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# 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::Prints 
=head1 SYNOPSIS
  Build a Prints factory
  my @params = ('DB',$dbfile);
  my $factory = Bio::Tools::Run::Prints->new($params);
  # Pass the factory a Bio::Seq object
  # @feats is an array of Bio::SeqFeature::Generic objects
  my @feats = $factory->run($seq);
=head1 DESCRIPTION
  FingerPRINTScan II is a PRINTS fingerprint identification algorithm.
  Copyright (C) 1998,1999  Phil Scordis
=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 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://bugzilla.open-bio.org/
=head1 AUTHOR - Bala
 Email savikalpa@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::Prints;
use vars qw($AUTOLOAD @ISA $PROGRAM  $PROGRAMDIR
            $PROGRAMNAME @PRINTS_PARAMS
                         %OK_FIELD);
use strict;
use Bio::SeqIO;
use Bio::Root::IO;
use Bio::Root::Root;
use Bio::Factory::ApplicationFactoryI;
use Bio::Tools::Prints;
use Bio::Tools::Run::WrapperBase;
@ISA = qw(Bio::Root::Root Bio::Tools::Run::WrapperBase);
BEGIN {
       @PRINTS_PARAMS=qw(DB PROGRAM VERBOSE);
       foreach my $attr ( @PRINTS_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 'FingerPRINTScan';
}
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=head2 program_dir
 Title   : program_dir
 Usage   : $factory->program_dir(@params)
 Function: returns the program directory, obtiained from ENV variable.
 Returns:  string
 Args    :
=cut
sub program_dir {
return Bio::Root::IO->catfile($ENV{PRINTSDIR}) if $ENV{PRINTSDIR};
}
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   : $prints->new(@params)
 Function: creates a new Prints factory
 Returns:  Bio::Tools::Run::Prints
 Args    :
=cut
sub new {
       my ($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( $attr =~ /^-/ ); # don't want named parameters
           if ($attr =~/PROGRAM/i) {
              $self->executable($value);
              next;
           }
           $self->$attr($value);
       }
       return $self;
}
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=head2 predict_protein_features
 Title   :   predict_protein_features()
 Usage   :   DEPRECATED. Use $obj->run($seqFile) instead.
 Function:   Runs Prints and creates an array of featrues
 Returns :   An array of Bio::SeqFeature::Generic objects
 Args    :   A Bio::PrimarySeqI
=cut
sub predict_protein_features{
        return shift->run(@_);
}
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=head2 run 
 Title   :   run 
 Usage   :   $obj->run($seq)
 Function:   Runs Prints 
 Returns :   An array of Bio::SeqFeature::Generic objects
 Args    :   A Bio::PrimarySeqI, or a Fasta file name
=cut
sub run{
    my ($self,$seq) = @_;
    my @feats;
    if  (ref($seq) ){# it is an object
         
        if (ref($seq) =~ /GLOB/) {
           $self->throw("cannot use filehandle");
        }
     
        my $infile1 = $self->_writeSeqFile($seq);
         
        $self->_input($infile1);
         
        @feats = $self->_run();
         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   :   obj->_input($seqFile)
 Function:   Internal(not to be used directly)
 Returns :
 Args    :
=cut
sub _input() {
     my ($self,$infile1) = @_;
      
     if(defined $infile1){
          
        $self->{'input'}=$infile1;
     }   
     return $self->{'input'};
}
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=head2 _run
 Title   :   _run
 Usage   :   $obj->_run()
 Function:   Internal(not to be used directly)
 Returns :   An array of Bio::SeqFeature::Generic objects
 Args    :
=cut
sub _run {
     my ($self)= @_;
     my ($tfh,$outfile) = $self->io->tempfile(-dir=>$self->tempdir());
     close($tfh);
     undef $tfh;
     my $str =$self->executable." ".$self->DB." ".$self->_input." -fjR >".$outfile;
     my $status = system($str);
     $self->throw( "Prints call ($str) crashed: $? \n") unless $status==0;
      
     my $filehandle;
     if (ref ($outfile) !~ /GLOB/) {
        open (PRINTS, "<".$outfile) or $self->throw ("Couldn't open file ".$outfile.": $!\n");
        $filehandle = \*PRINTS;
     }
     else {
        $filehandle = $outfile;
     }
     my $prints_parser = Bio::Tools::Prints->new(-fh=>$filehandle);
     my @prints_feat;
      
     while(my $prints_feat = $prints_parser->next_result){
         push @prints_feat, $prints_feat;
     }
      
      
     $self->cleanup();
     unlink $outfile;    
     return @prints_feat;
      
}
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=head2 _writeSeqFile
 Title   :   _writeSeqFile
 Usage   :   obj->_writeSeqFile($seq)
 Function:   Internal(not to be used directly)
 Returns :
 Args    :
=cut
sub _writeSeqFile{
    my ($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;