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.\" ========================================================================
.\"
.IX Title "GO::Parsers::base_parser 3pm"
.TH GO::Parsers::base_parser 3pm "2021-01-09" "perl v5.32.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH "NAME"
.Vb 1
\&  GO::Parsers::base_parser     \- base class for parsers
.Ve
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  do not use this class directly; use GO::Parser
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
.SH "AUTHOR"
.IX Header "AUTHOR"
.SS "show_messages"
.IX Subsection "show_messages"
.Vb 3
\&  Usage   \-
\&  Returns \-
\&  Args    \-
.Ve
.SS "normalize_files"
.IX Subsection "normalize_files"
.Vb 3
\&  Usage   \- @files = $parser\->normalize_files(@files)
\&  Returns \-
\&  Args    \-
.Ve
.PP
takes a list of filenames/paths, \*(L"glob\*(R"s them, uncompresses any compressed files and returns the new file list
.SS "litemode"
.IX Subsection "litemode"
.Vb 3
\&  Usage   \- $p\->litemode(1)
\&  Returns \-
\&  Args    \- bool
.Ve
.PP
when set, parser will only throw the following events:
.PP
id|name|is_a|relationship|namespace
.PP
(optimisation for fast parsing)
.SS "acc2name_h"
.IX Subsection "acc2name_h"
.Vb 3
\&  Usage   \- $n = $p\->acc2name_h\->{\*(AqGO:0003673\*(Aq}
\&  Returns \- hashref
\&  Args    \- hashref [optional]
.Ve
.PP
gets/sets a hash mapping IDs to names
.PP
this will be automatically set by an ontology parser
.PP
a non-ontology parser will use this index to verify the parsed data
(see \f(CW$p\fR\->acc_not_found($id), below)
.SS "acc_not_found"
.IX Subsection "acc_not_found"
.Vb 3
\&  Usage   \- if ($p\->acc_not_found($go_id)) { warn("$go_id not known") }
\&  Returns \- bool
\&  Args    \- acc string
.Ve
.PP
uses acc2name_h \- if this hash mapping has been created \s-1AND\s0 the acc is
not in the hash, \s-1THEN\s0 it is considered not found
.PP
This is useful for non-ontology parsers (xref_parser, go_assoc_parser)
to check whether a referenced \s-1ID\s0 is actually present in the ontology
.PP
note that if acc2name_h has not been created, then accs cannot be
considered not-found, and this will always return 0/false