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Bio::DB::EUtilities::ElinkData.3pm

NAME

Bio::DB::EUtilities::ElinkData

SYNOPSIS

*** Give standard usage here

DESCRIPTION

*** Describe the object here

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
 
 

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 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