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revision 1.31, Tue Aug 21 21:21:24 2007 UTC revision 1.32, Tue Aug 21 22:45:54 2007 UTC
# Line 1786  Line 1786 
1786          push(@$single_domain,$reg2);                           # permanent column          push(@$single_domain,$reg2);                           # permanent column
1787          push(@$single_domain,$thing->organism);                # permanent column          push(@$single_domain,$thing->organism);                # permanent column
1788          push(@$single_domain,$thing->function);                # permanent column          push(@$single_domain,$thing->function);                # permanent column
1789          push(@$single_domain,$subsystems_column{$id}) if (grep (/subsystem/, @$columns));          foreach my $col (@$columns){
1790          push(@$single_domain,$evidence_column{$id}) if (grep (/evidence/, @$columns));              (push(@$single_domain,$subsystems_column{$id}) && (next)) if ($col eq "subsystem");
1791          push(@$single_domain,&get_prefer($thing->acc, 'NCBI')) if (grep (/ncbi_id/, @$columns));              (push(@$single_domain,$evidence_column{$id}) && (next)) if ($col eq "evidence");
1792          push(@$single_domain,&get_prefer($thing->acc, 'RefSeq')) if (grep (/refseq_id/, @$columns));              (push(@$single_domain,&get_prefer($thing->acc, 'NCBI')) && (next)) if ($col eq "ncbi_id");
1793          push(@$single_domain,&get_prefer($thing->acc, 'SwissProt')) if (grep (/swissprot_id/, @$columns));              (push(@$single_domain,&get_prefer($thing->acc, 'RefSeq')) && (next)) if ($col eq "refseq_id");
1794          push(@$single_domain,&get_prefer($thing->acc, 'UniProt')) if (grep (/uniprot_id/, @$columns));              (push(@$single_domain,&get_prefer($thing->acc, 'SwissProt')) && (next)) if ($col eq "swissprot_id");
1795          push(@$single_domain,&get_prefer($thing->acc, 'TIGR')) if (grep (/tigr_id/, @$columns));              (push(@$single_domain,&get_prefer($thing->acc, 'UniProt')) && (next)) if ($col eq "uniprot_id");
1796          push(@$single_domain,&get_prefer($thing->acc, 'PIR')) if (grep (/pir_id/, @$columns));              (push(@$single_domain,&get_prefer($thing->acc, 'TIGR')) && (next)) if ($col eq "tigr_id");
1797          push(@$single_domain,&get_prefer($thing->acc, 'KEGG')) if (grep (/kegg_id/, @$columns));              (push(@$single_domain,&get_prefer($thing->acc, 'PIR')) && (next)) if ($col eq "pir_id");
1798          push(@$single_domain,&get_prefer($thing->acc, 'TrEMBL')) if (grep (/trembl_id/, @$columns));              (push(@$single_domain,&get_prefer($thing->acc, 'KEGG')) && (next)) if ($col eq "kegg_id");
1799          push(@$single_domain,&get_prefer($thing->acc, 'ASAP')) if (grep (/asap_id/, @$columns));              (push(@$single_domain,&get_prefer($thing->acc, 'TrEMBL')) && (next)) if ($col eq "trembl_id");
1800          push(@$single_domain,&get_prefer($thing->acc, 'JGI')) if (grep (/jgi_id/, @$columns));              (push(@$single_domain,&get_prefer($thing->acc, 'ASAP')) && (next)) if ($col eq "asap_id");
1801                (push(@$single_domain,&get_prefer($thing->acc, 'JGI')) && (next)) if ($col eq "jgi_id");
1802            }
1803          push(@$data,$single_domain);          push(@$data,$single_domain);
1804      }      }
1805    
# Line 1829  Line 1831 
1831      my %in_subs  = $fig->subsystems_for_pegs($ids);      my %in_subs  = $fig->subsystems_for_pegs($ids);
1832      my %column;      my %column;
1833      foreach my $id (@$ids){      foreach my $id (@$ids){
1834          my @in_sub = $in_subs{$id} if (defined $in_subs{$id});          my @in_sub = @{$in_subs{$id}} if (defined $in_subs{$id});
1835          my $in_sub;          my @subsystems;
1836    
1837          if (@in_sub > 0) {          if (@in_sub > 0) {
1838              $in_sub = @in_sub;              my $count = 1;
1839                foreach my $array(@in_sub){
1840              # RAE: add a javascript popup with all the subsystems                  push (@subsystems, $count . ". " . $$array[0]);
1841              my $ss_list=join "<br>", map { my $g = $_; $g =~ s/\_/ /g; $_ = $g } sort {$a cmp $b} @in_sub;                  $count++;
1842              $column{$id} = $cgi->a( {id=>"subsystems", onMouseover=>"javascript:if(!this.tooltip) this.tooltip=new Popup_Tooltip(this, 'Subsystems', '$ss_list', ''); this.tooltip.addHandler(); return false;"}, $in_sub);              }
1843                my $in_sub_line = join ("<br>", @subsystems);
1844                $column{$id} = $in_sub_line;
1845          } else {          } else {
1846              $column{$id} = "&nbsp;";              $column{$id} = "&nbsp;";
1847          }          }
# Line 2132  Line 2136 
2136      my %pch_already;      my %pch_already;
2137      foreach my $gene_peg (keys %all_genes)      foreach my $gene_peg (keys %all_genes)
2138      {      {
2139          if ($pch_already{$gene_peg}){next;};          if ($pch_already{$gene_peg}){(next);};
2140          my $gene_set = [$gene_peg];          my $gene_set = [$gene_peg];
2141          foreach my $pch_peg ($fig->in_pch_pin_with($gene_peg)) {          foreach my $pch_peg ($fig->in_pch_pin_with($gene_peg)) {
2142              $pch_peg =~ s/,.*$//;              $pch_peg =~ s/,.*$//;
# Line 2182  Line 2186 
2186  #    my $bbh_sets = [];  #    my $bbh_sets = [];
2187  #    my %already;  #    my %already;
2188  #    foreach my $gene_key (keys(%all_genes)){  #    foreach my $gene_key (keys(%all_genes)){
2189  #       if($already{$gene_key}){next;}  #       if($already{$gene_key}){(next);}
2190  #       my $gene_set = [$gene_key];  #       my $gene_set = [$gene_key];
2191  #  #
2192  #       my $gene_key_genome = $fig->genome_of($gene_key);  #       my $gene_key_genome = $fig->genome_of($gene_key);
2193  #  #
2194  #       foreach my $genome_key (keys(%all_genomes)){  #       foreach my $genome_key (keys(%all_genomes)){
2195  #           #next if ($gene_key_genome eq $genome_key);  #           #(next) if ($gene_key_genome eq $genome_key);
2196  #           my $return = $fig->bbh_list($genome_key,[$gene_key]);  #           my $return = $fig->bbh_list($genome_key,[$gene_key]);
2197  #  #
2198  #           my $feature_list = $return->{$gene_key};  #           my $feature_list = $return->{$gene_key};

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