/ 
Bio-FastParsers-0.221230
River stage one • 7 direct dependents • 8 total dependents
/ Bio::FastParsers::Blast::Xml::Hsp

NAME

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

VERSION

version 0.221230

SYNOPSIS

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

DESCRIPTION

This class implements the Hsp level of the XML BLAST parser.

METHODS

align_len

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

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

This method does not accept any arguments.

bit_score

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

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

This method does not accept any arguments.

density

Returns the value of the element <Hsp_density>.

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

This method does not accept any arguments.

evalue

Returns the value of the element <Hsp_evalue>.

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

This method does not accept any arguments.

gaps

Returns the value of the element <Hsp_gaps>.

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

This method does not accept any arguments.

hit_frame

Returns the value of the element <Hsp_hit-frame>.

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

This method does not accept any arguments.

hit_from

Returns the value of the element <Hsp_hit-from>.

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

This method does not accept any arguments.

hit_to

Returns the value of the element <Hsp_hit-to>.

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

This method does not accept any arguments.

hseq

Returns the value of the element <Hsp_hseq>.

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

This method does not accept any arguments.

identity

Returns the value of the element <Hsp_identity>.

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

This method does not accept any arguments.

midline

Returns the value of the element <Hsp_midline>.

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

This method does not accept any arguments.

num

Returns the value of the element <Hsp_num>.

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

This method does not accept any arguments.

pattern_from

Returns the value of the element <Hsp_pattern-from>.

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

This method does not accept any arguments.

pattern_to

Returns the value of the element <Hsp_pattern-to>.

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

This method does not accept any arguments.

positive

Returns the value of the element <Hsp_positive>.

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

This method does not accept any arguments.

qseq

Returns the value of the element <Hsp_qseq>.

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

This method does not accept any arguments.

query_frame

Returns the value of the element <Hsp_query-frame>.

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

This method does not accept any arguments.

query_from

Returns the value of the element <Hsp_query-from>.

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

This method does not accept any arguments.

query_to

Returns the value of the element <Hsp_query-to>.

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

This method does not accept any arguments.

score

Returns the value of the element <Hsp_score>.

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

This method does not accept any arguments.

hit_strand

Returns the strand of the hit. The strand can be either 1 or -1 depending on the sign of the element <Hsp_hit-frame>.

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

This method does not accept any arguments.

hit_start

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

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

This method does not accept any arguments.

hit_end

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

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

This method does not accept any arguments.

query_strand

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

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

This method does not accept any arguments.

query_start

Returns the start coordinate of the query. This value is taken either from the element <Hsp_query-from> or from the element <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 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.

query_end

Returns the end coordinate of the query. This value is taken either from the element <Hsp_query-to> or from the element <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 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.

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.

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.

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.

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.

ALIASES

expect

Alias for evalue method. For API consistency.

qcov

Alias for query_coverage method. For API consistency.

scov

Alias for subject_coverage method. For API consistency.

pident

Alias for percentage_identity method. For API consistency.

ppos

Alias for percentage_positive method. For API consistency.

query_len

Alias for query_len method in Hit object. For API completeness.

hit_len

Alias for len method in Hit object. For API completeness.

AUTHOR

Denis BAURAIN <denis.baurain@uliege.be>

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.