debian man page for bio::tools::eutilities::info

Bio::Tools::EUtilities::Info(3pm)			User Contributed Perl Documentation			 Bio::Tools::EUtilities::Info(3pm)

NAME
       Bio::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),"
";

	 # 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,"
";
	     print "Field name: ",$field->get_field_name,"
";
	     print "Field desc: ",$field->get_field_description,"
";
	     print "DB	: ",$field->get_database,"
";
	     print "Term ct   : ",$field->get_term_count,"
";
	     for my $att (qw(is_date is_singletoken is_hierarchy is_hidden is_numerical)) {
		 print "	Field $att
" 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,"
";
	     print "Link desc: ",$link->get_link_description,"
";
	     print "DBFrom: ",$link->get_dbfrom,"
"; # same as get_database()
	     print "DBTo: ",$link->get_dbto,"
"; # 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:

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

       o  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

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.

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

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 v5.14.2							    2012-03-02					 Bio::Tools::EUtilities::Info(3pm)