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revision 1.72, Tue Jan 25 19:14:40 2005 UTC revision 1.73, Tue Jan 25 21:30:55 2005 UTC
# Line 1235  Line 1235 
1235      $why_related = "";      $why_related = "";
1236      my %in_cluster = map { $_ => 1 } &in_cluster_with($fig_or_sprout,$peg);      my %in_cluster = map { $_ => 1 } &in_cluster_with($fig_or_sprout,$peg);
1237    
1238      my $col_hdrs = ["fid","starts","ends","size","","gap","req.<br>in<br>pin","fc","neigh","comment","aliases","Related"];      my $col_hdrs;
1239        if ($cgi->param('SPROUT'))
1240        {
1241            $col_hdrs = ["fid","starts","ends","size","","gap","req.<br>in<br>pin","fc","neigh","comment","","","aliases","Related"];
1242        }
1243        else
1244        {
1245            $col_hdrs = ["fid","starts","ends","size","","gap","req.<br>in<br>pin","fc","neigh","comment","aliases","Related"];
1246        }
1247    
1248      my($tab) = [];      my($tab) = [];
1249      my $genes = [];      my $genes = [];
1250    
# Line 1251  Line 1260 
1260          $fc = $in_cluster{$fid1} ? &pin_link($cgi,$fid1) : "";          $fc = $in_cluster{$fid1} ? &pin_link($cgi,$fid1) : "";
1261    
1262          my $aliases = join( ', ', &feature_aliasesL($fig_or_sprout,$fid1) );          my $aliases = join( ', ', &feature_aliasesL($fig_or_sprout,$fid1) );
         if ($cgi->param('SPROUT'))  
         {  
             $aliases .= ",$fid1";  
         }  
1263          my $uniprot;          my $uniprot;
1264          if ($aliases =~ /(uni[^,]+)/) {          if ($aliases =~ /(uni[^,]+)/) {
1265               # print STDERR "$1\n";               # print STDERR "$1\n";
# Line 1264  Line 1269 
1269          $aliases =~ s/SPROUT=1/SPROUT=0/g;          $aliases =~ s/SPROUT=1/SPROUT=0/g;
1270          $aliases =~ s/[&;]user=[^&;]+[;&]/;/g;          $aliases =~ s/[&;]user=[^&;]+[;&]/;/g;
1271    
1272            my($to_seed,$to_gbrowse);
1273            $to_seed = $to_gbrowse = "";
1274            if ($cgi->param('SPROUT') && ($fid1 =~ /peg/))
1275            {
1276                $to_seed     = &cgi_url . "/protein.cgi?prot=$fid1";
1277                $to_gbrowse  = &cgi_url . $fig_or_sprout->get_gbrowse_feature_link($fid1);
1278            }
1279    
1280    
1281          ($contig1,$beg1,$end1) = &boundaries_of($fig_or_sprout,&feature_locationS($fig_or_sprout,$fid1));;          ($contig1,$beg1,$end1) = &boundaries_of($fig_or_sprout,&feature_locationS($fig_or_sprout,$fid1));;
1282          $strand = ($beg1 < $end1) ? "+" : "-";          $strand = ($beg1 < $end1) ? "+" : "-";
1283    
# Line 1318  Line 1332 
1332                                                                                 -checked => 0,                                                                                 -checked => 0,
1333                                                                                 -override => 1,                                                                                 -override => 1,
1334                                                                                 -label => "");                                                                                 -label => "");
1335            if ($cgi->param('SPROUT'))
1336            {
1337          push(@$tab,[&HTML::fid_link($cgi,$fid1,"local"),$beg1,$end1,$sz,$strand,$gap,          push(@$tab,[&HTML::fid_link($cgi,$fid1,"local"),$beg1,$end1,$sz,$strand,$gap,
1338                      $must_have,                      $must_have,
1339                      $fc,$in_neighborhood,                      $fc,$in_neighborhood,
1340                      $comment,                      $comment,
1341                            "<a href=$to_seed>S</a>",
1342                            "<a href=$to_gbrowse>G</a>",
1343                      $aliases,                      $aliases,
1344                      $why_related]);                      $why_related]);
1345      }      }
1346            else
1347            {
1348                push(@$tab,[&HTML::fid_link($cgi,$fid1,"local"),$beg1,$end1,$sz,$strand,$gap,
1349                            $must_have,
1350                            $fc,$in_neighborhood,
1351                            $comment,
1352                            $aliases,
1353                            $why_related]);
1354            }
1355        }
1356      push(@$html,&HTML::make_table($col_hdrs,$tab,"Context on contig $contig1"));      push(@$html,&HTML::make_table($col_hdrs,$tab,"Context on contig $contig1"));
1357      push(@$html,$cgi->br,$cgi->submit('pin with checked genes'),$cgi->end_form,$cgi->br);      push(@$html,$cgi->br,$cgi->submit('pin with checked genes'),$cgi->end_form,$cgi->br);
1358      return ($beg,$end,$genes);      return ($beg,$end,$genes);

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