edu.upenn.gloDB.io
Class FASTAParserFly

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

public class FASTAParserFly
extends java.lang.Object
implements FASTAParser

Parses the header line at the beginning of each sequence. The header line is chopped into substrings at each space (" "). If a substring contains a ":" then it is assumed to be a key:value pair and is added to the attributes field as such. Otherwise, it is added as a value to the 'descriptors' key. An example of a parseable header is:

Version:
$Id: FASTAParserFly.java,v 1.7.2.4 2007/03/01 21:17:33 fisher Exp $
Notes:
can we assume that the header starts with a sequence ID?

Constructor Summary
FASTAParserFly()
           
 
Method Summary
 java.util.HashMap parseHeader(java.lang.String header)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

FASTAParserFly

public FASTAParserFly()
Method Detail

parseHeader

public java.util.HashMap parseHeader(java.lang.String header)
Specified by:
parseHeader in interface FASTAParser



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