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# BioPerl module for Profile
# Copyright Balamurugan Kumarasamy
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
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=head1 NAME
Bio::Tools::Run::Profile
=head1 SYNOPSIS
 Build a Profile factory
 # $paramfile is the full path to the seg binary file
 my @params = ('DB',$dbfile,'PROGRAM',$paramfile);
 my $factory = Bio::Tools::Run::Profile->new($param);
 # Pass the factory a Bio::PrimarySeqI object
 # @feats is an array of Bio::SeqFeature::Generic objects
 my @feats = $factory->run($seq);
=head1 DESCRIPTION
 Wrapper module for the pfscan program
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists.  Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
=head2 Support 
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and 
reponsive experts will be able look at the problem and quickly 
address it. Please include a thorough description of the problem 
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via the
web:
  http://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Balamurugan Kumarasamy
 Email: fugui@worf.fugu-sg.org
=head1 APPENDIX
 The rest of the documentation details each of the object
 methods. Internal methods are usually preceded with a _
=cut
package Bio::Tools::Run::Profile;
use vars qw($AUTOLOAD @ISA $PROGRAM  $PROGRAMDIR
             $PROGRAMNAME @PROFILE_PARAMS
                         %OK_FIELD);
use strict;
use Bio::SeqIO;
use Bio::Root::Root;
use Bio::Root::IO;
use Bio::Factory::ApplicationFactoryI;
use Bio::Tools::Profile;
use Bio::Tools::Run::WrapperBase;
@ISA = qw(Bio::Root::Root Bio::Tools::Run::WrapperBase);
BEGIN {
    @PROFILE_PARAMS=qw(DB PROGRAM VERBOSE);
    foreach my $attr ( @PROFILE_PARAMS)
    { $OK_FIELD{$attr}++; }
}
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=head2 program_name
 Title   : program_name
 Usage   : $factory>program_name()
 Function: holds the program name
 Returns:  string
 Args    : None
=cut
sub program_name {
    return 'pfscan';
}
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=head2 program_dir
 Title   : program_dir
 Usage   : $factory->program_dir(@params)
 Function: returns the program directory, obtained from ENV variable.
 Returns:  string
 Args    :
=cut
sub program_dir {
    return Bio::Root::IO->catfile($ENV{PROFILEDIR}) if $ENV{PROFILEDIR};
}
sub AUTOLOAD {
       my $self = shift;
       my $attr = $AUTOLOAD;
       $attr =~ s/.*:://;
       $attr = uc $attr;
       $self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr};
       $self->{$attr} = shift if @_;
       return $self->{$attr};
}
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=head2 new
 Title   : new
 Usage   : my $factory= Bio::Tools::Run::Profile->new($param);
 Function: creates a new Profile factory
 Returns:  Bio::Tools::Run::Profile
 Args    :
=cut
sub new {
       my ($class,@args) = @_;
       my $self = $class->SUPER::new(@args);
       $self->io->_initialize_io();
  
       my ($attr, $value);
       while (@args)  {
           $attr =   shift @args;
           $value =  shift @args;
           next if( $attr =~ /^-/ ); # don't want named parameters
           $self->$attr($value);
       }
       return $self;
}
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=head2 predict_protein_features
 Title   :   predict_protein_features
 Usage   :   DEPRECATED. Use $factory->run($seq) instead.
 Function:   Runs Profile and creates an array of featrues
 Returns :   An array of L<Bio::SeqFeature::FeaturePair> objects
 Args    :   A Bio::PrimarySeqI
=cut
sub predict_protein_features{
        return shift->run(@_);       
}
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=head2 run
 Title   :   run
 Usage   :   my @feats = $factory->run($seq)
 Function:   Runs Profile 
 Returns :   An array of L<Bio::SeqFeature::FeaturePair> objects
 Args    :   A Bio::PrimarySeqI
=cut
sub run{
    my ($self,$seq) = @_;
    my @feats;
     if (ref($seq) ) {
          
         if (ref($seq) =~ /GLOB/) {
             $self->throw("cannot use filehandle");
         }
          
        my $display_id = $seq->display_id;
         
        my $infile1 = $self->_writeSeqFile($seq);
         
        $self->_input($infile1);
         
         @feats = $self->_run($display_id);
         unlink $infile1;
        
    }
    else {
        #The clone object is not a seq object but a file.
        #Perhaps should check here or before if this file is fasta format...if not die
        #Here the file does not need to be created or deleted. Its already written and may be used by other runnables.
        $self->_input($seq);
         @feats = $self->_run();
         
    }
    
    return @feats;
}
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=head2 _input
 Title   :   _input
 Usage   :   $factory->_input($seqFile)
 Function:   get/set for input file
 Returns :
 Args    :
=cut
sub _input() {
     my ($self,$infile1) = @_;
     if(defined $infile1){
        $self->{'input'}=$infile1;
     }
      return $self->{'input'};
}
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=head2 _run
 Title   :   _run
 Usage   :   $factory->_run()
 Function:   Makes a system call and runs pfscan
 Returns :   An array of L<Bio::SeqFeature::FeaturePair> objects
 Args    :
=cut
sub _run {
     my ($self,$display_id)= @_;
     my ($tfh,$outfile) = $self->io->tempfile(-dir=>$self->tempdir());
     close($tfh);
     undef $tfh;
     my $str =$self->executable.' -fz '.$self->_input." ".$self->DB." > ".$outfile;
     my $status = system($str);
     $self->throw( "Profile call ($str) crashed: $? \n") unless $status==0;
      
     my $filehandle;
     if (ref ($outfile) !~ /GLOB/) {
        open (PROFILE, "<".$outfile) or $self->throw ("Couldn't open file ".$outfile.": $!\n");
        $filehandle = \*PROFILE;
     }
     else {
        $filehandle = $outfile;
     }
     my $profile_parser = Bio::Tools::Profile->new(-fh=>$filehandle);
     my @profile_feat;
     while(my $profile_feat = $profile_parser->next_result){
        $profile_feat->seq_id($display_id); 
         push @profile_feat, $profile_feat;
     }
      
     $self->cleanup();
      
     unlink $outfile;
     return @profile_feat;
}
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=head2 _writeSeqFile
 Title   :   _writeSeqFile
 Usage   :   $factory->_writeSeqFile($seq)
 Function:   Creates a file from the given seq object
 Returns :   A string(filename) 
 Args    :   Bio::PrimarySeqI
=cut
sub _writeSeqFile{
    my ($self,$seq) = @_;
    my ($tfh,$inputfile) = $self->io->tempfile(-dir=>$self->tempdir());
    my $in  = Bio::SeqIO->new(-fh => $tfh , '-format' => 'fasta');
    $in->write_seq($seq);
    $in->close();
    undef $in;
    close($tfh);
    undef $tfh;
    return $inputfile;
}
1;