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java.lang.Objectorg.biojava3.core.sequence.template.AbstractCompoundTranslator<NucleotideCompound,AminoAcidCompound>
org.biojava3.core.sequence.transcription.RNAToAminoAcidTranslator
public class RNAToAminoAcidTranslator
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.
Constructor Summary | |
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RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound> creator,
CompoundSet<NucleotideCompound> nucleotides,
CompoundSet<Table.Codon> codons,
CompoundSet<AminoAcidCompound> aminoAcids,
Table table,
boolean trimStops,
boolean initMetOnly,
boolean translateNCodons)
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Method Summary | |
---|---|
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.biojava3.core.sequence.template.AbstractCompoundTranslator |
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addCompounds, addCompoundsToList, addCompoundToLists, addStrings, createSequence, getCreator, getFromCompoundSet, getToCompoundSet, translate, translateMany, workingListToSequences |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound> creator, CompoundSet<NucleotideCompound> nucleotides, CompoundSet<Table.Codon> codons, CompoundSet<AminoAcidCompound> aminoAcids, Table table, boolean trimStops, boolean initMetOnly, boolean translateNCodons)
Method Detail |
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public List<Sequence<AminoAcidCompound>> createSequences(Sequence<NucleotideCompound> originalSequence)
WindowedSequence
.
createSequences
in interface CompoundTranslator<NucleotideCompound,AminoAcidCompound>
createSequences
in class AbstractCompoundTranslator<NucleotideCompound,AminoAcidCompound>
protected void postProcessCompoundLists(List<List<AminoAcidCompound>> compoundLists)
postProcessCompoundLists
in class AbstractCompoundTranslator<NucleotideCompound,AminoAcidCompound>
protected void trimStop(List<AminoAcidCompound> sequence)
public boolean translateNCodons()
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