Christopher Fields > BioPerl-1.6.1 > Bio::Tools::EUtilities::Info::FieldInfo

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Module Version: 1.006001   Source   Latest Release: BioPerl-1.6.901

NAME ^

Bio::Tools::EUtilities::Info::FieldInfo - class for storing einfo field 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->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)

    while (my $link = $info->next_Link) {
        print "Link name: ",$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_Links; # 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 _

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)

term_count

 Title    : term_count
 Usage    : my $ct = $field->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
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