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lib/Bio/FastParsers/Blast/Xml/Hsp.pm  view on Meta::CPAN

sub pattern_from {
    return shift->_root->{'Hsp_pattern-from'}->{'value'}
}


sub pattern_to {
    return shift->_root->{'Hsp_pattern-to'}->{'value'}
}


sub positive {
    return shift->_root->{'Hsp_positive'}->{'value'}
}


sub qseq {
    return shift->_root->{'Hsp_qseq'}->{'value'}
}


sub query_frame {
    return shift->_root->{'Hsp_query-frame'}->{'value'}
}


sub query_from {
    return shift->_root->{'Hsp_query-from'}->{'value'}
}


sub query_to {
    return shift->_root->{'Hsp_query-to'}->{'value'}
}


sub score {
    return shift->_root->{'Hsp_score'}->{'value'}
}


# public aliases


sub expect {
    return shift->evalue
}


sub qcov {
    return shift->query_coverage
}


sub scov {
    return shift->subject_coverage
}


sub pident {
    return shift->percentage_identity
}


sub ppos {
    return shift->percentage_positive
}



sub query_len {
    return shift->_parent->query_len
}



sub hit_len {
    return shift->_parent->len
}


# pseudo-aliases

use Const::Fast;
const my $NEGFRAME => qr{\A -}xms;


sub hit_strand {
    my $self = shift;
    return $self->hit_frame =~ $NEGFRAME ? -1 : 1;
}


sub hit_start {
    my $self = shift;
    return $self->hit_from < $self->hit_to ? $self->hit_from
                                           : $self->hit_to;
}


sub hit_end {
    my $self = shift;
    return $self->hit_to > $self->hit_from ? $self->hit_to
                                           : $self->hit_from;
}


sub query_strand {
    my $self = shift;
    return $self->query_frame =~ $NEGFRAME ? -1 : 1;
}


sub query_start {
    my $self = shift;
    return $self->query_from < $self->query_to ? $self->query_from
                                               : $self->query_to;
}


sub query_end {
    my $self = shift;
    return $self->query_to > $self->query_from ? $self->query_to
                                               : $self->query_from;
}


sub query_coverage {
    my $self = shift;
    return sprintf("%.1f",
        100 * ( $self->query_end - $self->query_start + 1 ) / $self->query_len
    );
}


sub subject_coverage {
    my $self = shift;
    return sprintf("%.1f",
        100 * ( $self->hit_end - $self->hit_start + 1 ) / $self->hit_len
    );
}


sub percentage_identity {
    my $self = shift;
    return sprintf("%.1f", 100 * ( $self->identity / $self->align_len ) );
}


sub percentage_positive {
    my $self = shift;
    return sprintf("%.1f", 100 * ( $self->positive / $self->align_len ) );
}


__PACKAGE__->meta->make_immutable;
1;

__END__

=pod

=head1 NAME

Bio::FastParsers::Blast::Xml::Hsp - NCBI BLAST DTD-derived internal class

=head1 VERSION

version 0.221230

=head1 SYNOPSIS

    # see Bio::FastParsers::Blast::Xml

=head1 DESCRIPTION

This class implements the C<Hsp> level of the XML BLAST parser.

=head1 METHODS

=head2 align_len

Returns the value of the element C<<Hsp_align-len>>.

    # $hsp is a Bio::FastParsers::Blast::Xml::Hsp
    my $align_len = $hsp->align_len;

This method does not accept any arguments.

=head2 bit_score

Returns the value of the element C<<Hsp_bit-score>>.

    # $hsp is a Bio::FastParsers::Blast::Xml::Hsp
    my $bit_score = $hsp->bit_score;

This method does not accept any arguments.

=head2 density

Returns the value of the element C<<Hsp_density>>.

    # $hsp is a Bio::FastParsers::Blast::Xml::Hsp
    my $density = $hsp->density;

This method does not accept any arguments.

=head2 evalue

Returns the value of the element C<<Hsp_evalue>>.

lib/Bio/FastParsers/Blast/Xml/Hsp.pm  view on Meta::CPAN

This method does not accept any arguments.

=head2 query_strand

Returns the strand of the query. The strand can be either 1 or -1 depending
on the sign of the element C<<Hsp_query-frame>>.

    # $hsp is a Bio::FastParsers::Blast::Xml::Hsp
    my $query_strand = $hsp->query_strand;

This method does not accept any arguments.

=head2 query_start

Returns the start coordinate of the query. This value is taken either from
the element C<<Hsp_query-from>> or from the element C<<Hsp_query-to>>
depending on the query orientation. The numerical value returned by this
method is guaranteed to be lower than the value returned by C<query_end>.

    # $hsp is a Bio::FastParsers::Blast::Xml::Hsp
    my ($query_start, $query_end) = ($hsp->query_start, $hsp->query_end);
    if ($query_start < $query_end) {    # always true
        ...
    }

This method does not accept any arguments.

=head2 query_end

Returns the end coordinate of the query. This value is taken either from the
element C<<Hsp_query-to>> or from the element C<<Hsp_query-from>> depending
on the query orientation. The numerical value returned by this method is
guaranteed to be greater than the value returned by C<query_start>.

    # $hsp is a Bio::FastParsers::Blast::Xml::Hsp
    my ($query_start, $query_end) = ($hsp->query_start, $hsp->query_end);
    if ($query_start < $query_end) {    # always true
        ...
    }

This method does not accept any arguments.

=head2 query_coverage

Returns the query coverage of the HSP.

    # $hsp is a Bio::FastParsers::Blast::Xml::Hsp
    my $query_coverage = $hsp->query_coverage;

This method does not accept any arguments.

=head2 subject_coverage

Returns the subject (hit) coverage of the HSP.

    # $hsp is a Bio::FastParsers::Blast::Xml::Hsp
    my $subject_coverage = $hsp->subject_coverage;

This method does not accept any arguments.

=head2 percentage_identity

Returns the percentage of identity of the HSP.

    # $hsp is a Bio::FastParsers::Blast::Xml::Hsp
    my $percentage_identity = $hsp->percentage_identity;

This method does not accept any arguments.

=head2 percentage_positive

Returns the percentage of positive matches of the HSP.

    # $hsp is a Bio::FastParsers::Blast::Xml::Hsp
    my $percentage_positive = $hsp->percentage_positive;

This method does not accept any arguments.

=head1 ALIASES

=head2 expect

Alias for C<evalue> method. For API consistency.

=head2 qcov

Alias for C<query_coverage> method. For API consistency.

=head2 scov

Alias for C<subject_coverage> method. For API consistency.

=head2 pident

Alias for C<percentage_identity> method. For API consistency.

=head2 ppos

Alias for C<percentage_positive> method. For API consistency.

=head2 query_len

Alias for C<query_len> method in Hit object. For API completeness.

=head2 hit_len

Alias for C<len> method in Hit object. For API completeness.

=head1 AUTHOR

Denis BAURAIN <denis.baurain@uliege.be>

=head1 COPYRIGHT AND LICENSE

This software is copyright (c) 2013 by University of Liege / Unit of Eukaryotic Phylogenomics / Denis BAURAIN.

This is free software; you can redistribute it and/or modify it under
the same terms as the Perl 5 programming language system itself.

=cut