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revision 1.90, Sat May 6 22:04:12 2006 UTC revision 1.99, Tue Sep 19 21:19:14 2006 UTC
# Line 831  Line 831 
831          }          }
832    
833          my $link;          my $link;
834            my $new_framework = $cgi->param('new_framework') ? 1 : 0;
835          #added to format prophage and path island links to feature.cgi          #added to format prophage and path island links to feature.cgi
836          if ($1 ne "peg")          my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";
837            if ($1 ne "peg" && ! $sprout)
838          {          {
839             my $user = $cgi->param('user');             my $user = $cgi->param('user');
840             if (! $user) { $user = "" }             if (! $user) { $user = "" }
841             my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";             $link = "$top/feature.cgi?feature=$fid&user=$user$sprout";
            $link = "$top/feature.cgi?feature=$fid&user=$user$trans$sprout";  
842             $link =~ s/[a-z_A-Z0-9]+\.cgi\?/feature.cgi?/;             $link =~ s/[a-z_A-Z0-9]+\.cgi\?/feature.cgi?/;
843          }          }
844          else          else
# Line 857  Line 858 
858    
859              #if (! $cgi_url) { $cgi_url = &FIG::cgi_url }              #if (! $cgi_url) { $cgi_url = &FIG::cgi_url }
860              #$link = $cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";              #$link = $cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
861              $link = "$top/protein.cgi?prot=$fid&user=$user$trans$sprout";              $link = "$top/protein.cgi?prot=$fid&user=$user$trans$sprout\&new_framework=$new_framework";
862              $link =~ s/[a-z_A-Z0-9]+\.cgi\?/protein.cgi?/;              $link =~ s/[a-z_A-Z0-9]+\.cgi\?/protein.cgi?/;
863          }          }
864          if ($just_url)          if ($just_url)
# Line 898  Line 899 
899          my $response = $ua->request($request);          my $response = $ua->request($request);
900          $out = $response->content;          $out = $response->content;
901      }      }
902      else  
903        if ($type =~/get/i)
904      {      {
905          @args = ();          @args = ();
906          foreach $x (@$kv_pairs)          foreach $x (@$kv_pairs)
# Line 1024  Line 1026 
1026          return &set_prot_links($cgi,$before) . &HTML::eric_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::eric_link($cgi,$match) . &set_prot_links($cgi,$after);
1027      }      }
1028    
1029      elsif ($x =~ /^(.*)\bbhb\|.*?\b(.*)/s)      elsif ($x =~ /^(.*)\b(bhb\|.*?)\b(.*)/s)
1030      {      {
1031          $before = $1;          $before = $1;
1032          $match = $2;          $match = $2;
# Line 1032  Line 1034 
1034          return &set_prot_links($cgi,$before) . &HTML::bhb_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::bhb_link($cgi,$match) . &set_prot_links($cgi,$after);
1035      }      }
1036    
1037      elsif ($x =~ /^(.*)\bapidb\|.*?\..*\b(.*)/s)      elsif ($x =~ /^(.*)\b(apidb\|[0-9\.a-z_]+)\b(.*)/s)
1038      {      {
1039          $before = $1;          $before = $1;
1040          $match = $2;          $match = $2;
# Line 1040  Line 1042 
1042          return &set_prot_links($cgi,$before) . &HTML::apidb_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::apidb_link($cgi,$match) . &set_prot_links($cgi,$after);
1043      }      }
1044    
1045      elsif ($x =~ /^(.*)\bpatric\|.*?\b(.*)/s)      elsif ($x =~ /^(.*)\b(patric\|.*?)\b(.*)/s)
1046      {      {
1047          $before = $1;          $before = $1;
1048          $match = $2;          $match = $2;
# Line 1048  Line 1050 
1050          return &set_prot_links($cgi,$before) . &HTML::patric_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::patric_link($cgi,$match) . &set_prot_links($cgi,$after);
1051      }      }
1052    
1053      elsif ($x =~ /^(.*)\bvbrc\|.*?\b(.*)/s)      elsif ($x =~ /^(.*)\b(vbrc\|.*?)\b(.*)/s)
1054      {      {
1055          $before = $1;          $before = $1;
1056          $match = $2;          $match = $2;
# Line 1056  Line 1058 
1058          return &set_prot_links($cgi,$before) . &HTML::vbrc_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::vbrc_link($cgi,$match) . &set_prot_links($cgi,$after);
1059      }      }
1060    
1061      elsif ($x =~ /^(.*)\bvectorbase\|.*?\b(.*)/s)      elsif ($x =~ /^(.*)\b(vectorbase\|.*?)\b(.*)/s)
1062      {      {
1063          $before = $1;          $before = $1;
1064          $match = $2;          $match = $2;
# Line 1170  Line 1172 
1172          $after = $3;          $after = $3;
1173          return &set_prot_links($cgi,$before) . &HTML::sgd_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::sgd_link($cgi,$match) . &set_prot_links($cgi,$after);
1174      }      }
1175        elsif ($x =~ /^(.*)(tr\|[a-zA-Z0-9]+)(.*)/s)
1176        {
1177    
1178          $before = $1;
1179          $match = $2;
1180          $after = $3;
1181    
1182          return &set_prot_links($cgi,$before) .  &HTML::trembl_link($cgi,$match) . &set_prot_links($cgi,$after);
1183        }
1184      return $x;      return $x;
1185  }  }
1186    
1187    sub trembl_link {
1188        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1189        my($cgi,$id) = @_;
1190    
1191        if ($id =~ /^tr\|(.*)/) {
1192          return "<a href='http://ca.expasy.org/uniprot/$1' target=_blank>$id</a>";
1193        } else {
1194          return "invalid call to trembl link";
1195        }
1196    }
1197    
1198  sub refseq_link {  sub refseq_link {
1199      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1200      my($cgi,$id) = @_;      my($cgi,$id) = @_;
1201    
1202      if ($id =~ /^[NXYZA]P_/)      if ($id =~ /^[NXYZA]P_/)
1203      {      {
1204          return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=search&term=$id>$id</a>";          return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=search&term=$id' target=_blank>$id</a>";
1205      }      }
1206      elsif ($id =~ /^[NXYZA]M_/)      elsif ($id =~ /^[NXYZA]M_/)
1207      {      {
1208          return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nuccore&cmd=search&term=$id>$id</a>";          return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nuccore&cmd=search&term=$id' target=_blank>$id</a>";
1209      }      }
1210  }  }
1211    
# Line 1193  Line 1215 
1215    
1216      if ($gi =~ /^gi\|(\d+)$/)      if ($gi =~ /^gi\|(\d+)$/)
1217      {      {
1218          return "<a href=http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=Protein&list_uids=$1&dopt=GenPept>$gi</a>";          return "<a href='http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=Protein&list_uids=$1&dopt=GenPept' target=_blank>$gi</a>";
1219      }      }
1220      return $gi;      return $gi;
1221  }  }
# Line 1205  Line 1227 
1227      if ($tigr =~ /^tigr\|(NT|ntbp|ntbpA|BA|BMAA|BXB|GBA)(\w+)$/)      if ($tigr =~ /^tigr\|(NT|ntbp|ntbpA|BA|BMAA|BXB|GBA)(\w+)$/)
1228      {      {
1229          my $id=$1.$2;          my $id=$1.$2;
1230          return "<a href=\"http://pathema.tigr.org/tigr-scripts/pathema/shared/GenePage.cgi?locus=$id\">$tigr</a> (Pathema)";          return "<a href=\"http://pathema.tigr.org/tigr-scripts/pathema/shared/GenePage.cgi?locus=$id\" target=_blank>$tigr</a> (Pathema)";
1231      }      }
1232      elsif ($tigr =~ /^tigr\|(\S+)$/)      elsif ($tigr =~ /^tigr\|(\S+)$/)
1233      {      {
1234          return "<a href=\"http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=$1\">$tigr</a>";          return "<a href=\"http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=$1\" target=_blank>$tigr</a>";
1235      }      }
1236      return $tigr;      return $tigr;
1237  }  }
# Line 1220  Line 1242 
1242    
1243      if ($eric =~ /^eric\|(\S+)/)      if ($eric =~ /^eric\|(\S+)/)
1244      {      {
1245          return "<a href=\"https://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=$1\">$eric</a>";          return "<a href=\"https://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=$1\" target=_blank>$eric</a>";
1246      }      }
1247      return $eric;      return $eric;
1248  }  }
# Line 1229  Line 1251 
1251      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1252      my($cgi,$bhb) = @_;      my($cgi,$bhb) = @_;
1253    
1254      return "<a href=\"http://www.biohealthbase.org\">$bhb</a>";      return "<a href=\"http://www.biohealthbase.org\" target=_blank>$bhb</a>";
1255  }  }
1256    
1257  sub apidb_link {  sub apidb_link {
# Line 1238  Line 1260 
1260    
1261      if ($api =~ /apidb\|(.*?)\.(.*)$/)      if ($api =~ /apidb\|(.*?)\.(.*)$/)
1262      {      {
1263          return "<a href=\"http://www.apidb.org/cgi-bin/redirect.cgi?taxon_id=$1&source_id=$2\">$api</a>";          return "<a href=\"http://www.apidb.org/cgi-bin/redirect.cgi?taxon_id=$1&source_id=$2\" target=_blank>$api</a>";
1264      }      }
1265      return $api;      return $api;
1266  }  }
# Line 1249  Line 1271 
1271    
1272      if ($patric =~ /patric\|(.*)/)      if ($patric =~ /patric\|(.*)/)
1273      {      {
1274          return "<a href=\"https://patric.vbi.vt.edu/software/curationTool/gep/pgiCuration.php?locus_name=$1\">$patric</a>";          return "<a href=\"https://patric.vbi.vt.edu/software/curationTool/gep/pgiCuration.php?locus_name=$1\" target=_blank>$patric</a>";
1275      }      }
1276      return $patric;      return $patric;
1277  }  }
# Line 1260  Line 1282 
1282    
1283      if ($vbrc =~ /vbrc\|(.*)/)      if ($vbrc =~ /vbrc\|(.*)/)
1284      {      {
1285          return "<a href=\"http://www.biovirus.org/gene_detail.asp?name=$1\">$vbrc</a>";          return "<a href=\"http://www.biovirus.org/gene_detail.asp?name=$1\" target=_blank>$vbrc</a>";
1286      }      }
1287      return $vbrc;      return $vbrc;
1288  }  }
# Line 1268  Line 1290 
1290  sub vectorbase_link {  sub vectorbase_link {
1291      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1292      my($cgi,$vec) = @_;      my($cgi,$vec) = @_;
1293      return "<a href=\"http://www.vectorbase.org\">$vec</a>";      return "<a href=\"http://www.vectorbase.org\" target=_blank>$vec</a>";
1294  }  }
1295    
1296    
# Line 1278  Line 1300 
1300    
1301      if ($uni =~ /^uni\|(\S+)$/)      if ($uni =~ /^uni\|(\S+)$/)
1302      {      {
1303          return "<a href=http://www.pir.uniprot.org/cgi-bin/upEntry?id=$1>$uni</a>";          #return "<a href=http://www.pir.uniprot.org/cgi-bin/upEntry?id=$1>$uni</a>";
1304            return "<a href='http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinAc=$1' target=_blank>$uni</a>";
1305      }      }
1306      return $uni;      return $uni;
1307  }  }
# Line 1289  Line 1312 
1312    
1313      if ($sp =~ /^sp\|(\S+)$/)      if ($sp =~ /^sp\|(\S+)$/)
1314      {      {
1315          return "<a href=http://us.expasy.org/cgi-bin/get-sprot-entry?$1>$sp</a>";          return "<a href='http://us.expasy.org/cgi-bin/get-sprot-entry?$1' target=_blank>$sp</a>";
1316      }      }
1317      return $sp;      return $sp;
1318  }  }
# Line 1300  Line 1323 
1323    
1324      if ($pir =~ /^pirnr\|(NF\d+)$/)      if ($pir =~ /^pirnr\|(NF\d+)$/)
1325      {      {
1326          return "<a href=http://pir.georgetown.edu/cgi-bin/nfEntry.pl?id=$1>$pir</a>";          return "<a href='http://pir.georgetown.edu/cgi-bin/nfEntry.pl?id=$1' target=_blank>$pir</a>";
1327      }      }
1328      return $pir;      return $pir;
1329  }  }
# Line 1311  Line 1334 
1334    
1335      if ($kegg =~ /^kegg\|([^:]+):(\S+)$/)      if ($kegg =~ /^kegg\|([^:]+):(\S+)$/)
1336      {      {
1337          return "<a href=http://www.genome.ad.jp/dbget-bin/www_bget?$1+$2>$kegg</a>";          return "<a href='http://www.genome.ad.jp/dbget-bin/www_bget?$1+$2' target=_blank>$kegg</a>";
1338      }      }
1339      return $kegg;      return $kegg;
1340  }  }
# Line 1333  Line 1356 
1356          #can't see how to do that without knowing the org name too, which          #can't see how to do that without knowing the org name too, which
1357          #I don't know at this point. (ensembl org name, not real org name)          #I don't know at this point. (ensembl org name, not real org name)
1358    
1359          return "<a href=http://www.ensembl.org/Homo_sapiens/searchview?species=all&idx=$idx&q=$key>$ensembl</a>";          return "<a href='http://www.ensembl.org/Homo_sapiens/searchview?species=all&idx=$idx&q=$key' target=_blank>$ensembl</a>";
1360      }      }
1361      return $ensembl;      return $ensembl;
1362  }  }
# Line 1344  Line 1367 
1367    
1368      if ($entrezgene =~ /^EntrezGene:(\S+)$/)      if ($entrezgene =~ /^EntrezGene:(\S+)$/)
1369      {      {
1370          return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=full_report&list_uids=$1>$entrezgene</a>";          return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=full_report&list_uids=$1' target=_blank>$entrezgene</a>";
1371      }      }
1372      return $entrezgene;      return $entrezgene;
1373  }  }
# Line 1355  Line 1378 
1378    
1379      if ($mim =~ /^MIM:(\S+)$/)      if ($mim =~ /^MIM:(\S+)$/)
1380      {      {
1381          return "<a href=http://www3.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=$1>$mim</a>";          return "<a href='http://www3.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=$1' target=_blank>$mim</a>";
1382      }      }
1383      return $mim;      return $mim;
1384  }  }
# Line 1366  Line 1389 
1389    
1390      if ($hgnc =~ /^HGNC:(\S+)$/)      if ($hgnc =~ /^HGNC:(\S+)$/)
1391      {      {
1392          return "<a href=http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl?field=symbol&anchor=equals&match=$1&symbol_search=Search&number=50&format=html&sortby=symbol>$hgnc</a>";          return "<a href='http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl?field=symbol&anchor=equals&match=$1&symbol_search=Search&number=50&format=html&sortby=symbol' target=_blank>$hgnc</a>";
1393      }      }
1394      return $mim;      return $mim;
1395  }  }
# Line 1377  Line 1400 
1400    
1401      if ($unigene =~ /^UniGene:(\S+)$/)      if ($unigene =~ /^UniGene:(\S+)$/)
1402      {      {
1403          return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene&cmd=search&term=$1>$unigene</a>";          return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene&cmd=search&term=$1' target=_blank>$unigene</a>";
1404      }      }
1405      return $unigene;      return $unigene;
1406  }  }
# Line 1388  Line 1411 
1411    
1412      if ($ipi =~ /^IPI:(\S+)$/)      if ($ipi =~ /^IPI:(\S+)$/)
1413      {      {
1414          return "<a href=http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+AEoS1R8Jnn+-e+[IPI:\'$1\']+-qnum+1+-enum+1>$ipi</a>";          return "<a href='http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+AEoS1R8Jnn+-e+[IPI:\'$1\']+-qnum+1+-enum+1' target=_blank>$ipi</a>";
1415      }      }
1416      return $ipi;      return $ipi;
1417  }  }
# Line 1401  Line 1424 
1424    
1425      if ($wp =~ /^WP:(\S+)$/)      if ($wp =~ /^WP:(\S+)$/)
1426      {      {
1427          return "<a href=http://www.wormbase.org/db/searches/basic?class=Any&query=$1&Search=Search>$wp</a>";          return "<a href='http://www.wormbase.org/db/searches/basic?class=Any&query=$1&Search=Search' target=_blank>$wp</a>";
1428      }      }
1429      return $wp;      return $wp;
1430  }  }
# Line 1414  Line 1437 
1437    
1438      if ($fb =~ /^FB:(\S+)$/)      if ($fb =~ /^FB:(\S+)$/)
1439      {      {
1440          return "<a href=http://flybase.bio.indiana.edu/.bin/fbidq.html?$1>$fb</a>";          return "<a href='http://flybase.bio.indiana.edu/.bin/fbidq.html?$1' target=_blank>$fb</a>";
1441      }      }
1442      return $fb;      return $fb;
1443  }  }
# Line 1427  Line 1450 
1450    
1451      if ($fb =~ /^FlyBaseORFNames:(\S+)$/)      if ($fb =~ /^FlyBaseORFNames:(\S+)$/)
1452      {      {
1453          return "<a href=http://flybase.bio.indiana.edu/.bin/fbidq.html?$1>$fb</a>";          return "<a href='http://flybase.bio.indiana.edu/.bin/fbidq.html?$1' target=_blank>$fb</a>";
1454      }      }
1455      return $fb;      return $fb;
1456  }  }
# Line 1440  Line 1463 
1463    
1464      if ($sgd =~ /^SGD_LOCUS:(\S+)$/)      if ($sgd =~ /^SGD_LOCUS:(\S+)$/)
1465      {      {
1466          return "<a href=http://db.yeastgenome.org/cgi-bin/locus.pl?locus=$1>$sgd</a>";          return "<a href='http://db.yeastgenome.org/cgi-bin/locus.pl?locus=$1' target=_blank>$sgd</a>";
1467      }      }
1468      return $sgd;      return $sgd;
1469  }  }
# Line 1518  Line 1541 
1541    
1542  sub reaction_link {  sub reaction_link {
1543      my($reaction) = @_;      my($reaction) = @_;
1544        if ($reaction =~ /^(\*)?(R\d+)/)
     if ($reaction =~ /^R\d+/)  
1545      {      {
1546          return "<a href=\"http://www.genome.ad.jp/dbget-bin/www_bget?rn+$reaction\" target=reaction$$>$reaction</a>";          return "<a href=\"http://www.genome.ad.jp/dbget-bin/www_bget?rn+$2\" target=reaction$$>$reaction</a>";
1547      }      }
1548      return $reaction;      return $reaction;
1549  }  }
1550    
1551    
1552  sub html_for_assignments {  sub html_for_assignments {
1553      my($fig,$user,$peg_sets) = @_;      my($fig,$user,$peg_sets) = @_;
1554      my $i;      my $i;

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