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 / blobdiff