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 01-21-2010 021 */ 022 023package org.biojava.nbio.core.sequence.io; 024 025import org.biojava.nbio.core.exceptions.CompoundNotFoundException; 026import org.biojava.nbio.core.sequence.DNASequence; 027import org.biojava.nbio.core.sequence.compound.NucleotideCompound; 028import org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface; 029import org.biojava.nbio.core.sequence.loader.ArrayListProxySequenceReader; 030import org.biojava.nbio.core.sequence.template.AbstractSequence; 031import org.biojava.nbio.core.sequence.template.CompoundSet; 032import org.biojava.nbio.core.sequence.template.ProxySequenceReader; 033 034import java.util.List; 035 036/** 037 * A helper class that allows different ways to read a string and create a DNA sequence. Used in FastaReaderHelper 038 * and probably a layer that isn't needed 039 * 040 * @author Scooter Willis <willishf at gmail dot com> 041 */ 042public class DNASequenceCreator implements 043 SequenceCreatorInterface<NucleotideCompound> { 044 045 private final CompoundSet<NucleotideCompound> compoundSet; 046 047 /** 048 * 049 * @param compoundSet 050 */ 051 public DNASequenceCreator(CompoundSet<NucleotideCompound> compoundSet) { 052 this.compoundSet = compoundSet; 053 } 054 055/** 056 * 057 * @param sequence The Sequence from a String 058 * @param index Currently not used 059 * @return 060 */ 061 @Override 062public AbstractSequence<NucleotideCompound> getSequence(String sequence, 063 long index) throws CompoundNotFoundException { 064 return new DNASequence(sequence, compoundSet); 065 } 066/** 067 * 068 * @param proxyLoader The Sequence from a ProxySequenceReader 069 * @param index Currently not used 070 * @return 071 */ 072 @Override 073public AbstractSequence<NucleotideCompound> getSequence( 074 ProxySequenceReader<NucleotideCompound> proxyLoader, long index) { 075 return new DNASequence(proxyLoader, compoundSet); 076 } 077 078 /** 079 * 080 * @param list 081 * @return 082 */ 083 @Override 084public AbstractSequence<NucleotideCompound> getSequence( 085 List<NucleotideCompound> list) { 086 ArrayListProxySequenceReader<NucleotideCompound> store = new ArrayListProxySequenceReader<NucleotideCompound>(); 087 store.setCompoundSet(compoundSet); 088 store.setContents(list); 089 return new DNASequence(store); 090 } 091}