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revision 1.1, Tue Apr 22 14:49:38 2014 UTC revision 1.2, Tue Apr 22 15:20:20 2014 UTC
# Line 226  Line 226 
226                                $genome_names{$4},                                $genome_names{$4},
227                                $3] : () }                                $3] : () }
228                     `cut -f1,2,4 $dataDF/families.all`;                     `cut -f1,2,4 $dataDF/families.all`;
229      push(@$html,$cgi->start_form(-action => "./families4_on_tree.cgi"));      push(@$html,$cgi->start_form(-action => "./families_on_tree.cgi"));
230      push(@$html,"<br><br>\n",&HTML::make_table($col_hdrs,\@tuples,"Distribution of Family $family: $func"),$cgi->hr,"\n");      push(@$html,"<br><br>\n",&HTML::make_table($col_hdrs,\@tuples,"Distribution of Family $family: $func"),$cgi->hr,"\n");
231      push(@$html,"<input type=hidden name=dataD value=$dataD>\n");      push(@$html,"<input type=hidden name=dataD value=$dataD>\n");
232      push(@$html,"<input type=hidden name=request value=show_ali_or_occurs_tree>\n");      push(@$html,"<input type=hidden name=request value=show_ali_or_occurs_tree>\n");
# Line 457  Line 457 
457      $dataDF =~ /([^\/]+)$/;      $dataDF =~ /([^\/]+)$/;
458      my $dataD = $1;      my $dataD = $1;
459    
460      return ("<a target=_blank href=http://bioseed.mcs.anl.gov/ross/FIG/families4_on_tree.cgi?request=show_family_tree&family=$fam&dataD=$dataD>tree</a>",      return ("<a target=_blank href=http://bioseed.mcs.anl.gov/ross/FIG/families_on_tree.cgi?request=show_family_tree&family=$fam&dataD=$dataD>tree</a>",
461              "<a target=_blank href=http://bioseed.mcs.anl.gov/ross/FIG/families4_on_tree.cgi?request=show_family_pegs&family=$fam&pegs=1&dataD=$dataD>PEGs:$fam</a>");              "<a target=_blank href=http://bioseed.mcs.anl.gov/ross/FIG/families_on_tree.cgi?request=show_family_pegs&family=$fam&pegs=1&dataD=$dataD>PEGs:$fam</a>");
462  }  }
463    
464  sub show_fam_table_link {  sub show_fam_table_link {
# Line 467  Line 467 
467      $dataDF =~ /([^\/]+)$/;      $dataDF =~ /([^\/]+)$/;
468      my $dataD = $1;      my $dataD = $1;
469    
470      return "<a target=_blank href=http://bioseed.mcs.anl.gov/ross/FIG/families4_on_tree.cgi?family=$fam&pegs=1&request=show_family_pegs&dataD=$dataD>$fam: PEGs</a>";      return "<a target=_blank href=http://bioseed.mcs.anl.gov/ross/FIG/families_on_tree.cgi?family=$fam&pegs=1&request=show_family_pegs&dataD=$dataD>$fam: PEGs</a>";
471  }  }
472    
473  sub show_func {  sub show_func {
# Line 682  Line 682 
682      print $cgi->header;      print $cgi->header;
683      print "<h3>$g</h3>\n";      print "<h3>$g</h3>\n";
684      print "<ol>\n";      print "<ol>\n";
685      print "<li> <a target=_blank href=http://bioseed.mcs.anl.gov/ross/FIG/families4_on_tree.cgi?request=show_otu_tree&dataD=$g>Gains/losses of Gene Families</a>\n";      print "<li> <a target=_blank href=http://bioseed.mcs.anl.gov/ross/FIG/families_on_tree.cgi?request=show_otu_tree&dataD=$g>Gains/losses of Gene Families</a>\n";
686      print "<li><a target=_blank href=http://bioseed.mcs.anl.gov/ross/FIG/families4_on_tree.cgi?request=show_kovbassa&dataD=$g>Genes that Distinguishing Families (Genes as Signatures)</a>\n";      print "<li><a target=_blank href=http://bioseed.mcs.anl.gov/ross/FIG/families_on_tree.cgi?request=show_kovbassa&dataD=$g>Genes that Distinguishing Families (Genes as Signatures)</a>\n";
687      print "<li><a target=_blank href=http://bioseed.mcs.anl.gov/ross/FIG/families4_on_tree.cgi?request=show_adjacency&dataD=$g>Changes in Adjacency</a>\n";      print "<li><a target=_blank href=http://bioseed.mcs.anl.gov/ross/FIG/families_on_tree.cgi?request=show_adjacency&dataD=$g>Changes in Adjacency</a>\n";
688      print "</ol>\n";      print "</ol>\n";
689    
690      push(@$html,"<br>",      push(@$html,"<br>",
691                  $cgi->start_form(-action => "./families4_on_tree.cgi"),                  $cgi->start_form(-action => "./families_on_tree.cgi"),
692                  $cgi->textfield(-name => 'keywords',-size => 100),                  $cgi->textfield(-name => 'keywords',-size => 100),
693                  $cgi->hidden(-override => 1,-name => 'request',-value => 'show_indexed_funcs'),                  $cgi->hidden(-override => 1,-name => 'request',-value => 'show_indexed_funcs'),
694                  $cgi->hidden(-override => 1,-name => 'dataD',-value => $dataD),                  $cgi->hidden(-override => 1,-name => 'dataD',-value => $dataD),
# Line 740  Line 740 
740          print "<h2>Genera Available</h2>\n";          print "<h2>Genera Available</h2>\n";
741          foreach my $g (sort @genera)          foreach my $g (sort @genera)
742          {          {
743              print "<h3><a target=_blank href=http://bioseed.mcs.anl.gov/ross/FIG/families4_on_tree.cgi?request=show_options_for_otu&dataD=$g>$g</a>\n";              print "<h3><a target=_blank href=http://bioseed.mcs.anl.gov/ross/FIG/families_on_tree.cgi?request=show_options_for_otu&dataD=$g>$g</a>\n";
744          }          }
745      }      }
746      else      else
# Line 768  Line 768 
768    
769      if (! $function) { return '' }      if (! $function) { return '' }
770      my $functionQ = uri_escape($function);      my $functionQ = uri_escape($function);
771      return "<a target=_blank href=http://bioseed.mcs.anl.gov/ross/FIG/families4_on_tree.cgi?request=show_func&function=$functionQ&dataD=$dataD>$function</a>"      return "<a target=_blank href=http://bioseed.mcs.anl.gov/ross/FIG/families_on_tree.cgi?request=show_func&function=$functionQ&dataD=$dataD>$function</a>"
772  }  }
773    
774  sub virulence_functions_link {  sub virulence_functions_link {
# Line 777  Line 777 
777      if ((-s "$dataDF/virulence.functions") && ($dataDF =~ /([^\/]+)$/))      if ((-s "$dataDF/virulence.functions") && ($dataDF =~ /([^\/]+)$/))
778      {      {
779          my $dataDQ = uri_escape($1);          my $dataDQ = uri_escape($1);
780          return "<a target=_blank href=http://bioseed.mcs.anl.gov/ross/FIG/families4_on_tree.cgi?request=show_virulence_functions&dataD=$dataDQ>Some Posssible Functions Associated with Virulence</a>";          return "<a target=_blank href=http://bioseed.mcs.anl.gov/ross/FIG/families_on_tree.cgi?request=show_virulence_functions&dataD=$dataDQ>Some Posssible Functions Associated with Virulence</a>";
781      }      }
782      return '';      return '';
783  }  }
# Line 789  Line 789 
789      if ($dataDF =~ /([^\/]+)$/)      if ($dataDF =~ /([^\/]+)$/)
790      {      {
791          my $dataDQ = uri_escape($1);          my $dataDQ = uri_escape($1);
792          return "<a target=_blank href=http://bioseed.mcs.anl.gov/ross/FIG/families4_on_tree.cgi?family=$fam&union=$union&dataD=$dataDQ&request=show_family_tree>Family on Tree</a>";          return "<a target=_blank href=http://bioseed.mcs.anl.gov/ross/FIG/families_on_tree.cgi?family=$fam&union=$union&dataD=$dataDQ&request=show_family_tree>Family on Tree</a>";
793      }      }
794      return '';      return '';
795  }  }
# Line 798  Line 798 
798      my($dataD,$node,$type) = @_;      my($dataD,$node,$type) = @_;
799      if ($type eq "families")      if ($type eq "families")
800      {      {
801          return "<a target=_blank href=http://bioseed.mcs.anl.gov/ross/FIG/families4_on_tree.cgi?request=show_node&dataD=$dataD&node=$node&type=families>$node</a>";          return "<a target=_blank href=http://bioseed.mcs.anl.gov/ross/FIG/families_on_tree.cgi?request=show_node&dataD=$dataD&node=$node&type=families>$node</a>";
802      }      }
803      else      else
804      {      {
805          return "<a target=_blank href=http://bioseed.mcs.anl.gov/ross/FIG/families4_on_tree.cgi?request=show_node&dataD=$dataD&node=$node&type=adjacency>$node</a>";          return "<a target=_blank href=http://bioseed.mcs.anl.gov/ross/FIG/families_on_tree.cgi?request=show_node&dataD=$dataD&node=$node&type=adjacency>$node</a>";
806      }      }
807  }  }
808    
# Line 810  Line 810 
810      my($dataD,$family,$coupled) = @_;      my($dataD,$family,$coupled) = @_;
811      my %tmp = map { $_ => 1 } ($family,@$coupled);      my %tmp = map { $_ => 1 } ($family,@$coupled);
812      my $families = join(",",sort { $a <=> $b} keys(%tmp));      my $families = join(",",sort { $a <=> $b} keys(%tmp));
813      return "<a target=_blank href=\"http://bioseed.mcs.anl.gov/ross/FIG/families4_on_tree.cgi?request=show_clusters&dataD=$dataD&families=$families\">$family</a>";      return "<a target=_blank href=\"http://bioseed.mcs.anl.gov/ross/FIG/families_on_tree.cgi?request=show_clusters&dataD=$dataD&families=$families\">$family</a>";
814  }  }
815    
816  sub show_clusters {  sub show_clusters {
# Line 891  Line 891 
891      }      }
892      my $tree = join("",@tree);      my $tree = join("",@tree);
893      push(@$html,"<br>",      push(@$html,"<br>",
894                  $cgi->start_form(-action => "./families4_on_tree.cgi"),                  $cgi->start_form(-action => "./families_on_tree.cgi"),
895                  $cgi->hidden(-override => 1,-name => 'request',-value => 'compute_kovbassa_sigs'),                  $cgi->hidden(-override => 1,-name => 'request',-value => 'compute_kovbassa_sigs'),
896                  $cgi->hidden(-override => 1,-name => 'dataD',-value => $dataD),                  $cgi->hidden(-override => 1,-name => 'dataD',-value => $dataD),
897                  "<pre>\n$tree\n</pre>\n",                  "<pre>\n$tree\n</pre>\n",

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