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package BioX::CLPM::Enzyme;
use base qw(BioX::CLPM::Base);
use Class::Std;
use Class::Std::Utils;

use warnings;
use strict;
use Carp;

use version; our $VERSION = qv('0.0.1');

{
        my %enzyme_id_of     :ATTR( :get<enzyme_id>      :set<enzyme_id>      :default<''>      :init_arg<enzyme_id> );
        my %name_of          :ATTR( :get<name>           :set<name>           :default<''>      :init_arg<name> );
        my %clvg_sites_of    :ATTR( :get<clvg_sites>     :set<clvg_sites>     :default<''>      :init_arg<clvg_sites> );
        my %clvg_position_of :ATTR( :get<clvg_position>  :set<clvg_position>  :default<''>      :init_arg<clvg_position> );
        my %rule_of          :ATTR( :get<rule>           :set<rule>           :default<''>      :init_arg<rule> );

        sub START {
                my ( $self, $ident, $arg_ref ) = @_;
                if ( $arg_ref ) { $self->_load( $arg_ref ); }
                return;
        }

        sub _load {
                my ( $self, $arg_ref ) = @_;
		# Update new enzyme_id if exists
                if ( defined $arg_ref->{enzyme_id} ) {
			my $enzyme_id = $arg_ref->{enzyme_id};
                	$self->set_enzyme_id($enzyme_id);

			# Load other enzyme data from db
	                my $sql  = 'select name, clvg_sites, clvg_position, rule ';
	                   $sql .= "from enzymes where enzyme_id = '$enzyme_id'";
	                my ( $enzyme_name, $clvg_sites, $clvg_position, $rule ) = $self->sqlexec( $sql, '@' );
			$self->set_name($enzyme_name);
			$self->set_clvg_sites($clvg_sites);
			$self->set_clvg_position($clvg_position);
			$self->set_rule($rule);
			warn "ENZYME _load() ( $enzyme_id, $enzyme_name, $clvg_sites, $clvg_position, $rule )\n";
		}
                elsif ( defined $arg_ref->{enzyme_name} ) {
			my $enzyme_name = $arg_ref->{enzyme_name};
                	$self->set_name($enzyme_name);

			# Load other enzyme data from db
	                my $sql  = 'select enzyme_id, clvg_sites, clvg_position, rule ';
	                   $sql .= "from enzymes where name = '$enzyme_name'";
	                my ( $enzyme_id, $clvg_sites, $clvg_position, $rule ) = $self->sqlexec( $sql, '@' );
                	$self->set_enzyme_id($enzyme_id);
			$self->set_clvg_sites($clvg_sites);
			$self->set_clvg_position($clvg_position);
			$self->set_rule($rule);
			warn "ENZYME _load() ( $enzyme_id, $enzyme_name, $clvg_sites, $clvg_position, $rule )\n";
		}
        }

	# API READ ONLY
	sub clvg_sites { my ( $self ) = @_; return split( //, $self->get_clvg_sites() ); }

	sub generate_fragments {
		my ($self, $arg_ref) = @_;
		my @clvg_sites;
		foreach my $sequence (@$arg_ref->{sequences}){
		        my @sequence = split(//, $sequence);
		        my $fragment;
		        my @initial_fragments;
		        foreach my $amino_acid (@sequence){
		                $fragment .= $amino_acid;
		                foreach my $clvg_site(@clvg_sites){
		                        if (uc($amino_acid) eq $clvg_site){
		                                push(@initial_fragments, $fragment);
		                                $fragment='';
		                        }
		                }
		        }
		        my @all_fragments = @initial_fragments;
		        for ( my $i = @initial_fragments - 1; $i > 1; $i--){
		                for ( my $j=0; $j<@initial_fragments-$i+1; $j++){
		                        my $new_fragment = '';
		                        $new_fragment.=$initial_fragments[$j];
		                        for ( my $k=0; $k<$i-1; $k++){
		                                $new_fragment.=$initial_fragments[$j+$k+1];
		                        }
		                        push (@all_fragments, $new_fragment);
		                }
		        }
		        foreach $fragment(@all_fragments){
		                if ($fragment=~m/.*[a-z]+.*/){
		                        #&SQLExec("insert into fragments(sequence_id, fragment_sequence) values ($sequence_id, '$fragment')");
		                }
		        }
		}	
	}
}

1; # Magic true value required at end of module
__END__

=head1 NAME

BioX::CLPM::Enzyme - Perl Tools for Mass Spec Peptide Matching


=head1 VERSION

This document describes BioX::CLPM::Enzyme version 0.0.1


=head1 SYNOPSIS

    use BioX::CLPM::Enzyme;

    my $obj = BioX::CLPM::Enzyme->new({attribute => 'value'});

    print $obj->get_attribute(), "\n";

    $obj->set_attribute('new value');

    print $obj->get_attribute(), "\n";

=for author to fill in:
    Brief code example(s) here showing commonest usage(s).
    This section will be as far as many users bother reading
    so make it as educational and exeplary as possible.
  
  
=head1 DESCRIPTION

=for author to fill in:
    Write a full description of the module and its features here.
    Use subsections (=head2, =head3) as appropriate.


=head1 INTERFACE 

=for author to fill in:
    Write a separate section listing the public components of the modules
    interface. These normally consist of either subroutines that may be
    exported, or methods that may be called on objects belonging to the
    classes provided by the module.


=head1 DIAGNOSTICS

=for author to fill in:
    List every single error and warning message that the module can
    generate (even the ones that will "never happen"), with a full
    explanation of each problem, one or more likely causes, and any
    suggested remedies.