Bio::Tools::EUtilitiesUserfContributed Perl DocBio::Tools::EUtilities::Info(3)NAMEBio::Tools::EUtilities::Info - interface class for storing einfo data
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: 1) a list of
all available databases (when called w/o parameters) and 2) 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 (Field and Link)
which can be iterated through or retrieved all at once, as demonstrated
above. NOTE: Methods described for the Link and Field 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
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 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.
http://bugzilla.open-bio.org/
AUTHOR
Email cjfields at bioperl dot org
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
rewind
Title : rewind
Usage : $info->rewind() # rewinds all (default)
$info->rewind('links') # rewinds only links
Function : 'rewinds' (resets) specified interators (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
perl v5.14.1 2011-07-22 Bio::Tools::EUtilities::Info(3)
