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revision 1.167, Fri Nov 11 19:55:27 2005 UTC revision 1.168, Wed Nov 23 20:34:59 2005 UTC
# Line 603  Line 603 
603    
604      if ((! $cgi->param('compare_region')) && $has_translation) {      if ((! $cgi->param('compare_region')) && $has_translation) {
605          my $link = $cgi->url(-relative => 1, -query => 1, -path_info => 1) . "&compare_region=1";          my $link = $cgi->url(-relative => 1, -query => 1, -path_info => 1) . "&compare_region=1";
         push(@$html,"<br><a href=$link>To Compare Region</a> &nbsp;");  
606          push(@$html,"<A href=\"Html/compare_regions.html\" class='help' target=\"SEED_or_SPROUT_help\">Help on compare regions</A>\n");          push(@$html,"<A href=\"Html/compare_regions.html\" class='help' target=\"SEED_or_SPROUT_help\">Help on compare regions</A>\n");
607          push(@$html, "<a href='proteinfamilies.cgi?user=$user&prot=$peg&equivalence=1'>Explore Protein Families</a><br>\n",          push(@$html,"<a href=$link>To Compare Region</a> &nbsp;\n<br>");
608          "\n<a href='Html/ProteinFamilies.html' class='help' target='help'>Help on Protein Families</a>\n");          push(@$html, "<a href='proteinfamilies.cgi?user=$user&prot=$peg&equivalence=1'>Explore Protein Families for $peg</a></br>\n");
609      } elsif ($cgi->param('compare_region')) {      } elsif ($cgi->param('compare_region')) {
610          &print_compared_regions($fig_or_sprout,$cgi,$html,$peg);          &print_compared_regions($fig_or_sprout,$cgi,$html,$peg);
611      }      }
# Line 764  Line 763 
763         my $link=$cgi->url(-relative => 1, -query => 1, -path_info => 1);         my $link=$cgi->url(-relative => 1, -query => 1, -path_info => 1);
764         foreach $_ (sort {$a->[0] cmp $b->[0]} @attr) {         foreach $_ (sort {$a->[0] cmp $b->[0]} @attr) {
765             my($peg,$tag,$val,$url) = @$_;             my($peg,$tag,$val,$url) = @$_;
            #next unless ($url =~ /^http/); #RAE Turned of hiding of attributes that don't have a URL per Ross' instructions  
766             push(@$tab,["<a href='$link&showtag=$tag'>$tag</a>",$url ? "<a href=\"$url\">$val</a>" : $val]);             push(@$tab,["<a href='$link&showtag=$tag'>$tag</a>",$url ? "<a href=\"$url\">$val</a>" : $val]);
767             if ($cgi->param("showtag") && $cgi->param("showtag") eq $tag) {             if ($cgi->param("showtag") && $cgi->param("showtag") eq $tag) {
768              my $data=&key_info($fig_or_sprout, $tag);              my $data=&key_info($fig_or_sprout, $tag);
# Line 781  Line 779 
779          push @$tab, [[$cgi->submit('Add Changes'), "td colspan=3 style=\"text-align: center\""]];          push @$tab, [[$cgi->submit('Add Changes'), "td colspan=3 style=\"text-align: center\""]];
780      }      }
781      elsif ($cgi->param('user')) {      elsif ($cgi->param('user')) {
782          push @$tab, [[$cgi->submit('Edit Attributes'), "td colspan=2 style=\"text-align: center\""]];          # RAE:
783            # I have turned off editing attributes at the moment. I think it is debateable that it has any value
784            # I am not aware of anyone editing attributes on a per-protein basis, although I know that people have
785            # edited them in bulk. The code is not working properly, and should be rewritten, so for now
786            # I have disabled them.
787    
788            #push @$tab, [[$cgi->submit('Edit Attributes'), "td colspan=2 style=\"text-align: center\""]];
789      }      }
790      push(@$html,$cgi->start_form(-action=>"protein.cgi"), $cgi->hidden("prot"), $cgi->hidden("user"));      push(@$html,$cgi->start_form(-action=>"protein.cgi"), $cgi->hidden("prot"), $cgi->hidden("user"));
791      if (($cgi->param('user') && $cgi->param('Edit Attributes')) || $cgi->param("showtag")) {      if (($cgi->param('user') && $cgi->param('Edit Attributes')) || $cgi->param("showtag")) {
# Line 849  Line 853 
853    
854      my $baseurl=$FIG_Config::cgi_base;      my $baseurl=$FIG_Config::cgi_base;
855    
856      push @$html, "<a href=\"javascript:toggleLayer('proteinfamilies');\" title=\"Show Protein Families\">Show/Hide Protein Families</a><br>";      push @$html, "<a href=\"javascript:toggleLayer('proteinfamilies');\" title=\"Show Protein Families\">Show/Hide Protein Families</a>";
857      foreach my $fam (@families)      foreach my $fam (@families)
858      {      {
859       my $link="<a href='proteinfamilies.cgi?user=$user&family=$fam'>$fam</a>";       my $link="<a href='proteinfamilies.cgi?user=$user&family=$fam'>$fam</a>";
# Line 857  Line 861 
861      }      }
862      my $col_hdrs=["Family ID<br><small>Link Investigates Family</small>", "Family Function", "Family Size"];      my $col_hdrs=["Family ID<br><small>Link Investigates Family</small>", "Family Function", "Family Size"];
863      push @$html, $cgi->br, $cgi->div({id=>"proteinfamilies"},      push @$html, $cgi->br, $cgi->div({id=>"proteinfamilies"},
         "<a href='proteinfamilies.cgi?user=$user&prot=$peg&equivalence=1'>Explore Protein Families</a><br>\n",  
864          "\n<a href='Html/ProteinFamilies.html' class='help' target='help'>Help on Protein Families</a>\n",          "\n<a href='Html/ProteinFamilies.html' class='help' target='help'>Help on Protein Families</a>\n",
865          &HTML::make_table($col_hdrs, $tab, "Protein Families")          &HTML::make_table($col_hdrs, $tab, "Protein Families")
866      );      );
# Line 1741  Line 1744 
1744      </select> &nbsp;&nbsp;      </select> &nbsp;&nbsp;
1745      Group by genome:<input type=checkbox name=group_by_genome value=1 $chk_group_by_genome>      Group by genome:<input type=checkbox name=group_by_genome value=1 $chk_group_by_genome>
1746      &nbsp;&nbsp;&nbsp;      &nbsp;&nbsp;&nbsp;
1747      <A href=\"Html/similarities_options.html\" target=\"SEED_or_SPROUT_help\">Help with SEED similarities options</A><BR />      <A href=\"Html/similarities_options.html\" target=\"SEED_or_SPROUT_help\" class=\"help\">Help with SEED similarities options</A><BR />
1748  </FORM>  </FORM>
1749    
1750  End_Short_Form  End_Short_Form
# Line 1814  Line 1817 
1817          <option value=bpp  $chk_sort_by_bpp>score per position</option>          <option value=bpp  $chk_sort_by_bpp>score per position</option>
1818      </select> &nbsp;&nbsp;      </select> &nbsp;&nbsp;
1819      Group by genome:<input type=checkbox name=group_by_genome value=1 $chk_group_by_genome> &nbsp;&nbsp;&nbsp;      Group by genome:<input type=checkbox name=group_by_genome value=1 $chk_group_by_genome> &nbsp;&nbsp;&nbsp;
1820      <A href=\"Html/similarities_options.html\" target=\"SEED_or_SPROUT_help\">Help with SEED similarities options</A><br />      <A href=\"Html/similarities_options.html\" target=\"SEED_or_SPROUT_help\" class=\"help\">Help with SEED similarities options</A><br />
1821  End_Default_Options  End_Default_Options
1822    
1823          #  Extra options          #  Extra options

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