org.biojava3.core.sequence.transcription
public class RNAToAminoAcidTranslator extends AbstractCompoundTranslator<NucleotideCompound,AminoAcidCompound>
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 and Description |
---|
RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound> creator,
CompoundSet<NucleotideCompound> nucleotides,
CompoundSet<Table.Codon> codons,
CompoundSet<AminoAcidCompound> aminoAcids,
Table table,
boolean trimStops,
boolean initMetOnly,
boolean translateNCodons) |
Modifier and Type | Method and Description |
---|---|
java.util.List<Sequence<AminoAcidCompound>> |
createSequences(Sequence<NucleotideCompound> originalSequence)
Performs the core conversion of RNA to Peptide.
|
protected void |
postProcessCompoundLists(java.util.List<java.util.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(java.util.List<AminoAcidCompound> sequence)
Imperfect code.
|
addCompounds, addCompoundsToList, addCompoundToLists, addStrings, createSequence, getCreator, getFromCompoundSet, getToCompoundSet, translate, translateMany, workingListToSequences
public RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound> creator, CompoundSet<NucleotideCompound> nucleotides, CompoundSet<Table.Codon> codons, CompoundSet<AminoAcidCompound> aminoAcids, Table table, boolean trimStops, boolean initMetOnly, boolean translateNCodons)
public java.util.List<Sequence<AminoAcidCompound>> createSequences(Sequence<NucleotideCompound> originalSequence)
WindowedSequence
.createSequences
in interface CompoundTranslator<NucleotideCompound,AminoAcidCompound>
createSequences
in class AbstractCompoundTranslator<NucleotideCompound,AminoAcidCompound>
protected void postProcessCompoundLists(java.util.List<java.util.List<AminoAcidCompound>> compoundLists)
postProcessCompoundLists
in class AbstractCompoundTranslator<NucleotideCompound,AminoAcidCompound>
protected void trimStop(java.util.List<AminoAcidCompound> sequence)
public boolean translateNCodons()