NAME¶
Bio::Tools::EUtilities::Link::LinkSet - class for EUtils LinkSets
SYNOPSIS¶
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DESCRIPTION¶
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FEEDBACK¶
Mailing Lists¶
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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.
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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
get_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 defined
get_link_name¶
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
next_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 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