#ifndef MAKE_MOMO_MOTIFS_H #define MAKE_MOMO_MOTIFS_H #include "alphabet.h" #include "array-list.h" #include "projrel.h" #include "utils.h" #include "hash_table.h" static const int MAX_ALPH_SIZE = 100; // Structure for tracking momo command line parameters. typedef enum filtertype { Le, // <= Lt, // < Eq, // = Gt, // > Ge // >= } FILTERTYPE_T; static const char *filtertype_names[] = {"<=", "<", "=", ">", ">="}; // Structure for tracking momo command line algorithm. typedef enum algorithm { No_algorithm, Unknown_algorithm, Simple, Motifx, Modl } ALGORITHM_T; static const char *algorithm_names[] ={"No algorithm", "Unknown algorithm", "simple", "motif-x", "MoDL"}; // Structure for tracking momo command line parameters. typedef enum filetype { Psm, Fasta, Raw } FILETYPE_T; static const char *filetype_names[] = {"PSM", "FASTA", "Raw"}; // Structure for tracking momo command line parameters. typedef struct options { ALGORITHM_T algorithm; ARRAYLST_T* phospho_filenames; // List of filenames containg PSMs. ARRAYLST_T* phospho_filesizes; // List of file sizes of above. bool allow_clobber; // Allow overwritting of files in output directory. bool filter; // Filter? bool db_background; // Use protein database as background (rather than shuffled foreground). bool hash_fasta; // Use a O(1) lookup table on protein database to speed up search bool remove_unknowns; // Remove sequences with unknown flanks bool single_motif_per_mass; // Create a single motif per mass ? bool harvard; // mimic original motif-x behavior by // truncating binomial p-value at 1e-16 and subtracting count*1e-6 // from log_p; this sorts ties by the number of matching peptides bool printp; // print normalized p-values for debuggin char* command_line; // Full command line char* filter_field; // Field to filter on char* html_path; // Path to MOMO HTML output file char* output_dirname; // Name of the output directory char* protein_database_filename; // Name of file file containg protein fasta database. char* psm_type; // Type of PSM file char* sequence_column; // Sequence column name in psm file char* text_path; // Path to MOMO motifs in meme format char* tsv_path; // Path to MOMO TSV output file char* paper; // Name of paper to cite. char* link; // Link of paper to cite. const char* HTML_FILENAME; // Name of HTML output file. const char* TEMPLATE_FILENAME; // Name of HTML template file. const char* TEXT_FILENAME; // Name of motifs in MEME format output file. const char* TSV_FILENAME; // Name of TSV output file. const char* usage; // Usage statment double filter_threshold; // Threshold to Filter on double score_threshold; // Motif-X Score Threshold FILETYPE_T filetype; // Type of PSM input file FILETYPE_T bg_filetype; // Type of protein database background file FILTERTYPE_T filter_type; // Type to filter int seed; // Random number seed int eliminate_repeat_width; // Eliminate Repeat length int hash_fasta_width; // Kmer length used for O(1) lookup table int max_iterations; // Maximum number of iterations for modl int max_motifs; // Maximum number of motifs for modl int min_occurrences; // Number of Occurrences int max_no_decrease; // Number of iterations of no decrease in MDL before stopping algorithm int width; // Motif Width int verbosity; } MOMO_OPTIONS_T; // Structure for tracking summary of results typedef struct summary { unsigned long num_mod; // Number of Modifications unsigned long num_modtype; // Number of Types of Modification unsigned long num_mod_passing; // Number of Modifications After Filtering unsigned long num_modtype_passing; // Number of Types of Modifications After Filtering unsigned long num_bg_mod; // Number of Background Modifications HASH_TABLE mod_table; // Hashes mod name to a modinfo struct ARRAYLST_T * mod_table_keys; // Arraylist containing pointers to mod_table key entries HASH_TABLE hash_fasta_table; // O(1) lookup table for sequences in protein database ALPH_T * alph; // Alphabet Used const char* alph_letters; ARRAY_T * bg_freqs; // Background frequencies (from protein database if provided) } SUMMARY_T; // Structure containing information for a given mod type typedef struct modinfo { char *mod_name; // Name of mod unsigned long mod_occurrences; // Number of times this mod occurs in the file ARRAYLST_T *seq_list; // If eliminate repeats, then this will be the keys // for seq_table. Otherwise, it is a list of sequences that pass filters HASH_TABLE seq_table; // If eliminate repeats, will hash from char* representation // for sequences of length eliminate_repeats that pass filters to respective // sequences. ARRAYLST_T *shuf_seq_list; // Shuffled foreground sequences. HASH_TABLE shuf_seq_table; // Shuffled foreground sequences. ARRAYLST_T *bg_seq_list; // From background file. HASH_TABLE bg_seq_table; // From background file. ARRAYLST_T *motifinfos; // the list of motifs for this mod. bool *amino_acids; // a boolean array for each amino acid. true if this mod is associated with the // amino acid. false otherwise. ARRAYLST_T* modl_ops; // Only used for MoDL algorithm. Contains a list of MODL_STEP_T*. } MOD_INFO_T; typedef struct motifinfo { MOTIF_T* motif; // Motif ARRAYLST_T* seqs; // Sequences that make up this motif double score; // motif score int n_tests; // number of tests made during search for motif int fg_matches; // matches in remaining foreground sequences (harvard-style) int fg_size; // possible sites in in remaining foreground sequences int bg_matches; // matches in remaining background sequences int bg_size; // possible sites in remaining background sequences int afg_matches; // matches in all foreground sequences int afg_size; // possible sites in in all foreground sequences int abg_matches; // matches in all background sequences int abg_size; // possible sites in in all background sequences } MOTIF_INFO_T; #endif