/ 
bioperl-1.5.2_004-RCd
/ Bio::DB::EUtilities::ElinkData

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 _

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