Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)


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


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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


  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


  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)


  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)


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


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


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


  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


  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


  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'


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


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


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


  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


  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