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revision 1.212, Sat Feb 5 04:12:35 2005 UTC revision 1.213, Mon Feb 7 00:27:34 2005 UTC
# Line 576  Line 576 
576    
577  =head3 get_local_hostname  =head3 get_local_hostname
578    
579    usage: my $result = $fig->get_local_hostname();
580    
581  =cut  =cut
582    #: Return Type $;
583  sub get_local_hostname {  sub get_local_hostname {
584    
585      #      #
# Line 671  Line 672 
672      }      }
673  }  }
674    
675    =head3 get_hostname_by_adapter
676    
677    usage: my $name = $fig->get_hostname_by_adapter();
678    
679    =cut
680    #: Return Type $;
681  sub get_hostname_by_adapter {  sub get_hostname_by_adapter {
682      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
683      #      #
# Line 821  Line 828 
828      return $ip;      return $ip;
829  }  }
830    
831    =head3 get_seed_id
832    
833    usage: my $id = $fig->get_seed_id();
834    
835    =cut
836    #: Return type $;
837  sub get_seed_id {  sub get_seed_id {
838      #      #
839      # Retrieve the seed identifer from FIGdisk/config/seed_id.      # Retrieve the seed identifer from FIGdisk/config/seed_id.
# Line 886  Line 899 
899  from this instance.  from this instance.
900    
901  =cut  =cut
902    #: Return Type @;
903  sub get_release_info  sub get_release_info
904  {  {
905      my($fig, $no_create) = @_;      my($fig, $no_create) = @_;
# Line 950  Line 963 
963    
964  =head1 get_peer_last_update  =head1 get_peer_last_update
965    
966    usage: my $date = $fig->get_peer_last_update($peer_id);
967    
968  Return the timestamp from the last successful peer-to-peer update with  Return the timestamp from the last successful peer-to-peer update with
969  the given peer.  the given peer.
970    
971  We store this information in FIG/Data/Global/Peers/<peer-id>.  We store this information in FIG/Data/Global/Peers/<peer-id>.
972    
973  =cut  =cut
974    #: Return Type $;
975  sub get_peer_last_update  sub get_peer_last_update
976  {  {
977      my($self, $peer_id) = @_;      my($self, $peer_id) = @_;
# Line 979  Line 994 
994      }      }
995  }  }
996    
997    =pod
998    
999    =head1 set_peer_last_update
1000    
1001    usage: $fig->set_peer_last_update($peer_id, $time);
1002    
1003    =cut
1004    #: Return Type ;
1005    
1006  sub set_peer_last_update  sub set_peer_last_update
1007  {  {
1008      my($self, $peer_id, $time) = @_;      my($self, $peer_id, $time) = @_;
# Line 994  Line 1018 
1018      close(F);      close(F);
1019  }  }
1020    
1021    =head3 cgi_url
1022    
1023    usage: my $url = $fig->cgi_url();
1024    
1025    =cut
1026    #: Return Type $;
1027  sub cgi_url {  sub cgi_url {
1028      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1029      return &plug_url($FIG_Config::cgi_url);      return &plug_url($FIG_Config::cgi_url);
1030  }  }
1031    
1032    =head3 temp_url
1033    
1034    usage: my $url = $fig->temp_url();
1035    
1036    =cut
1037    #: Return Type $;
1038  sub temp_url {  sub temp_url {
1039      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1040      return &plug_url($FIG_Config::temp_url);      return &plug_url($FIG_Config::temp_url);
1041  }  }
1042    
1043    =head3 plug_url
1044    
1045    usage: my $url2 = $fig->plug_url($url);
1046    
1047    =cut
1048    #: Return Type $;
1049  sub plug_url {  sub plug_url {
1050      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1051      my($url) = @_;      my($url) = @_;
# Line 1027  Line 1069 
1069      return $url;      return $url;
1070  }  }
1071    
1072    =head3 file_read
1073    
1074    usage: my $text = $fig->file_read($fileName);
1075    
1076    usage: my @lines = $fig->file_read($fileName);
1077    
1078    =cut
1079    #: Return Type $;
1080    #: Return Type @;
1081  sub file_read  sub file_read
1082  {  {
1083      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
# Line 1050  Line 1101 
1101  }  }
1102    
1103    
1104    =head3 file_head
1105    
1106    usage: my $text = $fig->file_read($fileName, $count);
1107    
1108    usage: my @lines = $fig->file_read($fileName, $count);
1109    
1110    =cut
1111    #: Return Type $;
1112    #: Return Type @;
1113  sub file_head  sub file_head
1114  {  {
1115      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
# Line 1135  Line 1195 
1195  Assumes @x contains numeric values.  Returns the minimum of the values.  Assumes @x contains numeric values.  Returns the minimum of the values.
1196    
1197  =cut  =cut
1198    #: Return Type $;
1199  sub min {  sub min {
1200      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1201      my(@x) = @_;      my(@x) = @_;
# Line 1159  Line 1219 
1219  Assumes @x contains numeric values.  Returns the maximum of the values.  Assumes @x contains numeric values.  Returns the maximum of the values.
1220    
1221  =cut  =cut
1222    #: Return Type $;
1223  sub max {  sub max {
1224      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1225      my(@x) = @_;      my(@x) = @_;
# Line 1183  Line 1243 
1243  Returns true iff $y is between $x and $z.  Returns true iff $y is between $x and $z.
1244    
1245  =cut  =cut
1246    #: Return Type $;
1247  sub between {  sub between {
1248      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1249      my($x,$y,$z) = @_;      my($x,$y,$z) = @_;
# Line 1208  Line 1268 
1268  codes using hashes that assumed uppercase DNA triplets as keys.  codes using hashes that assumed uppercase DNA triplets as keys.
1269    
1270  =cut  =cut
1271    #: Return Type $;
1272  sub standard_genetic_code {  sub standard_genetic_code {
1273      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1274    
# Line 1292  Line 1352 
1352  will translate initial TTG or GTG to 'M'.  will translate initial TTG or GTG to 'M'.
1353    
1354  =cut  =cut
1355    #: Return Type $;
1356  sub translate {  sub translate {
1357      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1358      my( $dna,$code,$start) = @_;      my( $dna,$code,$start) = @_;
# Line 1326  Line 1386 
1386    
1387  =pod  =pod
1388    
1389  =head1 reverse_comp and rev_comp  =head1 reverse_comp
1390    
1391  usage: $dnaR = &FIG::reverse_comp($dna) or  usage: $dnaR = &FIG::reverse_comp($dna) or
1392         $dnaRP = &FIG::rev_comp($seqP)         $dnaRP = &FIG::rev_comp($seqP)
# Line 1338  Line 1398 
1398  reasonable effeciency issue.  reasonable effeciency issue.
1399    
1400  =cut  =cut
1401    #: Return Type $;
1402  sub reverse_comp {  sub reverse_comp {
1403      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1404      my($seq) = @_;      my($seq) = @_;
# Line 1346  Line 1406 
1406      return ${&rev_comp(\$seq)};      return ${&rev_comp(\$seq)};
1407  }  }
1408    
1409    =head1 rev_comp
1410    
1411    =cut
1412    #: Return Type $;
1413  sub rev_comp {  sub rev_comp {
1414      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1415      my( $seqP ) = @_;      my( $seqP ) = @_;
# Line 1390  Line 1454 
1454    
1455  =cut  =cut
1456    
   
1457  sub run {  sub run {
1458      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1459      my($cmd) = @_;      my($cmd) = @_;
# Line 1420  Line 1483 
1483  Date:      2004-Feb-18  Date:      2004-Feb-18
1484    
1485  =cut  =cut
1486    #: Return Type @;
1487  sub read_fasta_record  sub read_fasta_record
1488  {  {
1489      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
# Line 2242  Line 2305 
2305  region (sorry).  region (sorry).
2306    
2307  =cut  =cut
2308    #: Return Type @;
   
2309  sub genes_in_region {  sub genes_in_region {
2310      my($self,$genome,$contig,$beg,$end) = @_;      my($self,$genome,$contig,$beg,$end) = @_;
2311      my($x,$relational_db_response,$feature_id,$b1,$e1,@feat,@tmp,$l,$u);      my($x,$relational_db_response,$feature_id,$b1,$e1,@feat,@tmp,$l,$u);

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