#ifndef STREME_SAX_H #define STREME_SAX_H #include #include /***************************************************************************** * Method for obtaining negative dataset enumeration ****************************************************************************/ enum streme_neg { STREME_NEG_SHUFFLED, // apply a shuffle to the positive set STREME_NEG_FILE, // use a supplied file for the negative dataset STREME_NEG_NONE // CD only: use no negative dataset }; typedef enum streme_neg STREME_NEG_EN; /***************************************************************************** * Strands ****************************************************************************/ enum streme_strands { STREME_STRANDS_BOTH, // use both strands STREME_STRANDS_FORWARD, // given strand STREME_STRANDS_NONE // single strand alphabet }; typedef enum streme_strands STREME_STRANDS_EN; /***************************************************************************** * Objective function ****************************************************************************/ enum streme_objfun { STREME_DIFFERENTIAL_ENRICHMENT, STREME_CENTRAL_DISTANCE }; typedef enum streme_objfun STREME_OBJFUN_EN; /***************************************************************************** * Test ****************************************************************************/ enum streme_test { STREME_FISHER_EXACT_TEST, STREME_BINOMIAL_TEST, STREME_CUMULATIVE_BATES_DISTRIBUTION }; typedef enum streme_test STREME_TEST_EN; /***************************************************************************** * Background sources enumeration ****************************************************************************/ enum streme_bg { STREME_BG_FROM_DATASET, // use negative dataset frequencies STREME_BG_FROM_FILE // use pre-calculated frequencies from a file }; typedef enum streme_bg STREME_BG_EN; struct streme_io_xml_callbacks { /***************************************************************************** * Error message handler ****************************************************************************/ void (*error)(void * ctx, const char *format, va_list args); /***************************************************************************** * streme * contains: model, motifs, reason_for_stopping, run_time * * release the release date. * version the program version. ****************************************************************************/ void (*start_streme)(void *ctx, int major_version, int minor_version, int patch_version, char *release_date); /***************************************************************************** * /streme ****************************************************************************/ void (*end_streme)(void *ctx); /***************************************************************************** * STREME > model * contains: command_line, train_positives, train_negatives, test_positives, * test_negatives, alphabet, strands, sequence_db, background_frequencies, * stop, objfun, srch, test, minw, maxw, kmer, hofract, neval, nref, * niter, mmr, seed, host ****************************************************************************/ void (*start_model)(void *ctx); /***************************************************************************** * STREME > /model ****************************************************************************/ void (*end_model)(void *ctx); /***************************************************************************** * STREME > model > command_line * the command-line used to run the program. ****************************************************************************/ void (*handle_command_line)(void *ctx, char *command_line); /***************************************************************************** * STREME > model > train_positives * * count the number of sequences in the positive input set * positions the number of characters in the positive training set * file the file containing the positive input set ****************************************************************************/ void (*handle_train_positives) (void *ctx, long sequence_count, long sequence_positions, char *positives_file_path); /***************************************************************************** * STREME > model > train_negatives * * count the number of sequences in the negative dataset * positions the number of characters in the negative training set * from the source of the negative dataset (eg shuffled positives) * file the file containing the negative dataset (optional) ****************************************************************************/ void (*handle_train_negatives) (void *ctx, long sequence_count, long sequence_positions, STREME_NEG_EN negatives_source, char *negatives_file_path); /***************************************************************************** * STREME > model > test_positives * * count the number of sequences in the positive training set * positions the number of characters in the positive training set ****************************************************************************/ void (*handle_test_positives) (void *ctx, long sequence_count, long sequence_positions); /***************************************************************************** * STREME > model > test_negatives * * count the number of sequences in the negative training set * positions the number of characters in the negative training set ****************************************************************************/ void (*handle_test_negatives) (void *ctx, long sequence_count, long sequence_positions); /***************************************************************************** * STREME > model > sequence_db * * This is a dummy entry with no contents. ****************************************************************************/ void (*handle_sequence_db) (void *ctx, int dummy); /***************************************************************************** * STREME > 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); /***************************************************************************** * STREME > model > /alphabet * * name is the name of the alphabet ****************************************************************************/ void (*end_alphabet) (void *ctx); /***************************************************************************** * STREME > 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); /***************************************************************************** * STREME > model > strands * * strands how is streme handling the strands ****************************************************************************/ void (*handle_strands) (void *ctx, STREME_STRANDS_EN strands); /***************************************************************************** * STREME > 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 positive dataset or a background file ****************************************************************************/ void (*handle_background) (void *ctx, int nfreqs, double* freqs, STREME_BG_EN background_source); void (*start_background_frequencies)(void *, char *); // source of data void (*end_background_frequencies)(void *); //start background frequencies void (*start_bf_alphabet_array)(void *); void (*end_bf_alphabet_array)(void *); //start alphabet_array void (*handle_bf_aa_value)(void *, char *, double); //end alphabet_array //end background frequencies /***************************************************************************** * STREME > model > stop * * pvt the maximum p-value threshold for motifs * nmotifs the maximum number of motifs to find * time the maximum time to run (seconds) ****************************************************************************/ void (*handle_stop) (void *ctx, double pvt, int nmotifs, double time); /***************************************************************************** * STREME > model > objfun ****************************************************************************/ void (*handle_objfun) (void *ctx, STREME_OBJFUN_EN objfun); /***************************************************************************** * STREME > model > test ****************************************************************************/ void (*handle_test) (void *ctx, STREME_TEST_EN test); /***************************************************************************** * STREME > model > minw ****************************************************************************/ void (*handle_minw) (void *ctx, int minw); /***************************************************************************** * STREME > model > maxw ****************************************************************************/ void (*handle_maxw) (void *ctx, int maxw); /***************************************************************************** * STREME > model > kmer ****************************************************************************/ void (*handle_kmer) (void *ctx, int kmer); /***************************************************************************** * STREME > model > hofract ****************************************************************************/ void (*handle_hofract) (void *ctx, double hofract); /***************************************************************************** * STREME > model > neval ****************************************************************************/ void (*handle_neval) (void *ctx, int neval); /***************************************************************************** * STREME > model > nref ****************************************************************************/ void (*handle_nref) (void *ctx, int nref); /***************************************************************************** * STREME > model > niter ****************************************************************************/ void (*handle_niter) (void *ctx, int niter); /***************************************************************************** * STREME > model > patience ****************************************************************************/ void (*handle_patience) (void *ctx, long patience); /***************************************************************************** * STREME > model > seed ****************************************************************************/ void (*handle_seed) (void *ctx, long seed); /***************************************************************************** * STREME > model > useer ****************************************************************************/ void (*handle_useer) (void *ctx, int useer); /***************************************************************************** * STREME > model > minscore ****************************************************************************/ void (*handle_minscore) (void *ctx, long minscore); /***************************************************************************** * STREME > model > ignore_depth ****************************************************************************/ void (*handle_ignore_depth) (void *ctx, long ignore_depth); /***************************************************************************** * STREME > model > nsubsets ****************************************************************************/ void (*handle_nsubsets) (void *ctx, long nsubsets); /***************************************************************************** * STREME > model > min_pal_ratio ****************************************************************************/ void (*handle_min_pal_ratio) (void *ctx, double min_pal_ratio); /***************************************************************************** * STREME > model > max_pal_ed ****************************************************************************/ void (*handle_max_pal_ed) (void *ctx, double max_pal_ed); /***************************************************************************** * STREME > model > cand ****************************************************************************/ void (*handle_cand) (void *ctx, int cand); /***************************************************************************** * STREME > model > experimental ****************************************************************************/ void (*handle_experimental) (void *ctx, int experimental); /***************************************************************************** * STREME > model > totallength ****************************************************************************/ void (*handle_totallength) (void *ctx, long totallength); /***************************************************************************** * STREME > model > align ****************************************************************************/ void (*handle_align) (void *ctx, long align); /***************************************************************************** * STREME > model > host ****************************************************************************/ void (*handle_host) (void *ctx, char *host); /***************************************************************************** * STREME > model > description ****************************************************************************/ void (*handle_description)(void *ctx, char *experiment_description); /***************************************************************************** * STREME > motifs * contains: motif* ****************************************************************************/ void (*start_motifs)(void *ctx); /***************************************************************************** * STREME > /motifs * contains: motif* ****************************************************************************/ void (*end_motifs)(void *ctx); /***************************************************************************** * STREME > motifs > motif * * id the identifier used by STREME * alt alternate identifier used by STREME * width the width of the motif * initial_width the width of the prefix seed for the motif * seed the seed word for the motif * score_threshold the log-odds score threshold for calling sites * train_pos_count positive training sites * train_neg_count negative training sites * train_log_pvalue log10 p-value on training set * train_pvalue p-value on training set * train_dtc CD only: average site distance to center in training set * train_bernoulli Binomial Test only: Bernoulli prob. in training set * test_pos_count positive test sites * test_neg_count negative test sites * test_log_pvalue log10 p-value on test set * test_pvalue p-value on test set * test_dtc CD only: average site distance to center in test set * test_bernoulli Binomial Test only: Bernoulli prob. in test set * is_palindromic is the motif a perfect palindrome? * elapsed time time elapsed until motif found (seconds) ****************************************************************************/ void (*start_motif)(void *ctx, char *id, char *alt, int width, int initial_width, char *seed, double score_threshold, long train_pos_count, long train_neg_count, double train_log_pvalue, char *train_pvalue, double train_dtc, double train_bernoulli, long test_pos_count, long test_neg_count, double test_log_pvalue, char *test_pvalue, double test_dtc, double test_bernoulli, char *is_palindromic, double elapsed_time); /***************************************************************************** * STREME > motifs > /motif * contains: pos+, match* ****************************************************************************/ void (*end_motif)(void *ctx); /***************************************************************************** * STREME > 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); /***************************************************************************** * STREME > reason_for_stopping ****************************************************************************/ void (*handle_reason_for_stopping)(void *ctx, char *reason_for_stopping); /***************************************************************************** * STREME > run_time * * cpu the time the program was running on a cpu. ****************************************************************************/ void (*handle_run_time)(void *ctx, double cpu_time); }; typedef struct streme_io_xml_callbacks STREME_IO_XML_CALLBACKS_T; /***************************************************************************** * Register handlers on the xmlSAXHandler structure ****************************************************************************/ void register_streme_io_xml_sax_handlers(xmlSAXHandler *handler); /***************************************************************************** * Creates the data to be passed to the SAX parser ****************************************************************************/ void* create_streme_io_xml_sax_context(void *user_data, STREME_IO_XML_CALLBACKS_T *callbacks); /***************************************************************************** * Destroys the data used by the SAX parser ****************************************************************************/ void destroy_streme_io_xml_sax_context(void *context); #endif