001 /* 002 * Copyright 2007, 2012 Stephen Fisher and Junhyong Kim, University of 003 * Pennsylvania. 004 * 005 * This file is part of Glo-DB. 006 * 007 * Glo-DB is free software: you can redistribute it and/or modify it 008 * under the terms of the GNU General Public License as published by 009 * the Free Software Foundation, either version 3 of the License, or 010 * (at your option) any later version. 011 * 012 * Glo-DB is distributed in the hope that it will be useful, but 013 * WITHOUT ANY WARRANTY; without even the implied warranty of 014 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 015 * General Public License for more details. 016 * 017 * You should have received a copy of the GNU General Public License 018 * along with Glo-DB. If not, see <http://www.gnu.org/licenses/>. 019 * 020 * @(#)FASTAParserDefault.java 021 */ 022 023 package edu.upenn.gloDB.io; 024 025 import java.util.HashMap; 026 027 /** 028 * The default parser for FASTA headers. It returns a HashMap that 029 * contains one entry: the key is "FASTA" and the value is the header 030 * line with the leading '>' removed. Thus no assumptions are made 031 * about the structure of the header, other than it beginning with a 032 * '>'. 033 * 034 * @author Stephen Fisher 035 * @version $Id: FASTAParserDefault.java,v 1.2.2.4 2007/03/01 21:17:33 fisher Exp $ 036 */ 037 038 public class FASTAParserDefault implements FASTAParser { 039 /** 040 * As the default parser, do not process the header at all, 041 * except to remove the leading '>'. Add the header to 042 * Sequence.attributes using the key 'FASTA'. 043 */ 044 public HashMap parseHeader(String header) { 045 HashMap attributes = new HashMap(); 046 attributes.put("FASTA", header.substring(1)); 047 return attributes; 048 } 049 } 050