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 Args     : string

=head1 Methods useful for multiple eutils

=head2 get_ids

 Title    : get_ids
 Usage    : my @ids = $parser->get_ids
 Function : returns array of requested IDs (see Notes for more specifics)
 Returns  : array
 Args     : [conditional] not required except when running elink queries against
            multiple databases. In case of the latter, the database name is
            optional but recommended when retrieving IDs as the ID list will
            be globbed together. In such cases, if a db name isn't provided a
            warning is issued as a reminder.
 Notes    : esearch    : returned ID list
            elink      : returned ID list (see Args above for caveats)
            all others : from parameter_base->id or undef

=head2 get_database

 Title    : get_database
 Usage    : my $db = $info->get_database;
 Function : returns single database name (eutil-compatible).  This is the
            queried database. For most eutils this is straightforward. For
            elinks (which have 'db' and 'dbfrom') this is db/dbto, for egquery,
            it is the first db in the list (you probably want get_databases
            instead)
 Returns  : string
 Args     : none
 Notes    : egquery    : first db in the query (you probably want get_databases)
            einfo      : the queried database
            espell     : the queried database
            all others : from parameter_base->db or undef

=head2 get_db (alias for get_database)

=head2 get_databases

 Title    : get_databases
 Usage    : my @dbs = $parser->get_databases
 Function : returns list of databases
 Returns  : array of strings
 Args     : none
 Notes    : This is guaranteed to return a list of databases. For a single
            database use the convenience method get_db/get_database

            egquery    : list of all databases in the query
            einfo      : the queried database, or the available databases
            espell     : the queried database
            elink      : collected from each LinkSet
            all others : from parameter_base->db or undef

=head2 get_dbs (alias for get_databases)

=head2 next_History

 Title    : next_History
 Usage    : while (my $hist=$parser->next_History) {...}
 Function : returns next HistoryI (if present).
 Returns  : Bio::Tools::EUtilities::HistoryI (Cookie or LinkSet)
 Args     : none
 Note     : esearch, epost, and elink are all capable of returning data which
            indicates search results (in the form of UIDs) is stored on the
            remote server. Access to this data is wrapped up in simple interface
            (HistoryI), which is implemented in two classes:
            Bio::DB::EUtilities::History (the simplest) and
            Bio::DB::EUtilities::LinkSet. In general, calls to epost and esearch
            will only return a single HistoryI object (formerly known as a
            Cookie), but calls to elink can generate many depending on the
            number of IDs, the correspondence, etc. Hence this iterator, which
            allows one to retrieve said data one piece at a time.

=head2 next_cookie (alias for next_History)

=head2 get_Histories

 Title    : get_Histories
 Usage    : my @hists = $parser->get_Histories
 Function : returns list of HistoryI objects.
 Returns  : list of Bio::Tools::EUtilities::HistoryI (History or LinkSet)
 Args     : none

=head1 Query-related methods

=head2 get_count

 Title    : get_count
 Usage    : my $ct = $parser->get_count
 Function : returns the count (hits for a search)
 Returns  : integer
 Args     : [CONDITIONAL] string with database name - used to retrieve
            count from specific database when using egquery
 Notes    : egquery    : count for specified database (specified above)
            esearch    : count for last search
            all others : undef

=head2 get_term

 Title    : get_term
 Usage    : $st = $qd->get_term;
 Function : retrieve the term for the global search
 Returns  : string
 Args     : none
 Notes    : egquery    : search term
            espell     : search term
            esearch    : from parameter_base->term or undef
            all others : undef

=head2 get_translation_from

 Title   : get_translation_from
 Usage   : $string = $qd->get_translation_from();
 Function: portion of the original query replaced with translated_to()
 Returns : string
 Args    : none
 Note    : only applicable for esearch

=head2 get_translation_to

 Title   : get_translation_to
 Usage   : $string = $qd->get_translation_to();
 Function: replaced string used in place of the original query term in translation_from()
 Returns : string
 Args    : none
 Note    : only applicable for esearch

=head2 get_retstart

 Title    : get_retstart

lib/Bio/Tools/EUtilities.pm  view on Meta::CPAN

 Returns  : LinkSet object
 Args     : none
 Notes    : only applicable for elink.  Uses callback() for filtering if defined
            for 'linksets'

=head2 get_LinkSets

 Title    : get_LinkSets
 Usage    : my @links = $info->get_LinkSets;
 Function : returns list of LinkSets objects
 Returns  : array (LinkSet objects)
 Args     : none
 Notes    : only applicable for elink.

=head2 print_LinkSets

 Title    : print_LinkSets
 Usage    : $info->print_LinkSets();
            $info->print_LinkSets(-fh => $fh, -cb => $coderef);
 Function : prints link data for each LinkSet object. The default is generated
            via LinkSet::to_string
 Returns  : none
 Args     : [optional]
           -file : file to print to
           -fh   : filehandle to print to (cannot be used concurrently with file)
           -cb   : coderef to use in place of default print method.  This is passed
                   in a LinkSet object
           -wrap : number of columns to wrap default text output to (def = 80)
 Notes    : only applicable for einfo.  If -file or -fh are not defined,
            prints to STDOUT

=head2 get_linked_databases

 Title    : get_linked_databases
 Usage    : my @dbs = $eutil->get_linked_databases
 Function : returns list of databases linked to in linksets
 Returns  : array of databases
 Args     : none
 Notes    : only applicable for elink.  Now defers to get_databases.

=head1 Iterator- and callback-related methods

=head2 rewind

 Title    : rewind
 Usage    : $esum->rewind()
            $esum->rewind('recursive')
 Function : retrieve a list of DocSum instances
 Returns  : array of Bio::Tools::EUtilities::Summary::DocSum
 Args     : [optional] Scalar; string ('all') to reset all iterators, or string
            describing the specific main object iterator to reset. The following
            are recognized (case-insensitive):

            'all' - rewind all objects and also recursively resets nested object
                    iterators (such as LinkSets and DocSums).
            'globalqueries' - GlobalQuery objects
            'fieldinfo' or 'fieldinfos' - FieldInfo objects
            'linkinfo' or 'linkinfos' - LinkInfo objects in this layer
            'linksets' - LinkSet objects
            'docsums' - DocSum objects
            'histories' - HistoryI objects (Cookies, LinkSets)

=head2 generate_iterator

 Title    : generate_iterator
 Usage    : my $coderef = $esum->generate_iterator('linkinfo')
 Function : generates an iterator (code reference) which iterates through
            the relevant object indicated by the args
 Returns  : code reference
 Args     : [REQUIRED] Scalar; string describing the specific object to iterate.
            The following are currently recognized (case-insensitive):

            'globalqueries'
            'fieldinfo' or 'fieldinfos' (the latter sounds clumsy, but I alias it JIC)
            'linkinfo' or 'linkinfos' (the latter sounds clumsy, but I alias it JIC)
            'linksets'
            'docsums'
            'histories'

 Note     : This function generates a simple coderef that one can use
            independently of the various next_* functions (in fact, the next_*
            functions use lazily created iterators generated via this method,
            while rewind() merely deletes them so they can be regenerated on the
            next call).

            A callback specified using callback() will be used to filter objects
            for any generated iterator. This behaviour is implemented for both
            normal and lazy iterator types and is the default. If you don't want
            this, make sure to reset any previously set callbacks via
            reset_callback() (which just deletes the code ref).  Note that setting
            callback() also changes the behavior of the next_* functions as the
            iterators are generated here (as described above); this is a feature
            and not a bug.

            'Lazy' iterators are considered an experimental feature and may be
            modified in the future. A 'lazy' iterator, which loops through and
            returns objects as they are created (instead of creating all data
            instances up front, then iterating through) is returned if the
            parser is set to 'lazy' mode. This mode is only present for elink
            and esummary output as they are the two formats parsed which can
            generate potentially thousands of individual objects (note efetch
            isn't parsed, so isn't counted). Use of rewind() with these
            iterators is not supported for the time being as we can't guarantee
            you can rewind(), as this depends on whether the data source is
            seek()able and thus 'rewindable'. We will add rewind() support at a
            later time which will work for 'seekable' data or possibly cached
            objects via Storable or BDB.

=head2 callback

 Title    : callback
 Usage    : $parser->callback(sub {$_[0]->get_database eq 'protein'});
 Function : Get/set callback code ref used to filter returned data objects
 Returns  : code ref if previously set
 Args     : single argument:
            code ref - evaluates a passed object and returns true or false value
                       (used in iterators)
            'reset' - string, resets the iterator.
            returns upon any other args

=head1 FEEDBACK