int main()
{
int n; // size of square matrix
int **A=NULL,**B=NULL,**C=NULL;
int **TA=NULL; // TA = traspose(A)
printf("Please input the size of matrix:");
scanf("%d",&n);
_flushall();
// Call the function - AllocIntMatrix to get the memory for matrix A and B
// --- write your codes here ---
A=AllocIntMatrix(n);
B=AllocIntMatrix(n);
int i,j;
// Ask the user to enter the matrix
printf("A=\n");
// --- write your codes here to get matrix A---
for(i=0; i<n; i++)
for(j=0; j<n; j++)
scanf(" %d", &A[i][j]);
printf("B=\n");
// --- write your codes here to get matrix B---
for(i=0; i<n; i++)
for(j=0; j<n; j++)
scanf(" %d", &B[i][j]);
// call the two functions for transpose(A) and C = transpose(A)*B
TA=matrix_transpose(&A[0], n); // share the ownership of the heap memory (i.e., A) with matrix_transpose() by call by reference (pointer)
// obtain the ownership of the heap memory (i.e., TA) requested in matrix_transpose()
//multiplication
C=matrix_multiplication(&TA[0], &B[0], n);// share the ownership of the heap memory (i.e., A, B) with matrix_multiplication() by call by reference (pointer)
// obtain the ownership of the heap memory (i.e., C) requested in matrix_multiplication()
system("cls");
printf("A=\n");
// --- write your codes here to print out A ---
int CNT=0;
for(i=0; i<n; i++){
for(j=0; j<n; j++){
printf("%d ", A[i][j]);
CNT++;
if(CNT == n){
printf("\n");
CNT=0;
}
}
}
printf("\n");
printf("TA=\n");
// --- write your codes here to print out TA ---
for(i=0; i<n; i++){
for(j=0; j<n; j++){
printf("%d ", TA[i][j]);
CNT++;
if(CNT == n){
printf("\n");
CNT=0;
}
}
}
printf("\n");
printf("B=\n");
// --- write your codes here to print out B ---
for(i=0; i<n; i++){
for(j=0; j<n; j++){
printf("%d ", B[i][j]);
CNT++;
if(CNT == n){
printf("\n");
CNT=0;
}
}
}
printf("\n");
printf("C=\n");
// --- write your codes here to print out C ---
for(i=0; i<n; i++){
for(j=0; j<n; j++){
printf("%d ", C[i][j]);
CNT++;
if(CNT == n){
printf("\n");
CNT=0;
}
}
}
// release heap memory explicitly preventing memory leakage
FreeIntMatrix(A ,n); // release A
FreeIntMatrix(B ,n); // relase B
FreeIntMatrix(C ,n); // relase C
FreeIntMatrix(TA ,n); // release TA
A = B = C = TA = NULL;
system("PAUSE");
return 0;
}
void CostCalculator::OptimizeCost(char ** haplotypes, int count, int markers)
{
LongCounter uniqueHaplotypes;
int bits = sizeof(long long) * 8 - 1;
int limit = count / 2;
long long * individualHaplotypes = new long long [count];
int ** uniqueCounts = AllocateIntMatrix(markers, bits);
// First we construct a matrix with the number of unique haplotypes
// along different portions of the current solution
for (int i = 0; i < markers; i++)
{
uniqueHaplotypes.Clear();
// Retrieve one marker haplotypes
for (int j = 0; j < count; j++)
{
individualHaplotypes[j] = haplotypes[j][i];
uniqueHaplotypes.IncrementCount(individualHaplotypes[j]);
}
// Count the number of unique haplotypes
uniqueCounts[i][0] = uniqueHaplotypes.Entries();
for (int j = 1; j < bits; j++)
{
if (uniqueHaplotypes.Entries() > limit || i + j >= markers)
{
uniqueCounts[i][j] = count;
continue;
}
uniqueHaplotypes.Clear();
for (int k = 0; k < count; k++)
{
individualHaplotypes[k] = individualHaplotypes[k] * 2 + haplotypes[k][i+j];
uniqueHaplotypes.IncrementCount(individualHaplotypes[k]);
}
uniqueCounts[i][j] = uniqueHaplotypes.Entries();
}
}
// Finally, we use dynamic programming to find the best cost path
if (cost != NULL) delete [] cost;
if (path != NULL) delete [] path;
cost = new double [markers];
path = new int [markers];
cost[0] = BasicCost(count);
path[0] = 0;
for (int i = 1; i < markers; i++)
{
cost[i] = cost[i - 1] + BasicCost(count);
path[i] = i;
for (int j = 1; j < bits; j++)
if (i - j >= 0)
{
double alternate_cost = cost[i - j]
+ ReducedCost(uniqueCounts[i-j][j], count) * j
+ TranslationCost(count);
if (alternate_cost < cost[i])
{
cost[i] = alternate_cost;
path[i] = i - j;
}
}
}
#ifdef _DEBUG
// Estimate savings
double naiveCost = markers * BasicCost(count);
printf("Reduced state space optimization would result in a speedup of about %.1f-fold\n",
naiveCost / cost[markers-1]);
int position = markers - 1;
printf(" Optimal Path: ");
while (position != 0)
if (path[position] == position)
printf(" Step(%d) ", position--);
else
{
printf(" Condense(%d -> %d)", position, path[position]);
position = path[position];
}
printf("\n");
#endif
// We are all done, free memory
FreeIntMatrix(uniqueCounts, markers);
delete [] individualHaplotypes;
}
