X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treegroupscommand.cpp;h=6633e5160559297c23a542c373ed1b1cc9a3ccdc;hb=5a4ac4f954c4b4445bcee272f1f8220ddcc9c1e4;hp=888f50202e3443855a99d82d71b126cf715ee380;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96;p=mothur.git

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 888f502..6633e51 100644
--- 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;