added logfile feature

[mothur.git] / sparsematrix.cpp

diff --git a/sparsematrix.cpp b/sparsematrix.cpp
index c4120f49d679ffc497ba72e7e0da8fc0fc22c00a..7f1c3c8564d29c6b1c551f7ee9bd16b58636af0a 100644 (file)
--- a/sparsematrix.cpp
+++ b/sparsematrix.cpp
@@ -35,13 +35,9 @@ void SparseMatrix::rmCell(MatData data){
        //  clustering and the clustering algorithm updates smallDist
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SparseMatrix class Function rmCell. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SparseMatrix", "rmCell");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SparseMatrix class function rmCell. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 /***********************************************************************/
@@ -55,13 +51,9 @@ void SparseMatrix::addCell(PCell value){
                }
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SparseMatrix class Function addCell. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SparseMatrix", "addCell");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SparseMatrix class function addCell. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 /***********************************************************************/
@@ -75,13 +67,9 @@ void SparseMatrix::clear(){
                smallDist = 1e6;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SparseMatrix class Function clear. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SparseMatrix", "clear");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SparseMatrix class function clear. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 /***********************************************************************/
@@ -101,22 +89,20 @@ MatData SparseMatrix::end(){
 void SparseMatrix::print(){
        try {
                int index = 0;
-       
-               cout << endl << "Index\tRow\tColumn\tDistance" << endl;
+               
+               mothurOutEndLine();
+               mothurOut("Index\tRow\tColumn\tDistance");
+               mothurOutEndLine();
        
                for(MatData currentCell=matrix.begin();currentCell!=matrix.end();currentCell++){
-                       cout << index << '\t' << currentCell->row  << '\t' << currentCell->column << '\t' << currentCell->dist << endl;
+                       mothurOut(toString(index) + "\t" + toString(currentCell->row)  + "\t" + toString(currentCell->column) + "\t" + toString(currentCell->dist)); mothurOutEndLine();
                        index++;
                }
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SparseMatrix class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SparseMatrix", "print");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SparseMatrix class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 /***********************************************************************/
@@ -125,21 +111,20 @@ void SparseMatrix::print(ListVector* list){
        try {
                int index = 0;
        
-               cout << endl << "Index\tRow\tColumn\tDistance" << endl;
+               mothurOutEndLine();
+               mothurOut("Index\tRow\tColumn\tDistance");
+               mothurOutEndLine();
+
        
                for(MatData currentCell=matrix.begin();currentCell!=matrix.end();currentCell++){
-                       cout << index << '\t' << list->get(currentCell->row)  << '\t' << list->get(currentCell->column) << '\t' << currentCell->dist << endl;
+                       mothurOut(toString(index) + "\t" + toString(list->get(currentCell->row))  + "\t" + toString(list->get(currentCell->column)) + "\t" + toString(currentCell->dist)); mothurOutEndLine();
                        index++;
                }
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SparseMatrix class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SparseMatrix", "print");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SparseMatrix class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 /***********************************************************************/
@@ -189,13 +174,9 @@ PCell* SparseMatrix::getSmallestCell(){
                return smallCell;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SparseMatrix class Function getSmallestCell. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SparseMatrix", "getSmallestCell");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SparseMatrix class function getSmallestCell. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 /***********************************************************************/