Bio::FastParsers::Blast::Xml::Hsp(3)

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.