#ifndef DREME_SAX_H #define DREME_SAX_H #include #include /***************************************************************************** * Method for obtaining negative dataset enumeration ****************************************************************************/ enum dreme_neg { DREME_NEG_SHUFFLED, // apply a dinucleotide shuffle to the positive set DREME_NEG_FILE // use a supplied file for the negative dataset }; typedef enum dreme_neg DREME_NEG_EN; /***************************************************************************** * Method for obtaining negative dataset enumeration ****************************************************************************/ enum dreme_strands { DREME_STRANDS_BOTH, // apply a dinucleotide shuffle to the positive set DREME_STRANDS_GIVEN,// use a supplied file for the negative dataset DREME_STRANDS_NONE }; typedef enum dreme_strands DREME_STRANDS_EN; /***************************************************************************** * Background sources enumeration ****************************************************************************/ enum dreme_bg { DREME_BG_FROM_DATASET, // use negative dataset frequencies DREME_BG_FROM_FILE // use pre-calculated frequencies from a file }; typedef enum dreme_bg DREME_BG_EN; /***************************************************************************** * Stopping reasons enumeration ****************************************************************************/ enum dreme_stop { DREME_STOP_EVALUE, // couldn't find a motif with a smaller evalue DREME_STOP_COUNT, // already found the expected number of motifs DREME_STOP_TIME // dreme has run longer than the maximum expected time }; typedef enum dreme_stop DREME_STOP_EN; struct dreme_io_xml_callbacks { /***************************************************************************** * Error message handler ****************************************************************************/ void (*error)(void * ctx, const char *format, va_list args); /***************************************************************************** * dreme * contains: model, motifs, run_time * * release the release date. * version the program version. ****************************************************************************/ void (*start_dreme)(void *ctx, int major_version, int minor_version, int patch_version, char *release_date); /***************************************************************************** * /dreme * contains: model, motifs, run_time ****************************************************************************/ void (*end_dreme)(void *ctx); /***************************************************************************** * dreme > model * contains: command_line, positives, negatives, background, stop, ngen, * add_pv_thresh, seed, host, when, description ****************************************************************************/ void (*start_model)(void *ctx); /***************************************************************************** * dreme > /model * contains: command_line, positives, negatives, background, stop, ngen, * add_pv_thresh, seed, host, when, description? ****************************************************************************/ void (*end_model)(void *ctx); /***************************************************************************** * dreme > model > command_line * the command-line used to run the program. ****************************************************************************/ void (*handle_command_line)(void *ctx, char *command_line); /***************************************************************************** * dreme > model > positives * * name the name of the positive input set * count the number of sequences in the positive input set * file the file containing the positive input set * last_mod_date the time the positive input set was last modified ****************************************************************************/ void (*handle_positives) (void *ctx, char *dataset_name, long sequence_count, char *positives_file_path, char *positives_file_last_modified_date); /***************************************************************************** * dreme > model > negatives * * name the name of the negative dataset * count the number of sequences in the negative dataset * from the source of the negative dataset (eg shuffled positives) * file the file containing the negative dataset (optional) * last_mod_date the last modified date of the file (optional) ****************************************************************************/ void (*handle_negatives) (void *ctx, char *dataset_name, long sequence_count, DREME_NEG_EN negatives_source, char *negatives_file_path, char *negatives_file_last_modified_date); /***************************************************************************** * dreme > model > alphabet * * name is the name of the alphabet * extends_flags is the alphabet being extended or 0 ****************************************************************************/ void (*start_alphabet) (void *ctx, char *name, int extends_flags); /***************************************************************************** * dreme > model > /alphabet * * name is the name of the alphabet ****************************************************************************/ void (*end_alphabet) (void *ctx); /***************************************************************************** * dreme > model > alphabet > letter * * id the identifier used to represent the symbol as XML attributes * symbol the symbol * aliases additional symbols that resolve to the same meaning * complement the complement symbol in a double stranded alphabet * equals the comprising symbols * name the name of the negative dataset * colour the colour in RGB triplet (first 3 bytes) ****************************************************************************/ void (*handle_alphabet_letter)(void *ctx, char *id, char symbol, char *aliases, char complement, char *equals, char *name, int color); /***************************************************************************** * dreme > model > strands * * strands how is dreme handling the strands ****************************************************************************/ void (*handle_strands) (void *ctx, DREME_STRANDS_EN strands); /***************************************************************************** * dreme > model > background * * nfreqs is the count of frequencies (same as alphabet core size) * freqs is the array of frequencies (ordered as in alphabet core) * from from the negative dataset or a background file * file the background file (optional) * last_mod_date the last modified date of the background file (optional) ****************************************************************************/ void (*handle_background) (void *ctx, int nfreqs, double* freqs, DREME_BG_EN background_source, char *background_file_path, char *background_file_last_modified_date); /***************************************************************************** * dreme > model > stop * * evalue the stopping evalue (in log base 10) (optional). * count the stopping count (optional). * time the stopping time (optional). ****************************************************************************/ void (*handle_stop) (void *ctx, double *log10_max_motif_evalue, int *max_motif_count, int *max_time_elapsed); /***************************************************************************** * dreme > model > ngen * the number of generations to check (or something like that). ****************************************************************************/ void (*handle_ngen) (void *ctx, int num_gen); /***************************************************************************** * dreme > model > add_pv_thresh * the p-value threshold (in log base 10) for adding a word to the list of * possible motif seed values (this description is probably wrong). ****************************************************************************/ void (*handle_add_pv_thresh)(void *ctx, double log10_add_pv_thresh); /***************************************************************************** * dreme > model > seed * the seed value used by the pseudo-random number generator. ****************************************************************************/ void (*handle_seed)(void *ctx, long seed); /***************************************************************************** * dreme > model > host * the name of the computer which ran DREME. ****************************************************************************/ void (*handle_host)(void *ctx, char *host_name); /***************************************************************************** * dreme > model > when * the time DREME was run. ****************************************************************************/ void (*handle_when)(void *ctx, char *start_date); /***************************************************************************** * dreme > model > description * an optional description of the experiment. ****************************************************************************/ void (*handle_description)(void *ctx, char *experiment_description); /***************************************************************************** * dreme > motifs * contains: motif* ****************************************************************************/ void (*start_motifs)(void *ctx); /***************************************************************************** * dreme > /motifs * contains: motif* ****************************************************************************/ void (*end_motifs)(void *ctx); /***************************************************************************** * dreme > motifs > motif * contains: pos+, match* * * id the identifier used by DREME * alt the alternate identifier used by DREME * seq the DNA iupac sequence representing the motif. * length the length of the motif * nsites the number of sites used to create the motif * p the number of sequences in the positive set with the motif * n the number of sequences in the negative set with the motif * pvalue the pvalue of the motif after erasing (in log base 10) * evalue the evalue of the motif after erasing (in log base 10) * unerased_evalue the evalue of the motif without erasing (in log base 10) ****************************************************************************/ void (*start_motif)(void *ctx, char *identifier, char *alt, char *iupac, int length, long sites, long positives_with_motif, long negatives_with_motif, double log10_pvalue, double log10_evalue, double log10_unerased_evalue); /***************************************************************************** * dreme > motifs > /motif * contains: pos+, match* ****************************************************************************/ void (*end_motif)(void *ctx); /***************************************************************************** * dreme > motifs > motif > pos * * position index of the motif position * nfreqs number of frequencies * freqs array of frequencies ****************************************************************************/ void (*handle_pos)(void *ctx, int position, int nfreqs, double* freqs); /***************************************************************************** * dreme > motifs > motif > match * * seq word which matches motif * p number of positive sequences which contain this word * n number of negative sequences which contain this word * pvalue the pvalue of this word (in log base 10) * evalue the evalue of this word (in log base 10) ****************************************************************************/ void (*handle_match)(void *ctx, char *matching_word, long positives_with_word, long negatives_with_word, double log10_pvalue, double log10_evalue); /***************************************************************************** * dreme > run_time * * cpu the time the program was running on a cpu. * real the real world time the program was running. * stop the reason dreme stopped. ****************************************************************************/ void (*handle_run_time)(void *ctx, double cpu_time, double real_time, DREME_STOP_EN stopping_reason); }; typedef struct dreme_io_xml_callbacks DREME_IO_XML_CALLBACKS_T; /***************************************************************************** * Register handlers on the xmlSAXHandler structure ****************************************************************************/ void register_dreme_io_xml_sax_handlers(xmlSAXHandler *handler); /***************************************************************************** * 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); /***************************************************************************** * Destroys the data used by the SAX parser ****************************************************************************/ void destroy_dreme_io_xml_sax_context(void *context); #endif