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revision 1.123, Tue Apr 29 05:43:12 2008 UTC revision 1.126, Thu Jun 5 19:50:12 2008 UTC
# Line 525  Line 525 
525      {      {
526          my $line = $_;          my $line = $_;
527          if (T(4)) {          if (T(4)) {
528              my $escapedLine = CGI::escapeHTML($line);              my $escapedLine = Tracer::Clean($line);
529              Trace("Printing:\n$escapedLine") if T(4);              Trace("Printing:\n$escapedLine") if T(4);
530          }          }
531          print $line;          print $line;
# Line 923  Line 923 
923          }          }
924          else          else
925          {          {
926              return "<a href='$link'>$n</a>";              return "<a target=_blank href='$link'>$n</a>";
927          }          }
928      }      }
929      return $fid;      return $fid;
# Line 1168  Line 1168 
1168        return "http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenePage.cgi?locus=".$id;        return "http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenePage.cgi?locus=".$id;
1169      }      }
1170    }    }
1171      elsif ($type eq "SwissProt"){ # 25
1172          return "http://www.uniprot.org/entry/$id";
1173      }
1174      elsif ($type eq "IMG"){ # 26
1175          return "http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?page=geneDetail&gene_oid=$id";
1176      }
1177      elsif ($type eq "KEGG") { # 27
1178          my ($pre,$post) = ($id) =~ /(.*):(.*)/;
1179          return "http://www.genome.ad.jp/dbget-bin/www_bget?" . $pre . "+" . $post;
1180      }
1181      elsif ($type eq "ASAP") { # 28
1182        return "https://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=$id";
1183      }
1184      elsif ($type eq "GenBank") { # 29
1185          return "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=$id";
1186      }
1187      elsif ($type eq "DBJ") { # 30
1188          return "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=$id";
1189      }
1190      elsif ($type eq "SCOP") { # 31
1191          $id =~ s/\:\w//;
1192          return "http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?pdb=$id";
1193      }
1194      elsif ($type eq "CATH") { # 32
1195          $id =~ s/\:\w//;
1196          return "http://www.cathdb.info/cgi-bin/CATHSrch.pl?type=PDB&query=$id";
1197      }
1198      elsif ($type eq "FSSP") { # 33
1199          $id =~ s/\:\w//;
1200          return "http://ekhidna.biocenter.helsinki.fi/dali/daliquery?find=$id";
1201      }
1202      elsif ($type eq "MMDB") { # 34
1203          $id =~ s/\:\w//;
1204          return "http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?form=6&db=tDopt=s&uid=$id";
1205      }
1206      elsif ($type eq "PDBsum") { # 35
1207          $id =~ s/\:\w//;
1208          return "http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=$id";
1209      }
1210    
1211    return undef;    return undef;
1212  }  }
# Line 1770  Line 1809 
1809      my $retVal;      my $retVal;
1810      # Clean the subsystem name for display purposes. This is a very      # Clean the subsystem name for display purposes. This is a very
1811      # different thing from URL-escaping.      # different thing from URL-escaping.
1812      my $cleaned = CGI::escapeHTML($sub);      my $cleaned = Tracer::Clean($sub);
1813      $cleaned =~ s/_/ /g;      $cleaned =~ s/_/ /g;
1814      # URL-escape the subsystem name for use in the link.      # URL-escape the subsystem name for use in the link.
1815      my $linkable = uri_escape($sub);      my $linkable = uri_escape($sub);

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