Package org.biojava.nbio.core.sequence.transcription

Class TranscriptionEngine

java.lang.Object

org.biojava.nbio.core.sequence.transcription.TranscriptionEngine

public class TranscriptionEngine
extends Object

Used as a way of encapsulating the data structures required to parse DNA to a Protein sequence. In order to build one look at @ TranscriptionEngine.Builder} which provides intelligent defaults and 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:

• Trim Stops
• Convert initiating codons to M
• Allow for the fuzzy translation of Codons i.e. if it contains an N that produces a Sequence<AminoAcidCompound> with an X at that position

Author:

ayates

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	TranscriptionEngine.Builder	This class is the way to create a TranscriptionEngine.

Method Summary

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()
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

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Details

getDefault

public static TranscriptionEngine getDefault()

Default instance to use when Transcribing from DNA -> RNA -> Protein. If you require anything that is not a default setting then look at @ TranscriptionEngine.Builder} for customisation options.

translate

public Sequence<AminoAcidCompound> translate(Sequence<NucleotideCompound> dna)

Quick method to let you go from a CDS to a Peptide quickly. It assumes you are translating only in the first frame

Parameters:

dna - The CDS to translate

Returns:

The Protein Sequence

multipleFrameTranslation

public Map<Frame,Sequence<AminoAcidCompound>> multipleFrameTranslation(Sequence<NucleotideCompound> dna,
 Frame... frames)

A way of translating DNA in a number of frames

Parameters:

dna - The CDS to translate

frames - The Frames to translate in

Returns:

All generated protein sequences in the given frames. Can have null entries

getTable

public Table getTable()

getRnaAminoAcidTranslator

public RNAToAminoAcidTranslator getRnaAminoAcidTranslator()

getDnaRnaTranslator

public DNAToRNATranslator getDnaRnaTranslator()

getProteinSequenceCreator

public SequenceCreatorInterface<AminoAcidCompound> getProteinSequenceCreator()

getRnaSequenceCreator

public SequenceCreatorInterface<NucleotideCompound> getRnaSequenceCreator()

getDnaCompounds

public CompoundSet<NucleotideCompound> getDnaCompounds()

getRnaCompounds

public CompoundSet<NucleotideCompound> getRnaCompounds()

getAminoAcidCompounds

public CompoundSet<AminoAcidCompound> getAminoAcidCompounds()