view release on metacpan or  search on metacpan

Bio/Tools/FootPrinter.pm  view on Meta::CPAN

 Returns : Bio::Tools::FootPrinter
 Args    : -fh/-file => $val, # for initing input, see Bio::Root::IO

=cut

sub new {
  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  $self->_initialize_io(@args);

  return $self;
}

=head2 next_feature

 Title   : next_feature
 Usage   : my $r = $footprint->next_feature
 Function: Get the next feature from parser data
 Returns : L<Bio::SeqFeature::Generic> 
 Args    : none

=cut

sub next_feature{
   my ($self) = @_;
   $self->_parse_predictions() unless $self->_predictions_parsed();
   return shift @{$self->{'_feature'}};

}

=head2 _add_feature

 Title   : _add_feature
 Usage   : $footprint->_add_feature($feat)
 Function: Add feature to array
 Returns : none
 Args    : none

=cut

sub _add_feature {
    my ($self,$feat) = @_;
    if($feat){
        push @{$self->{'_feature'}},$feat;
    }
}

=head2 _parse_predictions

 Title   : _parse_predictions
 Usage   : my $r = $footprint->_parse_predictions
 Function: do the parsing 
 Returns : none 
 Args    : none

=cut

sub _parse_predictions {
  my ($self) = @_;
  $/="";
  my ($seq,$second,$third,$name);
  while ($_ = $self->_readline) {
    chomp;
    my @array = split("\n",$_);
    if ($#array == 5) {
      # get rid of header
      shift(@array); shift(@array);
    }
    if($#array == 3){
        if($name){
            $name=~s/>//;
            my $feat = $self->_parse($name,$seq,$second,$third);
            $self->_add_feature($feat);
        }
        $name    = shift @array;
        $seq     = $array[0];
        $second  = $array[1];
        $third   = $array[2];
        next;
    }
    $seq        .= $array[0];
    $third      .= $array[2];
  }
  
  $seq || return;
  
  $name=~s/>//;
  my $feat = $self->_parse($name,$seq,$second,$third);
  $self->_add_feature($feat);

  $self->_predictions_parsed(1);
}

=head2 _predictions_parsed

 Title   : _predictions_parsed
 Usage   : $footprint->_predictions_parsed(1)
 Function: Get/Set for whether predictions parsed
 Returns : 1/0
 Args    : none

=cut

sub _predictions_parsed {
    my ($self,$val) = @_;
    if($val){
        $self->{'_predictions_parsed'} = $val;
    }
    return $self->{'_predictions_parsed'};
}


=head2 _parse

 Title   : _parse
 Usage   : $footprint->_parse($name,$seq,$pattern)
 Function: do the actual parsing
 Returns : L<Bio::SeqFeature::Generic>
 Args    : none