}
}
}
- else if (matrix == "sim2") {
- for(int i=0;i<nrows;i++) {
- start = 0.0;
- for(int j=0;j<ncols;j++) {
- probabilityMatrix[ncols * i + j] = start + 1/double(ncols);
- start = start + 1/double(ncols);
- }
- }
- }
+ //don't need a prob matrix because we just shuffle the rows, may use this in the future
+ else if (matrix == "sim2") { }
+// for(int i=0;i<nrows;i++) {
+// start = 0.0;
+// for(int j=0;j<ncols;j++) {
+// probabilityMatrix[ncols * i + j] = start + 1/double(ncols);
+// start = start + 1/double(ncols);
+// }
+// }
+// }
else if (matrix == "sim3") {
for(int j=0;j<ncols;j++) {
}
}
}
- else if (matrix == "sim9") { }
+ else if (matrix == "sim9" || matrix == "sim2") { }
else {
m->mothurOut("[ERROR]: No model selected! \n");
m->control_pressed = true;
double current;
double randnum;
int count;
-
- //burn-in
- for(int i=0;i<10000;i++){
- nullmatrix.clear();
- //zero-fill the null matrix
- nullmatrix.assign(nrows, vector<int>(ncols, 0));
-
- if(matrix == "sim1" || matrix == "sim6" || matrix == "sim8" || matrix == "sim7") {
- count = 0;
- while(count < n) {
- nextnum:
- previous = 0.0;
- randnum = rand() / double(RAND_MAX);
- for(int i=0;i<nrows;i++) {
- for(int j=0;j<ncols;j++) {
- current = probabilityMatrix[ncols * i + j];
- if(randnum <= current && randnum > previous) {
- nullmatrix[i][j] = 1;
- count++;
- if (count > n) break;
- else
- goto nextnum;
- }
- previous = current;
- }
- }
- }
- }
-
- else if(matrix == "sim2" || matrix == "sim4") {
- for(int i=0;i<nrows;i++) {
- previous = 0.0;
- count = 0;
- while(count < rowtotal[i]) {
- randnum = rand() / double(RAND_MAX);
- for(int j=0;j<ncols;j++) {
- current = probabilityMatrix[ncols * i + j];
- if(randnum <= current && randnum > previous && nullmatrix[i][j] != 1) {
- nullmatrix[i][j] = 1;
- count++;
- previous = 0.0;
- break;
- }
- previous = current;
- }
- }
- }
- }
-
- else if(matrix == "sim3" || matrix == "sim5") {
- //columns
- for(int j=0;j<ncols;j++) {
- count = 0;
- while(count < columntotal[j]) {
- randnum = rand() / double(RAND_MAX);
- for(int i=0;i<nrows;i++) {
- current = probabilityMatrix[ncols * i + j];
- if(randnum <= current && randnum > previous && nullmatrix[i][j] != 1) {
- nullmatrix[i][j] = 1;
- count++;
- previous = 0.0;
- break;
- }
- previous = current;
- }
- }
- }
- }
-
+
+ //burn-in for sim9
+ if(matrix == "sim9") {
+ for(int i=0;i<10000;i++) trial.swap_checkerboards (co_matrix, ncols, nrows);
}
-
+
//populate null matrix from probability matrix, do this a lot.
- for(int i=0;i<runs;i++){
+ for(int k=0;k<runs;k++){
nullmatrix.clear();
//zero-fill the null matrix
nullmatrix.assign(nrows, vector<int>(ncols, 0));
if(matrix == "sim1" || matrix == "sim6" || matrix == "sim8" || matrix == "sim7") {
count = 0;
while(count < n) {
+ if (m->control_pressed) { return 0; }
nextnum2:
previous = 0.0;
randnum = rand() / double(RAND_MAX);
}
}
- else if(matrix == "sim2" || matrix == "sim4") {
+ else if (matrix == "sim2") {
+ for(int i=0;i<nrows;i++) {
+ random_shuffle( co_matrix[i].begin(), co_matrix[i].end() );
+ }
+ //do this for the scoring since those all have nullmatrix as a parameter
+ //nullmatrix gets cleared at the begining of each run
+ nullmatrix = co_matrix;
+ }
+
+ else if(matrix == "sim4") {
for(int i=0;i<nrows;i++) {
- previous = 0.0;
count = 0;
while(count < rowtotal[i]) {
+ previous = 0.0;
+ if (m->control_pressed) { return 0; }
randnum = rand() / double(RAND_MAX);
for(int j=0;j<ncols;j++) {
current = probabilityMatrix[ncols * i + j];
for(int j=0;j<ncols;j++) {
count = 0;
while(count < columntotal[j]) {
+ if (m->control_pressed) { return 0; }
randnum = rand() / double(RAND_MAX);
for(int i=0;i<nrows;i++) {
current = probabilityMatrix[ncols * i + j];
//swap_checkerboards takes the original matrix and swaps checkerboards
else if(matrix == "sim9") {
- trial.swap_checkerboards (co_matrix, rowtotal, columntotal, ncols, nrows);
+ trial.swap_checkerboards (co_matrix, ncols, nrows);
+ nullmatrix = co_matrix;
}
else {
m->mothurOut("[ERROR]: No null model selected!\n\n"); m->control_pressed = true;