int ncols = thisLookUp.size();//groups
double initscore = 0.0;
- vector<int> initcolumntotal; initcolumntotal.resize(ncols, 0);
- vector<int> initrowtotal; initrowtotal.resize(nrows, 0);
+ vector<int> columntotal; columntotal.resize(ncols, 0);
+ vector<int> rowtotal; rowtotal.resize(nrows, 0);
vector<double> stats;
+ double probabilityMatrix[ncols * nrows];
+ vector<vector<int> > nullmatrix(nrows, vector<int>(ncols, 0));
TrialSwap2 trial;
- initcolumntotal = rowtotal;
- initrowtotal = columntotal;
- trial.update_row_col_totals(co_matrix, rowtotal, columntotal);
+ n = accumulate( columntotal.begin(), columntotal.end(), 0 );
- if (metric == "cscore") { initscore = trial.calc_c_score(co_matrix, rowtotal); }
- else if (metric == "checker") { initscore = trial.calc_checker(co_matrix, rowtotal); }
- else if (metric == "vratio") { initscore = trial.calc_vratio(rowtotal, columntotal); }
- else if (metric == "combo") { initscore = trial.calc_combo(co_matrix); }
+ //============================================================
+
+ //generate a probability matrix. Only do this once.
+ float start = 0.0;
+
+ if (matrix == "sim1") {
+ for(int i=0;i<nrows;i++) {
+ for(int j=0;j<ncols;j++) {
+ probabilityMatrix[ncols * i + j] = start + 1/double(nrows*ncols);
+ start = start + 1/double(nrows*ncols);
+ }
+ }
+ }
+ 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++) {
+ start = 0.0;
+ for(int i=0;i<nrows;i++) {
+ probabilityMatrix[ncols * i + j] = start + 1/double(nrows);
+ start = start + 1/double(nrows);
+ }
+ }
+ }
+
+ else if (matrix == "sim4") {
+ for(int i=0;i<nrows;i++) {
+ start = 0.0;
+ for(int j=0;j<ncols;j++) {
+ probabilityMatrix[ncols * i + j] = start + columntotal[j]/double(n);
+ start = start + columntotal[j]/double(n);
+ }
+ }
+ }
+
+ else if (matrix == "sim5") {
+ for(int j=0;j<ncols;j++) {
+ start = 0.0;
+ for(int i=0;i<nrows;i++) {
+ probabilityMatrix[ncols * i + j] = start + rowtotal[i]/double(n);
+ start = start + rowtotal[i]/double(n);
+ }
+ }
+ }
+
+ else if (matrix == "sim6") {
+ for(int i=0;i<nrows;i++) {
+ for(int j=0;j<ncols;j++) {
+ probabilityMatrix[ncols * i + j] = start + columntotal[j]/double(n*nrows);
+ start = start + columntotal[j]/double(n*nrows);
+ }
+ }
+ }
+
+
+ else if (matrix == "sim7") {
+ for(int i=0;i<nrows;i++) {
+ for(int j=0;j<ncols;j++) {
+ probabilityMatrix[ncols * i + j] = start + rowtotal[i]/double(n*ncols);
+ start = start + rowtotal[i]/double(n*ncols);
+ }
+ }
+ }
+
+ else if (matrix == "sim8") {
+ for(int i=0;i<nrows;i++) {
+ for(int j=0;j<ncols;j++) {
+ probabilityMatrix[ncols * i + j] = start + (rowtotal[i]*columntotal[j])/double(n*n);
+ start = start + (rowtotal[i]*columntotal[j])/double(n*n);
+ }
+ }
+ }
+
+ else {
+ if(sim != 9) {
+ m->mothurOut("[ERROR]: No model selected! \n");
+ m->control_pressed = true;
+ }
+ }
+
+
+
+ if (metric == "cscore") { initscore = trial.calc_c_score(initmatrix, rowtotal, ncols, nrows); }
+ else if (metric == "checker") { initscore = trial.calc_checker(initmatrix, rowtotal, ncols, nrows); }
+ else if (metric == "vratio") { initscore = trial.calc_vratio(nrows, ncols, rowtotal, columntotal); }
+ else if (metric == "combo") { initscore = trial.calc_combo(nrows, ncols, initmatrix); }
else { m->mothurOut("[ERROR]: No metric selected!\n"); m->control_pressed = true; return 1; }
m->mothurOut("Initial c score: " + toString(initscore)); m->mothurOutEndLine();
- //nullmatrix burn in
- for(int i=0;i<10000;i++) {
- if (m->control_pressed) { return 0; }
- if (matrix == "sim1") {
- trial.sim1(co_matrix);
- }else if (matrix == "sim2") {
- trial.sim2(co_matrix);
- }else if (matrix == "sim3") {
- trial.sim3(initmatrix);
- co_matrix = initmatrix;
- }else if (matrix == "sim4") {
- trial.sim4(columntotal, rowtotal, co_matrix);
- }else if (matrix == "sim5") {
- trial.sim5(initcolumntotal, initrowtotal, initmatrix);
- trial.transpose_matrix(initmatrix,co_matrix);
- }else if (matrix == "sim6") {
- trial.sim6(columntotal, co_matrix);
- }else if (matrix == "sim7") {
- trial.sim7(initcolumntotal, initmatrix);
- co_matrix = initmatrix;
- }else if (matrix == "sim8") {
- trial.sim8(columntotal, rowtotal, co_matrix);
- }else if (matrix == "sim9") {
- trial.swap_checkerboards (co_matrix);
- }else{
- m->mothurOut("[ERROR]: No model selected! \n");
- m->control_pressed = true;
+ double previous;
+ 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;
+ }
+ }
+ }
+ }
+
}
-
- //run
- for(int i=0;i<runs;i++) {
- if (m->control_pressed) { return 0; }
- //calc metric of nullmatrix
- if (matrix == "sim1") {
- trial.sim1(co_matrix);
- }else if (matrix == "sim2") {
- trial.sim2(co_matrix);
- }else if (matrix == "sim3") {
- trial.sim3(initmatrix);
- co_matrix = initmatrix;
- }else if (matrix == "sim4") {
- trial.sim4(columntotal, rowtotal, co_matrix);
- }else if (matrix == "sim5") {
- trial.sim5(initcolumntotal, initrowtotal, initmatrix);
- trial.transpose_matrix(initmatrix,co_matrix);
- }else if (matrix == "sim6") {
- trial.sim6(columntotal, co_matrix);
- }else if (matrix == "sim7") {
- trial.sim7(initcolumntotal, initmatrix);
- co_matrix = initmatrix;
- }else if (matrix == "sim8") {
- trial.sim8(columntotal, rowtotal, co_matrix);
- }else if (matrix == "sim9") {
- trial.swap_checkerboards (co_matrix);
- }else{
- m->mothurOut("[ERROR]: No model selected! \n");
- m->control_pressed = true;
+
+ //populate null matrix from probability matrix, do this a lot.
+ for(int i=0;i<runs;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;
+ }
+ }
+ }
}
- //
- //
- //trial.update_row_col_totals(co_matrix, rowtotal, columntotal);
- if (metric == "cscore") {
- stats.push_back(trial.calc_c_score(co_matrix, rowtotal));
- }else if (metric == "checker") {
- stats.push_back(trial.calc_checker(co_matrix, rowtotal));
- }else if (metric == "vratio") {
- stats.push_back(trial.calc_vratio(rowtotal, columntotal));
- }else if (metric == "combo") {
- stats.push_back(trial.calc_combo(co_matrix));
- }else {
- m->mothurOut("[ERROR]: No metric selected!\n");
- m->control_pressed = true;
+ //swap_checkerboards takes the original matrix and swaps checkerboards
+ else if(matrix == "sim9") {
+ trial.swap_checkerboards (initmatrix, rowtotal, columntotal, ncols, nrows);
+ }
+ else {
+ cout << "[ERROR]: No null model selected!\n" << endl;
return 1;
}
-
+
+ //run metric on null matrix and add score to the stats vector
+ if (metric == "cscore"){
+ stats.push_back(trial.calc_c_score(nullmatrix, rowtotal, ncols, nrows));
+ }
+ else if (metric == "checker") {
+ stats.push_back(trial.calc_checker(nullmatrix, rowtotal, ncols, nrows));
+ }
+ else if (metric == "vratio") {
+ stats.push_back(trial.calc_vratio(nrows, ncols, rowtotal, columntotal));
+ }
+ else if (metric == "combo") {
+ stats.push_back(trial.calc_combo(nrows, ncols, nullmatrix));
+ }
+ else {
+ cout << "[ERROR]: No metric selected!\n" << endl;
+ return 1;
+ }
+
}
+
+
double total = 0.0;
for (int i=0; i<stats.size();i++) { total+=stats[i]; }
}
}
/**************************************************************************************************/
-/* completely random matrix, all column and row totals are variable, matrix size is the same
- *
- *
- */
-/**************************************************************************************************/
-int TrialSwap2::sim1(vector<vector<int> > &co_matrix){
- try {
- vector<int> randRow;
- vector<vector<int> > tmpmatrix;
- int nrows = co_matrix.size();
- int ncols = co_matrix[0].size();
-
- //clear co_matrix
- // for(i=0;i<nrows;i++)
- // {
- // co_matrix.clear();
- // }
-
- //cout << "building matrix" << endl;
- for(int i=0;i<nrows;i++){
- if (m->control_pressed) { break; }
-
- for(int j=0;j<ncols;j++){
- double randNum = rand() / double(RAND_MAX);
- //cout << randNum << endl;
-
- if(randNum > 0.5) {
- randRow.push_back(1);
- }else{
- randRow.push_back(0);
- }
- }
- tmpmatrix.push_back(randRow);
- randRow.clear();
- //cout << endl;
- }
- co_matrix = tmpmatrix;
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "TrialSwap2", "sim1");
- exit(1);
- }
-}
-/**************************************************************************************************/
-/*
- *row sums fixed, columns equiprobable
- */
-void TrialSwap2::sim2(vector<vector<int> > &co_matrix)
-{
- try {
-
- for(int i=0;i<co_matrix.size();i++)
- {
- if (m->control_pressed) { break; }
- random_shuffle( co_matrix[i].begin(), co_matrix[i].end() );
- }
- }
- catch(exception& e) {
- m->errorOut(e, "TrialSwap2", "sim2");
- exit(1);
- }
-}
-/**************************************************************************************************/
-int TrialSwap2::sim2plus(vector<int> rowtotal, vector<vector<int> > &co_matrix)
-{
- try {
- int nrows = co_matrix.size();
- int ncols = co_matrix[0].size();
- double cellprob = 1.0/ncols;
- vector<double> cellprobvec;
- vector<int> tmprow;
- vector<vector<int> > tmpmatrix;
- //double randNum;
-
- double start = 0.0;
-
- for(int i=0; i<ncols; i++)
- {
- if (m->control_pressed) { return 0; }
- cellprobvec.push_back(start + cellprob);
- start = cellprobvec[i];
- }
-
- for(int i=0; i<nrows; i++)
- {
- tmprow.assign(ncols, 0);
-
- while( accumulate( tmprow.begin(), tmprow.end(), 0 ) < rowtotal[i])
- {
- if (m->control_pressed) { return 0; }
- double randNum = rand() / double(RAND_MAX);
- //cout << randNum << endl;
- if(randNum <= cellprobvec[0])
- {
- tmprow[0] = 1;
- continue;
- }
- for(int j=1;j<ncols;j++)
- {
- //cout << range[j] << endl;
- if(randNum <= cellprobvec[j] && randNum > cellprobvec[j-1] && tmprow[j] != 1)
- {
- tmprow[j] = 1;
- }
- }
- }
- tmpmatrix.push_back(tmprow);
- tmprow.clear();
- }
- co_matrix = tmpmatrix;
- tmpmatrix.clear();
- cellprobvec.clear();
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "TrialSwap2", "sim2plus");
- exit(1);
- }
-}
-/**************************************************************************************************/
-/*
- * same as sim2 but using initmatrix which is the initial co-occurrence matrix before transposition
- * may have to be changed depending on what matrix 'seed' is used. One way to use is to transpose
- * every null matrix before using an index and use the random matrix as a seed for the next null.
- */
-/**************************************************************************************************/
-void TrialSwap2::sim3(vector<vector<int> > &initmatrix)
-{
- try {
- for(int i=0;i<initmatrix.size();i++)
- {
- if (m->control_pressed) { break; }
- random_shuffle( initmatrix[i].begin(), initmatrix[i].end() );
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "TrialSwap2", "sim3");
- exit(1);
- }
-}
-/**************************************************************************************************/
-/*
- *
- *
- *
- */
-/**************************************************************************************************/
-int TrialSwap2::sim4(vector<int> columntotal, vector<int> rowtotal, vector<vector<int> > &co_matrix)
-{
- try {
- vector<double> colProb;
- vector<int> tmprow;//(ncols, 7);
- vector<vector<int> > tmpmatrix;
- vector<double> range;
- vector<double> randNums;
- int ncols = columntotal.size();
- int nrows = rowtotal.size();
- tmprow.clear();
-
- double colSum = accumulate( columntotal.begin(), columntotal.end(), 0 );
- //cout << "col sum: " << colSum << endl;
- for(int i=0;i<ncols;i++)
- {
- if (m->control_pressed) { return 0; }
- colProb.push_back(columntotal[i]/colSum);
- }
-
- double start = 0.0;
-
- for(int i=0;i<ncols;i++)
- {
- if (m->control_pressed) { return 0; }
- range.push_back(start + colProb[i]);
- start = range[i];
- }
-
- for(int i=0;i<nrows;i++)
- {
- tmprow.assign(ncols, 0);
- if (m->control_pressed) { return 0; }
-
- while ( accumulate( tmprow.begin(), tmprow.end(), 0 ) < rowtotal[i])
- {
- if (m->control_pressed) { return 0; }
-
- double randNum = rand() / double(RAND_MAX);
- if(randNum <= range[0])
- {
- tmprow[0] = 1;
- continue;
- }
- for(int j=1;j<ncols;j++)
- {
- if(randNum <= range[j] && randNum > range[j-1] && tmprow[j] != 1)
- {
- tmprow[j] = 1;
- }
-
- }
- }
- tmpmatrix.push_back(tmprow);
- tmprow.clear();
- }
-
- co_matrix = tmpmatrix;
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "TrialSwap2", "sim4");
- exit(1);
- }
-}
-/**************************************************************************************************/
-/*
- * inverse of sim4, MUST BE TRANSPOSED BEFORE CO-OCCURRENCE ANALYSIS
- *
- *
- */
-/**************************************************************************************************/
-int TrialSwap2::sim5(vector<int> initcolumntotal,vector<int> initrowtotal, vector<vector<int> > &initmatrix)
-{
- try {
- vector<double> colProb;
- vector<int> tmprow;//(ncols, 7);
- vector<vector<int> > tmpmatrix;
- vector<double> range;
- vector<double> randNums;
- int ncols = initcolumntotal.size();
- int nrows = initrowtotal.size();
-
- tmprow.clear();
-
- double colSum = accumulate( initcolumntotal.begin(), initcolumntotal.end(), 0 );
- //cout << "col sum: " << colSum << endl;
- for(int i=0;i<ncols;i++)
- {
- if (m->control_pressed) { return 0; }
- colProb.push_back(initcolumntotal[i]/colSum);
- }
-
- double start = 0.0;
-
- for(int i=0;i<ncols;i++)
- {
- if (m->control_pressed) { return 0; }
- range.push_back(start + colProb[i]);
- start = range[i];
- }
-
- for(int i=0;i<nrows;i++)
- {
- tmprow.assign(ncols, 0);
- if (m->control_pressed) { return 0; }
-
- while ( accumulate( tmprow.begin(), tmprow.end(), 0 ) < initrowtotal[i])
- {
- if (m->control_pressed) { return 0; }
-
- double randNum = rand() / double(RAND_MAX);
- if(randNum <= range[0])
- {
- tmprow[0] = 1;
- continue;
- }
- for(int j=1;j<ncols;j++)
- {
- if(randNum <= range[j] && randNum > range[j-1] && tmprow[j] != 1)
- {
- tmprow[j] = 1;
- }
-
- }
- }
- tmpmatrix.push_back(tmprow);
- tmprow.clear();
- }
-
- initmatrix = tmpmatrix;
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "TrialSwap2", "sim5");
- exit(1);
- }
-}
-/**************************************************************************************************/
-/*
- *
- *
- *
- */
-/**************************************************************************************************/
-int TrialSwap2::sim6(vector<int> columntotal, vector<vector<int> > &co_matrix)
-{
- try {
- vector<vector<int> > tmpmatrix;
- vector<double> colProb;
- vector<int> tmprow;
- vector<double> range;
- int ncols = columntotal.size();
- int nrows = co_matrix.size();
-
- int colSum = accumulate( columntotal.begin(), columntotal.end(), 0 );
-
- for(int i=0;i<ncols;i++)
- {
- if (m->control_pressed) { return 0; }
- colProb.push_back(columntotal[i]/double (colSum));
- }
-
- double start = 0.0;
-
- for(int i=0;i<ncols;i++)
- {
- if (m->control_pressed) { return 0; }
- range.push_back(start + colProb[i]);
- start = range[i];
- }
-
- for(int i=0;i<nrows;i++)
- {
- if (m->control_pressed) { return 0; }
- tmprow.assign(ncols, 0);
- int tmprowtotal;
- tmprowtotal = (rand() / double (RAND_MAX)) * 10;
- while ( tmprowtotal > ncols) {
- if (m->control_pressed) { return 0; }
- tmprowtotal = (rand() / double (RAND_MAX)) * 10;
- }
- //cout << tmprowtotal << endl;
- //cout << accumulate( tmprow.begin(), tmprow.end(), 0 ) << endl;
-
- while ( accumulate( tmprow.begin(), tmprow.end(), 0 ) < tmprowtotal)
- {
- if (m->control_pressed) { return 0; }
- double randNum = rand() / double(RAND_MAX);
- //cout << randNum << endl;
- if(randNum <= range[0])
- {
- tmprow[0] = 1;
- continue;
- }
- for(int j=1;j<ncols;j++)
- {
- //cout << range[j] << endl;
- if(randNum <= range[j] && randNum > range[j-1] && tmprow[j] != 1)
- {
- tmprow[j] = 1;
- }
-
- }
-
-
- }
-
- tmpmatrix.push_back(tmprow);
- tmprow.clear();
- }
-
- co_matrix = tmpmatrix;
- tmpmatrix.clear();
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "TrialSwap2", "sim6");
- exit(1);
- }
-}
-/**************************************************************************************************/
-/*
- * MUST BE TRANSPOSED BEFORE CO-OCCURRENCE ANALYSIS
- *
- *
- */
-/**************************************************************************************************/
-int TrialSwap2::sim7(vector<int> initrowtotal, vector<vector<int> > &co_matrix)
-{
- try {
- vector<vector<double> > probmatrix;
- vector<vector<int> > tmpmatrix;
- vector<double> colProb;
- vector<double> probrow;
- vector<int> tmprow;
- vector<double> range;
- double nc;
- int ncols = co_matrix[0].size(); int nrows = co_matrix.size();
-
- tmpmatrix.assign(nrows, vector<int>(ncols, 0.));
-
- int rowsum = accumulate( initrowtotal.begin(), initrowtotal.end(), 0 );
-
- nc = rowsum * ncols;
- //cout << nc << endl;
-
- //assign null matrix based on probabilities
-
- double start = 0.0; // don't reset start -- probs should be from 0-1 thoughout the entire matrix
-
- for(int i=0;i<nrows;i++)
- {
- if (m->control_pressed) { return 0; }
- //cout << initrowtotal[i]/double(nc) << endl;
- double cellprob = initrowtotal[i]/double(nc);
- //cout << cellprob << endl;
- for(int j=0;j<ncols;j++)
- {
-
- probrow.push_back(start + cellprob);
- //cout << probrow[j] << endl;
- //cout << start << endl;
- start = start + cellprob;
- }
- probmatrix.push_back(probrow);
- probrow.clear();
- }
-
-
- //while(tmprowsum < rowsum)
- //for(int k=0;k<rowsum;k++)
- int k = 0;
- while(k < rowsum)
- {
- if (m->control_pressed) { return 0; }
- done:
- //cout << k << endl;
- //tmprowsum = accumulate( tmprowtotal.begin(), tmprowtotal.end(), 0 );
- double randNum = rand() / double(RAND_MAX);
- //cout << randNum << "+" << endl;
- //special case for the first entry
- if(randNum <= probmatrix[0][0] && tmpmatrix[0][0] != 1)
- {
- tmpmatrix[0][0] = 1;
- k++;
- //cout << k << endl;
- continue;
- }
-
-
- for(int i=0;i<nrows;i++)
- {
- if (m->control_pressed) { return 0; }
- for(int j=0;j<ncols;j++)
- {
- //cout << probmatrix[i][j] << endl;
- if(randNum <= probmatrix[i][j] && randNum > probmatrix[i][j-1] && tmpmatrix[i][j] != 1)
- {
- tmpmatrix[i][j] = 1;
- k++;
- //cout << k << endl;
- goto done;
- }
- //else
- //k = k-1;
- }
-
- }
-
- }
-
- co_matrix = tmpmatrix;
- return 0;
- //build probibility matrix
- /* for(int i=0;i<nrows;i++)
- {
- for(int j=0;j<ncols;j++)
- {
- probrow.push_back(rowtotal[i]/nc);
- }
- probmatrix.pushback(probrow);
- probrow.clear;
- }
- */
-
- /* int colSum = accumulate( initcolumntotal.begin(), initcolumntotal.end(), 0 );
-
- for(int i=0;i<ncols;i++)
- {
- colProb.push_back(initcolumntotal[i]/double (colSum));
- }
-
- double start = 0.0;
-
- for(int i=0;i<ncols;i++)
- {
- range.push_back(start + colProb[i]);
- start = range[i];
- }
-
- for(int i=0;i<nrows;i++)
- {
- tmprow.assign(ncols, 0);
- int tmprowtotal;
- tmprowtotal = (rand() / double (RAND_MAX)) * 10;
- while ( tmprowtotal > ncols)
- tmprowtotal = (rand() / double (RAND_MAX)) * 10;
- //cout << tmprowtotal << endl;
- //cout << accumulate( tmprow.begin(), tmprow.end(), 0 ) << endl;
-
- while ( accumulate( tmprow.begin(), tmprow.end(), 0 ) < tmprowtotal)
- {
- double randNum = rand() / double(RAND_MAX);
- //cout << randNum << endl;
- if(randNum <= range[0])
- {
- tmprow[0] = 1;
- continue;
- }
- for(int j=1;j<ncols;j++)
- {
- //cout << range[j] << endl;
- if(randNum <= range[j] && randNum > range[j-1] && tmprow[j] != 1)
- {
- tmprow[j] = 1;
- }
- }
- }
-
- tmpmatrix.push_back(tmprow);
- tmprow.clear();
- }
- initmatrix = tmpmatrix;
- */
- }
- catch(exception& e) {
- m->errorOut(e, "TrialSwap2", "sim7");
- exit(1);
- }
-}
-/**************************************************************************************************/
-/*
- *
- *
- *
- */
/**************************************************************************************************/
-int TrialSwap2::sim8(vector<int> columntotal, vector<int> rowtotal, vector<vector<int> > &co_matrix)
-{
- try {
- double prob;
- double start = 0.0;
- int ncols = columntotal.size(); int nrows = rowtotal.size();
- double probarray[nrows * ncols];
- double randnum;
- int grandtotal;
- int total = 0;
-
- //double colSum = accumulate( columntotal.begin(), columntotal.end(), 0 );
- double rowSum = accumulate( rowtotal.begin(), rowtotal.end(), 0 );
-
- if (m->control_pressed) { return 0; }
-
- //cout << "rowsum: " << rowSum << endl;
-
- grandtotal = rowSum;
-
- //create probability matrix with each site being between 0 and 1
- for (int i=0;i<nrows;i++) {
- if (m->control_pressed) { return 0; }
- for (int j=0;j<ncols;j++) {
- prob = (rowtotal[i] * columntotal[j])/(rowSum*rowSum);
- if (prob == 0.0)
- probarray[ncols * i + j] = -1;
- else
- probarray[ncols * i + j] = start + prob;
- //probmatrixrow.pushback(start + prob);
- start += prob;
- }
- }
- //cout << "prbarray" << endl;
- //for(int i=0;i<(nrows*ncols);i++)
- //cout << probarray[i] << " ";
- //cout << endl;
-
- //generate random muber between 0 and 1 and interate through probarray until found
- while (total < grandtotal) {
- if (m->control_pressed) { return 0; }
- randnum = rand() / double(RAND_MAX);
- //cout << "rand num: " << randnum << endl;
- if((randnum <= probarray[0]) && (probarray[0] != 2) ) {
- probarray[0] = 2;
- total++;
- continue;
- }
- for(int i=1;i<(nrows*ncols);i++) {
- if (m->control_pressed) { return 0; }
- if((randnum <= probarray[i]) && (randnum > probarray[i-1]) && (probarray[i] != 2) ) {
- probarray[i] = 2;
- total++;
- break;
- }
- else
- continue;
- }
- }
- //cout << "prbarray" << endl;
- //for(int i=0;i<(nrows*ncols);i++)
- //cout << probarray[i] << " ";
- //cout << endl;
- for(int i=0;i<nrows;i++) {
- if (m->control_pressed) { return 0; }
- for(int j=0;j<ncols;j++) {
- if(probarray[ncols * i + j] == 2)
- co_matrix[i][j] = 1;
- else
- co_matrix[i][j] = 0;
- }
- }
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "TrialSwap2", "sim8");
- exit(1);
- }
-}
-/**************************************************************************************************/
-double TrialSwap2::calc_c_score (vector<vector<int> > &co_matrix,vector<int> rowtotal)
+double TrialSwap2::calc_c_score (vector<vector<int> > &co_matrix, vector<int> rowtotal, int ncols, int nrows)
{
try {
double cscore = 0.0;
double D;
double normcscore = 0.0;
int nonzeros = 0;
- int ncols = co_matrix[0].size(); int nrows = rowtotal.size();
+ //int ncols = co_matrix[0].size(); int nrows = rowtotal.size();
vector<vector<double> > s; s.resize(nrows);
for (int i = 0; i < nrows; i++) { s[i].resize(nrows,0.0); }//only fill half the matrix
}
}
/**************************************************************************************************/
-int TrialSwap2::calc_checker (vector<vector<int> > &co_matrix, vector<int> rowtotal)
+int TrialSwap2::calc_checker (vector<vector<int> > &co_matrix, vector<int> rowtotal, int ncols, int nrows)
{
try {
int cunits=0;
//int s[nrows][ncols];
- int ncols = co_matrix[0].size(); int nrows = rowtotal.size();
+ //int ncols = co_matrix[0].size(); int nrows = rowtotal.size();
vector<vector<int> > s; s.resize(nrows);
for (int i = 0; i < nrows; i++) { s[i].resize(nrows,0); }//only fill half the matrix
}
}
/**************************************************************************************************/
-double TrialSwap2::calc_vratio (vector<int> rowtotal, vector<int> columntotal)
+double TrialSwap2::calc_vratio (int nrows, int ncols, vector<int> rowtotal, vector<int> columntotal)
{
try {
- int nrows = rowtotal.size();
- int ncols = columntotal.size();
+ //int nrows = rowtotal.size();
+ //int ncols = columntotal.size();
int sumCol = accumulate(columntotal.begin(), columntotal.end(), 0 );
// int sumRow = accumulate(rowtotal.begin(), rowtotal.end(), 0 );
}
/**************************************************************************************************/
-int TrialSwap2::calc_combo (vector<vector<int> > &initmatrix)
+int TrialSwap2::calc_combo (int nrows, int ncols, vector<vector<int> > &nullmatrix)
{
try {
- int initrows = initmatrix.size();
+ //need to transpose so we can compare rows (row-major order)
+ int tmpnrows = nrows;
+ vector<vector<int> > tmpmatrix;
+
+ vector<int> tmprow;
+ if(!tmpmatrix.empty())
+ tmpmatrix.clear();
+ for (int i=0;i<ncols;i++)
+ {
+ for (int j=0;j<nrows;j++)
+ {
+ tmprow.push_back(nullmatrix[j][i]);
+ }
+
+ tmpmatrix.push_back(tmprow);
+ tmprow.clear();
+ }
+
int unique = 0;
int match = 0;
- int matches = 0;
- for(int i=0;i<initrows;i++)
+ for(int j=0;j<ncols;j++)
{
match = 0;
- for(int j=i+1;j<=initrows;j++)
+ for(int i=j+1;i<=ncols;i++)
{
- if (m->control_pressed) { return 0; }
- if( (initmatrix[i] == initmatrix[j]))
+ //comparing matrix rows
+ if( (tmpmatrix[j] == tmpmatrix[i]))
{
match++;
- matches++;
break;
}
}
-
+
//on the last iteration of a previously matched row it will add itself because it doesn't match any following rows, so that combination is counted
if (match == 0)
unique++;
- }
- return unique;
+ }
+ return unique;
}
catch(exception& e) {
m->errorOut(e, "TrialSwap2", "calc_combo");
while((j = m->getRandomIndex(nrows-1) ) == i ) {;if (m->control_pressed) { return 0; }}
k = m->getRandomIndex(ncols-1);
while((l = m->getRandomIndex(ncols-1)) == k ) {;if (m->control_pressed) { return 0; }}
-
- //cout << co_matrix[i][k] << " " << co_matrix[j][l] << endl;
- //cout << co_matrix[i][l] << " " << co_matrix[j][k] << endl;
- //cout << co_matrix[i][l] << " " << co_matrix[j][k] << endl;
- //cout << co_matrix[i][l] << " " << co_matrix[j][k] << endl;
+
if((co_matrix[i][k]*co_matrix[j][l]==1 && co_matrix[i][l]+co_matrix[j][k]==0)||(co_matrix[i][k]+co_matrix[j][l]==0 && co_matrix[i][l]*co_matrix[j][k]==1)) //checking for checkerboard value and swap
{
co_matrix[i][k]=1-co_matrix[i][k];
co_matrix[i][l]=1-co_matrix[i][l];
co_matrix[j][k]=1-co_matrix[j][k];
co_matrix[j][l]=1-co_matrix[j][l];
- //cout << "swapped!" << endl;
+
}
- //cout << "i: " << i << " j: " << j << " k: " << " l: " << l << endl;
+
return 0;
}
catch(exception& e) {
}
}
/**************************************************************************************************/
-int TrialSwap2::transpose_matrix (vector<vector<int> > &initmatrix, vector<vector<int> > &co_matrix)//, int nrows, int nocols)
-{
- try {
- int ncols = initmatrix.size(); int nrows = initmatrix[0].size();
- int tmpnrows = nrows;
- //vector<vector<int> > tmpvec;
- vector<int> tmprow;
- if(!co_matrix.empty())
- co_matrix.clear();
- for (int i=0;i<nrows;i++)
- {
- if (m->control_pressed) { return 0; }
- for (int j=0;j<ncols;j++)
- {
- tmprow.push_back(initmatrix[j][i]);
- }
- /*if (accumulate( tmprow.begin(), tmprow.end(), 0 ) == 0)
- {
- tmpnrows--;
- }
- else */
- co_matrix.push_back(tmprow);
- tmprow.clear();
- }
- nrows = tmpnrows;
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "TrialSwap2", "transpose_matrix");
- exit(1);
- }
-}
-/**************************************************************************************************/
-int TrialSwap2::update_row_col_totals(vector<vector<int> > &co_matrix, vector<int> &rowtotal, vector<int> &columntotal)
-{
- try {
- //rowtotal.clear();
- //columntotal.clear();
- //generate (rowtotal.begin(), rowtotal.end(), 0);
- //generate (columntotal.begin(), columntotal.end(), 0);
- int nrows = co_matrix.size();
- int ncols = co_matrix[0].size();
- vector<int> tmpcolumntotal; tmpcolumntotal.resize(ncols, 0);
- vector<int> tmprowtotal; tmprowtotal.resize(nrows, 0);
-
- int rowcount = 0;
-
- for (int i = 0; i < nrows; i++)
- {
- if (m->control_pressed) { return 0; }
- for (int j = 0; j < ncols; j++)
- {
- if (co_matrix[i][j] == 1)
- {
- rowcount++;
- tmpcolumntotal[j]++;
- }
- }
- tmprowtotal[i] = rowcount;
- rowcount = 0;
- }
- columntotal = tmpcolumntotal;
- rowtotal = tmprowtotal;
- /*cout << "rowtotal: ";
- for(int i = 0; i<nrows; i++) { cout << rowtotal[i]; }
- cout << " ";
- cout << " coltotal: ";
- for(int i = 0; i<ncols; i++) { cout << columntotal[i]; }
- cout << endl;*/
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "TrialSwap2", "update_row_col_totals");
- exit(1);
- }
-}
-/**************************************************************************************************/
+
projects / mothur.git / commitdiff