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 */ 022package org.biojava.nbio.core.sequence.io; 023 024import org.biojava.nbio.core.sequence.AccessionID; 025import org.biojava.nbio.core.sequence.io.template.FastaHeaderFormatInterface; 026import org.biojava.nbio.core.sequence.template.AbstractSequence; 027import org.biojava.nbio.core.sequence.template.Compound; 028 029/** 030 * We store the original header if the sequence is parsed from a fasta file and will use that exact 031 * sequence if we write out the sequences to a fasta file. If we don't have an orginal header then 032 * use the accession id. This allows the implementation by the user to write out complex header 033 * with id notes etc without rewriting the fasta writer 034 * 035 * @author Scooter Willis <willishf at gmail dot com> 036 */ 037public class GenericFastaHeaderFormat<S extends AbstractSequence<?>, C extends Compound> implements FastaHeaderFormatInterface<S, C> { 038 039 @Override 040 public String getHeader(S sequence) { 041 String header = ""; 042 043 if (sequence.getOriginalHeader() != null && sequence.getOriginalHeader().length() > 0) { 044 header = sequence.getOriginalHeader(); 045 } else { 046 AccessionID accessionID = sequence.getAccession(); 047 if (accessionID != null) { 048 header = accessionID.getID(); 049 } 050 } 051 052 return header; 053 } 054}