Christopher Fields > BioPerl-1.6.901 > Bio::Tools::EUtilities::Info::LinkInfo



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Module Version: 1.006901   Source  


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 both einfo and elink, and centers on describing data that either describes how NCBI databases are linked together via link names, or how databases are linked to outside databases (LinkOut).

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

get_db (alias for get_database)

get_dbto (alias for get_database)


 Title    : get_dbfrom
 Usage    : my $origdb = $link->get_dbfrom;
 Function : returns referring database
 Returns  : string
 Args     : none
 Note     :


 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
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