Bio::Tools::EUtilities::Link::LinkSet.3pm

Langue: en

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

Section: 3 (Bibliothèques de fonctions)

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
 
 
  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
 
 

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
 
 
  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     :
 
 

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