Bio::Tools::EUtilities::Info::LinkInfo - class for storing einfo link data
## should not create instance directly; Bio::Tools::EUtilities does this ## # get a LinkInfo object using Bio:Tools::EUtilities print "Link name: ",$link->get_link_name,"\n"; print "Link name: ",$link->get_link_menu_name,"\n"; print "Link desc: ",$link->get_link_description,"\n"; print "DBFrom: ",$link->get_dbfrom,"\n"; # database linked from print "DBTo: ",$link->get_dbto,"\n"; # database linked to
This class handles data output (XML) from einfo and elink.
einfo is capable of returning two types of information: 1) a list of all available databases (when called w/o parameters) and 2) information about a specific database. The latter information includes the database description, record count, and date/time stamp for the last update, among other things. It also includes a list of fields (indices by which record data is stored which can be used in queries) and links (crossrefs between related records in other databases at NCBI). Data from the latter two are stored in two small subclasses (Field and Link) which can be iterated through or retrieved all at once, as demonstrated above. NOTE: Methods described for the Link and Field subclasses are unique to those classes (as they retrieve data unique to those data types).
Further documentation for Link and Field subclass methods is included below.
For more information on einfo see:
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Note : *** should not be called by end-users *** Usage : my $ct = Bio::Tools::EUtilities::Info::LinkInfo; Function : returns new LinkInfo instance Returns : Bio::Tools::EUtilities::Info::LinkInfo instance Args : none (all data added via _add_data, most methods are getters only)
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) Returns : string Args : none
Title : get_dbfrom Usage : my $origdb = $link->get_dbfrom; Function : returns referring database Returns : string Args : none Note : alias for get_db()
Title : get_link_name Usage : $ln = $link->get_link_name; Function : returns raw link name (eutil-compatible) Returns : string Args : none
Title : get_link_description Usage : $desc = $link->get_link_description; Function : returns the (more detailed) link description Returns : string Args : none
Title : get_link_menu_name Usage : my $mn = $link->get_link_menu_name; Function : returns formal menu name Returns : string Args : none
Title : get_priority Usage : my $mn = $link->get_priority; Function : returns priority ranking Returns : integer Args : none Note : only set when using elink and cmd set to 'acheck'
Title : get_html_tag Usage : my $tag = $link->get_html_tag; Function : returns HTML tag Returns : string Args : none Note : only set when using elink and cmd set to 'acheck'
Title : get_url Usage : my $url = $link->get_url; Function : returns URL string; note that the string isn't usable directly but has the ID replaced with the tag <@UID@> Returns : string Args : none Note : only set when using elink and cmd set to 'acheck'
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