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revision 1.18, Wed Nov 29 15:19:19 2006 UTC revision 1.19, Thu Dec 6 13:59:34 2007 UTC
# Line 103  Line 103 
103    
104  =head3 new  =head3 new
105    
106  C<< my $usub = UnvSubsys->new($ssa, $fig, $active_subsetR, $focus, $show_clusters, $aliases, \@peg_colors); >>      my $usub = UnvSubsys->new($ssa, $fig, $active_subsetR, $focus, $show_clusters, $aliases, \@peg_colors);
107    
108  Construct a new universal subsystem object for a specified subsystem.  Construct a new universal subsystem object for a specified subsystem.
109    
# Line 308  Line 308 
308    
309  =head3 get_ssa  =head3 get_ssa
310    
311  C<< my $ssa = $unvsub->get_ssa(); >>      my $ssa = $unvsub->get_ssa();
312    
313  Return the name of the subsystem  Return the name of the subsystem
314    
# Line 321  Line 321 
321    
322  =head3 get_ssa_pretty  =head3 get_ssa_pretty
323    
324  C<< my $ssa = $unvsub->get_ssa_pretty(); >>      my $ssa = $unvsub->get_ssa_pretty();
325    
326  Return the 'prettyfied' name of the subsystem  Return the 'prettyfied' name of the subsystem
327    
# Line 337  Line 337 
337    
338  =head3 get_subset_namesR  =head3 get_subset_namesR
339    
340  C<< my @names = $unvsub->get_subset_namesR(); >>      my @names = $unvsub->get_subset_namesR();
341    
342  Return the names of the genome (row) subsets.  Return the names of the genome (row) subsets.
343    
# Line 351  Line 351 
351    
352  =head3 get_subsetR  =head3 get_subsetR
353    
354  C<< my @genomes = $unvsub->get_subsetR($set); >>      my @genomes = $unvsub->get_subsetR($set);
355    
356  Return a list of the genome IDs covered by a row subset.  Return a list of the genome IDs covered by a row subset.
357    
# Line 393  Line 393 
393    
394  =head3 get_subsetR  =head3 get_subsetR
395    
396  C<< my @pairs = $unvsub->get_subsetsR(); >>      my @pairs = $unvsub->get_subsetsR();
397    
398  Return a list of all the row subsets. The subsets are returned in the form  Return a list of all the row subsets. The subsets are returned in the form
399  of 2-tuples, each consisting of a subset name followed by a reference to a  of 2-tuples, each consisting of a subset name followed by a reference to a
# Line 424  Line 424 
424    
425  =head3 row_subsets  =head3 row_subsets
426    
427  C<< my $subsetList = UnvSubsys::row_subsets($fig, \%genomeH); >>      my $subsetList = UnvSubsys::row_subsets($fig, \%genomeH);
428    
429  This method computes the taxonomic row subsets for a subsystem. It takes  This method computes the taxonomic row subsets for a subsystem. It takes
430  as input a hash that maps genome IDs to column indices and a FIG object.  as input a hash that maps genome IDs to column indices and a FIG object.
# Line 497  Line 497 
497    
498  =head3 set_aliases  =head3 set_aliases
499    
500  C<< my $aliasHash = UnvSubsys::set_aliases($fig, $pegH, $active_genomes); >>      my $aliasHash = UnvSubsys::set_aliases($fig, $pegH, $active_genomes);
501    
502  Return a hash mapping PEG IDs to aliases.  Return a hash mapping PEG IDs to aliases.
503    
# Line 573  Line 573 
573    
574  =head3 set_colors  =head3 set_colors
575    
576  C<< my $colorHash = UnvSubsys::set_colors($fig, $sub, \%pegH, \%active_genomes); >>      my $colorHash = UnvSubsys::set_colors($fig, $sub, \%pegH, \%active_genomes);
577    
578  Return a hash that maps each PEG in the subsystem spreadsheet to a display  Return a hash that maps each PEG in the subsystem spreadsheet to a display
579  color. Not all PEGs need to be mapped. Those that do not have a color  color. Not all PEGs need to be mapped. Those that do not have a color
# Line 663  Line 663 
663    
664  =head3 set_colors_for_genome  =head3 set_colors_for_genome
665    
666  C<< my $colorHash = UnvSubsys::set_colors_for_genome($fig, $sub, \@pegs); >>      my $colorHash = UnvSubsys::set_colors_for_genome($fig, $sub, \@pegs);
667    
668  Return a reference to a hash mapping the specified pegs to colors. PEGs that  Return a reference to a hash mapping the specified pegs to colors. PEGs that
669  are physically close to each other will be painted the same color.  are physically close to each other will be painted the same color.
# Line 719  Line 719 
719    
720  =head3 cool_colors  =head3 cool_colors
721    
722  C<< my @colorList = UnvSubsys::cool_colors(); >>      my @colorList = UnvSubsys::cool_colors();
723    
724  Return a list of web-safe colors.  Return a list of web-safe colors.
725    
# Line 748  Line 748 
748    
749  =head3 ext_id  =head3 ext_id
750    
751  C<< my $externalID = UnvSubsys::ext_id($fig, $peg); >>      my $externalID = UnvSubsys::ext_id($fig, $peg);
752    
753  or  or
754    
755  C<< my @externalIDs = UnvSubsys::ext_id($fig, $peg); >>      my @externalIDs = UnvSubsys::ext_id($fig, $peg);
756    
757  Return a list of non-FIG IDs for the specified feature. In a scalar context, return  Return a list of non-FIG IDs for the specified feature. In a scalar context, return
758  a single non-FIG ID for the specified feature.  a single non-FIG ID for the specified feature.
# Line 821  Line 821 
821    
822  =head3 subsystem_curator  =head3 subsystem_curator
823    
824  C<< my $name = $unvsub->subsystem_curator(); >>      my $name = $unvsub->subsystem_curator();
825    
826  Return the name of the subsystem curator. The database stores user names as  Return the name of the subsystem curator. The database stores user names as
827  C<master:>I<name>. This method strips off the C<master:> prefix before it  C<master:>I<name>. This method strips off the C<master:> prefix before it
# Line 839  Line 839 
839    
840  =head3 get_roles  =head3 get_roles
841    
842  C<< my @roles = $unvsub->get_roles(); >>      my @roles = $unvsub->get_roles();
843    
844  Return a list of the roles (columns) for this subsystem. The roles will be  Return a list of the roles (columns) for this subsystem. The roles will be
845  returned in column order, so that if you access the sixth element of the  returned in column order, so that if you access the sixth element of the
# Line 856  Line 856 
856    
857  =head3 get_genome_index  =head3 get_genome_index
858    
859  C<< my $index = $unvsub->get_genome_index($genome); >>      my $index = $unvsub->get_genome_index($genome);
860    
861  Return the row index of the specified genome.  Return the row index of the specified genome.
862    
# Line 884  Line 884 
884    
885  =head3 get_genomes  =head3 get_genomes
886    
887  C<< my @genomes = $unvsub->get_genomes(); >>      my @genomes = $unvsub->get_genomes();
888    
889  Return a list of the genome IDs for the subsystem. The genomes will be  Return a list of the genome IDs for the subsystem. The genomes will be
890  presented in row order. In other words, if you index into the sixth  presented in row order. In other words, if you index into the sixth
# Line 902  Line 902 
902    
903  =head3 get_variant_code  =head3 get_variant_code
904    
905  C<< my $code = $unvsub->get_variant_code($genome); >>      my $code = $unvsub->get_variant_code($genome);
906    
907  Return the variant code for a genome. Each subsystem has several variations.  Return the variant code for a genome. Each subsystem has several variations.
908  The variant code indicates which variation of a subsystem is used by a  The variant code indicates which variation of a subsystem is used by a
# Line 944  Line 944 
944    
945  =head3 get_pegs_from_cell  =head3 get_pegs_from_cell
946    
947  C<< my @pegs = $unvsub->get_pegs_from_cell($genome, $role); >>      my @pegs = $unvsub->get_pegs_from_cell($genome, $role);
948    
949  Return a list of the features in a specified spreadsheet cell. The cell is specified  Return a list of the features in a specified spreadsheet cell. The cell is specified
950  by genome ID and role ID.  by genome ID and role ID.
# Line 979  Line 979 
979    
980  =head3 get_diagrams  =head3 get_diagrams
981    
982  C<< my @list = $sub->get_diagrams(); >>      my @list = $sub->get_diagrams();
983    
984  Return a list of the diagrams associated with this subsystem. Each diagram  Return a list of the diagrams associated with this subsystem. Each diagram
985  is represented in the return list as a 4-tuple C<[diagram_id, diagram_name,  is represented in the return list as a 4-tuple C<[diagram_id, diagram_name,
# Line 1080  Line 1080 
1080    
1081  =head3 active_genomes  =head3 active_genomes
1082    
1083  C<< my $activeHash = UnvSubsys::active_genomes(\@row_subsets, $active_subsetR, $focus, \%genomeH, \@genomes_info); >>      my $activeHash = UnvSubsys::active_genomes(\@row_subsets, $active_subsetR, $focus, \%genomeH, \@genomes_info);
1084    
1085  Return a hash containing the active genomes for this subsystem display. The  Return a hash containing the active genomes for this subsystem display. The
1086  keys of the hash will be the row indices of the genomes to be highlighted on the  keys of the hash will be the row indices of the genomes to be highlighted on the

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