Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

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

SYNOPSIS

         # ...

DESCRIPTION

         # ...

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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