XrefMapper db
Package variablesGeneral documentationMethods
Toolbar
WebCvsRaw content
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::DBSQL::DBConnection
Cwd
Synopsis
No synopsis!
Description
No description!
Methods
dbc
No description
Code
dirDescriptionCode
dna_fileDescriptionCode
new
No description
Code
process_dir
No description
Code
protein_fileDescriptionCode
species
No description
Code
Methods description
dircode    nextTop
                                                                                
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
dna_filecodeprevnextTop
 
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
protein_filecodeprevnextTop
 
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
Methods code
dbcdescriptionprevnextTop
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 $self->{_dbc};
}
dirdescriptionprevnextTop
sub dir {
  my ($self, $arg) = @_;

  (defined $arg) &&
    ($self->{_dir} = process_dir($arg) );
  return $self->{_dir};
}
dna_filedescriptionprevnextTop
sub dna_file {
  my ($self, $arg) = @_;

  (defined $arg) &&
    ($self->{_ens_dna_file} = $arg );
  return $self->{_ens_dna_file};
}
newdescriptionprevnextTop
sub new {
  my($class, @args) = @_;

  my $self ={};
  bless $self,$class;

   $self->dbc(new Bio::EnsEMBL::DBSQL::DBConnection(@args));

  return $self;
}
process_dirdescriptionprevnextTop
sub process_dir {
  my ($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 $dir; } 1;
}
protein_filedescriptionprevnextTop
sub protein_file {
  my ($self, $arg) = @_;

  (defined $arg) &&
    ($self->{_ens_prot_file} = $arg );
  return $self->{_ens_prot_file};
}
speciesdescriptionprevnextTop
sub species {
  my ($self, $arg) = @_;

  (defined $arg) &&
    ($self->{_species} = $arg );
  return $self->{_species};
}
General documentation
No general documentation available.