1 #define GETDATA_INCLUDE 2 3 #ifndef RECOMBINE_INCLUDE 4 #include "recombine.h" 5 #endif 6 7 #define OUTLINESIZE 50 /* the maximum number of characters allowed 8 for line-output used in printdnadata */ 9 10 char uppercase(char ch); 11 12 void setupdata(data_fmt *data, char datatype, long numpop, long numloci, 13 long numind, long *numsites, char *title); 14 void freedata(data_fmt *data); 15 long getdata_nummarkers(option_struct *op, data_fmt *data); 16 long getdata_numtips(option_struct *op, data_fmt *data); 17 long getdata_numseq(option_struct *op, data_fmt *data); 18 long getdata_numloci(option_struct *op, data_fmt *data); 19 long getdata_numpop(option_struct *op, data_fmt *data); 20 long getdata_sitecount(option_struct *op, data_fmt *data, long marker); 21 long getdata_markersite(option_struct *op, data_fmt *data, long marker); 22 double getdata_space(option_struct *op, data_fmt *data, long target); 23 24 void read_spacefile(FILE *file, option_struct *op, data_fmt *data); 25 int longcmp (const void *v1, const void *v2); 26 int doublecmp (const void *v1, const void *v2); 27 void read_flipfile(option_struct *op, data_fmt *data, tree *tr, FILE *file); 28 void pruneflips(option_struct *op, data_fmt *data, tree *tr); 29 30 31 void read_data(FILE *infile, data_fmt *data, char datatype, long pop); 32 void setpopstuff(data_fmt *data, long pop, long numind, 33 char *poptitle, char datatype); 34 void read_popdata(FILE *infile, data_fmt *data, long pop, 35 option_struct *op); 36 void read_indname(FILE *infile, data_fmt *data, long pop, long lowcus, 37 long ind, long namelngth, char datatype); 38 39 void read_microalleles(FILE *infile, msatdata *data, long pop, 40 long ind); 41 42 long read_ind_seq(FILE *infile, dnadata *data, option_struct *op, 43 long lowcus, long pop, long ind, long baseread); 44 void finish_read_seq(FILE *infile, data_fmt *data, option_struct *op, 45 long pop, long baseread); 46 47 void setupdnadata(dnadata **dna, long *sites, long numseq, long numloci, 48 long numpop); 49 void freednadata(dnadata *dna); 50 void printdnadata(option_struct *op, data_fmt *data, FILE *out); 51 void initinvartips(option_struct *op, data_fmt *data, long categs, 52 tree *curtree); 53 void makednavalues(option_struct *op, data_fmt *data, long categs, 54 tree *curtree); 55 void empiricaldnafreqs(option_struct *op, data_fmt *data, tree *curtree); 56 void getbasednafreqs(dnadata *dna, option_struct *op, double 57 locus_ttratio, FILE *outfile); 58 void inputdnaweights(long numchars, dnadata *dna, option_struct *op); 59 60 long hapdist(option_struct *op,data_fmt *hap1, data_fmt *hap2, creature *critter); 61 void readtruehaps(option_struct *op, data_fmt *hap, long numpop, long 62 numloci, long numind, long *numsites); 63 void copyhaps(option_struct *op, data_fmt *oldhap, data_fmt *newhap, 64 long numpop, long numloci, long numind, long *numsites); 65