added sparseDistanceMatrix class. Modified cluster commands to use the new sparse...

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 888f50202e3443855a99d82d71b126cf715ee380..6633e5160559297c23a542c373ed1b1cc9a3ccdc 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -286,7 +286,7 @@ TreeGroupCommand::TreeGroupCommand(string option)  {
 TreeGroupCommand::~TreeGroupCommand(){
        if (abort == false) {
                if (format == "sharedfile") {  delete input; }
-               else { delete readMatrix;  delete matrix; delete list; }
+               else { delete list; }
                delete tmap;  
        }
        
@@ -418,7 +418,8 @@ int TreeGroupCommand::execute(){
                }else{
                        //read in dist file
                        filename = inputfile;
-               
+            
+            ReadMatrix* readMatrix;
                        if (format == "column") { readMatrix = new ReadColumnMatrix(filename); }        
                        else if (format == "phylip") { readMatrix = new ReadPhylipMatrix(filename); }
                                
@@ -434,7 +435,7 @@ int TreeGroupCommand::execute(){
        
                        readMatrix->read(nameMap);
                        list = readMatrix->getListVector();
-                       matrix = readMatrix->getMatrix();
+                       SparseDistanceMatrix* dMatrix = readMatrix->getDMatrix();
 
                        //make treemap
                        tmap = new TreeMap();
@@ -457,7 +458,9 @@ int TreeGroupCommand::execute(){
                        
                        if (m->control_pressed) { return 0; }
                        
-                       vector< vector<double> > matrix = makeSimsDist();
+                       vector< vector<double> > matrix = makeSimsDist(dMatrix);
+            delete readMatrix;
+            delete dMatrix;
                        
                        if (m->control_pressed) { return 0; }
 
@@ -554,7 +557,7 @@ void TreeGroupCommand::printSims(ostream& out, vector< vector<double> >& simMatr
        }
 }
 /***********************************************************/
-vector< vector<double> > TreeGroupCommand::makeSimsDist() {
+vector< vector<double> > TreeGroupCommand::makeSimsDist(SparseDistanceMatrix* matrix) {
        try {
                numGroups = list->size();
                
@@ -569,13 +572,17 @@ vector< vector<double> > TreeGroupCommand::makeSimsDist() {
                
                //go through sparse matrix and fill sims
                //go through each cell in the sparsematrix
-               for(MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++){
-                       //similairity = -(distance-1)
-                       simMatrix[currentCell->row][currentCell->column] = -(currentCell->dist -1.0);   
-                       simMatrix[currentCell->column][currentCell->row] = -(currentCell->dist -1.0);   
-                       
-                       if (m->control_pressed) { return simMatrix; }
+        for (int i = 0; i < matrix->seqVec.size(); i++) {
+            for (int j = 0; j < matrix->seqVec[i].size(); j++) {
+                
+                //already checked everyone else in row
+                if (i < matrix->seqVec[i][j].index) {   
+                    simMatrix[i][matrix->seqVec[i][j].index] = -(matrix->seqVec[i][j].dist -1.0);      
+                    simMatrix[matrix->seqVec[i][j].index][i] = -(matrix->seqVec[i][j].dist -1.0);      
                        
+                    if (m->control_pressed) { return simMatrix; }
+                }
+            }
                }
 
                return simMatrix;