svndigest - svndigest

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/vcf/InfoFactory.java

: Code
: Comments
: Other

Rev	Date	Author	Line
5729	18 Nov 19	nicklas	1	package net.sf.basedb.reggie.vcf;
5729	18 Nov 19	nicklas	2
5729	18 Nov 19	nicklas	3	/**
5729	18 Nov 19	nicklas	4	Factory class for extracting information from the
5729	18 Nov 19	nicklas	5	INFO field of a VCF. Implementations will get notified
5729	18 Nov 19	nicklas	6	for each ##INFO header via {@link #addInfoHeader(String, String)}
5729	18 Nov 19	nicklas	7	and then, for each entry, the INFO column via {@link #getInfo(String)}
5729	18 Nov 19	nicklas	8
5729	18 Nov 19	nicklas	9	@since 4.24
5729	18 Nov 19	nicklas	10	*/
5729	18 Nov 19	nicklas	11	public interface InfoFactory
5729	18 Nov 19	nicklas	12	{
5729	18 Nov 19	nicklas	13
5729	18 Nov 19	nicklas	14	/**
5729	18 Nov 19	nicklas	15	This method is called by the VcfParser once for every
5729	18 Nov 19	nicklas	16	##INFO header in the VCF. The ID attribute has been
5729	18 Nov 19	nicklas	17	extracted and is passed as the id parameter. The
5729	18 Nov 19	nicklas	18	other attributes are not parsed but passed as a
5729	18 Nov 19	nicklas	19	the data string. The following pattern is
5729	18 Nov 19	nicklas	20	used to parse the header: ##INFO=<ID=(\w+),(.*)>
5729	18 Nov 19	nicklas	21	*/
5729	18 Nov 19	nicklas	22	public void addInfoHeader(String id, String data);
5729	18 Nov 19	nicklas	23
5729	18 Nov 19	nicklas	24	/**
5729	18 Nov 19	nicklas	25	This method is called by the VcfParser once for
5729	18 Nov 19	nicklas	26	every data line in the VCF with data for the info
5729	18 Nov 19	nicklas	27	column and the information about the SNP that
5729	18 Nov 19	nicklas	28	has already been extracted.
5729	18 Nov 19	nicklas	29	@return An InfoData object or null
5729	18 Nov 19	nicklas	30	*/
5729	18 Nov 19	nicklas	31	public InfoData getInfo(String info, SnpData snp);
5729	18 Nov 19	nicklas	32
5729	18 Nov 19	nicklas	33	}