#ifndef __SWAT_PARAM_H__
#define __SWAT_PARAM_H__

#include <stdio.h>
#include <stdlib.h>
#include <string.h>

float blosum62[4][4] = {
/*	        a       c       g       t   */
/* a */{   4.0,    0.0,    0.0,    0.0 },
/* c */{   0.0,    9.0,    -3.0,   -1.0},
/* g */{   0.0,    -3.0,   6.0,    -2.0},
/* t */{   0.0,    -1.0,   -2.0,   5.0}};


void PrintResult(char *, char *, int, int, float, float);
int char2index1(char);

void PrintResult(char *outstr1, 
				 char *outstr2, 
				 int noutLen, 
				 int nCharsPerLine, 
				 float fopen_pa, 
				 float fext_pa)
{
	int i, j, npos;
	int nstart1, nstart2;
	int nstartmiss;
	char *interstring;
	int ninterpos;
	int nflag;

	interstring = new char[noutLen];
	if (interstring == NULL)
	{
		printf("Allocate interstring error!\n");
		return;
	}
	ninterpos = 0;
	nflag = 0;
	nstartmiss = 0;
	nstart1 = 0;
	nstart2 = 0;

	for (i = 0; i < noutLen; i++)
	{
		if (nflag == 0)
		{
			if (outstr1[noutLen - 1 - i] != outstr2[noutLen - 1 - i])
			{
				if (outstr1[noutLen - 1 - i] != '-')
					nstart1++;

				if (outstr2[noutLen - 1 - i] != '-')
					nstart2++;
				nstartmiss++;
				continue;
			}
			else
			{
				nflag = 1;
			}
		}

		if (outstr1[noutLen - 1 - i] == '-' || outstr2[noutLen - 1 - i] == '-')
		{
			interstring[ninterpos++] = ' ';
		}
		else if (outstr1[noutLen - 1 - i] != outstr2[noutLen - 1 - i])
		{
			interstring[ninterpos++] = '.';
		}
		else
		{
			interstring[ninterpos++] = '|';
		}
	}

	int nOutLine = (noutLen - nstartmiss)/nCharsPerLine;
	for (i = 0; i < nOutLine; i++)
	{
		for (j = 0; j < nCharsPerLine; j++)
		{
			npos = i * nCharsPerLine + nstartmiss + j;
			printf("%c", outstr1[noutLen - 1 - npos]);
		}
		printf("\n");

		for (j = 0; j < nCharsPerLine; j++)
		{
			npos = i * nCharsPerLine + j;
			printf("%c", interstring[npos]);
		}
		printf("\n");

		for (j = 0; j < nCharsPerLine; j++)
		{
			npos = i * nCharsPerLine + nstartmiss + j;
			printf("%c", outstr2[noutLen - 1 - npos]);
		}
		printf("\n\n");
	}

	int nRemainingCh = noutLen - nstartmiss - nOutLine * nCharsPerLine;
	if (nRemainingCh > 0)
	{
		for (j = 0; j < nRemainingCh; j++)
		{
			printf("%c", outstr1[nRemainingCh - 1 - j]);
		}
		printf("\n");

        for (j = 0; j < nRemainingCh; j++)
		{
			npos = nOutLine * nCharsPerLine + j;
			printf("%c", interstring[npos]);
		}
		printf("\n");
		
		for (j = 0; j < nRemainingCh; j++)
		{
			printf("%c", outstr2[nRemainingCh - 1 - j]);
		}
		printf("\n\n");
	}

	printf("output string length: 	  %d\n", noutLen - nstartmiss);
	printf("open gap penalty is:      %.1f\n", fopen_pa);
	printf("extension gap penalty is: %.1f\n", fext_pa);

	return;
}

int char2index1(char inch)
{
	int result;
	if ((inch == 'a') || (inch == 'A'))
	{
		result = 0;
	}
	else if ((inch == 'c') || (inch == 'C'))
	{
		result = 1;
	}
	else if ((inch == 'g') || (inch == 'G'))
	{
		result = 2;
	}
	else if ((inch == 't') || (inch == 'T'))
	{
		result = 3;
	}
	else
	{
		return -1;
	}

	return result;
}

#endif