Bio::Tools::EUtilities::Link::LinkSet man page on Pidora

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Bio::Tools::EUtilitiesUsernContributedBio::Tools::EUtilities::Link::LinkSet(3)

NAME
       Bio::Tools::EUtilities::Link::LinkSet - class for EUtils LinkSets

SYNOPSIS
	 # ...

DESCRIPTION
	 # ...

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 _

   get_ids
	Title	 : get_ids
	Usage	 : my @ids = $linkset->get_ids
	Function : returns list of retrieved IDs
	Returns	 : array of IDs
	Args	 : none
	Notes	 : Cmd			 Description
		   acheck		 same as get_submitted_ids
		   lcheck		 same as get_submitted_ids
		   ncheck		 same as get_submitted_ids
		   prlinks		 same as get_submitted_ids
		   llinks		 same as get_submitted_ids
		   llinkslib		 same as get_submitted_ids
		   neighbor		 linked IDs for database in get_database
		   neighbor_history	 linked IDs for database in get_database

   get_database
	Title	 : get_database
	Usage	 : my $db = $info->get_database;
	Function : returns single database name (eutil-compatible).  This is the
		   queried database. For elinks (which have 'db' and 'dbfrom')
		   this is equivalent to db/dbto (use get_dbfrom() to for the latter).
		   Note that this only returns the first db; in some cases this may
		   not be what you want (when multiple dbs are queried, for instance)
	Returns	 : string
	Args	 : none
	Notes	 : with all elink cmd arguments

   get_db (alias for get_database)
   get_dbto (alias for get_database)
   get_databases
	Title	 : get_databases
	Usage	 : my $string = $linkset->get_databases;
	Function : retrieve databases referred to for this linkset
		   these may be present as a single database or embedded in
	Returns	 : array of strings
	Args	 : none

   get_dbs (alias for get_databases)
   get_dbfrom
	Title	 : get_dbfrom
	Usage	 : my $string = $linkset->get_dbfrom;
	Function : retrieve originating database for this linkset
	Returns	 : string
	Args	 : none

   get_link_names
	Title	 : get_link_names
	Usage	 : my $string = $linkset->get_link_names;
	Function : retrieve eutil-compatible link names
	Returns	 : array of strings
	Args	 : none
	Notes	 : Each LinkSet can hold multiple LinkInfo objects (each containing
		   a link name). Also, some LinkSets define a single link name. This
		   returns an array with all unique linknames globbed both sources, if
		   present and defined

   get_link_name
	Title	 : get_link_name
	Usage	 : my $string = $linkset->get_link_name;
	Function : retrieve eutil-compatible link name
	Returns	 : single link name
	Args	 : none

   get_submitted_ids
	Title	 : get_submitted_ids
	Usage	 : my $string = $linkset->get_submitted_ids;
	Function : retrieve original ID list
	Returns	 : string
	Args	 : none

   has_scores
	Title	 : has_scores
	Usage	 : if (my $linkset->has_scores) {...}
	Function : returns TRUE if score data is present
	Returns	 : Boolean
	Args	 : none

   get_scores
	Title	 : get_scores
	Usage	 : %scores = $linkset->get_scores;
	Function : returns flattened list or hash ref containing ID => score pairs
	Returns	 : hash or hash ref (based on list or scalar context)
	Args	 : none

   get_score_by_id
	Title	 : get_score_by_id
	Usage	 : $score = $linkset->get_score_by_id($id);
	Function : returns the score for a particular primary ID
	Returns	 : integer
	Args	 : [REQUIRED] Primary ID for the score lookup

   has_linkout
	Title	 : has_linkout
	Usage	 : if ($linkset->has_linkout) {...}
	Function : returns TRUE if the single ID present in this linkset has a linkout
	Returns	 : boolean
	Args	 : none
	Notes	 : this checks cmd=lcheck (boolean for a linkout) and also backchecks
		   cmd=acheck for databases with name 'LinkOut'

   has_neighbor
	Title	 : has_neighbor
	Usage	 : if ($linkset->has_neighbor) {...}
	Function : returns TRUE if the single ID present in this linkset has a neighbor
		   in the same database
	Returns	 : boolean
	Args	 : none
	Notes	 : this checks cmd=ncheck (boolean for a neighbor in same database); no
		   other checks performed at this time

   next_UrlLink
	Title	 : next_UrlLink
	Usage	 : while (my $url = $linkset->next_UrlLink) {...}
	Function : iterate through UrlLink objects
	Returns	 : Bio::Tools::EUtilities::Link::UrlLink
	Args	 :

   get_UrlLinks
	Title	 : get_UrlLinks
	Usage	 : my @urls = $linkset->get_UrlLinks
	Function : returns all UrlLink objects
	Returns	 : list of Bio::Tools::EUtilities::Link::UrlLink
	Args	 :

   next_LinkInfo
	Title	 : next_LinkInfo
	Usage	 : while (my $info = $linkset->next_LinkInfo) {...}
	Function : iterate through LinkInfo objects
	Returns	 : Bio::Tools::EUtilities::Link::LinkInfo
	Args	 :

   get_LinkInfo
	Title	 : get_LinkInfo
	Usage	 : my @links = $linkset->get_LinkInfo
	Function : returns all LinkInfo objects
	Returns	 : list of Bio::Tools::EUtilities::Link::LinkInfo
	Args	 :

   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' or 'linkinfos'  - LinkInfo objects only
		   'urllinks'	- UrlLink 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			  2011Bio::Tools::EUtilities::Link::LinkSet(3)
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