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revision 1.54, Mon Feb 18 20:40:19 2008 UTC revision 1.55, Sat Feb 23 06:48:43 2008 UTC
# Line 14  Line 14 
14  #use strict;  #use strict;
15  #use warnings;  #use warnings;
16  use HTML;  use HTML;
17  use FigFams;  use FFs;
18    
19  1;  1;
20    
# Line 1686  Line 1686 
1686    
1687      my %in_subs  = $fig->subsystems_for_pegs(\@ids);      my %in_subs  = $fig->subsystems_for_pegs(\@ids);
1688    
1689        my %sims_objects_evalue;
1690        my $count = 0;
1691      foreach my $thing (@$array){      foreach my $thing (@$array){
1692          if ($thing->class eq "SIM"){          if ($thing->class eq "SIM"){
1693                $sims_objects_evalue{$count} = $thing->evalue;
1694            }
1695            $count++;
1696        }
1697    
1698        foreach my $index (sort {$sims_objects_evalue{$a}<=>$sims_objects_evalue{$b}} keys %sims_objects_evalue){
1699    #    foreach my $thing ( @$array){
1700            my $thing = $array->[$index];
1701            if ($thing->class eq "SIM"){
1702              my $peg = $thing->acc;              my $peg = $thing->acc;
1703              my $query = $thing->query;              my $query = $thing->query;
1704    
# Line 1954  Line 1964 
1964      #my $alias_col = {};      #my $alias_col = {};
1965    
1966      my $figfam_data = "$FIG_Config::FigfamsData";      my $figfam_data = "$FIG_Config::FigfamsData";
1967      my $figfams = new FigFams($fig,$figfam_data);      my $figfams = new FFs($figfam_data);
1968      my $ff_hash = $figfams->families_containing_peg_bulk(\@ids);  #    my $ff_hash = $figfams->families_containing_peg_bulk(\@ids);
1969    
1970        my %sims_objects_evalue;
1971        my $simcount = 0;
1972      foreach my $thing (@$dataset) {      foreach my $thing (@$dataset) {
1973            if ($thing->class eq "SIM"){
1974                $sims_objects_evalue{$simcount} = $thing->evalue;
1975            }
1976            $simcount++;
1977        }
1978    
1979        foreach my $index (sort {$sims_objects_evalue{$a}<=>$sims_objects_evalue{$b}} keys %sims_objects_evalue){
1980    #    foreach my $thing ( @$dataset){
1981            my $thing = $dataset->[$index];
1982    
1983          next if ($thing->class ne "SIM");          next if ($thing->class ne "SIM");
1984          my $single_domain = [];          my $single_domain = [];
1985          $count++;          $count++;
# Line 1994  Line 2016 
2016          push (@$single_domain, $box_col, $fig_col, $thing->evalue,          push (@$single_domain, $box_col, $fig_col, $thing->evalue,
2017                "$iden\%", $reg1, $reg2, $thing->organism, $thing->function);   # permanent columns                "$iden\%", $reg1, $reg2, $thing->organism, $thing->function);   # permanent columns
2018    
2019            my ($ff) = $figfams->families_containing_peg($id);
2020    
2021          foreach my $col (sort keys %$scroll_list){          foreach my $col (sort keys %$scroll_list){
2022              if ($col =~ /associated_subsystem/)          {push(@$single_domain,$subsystems_column{$id});}              if ($col =~ /associated_subsystem/)          {push(@$single_domain,$subsystems_column{$id});}
2023              elsif ($col =~ /evidence/)                   {push(@$single_domain,$evidence_column{$id});}              elsif ($col =~ /evidence/)                   {push(@$single_domain,$evidence_column{$id});}
# Line 2010  Line 2034 
2034              elsif ($col =~ /jgi_id/)                     {push(@$single_domain,$alias_col->{$id}->{"JGI"});}              elsif ($col =~ /jgi_id/)                     {push(@$single_domain,$alias_col->{$id}->{"JGI"});}
2035              elsif ($col =~ /taxonomy/)                   {push(@$single_domain,$lineages->{$tax});}              elsif ($col =~ /taxonomy/)                   {push(@$single_domain,$lineages->{$tax});}
2036              #elsif ($col =~ /taxonomy/)                   {push(@$single_domain,$fig->taxonomy_of($taxid));}              #elsif ($col =~ /taxonomy/)                   {push(@$single_domain,$fig->taxonomy_of($taxid));}
2037              elsif ($col =~ /figfam/)                     {push(@$single_domain,"<a href='?page=FigFamViewer&figfam=" . $ff_hash->{$id} . "' target='_new'>" . $ff_hash->{$id} . "</a>");}              #elsif ($col =~ /figfam/)                     {push(@$single_domain,"<a href='?page=FigFamViewer&figfam=" . $ff_hash->{$id} . "' target='_new'>" . $ff_hash->{$id} . "</a>");}
2038                elsif ($col =~ /figfam/)                     {push(@$single_domain,"<a href='?page=FigFamViewer&figfam=" . $ff . "' target='_new'>" . $ff . "</a>");}
2039          }          }
2040          push(@$data,$single_domain);          push(@$data,$single_domain);
2041      }      }

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