NAME

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

VERSION

version 0.221230

SYNOPSIS

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

DESCRIPTION

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

ATTRIBUTES

hsps

ArrayRef of Bio::FastParsers::Blast::Xml::Hsp

METHODS

count_hsps

Returns the number of Hsps of the Hit.

# $hit is a Bio::FastParsers::Blast::Xml::Hit
my $count = $hit->count_hsps;

This method does not accept any arguments.

all_hsps

Returns all the Hsps of the Hit (not an array reference).

# $hit is a Bio::FastParsers::Blast::Xml::Hit
my @hsps = $hit->all_hsps;

This method does not accept any arguments.

get_hsp

Returns one Hsp of the Hit by its index. You can also use negative index numbers, just as with Perl's core array handling. If the specified Hsp does not exist, this method will return undef.

# $hit is a Bio::FastParsers::Blast::Xml::Hit
my $hsp = $hit->get_hsp($index);
croak "Hsp $index not found!" unless defined $hsp;

This method accepts just one argument (and not an array slice).

next_hsp

Shifts the first Hsp of the array off and returns it, shortening the array by 1 and moving everything down. If there are no more Hsps in the array, returns undef.

# $hit is a Bio::FastParsers::Blast::Xml::Hit
while (my $hsp = $hit->next_hsp) {
    # process $hsp
    # ...
}

This method does not accept any arguments.

accession

Returns the value of the element <Hit_accession>.

# $hit is a Bio::FastParsers::Blast::Xml::Hit
my $accession = $hit->accession;

This method does not accept any arguments.

def

Returns the value of the element <Hit_def>.

# $hit is a Bio::FastParsers::Blast::Xml::Hit
my $def = $hit->def;

This method does not accept any arguments.

id

Returns the value of the element <Hit_id>.

# $hit is a Bio::FastParsers::Blast::Xml::Hit
my $id = $hit->id;

This method does not accept any arguments.

len

Returns the value of the element <Hit_len>.

# $hit is a Bio::FastParsers::Blast::Xml::Hit
my $len = $hit->len;

This method does not accept any arguments.

num

Returns the value of the element <Hit_num>.

# $hit is a Bio::FastParsers::Blast::Xml::Hit
my $num = $hit->num;

This method does not accept any arguments.

ALIASES

query_len

Alias for query_len method in Iteration 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.

cpanm Bio::FastParsers

perl -MCPAN -e shell
install Bio::FastParsers