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
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Constructor Summary
ConstructorsConstructorDescriptionRNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound> creator, CompoundSet<NucleotideCompound> nucleotides, CompoundSet<Table.Codon> codons, CompoundSet<AminoAcidCompound> aminoAcids, Table table, boolean trimStops, boolean initMetOnly, boolean translateNCodons) 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) 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 TypeMethodDescriptioncreateSequences(Sequence<NucleotideCompound> originalSequence) Performs the core conversion of RNA to Peptide.protected voidpostProcessCompoundLists(List<List<AminoAcidCompound>> compoundLists) Performs the trimming of stop codons and the conversion of a valid start amino acid to MbooleanIndicates if we want to force exact translation of compounds or not i.e.protected voidtrimStop(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
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Constructor Details
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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, settingstopAtStopCodonstofalse -
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)
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Method Details
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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 ofWindowedSequence.- Specified by:
createSequencesin interfaceCompoundTranslator<NucleotideCompound,AminoAcidCompound> - Overrides:
createSequencesin classAbstractCompoundTranslator<NucleotideCompound,AminoAcidCompound>
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postProcessCompoundLists
Performs the trimming of stop codons and the conversion of a valid start amino acid to M- Specified by:
postProcessCompoundListsin classAbstractCompoundTranslator<NucleotideCompound,AminoAcidCompound>
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trimStop
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
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stopAtStopCodonstofalse