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 & 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<{@link{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 TranslationEngine.
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()

Class TranscriptionEngine

Nested Class Summary

Method Summary

Methods inherited from class java.lang.Object

Method Details

getDefault

translate

multipleFrameTranslation

getTable

getRnaAminoAcidTranslator

getDnaRnaTranslator

getProteinSequenceCreator

getRnaSequenceCreator

getDnaCompounds

getRnaCompounds

getAminoAcidCompounds