001/* 002 * BioJava development code 003 * 004 * This code may be freely distributed and modified under the 005 * terms of the GNU Lesser General Public Licence. This should 006 * be distributed with the code. If you do not have a copy, 007 * see: 008 * 009 * http://www.gnu.org/copyleft/lesser.html 010 * 011 * Copyright for this code is held jointly by the individual 012 * authors. These should be listed in @author doc comments. 013 * 014 * For more information on the BioJava project and its aims, 015 * or to join the biojava-l mailing list, visit the home page 016 * at: 017 * 018 * http://www.biojava.org/ 019 * 020 */ 021package org.biojava.nbio.core.sequence.transcription; 022 023import org.biojava.nbio.core.sequence.RNASequence; 024import org.biojava.nbio.core.sequence.compound.NucleotideCompound; 025import org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface; 026import org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator; 027import org.biojava.nbio.core.sequence.template.CompoundSet; 028import org.biojava.nbio.core.sequence.template.ProxySequenceReader; 029import org.biojava.nbio.core.sequence.template.Sequence; 030import org.biojava.nbio.core.sequence.views.RnaSequenceView; 031 032import java.util.ArrayList; 033import java.util.List; 034 035/** 036 * Performs the first stage of transcription by going from DNA to RNA. This 037 * class will first delegate to {@link Frame} in order to be in the correctly 038 * specified translation frame and then translates T to U. The other 039 * translation carried out is to convert an equivalent compound in DNA to RNA 040 * i.e. for the base A in DNA fetching the equivalent A base in the RNA 041 * {@link CompoundSet}. 042 * 043 * @author ayates 044 */ 045public class DNAToRNATranslator extends AbstractCompoundTranslator<NucleotideCompound, NucleotideCompound> { 046 047 private final boolean shortCutTranslation; 048 049 public DNAToRNATranslator(SequenceCreatorInterface<NucleotideCompound> rnaCreator, 050 CompoundSet<NucleotideCompound> dna, CompoundSet<NucleotideCompound> rna, 051 boolean shortCutTranslation) { 052 super(rnaCreator, dna, rna); 053 this.shortCutTranslation = shortCutTranslation; 054 defaultMappings(); 055 thyamineToUracil(); 056 } 057 058 /** 059 * Overloaded local version which delegates to an optional translator 060 * when told to (specified during construction). 061 * 062 * @param originalSequence The DNA sequence to translate 063 * @return The translated single sequence 064 */ 065 @Override 066 public List<Sequence<NucleotideCompound>> createSequences(Sequence<NucleotideCompound> originalSequence) { 067 if(shortCutTranslation) { 068 List<Sequence<NucleotideCompound>> result = new ArrayList<Sequence<NucleotideCompound>>(1); 069 result.add(wrapToRna(originalSequence)); 070 return result; 071 } 072 else { 073 return super.createSequences(originalSequence); 074 } 075 } 076 077 /** 078 * Takes in the given DNA Sequence and returns an instance of RNASequence 079 * which is using {@link RnaSequenceView} as a 080 * {@link ProxySequenceReader}. 081 */ 082 protected RNASequence wrapToRna(Sequence<NucleotideCompound> dna) { 083 ProxySequenceReader<NucleotideCompound> rnaView = new RnaSequenceView(dna); 084 return new RNASequence(rnaView); 085 } 086 087 private void defaultMappings() { 088 NucleotideCompound thymine = getFromCompoundSet().getCompoundForString("T"); 089 for(NucleotideCompound dnaBase: getFromCompoundSet().getAllCompounds()) { 090 if(dnaBase.equalsIgnoreCase(thymine)) { 091 continue; 092 } 093 NucleotideCompound rnaBase = getToCompoundSet().getCompoundForString( 094 dnaBase.toString()); 095 addCompounds(dnaBase, rnaBase); 096 } 097 098 } 099 100 private void thyamineToUracil() { 101 addCompounds(getFromCompoundSet().getCompoundForString("T"), 102 getToCompoundSet().getCompoundForString("U")); 103 addCompounds(getFromCompoundSet().getCompoundForString("t"), 104 getToCompoundSet().getCompoundForString("u")); 105 } 106 107 public Sequence<NucleotideCompound> createSequence(Sequence<NucleotideCompound> originalSequence, Frame frame) { 108 Sequence<NucleotideCompound> wrapped = frame.wrap(originalSequence); 109 return super.createSequence(wrapped); 110 } 111 112 @Override 113 public Sequence<NucleotideCompound> createSequence(Sequence<NucleotideCompound> originalSequence) { 114 return createSequence(originalSequence, Frame.getDefaultFrame()); 115 } 116 117 @Override 118 protected void postProcessCompoundLists( 119 List<List<NucleotideCompound>> compoundLists) { 120 //No post processing needed 121 } 122}