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.\" ========================================================================
.\"
.IX Title "GO::Model::Association 3pm"
.TH GO::Model::Association 3pm "2014-02-01" "perl v5.18.2" "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::Model::Association \- association between a GO term and a gene product
.Ve
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 9
\&  # print all gene products associated with a GO::Model::Term
\&  my $assoc_l = $term\->association_list;
\&  foreach my $assoc (@$assoc_l) {
\&    printf "gene product:%s %s %s (evidence: %s)\en",
\&      $assoc\->gene_product\->symbol,
\&      $assoc\->is_not ? "IS NOT" : "IS",
\&      $term\->name,
\&      map {$_\->code} @{$assoc\->evidence_list};
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Represents an association between a \s-1GO\s0 term (GO::Model::Term) and a
gene product (GO::Model::GeneProduct)
.SS "go_public_acc"
.IX Subsection "go_public_acc"
.Vb 3
\&  Usage   \-
\&  Returns \-
\&  Args    \-
.Ve
.SS "add_evidence"
.IX Subsection "add_evidence"
.Vb 3
\&  Usage   \- $assoc\->add_evidence($my_evid);
\&  Returns \-
\&  Args    \- GO::Model::Evidence
.Ve
.SS "evidence_list"
.IX Subsection "evidence_list"
.Vb 3
\&  Usage   \- my $ev_l = $assoc\->evidence_list;
\&  Returns \-
\&  Args    \-
.Ve
.PP
gets/sets arrayref of GO::Model::Evidence
.SS "evidence_as_str"
.IX Subsection "evidence_as_str"
.Vb 4
\&  Usage   \- print $assoc\->evidence_as_str
\&  Usage   \- print $assoc\->evidence_as_str(1); #verbose
\&  Returns \-
\&  Args    \- verbose
.Ve
.PP
concatenates evcodes together, for display
.SS "has_evcode"
.IX Subsection "has_evcode"
.Vb 3
\&  Usage   \- if $assoc\->has_evcode("IEA");
\&  Returns \- boolean
\&  Args    \- evcode [string]
.Ve
.SS "remove_evcode"
.IX Subsection "remove_evcode"
.Vb 3
\&  Usage   \- $assoc\->remove_evcode("IEA");
\&  Returns \- 
\&  Args    \- evcode [string]
.Ve
.PP
removes all evidence of the specified type from the
association; useful for filtering
.SS "evidence_score"
.IX Subsection "evidence_score"
.Vb 3
\&  Usage   \- my $score = $assoc\->evidence_score
\&  Returns \- 0 <= float <= 1
\&  Args    \-
.Ve
.PP
returns a score for the association based on the evidence;
.PP
This is an \s-1EXPERIMENTAL\s0 method; it may be removed in future versions.
.PP
The evidence fields can be thought of in a loose hierachy:
.PP
\&\s-1TAS
   IDA
      IMP/IGI/IPI
                 ISS
                    NAS\s0
.PP
see http://www.geneontology.org/GO.evidence.html
.SS "gene_product"
.IX Subsection "gene_product"
.Vb 3
\&  Usage   \- my $gp = $assoc\->gene_product
\&  Returns \-
\&  Args    \-
.Ve
.PP
gets sets GO::Model::GeneProduct
.SS "assigned_by"
.IX Subsection "assigned_by"
.Vb 3
\&  Usage   \-
\&  Returns \-
\&  Args    \-
.Ve
.SS "is_not"
.IX Subsection "is_not"
.Vb 3
\&  Usage   \-
\&  Returns \-
\&  Args    \-
.Ve
.PP
gets/sets boolean representing whether this relationship is negated
.SS "assocdate"
.IX Subsection "assocdate"
.Vb 3
\&  Usage   \-
\&  Returns \-
\&  Args    \-
.Ve
.SS "assocdate"
.IX Subsection "assocdate"
.Vb 3
\&  Usage   \-
\&  Returns \-
\&  Args    \-
.Ve
.PP
gets/sets integer representing the date of the association (\s-1YYYYMMDD\s0 format)
.SS "role_group"
.IX Subsection "role_group"
.Vb 3
\&  Usage   \-
\&  Returns \-
\&  Args    \-
.Ve
.PP
gets/sets integer to indicate which associations go together