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

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

VERSION
version 0.221230

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

DESCRIPTION
This class implements the "Iteration" level of the XML BLAST parser.

ATTRIBUTES

  hits
ArrayRef of Bio::FastParsers::Blast::Xml::Hit

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

METHODS

  count_hits
Returns the number of Hits of the Iteration.

    # $iteration is a Bio::FastParsers::Blast::Xml::Iteration
    my $count = $iteration->count_hits;

This method does not accept any arguments.

  all_hits
Returns all the Hits of the Iteration (not an array reference).

    # $iteration is a Bio::FastParsers::Blast::Xml::Iteration
    my @hits = $iteration->all_hits;

This method does not accept any arguments.

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

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

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

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

    # $iteration is a Bio::FastParsers::Blast::Xml::Iteration
    while (my $hit = $iteration->next_hit) {
        # process $hit
        # ...
    }

This method does not accept any arguments.

  iter_num
Returns the value of the element "<Iteration_iter-num">.

    # $iteration is a Bio::FastParsers::Blast::Xml::Iteration
    my $iter_num = $iteration->iter_num;

This method does not accept any arguments.

  message
Returns the value of the element "<Iteration_message">.

    # $iteration is a Bio::FastParsers::Blast::Xml::Iteration
    my $message = $iteration->message;

This method does not accept any arguments.

  query_def
Returns the value of the element "<Iteration_query-def">.

    # $iteration is a Bio::FastParsers::Blast::Xml::Iteration
    my $query_def = $iteration->query_def;

This method does not accept any arguments.

  query_id
Returns the value of the element "<Iteration_query-ID">.

    # $iteration is a Bio::FastParsers::Blast::Xml::Iteration
    my $query_id = $iteration->query_id;

This method does not accept any arguments.

  query_len
Returns the value of the element "<Iteration_query-len">.

    # $iteration is a Bio::FastParsers::Blast::Xml::Iteration
    my $query_len = $iteration->query_len;

This method does not accept any arguments.

ALIASES

  statistics
Alias for "stat" method. For API consistency.

  num
Alias for "iter_num" 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.