=head1 LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2019] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

=cut

package XrefMapper::db;

use vars '@ISA';
use Bio::EnsEMBL::DBSQL::DBConnection;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
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};
}

sub dba {
    my $self = shift;
    my $dbc = $self->dbc;
    return Bio::EnsEMBL::DBSQL::DBAdaptor->new(-dbconn => $dbc, -species => $self->species);
}

=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;
}


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