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java.lang.Objectorg.biojava3.core.sequence.transcription.TranscriptionEngine
public class TranscriptionEngine
Used as a way of encapsulating the data structures required to parse DNA to a Protein sequence. In order to build one look at which provides intelligent defaults & allows you to build an engine which is nearly the same as the default one but with a few changes. All of the engine is customisable. By default the code will attempt to:
Sequence
<>
with an X at that position
Nested Class Summary | |
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static class |
TranscriptionEngine.Builder
This class is the way to create a TranslationEngine . |
Method Summary | |
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CompoundSet<AminoAcidCompound> |
getAminoAcidCompounds()
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static TranscriptionEngine |
getDefault()
Default instance to use when Transcribing from DNA -> RNA -> Protein. |
CompoundSet<NucleotideCompound> |
getDnaCompounds()
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DNAToRNATranslator |
getDnaRnaTranslator()
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SequenceCreatorInterface<AminoAcidCompound> |
getProteinSequenceCreator()
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RNAToAminoAcidTranslator |
getRnaAminoAcidTranslator()
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CompoundSet<NucleotideCompound> |
getRnaCompounds()
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SequenceCreatorInterface<NucleotideCompound> |
getRnaSequenceCreator()
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Table |
getTable()
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Map<Frame,Sequence<AminoAcidCompound>> |
multipleFrameTranslation(Sequence<NucleotideCompound> dna,
Frame... frames)
A way of translating DNA in a number of frames |
Sequence<AminoAcidCompound> |
translate(Sequence<NucleotideCompound> dna)
Quick method to let you go from a CDS to a Peptide quickly. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Method Detail |
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public static TranscriptionEngine getDefault()
public Sequence<AminoAcidCompound> translate(Sequence<NucleotideCompound> dna)
dna
- The CDS to translate
public Map<Frame,Sequence<AminoAcidCompound>> multipleFrameTranslation(Sequence<NucleotideCompound> dna, Frame... frames)
dna
- The CDS to translateframes
- The Frames to translate in
public Table getTable()
public RNAToAminoAcidTranslator getRnaAminoAcidTranslator()
public DNAToRNATranslator getDnaRnaTranslator()
public SequenceCreatorInterface<AminoAcidCompound> getProteinSequenceCreator()
public SequenceCreatorInterface<NucleotideCompound> getRnaSequenceCreator()
public CompoundSet<NucleotideCompound> getDnaCompounds()
public CompoundSet<NucleotideCompound> getRnaCompounds()
public CompoundSet<AminoAcidCompound> getAminoAcidCompounds()
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