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

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.