public class TranscriptionEngine
extends java.lang.Object
Sequence
<{@link{AminoAcidCompound}> with an X at
that position
Modifier and Type | Class | Description |
---|---|---|
static class |
TranscriptionEngine.Builder |
This class is the way to create a
TranslationEngine . |
Modifier and Type | Method | Description |
---|---|---|
CompoundSet<AminoAcidCompound> |
getAminoAcidCompounds() |
|
static TranscriptionEngine |
getDefault() |
Default instance to use when Transcribing from DNA -> RNA ->
Protein.
|
CompoundSet<NucleotideCompound> |
getDnaCompounds() |
|
DNAToRNATranslator |
getDnaRnaTranslator() |
|
SequenceCreatorInterface<AminoAcidCompound> |
getProteinSequenceCreator() |
|
RNAToAminoAcidTranslator |
getRnaAminoAcidTranslator() |
|
CompoundSet<NucleotideCompound> |
getRnaCompounds() |
|
SequenceCreatorInterface<NucleotideCompound> |
getRnaSequenceCreator() |
|
Table |
getTable() |
|
java.util.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.
|
public static TranscriptionEngine getDefault()
public Sequence<AminoAcidCompound> translate(Sequence<NucleotideCompound> dna)
dna
- The CDS to translatepublic java.util.Map<Frame,Sequence<AminoAcidCompound>> multipleFrameTranslation(Sequence<NucleotideCompound> dna, Frame... frames)
dna
- The CDS to translateframes
- The Frames to translate inpublic 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()