changes while testing

[mothur.git] / sparsematrix.cpp

diff --git a/sparsematrix.cpp b/sparsematrix.cpp
index 8a873f74c2441c4dd50f20450ebe4882227ce32b..3a0ec6521720c1f89eb7c54ce47f60a2f81d364a 100644 (file)
--- a/sparsematrix.cpp
+++ b/sparsematrix.cpp
@@ -5,7 +5,7 @@
 
 /***********************************************************************/
 
-SparseMatrix::SparseMatrix() : numNodes(0), minsIndex(0), smallDist(1e6){}
+SparseMatrix::SparseMatrix() : numNodes(0), minsIndex(0), smallDist(1e6){  m = MothurOut::getInstance();  }
 
 /***********************************************************************/
 
@@ -34,7 +34,7 @@ MatData SparseMatrix::rmCell(MatData data){
        //  clustering and the clustering algorithm updates smallDist
        }
        catch(exception& e) {
-               errorOut(e, "SparseMatrix", "rmCell");
+               m->errorOut(e, "SparseMatrix", "rmCell");
                exit(1);
        }
 }
@@ -50,7 +50,7 @@ void SparseMatrix::addCell(PCell value){
                }
        }
        catch(exception& e) {
-               errorOut(e, "SparseMatrix", "addCell");
+               m->errorOut(e, "SparseMatrix", "addCell");
                exit(1);
        }
 }
@@ -66,7 +66,7 @@ void SparseMatrix::clear(){
                smallDist = 1e6;
        }
        catch(exception& e) {
-               errorOut(e, "SparseMatrix", "clear");
+               m->errorOut(e, "SparseMatrix", "clear");
                exit(1);
        }
 }
@@ -97,7 +97,7 @@ void SparseMatrix::print(){
                }
        }
        catch(exception& e) {
-               errorOut(e, "SparseMatrix", "print");
+               m->errorOut(e, "SparseMatrix", "print");
                exit(1);
        }
 }
@@ -108,15 +108,15 @@ void SparseMatrix::print(ListVector* list){
        try {
                int index = 0;
        
-               mothurOutEndLine(); mothurOut("Index\tRow\tColumn\tDistance"); mothurOutEndLine();
+               m->mothurOutEndLine(); m->mothurOut("Index\tRow\tColumn\tDistance"); m->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();
+                       m->mothurOut(toString(index) + "\t" + toString(list->get(currentCell->row))  + "\t" + toString(list->get(currentCell->column)) + "\t" + toString(currentCell->dist)); m->mothurOutEndLine();
                        index++;
                }
        }
        catch(exception& e) {
-               errorOut(e, "SparseMatrix", "print");
+               m->errorOut(e, "SparseMatrix", "print");
                exit(1);
        }
 }
@@ -136,7 +136,7 @@ PCell* SparseMatrix::getSmallestCell(){
        //      if the mins vector is empty go here...
                if(mins.empty()){               
                        mins.clear();
-               
+       
                        smallDist = begin()->dist;  //set the first candidate small distance
                
                        for(MatData currentCell=begin();currentCell!=end();currentCell++){
@@ -153,7 +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
@@ -168,7 +168,7 @@ PCell* SparseMatrix::getSmallestCell(){
                return smallCell;
        }
        catch(exception& e) {
-               errorOut(e, "SparseMatrix", "getSmallestCell");
+               m->errorOut(e, "SparseMatrix", "getSmallestCell");
                exit(1);
        }
 }