Bio::Restriction::IO::bairoch - bairoch enzyme set

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 Title   : read
 Usage   : $renzs = $stream->read
 Function: reads all the restrction enzymes from the stream
 Returns : a Bio::Restriction::Restriction object
 Args    : none

 Title   : write
 Usage   : $stream->write($renzs)
 Function: writes restriction enzymes into the stream
 Returns : 1 for success and 0 for error
 Args    : a Bio::Restriction::Enzyme
           or a Bio::Restriction::EnzymeCollection object

# BioPerl module for Bio::Restriction::IO::withrefm
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Rob Edwards <redwards@utmem.edu>
#
# Copyright Rob Edwards
#
# You may distribute this module under the same terms as perl itself
#

# POD documentation - main docs before the code

# Let the code begin...

package Bio::Restriction::IO::bairoch;

use vars qw(%WITH_REFM_FIELD);
use strict;

use Bio::Restriction::Enzyme;
use Bio::Restriction::Enzyme::MultiCut;
use Bio::Restriction::Enzyme::MultiSite;
use Bio::Restriction::EnzymeCollection;

use Data::Dumper;

use base qw(Bio::Restriction::IO::base);

sub read {
    my $self = shift;

    my $renzs = Bio::Restriction::EnzymeCollection->new(-empty => 1);

    local $/ = '//';
    while (defined(my $entry=$self->_readline()) ) {
        $self->debug("|$entry|\n");

        #
        # Minimal information
        #
        my ($name) = $entry =~ /ID\s+(\S+)/;
        my ($site) = $entry =~ /RS\s+([^\n]+)/;
        next unless ($name && $site);
       
        # the standard sequence format for these guys is:
        # GATC, 2;
        # or, for enzymes that cut more than once
        # GATC, 2; GTAC, 2; 

        # there are a couple of sequences that have multiple
        # recognition sites. 

        my @sequences;
        if ($site =~ /\;/) {
            @sequences = split /\;/, $site;
            $self->debug(@sequences,"\n");
            $site=shift @sequences;
        }
        
        my ($seq, $cut)=split /,\s+/, $site;
        $self->debug("SITE: |$site| GAVE: |$seq| and |$cut|\n");
        if ($seq eq '?') {
           $self->warn("$name: no site. Skipping") if $self->verbose > 1;
           next;
        }
        
            # this is mainly an error check to make sure that I am adding what I think I am!	
        if ($seq !~ /[NGATC]/i) {
          $self->throw("Sequence $name has weird sequence: |$seq|");
        }
        my $re;
        if ($cut eq "?") {
              $re = Bio::Restriction::Enzyme->new(-name=>$name, -seq => $seq);
        }
        else {
               if ($cut !~ /^-?\d+$/) {
             $self->throw("Cut site from $name is weird: |$cut|\n");
               }
        
               $re = Bio::Restriction::Enzyme->new(-name=>$name,
                                                  -cut => $cut,
                                                  -seq => $seq
                                                  );
        }
        $renzs->enzymes($re);

        #
        # prototype / isoschizomers
        #
        my ($prototype) = $entry =~ /PT\s+([^\n]+)/;

        if ($prototype) {
            #$re->isoschizomers(split /\,/, $isoschizomers);
            #NOTE: Need to add a method so that we can add isoschosomers to enzymes that may not exist!
	    $re->is_prototype(0);
        } else {
            $re->is_prototype(1);
        }

        #
        # methylation
        #

        my ($meth) = $entry =~ /MS\s+([^\n]+)/;
        my @meths;
        if ($meth) {
            # this can be either X(Y) or X(Y),X2(Y2)
            # where X is the base and y is the type of methylation
            if ( $meth =~ /(\S+)\((\d+)\),(\S+)\((\d+)\)/ ) { # two msites per site
                #my ($p1, $m1, $p2, $m2) = ($1, $2, $3, $4);
                $re->methylation_sites($self->_meth($re,$1, $2),
                                       $self->_meth($re,$3,$4));
            }
            elsif ($meth =~ /(\S+)\((\d+)\)/ ) { # one msite per site or more sites
                #print Dumper $meth;
                $re->methylation_sites( $self->_meth($re,$1,$2) );
                @meths = split /, /, $meth;
                $meth=shift @meths;
            } else {
                $self->warn("Unknown methylation format [$meth]") if $self->verbose >0;
            }
        }

        #
        # microbe
        #
        my ($microbe) = $entry =~ /OS\s+([^\n]+)/;
        $re->microbe($microbe) if $microbe;

        #
        # source
        #
        #my ($source) = $entry =~ /<6>([^\n]+)/;
        #$re->source($source) if $source;

        #
        # vendors
        #
        my ($vendors) = $entry =~ /CR\s+([^\n]+)/;
        $re->vendors(split /,\s*/, $vendors) if $vendors;

        #
        # references
        #
        #my ($refs) = $entry =~ /<8>(.+)/s;
        #$re->references(map {split /\n+/} $refs) if $refs;

        #
        # create special types of Enzymes
        #
        $self->warn("Current issues with multisite enzymes using bairoch format\n".
                    "Recommend using itype2 or withrefm formats for now") if @sequences;
        #$self->_make_multisites($renzs, $re, \@sequences, \@meths) if @sequences;

    }

    return $renzs;
}

sub write {
    my ($self,@h) = @_;
    $self->throw_not_implemented;
}

1;