profile.h

#include <stdio.h>

//size of all hash tables made
#define HASHSIZE 31
//size of char array holding helix id
#define ARRAYSIZE 20
//default noise threshold in percent; used to define h and p
#define DEF_NOISE 10
//default value that looking for h dropoff starts at (in percent)
#define H_START 10
//default value that looking for p dropoff starts at (in percent)
#define P_START 5
//default minimum significant helix size
#define DEF_MIN_HEL_LEN 1
//default frequency threshold in percentage
#define DEF_THRESH_FREQ 10.0
//default frequency for a helix to be a given
#define DEF_THRESH_COMMON 99.0
//default total number of freq helices
#define DEF_NUMFREQ 7
//default profile frequency threshold in percentage
#define DEF_PROF_FREQ 2.0
//default percentage of structures represented by final profiles
#define DEF_THRESH_STRUCT 85.0
//initial size of memory allocated = ARRAYSIZE * SIZE
#define INIT_SIZE 2
//default output file name
#define DEF_OUTPUT "profile.dot"

extern HASHTBL *bp;
extern HASHTBL *marginals;
extern HASHTBL *idhash;
extern HASHTBL *freq;
extern HASHTBL *cluster;
extern HASHTBL *binary;
extern HASHTBL *bracket;
extern HASHTBL *avetrip;
extern HASHTBL *freqprofs;
//file name to write output
extern char *OUTPUT;
//file name contains input structure(s)
extern char *INPUT;
//file name contains native structure
extern char *NATIVE;
//if filter is 1, keep number of freq helices under 10
extern int FILTER; 
//defines h and p st they cut off no more than NOISE percentage of area  
extern int NOISE;
//if 1, prints additional info
extern int VERBOSE;
//minimum size a helix must be to be considered significant
extern int MIN_HEL_LEN;
//if freq > thresh_freq, is significant (in percentage)
extern double THRESH_FREQ;
//if freq > thresh_common, assume is in everything
extern double THRESH_COMMON;
//limit to number of frequent helices
extern int NUMFREQ;
//limit to number of profiles made
extern int NUMPROF;
//profiles must have freq at least PROF_FREQ
extern double PROF_FREQ;
//number of structures processed; sfold generates 1000
extern int NUMSTRUCTS;
//lower bound for percent of structures represented by final profiles
extern double THRESH_STRUCT;
//sets minimum length a freq helix must be
extern int LENGTH;
//makes triplet stats in process_structs
extern int STATS;
//turns on or off making representative structures by consensus
extern int REP_STRUCT;

typedef struct linkedlist {
  int data;
  struct linkedlist *next;
} LIST;

//in cluster.c
char* input_seq(char *seqfile);
int process_structs(char *seqfile,char *name);
void longest_possible(int i,int j,int k,int id);
int match(int i,int j);
void reorder_helices(int total);
double set_h_dropoff(HASHTBL *hash, int start);
int print_all_helices(int total);

char** find_freq(int total);
double calc_entropy(int marg);
int charcompare(const void *v1, const void *v2);
void filter(char *key,char **mostfreq, int count);
int freqcompare(const void *v1, const void *v2);
int binsearch(char **mostfreq, char *key);
void freq_insert(char *key,int marg,int length);
//int make_graph(HASHTBL *marg, HASHTBL *max,HASHTBL *idhash,int total, char *name, FILE *fp);
int make_profiles(char *name);
void make_rep_struct(char *profile, char* trips);
int print_profiles();
int select_profiles(char **mostfreq,int notcommon);
int profcompare(const void *v1, const void *v2);
char* process_profile(HASHTBL *halfbrac,char *profile,int numhelix,int *size);
void make_brackets(HASHTBL *brac, int i, int j, int id);
void make_bracket_rep(HASHTBL *brac,char *profile);
char* resize(int *size,int total,char *s);
char* quicksort(char *profile,char *dup);
int compare(const void *v1, const void *v2);
char* strcat_front(char *s, char *ct);
void prune_profiles(char **mostfreq);
char *delete_helix(char *origprof, char *least,char *modprofile, int *m);
void find_consensus();
int print_consensus(char *seqfile);
int print_cluster(char *seqfile);