some changes while testing 1.9

[mothur.git] / cluster.cpp

diff --git a/cluster.cpp b/cluster.cpp
index e2d307e1bfbce54162b55a7368b58180205f87e5..96ca44061436f873ee8b663e248ddcc386c995cb 100644 (file)
--- a/cluster.cpp
+++ b/cluster.cpp
@@ -50,14 +50,17 @@ rabund(rav), list(lv), dMatrix(dm), method(f)
        // a list contains pointers (iterators) to the all distances related
        // to a certain sequence. The Vector is accessed via the index of a 
        // sequence in the distance matrix.
-       
-
+//ofstream outtemp;
+//string temp = "temp";
+//openOutputFile(temp, outtemp);       
+//cout << lv->size() << endl;
        seqVec = vector<MatVec>(lv->size());
        for (MatData currentCell = dMatrix->begin(); currentCell != dMatrix->end(); currentCell++) {
+//outtemp << currentCell->row << '\t' << currentCell->column  << '\t' << currentCell->dist << endl;
                seqVec[currentCell->row].push_back(currentCell);
                seqVec[currentCell->column].push_back(currentCell);
        }
-
+//outtemp.close();
        mapWanted = false;  //set to true by mgcluster to speed up overlap merge
        
        //save so you can modify as it changes in average neighbor
@@ -74,11 +77,16 @@ void Cluster::getRowColCells() {
                smallRow = smallCell->row;              // get its row
                smallCol = smallCell->column;   // get its column
                smallDist = smallCell->dist;    // get the smallest distance
-       
+       //cout << "small row = " << smallRow << "small col = " << smallCol << "small dist = " << smallDist << endl;
+        
                rowCells = seqVec[smallRow];    // all distances related to the row index
                colCells = seqVec[smallCol];    // all distances related to the column index
                nRowCells = rowCells.size();
                nColCells = colCells.size();
+//cout << "num rows = " << nRowCells << "num col = " << nColCells << endl;
+               
+               //for (int i = 0; i < nColCells; i++) { cout << colCells[i]->row << '\t' << colCells[i]->column << endl;  }
+               //for (int i = 0; i < nRowCells; i++) { cout << rowCells[i]->row << '\t' << rowCells[i]->column << endl;  }
        }
        catch(exception& e) {
                m->errorOut(e, "Cluster", "getRowColCells");
@@ -132,7 +140,9 @@ void Cluster::removeCell(const MatData& cell, int vrow, int vcol, bool rmMatrix)
                        seqVec[dcol].erase(seqVec[dcol].begin()+vcol);
                
                        if (rmMatrix) {
+                       //cout << " removing = " << cell->row << '\t' << cell->column  << '\t' << cell->dist << endl;
                                dMatrix->rmCell(cell);
+               //      cout << "done" << endl;
                        }
                
        }
@@ -188,6 +198,7 @@ void Cluster::clusterNames(){
 void Cluster::update(double& cutOFF){
        try {
                getRowColCells();       
+//cout << "got rowcells" << endl;
 
                vector<int> foundCol(nColCells, 0);