NAME
Bio::Tools::EUtilities::Link::LinkSet - Class for EUtils LinkSets.
VERSION
version 1.74
SYNOPSIS
# ...DESCRIPTION
# ...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_databaseget_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 argumentsget_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 : noneget_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 : noneget_link_names
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 definedget_link_name
Title : get_link_name
Usage : my $string = $linkset->get_link_name;
Function : retrieve eutil-compatible link name
Returns : single link name
Args : noneget_submitted_ids
Title : get_submitted_ids
Usage : my $string = $linkset->get_submitted_ids;
Function : retrieve original ID list
Returns : string
Args : nonehas_scores
Title : has_scores
Usage : if (my $linkset->has_scores) {...}
Function : returns TRUE if score data is present
Returns : Boolean
Args : noneget_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 : noneget_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 lookuphas_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 timenext_UrlLink
Title : next_UrlLink
Usage : while (my $url = $linkset->next_UrlLink) {...}
Function : iterate through UrlLink objects
Returns : Bio::Tools::EUtilities::Link::UrlLink
Args :get_UrlLinks
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 onlyto_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 methodsFEEDBACK
Mailing lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing listsSupport
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 of the bugs and their resolution. Bug reports can be submitted via the web:
https://github.com/bioperl/%%7Bdist%7DAUTHOR
Chris Fields <cjfields@bioperl.org>
COPYRIGHT
This software is copyright (c) 2006-2013 by Chris Fields.
This software is available under the same terms as the perl 5 programming language system itself.