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

NAME

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

VERSION

version 0.221230

SYNOPSIS

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

DESCRIPTION

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

ATTRIBUTES

iterations

ArrayRef of Bio::FastParsers::Blast::Xml::Iteration

mbstat

Bio::FastParsers::Blast::Xml::Statistics composed object

param

Bio::FastParsers::Blast::Xml::Parameters composed object

METHODS

count_iterations

Returns the number of Iterations of the BlastOutput.

# $blast_output is a Bio::FastParsers::Blast::Xml::BlastOutput
my $count = $blast_output->count_iterations;

This method does not accept any arguments.

all_iterations

Returns all the Iterations of the BlastOutput (not an array reference).

# $blast_output is a Bio::FastParsers::Blast::Xml::BlastOutput
my @iterations = $blast_output->all_iterations;

This method does not accept any arguments.

get_iteration

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

# $blast_output is a Bio::FastParsers::Blast::Xml::BlastOutput
my $iteration = $blast_output->get_iteration($index);
croak "Iteration $index not found!" unless defined $iteration;

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

next_iteration

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

# $blast_output is a Bio::FastParsers::Blast::Xml::BlastOutput
while (my $iteration = $blast_output->next_iteration) {
    # process $iteration
    # ...
}

This method does not accept any arguments.

db

Returns the value of the element <BlastOutput_db>.

# $blast_output is a Bio::FastParsers::Blast::Xml::BlastOutput
my $db = $blast_output->db;

This method does not accept any arguments.

program

Returns the value of the element <BlastOutput_program>.

# $blast_output is a Bio::FastParsers::Blast::Xml::BlastOutput
my $program = $blast_output->program;

This method does not accept any arguments.

query_def

Returns the value of the element <BlastOutput_query-def>.

# $blast_output is a Bio::FastParsers::Blast::Xml::BlastOutput
my $query_def = $blast_output->query_def;

This method does not accept any arguments.

query_id

Returns the value of the element <BlastOutput_query-ID>.

# $blast_output is a Bio::FastParsers::Blast::Xml::BlastOutput
my $query_id = $blast_output->query_id;

This method does not accept any arguments.

query_len

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

# $blast_output is a Bio::FastParsers::Blast::Xml::BlastOutput
my $query_len = $blast_output->query_len;

This method does not accept any arguments.

query_seq

Returns the value of the element <BlastOutput_query-seq>.

# $blast_output is a Bio::FastParsers::Blast::Xml::BlastOutput
my $query_seq = $blast_output->query_seq;

This method does not accept any arguments.

reference

Returns the value of the element <BlastOutput_reference>.

# $blast_output is a Bio::FastParsers::Blast::Xml::BlastOutput
my $reference = $blast_output->reference;

This method does not accept any arguments.

version

Returns the value of the element <BlastOutput_version>.

# $blast_output is a Bio::FastParsers::Blast::Xml::BlastOutput
my $version = $blast_output->version;

This method does not accept any arguments.

ALIASES

statistics

Alias for mbstat method. For API consistency.

parameters

Alias for param method. For API consistency.

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.