//see header file for "how to use" documentation
void quickSort(int *array, int n, bool isOrderASC)
{
//always sort in ascending order
quickSort_Internal(array, 0, n-1);
//if the specified order is descending, just inverse the array
if(!isOrderASC)
{
inverseArray(array, n);
}
}
/*
** 从集中器返回帧, 读取集中器号.
** @gatewatId: 集中器号, 从消息中的反序, 变为正序
** @idLen: 集中器号的长度
** @buf: 返回帧
** @bufSize: 返回帧的长度
*/
U8 protoA_radioReadId(U8 *gatewayId, U8 idLen, U8* buf, U16 bufSize)
{
//检查消息合法性
if (protoA_retFrameLen(buf, bufSize) == ERROR)
return ERROR;
buf += GATEWAY_RETID_OFFSET;
memcpy(gatewayId, buf, GATEWAY_OADD_LEN);
inverseArray(gatewayId, GATEWAY_OADD_LEN);
return NO_ERR;
}
/*
** 反序输入的字符串至BCD码.
** @s: 源字符串
** @sLen: 源字符串长度
** @t: 目标字符串
** @tLen: 目标字符串长度
*/
U8 inverseStrToBCD(U8* s, U16 sLen, U8* t, U16 tLen)
{
U16 i = 0;
if (sLen % 2)
return ERROR;
for (i = 0;i < sLen/2;i++, s += 2) {//convert ascii to hex each two chars
t[i] = (ASCII_TO_HEX(s[0]) << 4 | ASCII_TO_HEX(s[1]));
}
inverseArray(t, i);
return NO_ERR;
}
void getAlignment(int* matrix, char* matsub, int sizeM,
short gapVal, short expandGap,
char* seq1, int size1,
char* seq2, int size2,
char** res1, char** res2)
{
*res2 = (char*) malloc((size1+size2)*sizeof(char));
*res1 = (char*) malloc((size1+size2)*sizeof(char));
int indiceRes = 0;
int indiceSeq1 = size1-1;
int indiceSeq2 = size2-1;
int x, y, tmp;
findScorePositionInMatrix(matrix, size1, size2, &x, &y);
// viewMatrix(matrix, size1, size2);
//printf("position x: %d, y:%d\n", x, y);
for(size_t i = x; i < size2; i++)
{
(*res2)[indiceRes] = seq2[indiceSeq2--];
(*res1)[indiceRes++] = -1;
}
for(size_t i = y; i < size1; i++)
{
(*res1)[indiceRes] = seq1[indiceSeq1--];
(*res2)[indiceRes++] = -1;
}
while(x != 0 && y != 0)
{
/*
printf("Comp %d + %d(%d,%d) == %d \n", matrix[(x-1)*SIZE+y-1],
blosumValue(matsub, sizeM, seq1[y-1], seq2[x-1]), seq1[y-1], seq2[x-1],
matrix[x*SIZE+y] );
*/
if( matrix[(x-1)*SIZE+y-1]+blosumValue(matsub, sizeM, seq1[y-1], seq2[x-1]) == matrix[x*SIZE+y] )
{
(*res1)[indiceRes] = seq1[indiceSeq1--];
(*res2)[indiceRes++] = seq2[indiceSeq2--];
x -= 1;
y -= 1;
}
else if( 0 < (tmp=findEndGap(matrix, gapVal, expandGap, x*SIZE+y, 1, x*SIZE)) )
{
// printf("Decalage %d\n", tmp);
for(int i = 0; i < tmp; i++)
{
(*res1)[indiceRes] = seq1[indiceSeq1--];
(*res2)[indiceRes++] = -1;// seq2[indiceSeq2--];
y -= 1;
}
}
else if( 0 < (tmp=findEndGap(matrix, gapVal, expandGap, x*SIZE+y, SIZE, 0)) )
{
for(int i = 0; i < tmp; i++)
{
(*res1)[indiceRes] = -1; //seq1[indiceSeq1--];
(*res2)[indiceRes++] = seq2[indiceSeq2--];
x -= 1;
}
}
else exit(0);
}
for(size_t i = 0; i < x; i++)
{
(*res2)[indiceRes] = seq2[indiceSeq2--];
(*res1)[indiceRes++] = -1;
}
for(size_t i = 0; i < y; i++)
{
(*res1)[indiceRes] = seq1[indiceSeq1--];
(*res2)[indiceRes++] = -1;
}
// printf("indice Res = %d \n", indiceRes);
(*res1)[indiceRes] = '\0';
(*res2)[indiceRes] = '\0';
inverseArray(*res1, strlen(*res1));
inverseArray(*res2, strlen(*res2));
}
