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.\" ========================================================================
.\"
.IX Title "GO::Model::Evidence 3pm"
.TH GO::Model::Evidence 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.
.if n .ad l
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.SH "NAME"
.Vb 1
\&  GO::Model::Evidence \- evidence for an association
.Ve
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 6
\&  my $ev_l = $association\->evidence_list;
\&  foreach my $ev (@$ev_l) {
\&    print "Evidence for association %s : %s\en",
\&      $association\->gene_product\->symbol,
\&      $ev\->code;
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
evidence for an association
.PP
see http://www.geneontology.org/GO.evidence.html
for a list of evidence codes
.SS "code"
.IX Subsection "code"
.Vb 3
\&  Usage   \- $ev\->code("IEA");
\&  Returns \-
\&  Args    \-
.Ve
.PP
gets/sets the evidence code
.PP
see http://www.geneontology.org/GO.evidence.html
.SS "seq_acc"
.IX Subsection "seq_acc"
.Vb 3
\&  Usage   \-
\&  Returns \-
\&  Args    \-
.Ve
.PP
gets/sets the sequence accesion GO::Model::Xref
.PP
\&\s-1ALPHA CODE\s0  \- \s-1API\s0 may change
.PP
used to set the GO::Model::Xref list from a text string. eg
.PP
.Vb 1
\&  $ev\->seq_acc("SGD:RRP41; SGDID:L0003550");
.Ve
.PP
will actually add two GO::Model::Xref objects
.PP
This method doesn't really belong in the GO::Model::* hierarchy as it
contains parsing code. Its a minor hack mainly due to the fact that
this data is still denormalized in the database.
.SS "add_seq_xref"
.IX Subsection "add_seq_xref"
.Vb 3
\&  Usage   \-
\&  Returns \-
\&  Args    \-
.Ve
.PP
equivalent to \s-1WITH\s0 column in gene_association files, and evidence_dbxref tables in db
.SS "add_pub_xref"
.IX Subsection "add_pub_xref"
.Vb 3
\&  Usage   \-
\&  Returns \-
\&  Args    \-
.Ve
.SS "xref"
.IX Subsection "xref"
.Vb 3
\&  Usage   \-
\&  Returns \-
\&  Args    \-
.Ve
.PP
gets/sets the literature or sequence reference GO::Model::Xref
.PP
\&\s-1NOTE:\s0 at some point we may want to deprecate this method and persuade
\&\s-1API\s0 client code to call
.PP
.Vb 1
\&  $ev\->literature_xref
.Ve
.PP
instead, to make explicit the fact that this is a literature reference
as opposed to a sequence reference
.SS "xref_list"
.IX Subsection "xref_list"
.Vb 3
\&  Usage   \-
\&  Returns \- GO::Model::Xref listref
\&  Args    \-
.Ve
.PP
returns all (sequence and literature) references
.SS "xref"
.IX Subsection "xref"
.Vb 3
\&  Usage   \-
\&  Returns \-
\&  Args    \-
.Ve
.PP
deprecated \- sets first pub_xref_list
.SS "valid_codes"
.IX Subsection "valid_codes"
.Vb 3
\&  Usage   \- print join("; ", GO::Model::Evidence\->valid_codes);
\&  Returns \- string array
\&  Args    \-
.Ve
.PP
list of valid evidence codes