//reset groups parameter
delete input;
+ m->clearGroups();
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
int CooccurrenceCommand::getCooccurrence(vector<SharedRAbundVector*>& thisLookUp, ofstream& out){
try {
int numOTUS = thisLookUp[0]->getNumBins();
- vector< vector<int> > initmatrix (thisLookUp.size());
- vector< vector<int> > co_matrix (thisLookUp[0]->getNumBins());
+ vector< vector<int> > initmatrix; initmatrix.resize(thisLookUp.size());
+ vector< vector<int> > co_matrix; co_matrix.resize(thisLookUp[0]->getNumBins());
for (int i = 0; i < thisLookUp[0]->getNumBins(); i++) { co_matrix[i].resize((thisLookUp.size()), 0); }
for (int i = 0; i < thisLookUp.size(); i++) { initmatrix[i].resize((thisLookUp[i]->getNumBins()), 0); }
- vector<int> columntotal(thisLookUp.size(), 0);
- vector<int> rowtotal(numOTUS, 0);
+ vector<int> columntotal; columntotal.resize(thisLookUp.size(), 0);
+ vector<int> rowtotal; rowtotal.resize(numOTUS, 0);
int rowcount = 0;
for (int i = 0; i < thisLookUp.size(); i++) {
//nrows is ncols of inital matrix. All the functions need this value. They assume the transposition has already taken place and nrows and ncols refer to that matrix.
//comatrix and initmatrix are still vectors of vectors of ints as in the original script. The abundancevector is only what was read in ie not a co-occurrence matrix!
int ncols = numOTUS;//rows of inital matrix
- int nrows = thisLookUp.size();//OTUs
+ int nrows = thisLookUp.size();//groups
double initscore = 0.0;
//transpose matrix
int newmatrows = ncols;
nrows = newmatrows;//ncols;
ncols = newmatcols;//nrows;
- vector<int> initcolumntotal(ncols, 0);
- vector<int> initrowtotal(nrows, 0);
+ vector<int> initcolumntotal; initcolumntotal.resize(ncols, 0);
+ vector<int> initrowtotal; initrowtotal.resize(nrows, 0);
vector<double> stats;
TrialSwap2 trial;