bio::tools::eutilities::summary(3pm) [debian man page]

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

NAME

       Bio::Tools::EUtilities::Summary - class for handling data output (XML) from esummary.

SYNOPSIS

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

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

	 while (my $docsum = $esum->next_DocSum) {
	     my $id = $docsum->get_ids;  # EUtilDataI compliant method, returns docsum ID
	     my @names = $docsum->get_item_names;
	 }

DESCRIPTION

       This class handles data output (XML) from esummary.

       esummary retrieves information in the form of document summaries (docsums) when passed a list of primary IDs or if using a previous search
       history.

       This module breaks down the returned data from esummary into individual document summaries per ID (using a DocSum object). As the data in a
       docsum can be nested, subclasses of DocSums (Item, ListItem, Structure) are also present.

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

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 _

   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 the print_* methods

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

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

NAME

       Bio::Tools::EUtilities::HistoryI - simple extension of EUtilDataI interface class for classes which hold NCBI server history data

SYNOPSIS

	 #should work for any class which is-a HistoryI

	 if ($obj->has_History) {
	     # do something here
	 }

	 ($webenv, $querykey) = $obj->history;

	 $obj->history($webenv, $querykey);

	 $webenv = $obj->get_webenv;

	 $query_key = $obj->get_query_key;

DESCRIPTION

       This class extends methods for any EUtilDataI implementation allow instances to dealwith NCBI history data (WebEnv and query_key).  These
       can be used as parameters for further queries against data sets stored on the NCBI server, much like NCBI's Entrez search history. These
       are important when one wants to run complex queries using esearch, retrieve related data using elink, and retrieve large datasets using
       epost/efetch.

       The simplest implementation is Bio::Tools::EUtilities::History, which holds the history data for epost.	See also
       Bio::Tools::EUtilities::Query (esearch) and Bio::Tools::EUtilities::LinkSet (elink), which also implement HistoryI.

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 _

   history
	Title	 : history
	Usage	 : my ($webenv, $qk) = $hist->history
	Function : Get/Set two-element list of webenv() and query_key()
	Returns  : array
	Args	 : two-element list of webenv, querykey

   get_webenv
	Title	 : get_webenv
	Usage	 : my $webenv = $hist->get_webenv
	Function : returns web environment key needed to retrieve results from
		   NCBI server
	Returns  : string (encoded key)
	Args	 : none

   get_query_key
	Title	 : get_query_key
	Usage	 : my $qk = $hist->get_query_key
	Function : returns query key (integer) for the history number for this session
	Returns  : integer
	Args	 : none

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