edu.upenn.gloDB.io
Class FASTAParserMinimal

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

public class FASTAParserMinimal
extends java.lang.Object
implements FASTAParser

Parses the header line at the beginning of each FASTA 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. This is very similar to FASTAParserFly.java, however it doesn't processes the gene_boundaries in any special way. Thus this should not be used for FASTA files that contain Features.

Version:
$Id: FASTAParserMinimal.java,v 1.7.2.4 2007/03/01 21:17:33 fisher Exp $
Notes:
this assumes that the header starts with a sequence ID.

Constructor Summary
FASTAParserMinimal()
           
 
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

FASTAParserMinimal

public FASTAParserMinimal()
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.