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 * Created on DATE 021 * 022 */ 023package org.biojava.nbio.core.sequence; 024 025/** 026 * @author Scooter Willis 027 * 028 */ 029import org.biojava.nbio.core.exceptions.CompoundNotFoundException; 030import org.biojava.nbio.core.sequence.compound.NucleotideCompound; 031import org.biojava.nbio.core.sequence.compound.RNACompoundSet; 032import org.biojava.nbio.core.sequence.template.AbstractSequence; 033import org.biojava.nbio.core.sequence.template.CompoundSet; 034import org.biojava.nbio.core.sequence.template.ProxySequenceReader; 035import org.biojava.nbio.core.sequence.template.SequenceView; 036import org.biojava.nbio.core.sequence.transcription.TranscriptionEngine; 037import org.biojava.nbio.core.sequence.views.ComplementSequenceView; 038import org.biojava.nbio.core.sequence.views.ReversedSequenceView; 039 040/** 041 * RNASequence where RNACompoundSet are the allowed values 042 * @author Scooter Willis <willishf at gmail dot com> 043 */ 044 045public class RNASequence extends AbstractSequence<NucleotideCompound> { 046 047 /** 048 * Create a RNA sequence from a String 049 * @param seqString 050 * @throws CompoundNotFoundException 051 */ 052 public RNASequence(String seqString) throws CompoundNotFoundException { 053 super(seqString, RNACompoundSet.getRNACompoundSet()); 054 } 055 056 /** 057 * Create a RNA aequence from a proxy reader 058 * @param proxyLoader 059 */ 060 public RNASequence(ProxySequenceReader<NucleotideCompound> proxyLoader) { 061 super(proxyLoader, RNACompoundSet.getRNACompoundSet()); 062 } 063 064 /** 065 * Create a RNA sequence from a string with a user defined RNA compound set 066 * @param seqString 067 * @param compoundSet 068 * @throws CompoundNotFoundException 069 */ 070 public RNASequence(String seqString, CompoundSet<NucleotideCompound> compoundSet) throws CompoundNotFoundException { 071 super(seqString, compoundSet); 072 } 073 074 /** 075 * Create a RNA sequence from a proxy reader and user defined RNA compound set 076 * @param proxyLoader 077 * @param compoundSet 078 */ 079 public RNASequence(ProxySequenceReader<NucleotideCompound> proxyLoader, 080 CompoundSet<NucleotideCompound> compoundSet) { 081 super(proxyLoader, compoundSet); 082 } 083 084 /** 085 * Get reverse complement view of the sequence 086 * @return 087 */ 088 public SequenceView<NucleotideCompound> getReverseComplement() { 089 return new ComplementSequenceView<NucleotideCompound>(getInverse()); 090 } 091 092 /** 093 * Get the inverse view of the sequence. It is the reverse sequence from 094 * end to begin where use reverse could imply complement. Called getInverse() 095 * in the hopes of making less confusing. 096 * @return 097 */ 098 @Override 099public SequenceView<NucleotideCompound> getInverse() { 100 return new ReversedSequenceView<NucleotideCompound>(this); 101 } 102 103 /** 104 * Get the complement view of the RNA sequence 105 * @return 106 */ 107 public SequenceView<NucleotideCompound> getComplement() { 108 return new ComplementSequenceView<NucleotideCompound>(this); 109 } 110 111 /** 112 * Get the ProteinSequence from the RNA sequence 113 * @return 114 */ 115 public ProteinSequence getProteinSequence() { 116 return getProteinSequence(TranscriptionEngine.getDefault()); 117 } 118 119 /** 120 * Get the ProteinSequene from the RNA sequence with user defined 121 * transcription engine 122 * 123 * @param engine 124 * @return 125 */ 126 public ProteinSequence getProteinSequence(TranscriptionEngine engine) { 127 return (ProteinSequence)engine.getRnaAminoAcidTranslator().createSequence(this); 128 } 129 130 public double getGC() { 131 throw new UnsupportedOperationException("Not supported yet"); 132 } 133}