SYNOPSIS
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DESCRIPTION
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AUTHOR
Email cjfields at bioperl dot orgAPPENDIX
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