edu.upenn.gloDB.io
Class FASTAParserDefault

java.lang.Object
  extended by edu.upenn.gloDB.io.FASTAParserDefault
All Implemented Interfaces:
FASTAParser

public class FASTAParserDefault
extends java.lang.Object
implements FASTAParser

The default parser for FASTA headers. It returns a HashMap that contains one entry: the key is "FASTA" and the value is the header line with the leading '>' removed. Thus no assumptions are made about the structure of the header, other than it beginning with a '>'.

Version:
$Id: FASTAParserDefault.java,v 1.2.2.4 2007/03/01 21:17:33 fisher Exp $

Constructor Summary
FASTAParserDefault()
           
 
Method Summary
 java.util.HashMap parseHeader(java.lang.String header)
          As the default parser, do not process the header at all, except to remove the leading '>'.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

FASTAParserDefault

public FASTAParserDefault()
Method Detail

parseHeader

public java.util.HashMap parseHeader(java.lang.String header)
As the default parser, do not process the header at all, except to remove the leading '>'. Add the header to Sequence.attributes using the key 'FASTA'.

Specified by:
parseHeader in interface FASTAParser



Copyright 2012 Stephen Fisher and Junhyong Kim, University of Pennsylvania. All Rights Reserved.