#include<stdio.h>
#include"dictionary.h"

typedef struct {
  char *chr;
  int Nsites;
  int *site;
  char *ok;
  int Ncol;
  int max;
  char **col;
  char **allele;
  char ***complete;
  int *index;
  char **sdp;
} ALLELE_DATA;

typedef struct {
  int chr, from, to, id;
  double error;
} SEGMENTS;

typedef struct {
  int id, acc, chr, frombp, tobp, fromsite, tosite, errors;
} MOSAIC_SEGMENT;

typedef struct {
  char *name;
  int len;
  int *bp;
  int *chr;
  int nchr;
  char **chroms;
  char *allele;
  char *ref;
  char **founder;
  int Nfounders;
  char **founder_name;
  int *chr_start;
  int *chr_end;
  SEGMENTS **mosaic;
  int *nseg;
} SEQ_CALL;

typedef struct {
  int nsegmax, nsegs, nseqs;
  MOSAIC_SEGMENT *seg;
  int *idx;
  DICTIONARY *dict_ids;
  DICTIONARY *dict_accs;
} MOSAIC;

typedef struct {
  int nobs;
  char **id;
  double *x;
  char *name;
} PHENOTYPE_TABLE;

typedef struct {
  int nseq, nsdp, nsite, chr, haplotype, uncompressed;
  char **mat;
  char **id;
  int *sdp;
  int *site;
} BINARY_DATA;

typedef struct {
  double *logP;
  int *chr;
  int *bp;
  int *site;
  int N;
} SCAN_DATA;

typedef struct {
  int nalleles;
  int *allele;
  double *estimate;
  int *count;
  double logP;
  double sigma;
} SCAN_STATISTICS;

typedef struct {
  int nlevels, nobs, debug;
  double TSS, FSS, RSS, df, rdf, F, log10pval, gm;
  double N[256], mean[256], SS[256];
} ANOVA_TABLE;

     
typedef struct {
  int idx;
  char *id;
}  CHAR_INDEX;

typedef struct {
  int nperm, nobs;
  double **y;
  double *maxlogP;
  double q50, q90, q95, pval;
  double mx;
} PERMUTATIONS;

ALLELE_DATA *ReadAlleleData( char *fileame, int format );
ALLELE_DATA **ReadGenomeAlleleData( char *dir, char *maskfile, int format, int nchr, char **chroms );
SEQ_CALL **ReadSeqCalls( char *dir, char *suffix, ALLELE_DATA **add, int nchr, char **chroms, int *nseq );
SEQ_CALL *ReadSeqCall( char *filename, ALLELE_DATA **add, int nchr, char **chroms );
void FreeSeqCall ( SEQ_CALL *sq );
SEGMENTS *ReadGFF( char *filename, int *nsegments );
int ReconstructMosaicDiploid( SEQ_CALL *sq, int penalty, int chr, char *chrom, FILE *fp );
int ReconstructMosaic( SEQ_CALL *sq, int penalty, int chr, char *chrom, FILE *fp, int backcross );
int IntersectIds ( char **id1, char **id2, int N1, int N2, int**Index1, int **Index2 );
BINARY_DATA *ReadBinaryData( char *filename );
BINARY_DATA **ReadBinaryGenome( int nchr, char *dir, int uncompressed, int haplotype );
PHENOTYPE_TABLE *ReadPhenotype( char *filename, char *phenotype );
PHENOTYPE_TABLE **ReadPhenotypes( char *filename, char **phenotypes, int nphen );
double OneWayAnovaLog10pval( int nobs, double *phenotype, char *genotype, double *residuals, int *df, ANOVA_TABLE *anova );
SCAN_STATISTICS *ChromosomeScan(  PHENOTYPE_TABLE *pt, BINARY_DATA *bd, PERMUTATIONS *perm );
SCAN_STATISTICS **GenomeScan( PHENOTYPE_TABLE *pt, BINARY_DATA **genome, int nchr,PERMUTATIONS *perm  );
void FreeScanStatistics( SCAN_STATISTICS *stats, int len );
char **TheChromosomes( char *species, int *nchr  );
void ProcessSeqCalls( char *dir, char *suffix, ALLELE_DATA **add, int nchr, char **chroms, int *nseq, int penalty, int backcross, int diploid, FILE *outfp, double window );

double FDistribution(double f, int v1, int v2);
double CompFDistribution(double f, int v1, int v2);
void InitFcache( int df );
double Log10Fpval( double F, double df1, double df2 );
double OneWayAnovaLog10pvalFast( double *phenotype, char *genotype, ANOVA_TABLE *an);

void WriteGenomeScan( SCAN_STATISTICS **stats, int nchr, BINARY_DATA **genome, char *filename, double threshold );
void WriteGenomeScanEstimate( SCAN_STATISTICS **stats, int nchr, BINARY_DATA **genome, ALLELE_DATA **ad, char *filename, double threshold );
void WriteHaplotypeGenomeScanEstimate( SCAN_STATISTICS **stats, int nchr, BINARY_DATA **genome,  char *filename, double threshold );

static int sdpcmp( const void *a, const void *b );
char *suffix( char *s, char sep );
SCAN_DATA *ForwardSelection( PHENOTYPE_TABLE *pt, int nchr, BINARY_DATA **gd, ALLELE_DATA **ad, SCAN_STATISTICS **stats, double thresh, char *outfile ); 
SCAN_DATA *NewScanData(int N );
SCAN_DATA *PopulateScanData ( BINARY_DATA **gd, SCAN_STATISTICS **stats, int nchr, double thresh  );
ALLELE_DATA *ReadBinaryAlleleData( char *filename, int index_all );
ALLELE_DATA **ReadAllBinaryAlleleData( char *dir, int index_all, int nchr, char **chroms );
int WriteBinaryAlleleData( ALLELE_DATA *ad, char *filename );
int scan_data_cmp( const void *A, const void *B);
int scan_data_cmp2( const void *A, const void *B);
void WriteAnnotatedScan( PHENOTYPE_TABLE *pt, int nchr, SCAN_STATISTICS **stats, BINARY_DATA **bd, ALLELE_DATA **ad, double thresh, int max, char *filename );
int WriteLarsData(  PHENOTYPE_TABLE *pt, SCAN_STATISTICS **stats, int nchr, BINARY_DATA **genome, char *filename, double threshold );
int WriteSeqCalls ( SEQ_CALL **sq, int n, char *dir );
int WriteSeqCall( char *filename, SEQ_CALL *sq);
int idx_cmp( const void *A, const void *B);
void ImputeGenomes( ALLELE_DATA **add, int nchr, char **chroms, SEQ_CALL **sqq, int nseq, char *dir);


double PermutationPvalue( double **logP, PHENOTYPE_TABLE *pt, BINARY_DATA **genome, int nchr, int nperm, double *q50, double *q90, double *q95, double *mx );
PHENOTYPE_TABLE *PermutePhenotypes( PHENOTYPE_TABLE *pt, int in_place );
double *PermutedGenomeScans( PHENOTYPE_TABLE *pt, BINARY_DATA **genome, int nchr, int nperm );
PERMUTATIONS *MakePermutations( PHENOTYPE_TABLE *pt, BINARY_DATA *bd, int nperm );
void FreePermutations( PERMUTATIONS *perm );
int pair_cmp( const void *A, const void *B);
int double_cmp( const void *A, const void *B);
void PermuteArray( int *array, int n );
double surand();
double urand(double low, double high);
double genexp(double lambda);
double gennor();

void ImputeFromMosaic( MOSAIC *mosaic,  ALLELE_DATA **ad, int nchr, char *outdir );
MOSAIC *ReadMosaic( char *mosaicfile, char **strings, int nstrings );
int **IUBcodes();