funcs.h

hmmer源程序

 * Miscellaneous functions with no home
 */
extern char *Getword(FILE *fp, int type); 
extern char *Getline(char *s, int n, FILE *fp);
extern int   SetAutocuts(struct threshold_s *thresh, struct plan7_s *hmm);

/* from modelmakers.c
 * Model construction algorithms
 */
extern void P7Handmodelmaker(MSA *msa, char **dsq, struct plan7_s **ret_hmm,
			     struct p7trace_s ***ret_tr);
extern void P7Fastmodelmaker(MSA *msa, char **dsq, 
			     float maxgap, struct plan7_s **ret_hmm, 
			     struct p7trace_s ***ret_tr);
extern void P7Maxmodelmaker(MSA *msa, char **dsq, 
			    float maxgap, struct p7prior_s *prior, 
			    float *null, float null_p1, float mpri, 
			    struct plan7_s **ret_hmm,
			    struct p7trace_s  ***ret_tr);

/* from plan7.c
 * Plan7 HMM structure support
 */
extern struct plan7_s *AllocPlan7(int M);
extern struct plan7_s *AllocPlan7Shell(void);
extern void AllocPlan7Body(struct plan7_s *hmm, int M);
extern void FreePlan7(struct plan7_s *hmm);
extern void ZeroPlan7(struct plan7_s *hmm);
extern void Plan7SetName(struct plan7_s *hmm, char *name);
extern void Plan7SetAccession(struct plan7_s *hmm, char *acc);
extern void Plan7SetDescription(struct plan7_s *hmm, char *desc);
extern void Plan7ComlogAppend(struct plan7_s *hmm, int argc, char **argv);
extern void Plan7SetCtime(struct plan7_s *hmm);
extern void Plan7SetNullModel(struct plan7_s *hmm, float null[MAXABET], float p1);
extern void P7Logoddsify(struct plan7_s *hmm, int viterbi_mode);
extern void Plan7Renormalize(struct plan7_s *hmm);
extern void Plan7RenormalizeExits(struct plan7_s *hmm);
extern void Plan7NakedConfig(struct plan7_s *hmm);
extern void Plan7GlobalConfig(struct plan7_s *hmm);
extern void Plan7LSConfig(struct plan7_s *hmm);
extern void Plan7SWConfig(struct plan7_s *hmm, float pentry, float pexit);
extern void Plan7FSConfig(struct plan7_s *hmm, float pentry, float pexit); 
extern void PrintPlan7Stats(FILE *fp, struct plan7_s *hmm, char **dsq, 
			    int nseq, struct p7trace_s **tr);
extern int  DegenerateSymbolScore(float *p, float *null, int ambig);
extern void Plan9toPlan7(struct plan9_s *hmm, struct plan7_s **ret_plan7);

/* 
 * from plan9.c
 * Backwards compatibility for the Plan 9 data structures of HMMER 1.x
 */
extern struct plan9_s *P9AllocHMM(int M);
extern void P9ZeroHMM(struct plan9_s *hmm);
extern int  P9FreeHMM(struct plan9_s *hmm);
extern void P9Renormalize(struct plan9_s *hmm);
extern void P9DefaultNullModel(float *null);

/* 
 * from postprob.c
 * Functions for working with posterior probabilities within alignments
 */
extern float P7OptimalAccuracy(char *dsq, int L, struct plan7_s *hmm, struct p7trace_s **ret_tr);
extern float P7Backward(char *dsq, int L, struct plan7_s *hmm, 	struct dpmatrix_s **ret_mx);
extern void  P7EmitterPosterior(int L, struct plan7_s *hmm, struct dpmatrix_s *forward,
				struct dpmatrix_s *backward, struct dpmatrix_s *mx);
extern float P7FillOptimalAccuracy(int L, int M, struct dpmatrix_s *posterior,
				   struct dpmatrix_s *mx, struct p7trace_s **ret_tr);
extern void  P7OptimalAccuracyTrace(int L, int M, struct dpmatrix_s *posterior,
				    struct dpmatrix_s *mx, struct p7trace_s **ret_tr);
extern char *PostalCode(int L, struct dpmatrix_s *mx, struct p7trace_s *tr);

/* from prior.c
 * Dirichlet priors
 */
extern struct p7prior_s *P7AllocPrior(void);
extern struct p7prior_s *P7LaplacePrior(void);
extern struct p7prior_s *P7DefaultPrior(void);
extern struct p7prior_s *P7ReadPrior(char *prifile);
extern void P7FreePrior(struct p7prior_s *pri);
extern void PAMPrior(char *pamfile, struct p7prior_s *pri, float pamwgt);
extern void P7DefaultNullModel(float *null, float *ret_p1);
extern void P7ReadNullModel(char *rndfile, float *null, float *ret_p1);
extern void P7PriorifyHMM(struct plan7_s *hmm, struct p7prior_s *pri);
extern void P7PriorifyTransitionVector(float *t, struct p7prior_s *prior, 
				       float tq[MAXDCHLET]);
extern void P7PriorifyEmissionVector(float *vec, struct p7prior_s *pri, 
				     int num, float eq[MAXDCHLET], 
				     float e[MAXDCHLET][MAXABET],
				     float *ret_mix);


#ifdef HMMER_PVM
/* from pvm.c
 * PVM Parallel Virtual Machine implementation
 */
extern void              PVMSpawnSlaves(char *slave, int **ret_tid, int *ret_nslaves);
extern void              PVMConfirmSlaves(int *slave_tid, int nslaves);
extern void              PVMCheckSlaves(int *slave_tid, int nslaves);
extern void              PVMKillSlaves(int *slave_tid, int nslaves);
extern int               PVMPackString(char *s);
extern char *            PVMUnpackString(void);
extern int               PVMPackTrace(struct p7trace_s *tr);
extern struct p7trace_s *PVMUnpackTrace(void);
extern int               PVMPackHMM(struct plan7_s *hmm);
extern struct plan7_s *  PVMUnpackHMM(void);
#endif /*HMMER_PVM*/

#ifdef HMMER_THREADS
/* from threads.c
 * POSIX threads implementation
 */
extern int   ThreadNumber(void);
#endif /*HMMER_THREADS*/


/* from tophits.c
 * Support for keeping/sorting top scoring hit/alignment lists
 */
extern struct tophit_s *AllocTophits(int lumpsize);
extern void   GrowTophits(struct tophit_s *h);
extern void   FreeTophits(struct tophit_s *h);
extern struct fancyali_s *AllocFancyAli(void);
extern void   FreeFancyAli(struct fancyali_s *ali);
extern void   RegisterHit(struct tophit_s *h, double sortkey, 
			  double pvalue, float score, 
			  double motherp, float mothersc,
			  char *name, char *acc, char *desc, 
			  int sqfrom, int sqto, int sqlen, 
			  int hmmfrom, int hmmto, int hmmlen, 
			  int domidx, int ndom, 
			  struct fancyali_s *ali);
extern void GetRankedHit(struct tophit_s *h, int rank, 
			 double *r_pvalue, float *r_score, 
			 double *r_motherp, float *r_mothersc,
			 char **r_name, char **r_acc, char **r_desc,
			 int *r_sqfrom, int *r_sqto, int *r_sqlen,
			 int *r_hmmfrom, int *r_hmmto, int *r_hmmlen,
			 int *r_domidx, int *r_ndom,
			 struct fancyali_s **r_ali);
extern int    TophitsMaxName(struct tophit_s *h);
extern void   FullSortTophits(struct tophit_s *h);
extern void   TophitsReport(struct tophit_s *h, double E, int nseq);

/* from trace.c
 * Support for traceback (state path) structure
 */
extern void  P7AllocTrace(int tlen, struct p7trace_s **ret_tr);
extern void  P7ReallocTrace(struct p7trace_s *tr, int tlen);
extern void  P7FreeTrace(struct p7trace_s *tr);
extern void  TraceSet(struct p7trace_s *tr, int tpos, char type, int idx, int pos);
extern struct p7trace_s **MergeTraceArrays(struct p7trace_s **t1, int n1, struct p7trace_s **t2, int n2);
extern void  P7ReverseTrace(struct p7trace_s *tr);
extern void  P7TraceCount(struct plan7_s *hmm, char *dsq, float wt, 
			  struct p7trace_s *tr);
extern float P7TraceScore(struct plan7_s *hmm, char *dsq, struct p7trace_s *tr);
extern MSA  *P7Traces2Alignment(char **dsq, SQINFO *sqinfo, float *wgt, 
				int nseq, int M, 
				struct p7trace_s **tr, int matchonly);
extern int  TransitionScoreLookup(struct plan7_s *hmm, char st1, 
				  int k1, char st2, int k2);
extern struct fancyali_s *CreateFancyAli(struct p7trace_s *tr, struct plan7_s *hmm,
					 char *dsq, char *name);
extern void PrintFancyAli(FILE *fp, struct fancyali_s *ali);
extern void TraceDecompose(struct p7trace_s *otr, struct p7trace_s ***ret_tr,
			   int *ret_ntr);
extern int  TraceDomainNumber(struct p7trace_s *tr);
extern void TraceSimpleBounds(struct p7trace_s *tr, int *ret_i1, int *ret_i2, 
			      int *ret_k1,  int *ret_k2);
extern struct p7trace_s *MasterTraceFromMap(int *map, int M, int alen);
extern void ImposeMasterTrace(char **aseq, int nseq, struct p7trace_s *mtr, 
			      struct p7trace_s ***ret_tr);


#endif /*FUNCSH_INCLUDED*/