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has 'similarity'             => ( is => 'rw', isa => 'Num',  default  => 1 );
has 'sequences_unaligned'    => ( is => 'rw', isa => 'Bool', default  => 0 );

has '_input_seqio'  => ( is => 'ro', isa => 'Bio::SeqIO', lazy => 1, builder => '_build__input_seqio' );
has '_output_seqio' => ( is => 'ro', isa => 'Bio::SeqIO', lazy => 1, builder => '_build__output_seqio' );

sub _build_output_filename {
    my ($self) = @_;
    return $self->input_filename . ".sorted.fa";
}

sub _build__input_seqio {
    my ($self) = @_;
    return Bio::SeqIO->new( -file => $self->input_filename, -format => 'Fasta' );
}

sub _build__output_seqio {
    my ($self) = @_;
    return Bio::SeqIO->new( -file => ">" . $self->output_filename, -format => 'Fasta' );
}

sub _add_padding_to_make_sequence_length_multiple_of_three {
    my ( $self, $input_seq ) = @_;

    my $seq_length = $input_seq->length();
    if ( $seq_length % 3 == 1 ) {
        $input_seq->seq( $input_seq->seq() . "NN" );
    }
    elsif ( $seq_length % 3 == 2 ) {
        $input_seq->seq( $input_seq->seq() . "N" );
    }

    return $input_seq;
}

sub _remove_nnn_from_all_sequences {
    my ( $self, $input_sequences ) = @_;

    for my $sequence_name ( sort keys %{$input_sequences} ) {
        my $sequence = $input_sequences->{$sequence_name}->seq();
        $sequence =~ s/NNN$//i;
        $input_sequences->{$sequence_name}->seq($sequence);
    }
    return $input_sequences;
}

sub sort_fasta {
    my ($self) = @_;

    my %input_sequences;

    my $nnn_at_end_of_all_sequences = 1;
	my $sequence;
	my $variation_detected = 0;
    while ( my $input_seq = $self->_input_seqio->next_seq() ) {
		$sequence = $input_seq->seq if(!defined($sequence));
        $self->_add_padding_to_make_sequence_length_multiple_of_three($input_seq) if ( $self->make_multiple_of_three );
        $nnn_at_end_of_all_sequences = 0 if ( $nnn_at_end_of_all_sequences == 1 && !( $input_seq->seq() =~ /NNN$/i ) );
        $input_sequences{ $input_seq->display_id } = $input_seq;
        
		my $factor = $self->_percentage_similarity($sequence, $input_seq->seq);
        if($factor < $self->similarity)
        {
            $self->similarity($factor);
        }
    }

    $self->_remove_nnn_from_all_sequences( \%input_sequences ) if ( $self->remove_nnn_from_end && $nnn_at_end_of_all_sequences );

    my $sequence_length = 0;
    my $sequences_unaligned = 0;
    for my $sequence_name ( sort keys %input_sequences ) {
        $sequence_length = $input_sequences{$sequence_name}->length if($sequence_length == 0);
        $self->sequences_unaligned(1) if($input_sequences{$sequence_name}->length != $sequence_length);
        $self->_output_seqio->write_seq( $input_sequences{$sequence_name} );
    }
    return $self;
}

sub replace_input_with_output_file {
    my ($self) = @_;
    move( $self->output_filename, $self->input_filename );
    return $self;
}

sub _percentage_similarity
{
    my ($self, $string1, $string2) = @_;
    my $num_differences = 0;
    my $string1_length = length($string1);
    for(my $i = 0; $i < $string1_length && $i< length($string2); $i++)
    {
        $num_differences++ if( substr($string1, $i, 1) ne substr($string2, $i, 1));
    }
    return 1 if($num_differences == 0);
    return 0 if($string1_length == 0);
    return (1.0 - ($num_differences/$string1_length));
}

no Moose;
__PACKAGE__->meta->make_immutable;

1;

__END__

=pod

=encoding UTF-8

=head1 NAME

Bio::Roary::SortFasta - sort a fasta file by name

=head1 VERSION

version 3.13.0

=head1 SYNOPSIS

sort a fasta file by name
   use Bio::Roary::SortFasta;

   my $obj = Bio::Roary::SortFasta->new(
     input_filename   => 'infasta.fa',
   );
   $obj->sort_fasta->replace_input_with_output_file;

=head1 AUTHOR

Andrew J. Page <ap13@sanger.ac.uk>

=head1 COPYRIGHT AND LICENSE

This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.

This is free software, licensed under:

  The GNU General Public License, Version 3, June 2007

=cut