/*****************************************************************************
   Major portions of this software are copyrighted by the Medical College
   of Wisconsin, 1994-2000, and are released under the Gnu General Public
   License, Version 2.  See the file README.Copyright for details.
******************************************************************************/

#ifndef _MCW_CS_STUFF_HEADER_
#define _MCW_CS_STUFF_HEADER_

/*----- Miscellaneous "computer science" stuff
        [legacy of when I was a professor of Computer Science -- RWCox] -----*/

#include <stdlib.h>
#include <stdio.h>
#include <unistd.h>
#include <math.h>

#include "mcw_malloc.h"

#ifdef  __cplusplus
extern "C" {
#endif

/***** Quicksort routines in various flavonoids *****/

extern void qsort_floatint  ( int , float *  , int * ) ;
extern void qsort_doubleint ( int , double * , int * ) ;
extern void qsort_intint    ( int , int *    , int * ) ;
extern void qsort_floatfloat( int , float *  , float * ) ;  /* 30 Jan 2000 */
extern void qsort_floatstuff( int , float *  , void ** ) ;  /* 06 Feb 2000 */
extern void qsort_doublestuff( int, double * , void ** ) ;  /* 18 Dec 2006 */

/***** Quicksort-ish median *****/

extern float qmed_float     ( int , float * ) ;
extern void  qmedmad_float  ( int,float *,float *,float * ) ; /* 08 Mar 2001 */
extern void  meansigma_float( int,float *,float *,float * ) ; /* 07 Dec 2006 */

/***** Eigensolutions *****/

extern void symeig_double( int , double * , double * ) ;
extern void symeigval_double( int , double * , double * ) ;
extern void svd_double( int, int, double *, double *, double *, double * ) ;
extern void svd_float ( int, int, float *, float *, float *, float * ) ;
extern void set_svd_sort(int) ;

extern void symeig_3( double *, double *, int ) ;  /* 30 Sep 2005 */
extern void symeig_2( double *, double *, int ) ;
extern void symeig_forbid_23( int ) ;

/***** Argument list mangling *****/

extern void addto_args( int , char ** , int * , char *** ) ;
extern void append_string_to_args ( char *, int, char **, int *, char *** ) ;
extern void prepend_string_to_args( char *, int, char **, int *, char *** ) ;

/***** Misc stuff *****/

extern void get_laguerre_table( int , double ** , double ** ) ;  /* 12 Mar 2000 */

extern int qhull_wrap( int , float * , int ** ) ; /* 07 Jun 2001 */
extern int sphere_voronoi_angles( int , float *, float *, float ** ) ;
extern int sphere_voronoi_vectors( int , float *, float ** ) ;

extern float cl1_solve    ( int, int, float *, float **, float *,int ) ; /* cl1.c */
extern float cl1_solve_res( int, int, float *, float **, float *,int, float*,int ) ; /* cl1.c */

extern int powell_newuoa( int ndim , double *x ,
                          double rstart , double rend ,
                          int maxcall , double (*ufunc)(int,double *) ) ;
extern void powell_set_mfac( float mm , float aa ) ;
extern void powell_set_verbose( int ) ;
extern int powell_newuoa_con( int ndim , double *x , double *xb, double *xt ,
                              int nrand, double rstart , double rend ,
                              int maxcall , double (*ufunc)(int,double *) ) ;

extern int powell_newuoa_constrained(
                               int ndim, double *x, double *cost ,
                               double *xbot, double *xtop ,
                               int nrand, int nkeep, int ntry ,
                               double rstart , double rend ,
                               int maxcall , double (*ufunc)(int,double *) ) ;

extern char *approximate_number_string( double ) ;  /* 16 Jan 2004 */

extern int strcmp_aboot( char * , char * ) ;        /* 12 Mar 2007 */

#ifndef DEBLANK
#define DEBLANK(cc) do{ if( (cc) != NULL ){                   \
                          char *qc ;                          \
                          for( qc=(cc) ; *qc != '\0' ; qc++ ) \
                            if( isspace(*qc) ) *qc = '_' ;    \
                       }} while(0)
#endif

typedef struct {
      float x;
      int Index;
} Z_QSORT_FLOAT;

typedef struct {
      int x;
      int Index;
} Z_QSORT_INT;

extern int compare_Z_IQSORT_FLOAT (Z_QSORT_FLOAT *a, Z_QSORT_FLOAT *b );
extern int compare_Z_IQSORT_INT (Z_QSORT_INT *a, Z_QSORT_INT *b );
extern int compare_double (double *a, double *b );
extern int compare_float (float *a, float *b );
extern int compare_int (int *a, int *b );
extern int compare_short (short *a, short *b );
extern int compare_char (char *a, char *b );

/***** pca calc *****/
double covariance(float *data_mat, double *cov_mat, unsigned char * row_mask, int num_rows, int num_cols, int norm, int remove_mean, int be_quiet);
void pca (float *data_mat, unsigned char * row_mask, int num_rows, int num_cols, int be_quiet);
double pca_fast3 (float *data_mat, int num_rows, int be_quiet, double *pca_vec, double *pca_eig);

#ifdef  __cplusplus
}
#endif

#endif