequence

wrapToRna

protected RNASequence wrapToRna(Sequence<NucleotideCompound> dna)

Takes in the given DNA Sequence and returns an instance of RNASequence which is using RnaSequenceView as a ProxySequenceReader.

createSequence

public Sequence<NucleotideCompound> createSequence(Sequence<NucleotideCompound> originalSequence,
                                                   Frame frame)

createSequence

public Sequence<NucleotideCompound> createSequence(Sequence<NucleotideCompound> originalSequence)

Specified by:

createSequence in interface CompoundTranslator<NucleotideCompound,NucleotideCompound>

Overrides:

createSequence in class AbstractCompoundTranslator<NucleotideCompound,NucleotideCompound>

postProcessCompoundLists

protected void postProcessCompoundLists(List<List<NucleotideCompound>> compoundLists)

Specified by:

postProcessCompoundLists in class AbstractCompoundTranslator<NucleotideCompound,NucleotideCompound>