Raw content of XrefMapper::db
<![CDATA[package XrefMapper::db;
use vars '@ISA';
use Bio::EnsEMBL::DBSQL::DBConnection;
use Cwd;
sub new{
my($class, @args) = @_;
my $self ={};
bless $self,$class;
$self->dbc(new Bio::EnsEMBL::DBSQL::DBConnection(@args));
return $self;
}
sub species{
my ($self, $arg) = @_;
(defined $arg) &&
($self->{_species} = $arg );
return $self->{_species};
}
sub dbc{
my $self = shift;
if(@_){
my $arg = shift;
if(defined($arg)){
if(!$arg->isa('Bio::EnsEMBL::DBSQL::DBConnection')){
throw("$arg is no a DBConnection\n");
}
}
$self->{_dbc} = $arg;
}
return $self->{_dbc};
}
=head2 dir
Arg [1] : (optional) string $arg
The new value of the dir used
Example : $dir = $db->dir()
Description: Getter/Setter for the directory used in the creation of fasta file
Returntype : string
Exceptions : none
Caller : new
=cut
sub dir {
my ($self, $arg) = @_;
(defined $arg) &&
($self->{_dir} = process_dir($arg) );
return $self->{_dir};
}
=head2 protein_file
Arg [1] : (optional) string $arg
the fasta file name for the ensembl proteins
Example : $file_name = $self->ensembl_protein_file();
Description: Getter / Setter for the protien ensembl fasta file
Returntype : string
Exceptions : none
=cut
sub protein_file{
my ($self, $arg) = @_;
(defined $arg) &&
($self->{_ens_prot_file} = $arg );
return $self->{_ens_prot_file};
}
=head2 dna_file
Arg [1] : (optional) string $arg
the fasta file name for the ensembl dna
Example : $file_name = $self->ensembl_dna_file();
Description: Getter / Setter for the protien ensembl fasta file
Returntype : string
Exceptions : none
=cut
sub dna_file{
my ($self, $arg) = @_;
(defined $arg) &&
($self->{_ens_dna_file} = $arg );
return $self->{_ens_dna_file};
}
sub process_dir {
my ($dir) = @_;
if($dir =~ "^\/" ) { # if it start with / then its not from pwd
if(! -d $dir){
die "directory does not exist $dir\n";
}
}
elsif($dir eq "."){
$dir = cwd();
}
elsif($dir =~ "^\.\/"){
my $tmp = $dir;
$dir = cwd() . "/" . substr( $tmp, 2 );
if(! -d $dir){
die "directory does not exist $dir\n";
}
}
else{
die "directory does not exist $dir\n";
}
return $dir;
}
1;
]]>