}
}
/**************************************************************************************************/
+/*
+ * 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;
projects / mothur.git / commitdiff