org.biojava3.core.sequence.transcription
Class TranscriptionEngine

java.lang.Object
  extended by org.biojava3.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 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:

Author:
ayates

Nested Class Summary
static class TranscriptionEngine.Builder
          This class is the way to create a TranslationEngine.
 
Method Summary
 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 Detail

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 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()