#ifndef GLOBALS_H
#define GLOBALS_H
/** user specified compilation parameters  **/
#undef USERHOD /* define (undef), uses (does not use) correlation of delta  */
#define MUNONNEG /* define (undef), restricts (does not restrict) mu_x, mu_y to be non-negative on mu optimization */
/*** end user specified compilation compilation parameters **/
#include <stdio.h>
#include <stdlib.h>
#include <time.h>
#include "util.h" 

#define NRANSI

/** global variables **/
extern int Nheader; 
/* Number of lines in header */
/* declared here since it will be used by output routine write_llr */

extern bool RunVERA;
extern bool RunSAM;
extern bool alt_sam;
extern CString temp_in_model, VERA_input, ALT_SAM_INPUT;
extern double new_eps_beta;
extern bool disp_iter;  /* flag=1 to display progress of iterations run */
extern bool s_disp_iter;  /* flag=1 to display progress of iterations run */
extern bool start_mod;  /* flag=1  if starting guess to be used for optimization */
extern bool evolution;  /* flag=1 to display parameter evolution during optimization */
extern bool stop_crit; /* flag=1 to specify stop criterion for optimization */
extern int N;  /* number of genes, maximum no. of repeats */
extern char **yorf; /* unique gene name identifiers for each gene */
extern char **gene_name; /* common use gene name */ 
extern int *m; /* number of samples for each gene */
extern float **X, **Y, *muX, *muY; /* intensities for all genes&repeats and mu parameters for all genes*/
extern int *m1, *m2; /* number of samples in each case for reference comparison */
extern float **X1, **Y1, **X2, **Y2; /* intensities for data sets involved in reference comparison */
extern float LINMIN_TOL; /* tolerance for linmin.c */
extern double *cov;   /* parameters of covariance matrix */
extern double *cov1, *cov2;   /* parameters of covariance matrices for reference sample comparisons */

extern int gene_index; /* gene index for Z_gene.c and gradZ_gene.c */
extern int gene_index_1, gene_index_2; /* gene index needed for two sample comparisons */
extern int Nfull, *full2internal, *internal2full; 
/* total number of genes in original data set Nfull and mapping to N genes used for internal code  */
                          /* full2internal[i] = -1 if gene i was excluded */

#ifdef USERHOD
#define NDIM 6 /* number of dimensions for gamma */
#else
#define NDIM 5
#endif

#define NDIM_MU 2 /* number of dimensions for single gene mu_x mu_y */



#endif