Package org.biojava3.core.sequence.transcription

Class RNAToAminoAcidTranslator

java.lang.Object

org.biojava3.core.sequence.template.AbstractCompoundTranslator<NucleotideCompound,AminoAcidCompound>

org.biojava3.core.sequence.transcription.RNAToAminoAcidTranslator

All Implemented Interfaces:

CompoundTranslator<NucleotideCompound,AminoAcidCompound>

public class RNAToAminoAcidTranslator
extends AbstractCompoundTranslator<NucleotideCompound,AminoAcidCompound>

Takes a Sequence of NucleotideCompound which should represent an RNA sequence (RNASequence is good for this) and returns a list of Sequence which hold AminoAcidCompound. The translator can also trim stop codons as well as changing any valid start codon to an initiating met.

Author:

ayates

Constructor Summary

Constructors

Constructor	Description
RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound> creator, CompoundSet<NucleotideCompound> nucleotides, CompoundSet<Table.Codon> codons, CompoundSet<AminoAcidCompound> aminoAcids, Table table, boolean trimStops, boolean initMetOnly, boolean translateNCodons)

Method Summary

Modifier and Type	Method	Description
List<Sequence<AminoAcidCompound>>	createSequences(Sequence<NucleotideCompound> originalSequence)	Performs the core conversion of RNA to Peptide.
boolean	translateNCodons()	Indicates if we want to force exact translation of compounds or not i.e. those with internal N RNA bases.

Methods inherited from class org.biojava3.core.sequence.template.AbstractCompoundTranslator

createSequence, getCreator, getFromCompoundSet, getToCompoundSet, translate, translateMany

Methods inherited from class java.lang.Object

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

Constructor Details

RNAToAminoAcidTranslator

public RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound> creator,
 CompoundSet<NucleotideCompound> nucleotides,
 CompoundSet<Table.Codon> codons,
 CompoundSet<AminoAcidCompound> aminoAcids,
 Table table,
 boolean trimStops,
 boolean initMetOnly,
 boolean translateNCodons)

Method Details

createSequences

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

Performs the core conversion of RNA to Peptide. It does this by walking a windowed version of the given sequence. Any trailing DNA base pairs are ignored according to the specification of WindowedSequence.

Specified by:

createSequences in interface CompoundTranslator<NucleotideCompound,AminoAcidCompound>

Overrides:

createSequences in class AbstractCompoundTranslator<NucleotideCompound,AminoAcidCompound>

translateNCodons

public boolean translateNCodons()

Indicates if we want to force exact translation of compounds or not i.e. those with internal N RNA bases. This will cause a translation to an X amino acid