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revision 1.12, Wed Oct 12 02:47:56 2005 UTC revision 1.14, Mon Nov 28 22:41:16 2005 UTC
# Line 4  Line 4 
4  use Carp;  use Carp;
5  use FIG;  use FIG;
6  use SFXlate;  use SFXlate;
   
7  use Data::Dumper;  use Data::Dumper;
8  use strict;  use strict;
9  use Tracer;  use Tracer;
# Line 148  Line 147 
147          my $reactions = $subsystem->get_reactions;          my $reactions = $subsystem->get_reactions;
148          my @genomes = $subsystem->get_genomes;          my @genomes = $subsystem->get_genomes;
149          my @col_subsets = $subsystem->get_subset_namesC;          my @col_subsets = $subsystem->get_subset_namesC;
150            my @diagrams = $subsystem->get_diagrams();
151          # Create the data structures for the role list and the role index.          # Create the data structures for the role list and the role index.
152          my $role_info = [];          my $role_info = [];
153          my $roleH     = {};          my $roleH     = {};
# Line 224  Line 224 
224          # parameters. If, for example, we are using this object to generate          # parameters. If, for example, we are using this object to generate
225          # a subsystem web page, the focus information would steer us to          # a subsystem web page, the focus information would steer us to
226          # whatever the user wants to look at on the page.          # whatever the user wants to look at on the page.
227          my $active_genomes = &active_genomes($row_subsets,$active_subsetR,$focus,          my $active_genomes = &active_genomes($fig, $row_subsets,$active_subsetR,$focus,
228                                               $genomeH,$genomes_info);                                               $genomeH,$genomes_info);
229    
230          # Now we generate a table of colors for the various PEGs. If the          # Now we generate a table of colors for the various PEGs. If the
# Line 273  Line 273 
273                       Aliases => $aliasesH,                       Aliases => $aliasesH,
274                       Curator => $curator,                       Curator => $curator,
275                       Notes => $notes,                       Notes => $notes,
276                       Reactions => $reactions                       Reactions => $reactions,
277                         Diagrams => \@diagrams,
278                     };                     };
279          bless($self, $class);          bless($self, $class);
280          # Return the object.          # Return the object.
# Line 923  Line 924 
924      return $pegs ? @$pegs : ();      return $pegs ? @$pegs : ();
925  }  }
926    
927    =head3 get_diagrams
928    
929    C<< my @list = $sub->get_diagrams(); >>
930    
931    Return a list of the diagrams associated with this subsystem. Each diagram
932    is represented in the return list as a 4-tuple C<[diagram_id, diagram_name,
933    page_link, img_link]> where
934    
935    =over 4
936    
937    =item diagram_id
938    
939    ID code for this diagram.
940    
941    =item diagram_name
942    
943    Displayable name of the diagram.
944    
945    =item page_link
946    
947    URL of an HTML page containing information about the diagram.
948    
949    =item img_link
950    
951    URL of an HTML page containing an image for the diagram.
952    
953    =back
954    
955    Note that the URLs are in fact for CGI scripts with parameters that point them
956    to the correct place. Though Sprout has diagram information in it, it has
957    no relationship to the diagrams displayed in SEED, so the work is done entirely
958    on the SEED side.
959    
960    =cut
961    
962    sub get_diagrams {
963        # Get the parameters.
964        my ($self) = @_;
965        # Return the diagram list.
966        return @{$self->{Diagrams}};
967    }
968    
969  sub get_notes {  sub get_notes {
970      my($self) = @_;      my($self) = @_;
971    

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