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revision 1.3, Fri Jan 15 12:54:57 2010 UTC revision 1.4, Thu Mar 25 16:05:50 2010 UTC
# Line 52  Line 52 
52                              call_genes                              call_genes
53                              find_rnas                              find_rnas
54                              assign_functions_to_DNA                              assign_functions_to_DNA
55                                find_special_proteins
56                          )];                          )];
57    
58  sub methods {  sub methods {
# Line 65  Line 66 
66  # Docs are in ANNOserver.pm.  # Docs are in ANNOserver.pm.
67  #  #
68    
69    sub find_special_proteins {
70        # Get the parameters.
71        my ($self, $args) = @_;
72        # Pull in the special protein finder.
73        require find_special_proteins;
74        # Convert the hash to the form expected by find_special_proteins.
75        my $params = {
76            contigs => $args->{-contigs},
77            is_init => $args->{-is_init},
78            is_alt => $args->{-is_alt},
79            is_term => $args->{-is_term},
80            comment => $args->{-comment}
81            };
82        if (exists $args->{-templates}) {
83            my $templates = $args->{-templates};
84            if (ref $templates eq 'ARRAY') {
85                $params->{references} = $templates;
86            } elsif ($templates =~ /^pyr/) {
87                $params->{pyrrolysine} = 1
88            }
89        }
90        # Process the input.
91        my @retVal = find_special_proteins::find_selenoproteins($params);
92        # Return the result.
93        return \@retVal;
94    }
95    
96  sub metabolic_reconstruction {  sub metabolic_reconstruction {
97      # Get the parameters.      # Get the parameters.
98      my ($self, $args) = @_;      my ($self, $args) = @_;

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