Bio::DB::EUtilities::ElinkData(3)

NAME
Bio::DB::EUtilities::ElinkData

SYNOPSIS
*** Give standard usage here

DESCRIPTION
*** Describe the object here

FEEDBACK

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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
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  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.

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AUTHOR
Email cjfields at uiuc dot edu

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

  elink_dbfrom
 Title   : elink_dbfrom
 Usage   : $dbfrom = $linkset->elink_dbfrom;
 Function: gets/sets dbfrom value
 Returns : originating database
 Args    : originating database

  elink_queryids
 Title   : elink_queryids
 Usage   : @ids = $linkset->elink_queryids;
 Function: gets/sets original query ID values (ref to array)
 Returns : array or array ref of IDs (based on wantarray)
 Args    : array ref of IDs

  elink_command
 Title   : elink_command
 Usage   : $cmd = $linkset->elink_command;
 Function: gets/sets cmd used for elink query
 Returns : string (cmd parameter)
 Args    : string (cmd parameter)

  get_LinkIds_by_db
 Title   : get_LinkIds_by_db
 Usage   : @ids = $linkset->get_LinkIds_by_db('protein');
 Function: retrieves primary ID list based on the database for the object
 Returns : array or array ref of IDs (based on wantarray)
 Args    : None

  next_linkdb
 Title   : next_linkdb
 Usage   : while (my $db = $linkset->next_linkdb) {
 Function: iterates through list of database names in internal queue
 Returns : String (name of database)
 Args    : None

  get_all_linkdbs
 Title   : get_all_linkdbs
 Usage   : @dbs = $linkset->get_all_linkdbs;
 Function: returns all database names which contain IDs
 Returns : array or array ref of databases (based on wantarray)
 Args    : None

  next_scoredb
 Title   : next_scoredb
 Usage   : while (my $db = $linkset->next_scoredb) {
 Function: iterates through list of database with score values
 Returns : String (name of database)
 Args    : None

  get_all_scoredbs
 Title   : get_all_scoredbs
 Usage   : @dbs = $linkset->get_all_scoredbs;
 Function: returns database names which contain scores
 Returns : array or array ref of databases (based on wantarray)
 Args    : None

  get_score
 Title   : get_score
 Usage   : $score = $linkset->get_score($id);
 Function: returns score value for ID
 Returns : score value
 Args    : ID
 Note    : if multiple databases are returned with scores (rare but possible),
         : you must set the default score database using set_scoredb.  If you
         : use next_scoredb to iterate through the databases, this is done for you

  get_score_hash
 Title   : get_score_hash
 Usage   : %scores = $linkset->get_score_hash($database);
 Function: returns ID(key)-score(value) hash based on database name
 Returns : score value
 Args    : OPTIONAL : database name.  If there is only one score hash, returns
         : that hash, otherwise throws an exception

  set_scoredb
 Title   : set_scoredb
 Usage   : $linkset->set_scoredb('protein');
 Function: sets the database to retrieve scores from
 Returns : None
 Args    : database name

  rewind_linkdbs
 Title   : rewind_linkdbs
 Usage   : $linkset->rewind_linkdbs;
 Function: resets the iterator for next_database
 Returns : None
 Args    : None

  rewind_scoredbs
 Title   : rewind_scoredbs
 Usage   : $linkset->rewind_scoredbs;
 Function: resets the iterator, current database for next_scoredb
 Returns : None
 Args    : None