Bio::DB EUtilities
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Summary
Bio::DB::EUtilities - webagent which interacts with and retrieves data from
NCBI's eUtils
Package variables
No package variables defined.
Included modules
Bio::Tools::EUtilities
Bio::Tools::EUtilities::EUtilParameters
Inherit
Bio::DB::GenericWebAgent
Synopsis
  my $eutil = Bio::DB::EUtilities->new(
-eutil => 'esearch',
-term => 'BRCA1',
-db => 'pubmed',
-retmax => 10000,
-email => 'foo@bar.org'); # please use your real email
# eutil => any of esearch, esummary, elink @ids = $eutil->get_ids(); # returns array or array ref of IDs # eutil => any of egquery, espell $term = $eutil->get_term(); # returns array or array ref of IDs # eutil => any of elink, einfo $db = $eutil->get_database(); # returns database # Query-related methods (esearch, egquery, espell data) # eutil data centered on use of search terms my $ct = $eutil->get_count; # uses optional database for egquery count my $translation = $eutil->get_count; my $corrected = $eutil->get_corrected_query; # espell while (my $gquery = $eutil->next_GlobalQuery) { # iterates through egquery data } # Info-related methods (einfo data) # database-related information my $desc = $eutil->get_description; my $update = $eutil->get_last_update; my $nm = $eutil->get_menu_name; my $ct = $eutil->get_record_count; while (my $field = $eutil->next_FieldInfo) { # ... } while (my $field = $eutil->next_LinkInfo) { # ... } # History methods (epost data, some data returned from elink) # data which enables one to retrieve and query against user-stored # information on the NCBI server while (my $cookie = $eutil->next_History) { # ... } my @hists = $eutil->get_Histories; # Bio::Tools::EUtilities::Summary (esummary data) # information on a specific database record # retrieve nested docsum data while (my $docsum = $eutil->next_DocSum) { print "ID:",$docsum->get_ids,"\n"; while (my $item = $docsum->next_Item) { # do stuff here... while (my $listitem = $docsum->next_ListItem) { # do stuff here... while (my $listitem = $docsum->next_Structure) { # do stuff here... } } } } # retrieve flattened item list per DocSum while (my $docsum = $eutil->next_DocSum) { my @items = $docsum->get_all_DocSum_Items; }
Description
This is a general webagent which posts and retrieves data to NCBI's eUtils
service using their CGI interface. A separate project, currently present in
BioPerl-Run, utilizes the SOAP-based interface for eUtils.
A full explanation of the eUtils interfaces are not possible within this short
module; please see the BioPerl wiki HOWTO for more details.
Methods
new
No description
Code
get_ResponseDescriptionCode
delay_policyDescriptionCode
get_ParserDescriptionCode
set_parametersDescriptionCode
reset_parametersDescriptionCode
available_parametersDescriptionCode
get_parametersDescriptionCode
get_parameter_valuesDescriptionCode
eutilDescriptionCode
datatypeDescriptionCode
to_stringDescriptionCode
print_allDescriptionCode
get_idsDescriptionCode
get_databaseDescriptionCode
get_dbDescriptionCode
get_databasesDescriptionCode
get_dbsDescriptionCode
next_HistoryDescriptionCode
next_cookieDescriptionCode
get_HistoriesDescriptionCode
get_countDescriptionCode
get_termDescriptionCode
get_translation_fromDescriptionCode
get_translation_toDescriptionCode
get_retstartDescriptionCode
get_retmaxDescriptionCode
get_query_translationDescriptionCode
get_corrected_queryDescriptionCode
get_replaced_termsDescriptionCode
next_GlobalQueryDescriptionCode
get_GlobalQueriesDescriptionCode
print_GlobalQueriesDescriptionCode
next_DocSumDescriptionCode
get_DocSumsDescriptionCode
print_DocSumsDescriptionCode
get_available_databasesDescriptionCode
get_record_countDescriptionCode
get_last_updateDescriptionCode
get_menu_nameDescriptionCode
get_descriptionDescriptionCode
next_FieldInfoDescriptionCode
get_FieldInfoDescriptionCode
next_LinkInfoDescriptionCode
get_LinkInfoDescriptionCode
print_FieldInfoDescriptionCode
print_LinkInfoDescriptionCode
next_LinkSetDescriptionCode
get_LinkSetsDescriptionCode
print_LinkSetsDescriptionCode
get_linked_databasesDescriptionCode
rewindDescriptionCode
generate_iteratorDescriptionCode
callbackDescriptionCode
Methods description
get_Responsecode    nextTop
 Title   : get_Response
Usage : $agent->get_Response;
Function: Get the HTTP::Response object by passing it an HTTP::Request (generated from
Bio::ParameterBaseI implementation).
Returns : HTTP::Response object or data if callback is used
Args : (optional)
-cache_response - flag to cache HTTP::Response object; Default is 1 (TRUE, caching ON) These are passed on to LWP::UserAgent::request() if stipulated -cb - use a LWP::UserAgent-compliant callback -file - dumps the response to a file (handy for large responses) Note: can't use file and callback at the same time -read_size_hint - bytes of content to read in at a time to pass to callback Note : Caching and parameter checking are set
delay_policycodeprevnextTop
  Title   : delay_policy
Usage : $secs = $self->delay_policy
Function: return number of seconds to delay between calls to remote db
Returns : number of seconds to delay
Args : none
NOTE: NCBI requests a delay of 3 requests per second. This method implements that policy. This will likely change to check time of day or number of requests for lengthening delays.
get_ParsercodeprevnextTop
 Title   : get_Parser
Usage : $agent->get_Parser;
Function: Retrieve the parser used for last agent request
Returns : The Bio::Tools::EUtilities parser used to parse the HTTP::Response
content
Args : None
Note : Abstract method; defined by implementation
set_parameterscodeprevnextTop
 Title   : set_parameters
Usage : $pobj->set_parameters(@params);
Function: sets the NCBI parameters listed in the hash or array
Returns : None
Args : [optional] hash or array of parameter/values.
Note : This sets any parameter (i.e. doesn't screen them). In addition to
regular eutil-specific parameters, you can set the following:
-eutil - the eUtil to be used (default 'efetch') -history - pass a HistoryI-implementing object, which sets the WebEnv, query_key, and possibly db and linkname (the latter two only for LinkSets) -correspondence - Boolean flag, set to TRUE or FALSE; indicates how IDs are to be added together for elink request where ID correspondence might be needed (default 0)
reset_parameterscodeprevnextTop
 Title   : reset_parameters
Usage : resets values
Function: resets parameters to either undef or value in passed hash
Returns : none
Args : [optional] hash of parameter-value pairs
Note : this also resets eutil(), correspondence(), and the history and request
cache
available_parameterscodeprevnextTop
 Title   : available_parameters
Usage : @params = $pobj->available_parameters()
Function: Returns a list of the available parameters
Returns : Array of available parameters (no values)
Args : [optional] A string; either eutil name (for returning eutil-specific
parameters) or 'history' (for those parameters allowed when retrieving
data stored on the remote server using a 'History' object).
get_parameterscodeprevnextTop
 Title   : get_parameters
Usage : @params = $pobj->get_parameters;
%params = $pobj->get_parameters;
Function: Returns list of key/value pairs, parameter => value
Returns : Flattened list of key-value pairs. All key-value pairs returned,
though subsets can be returned based on the '-type' parameter.
Data passed as an array ref are returned based on whether the
'-join_id' flag is set (default is the same array ref).
Args : -type : the eutil name or 'history', for returning a subset of
parameters (Default: returns all)
-join_ids : Boolean; join IDs based on correspondence (Default: no join)
get_parameter_valuescodeprevnextTop
 Title   : get_parameter_values
Usage : @vals = $factory->get_parameter_value('id'); # always get array
Function: Returns the specific parameter values.
Returns : For consistency returns a list of values for this parameter. If only
one is expected, use:
($val) = $factory->get_parameter_value('id'); Args : parameter expected
eutilcodeprevnextTop
 Title    : eutil
Usage : $eutil->$foo->eutil
Function : Get/Set eutil
Returns : string
Args : string (eutil)
Throws : on invalid eutil
datatypecodeprevnextTop
 Title    : datatype
Usage : $type = $foo->datatype;
Function : Get/Set data object type
Returns : string
Args : string
to_stringcodeprevnextTop
 Title    : to_string
Usage : $foo->to_string()
Function : converts current object to string
Returns : none
Args : (optional) simple data for text formatting
Note : Implemented in plugins
print_allcodeprevnextTop
 Title    : print_all
Usage : $info->print_all();
$info->print_all(-fh => $fh, -cb => $coderef);
Function : prints (dumps) all data in parser. Unless a coderef is supplied,
this just dumps the parser-specific to_string method to either a
file/fh or STDOUT
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
get_idscodeprevnextTop
 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
get_databasecodeprevnextTop
 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 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
elink : from parameter_base->dbfrom or undef
all others : from parameter_base->db or undef
get_db (alias for get_database)codeprevnextTop
get_databasescodeprevnextTop
 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
espell : the queried database
all others : from parameter_base->db or undef
get_dbs (alias for get_databases)codeprevnextTop
next_HistorycodeprevnextTop
 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.
next_cookie (alias for next_History)codeprevnextTop
get_HistoriescodeprevnextTop
 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
get_countcodeprevnextTop
 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
get_termcodeprevnextTop
 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
get_translation_fromcodeprevnextTop
 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
get_translation_tocodeprevnextTop
 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
get_retstartcodeprevnextTop
 Title    : get_retstart
Usage : $start = $qd->get_retstart();
Function : retstart setting for the query (either set or NCBI default)
Returns : Integer
Args : none
Notes : esearch : retstart
esummary : retstart
all others : from parameter_base->retstart or undef
get_retmaxcodeprevnextTop
 Title    : get_retmax
Usage : $max = $qd->get_retmax();
Function : retmax setting for the query (either set or NCBI default)
Returns : Integer
Args : none
Notes : esearch : retmax
esummary : retmax
all others : from parameter_base->retmax or undef
get_query_translationcodeprevnextTop
 Title   : get_query_translation
Usage : $string = $qd->get_query_translation();
Function: returns the translated query used for the search (if any)
Returns : string
Args : none
Notes : only applicable for esearch. This is the actual term used for
esearch.
get_corrected_querycodeprevnextTop
 Title    : get_corrected_query
Usage : my $cor = $eutil->get_corrected_query;
Function : retrieves the corrected query when using espell
Returns : string
Args : none
Notes : only applicable for espell.
get_replaced_termscodeprevnextTop
 Title    : get_replaced_terms
Usage : my $term = $eutil->get_replaced_terms
Function : returns array of strings replaced in the query
Returns : string
Args : none
Notes : only applicable for espell
next_GlobalQuerycodeprevnextTop
 Title    : next_GlobalQuery
Usage : while (my $query = $eutil->next_GlobalQuery) {...}
Function : iterates through the queries returned from an egquery search
Returns : GlobalQuery object
Args : none
Notes : only applicable for egquery
get_GlobalQueriescodeprevnextTop
 Title    : get_GlobalQueries
Usage : @queries = $eutil->get_GlobalQueries
Function : returns list of GlobalQuery objects
Returns : array of GlobalQuery objects
Args : none
Notes : only applicable for egquery
print_GlobalQueriescodeprevnextTop
 Title    : print_GlobalQueries
Usage : $docsum->print_GlobalQueries();
$docsum->print_GlobalQueries(-fh => $fh, -cb => $coderef);
Function : prints item data for all global queries. The default printing
method is each item per DocSum is printed with relevant values if
present in a simple table using Text::Wrap.
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 GlobalQuery object;
-wrap : number of columns to wrap default text output to (def = 80)
Notes : only applicable for esummary. If -file or -fh are not defined,
prints to STDOUT
next_DocSumcodeprevnextTop
 Title    : next_DocSum
Usage : while (my $ds = $esum->next_DocSum) {...}
Function : iterate through DocSum instances
Returns : single Bio::Tools::EUtilities::Summary::DocSum
Args : none yet
Notes : only applicable for esummary
get_DocSumscodeprevnextTop
 Title    : get_DocSums
Usage : my @docsums = $esum->get_DocSums
Function : retrieve a list of DocSum instances
Returns : array of Bio::Tools::EUtilities::Summary::DocSum
Args : none
Notes : only applicable for esummary
print_DocSumscodeprevnextTop
 Title    : print_DocSums
Usage : $docsum->print_DocSums();
$docsum->print_DocSums(-fh => $fh, -cb => $coderef);
Function : prints item data for all docsums. The default printing method is
each item per DocSum is printed with relevant values if present
in a simple table using Text::Wrap.
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 DocSum object;
-wrap : number of columns to wrap default text output to (def = 80)
Notes : only applicable for esummary. If -file or -fh are not defined,
prints to STDOUT
get_available_databasescodeprevnextTop
 Title    : get_available_databases
Usage : my @dbs = $info->get_available_databases
Function : returns list of available eutil-compatible database names
Returns : Array of strings
Args : none
Notes : only applicable for einfo.
get_record_countcodeprevnextTop
 Title    : get_record_count
Usage : my $ct = $eutil->get_record_count;
Function : returns database record count
Returns : integer
Args : none
Notes : only applicable for einfo.
get_last_updatecodeprevnextTop
 Title    : get_last_update
Usage : my $time = $info->get_last_update;
Function : returns string containing time/date stamp for last database update
Returns : integer
Args : none
Notes : only applicable for einfo.
get_menu_namecodeprevnextTop
 Title    : get_menu_name
Usage : my $nm = $info->get_menu_name;
Function : returns string of database menu name
Returns : string
Args : none
Notes : only applicable for einfo.
get_descriptioncodeprevnextTop
 Title    : get_description
Usage : my $desc = $info->get_description;
Function : returns database description
Returns : string
Args : none
Notes : only applicable for einfo.
next_FieldInfocodeprevnextTop
 Title    : next_FieldInfo
Usage : while (my $field = $info->next_FieldInfo) {...}
Function : iterate through FieldInfo objects
Returns : Field object
Args : none
Notes : only applicable for einfo. Uses callback() for filtering if defined
for 'fields'
get_FieldInfocodeprevnextTop
 Title    : get_FieldInfo
Usage : my @fields = $info->get_FieldInfo;
Function : returns list of FieldInfo objects
Returns : array (FieldInfo objects)
Args : none
Notes : only applicable for einfo.
next_LinkInfocodeprevnextTop
 Title    : next_LinkInfo
Usage : while (my $link = $info->next_LinkInfo) {...}
Function : iterate through LinkInfo objects
Returns : LinkInfo object
Args : none
Notes : only applicable for einfo. Uses callback() for filtering if defined
for 'linkinfo'
get_LinkInfocodeprevnextTop
 Title    : get_LinkInfo
Usage : my @links = $info->get_LinkInfo;
Function : returns list of LinkInfo objects
Returns : array (LinkInfo objects)
Args : none
Notes : only applicable for einfo.
print_FieldInfocodeprevnextTop
 Title    : print_FieldInfo
Usage : $info->print_FieldInfo();
$info->print_FieldInfo(-fh => $fh, -cb => $coderef);
Function : prints field data for each FieldInfo object. The default method
prints data from each FieldInfo in a simple table using Text::Wrap.
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.
-wrap : number of columns to wrap default text output to (def = 80)
Note : if -file or -fh are not defined, prints to STDOUT
print_LinkInfocodeprevnextTop
 Title    : print_LinkInfo
Usage : $info->print_LinkInfo();
$info->print_LinkInfo(-fh => $fh, -cb => $coderef);
Function : prints link data for each LinkInfo object. The default is generated
via LinkInfo::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 LinkInfo 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
next_LinkSetcodeprevnextTop
 Title    : next_LinkSet
Usage : while (my $ls = $eutil->next_LinkSet {...}
Function : iterate through LinkSet objects
Returns : LinkSet object
Args : none
Notes : only applicable for elink. Uses callback() for filtering if defined
for 'linksets'
get_LinkSetscodeprevnextTop
 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.
print_LinkSetscodeprevnextTop
 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
get_linked_databasescodeprevnextTop
 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.
rewindcodeprevnextTop
 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 interators (such as LinkSets and DocSums). 'globalqueries' 'fieldinfo' or 'fieldinfos' 'linkinfo' or 'linkinfos' 'linksets' 'docsums'
generate_iteratorcodeprevnextTop
 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' 'linkinfo' or 'linkinfos' 'linksets' 'docsums' A second argument can also be passed to generate a 'lazy' iterator, which loops through and returns objects as they are created (instead of creating all data instances up front, then iterating through, which is the default). Use of these iterators precludes use of rewind() 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. 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). TODO : generate seekable iterators ala HOP for seekable fh data
callbackcodeprevnextTop
 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
Methods code
newdescriptionprevnextTop
sub new {
    my($class,@args) = @_;
    my $self = $class->SUPER::new(@args);
    my $params = Bio::Tools::EUtilities::EUtilParameters->new(-verbose => $self->verbose,
                                               @args);
    # cache parameters
$self->parameter_base($params); return $self;
}
get_ResponsedescriptionprevnextTop
sub get_Response {
    my $self = shift;
    $self->parameter_base->email() || $self->warn('The -email parameter is now required, per NCBI E-utilities policy');
    $self->SUPER::get_Response(@_);
}
delay_policydescriptionprevnextTop
sub delay_policy {
    my $self = shift;
    return 1/3;
}
get_ParserdescriptionprevnextTop
sub get_Parser {
    my ($self) = @_;
    my $pobj = $self->parameter_base;
    if ($pobj->parameters_changed || !$self->{'_parser'}) {
        my $eutil = $pobj->eutil ;
        if ($eutil eq 'efetch') {
            $self->throw("No parser defined for efetch; use get_Response() directly");
        };
        # if we are to add pipe/tempfile support this would probably be the
# place to add it....
my $parser = Bio::Tools::EUtilities->new( -eutil => $eutil, -response => $self->get_Response, -parameters => $pobj, -verbose => $self->verbose); return $self->{'_parser'} = $parser; } return $self->{'_parser'};
}
set_parametersdescriptionprevnextTop
sub set_parameters {
    my ($self, @args) = @_;
    # just ensures that parser instance isn't reused
delete $self->{'_parser'}; $self->parameter_base->set_parameters(@args);
}
reset_parametersdescriptionprevnextTop
sub reset_parameters {
    my ($self, @args) = @_;
    # just ensures that parser instance isn't reused
delete $self->{'_parser'}; $self->parameter_base->reset_parameters(@args);
}
available_parametersdescriptionprevnextTop
sub available_parameters {
    my ($self, @args) = @_;
    return $self->parameter_base->available_parameters(@args);
}
get_parametersdescriptionprevnextTop
sub get_parameters {
    my ($self, @args) = @_;
    return $self->parameter_base->get_parameters(@args);
}
get_parameter_valuesdescriptionprevnextTop
sub get_parameter_values {
    my ($self, $p) = @_;
    my %params = $self->parameter_base->get_parameters(-list => [$p]);
    if (exists $params{$p}) {
        return ref $params{$p} eq 'ARRAY' ? @{$params{$p}} : $params{$p};
    }
    return;
}
eutildescriptionprevnextTop
sub eutil {
    my ($self, @args) = @_;
    return $self->get_Parser->eutil(@args);
}
datatypedescriptionprevnextTop
sub datatype {
    my ($self, @args) = @_;
    return $self->get_Parser->datatype(@args);
}
to_stringdescriptionprevnextTop
sub to_string {
    my ($self, @args) = @_;
    return $self->get_Parser->to_string(@args);
}
print_alldescriptionprevnextTop
sub print_all {
    my ($self, @args) = @_;
    return $self->get_Parser->print_all(@args);
}
get_idsdescriptionprevnextTop
sub get_ids {
    my ($self, @args) = @_;
    return $self->get_Parser->get_ids(@args);
}
get_databasedescriptionprevnextTop
sub get_database {
    my ($self, @args) = @_;
    return $self->get_Parser->get_database(@args);
}
get_dbdescriptionprevnextTop
sub get_db {
    my ($self, @args) = @_;
    return $self->get_Parser->get_db(@args);
}
get_databasesdescriptionprevnextTop
sub get_databases {
    my ($self, @args) = @_;
    return $self->get_Parser->get_databases(@args);
}
get_dbsdescriptionprevnextTop
sub get_dbs {
    my ($self, @args) = @_;
    return $self->get_Parser->get_databases(@args);
}
next_HistorydescriptionprevnextTop
sub next_History {
    my ($self, @args) = @_;
    return $self->get_Parser->next_History(@args);
}
next_cookiedescriptionprevnextTop
sub next_cookie {
    my ($self, @args) = @_;
    return $self->get_Parser->next_History(@args);
}
get_HistoriesdescriptionprevnextTop
sub get_Histories {
    my ($self, @args) = @_;
    return $self->get_Parser->get_Histories(@args);
}
get_countdescriptionprevnextTop
sub get_count {
    my ($self, @args) = @_;
    return $self->get_Parser->get_count(@args);
}
get_termdescriptionprevnextTop
sub get_term {
    my ($self, @args) = @_;
    return $self->get_Parser->get_term(@args);
}
get_translation_fromdescriptionprevnextTop
sub get_translation_from {
    my ($self, @args) = @_;
    return $self->get_Parser->get_translation_from(@args);
}
get_translation_todescriptionprevnextTop
sub get_translation_to {
    my ($self, @args) = @_;
    return $self->get_Parser->get_translation_to(@args);
}
get_retstartdescriptionprevnextTop
sub get_retstart {
    my ($self, @args) = @_;
    return $self->get_Parser->get_retstart(@args);
}
get_retmaxdescriptionprevnextTop
sub get_retmax {
    my ($self, @args) = @_;
    return $self->get_Parser->get_retmax(@args);
}
get_query_translationdescriptionprevnextTop
sub get_query_translation {
    my ($self, @args) = @_;
    return $self->get_Parser->get_query_translation(@args);
}
get_corrected_querydescriptionprevnextTop
sub get_corrected_query {
    my ($self, @args) = @_;
    return $self->get_Parser->get_corrected_query(@args);
}
get_replaced_termsdescriptionprevnextTop
sub get_replaced_terms {
    my ($self, @args) = @_;
    return $self->get_Parser->get_replaced_terms(@args);
}
next_GlobalQuerydescriptionprevnextTop
sub next_GlobalQuery {
    my ($self, @args) = @_;
    return $self->get_Parser->next_GlobalQuery(@args);
}
get_GlobalQueriesdescriptionprevnextTop
sub get_GlobalQueries {
    my ($self, @args) = @_;
    return $self->get_Parser->get_GlobalQueries(@args);
}
print_GlobalQueriesdescriptionprevnextTop
sub print_GlobalQueries {
    my ($self, @args) = @_;
    return $self->get_Parser->print_GlobalQueries(@args);
}
next_DocSumdescriptionprevnextTop
sub next_DocSum {
    my ($self, @args) = @_;
    return $self->get_Parser->next_DocSum(@args);
}
get_DocSumsdescriptionprevnextTop
sub get_DocSums {
    my ($self, @args) = @_;
    return $self->get_Parser->get_DocSums(@args);
}
print_DocSumsdescriptionprevnextTop
sub print_DocSums {
    my ($self, @args) = @_;
    return $self->get_Parser->print_DocSums(@args);
}
get_available_databasesdescriptionprevnextTop
sub get_available_databases {
    my ($self, @args) = @_;
    return $self->get_Parser->get_available_databases(@args);
}
get_record_countdescriptionprevnextTop
sub get_record_count {
    my ($self, @args) = @_;
    return $self->get_Parser->get_record_count(@args);
}
get_last_updatedescriptionprevnextTop
sub get_last_update {
    my ($self, @args) = @_;
    return $self->get_Parser->get_last_update(@args);
}
get_menu_namedescriptionprevnextTop
sub get_menu_name {
    my ($self, @args) = @_;
    return $self->get_Parser->get_menu_name(@args);
}
get_descriptiondescriptionprevnextTop
sub get_description {
    my ($self, @args) = @_;
    return $self->get_Parser->get_description(@args);
}
next_FieldInfodescriptionprevnextTop
sub next_FieldInfo {
    my ($self, @args) = @_;
    return $self->get_Parser->next_FieldInfo(@args);
}
get_FieldInfodescriptionprevnextTop
sub get_FieldInfo {
    my ($self, @args) = @_;
    return $self->get_Parser->get_FieldInfo(@args);
}

*get_FieldInfos =\& get_FieldInfo;
}
next_LinkInfodescriptionprevnextTop
sub next_LinkInfo {
    my ($self, @args) = @_;
    return $self->get_Parser->next_LinkInfo(@args);
}
get_LinkInfodescriptionprevnextTop
sub get_LinkInfo {
    my ($self, @args) = @_;
    return $self->get_Parser->get_LinkInfo(@args);
}

*get_LinkInfos =\& get_LinkInfo;
}
print_FieldInfodescriptionprevnextTop
sub print_FieldInfo {
    my ($self, @args) = @_;
    return $self->get_Parser->print_FieldInfo(@args);
}
print_LinkInfodescriptionprevnextTop
sub print_LinkInfo {
    my ($self, @args) = @_;
    return $self->get_Parser->print_LinkInfo(@args);
}
next_LinkSetdescriptionprevnextTop
sub next_LinkSet {
    my ($self, @args) = @_;
    return $self->get_Parser->next_LinkSet(@args);
}
get_LinkSetsdescriptionprevnextTop
sub get_LinkSets {
    my ($self, @args) = @_;
    return $self->get_Parser->get_LinkSets(@args);
}
print_LinkSetsdescriptionprevnextTop
sub print_LinkSets {
    my ($self, @args) = @_;
    return $self->get_Parser->print_LinkSets(@args);
}
get_linked_databasesdescriptionprevnextTop
sub get_linked_databases {
    my ($self, @args) = @_;
    return $self->get_Parser->get_linked_databases(@args);
}
rewinddescriptionprevnextTop
sub rewind {
    my ($self, $string) = @_;
    return $self->get_Parser->rewind($string);
}
generate_iteratordescriptionprevnextTop
sub generate_iterator {
    my ($self, @args) = @_;
    return $self->get_Parser->generate_iterator(@args);
}
callbackdescriptionprevnextTop
sub callback {
    my ($self, @args) = @_;
    return $self->get_Parser->callback(@args);
}

1;
__END__
}
General documentation
TODOTop
   * Finish documentation
   HOWTOs (both standard and Cookbook).
   * Cookbook tests
   Set up dev-only tests for Cookbook examples to make sure they are consistently
updated.
   * 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).
   * Carryover of parameters
   Maybe add a default but configurable list of parameters that can be carried over
between calls.
   * Make setting certain parameters consistent
   Setting history is a bit inconsistent, so maybe use a common alias for this?
   * Splitting out of core
   This could easily belong in its own distribution, the only tie to BioPerl is the
use of Bio::Root::Root.
   * Moosify?
   Not necessary, but it might make things easier and more maintainable in the long
run.
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the
evolution of this and other Bioperl modules. Send
your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation
is much appreciated.
  bioperl-l@lists.open-bio.org               - General discussion
http://www.bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to
help us keep track the bugs and their resolution.
Bug reports can be submitted via the web.
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR Top
Email cjfields at bioperl dot org
APPENDIXTop
The rest of the documentation details each of the
object methods. Internal methods are usually
preceded with a _
Bio::DB::GenericWebAgent methodsTop
GenericWebDBI methodsTop
parameter_baseTop
 Title   : parameter_base
Usage : $dbi->parameter_base($pobj);
Function: Get/Set Bio::ParameterBaseI.
Returns : Bio::ParameterBaseI object
Args : Bio::ParameterBaseI object
uaTop
 Title   : ua
Usage : $dbi->ua;
Function: Get/Set LWP::UserAgent.
Returns : LWP::UserAgent
Args : LWP::UserAgent
delayTop
 Title   : delay
Usage : $secs = $self->delay([$secs])
Function: get/set number of seconds to delay between fetches
Returns : number of seconds to delay
Args : new value
NOTE: the default is to use the value specified by delay_policy().
This can be overridden by calling this method.
LWP::UserAgent related methodsTop
proxyTop
 Title   : proxy
Usage : $httpproxy = $db->proxy('http') or
$db->proxy(['http','ftp'], 'http://myproxy' )
Function: Get/Set a proxy for use of proxy
Returns : a string indicating the proxy
Args : $protocol : an array ref of the protocol(s) to set/get
$proxyurl : url of the proxy to use for the specified protocol
$username : username (if proxy requires authentication)
$password : password (if proxy requires authentication)
authenticationTop
 Title   : authentication
Usage : $db->authentication($user,$pass)
Function: Get/Set authentication credentials
Returns : Array of user/pass
Args : Array or user/pass
Bio::Tools::EUtilities::EUtilParameters-delegating methodsTop
This is only a subset of parameters available from Bio::Tools::EUtilities::EUtilParameters (the
ones deemed absolutely necessary). All others are available by calling
'parameter_base->method' when needed.
Bio::Tools::EUtilities-delegating methodsTop
Bio::Tools::EUtilities::EUtilDataI methodsTop
Methods useful for multiple eutilsTop
Query-related methodsTop
Summary-related methodsTop
Info-related methodsTop
Bio::Tools::EUtilities::Link-related methodsTop
Iterator- and callback-related methodsTop