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/***************** seqset.h - sequence set data type. ********************/
/*************************** Sequence Set ADT ******************************
Define: P = <S,A>
where
S is a set of sequences
A is the sequence alphabet
**************************************************************************/
#if !defined (SEQSET)
#define SEQSET
#include "stdinc.h"
#include "afnio.h"
#include "alphabet.h"
#include "karlin.h"
#include "sequence.h"
#include "random.h"
/******************************* PRIVATE ***********************************/
/****************************** seqset type ****************************/
typedef struct {
char *name; /* input filename for entities */
e_type *entity; /* array of sequence entities */
long nent; /* number of input entities */
long max_leng; /* sequence entity maximumlength */
long min_leng; /* sequence entity minimum length */
Boolean xnu; /* has data been xnu'ed? */
long *counts; /* number of b residues */
long total; /* total # residues */
double *tfreq; /* residue total freqs for seqs */
a_type A; /* sequence alphabet */
} seqset_type;
typedef seqset_type *ss_type;
/******************************* private *************************************/
void seqset_error(char *s);
ss_type calcseqsetfreq(ss_type P);
ss_type xnu_seqset(ss_type P);
long count_seqset_entities(FILE *fptr, ss_type P,long nsize[]);
FILE *OpenSeqSetFile(ss_type P);
ss_type seqset(char *filename,a_type A);
ss_type fptr_seqset(FILE *fptr,a_type A);
ss_type SeqSet_fptr(FILE *fptr,a_type A);
ss_type MkXnuSeqSet_fptr(FILE *fptr,a_type A);
/******************************* PUBLIC *************************************/
/************************** seqset operations ***************************/
ss_type SeqSet(char *name,a_type A);
ss_type SeqSet1(char *filename,e_type E,a_type A);
ss_type MkXnuSeqSet(char *filename,a_type A);
ss_type MkXnuSeqSet1(char *filename,e_type E,a_type A);
ss_type RmSeqSet(e_type E, ss_type P);
ss_type NilSeqSet(ss_type P);
double SeqSetEntropy(ss_type P);
long *LengthsSeqSet(ss_type P);
ss_type PutSeqSet(FILE *fptr,ss_type P); /* show seqset data */
ss_type PutSeqSetPIDs(FILE *fptr, ss_type P);
ss_type PutSeqSetEs(FILE *fptr,ss_type P);
ss_type PutSeqSetE(FILE *fptr,long i, ss_type P);
ss_type PutSeqSettFreqs(FILE *fptr,ss_type P);
ss_type ShuffleSeqSet(ss_type P); /* shuffle seqset */
ss_type ShuffleSeqSet2(ss_type P);
double LogL0SeqSet(ss_type P);
/************************** sequence set defines ***************************/
#define MAX_NUMBER_SEQS 15000
#define SeqSetA(P) (P->A)
#define nLetSeqSet(P) (nAlpha(P->A))
#define CountsSeqSet(r,P) ((P)->counts[(r)])
#define TotalSeqSet(P) ((P)->total)
#define tFreqSeqSet(P) ((P)->tfreq)
#define SeqP(n,i,P) ResSeq(i,(P)->entity[(n)])
#define NSeqsSeqSet(P) ((P)->nent)
#define SqLenSeqSet(n,P) LenSeq((P)->entity[(n)])
#define SeqSeqSet2(n,P) SeqPtr((P)->entity[(n)])
#define SeqSeqSet(n,P) XnuSeqPtr((P)->entity[(n)])
#define SeqSetE(n,P) ((P)->entity[(n)])
#define NameSeqSet(P) ((P)->name)
#define MinSeqSeqSet(P) ((P)->min_leng)
#define MaxSeqSeqSet(P) ((P)->max_leng)
#define CntsSeqSet(P) ((P)->counts)
#define XnuSeqSet(P) xnu_seqset(P)
#endif
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