#!@@_perl_root_@@/bin/perl.exe 
package SeqParamTranslator;

##########################################################
#                                                        #
# dictyBase Extension of SeqParamTranslator              #
#                                                        #
##########################################################

use SeqParamTranslator_base;

BEGIN { %SeqParamTranslator:: = %SeqParamTranslator_base:: }


#########################################################################
#sub getMatchList {
#########################################################################
#    my ($self) = @_;
#
#    $self->_initFilePath;
#
#    $self->{'_query'} =~ s/\*/\%/g;
#    my $sth = $dbh->prepare("
#        SELECT feature_name
#        FROM   CGM_DDB.feature
#        WHERE  upper(feature_name) like ?
#        UNION
#        SELECT locus_name
#        FROM   CGM_DDB.locus
#        WHERE  upper(locus_name) like ?
#        UNION  
#        SELECT alias_name
#        FROM   CGM_DDB.alias
#        WHERE  upper(alias_name) like ?
#    ");
#    $sth->execute(uc($self->{'_query'}), uc($self->{'_query'}),
#		  uc($self->{'_query'}));
#    my $matchList;
#    while(my ($name) = $sth->fetchrow()) {
#	$matchList .= ":".$name;
#    }
#    
#    my $query = $self->{'_query'};
#    $query =~ s/\%/\*/g;
#    $query =~ s/\*$/\.\*/;
##
##  dictyBase took out next section (were not using basepairs file)
##
##
#
##    my $basepairsfile = $GCGDataDir."basepairs.table";
##    open(BASEPAIR, "$basepairsfile") ||
##	die "getSeq: Can't open '$basepairsfile' for reading:$!\n";
##    while(<BASEPAIR>) {
##	chomp;
##	my ($seqname, $GB, $num1, $num2) = split(/\t/);
##	if ($seqname =~ /^$query/i) {
##	    if ($GB =~ / \(GB\)$/) {
##	       $matchList .= ":".$seqname;
##	    }
##	}
##    }
##    close(BASEPAIR);
##
##    my $seqfile = $GCGDataDir."seqnames.table";
##    open(SEQFILE, "$seqfile") ||
##	die "getSeq: Can't open '$seqfile' for reading:$!\n";
##    while(<SEQFILE>) {
##	chomp;
##	if ($_ =~ /^$query \(GB\)$/i) {
##	    $matchList .= ":".$_;
##	}
##    }
##    close(SEQFILE);
#
#    $matchList =~ s/^\://;
#    $self->{'_matchList'} = $matchList;
#    if (!$self->{'_matchList'}) {
#	$self->{'_error'} = "No sequences were found in dictyBase with the name $query";
#    }
#    
#    if ($self->{'_matchList'} !~ /\:/) {
#	$self->{'_query'} = $self->{'_matchList'};
#	$self->{'_matchList'} = "";
#	$self->initInfo;
#    }
#}


########################################################################
1;
########################################################################