#include "CipresNativeC.h"
#ifdef __cplusplus
#	include <cstdlib>
#	include <cassert>
#	include <cstdio>
#	include <cstring>

extern "C" 
{
#else
#	include <stdlib.h>
#	include <assert.h>
#	include <stdio.h>
#	include <string.h>
#endif

static void *SetMatrixRowPtrs(void *a_arg, void *p_arg, unsigned nrows, unsigned ncols, size_t elSize)
	{
	char		*p, **a;
	unsigned	i;
	size_t		rowBytes;

	a = (char **)a_arg;
	p = (char *)p_arg;

	rowBytes = ncols*elSize;
	for (i = 0; i < nrows; i++)
		{
		a[i] = p;
		p += rowBytes;
		}
		
	return a_arg;
	}

//@ move to a CIPR_Matrix file
int CIPR_AllocMatrix(void *pA, size_t elSize, unsigned nrows, unsigned ncols)
	{
	char **a;
	void **pblock;

	assert(pA != NULL);
	assert(elSize != 0);
	assert(nrows != 0);

	/* Allocate array of row pointers */
	a = (char **)calloc(nrows, sizeof(void *));
	if (a == NULL)
		return 1;
	
	pblock = (void **)pA;
	*pblock = a;

	if (ncols != 0)
		{
		/* Allocate block for data and set pointers to each matrix row */
		a[0] = (char *)calloc(nrows*ncols, elSize);
		if (a[0] == NULL)
			return 1;

		(void)SetMatrixRowPtrs(a, a[0], nrows, ncols, elSize);
		}

	return 0;
	}

const char * datatypeEnumToString(const CIPR_Datatypes d)
	{
	switch(d)
		{
		case CIPR_DNA_Datatype: 	return "DNA";
		case CIPR_RNA_Datatype: 	return "RNA";
		case CIPR_AA_Datatype: 		return "AA";
		case CIPR_Codon_Datatype: 	return "Codon";
		case CIPR_Generic_Datatype: return "Generic";
		default:
			assert(0);
			return NULL;
		}
	}
#if defined(OLD_CIPRES_MATRIX)
	void showMatrix(const CIPR_Matrix matrix, int m, int n)
		{	 
		int i, j;
		char *dna = "ACGT";
	
		printf("Data matrix\n");
		for (i = 0; i < m; i++)
			{
			for (j = 0; j < n; j++)			
				printf("%c", dna[(int)matrix[i][j]]);
			printf("\n");
			}
		}
#else
	void showMatrix(const CIPR_Matrix matrix)
		{
		unsigned i, j, k;
		int index;
		const int nSymbols = strlen(matrix.symbolsList);		
		printf("Data matrix\n");
		printf(" type = %s\n", datatypeEnumToString(matrix.datatype));
		printf(" symbols = %s\n", matrix.symbolsList);
		printf(" nStates = %d\n", matrix.nStates);
		printf(" nChar = %d\n", matrix.nChar);
		printf(" nTax = %d\n", matrix.nTax);
		printf(" %d different state sets were observed:\n", matrix.nObservedStateSets);
		for (i = 0; i < matrix.nObservedStateSets; ++i)
			{
			const int stateListInd = matrix.stateListPos[i];
			const unsigned nAmbigElements = matrix.stateList[stateListInd];
			printf("\tstateListPos[%d] = %d\tstateList[%d] = %d\n", i, stateListInd, stateListInd, nAmbigElements);
			for (j = 1 ; j <= nAmbigElements; ++j)
				printf("\t\t\t\t\tstateList[%d] = %d\n", stateListInd + j, matrix.stateList[stateListInd + j]);
			}
		printf("Matrix:\n");
		for (i = 0; i < matrix.nTax; ++i)
			{
			printf("%d\t", i);
			for (j = 0; j < matrix.nChar; ++j)
				printf("%2d", (int)matrix.matrix[i][j]);
			printf("\n");
			}
		printf("Decoded Matrix:\n");
		for (i = 0; i < matrix.nTax; ++i)
			{
			printf("%d\t", i);
			for (j = 0; j < matrix.nChar; ++j)
				{
				index = matrix.matrix[i][j];
				if (index >= nSymbols || matrix.symbolsList[index] == ' ')
					{
					const int stateListInd = matrix.stateListPos[j];
					const int nSymbols = (int)matrix.stateList[stateListInd];
					assert(nSymbols >= 0);
					printf("{");
					for (k = 0; k < (unsigned)nSymbols; ++k)
						printf("%c", matrix.symbolsList[matrix.stateList[stateListInd + 1 + k]]);
					printf("}");
					}
				else
					printf("%c", matrix.symbolsList[index]);
				}
			printf("\n");
			}
		
		}
#endif

#ifdef __cplusplus
} /*extern C */
#endif