void* dxml_create(const char *optional_filename, int options) {
DXML_T *parser;
// allocate the structure to hold the parser information
parser = (DXML_T*)mm_malloc(sizeof(DXML_T));
// setup data store
parser->data = create_parser_data(options, optional_filename);
// setup meme xml callbacks
parser->callbacks = (DREME_IO_XML_CALLBACKS_T*)mm_malloc(sizeof(DREME_IO_XML_CALLBACKS_T));
memset(parser->callbacks, 0, sizeof(DREME_IO_XML_CALLBACKS_T));
//start callbacks
parser->callbacks->error = dxml_error;
parser->callbacks->start_dreme = dxml_start_dreme;
// start dreme
// start model
parser->callbacks->handle_background = dxml_handle_background;
// end model
// start motifs
parser->callbacks->start_motif = dxml_start_motif;
parser->callbacks->end_motif = dxml_end_motif;
// start motif
parser->callbacks->handle_pos = dxml_handle_pos;
// end motif
// end motifs
// end dreme
// end callbacks
// setup context for SAX parser
parser->sax_context = create_dreme_io_xml_sax_context(parser->data, parser->callbacks);
// setup SAX handler
parser->handler = (xmlSAXHandler*)mm_malloc(sizeof(xmlSAXHandler));
register_dreme_io_xml_sax_handlers(parser->handler);
// create the push parser context
parser->ctxt = xmlCreatePushParserCtxt(parser->handler, parser->sax_context, NULL, 0, optional_filename);
return parser;
}
/*****************************************************************************
* Create a parser for MEME's XML format.
****************************************************************************/
void* mxml_create(const char *optional_filename, int options) {
MXML_T *parser;
// allocate the structure to hold the parser information
parser = (MXML_T*)mm_malloc(sizeof(MXML_T));
// setup data store
parser->data = create_parser_data(options, optional_filename);
// setup meme xml callbacks
parser->callbacks = (MEME_IO_XML_CALLBACKS_T*)mm_malloc(sizeof(MEME_IO_XML_CALLBACKS_T));
memset(parser->callbacks, 0, sizeof(MEME_IO_XML_CALLBACKS_T));
parser->callbacks->error = mxml_error;
parser->callbacks->start_meme = mxml_start_meme;
parser->callbacks->start_alphabet = mxml_start_alphabet;
parser->callbacks->handle_alphabet_letter = mxml_alphabet_letter;
parser->callbacks->end_alphabet = mxml_end_alphabet;
parser->callbacks->handle_ambigs_letter = mxml_ambigs_letter;
parser->callbacks->handle_strands = mxml_handle_strands;
parser->callbacks->handle_bf_aa_value = mxml_background_value;
parser->callbacks->end_background_frequencies = mxml_end_background;
parser->callbacks->start_motif = mxml_start_motif;
parser->callbacks->end_motif = mxml_end_motif;
parser->callbacks->start_scores = mxml_start_scores;
parser->callbacks->end_sc_am_alphabet_array = mxml_end_score_pos;
parser->callbacks->handle_sc_am_aa_value = mxml_score_value;
parser->callbacks->start_probabilities = mxml_start_probabilities;
parser->callbacks->end_pr_am_alphabet_array = mxml_end_probability_pos;
parser->callbacks->handle_pr_am_aa_value = mxml_probability_value;
if (options & SCANNED_SITES) {
parser->callbacks->handle_sequence = mxml_sequence;
parser->callbacks->start_scanned_sites_summary = mxml_start_scanned_sites;
parser->callbacks->end_scanned_sites_summary = mxml_end_scanned_sites;
parser->callbacks->start_scanned_sites = mxml_start_scanned_seq;
parser->callbacks->handle_scanned_site = mxml_scanned_site;
}
// setup context for SAX parser
parser->sax_context = create_meme_io_xml_sax_context(parser->data, parser->callbacks);
// setup SAX handler
parser->handler = (xmlSAXHandler*)mm_malloc(sizeof(xmlSAXHandler));
register_meme_io_xml_sax_handlers(parser->handler);
// create the push parser context
parser->ctxt = xmlCreatePushParserCtxt(parser->handler, parser->sax_context, NULL, 0, optional_filename);
return parser;
}
