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.ProteinSequence; 027import org.biojava.nbio.core.sequence.compound.AminoAcidCompound; 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 * Used to create a ProteinSequence from a String to allow for details 038 * about the location of the sequence etc. 039 * 040 * @author Scooter Willis <willishf at gmail dot com> 041 */ 042public class ProteinSequenceCreator implements 043 SequenceCreatorInterface<AminoAcidCompound> { 044 045 private CompoundSet<AminoAcidCompound> compoundSet; 046/** 047 * 048 * @param compoundSet 049 */ 050 public ProteinSequenceCreator(CompoundSet<AminoAcidCompound> compoundSet) { 051 this.compoundSet = compoundSet; 052 } 053/** 054 * 055 * @param sequence 056 * @param index not used in this implementation 057 * @return 058 * @throws CompoundNotFoundException 059 */ 060 @Override 061public AbstractSequence<AminoAcidCompound> getSequence(String sequence, 062 long index) throws CompoundNotFoundException { 063 return new ProteinSequence(sequence, compoundSet); 064 } 065/** 066 * 067 * @param list 068 * @return 069 */ 070 @Override 071public AbstractSequence<AminoAcidCompound> getSequence( 072 List<AminoAcidCompound> list) { 073 ArrayListProxySequenceReader<AminoAcidCompound> store = new ArrayListProxySequenceReader<AminoAcidCompound>(); 074 store.setCompoundSet(compoundSet); 075 store.setContents(list); 076 return new ProteinSequence(store); 077 } 078/** 079 * 080 * @param proxyLoader 081 * @param index not used in this implementation 082 * @return 083 */ 084 @Override 085public AbstractSequence<AminoAcidCompound> getSequence( 086 ProxySequenceReader<AminoAcidCompound> proxyLoader, long index) { 087 return new ProteinSequence(proxyLoader, compoundSet); 088 } 089}