Bio::Tools::EUtilities::Summary - class for handling data output (XML) from

BioPerl documentation Contained in the BioPerl distribution.

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NAME

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Bio::Tools::EUtilities::Summary - class for handling data output (XML) from esummary.

SYNOPSIS

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  #### should not create instance directly; Bio::Tools::EUtilities does this ####

  my $esum = Bio::Tools::EUtilities->new(-eutil => 'esummary',
                                         -file => 'summary.xml');
  # can also use '-response' (for HTTP::Response objects) or '-fh' (for filehandles)

  while (my $docsum = $esum->next_DocSum) {
      my $id = $docsum->get_ids;  # EUtilDataI compliant method, returns docsum ID
      my @names = $docsum->get_item_names;
  }

DESCRIPTION

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This class handles data output (XML) from esummary.

esummary retrieves information in the form of document summaries (docsums) when passed a list of primary IDs or if using a previous search history.

This module breaks down the returned data from esummary into individual document summaries per ID (using a DocSum object). As the data in a docsum can be nested, subclasses of DocSums (Item, ListItem, Structure) are also present.

Further documentation for Link and Field subclass methods is included below.

FEEDBACK

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Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@lists.open-bio.org               - General discussion
  http://www.bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web.

  https://redmine.open-bio.org/projects/bioperl/

AUTHOR

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Email cjfields at bioperl dot org

APPENDIX

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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

to_string

 Title    : to_string
 Usage    : $foo->to_string()
 Function : converts current object to string
 Returns  : none
 Args     : (optional) simple data for text formatting
 Note     : Used generally for debugging and for the print_* methods
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::Tools::EUtilities::DocSum
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Chris Fields
#
# Copyright Chris Fields
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
# 
# Part of the EUtilities BioPerl package


# Let the code begin...

package Bio::Tools::EUtilities::Summary;
use strict;
use warnings;

use base qw(Bio::Tools::EUtilities Bio::Tools::EUtilities::EUtilDataI);

use Bio::Tools::EUtilities::Summary::DocSum;

# private EUtilDataI method

sub _add_data {
    my ($self, $data) = @_;
    if (!exists $data->{DocSum}) {
        $self->warn('No returned docsums.');
        return;
    }
    
    my @docs;
    for my $docsum (@{ $data->{DocSum} }) {
        my $ds = Bio::Tools::EUtilities::Summary::DocSum->new(-datatype => 'docsum',
                                                              -verbose => $self->verbose);
        $ds->_add_data($docsum);
        push @{ $self->{'_docsums'} }, $ds;
    }
}


sub to_string {
    my $self = shift;
    my %data = (
        'DB'    => [1, join(', ',$self->get_databases) || ''],
    );
    my $string = $self->SUPER::to_string."\n";
    for my $k (sort {$data{$a}->[0] <=> $data{$b}->[0]} keys %data) {
        $string .= sprintf("%-20s:%s\n\n",$k, $self->_text_wrap('',' 'x 20 .':', $data{$k}->[1]));
    }
    while (my $ds = $self->next_DocSum) {
        $string .= $ds->to_string."\n";
    }
    return $string;
}

1;

__END__