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Bio-EUtilities-1.77
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/ Bio::Tools::EUtilities::Info

NAME

Bio::Tools::EUtilities::Info - Interface class for storing einfo data.

VERSION

version 1.77

SYNOPSIS

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

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

# print available databases (if data is present)

print join(', ',$info->get_available_databases),"\n";

# get database info

my $db = $info->get_database; # in case you forgot...
my $desc = $info->get_description;
my $nm = $info->get_menu_name;
my $ct = $info->get_record_count;
my $dt = $info->get_last_update;

# EUtilDataI interface methods

my $eutil = $info->eutil;
my $type = $info->datatype;

# iterate through Field and Link objects

while (my $field = $info->next_Field) {
    print "Field code: ",$field->get_field_code,"\n";
    print "Field name: ",$field->get_field_name,"\n";
    print "Field desc: ",$field->get_field_description,"\n";
    print "DB  : ",$field->get_database,"\n";
    print "Term ct   : ",$field->get_term_count,"\n";
    for my $att (qw(is_date is_singletoken is_hierarchy is_hidden is_numerical)) {
        print "\tField $att\n" if $field->$att;
    }
}

my @fields = $info->get_Fields; # grab them all (useful for grep)

while (my $link = $info->next_LinkInfo) {
    print "Link name: ",$link->get_link_name,"\n";
    print "Link desc: ",$link->get_link_description,"\n";
    print "DBFrom: ",$link->get_dbfrom,"\n"; # same as get_database()
    print "DBTo: ",$link->get_dbto,"\n"; # database linked to
}

my @links = $info->get_LinkInfo; # grab them all (useful for grep)

$info->rewind(); # rewinds all iterators
$info->rewind('links'); # rewinds Link iterator
$info->rewind('fields'); # rewinds Field iterator

DESCRIPTION

This class handles data output (XML) from einfo.

Einfo is capable of returning two types of information:

  • A list of all available databases (when called w/o parameters)

  • Information about a specific database.

The latter information includes the database description, record count, and date/time stamp for the last update, among other things. It also includes a list of fields (indices by which record data is stored which can be used in queries) and links (crossrefs between related records in other databases at NCBI). Data from the latter two are stored in two small subclasses (FieldInfo and LinkInfo) which can be iterated through or retrieved all at once, as demonstrated above. NOTE: Methods described for the LinkInfo and FieldInfo subclasses are unique to those classes (as they retrieve data unique to those data types).

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

For more information on einfo see:

http://eutils.ncbi.nlm.nih.gov/entrez/query/static/einfo_help.html

rewind

Title    : rewind
Usage    : $info->rewind() # rewinds all (default)
           $info->rewind('links') # rewinds only links
Function : 'rewinds' (resets) specified iterators (all if no arg)
Returns  : none
Args     : [OPTIONAL] String:
           'all'    - all iterators (default)
           'linkinfo'  - LinkInfo objects only
           'fieldinfo' - FieldInfo objects only

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 various print methods

FEEDBACK

Mailing lists

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

bioperl-l@bioperl.org               - General discussion
https://bioperl.org/Support.html    - 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 of the bugs and their resolution. Bug reports can be submitted via the web:

https://github.com/bioperl/bio-eutilities/issues

AUTHOR

Chris Fields <cjfields@bioperl.org>

COPYRIGHT

This software is copyright (c) 2006-2013 by Chris Fields.

This software is available under the same terms as the perl 5 programming language system itself.