Bio::FastParsers::Blast::Xml::Hsp - NCBI BLAST DTD-derived internal class
version 0.173640
# TODO
Returns the value of the element <Hsp_align-len>.
<Hsp_align-len
# $hsp is a Bio::FastParsers::Blast::Xml::Hsp my $align_len = $hsp->align_len;
This method does not accept any arguments.
Returns the value of the element <Hsp_bit-score>.
<Hsp_bit-score
# $hsp is a Bio::FastParsers::Blast::Xml::Hsp my $bit_score = $hsp->bit_score;
Returns the value of the element <Hsp_density>.
<Hsp_density
# $hsp is a Bio::FastParsers::Blast::Xml::Hsp my $density = $hsp->density;
Returns the value of the element <Hsp_evalue>.
<Hsp_evalue
# $hsp is a Bio::FastParsers::Blast::Xml::Hsp my $evalue = $hsp->evalue;
Returns the value of the element <Hsp_gaps>.
<Hsp_gaps
# $hsp is a Bio::FastParsers::Blast::Xml::Hsp my $gaps = $hsp->gaps;
Returns the value of the element <Hsp_hit-frame>.
<Hsp_hit-frame
# $hsp is a Bio::FastParsers::Blast::Xml::Hsp my $hit_frame = $hsp->hit_frame;
Returns the value of the element <Hsp_hit-from>.
<Hsp_hit-from
# $hsp is a Bio::FastParsers::Blast::Xml::Hsp my $hit_from = $hsp->hit_from;
Returns the value of the element <Hsp_hit-to>.
<Hsp_hit-to
# $hsp is a Bio::FastParsers::Blast::Xml::Hsp my $hit_to = $hsp->hit_to;
Returns the value of the element <Hsp_hseq>.
<Hsp_hseq
# $hsp is a Bio::FastParsers::Blast::Xml::Hsp my $hseq = $hsp->hseq;
Returns the value of the element <Hsp_identity>.
<Hsp_identity
# $hsp is a Bio::FastParsers::Blast::Xml::Hsp my $identity = $hsp->identity;
Returns the value of the element <Hsp_midline>.
<Hsp_midline
# $hsp is a Bio::FastParsers::Blast::Xml::Hsp my $midline = $hsp->midline;
Returns the value of the element <Hsp_num>.
<Hsp_num
# $hsp is a Bio::FastParsers::Blast::Xml::Hsp my $num = $hsp->num;
Returns the value of the element <Hsp_pattern-from>.
<Hsp_pattern-from
# $hsp is a Bio::FastParsers::Blast::Xml::Hsp my $pattern_from = $hsp->pattern_from;
Returns the value of the element <Hsp_pattern-to>.
<Hsp_pattern-to
# $hsp is a Bio::FastParsers::Blast::Xml::Hsp my $pattern_to = $hsp->pattern_to;
Returns the value of the element <Hsp_positive>.
<Hsp_positive
# $hsp is a Bio::FastParsers::Blast::Xml::Hsp my $positive = $hsp->positive;
Returns the value of the element <Hsp_qseq>.
<Hsp_qseq
# $hsp is a Bio::FastParsers::Blast::Xml::Hsp my $qseq = $hsp->qseq;
Returns the value of the element <Hsp_query-frame>.
<Hsp_query-frame
# $hsp is a Bio::FastParsers::Blast::Xml::Hsp my $query_frame = $hsp->query_frame;
Returns the value of the element <Hsp_query-from>.
<Hsp_query-from
# $hsp is a Bio::FastParsers::Blast::Xml::Hsp my $query_from = $hsp->query_from;
Returns the value of the element <Hsp_query-to>.
<Hsp_query-to
# $hsp is a Bio::FastParsers::Blast::Xml::Hsp my $query_to = $hsp->query_to;
Returns the value of the element <Hsp_score>.
<Hsp_score
# $hsp is a Bio::FastParsers::Blast::Xml::Hsp my $score = $hsp->score;
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;
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.
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 ... }
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.
hit_start
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;
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.
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 ... }
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.
query_start
Alias for evalue method. For API consistency.
evalue
Denis BAURAIN <denis.baurain@uliege.be>
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.
To install Bio::FastParsers, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::FastParsers
CPAN shell
perl -MCPAN -e shell install Bio::FastParsers
For more information on module installation, please visit the detailed CPAN module installation guide.