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# $Id: Prints.pm,v 1.13.4.1 2006/10/02 23:10:32 sendu Exp $
#
# BioPerl module for Bio::Tools::Prints
#
# Cared for by  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::Prints - Parser for FingerPRINTScanII program 
=head1 SYNOPSIS
  use Bio::Tools::Prints;
  my $prints_parser = new Bio::Tools::Prints(-fh =>$filehandle );
  while( my $prints_feat = $prints_parser->next_result ) {
        push @prints_feat, $prints_feat;
  }
=head1 DESCRIPTION
 PRINTScan 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
 the Bioperl mailing list.  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
 of the bugs and their resolution. Bug reports can be submitted via
 the web:
  http://bugzilla.open-bio.org/
=head1 AUTHOR - Balamurugan Kumarasamy
 bala@tll.org.sg
 juguang@tll.org.sg
=head1 APPENDIX
 The rest of the documentation details each of the object methods.
 Internal methods are usually preceded with a _
=cut
package Bio::Tools::Prints;
use strict;
use Bio::SeqFeature::FeaturePair;
use Bio::SeqFeature::Generic;
use base qw(Bio::Root::Root Bio::Root::IO);
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=head2 new
 Title   : new
 Usage   : my $obj = new Bio::Tools::Prints(-fh=>$filehandle);
 Function: Builds a new Bio::Tools::Prints object
 Returns : Bio::Tools::Prints
 Args    : -filename
           -fh (filehandle)
=cut
sub new {
      my($class,@args) = @_;
      my $self = $class->SUPER::new(@args);
      $self->_initialize_io(@args);
      return $self;
}
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=head2 next_result
 Title   : next_result
 Usage   : my $feat = $prints_parser->next_result
 Function: Get the next result set from parser data
 Returns : L<Bio::SeqFeature::Generic>
 Args    : none
=cut
sub next_result {
    my ($self) = @_;
    my %printsac;
    my @features;
    my $line;
    my $sequenceId;
      
    while ($_=$self->_readline()) {
       
           $line = $_;
           chomp $line;
           if ($line =~ s/^Sn;//) { # We have identified a Sn; line so there should be the following:
              ($sequenceId) = $line =~ /^\s*(\w+)/;
              $self->seqname($sequenceId);
              next;
           }
               
           if ($line =~ s/^1TBH//) {
               my  ($id) = $line =~ /^\s*(\w+)/;
               my ($ac) = $line =~ /(PR\w+)\s*$/;
               $printsac{$id} = $ac;
               $self->print_sac(\%printsac);
               next;
           }
              
           if ($line =~ s/^3TB//) {
               
              if ($line =~ s/^[HN]//) {
                   my($num)="";
                   $line =~ s/^\s+//;
                   my @elements = split /\s+/, $line;
                   my ($fingerprintName,$motifNumber,$temp,$tot,$percentageIdentity,$profileScore,$pvalue,$subsequence,$motifLength,$lowestMotifPosition,$matchPosition,$highestMotifPosition) = @elements;
     
                   my $start = $matchPosition;
                   my $end = $matchPosition + $motifLength - 1;
                   my $print_sac = $self->print_sac;
                    
                   my %printsac =  %{$print_sac};
                   my $print =  $printsac{$fingerprintName};
                   my $seqname=$self->seqname;
                   my $feat = "$print,$start,$end,$percentageIdentity,$profileScore,$pvalue";
                   my $new_feat =  $self->create_feature($feat,$seqname);
                   return $new_feat;
               }
               if ($line =~ s/^F//) {
                   return;  
               }
                   next;                                                       
               }
            next;         
  
      }
}
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=head2 create_feature
 Title   : create_feature
 Usage   : my $feat=$prints_parser->create_feature($feature,$seqname)
 Function: creates a SeqFeature Generic object
 Returns : L<Bio::SeqFeature::FeaturePair>
 Args    :
=cut
sub create_feature {
    my ($self, $feat,$sequenceId) = @_;
    my @f = split (/,/,$feat);
    # create feature object
    my $feature= Bio::SeqFeature::Generic->new(
        -seq_id    =>$sequenceId,
        -start=>$f[1],
        -end  => $f[2],
        -score      => $f[4],
        -source     => "PRINTS",
        -primary    =>$f[0],
        -logic_name => "PRINTS",
    );
    $feature->add_tag_value('evalue',$f[5]);
    $feature->add_tag_value('percent_id',$f[3]);
         
    my $feature2 = Bio::SeqFeature::Generic->new(
        -seq_id => $f[0],
        -start => 0,
        -end => 0,
    );
    my $fp = Bio::SeqFeature::FeaturePair->new(
        -feature1 => $feature,
        -feature2 => $feature2
    );
    return  $fp; 
}
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=head2 print_sac
 Title   : print_sac
 Usage   : $prints_parser->print_sac($print_sac)
 Function: get/set for print_sac
 Returns :
 Args    :
=cut
sub print_sac {
    my $self = shift;
    return $self->{'print_sac'} = shift if @_;
    return $self->{'print_sac'};
}
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=head2 seqname 
 Title   : seqname
 Usage   : $prints_parser->seqname($seqname)
 Function: get/set for seqname
 Returns :
 Args    :
=cut
sub seqname {
    my($self,$seqname)=@_;
    return $self->{'seqname'}=$seqname if(defined($seqname));
    return $self->{'seqname'};
}
1;