Thallinger changes to cluster command.

[mothur.git] / sparsematrix.cpp

diff --git a/sparsematrix.cpp b/sparsematrix.cpp
index 7f1c3c8564d29c6b1c551f7ee9bd16b58636af0a..8a873f74c2441c4dd50f20450ebe4882227ce32b 100644 (file)
--- a/sparsematrix.cpp
+++ b/sparsematrix.cpp
@@ -2,7 +2,6 @@
 #include "sparsematrix.hpp"
 #include "listvector.hpp"
 
-typedef list<PCell>::iterator MatData;
 
 /***********************************************************************/
 
@@ -22,15 +21,15 @@ float SparseMatrix::getSmallDist(){
 
 /***********************************************************************/
 
-void SparseMatrix::rmCell(MatData data){
+MatData SparseMatrix::rmCell(MatData data){
        try {
                if(data->vectorMap != NULL ){
                        *(data->vectorMap) = NULL;
                        data->vectorMap = NULL;
                }
-               matrix.erase(data);             
+               data = matrix.erase(data);              
                numNodes--;
-       
+               return(data);
        //  seems like i should be updating smallDist here, but the only time we remove cells is when
        //  clustering and the clustering algorithm updates smallDist
        }
@@ -89,13 +88,11 @@ MatData SparseMatrix::end(){
 void SparseMatrix::print(){
        try {
                int index = 0;
-               
-               mothurOutEndLine();
-               mothurOut("Index\tRow\tColumn\tDistance");
-               mothurOutEndLine();
+       
+               cout << endl << "Index\tRow\tColumn\tDistance" << endl;
        
                for(MatData currentCell=matrix.begin();currentCell!=matrix.end();currentCell++){
-                       mothurOut(toString(index) + "\t" + toString(currentCell->row)  + "\t" + toString(currentCell->column) + "\t" + toString(currentCell->dist)); mothurOutEndLine();
+                       cout << index << '\t' << currentCell->row  << '\t' << currentCell->column << '\t' << currentCell->dist << endl;
                        index++;
                }
        }
@@ -111,10 +108,7 @@ void SparseMatrix::print(ListVector* list){
        try {
                int index = 0;
        
-               mothurOutEndLine();
-               mothurOut("Index\tRow\tColumn\tDistance");
-               mothurOutEndLine();
-
+               mothurOutEndLine(); mothurOut("Index\tRow\tColumn\tDistance"); mothurOutEndLine();
        
                for(MatData currentCell=matrix.begin();currentCell!=matrix.end();currentCell++){
                        mothurOut(toString(index) + "\t" + toString(list->get(currentCell->row))  + "\t" + toString(list->get(currentCell->column)) + "\t" + toString(currentCell->dist)); mothurOutEndLine();
@@ -159,7 +153,7 @@ PCell* SparseMatrix::getSmallestCell(){
                                }
 
                        }
-                       random_shuffle(mins.begin(), mins.end());  //randomize the order of the iterators in the mins vector
+//                     random_shuffle(mins.begin(), mins.end());  //randomize the order of the iterators in the mins vector
 
                        for(int i=0;i<mins.size();i++){
                                mins[i]->vectorMap = &mins[i];  //assign vectorMap to the address for the container