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revision 1.43, Wed Jan 25 04:12:20 2006 UTC revision 1.44, Fri Jan 27 05:05:36 2006 UTC
# Line 151  Line 151 
151               $cgi->p("You can enter a protein ID . You will recieve a list of all the families that protein is in. \n",               $cgi->p("You can enter a protein ID . You will recieve a list of all the families that protein is in. \n",
152               "You can use a FIG ID such as fig|83333.1.peg.3, or an ID from SwissProt, KEGG, NCBI, and others.\n"),               "You can use a FIG ID such as fig|83333.1.peg.3, or an ID from SwissProt, KEGG, NCBI, and others.\n"),
153               "Please enter a protein id: ", $cgi->textfield(-name=>"prot", -size=>40), "<br>\n",               "Please enter a protein id: ", $cgi->textfield(-name=>"prot", -size=>40), "<br>\n",
154                 $cgi->p("You can enter a family ID. You will receive a list of all proteins in that family. \n",
155                 "You can use a family ID such as fig|PF003462 or pir|PIRSF012283.\n"),
156                 "Please enter a family id: ", $cgi->textfield(-name=>"family", -size=>40), "<br>\n",
157               $cgi->submit(-name=>'equivalence', -value=>"Show Protein Families"), "\n", $cgi->reset,               $cgi->submit(-name=>'equivalence', -value=>"Show Protein Families"), "\n", $cgi->reset,
158               $cgi->end_form(),               $cgi->end_form(),
159             ),             ),
# Line 312  Line 315 
315          $cgi->p("<h1>Protein <b>$peg</b>: $genusspecies</h1>"), "\n",          $cgi->p("<h1>Protein <b>$peg</b>: $genusspecies</h1>"), "\n",
316          "<div class=\"bordermargin\">",          "<div class=\"bordermargin\">",
317          $cgi->hidden(-name=>'querycid', -value=>$fig->prot_to_cid($peg)), "\n",          $cgi->hidden(-name=>'querycid', -value=>$fig->prot_to_cid($peg)), "\n",
318          $cgi->a({class=>"help", onMouseover=>"javascript:if(!this.tooltip) this.tooltip=new Popup_Tooltip(this, 'Help', 'The table below shows all the families that contain a protein with the same sequence as <b>$peg</b>, although each family uses different IDs. The number of different IDs in each protein family and the number of unique protein sequences in each family are also shown. The latter is often less than the former since many databases contain identical proteins with different identifiers (for example the same protein from different <i>$genusspecies</i> genome sequences).', ''); this.tooltip.addHandler(); return false;", href=>"Html/ProteinFamilies.html"}, "Help"),          $cgi->p("This table shows all the families that contain a protein with the same sequence as <b>$peg</b>, although each family uses different IDs. The number of different IDs in each protein family and the number of unique protein sequences in each family are also shown. The latter is often less than the former since many databases contain identical proteins with different identifiers (for example the same protein from different <i>$genusspecies</i> genome sequences)."),
319         );         );
320    
321     foreach my $fam ($fig->families_for_protein($peg))     foreach my $fam ($fig->families_for_protein($peg))
# Line 568  Line 571 
571    # put here the link to the site for the proteins.    # put here the link to the site for the proteins.
572    # Note the use of single quotes. Later, anywhere where the protein ID should be I'll replace \$p with the protein id.    # Note the use of single quotes. Later, anywhere where the protein ID should be I'll replace \$p with the protein id.
573    # This is because for some reason cog needs the protein ID twice.    # This is because for some reason cog needs the protein ID twice.
574    "fig"         => 'protein.cgi?user=$user&prot=fig|$p',    "fig"         => "protein.cgi?user=$user&prot=fig|".'$p',
575    "cog"  => 'http://www.ncbi.nlm.nih.gov/COG/old/blux.cgi?cog=$p&$p',    "cog"  => 'http://www.ncbi.nlm.nih.gov/COG/old/blux.cgi?cog=$p&$p',
576    "sp"   => 'http://www.expasy.org/uniprot/$p',    "sp"   => 'http://www.expasy.org/uniprot/$p',
577    "tr"   => 'http://www.expasy.org/uniprot/$p',    "tr"   => 'http://www.expasy.org/uniprot/$p',
# Line 585  Line 588 
588   {   {
589          $mouseovertitle="<i>Column family: " . $fig->family_function($fam) . " ($fam)</i>";          $mouseovertitle="<i>Column family: " . $fig->family_function($fam) . " ($fam)</i>";
590   }   }
591   my $familiesforp = "<b>Families for $p:</b><br>";   my $familiesforp = "<b>Families for $p from ".$fig->genus_species($fig->genome_of($p))."</b><br>";
592   my ($hcolor, $bgcolor)=('#11AA66','#BBFFBB'); # text background color.   my ($hcolor, $bgcolor)=('#11AA66','#BBFFBB'); # text background color.
593    
594   # if the protein is in our family of interest show just that, otherwise show all the families   # if the protein is in our family of interest show just that, otherwise show all the families

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