static CTX_T* create_parser_data(int options, const char *optional_filename) {
CTX_T *data;
data = mm_malloc(sizeof(CTX_T));
memset(data, 0, sizeof(CTX_T));
data->options = options;
data->motif_queue = linklst_create();
data->errors = linklst_create();
data->file_type_match = file_name_match("dreme", "xml", optional_filename);
return data;
}
/*****************************************************************************
* Creates the data to be passed to the SAX parser
****************************************************************************/
void* create_dreme_io_xml_sax_context(void *user_data, DREME_IO_XML_CALLBACKS_T *callbacks) {
PS_T *ps;
CHARBUF_T *buf;
ps = (PS_T*)mm_malloc(sizeof(PS_T));
memset(ps, 0, sizeof(PS_T));
ps->state = PS_START;
ps->udepth = 0;
ps->callbacks = callbacks;
ps->user_data = user_data;
ps->seen_alphabet = false;
ps->seen_ambig = false;
ps->alph_ids = rbtree_create(rbtree_strcmp, rbtree_strcpy, free, rbtree_intcpy, free);
ps->freqs = NULL;
ps->motif_id = NULL;
ps->last_pos = 0;
//set up character buffer
buf = &(ps->characters);
buf->buffer = mm_malloc(sizeof(char)*10);
buf->buffer[0] = '\0';
buf->size = 10;
buf->pos = 0;
attrbuf_init(&(ps->attrbuf));
//set up expected queue
ps->expected_stack = linklst_create();
return ps;
}
/**************************************************************************
* Create a group with a good secondary motif and a group
* of redundant secondary motifs.
**************************************************************************/
GROUPED_MOTIF_T* create_grouped_motif(SECONDARY_MOTIF_T* best) {
GROUPED_MOTIF_T *group;
group = (GROUPED_MOTIF_T*)mm_malloc(sizeof(GROUPED_MOTIF_T));
group->best = best;
group->others = linklst_create();
return group;
}
/*****************************************************************************
* Create the datastructure for storing motifs while their content is
* still being parsed.
****************************************************************************/
static CTX_T* create_parser_data(int options, const char *optional_file_name) {
CTX_T *data;
data = (CTX_T*)mm_malloc(sizeof(CTX_T));
memset(data, 0, sizeof(CTX_T));
data->format_match = file_name_match("meme", "xml", optional_file_name);
data->warnings = linklst_create();
data->errors = linklst_create();
data->motif_queue = linklst_create();
data->options = options;
data->letter_lookup = rbtree_create(rbtree_strcmp, rbtree_strcpy, free, rbtree_strcpy, free);
data->alph = NULL;
data->alph_rdr = NULL;
data->nums = NULL;
if (options & SCANNED_SITES) {
data->sequence_lookup = rbtree_create(rbtree_strcmp, rbtree_strcpy, free, NULL, destroy_seqinfo);
data->motif_lookup = rbtree_create(rbtree_strcmp, rbtree_strcpy, free, rbtree_intcpy, free);
}
return data;
}
/*
* jsonwr_open
* Opens a JSON writer which aims to make human readable JSON
* indented min_cols with each sub-section indented another tab_cols
* aiming for a maximum line length of line_cols.
*/
JSONWR_T* jsonwr_open(FILE *dest, int min_cols, int tab_cols, int line_cols) {
JSONWR_T *jsonwr;
jsonwr = mm_malloc(sizeof(JSONWR_T));
memset(jsonwr, 0, sizeof(JSONWR_T));
jsonwr->file = dest;
jsonwr->min_cols = min_cols;
jsonwr->tab_cols = tab_cols;
jsonwr->line_cols = line_cols;
jsonwr->indent = min_cols + tab_cols;
jsonwr->column = 0;
jsonwr->value_buf = str_create(10);
jsonwr->line_buf = str_create(line_cols);
jsonwr->state = JSON_EMPTY_OBJECT;
jsonwr->stack = linklst_create();
push_state(jsonwr->stack, JSON_DONE);
fputc('{', jsonwr->file);
return jsonwr;
}
/*****************************************************************************
* Creates the data to be passed to the SAX parser
****************************************************************************/
void* create_dreme_io_xml_sax_context(void *user_data, DREME_IO_XML_CALLBACKS_T *callbacks) {
PS_T *ps;
CHARBUF_T *buf;
ps = (PS_T*)mm_malloc(sizeof(PS_T));
memset(ps, 0, sizeof(PS_T));
ps->state = PS_START;
ps->udepth = 0;
ps->callbacks = callbacks;
ps->user_data = user_data;
ps->motif_id = NULL;
ps->last_pos = 0;
//set up character buffer
buf = &(ps->characters);
buf->buffer = mm_malloc(sizeof(char)*10);
buf->buffer[0] = '\0';
buf->size = 10;
buf->pos = 0;
//set up expected queue
ps->expected_stack = linklst_create();
return ps;
}
