// vera_sam.cpp : Defines the class behaviors for the application.
//

#include "stdafx.h"
#include "vera_sam.h"
#include "vera_samDlg.h"

#ifdef _DEBUG
#define new DEBUG_NEW
#undef THIS_FILE
static char THIS_FILE[] = __FILE__;
#endif

int Nheader; 
/* Number of lines in header */
/* declared here since it will be used by output routine write_llr */
bool RunVERA   = true;
bool RunSAM    = true;
bool alt_sam   = false;
CString temp_in_model = "",VERA_input = "", ALT_SAM_INPUT = "";
double new_eps_beta = 0.0005;
bool disp_iter = false;  /* flag=1 to display progress of iterations run */
bool s_disp_iter = false;  /* flag=1 to display progress of iterations run */
bool start_mod = false;  /* flag=1  if starting guess to be used for optimization */
bool evolution = false;  /* flag=1 to display parameter evolution during optimization */
bool stop_crit = false; /* flag=1 to specify stop criterion for optimization */
int N;  /* number of genes, maximum no. of repeats */
char **yorf; /* unique gene name identifiers for each gene */
char **gene_name; /* common use gene name */ 
int *m; /* number of samples for each gene */
float **X, **Y, *muX, *muY; /* intensities for all genes&repeats and mu parameters for all genes*/
int *m1, *m2; /* number of samples in each case for reference comparison */
float **X1, **Y1, **X2, **Y2; /* intensities for data sets involved in reference comparison */
float LINMIN_TOL; /* tolerance for linmin.c */
double *cov;   /* parameters of covariance matrix */
double *cov1, *cov2;   /* parameters of covariance matrices for reference sample comparisons */

int gene_index; /* gene index for Z_gene.c and gradZ_gene.c */
int gene_index_1, gene_index_2; /* gene index needed for two sample comparisons */
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 */

/////////////////////////////////////////////////////////////////////////////
// CVera_samApp

BEGIN_MESSAGE_MAP(CVera_samApp, CWinApp)
	//{{AFX_MSG_MAP(CVera_samApp)
		// NOTE - the ClassWizard will add and remove mapping macros here.
		//    DO NOT EDIT what you see in these blocks of generated code!
	//}}AFX_MSG
	ON_COMMAND(ID_HELP, CWinApp::OnHelp)
END_MESSAGE_MAP()

/////////////////////////////////////////////////////////////////////////////
// CVera_samApp construction

CVera_samApp::CVera_samApp()
{
	// TODO: add construction code here,
	// Place all significant initialization in InitInstance
}

/////////////////////////////////////////////////////////////////////////////
// The one and only CVera_samApp object

CVera_samApp theApp;

/////////////////////////////////////////////////////////////////////////////
// CVera_samApp initialization

BOOL CVera_samApp::InitInstance()
{
	AfxEnableControlContainer();

	// Standard initialization
	// If you are not using these features and wish to reduce the size
	//  of your final executable, you should remove from the following
	//  the specific initialization routines you do not need.


#ifdef _AFXDLL
	Enable3dControls();			// Call this when using MFC in a shared DLL
#else
	Enable3dControlsStatic();	// Call this when linking to MFC statically
#endif
	CVera_samDlg dlg;
	m_pMainWnd = &dlg;
	int nResponse = dlg.DoModal();
	if (nResponse == IDOK)
	{
		// TODO: Place code here to handle when the dialog is
		//  dismissed with OK
	}
	else if (nResponse == IDCANCEL)
	{
		// TODO: Place code here to handle when the dialog is
		//  dismissed with Cancel
	}

	// Since the dialog has been closed, return FALSE so that we exit the
	//  application, rather than start the application's message pump.
	return FALSE;
}