org.biojava.nbio.core.sequence.transcription

Class RNAToAminoAcidTranslator

java.lang.Object

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

org.biojava.nbio.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 and Description
RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound> creator, CompoundSet<NucleotideCompound> nucleotides, CompoundSet<Table.Codon> codons, CompoundSet<AminoAcidCompound> aminoAcids, Table table, boolean trimStops, boolean initMetOnly, boolean translateNCodons) Deprecated. Retained for backwards compatability, setting stopAtStopCodons to false
RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound> creator, CompoundSet<NucleotideCompound> nucleotides, CompoundSet<Table.Codon> codons, CompoundSet<AminoAcidCompound> aminoAcids, Table table, boolean trimStops, boolean initMetOnly, boolean translateNCodons, boolean stopAtStopCodons) Deprecated.
RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound> creator, CompoundSet<NucleotideCompound> nucleotides, CompoundSet<Table.Codon> codons, CompoundSet<AminoAcidCompound> aminoAcids, Table table, boolean trimStops, boolean initMetOnly, boolean translateNCodons, boolean stopAtStopCodons, boolean waitForStartCodon)

Method Summary

Modifier and Type	Method and Description
List<Sequence<AminoAcidCompound>>	createSequences(Sequence<NucleotideCompound> originalSequence) Performs the core conversion of RNA to Peptide.
protected void	postProcessCompoundLists(List<List<AminoAcidCompound>> compoundLists) Performs the trimming of stop codons and the conversion of a valid start amino acid to M
boolean	translateNCodons() Indicates if we want to force exact translation of compounds or not i.e.
protected void	trimStop(List<AminoAcidCompound> sequence) Imperfect code.

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

addCompounds, addCompoundsToList, addCompoundToLists, addStrings, createSequence, 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

RNAToAminoAcidTranslator

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

Deprecated. Retained for backwards compatability, setting stopAtStopCodons to false

RNAToAminoAcidTranslator

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

Deprecated.

RNAToAminoAcidTranslator

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

Method Detail

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>

postProcessCompoundLists

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

Performs the trimming of stop codons and the conversion of a valid start amino acid to M

Specified by:

postProcessCompoundLists in class AbstractCompoundTranslator<NucleotideCompound,AminoAcidCompound>

trimStop

protected void trimStop(List<AminoAcidCompound> sequence)

Imperfect code. Checks the last amino acid to see if a codon could have translated a stop for it. Left in for the moment

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