Bio-EUtilities

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

=head1 METHODS

=head2

=head1 TODO

=over 3

=item * Finish documentation

HOWTOs (both standard and Cookbook).

=item * Cookbook tests

Set up dev-only tests for Cookbook examples to make sure they are consistently
updated.

=item * API

Mark Jensen has written up the SOAP-based eUtil modules, maybe we should
coalesce around a consistent API between the two (they are close).

=item * Carryover of parameters

Maybe add a default but configurable list of parameters that can be carried over

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

            espell     : the queried database
            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 (Cookie 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

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

            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.

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

            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):