NAME

Bio::Tools::EUtilities::Info::FieldInfo - Class for storing einfo field 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->type;
# 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)
$info->rewind('fields'); # rewinds Field iterator
            
          

DESCRIPTION

This class handles simple field data output (XML) from einfo.

For more information on einfo see:

            

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

new

            

              
              
Title    : new
Note     : *** should not be called by end-users ***
Usage    : my $ct = Bio::Tools::EUtilities::Info::FieldInfo;
Function : returns new FieldInfo instance
Returns  : Bio::Tools::EUtilities::Info::FieldInfo instance
Args     : none (all data added via _add_data, most methods are getters only)
            
          

get_term_count

            

              
              
Title    : get_term_count
Usage    : my $ct = $field->get_term_count;
Function : returns number of terms for field
Returns  : integer
Args     : none
            
          

get_field_name

            

              
              
Title    : get_field_name
Usage    : my $nm = $field->get_field_name;
Function : returns the full name of the field
Returns  : string
Args     : none
            
          

get_full_name

            

              
              
Title    : get_full_name
Note     : alias of get_field_name()
            
          

get_field_code

            

              
              
Title    : get_field_code
Usage    : $field->get_field_code()
Function : returns field code (abbreviation) used for queries
Returns  : string
Args     : none
            
          

get_field_description

            

              
              
Title    : get_field_description
Usage    : $field->get_field_description
Function : returns field description
Returns  : string
Args     : none
Note     : alias of get_description()
            
          

is_date

            

              
              
Title    : is_date
Usage    : if ($field->is_date) {...}
Function : returns true if field contains date information
Returns  : Boolean
Args     : none
            
          

is_singletoken

            

              
              
Title    : is_singletoken
Usage    : if ($field->is_singletoken) {...}
Function : returns true if field has single value in docsums
Returns  : Boolean
Args     : none
            
          

is_hierarchy

            

              
              
Title    : is_hierarchy
Usage    : if ($field->is_hierarchy) {...}
Function : returns true if field contains hierarchal values
Returns  : Boolean
Args     : none
            
          

is_hidden

            

              
              
Title    : is_hidden
Usage    : if ($field->is_hidden) {...}
Function : returns true if field is hidden in docsums
Returns  : Boolean
Args     : none
            
          

is_numerical

            

              
              
Title    : is_numerical
Usage    : if ($field->is_numerical) {...}
Function : returns true if field contains a numerical value
Returns  : Boolean
Args     : none
            
          

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.

cpanm Bio::EUtilities

perl -MCPAN -e shell
install Bio::EUtilities