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BioPerl-1.6.901
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Tools::EUtilities::Link::LinkSet

NAME

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

SYNOPSIS

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DESCRIPTION

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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.

https://redmine.open-bio.org/projects/bioperl/

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