GO::Parsers::base_parser(3pm)				User Contributed Perl Documentation			     GO::Parsers::base_parser(3pm)

NAME

	 GO::Parsers::base_parser     - base class for parsers

SYNOPSIS

	 do not use this class directly; use GO::Parser

DESCRIPTION

AUTHOR

   show_messages
	 Usage	 -
	 Returns -
	 Args	 -

   normalize_files
	 Usage	 - @files = $parser->normalize_files(@files)
	 Returns -
	 Args	 -

       takes a list of filenames/paths, "glob"s them, uncompresses any compressed files and returns the new file list

   litemode
	 Usage	 - $p->litemode(1)
	 Returns -
	 Args	 - bool

       when set, parser will only throw the following events:

       id|name|is_a|relationship|namespace

       (optimisation for fast parsing)

   acc2name_h
	 Usage	 - $n = $p->acc2name_h->{'GO:0003673'}
	 Returns - hashref
	 Args	 - hashref [optional]

       gets/sets a hash mapping IDs to names

       this will be automatically set by an ontology parser

       a non-ontology parser will use this index to verify the parsed data (see $p->acc_not_found($id), below)

   acc_not_found
	 Usage	 - if ($p->acc_not_found($go_id)) { warn("$go_id not known") }
	 Returns - bool
	 Args	 - acc string

       uses acc2name_h - if this hash mapping has been created AND the acc is not in the hash, THEN it is considered not found

       This is useful for non-ontology parsers (xref_parser, go_assoc_parser) to check whether a referenced ID is actually present in the ontology

       note that if acc2name_h has not been created, then accs cannot be considered not-found, and this will always return 0/false

perl v5.14.2							    2010-07-24					     GO::Parsers::base_parser(3pm)