# $Id: Cap3.pm,v 1.1.1.1 2003/01/29 02:07:55 marcl Exp $
package Bio::Tools::Run::Cap3;
use vars qw(@ISA %OK_FIELD @PARAMS *AUTOLOAD $PROGRAMDIR);

use strict;
use Bio::Root::Root;
use Bio::Root::IO;
use Bio::Seq;
use Bio::SeqIO;
use Bio::Tools::Run::WrapperBase;
use Bio::Factory::ApplicationFactoryI;

BEGIN
{

    @PARAMS     = qw(a b c d e f g m n o p s u v x);
    $PROGRAMDIR = '/usr/local/bin';

    # Authorize attribute fields
    foreach my $attr (@PARAMS) { $OK_FIELD{$attr}++; }
}

@ISA = qw(Bio::Root::Root
  Bio::Tools::Run::WrapperBase
  Bio::Factory::ApplicationFactoryI);

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

    # chained new
    my $self = $caller->SUPER::new(@args);

    # to facilitiate tempfile cleanup
    my ( undef, $tempfile ) = $self->io->tempfile();
    $self->outfile_name($tempfile);
    while (@args)
    {
        my $attr  = shift @args;
        my $value = shift @args;
        $self->$attr($value);
    }
    return $self;
}

sub AUTOLOAD
{
    my $self = shift;
    my $attr = $AUTOLOAD;
    $attr =~ s/.*:://;
    my $attr_letter = substr( $attr, 0, 1 );

    # actual key is first letter of $attr unless first attribute
    # letter is underscore (as in _READMETHOD), the $attr is a BLAST
    # parameter and should be truncated to its first letter only
    $attr = ( $attr_letter eq '_' ) ? $attr : $attr_letter;
    $self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr};
    $self->{$attr_letter} = shift if @_;
    return $self->{$attr_letter};
}

sub program_dir
{
    $PROGRAMDIR;
}

sub program_name
{
    'cap3';
}

sub run
{
    my ($self, $input) = @_;
    my $param_string = $self->_setparams;
    my $exe = $self->executable;
# Create input file pointer
    my $infilename1 = $self->_setinput($input);
    if (! $infilename1) {$self->throw(" $input ($infilename1) not array of Bio::Seq objects or file name!");}

    my $commandstring = $exe. $param_string . " $infilename1";

    open(CAP3, "$commandstring |") || $self->throw(sprintf("%s call crashed: %s %s\n", $self->program_name, $!, $commandstring));
    local $/ = undef;
    my ($result) = <CAP3>;
    close CAP3;
    return $result;
}

sub _setparams
{
    my $self = shift;
    my ( $attr, $value, @execparams );

    @execparams = @PARAMS;

    my $param_string = "";
    for $attr (@execparams)
    {
        $value = $self->$attr();
        next unless ( defined $value );

        # put params in format expected by cap3
        $attr = '-' . $attr;
        $param_string .= " $attr  $value ";
    }
    return $param_string;
}


sub _setinput {
    my ($self, $input1) = @_;
    my ($seq, $temp, $infilename1, $fh ) ;
#  If $input1 is not a reference it better be the name of a file with
#  the sequence data...
    $self->io->_io_cleanup();

  SWITCH:  {
      unless (ref $input1) {
	  $infilename1 = (-e $input1) ? $input1 : 0 ;
	  last SWITCH; 
      }
#  $input may be an array of BioSeq objects...
      if (ref($input1) =~ /ARRAY/i ) {
	  ($fh,$infilename1) = $self->io->tempfile();
	  $temp =  Bio::SeqIO->new(-fh=> $fh, '-format' => 'Fasta');
	  foreach $seq (@$input1) {
	      unless ($seq->isa("Bio::PrimarySeqI")) {return 0;}
	      $temp->write_seq($seq);
	  }
	  close $fh;
	  $fh = undef;
	  last SWITCH;
      }
      $infilename1 = 0;		# Set error flag if you get here
  }				# End SWITCH
    return ($infilename1);
}