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revision 1.7, Sun Sep 18 14:11:22 2005 UTC revision 1.8, Tue Sep 20 16:58:48 2005 UTC
# Line 9  Line 9 
9    
10  sub new  sub new
11  {  {
12      my($class, $ssa, $fig, $active_subsetR, $focus, $show_clusters, $aliases) = @_;      my($class, $ssa, $fig, $active_subsetR, $focus, $show_clusters, $aliases, $peg_colors) = @_;
13    
14      $ssa =~ s/ /_/g;      $ssa =~ s/ /_/g;
15    
# Line 105  Line 105 
105    
106          my $row_subsets    = &row_subsets($fig,$genomeH,$genomes_info);          my $row_subsets    = &row_subsets($fig,$genomeH,$genomes_info);
107          my $active_genomes = &active_genomes($row_subsets,$active_subsetR,$focus,$genomeH,$genomes_info);          my $active_genomes = &active_genomes($row_subsets,$active_subsetR,$focus,$genomeH,$genomes_info);
108          my $colorsH  = $show_clusters  ? &set_colors($fig,$pegH,$active_genomes)  : {};  
109            my $colorsH;
110            if ($peg_colors)
111            {
112                $colorsH = {};
113                foreach $_ (@$peg_colors)
114                {
115                    my($peg,$color) = @$_;
116                    $colorsH->{$peg} = $color;
117                }
118            }
119            elsif ($show_clusters)
120            {
121                $colorsH  = &set_colors($fig,$pegH,$active_genomes);
122            }
123            else
124            {
125                $colorsH = {};
126            }
127    
128          my $aliasesH = $aliases ? &set_aliases($fig,$pegH,$active_genomes) : {};          my $aliasesH = $aliases ? &set_aliases($fig,$pegH,$active_genomes) : {};
129          my $reactions = $subsystem->get_reactions;          my $reactions = $subsystem->get_reactions;
130          my $self = { Roles => $role_info,          my $self = { Roles => $role_info,

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