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NAMEBio::Event::EventHandlerI - An Event Handler InterfaceSYNOPSIS# do not use this module directly # See Bio::SearchIO::SearchResultEventHandler for an example of # implementation. DESCRIPTIONThis interface describes the basic methods required for EventHandlers. These are essentially SAX methods.Developer NotesEventHandlerI implementations are used in the BioPerl IO systems to decouple the task of tokenizing the input stream into data elements and their attributes, which is format-specific, and the task of collecting those elements and attributes into whatever is the result of a parser, which is specific to the kind of result to be produced, such as BioPerl objects, a tabular or array data structure, etc.You can think of EventHandlerI-compliant parsers as faking a SAX XML parser, making their input (typically a non-XML document) behave as if it were XML. The overhead to do this can be quite substantial, at the gain of not having to duplicate the parsing code in order to change the parsing result, and not having to duplicate the logic of instantiating objects between parsers for different formats that all give rise to the same types of objects. This is perhaps best illustrated by the Bio::SearchIO system, where many different formats exist for sequence similarity and pairwise sequence alignment exist that essentially all result in Bio::Search objects. The method names and their invocation semantics follow their XML SAX equivalents, see http://www.saxproject.org/apidoc/, especially the org.xml.sax.ContentHandler interface. FEEDBACKMailing ListsUser feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists SupportPlease 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 BugsReport bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:https://github.com/bioperl/bioperl-live/issues AUTHOR - Jason StajichEmail jason@bioperl.orgAPPENDIXThe rest of the documentation details each of the object methods. Internal methods are usually preceded with a _will_handleTitle : will_handle Usage : if( $handler->will_handle($event_type) ) { ... } Function: Tests if this event builder knows how to process a specific event Returns : boolean Args : event type name SAX methodsstart_documentTitle : start_document Usage : $resultObj = $parser->start_document(); Function: Receive notification of the beginning of a document (the input file of a parser). The parser will invoke this method only once, before any other event callbacks. Usually, a handler will reset any internal state structures when this method is called. Returns : none Args : none end_documentTitle : end_document Usage : $parser->end_document(); Function: Receive notification of the end of a document (normally the input file of a parser). The parser will invoke this method only once, and it will be the last method invoked during the parse of the document. The parser shall not invoke this method until it has either abandoned parsing (because of an unrecoverable error) or reached the end of input. Unlike the XML SAX signature of this method, this method is expected to return the object representing the result of parsing the document. Returns : The object representing the result of parsing the input stream between the calls to start_document() and this method. Args : none start_elementTitle : start_element Usage : $parser->start_element Function: Receive notification of the beginning of an element. The Parser will invoke this method at the beginning of every element in the input stream; there will be a corresponding end_element() event for every start_element() event (even when the element is empty). All of the element's content will be reported, in order, before the corresponding end_element() event. Returns : none Args : A hashref with at least 2 keys: 'Data' and 'Name'. The value for 'Name' is expected to be the type of element being encountered; the understood values will depend on the IO parser to which this interface is being applied. Likewise, the value for 'Data' will be specific to event handler implementions, and the specific data chunking needs of input formats to be handled efficiently. end_elementTitle : end_element Usage : $parser->end_element Function: Receive notification of the end of an element. The parser will invoke this method at the end of every element in the input stream; there will be a corresponding start_element() event for every end_element() event (even when the element is empty). Returns : none Args : hashref with at least 2 keys, 'Data' and 'Name'. The semantics are the same as for start_element(). in_elementTitle : in_element Usage : if( $handler->in_element($element) ) {} Function: Test if we are in a particular element. Normally, in_element() will test for particular attributes, or nested elements, within a containing element. Conversely, the containing element can be queries with within_element(). The names understood as argument should be the same as the ones understood for the 'Name' key in start_element() and end_element(). Typically, handler implementations will call this method from within the characters() method to determine the context of the data that were passed to characters(). Returns : boolean Args : A string, the name of the element (normally an attribute name or nested sub-element name). within_elementTitle : within_element Usage : if( $handler->within_element($element) ) {} Function: Test if we are within a particular kind of element. Normally, the element type names understood as argument values will be for containing elements or data chunks. Conversely, in_element() can be used to test whether an attribute or nested element is the ccurrent context. Typically, a handler will call this method from within the characters() method to determine the context for the data that were passed to characters(). Returns : boolean Args : string element name charactersTitle : characters Usage : $parser->characters($str) Function: Receive notification of character data. The parser will call this method to report values of attributes, or larger data chunks, depending on the IO subsystem and event handler implementation. Values may be whitespace-padded even if the whitespace is insignificant for the format. The context of the character data being passed can be determined by calling the in_element() and within_element() methods. Returns : none Args : string, the character data
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