Provided by: libbio-eutilities-perl_1.77-2_all bug

NAME

       Bio::Tools::EUtilities::Link::LinkSet - Class for EUtils LinkSets.

VERSION

       version 1.77

SYNOPSIS

         # ...

DESCRIPTION

         # ...

   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 iterators (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

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.