Bio::SearchIO::sim4 - parser for Sim4 alignments # do not use this module directly, it is a driver for SearchIO use Bio::SearchIO; my $searchio = new Bio::SearchIO(-file => 'results.sim4', -format => 'sim4'); while ( my $result = $searchio->next_result ) { while ( my $hit = $result->next_hit ) { while ( my $hsp = $hit->next_hsp ) { # ... } } } This is a driver for the SearchIO system for parsing Sim4. http://globin.cse.psu.edu/html/docs/sim4.html

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Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bioperl.org http://bioperl.org/bioperl-bugs/ Email jason-at-bioperl-dot-org Luc Gauthier (lgauthie@hotmail.com) The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $obj = new Bio::SearchIO::sim4(); Function: Builds a new Bio::SearchIO::sim4 object Returns : an instance of Bio::SearchIO::sim4 Args :

next_result
Title : next_result Usage : my $result = $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: Convience method that calls start_element, characters, end_element Returns : none Args : Hash ref with the keys 'Name' and 'Data'

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 'in' because within can be tested for a whole block. 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

_will_handle
Title : _will_handle Usage : Private method. For internal use only. if( $self->_will_handle($type) ) { ... } Function: Provides an optimized way to check whether or not an element of a given type is to be handled. Returns : Reference to EventHandler object if the element type is to be handled. undef if the element type is not to be handled. Args : string containing type of element. Optimizations: 1. Using the cached pointer to the EventHandler to minimize repeated lookups. 2. Caching the will_handle status for each type that is encountered so that it only need be checked by calling handler->will_handle($type) once. This does not lead to a major savings by itself (only 5-10%). In combination with other optimizations, or for large parse jobs, the savings good be significant. To test against the unoptimized version, remove the parentheses from around the third term in the ternary " ? : " operator and add two calls to $self->_eventHandler().