Bio::Tools::EUtilities::Link::LinkSet - Class for EUtils LinkSets.
version 1.75
# ...
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
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
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
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
Title : get_submitted_ids Usage : my $string = $linkset->get_submitted_ids; Function : retrieve original ID list Returns : string Args : none
Title : has_scores Usage : if (my $linkset->has_scores) {...} Function : returns TRUE if score data is present Returns : Boolean Args : none
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
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
Title : has_linkout Usage : if ($linkset->has_linkout) {...} Function : returns TRUE if the single ID present in this linkset has a linkout Returns : boolean Args : none Notes : this checks cmd=lcheck (boolean for a linkout) and also backchecks cmd=acheck for databases with name 'LinkOut'
Title : has_neighbor Usage : if ($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 :
Title : next_LinkInfo Usage : while (my $info = $linkset->next_LinkInfo) {...} Function : iterate through LinkInfo objects Returns : Bio::Tools::EUtilities::Link::LinkInfo Args :
Title : get_LinkInfo Usage : my @links = $linkset->get_LinkInfo Function : returns all LinkInfo objects Returns : list of Bio::Tools::EUtilities::Link::LinkInfo Args :
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
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
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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.
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%7D
Chris Fields <cjfields@bioperl.org>
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.
To install Bio::DB::EUtilities, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::DB::EUtilities
CPAN shell
perl -MCPAN -e shell install Bio::DB::EUtilities
For more information on module installation, please visit the detailed CPAN module installation guide.