org.biojava3.core.sequence.transcription
Class DNAToRNATranslator
java.lang.Object
org.biojava3.core.sequence.template.AbstractCompoundTranslator<NucleotideCompound,NucleotideCompound>
org.biojava3.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
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
DNAToRNATranslator
public DNAToRNATranslator(SequenceCreatorInterface<NucleotideCompound> rnaCreator,
CompoundSet<NucleotideCompound> dna,
CompoundSet<NucleotideCompound> rna,
boolean shortCutTranslation)
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>