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revision 1.95, Tue Jun 27 22:40:49 2006 UTC revision 1.101, Mon Sep 25 19:34:14 2006 UTC
# Line 17  Line 17 
17    
18  package HTML;  package HTML;
19    
20    use strict;
21  use Tracer;  use Tracer;
22  use FIG;  use FIG;
23  use Carp;  use Carp;
# Line 28  Line 29 
29  use HTTP::Request::Common;  use HTTP::Request::Common;
30  use POSIX;  use POSIX;
31    
32  use raelib; # now used for the excel function, that should eventually end up in here. Way too experimental!  #use raelib; # now used for the excel function, that should eventually end up in here. Way too experimental!
33  my $raelib=new raelib;  my $raelib;
34    
35    
36  my $top_link_cache;  my $top_link_cache;
# Line 181  Line 182 
182      # Find the HTML header      # Find the HTML header
183      #      #
184    
185        my $tail_name = $options->{tail_name} ? $options->{tail_name} : "html.tail";
186      my $html_tail_file = "./Html/$tail_name";      my $html_tail_file = "./Html/$tail_name";
187      if (! -f $html_tail_file)      if (! -f $html_tail_file)
188      {      {
# Line 415  Line 417 
417          # BASE href needs to be absolute. RDO.          # BASE href needs to be absolute. RDO.
418          #          #
419          #          #
420          $base_url = &FIG::cgi_url;  #        $base_url = &FIG::cgi_url;
421  #       my $base_url = $FIG_Config::cgi_base;  #       my $base_url = $FIG_Config::cgi_base;
422  #       if ( ! $base_url )                      # if cgi_base was not defined  #       if ( ! $base_url )                      # if cgi_base was not defined
423  #       {  #       {
# Line 558  Line 560 
560      push(@tab,"</table>\n");      push(@tab,"</table>\n");
561    
562      # excelfile should be appropriate for a filename (no spaces/special characters)      # excelfile should be appropriate for a filename (no spaces/special characters)
563      if (defined $options{"excelfile"}) {push @tab, $raelib->tab2excel($col_hdrs,$tab,$title,\%options,$options{"excelfile"})}      if (defined $options{"excelfile"}) {
564            if (! defined($raelib)) {
565                require raelib;
566                $raelib = new raelib;
567            }
568            push @tab, $raelib->tab2excel($col_hdrs,$tab,$title,\%options,$options{"excelfile"})}
569    
570      return join("",@tab);      return join("",@tab);
571  }  }
# Line 833  Line 840 
840          my $link;          my $link;
841          my $new_framework = $cgi->param('new_framework') ? 1 : 0;          my $new_framework = $cgi->param('new_framework') ? 1 : 0;
842          #added to format prophage and path island links to feature.cgi          #added to format prophage and path island links to feature.cgi
843          if ($1 ne "peg")          my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";
844            if ($1 ne "peg" && ! $sprout)
845          {          {
846             my $user = $cgi->param('user');             my $user = $cgi->param('user');
847             if (! $user) { $user = "" }             if (! $user) { $user = "" }
848             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";  
849             $link =~ s/[a-z_A-Z0-9]+\.cgi\?/feature.cgi?/;             $link =~ s/[a-z_A-Z0-9]+\.cgi\?/feature.cgi?/;
850          }          }
851          else          else
# Line 912  Line 919 
919          {          {
920              $url .= "?" . join("&",@args);              $url .= "?" . join("&",@args);
921          }          }
922          $request = new HTTP::Request('GET', $url);          my $request = new HTTP::Request('GET', $url);
923          my $response = $ua->request($request);          my $response = $ua->request($request);
924    
925          if ($response->is_success)          if ($response->is_success)
# Line 930  Line 937 
937    
938  #   Now splice in a line of the form <base href=URL> to cause all relative links to work  #   Now splice in a line of the form <base href=URL> to cause all relative links to work
939  #   properly.  Remove the header.  #   properly.  Remove the header.
940        my $i;
941      for ($i=0; ($i < @output) && ($output[$i] !~ /^\s*\</); $i++) {}      for ($i=0; ($i < @output) && ($output[$i] !~ /^\s*\</); $i++) {}
942      if ($i < @output)      if ($i < @output) {
     {  
   
943          splice(@output,0,$i);          splice(@output,0,$i);
944      }      }
945    
# Line 950  Line 955 
955  sub trim_output {  sub trim_output {
956      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
957      my($out) = @_;      my($out) = @_;
958      my $i;      my ($i, $j);
959    
960      for ($i=0; ($i < @$out) && ($out->[$i] !~ /^\</); $i++) {}      for ($i=0; ($i < @$out) && ($out->[$i] !~ /^\</); $i++) {}
961      splice(@$out,0,$i);      splice(@$out,0,$i);
# Line 979  Line 984 
984      for ($j=$i-1; ($j > 0) && ($out->[$j] !~ /FIG search/); $j--) {}      for ($j=$i-1; ($j > 0) && ($out->[$j] !~ /FIG search/); $j--) {}
985      if ($j > 0)      if ($j > 0)
986      {      {
987            #
988            # Hm. We would have tried using the options here:
989            # my $tail_name = $options{tail_name} ? $options{tail_name} : "html.tail";
990            # but they're not passed in. So use the default html.tail.
991            #
992            my $html_tail_file = "./Html/html.tail";
993          my @tmp = `cat $html_tail_file`;          my @tmp = `cat $html_tail_file`;
994          my $n = @tmp;          my $n = @tmp;
995          splice(@$out,$j-$n,$n+1);          splice(@$out,$j-$n,$n+1);
# Line 1172  Line 1183 
1183          $after = $3;          $after = $3;
1184          return &set_prot_links($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,$after);
1185      }      }
1186        elsif ($x =~ /^(.*)(tr\|[a-zA-Z0-9]+)(.*)/s)
1187        {
1188    
1189          $before = $1;
1190          $match = $2;
1191          $after = $3;
1192    
1193          return &set_prot_links($cgi,$before) .  &HTML::trembl_link($cgi,$match) . &set_prot_links($cgi,$after);
1194        }
1195      return $x;      return $x;
1196  }  }
1197    
1198    sub trembl_link {
1199        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1200        my($cgi,$id) = @_;
1201    
1202        if ($id =~ /^tr\|(.*)/) {
1203          return "<a href='http://ca.expasy.org/uniprot/$1' target=_blank>$id</a>";
1204        } else {
1205          return "invalid call to trembl link";
1206        }
1207    }
1208    
1209  sub refseq_link {  sub refseq_link {
1210      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1211      my($cgi,$id) = @_;      my($cgi,$id) = @_;
1212    
1213      if ($id =~ /^[NXYZA]P_/)      if ($id =~ /^[NXYZA]P_/)
1214      {      {
1215          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>";
1216      }      }
1217      elsif ($id =~ /^[NXYZA]M_/)      elsif ($id =~ /^[NXYZA]M_/)
1218      {      {
1219          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>";
1220      }      }
1221  }  }
1222    
# Line 1195  Line 1226 
1226    
1227      if ($gi =~ /^gi\|(\d+)$/)      if ($gi =~ /^gi\|(\d+)$/)
1228      {      {
1229          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>";
1230      }      }
1231      return $gi;      return $gi;
1232  }  }
# Line 1207  Line 1238 
1238      if ($tigr =~ /^tigr\|(NT|ntbp|ntbpA|BA|BMAA|BXB|GBA)(\w+)$/)      if ($tigr =~ /^tigr\|(NT|ntbp|ntbpA|BA|BMAA|BXB|GBA)(\w+)$/)
1239      {      {
1240          my $id=$1.$2;          my $id=$1.$2;
1241          return "<a href=\"http://pathema.tigr.org/tigr-scripts/pathema/shared/GenePage.cgi?locus=$id\">$tigr</a> (Pathema)";          return "<a href=\"http://pathema.tigr.org/tigr-scripts/pathema/shared/GenePage.cgi?locus=$id\" target=_blank>$tigr</a> (Pathema)";
1242      }      }
1243      elsif ($tigr =~ /^tigr\|(\S+)$/)      elsif ($tigr =~ /^tigr\|(\S+)$/)
1244      {      {
1245          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>";
1246      }      }
1247      return $tigr;      return $tigr;
1248  }  }
# Line 1222  Line 1253 
1253    
1254      if ($eric =~ /^eric\|(\S+)/)      if ($eric =~ /^eric\|(\S+)/)
1255      {      {
1256          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>";
1257      }      }
1258      return $eric;      return $eric;
1259  }  }
# Line 1231  Line 1262 
1262      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1263      my($cgi,$bhb) = @_;      my($cgi,$bhb) = @_;
1264    
1265      return "<a href=\"http://www.biohealthbase.org\">$bhb</a>";      return "<a href=\"http://www.biohealthbase.org\" target=_blank>$bhb</a>";
1266  }  }
1267    
1268  sub apidb_link {  sub apidb_link {
# Line 1240  Line 1271 
1271    
1272      if ($api =~ /apidb\|(.*?)\.(.*)$/)      if ($api =~ /apidb\|(.*?)\.(.*)$/)
1273      {      {
1274          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>";
1275      }      }
1276      return $api;      return $api;
1277  }  }
# Line 1251  Line 1282 
1282    
1283      if ($patric =~ /patric\|(.*)/)      if ($patric =~ /patric\|(.*)/)
1284      {      {
1285          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>";
1286      }      }
1287      return $patric;      return $patric;
1288  }  }
# Line 1262  Line 1293 
1293    
1294      if ($vbrc =~ /vbrc\|(.*)/)      if ($vbrc =~ /vbrc\|(.*)/)
1295      {      {
1296          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>";
1297      }      }
1298      return $vbrc;      return $vbrc;
1299  }  }
# Line 1270  Line 1301 
1301  sub vectorbase_link {  sub vectorbase_link {
1302      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1303      my($cgi,$vec) = @_;      my($cgi,$vec) = @_;
1304      return "<a href=\"http://www.vectorbase.org\">$vec</a>";      return "<a href=\"http://www.vectorbase.org\" target=_blank>$vec</a>";
1305  }  }
1306    
1307    
# Line 1281  Line 1312 
1312      if ($uni =~ /^uni\|(\S+)$/)      if ($uni =~ /^uni\|(\S+)$/)
1313      {      {
1314          #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>";
1315          return "<a href='http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinAc=$1'>$uni</a>";          return "<a href='http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinAc=$1' target=_blank>$uni</a>";
1316      }      }
1317      return $uni;      return $uni;
1318  }  }
# Line 1292  Line 1323 
1323    
1324      if ($sp =~ /^sp\|(\S+)$/)      if ($sp =~ /^sp\|(\S+)$/)
1325      {      {
1326          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>";
1327      }      }
1328      return $sp;      return $sp;
1329  }  }
# Line 1303  Line 1334 
1334    
1335      if ($pir =~ /^pirnr\|(NF\d+)$/)      if ($pir =~ /^pirnr\|(NF\d+)$/)
1336      {      {
1337          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>";
1338      }      }
1339      return $pir;      return $pir;
1340  }  }
# Line 1314  Line 1345 
1345    
1346      if ($kegg =~ /^kegg\|([^:]+):(\S+)$/)      if ($kegg =~ /^kegg\|([^:]+):(\S+)$/)
1347      {      {
1348          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>";
1349      }      }
1350      return $kegg;      return $kegg;
1351  }  }
# Line 1336  Line 1367 
1367          #can't see how to do that without knowing the org name too, which          #can't see how to do that without knowing the org name too, which
1368          #I don't know at this point. (ensembl org name, not real org name)          #I don't know at this point. (ensembl org name, not real org name)
1369    
1370          return "<a href=http://www.ensembl.org/Homo_sapiens/searchview?species=all&idx=$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>";
1371      }      }
1372      return $ensembl;      return $ensembl;
1373  }  }
# Line 1347  Line 1378 
1378    
1379      if ($entrezgene =~ /^EntrezGene:(\S+)$/)      if ($entrezgene =~ /^EntrezGene:(\S+)$/)
1380      {      {
1381          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>";
1382      }      }
1383      return $entrezgene;      return $entrezgene;
1384  }  }
# Line 1358  Line 1389 
1389    
1390      if ($mim =~ /^MIM:(\S+)$/)      if ($mim =~ /^MIM:(\S+)$/)
1391      {      {
1392          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>";
1393      }      }
1394      return $mim;      return $mim;
1395  }  }
# Line 1369  Line 1400 
1400    
1401      if ($hgnc =~ /^HGNC:(\S+)$/)      if ($hgnc =~ /^HGNC:(\S+)$/)
1402      {      {
1403          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>";
1404      }      }
1405      return $mim;  
1406        return $hgnc;
1407  }  }
1408    
1409  sub unigene_link {  sub unigene_link {
# Line 1380  Line 1412 
1412    
1413      if ($unigene =~ /^UniGene:(\S+)$/)      if ($unigene =~ /^UniGene:(\S+)$/)
1414      {      {
1415          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>";
1416      }      }
1417      return $unigene;      return $unigene;
1418  }  }
# Line 1391  Line 1423 
1423    
1424      if ($ipi =~ /^IPI:(\S+)$/)      if ($ipi =~ /^IPI:(\S+)$/)
1425      {      {
1426          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>";
1427      }      }
1428      return $ipi;      return $ipi;
1429  }  }
# Line 1404  Line 1436 
1436    
1437      if ($wp =~ /^WP:(\S+)$/)      if ($wp =~ /^WP:(\S+)$/)
1438      {      {
1439          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>";
1440      }      }
1441      return $wp;      return $wp;
1442  }  }
# Line 1417  Line 1449 
1449    
1450      if ($fb =~ /^FB:(\S+)$/)      if ($fb =~ /^FB:(\S+)$/)
1451      {      {
1452          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>";
1453      }      }
1454      return $fb;      return $fb;
1455  }  }
# Line 1430  Line 1462 
1462    
1463      if ($fb =~ /^FlyBaseORFNames:(\S+)$/)      if ($fb =~ /^FlyBaseORFNames:(\S+)$/)
1464      {      {
1465          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>";
1466      }      }
1467      return $fb;      return $fb;
1468  }  }
# Line 1443  Line 1475 
1475    
1476      if ($sgd =~ /^SGD_LOCUS:(\S+)$/)      if ($sgd =~ /^SGD_LOCUS:(\S+)$/)
1477      {      {
1478          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>";
1479      }      }
1480      return $sgd;      return $sgd;
1481  }  }
# Line 1474  Line 1506 
1506      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1507      my($cgi,$map,$org) = @_;      my($cgi,$map,$org) = @_;
1508    
1509      $user = $cgi->param('user');      my $user = $cgi->param('user');
1510      $user = $user ? $user : "";      $user = $user ? $user : "";
1511      $org = $org ? $org : "";      $org = $org ? $org : "";
1512    
# Line 1492  Line 1524 
1524    # -name => field and the checkbox name    # -name => field and the checkbox name
1525    my ($form, $button)=@_;    my ($form, $button)=@_;
1526    
1527    $java_script="<input type=\"button\" name=\"CheckAll\" value=\"Check All\"\nonClick=\"checkAll(document.$form.$button)\">\n";    my $java_script="<input type=\"button\" name=\"CheckAll\" value=\"Check All\"\nonClick=\"checkAll(document.$form.$button)\">\n";
1528    $java_script.="<input type=\"button\" name=\"CheckFirst\" value=\"Check First Half\"\nonClick=\"checkFirst(document.$form.$button)\">\n";    $java_script.="<input type=\"button\" name=\"CheckFirst\" value=\"Check First Half\"\nonClick=\"checkFirst(document.$form.$button)\">\n";
1529    $java_script.="<input type=\"button\" name=\"CheckSecond\" value=\"Check Second Half\"\nonClick=\"checkSecond(document.$form.$button)\">\n";    $java_script.="<input type=\"button\" name=\"CheckSecond\" value=\"Check Second Half\"\nonClick=\"checkSecond(document.$form.$button)\">\n";
1530    $java_script.="<input type=\"button\" name=\"UnCheckAll\" value=\"Uncheck All\"\nonClick=\"uncheckAll(document.$form.$button)\">\n";    $java_script.="<input type=\"button\" name=\"UnCheckAll\" value=\"Uncheck All\"\nonClick=\"uncheckAll(document.$form.$button)\">\n";
# Line 1521  Line 1553 
1553    
1554  sub reaction_link {  sub reaction_link {
1555      my($reaction) = @_;      my($reaction) = @_;
1556        if ($reaction =~ /^(\*)?(R\d+)/)
     if ($reaction =~ /^R\d+/)  
1557      {      {
1558          return "<a href=\"http://www.genome.ad.jp/dbget-bin/www_bget?rn+$reaction\" target=reaction$$>$reaction</a>";          return "<a href=\"http://www.genome.ad.jp/dbget-bin/www_bget?rn+$2\" target=reaction$$>$reaction</a>";
1559      }      }
1560      return $reaction;      return $reaction;
1561  }  }
1562    
1563    
1564  sub html_for_assignments {  sub html_for_assignments {
1565      my($fig,$user,$peg_sets) = @_;      my($fig,$user,$peg_sets) = @_;
1566      my $i;      my $i;
1567    
1568      my @vals = ();      my @vals = ();
1569      my $set = 1;      my $set = 1;
1570      foreach $peg_set (@$peg_sets)      foreach my $peg_set (@$peg_sets)
1571      {      {
1572          for ($i=0; ($i < @$peg_set); $i++)          for ($i=0; ($i < @$peg_set); $i++)
1573          {          {
1574              $peg = $peg_set->[$i];              my $peg = $peg_set->[$i];
1575              push(@vals,'show=' . join("@",($set,$i+1,$peg,&FIG::abbrev($fig->org_of($peg)),"")));              push(@vals,'show=' . join("@",($set,$i+1,$peg,&FIG::abbrev($fig->org_of($peg)),"")));
1576          }          }
1577          $set++;          $set++;
# Line 1650  Line 1682 
1682    
1683    
1684   my @files=("SEED.rss");   my @files=("SEED.rss");
1685   if ($args->{"type"}) {push @files, "SEED.$type.rss"}   if ($args->{"type"}) {
1686        my $type = $args->{type};
1687        push @files, "SEED.$type.rss"
1688    }
1689    
1690   foreach my $file ("SEED.rss", @$files)   foreach my $file ("SEED.rss", @$files)
1691   {   {

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