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Bio/Prospect/LocalClient.pm  view on Meta::CPAN

 Purpose:   constructor
 Arguments: hash reference with following key/value pairs
  options => Bio::Prospect::Options object (required)
 Returns:   Bio::Prospect::LocalClient

=cut


sub new(;%) {
  my $self = shift->SUPER::new(@_);
  $self->_setenv();
  $self->_prepare_options();
  $self->{'xmlCacheName'}  = 'xmlCache';   # name of xml file cache
  $self->{'sortCacheName'} = 'sortCache';  # name of sort file cache
  return $self;
}


#-------------------------------------------------------------------------------
# thread()
#-------------------------------------------------------------------------------

Bio/Prospect/LocalClient.pm  view on Meta::CPAN

  throw Bio::Prospect::RuntimeError
    ( 'failed to execute Prospect',
    "system($cmd) exited with status $s",
    'check your prospect installation manually' );
  }
  # sanity checks on the sort output??
  return $sfn;
}


sub _setenv {
  if (not -d $Bio::Prospect::Init::PROSPECT_PATH ) {
    throw Bio::Prospect::Exception
      ( "PROSPECT_PATH is not set correctly",
      "PROSPECT_PATH ($Bio::Prospect::Init::PROSPECT_PATH}) is not a valid directory",
      "Check your prospect installation and set PROSPECT_PATH in Bio::Prospect::Init or as an environment variable" );
  } else {
    $ENV{'PROSPECT_PATH'} =  $Bio::Prospect::Init::PROSPECT_PATH;
  }
  if (not -d $Bio::Prospect::Init::PDB_PATH) {
    throw Bio::Prospect::Exception