The rest of the documentation details each of the object methods. Internal methods are usually preceded
with a _
new
Title : new
Usage : my $obj = Bio::SearchIO::infernal->new();
Function: Builds a new Bio::SearchIO::infernal object
Returns : Bio::SearchIO::infernal
Args : -fh/-file => cmsearch (infernal) filename
-format => 'infernal'
-model => query model (Rfam ID) (default undef)
-database => database name (default undef)
-query_acc => query accession, eg. Rfam accession RF####
-query_desc => query description, eg. Rfam description
-hsp_minscore => minimum HSP score cutoff
-convert_meta => boolean, set to convert meta string to simple WUSS format
-symbols => hash ref of structure symbols to use
(default symbols in %STRUCTURE_SYMBOLS hash)
next_result
Title : next_result
Usage : my $hit = $searchio->next_result;
Function: Returns the next Result from a search
Returns : Bio::Search::Result::ResultI object
Args : none
start_element
Title : start_element
Usage : $eventgenerator->start_element
Function: Handles a start element event
Returns : none
Args : hashref with at least 2 keys 'Data' and 'Name'
end_element
Title : start_element
Usage : $eventgenerator->end_element
Function: Handles an end element event
Returns : none
Args : hashref with at least 2 keys, 'Data' and 'Name'
element
Title : element
Usage : $eventhandler->element({'Name' => $name, 'Data' => $str});
Function: Convenience method that calls start_element, characters, end_element
Returns : none
Args : Hash ref with the keys 'Name' and 'Data'
element_hash
Title : element
Usage : $eventhandler->element_hash({'Hsp_hit-from' => $start,
'Hsp_hit-to' => $end,
'Hsp_score' => $lastscore});
Function: Convenience method that takes multiple simple data elements and
maps to appropriate parameters
Returns : none
Args : Hash ref with the mapped key (in %MAPPING) and value
characters
Title : characters
Usage : $eventgenerator->characters($str)
Function: Send a character events
Returns : none
Args : string
within_element
Title : within_element
Usage : if( $eventgenerator->within_element($element) ) {}
Function: Test if we are within a particular element
This is different than 'in' because within can be tested
for a whole block.
Returns : boolean
Args : string element name
in_element
Title : in_element
Usage : if( $eventgenerator->in_element($element) ) {}
Function: Test if we are in a particular element
This is different than 'within' because 'in' only
tests its immediate parent.
Returns : boolean
Args : string element name
start_document
Title : start_document
Usage : $eventgenerator->start_document
Function: Handle a start document event
Returns : none
Args : none
end_document
Title : end_document
Usage : $eventgenerator->end_document
Function: Handles an end document event
Returns : Bio::Search::Result::ResultI object
Args : none
result_count
Title : result_count
Usage : my $count = $searchio->result_count
Function: Returns the number of results we have processed
Returns : integer
Args : none
model
Title : model
Usage : my $model = $parser->model();
Function: Get/Set model; Infernal currently does not output
the model name (Rfam ID)
Returns : String (name of model)
Args : [optional] String (name of model)
database
Title : database
Usage : my $database = $parser->database();
Function: Get/Set database; pre-v.1 versions of Infernal do not output
the database name
Returns : String (database name)
Args : [optional] String (database name)
algorithm
Title : algorithm
Usage : my $algorithm = $parser->algorithm();
Function: Get/Set algorithm; pre-v.1 versions of Infernal do not output
the algorithm name
Returns : String (algorithm name)
Args : [optional] String (algorithm name)
query_accession
Title : query_accession
Usage : my $acc = $parser->query_accession();
Function: Get/Set query (model) accession; pre-v1.1 Infernal does not output
the accession number (Rfam accession #)
Returns : String (accession)
Args : [optional] String (accession)
query_description
Title : query_description
Usage : my $acc = $parser->query_description();
Function: Get/Set query (model) description; pre-v1.1 Infernal does not output
the Rfam description
Returns : String (description)
Args : [optional] String (description)
hsp_minscore
Title : hsp_minscore
Usage : my $cutoff = $parser->hsp_minscore();
Function: Get/Set min bit score cutoff (for generating Hits/HSPs)
Returns : score (number)
Args : [optional] score (number)
convert_meta
Title : convert_meta
Usage : $parser->convert_meta(1);
Function: Get/Set boolean flag for converting Infernal WUSS format
to a simple bracketed format (simple WUSS by default)
Returns : boolean flag (TRUE or FALSE)
Args : [optional] boolean (eval's to TRUE or FALSE)
version
Title : version
Usage : $parser->version();
Function: Set the Infernal cmsearch version
Returns : version
Args : [optional] version
structure_symbols
Title : structure_symbols
Usage : my $hashref = $parser->structure_symbols();
Function: Get/Set RNA structure symbols
Returns : Hash ref of delimiters (5' stem, 3' stem, single-strand, etc)
: default = < (5-prime)
> (3-prime)
: (single-strand)
? (unknown)
. (gap)
Args : Hash ref of substitute delimiters, using above keys.
simple_meta
Title : simple_meta
Usage : my $string = $parser->simple_meta($str);
Function: converts more complex WUSS meta format into simple bracket format
using symbols defined in structure_symbols()
Returns : converted string
Args : [required] string to convert
Note : This is a very simple conversion method to get simple bracketed
format from Infernal data. If the convert_meta() flag is set,
this is the method used to convert the strings.
perl v5.32.1 2021-08-15 Bio::SearchIO::infernal(3pm)
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