NCBIFastaHeaderParser

java.lang.Object

bacnet.reader.NCBIFastaHeaderParser<S,C>

All Implemented Interfaces:: FastaHeaderParserInterface<S,C>

public class NCBIFastaHeaderParser<S extends AbstractSequence<C>,C extends Compound> extends Object implements FastaHeaderParserInterface<S,C>

My own implementation of a FastaHeaderParserInterface to parse Fasta files from NCBI ftp NCBI fna (genome and plasmids) gi|gi-number|ref|accession|name gi|16802048|ref|NC_003210.1| Listeria monocytogenes EGD-e, complete genome NCBI ffn (coding) ref|refGenome gi-number|:start-end name ref|NC_003210.1|:318-1673 chromosomal replication initiation protein [Listeria monocytogenes EGD-e] NCBI frn (non-coding) ref|refGenome gi-number|:start-end| name| [locus-tag] ref|NC_003210|:82705-82777|Lys tRNA| [locus_tag=lmot01] NCBI faa (proteins) gi|gi-number|ref|accession|name gi|16802049|ref|NP_463534.1| chromosomal replication initiation protein [Listeria monocytogenes EGD-e]

Author:: Christophe Becavin

Constructor Summary

Constructors

Constructor

Description

NCBIFastaHeaderParser()
Method Summary

Modifier and Type

Method

Description

String[]

getHeaderValues(String header)

Parse out the components where some have a | and others do not

void

parseHeader(String header, S sequence)

Parse the header and set the values in the sequence

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- NCBIFastaHeaderParser
  
  public NCBIFastaHeaderParser()
Method Details
- getHeaderValues
  
  public String[] getHeaderValues(String header)
  
  Parse out the components where some have a | and others do not
  
  Parameters:
  
  header -
  
  Returns:
- parseHeader
  
  public void parseHeader(String header, S sequence)
  
  Parse the header and set the values in the sequence
  
  Specified by:
  
  parseHeader in interface FastaHeaderParserInterface<S extends AbstractSequence<C>,C extends Compound>
  
  Parameters:
  
  header -
  
  sequence -