added logfile feature

[mothur.git] / fullmatrix.cpp

diff --git a/fullmatrix.cpp b/fullmatrix.cpp
index bc53b7db926cca543449fe58b5182d7d1ed6af67..5bb2d2336d6ea263a1b0596511abf5f66cb7a248 100644 (file)
--- a/fullmatrix.cpp
+++ b/fullmatrix.cpp
@@ -27,7 +27,7 @@ FullMatrix::FullMatrix(ifstream& filehandle) {
                }
                
                group = groupmap->getGroup(name);
-               if(group == "not found") {      cout << "Error: Sequence '" << name << "' was not found in the group file, please correct." << endl; exit(1); }
+               if(group == "not found") {      mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); mothurOutEndLine(); exit(1); }
                index.resize(numSeqs);
                index[0].groupName = group; 
                index[0].seqName = name;
@@ -78,11 +78,7 @@ FullMatrix::FullMatrix(ifstream& filehandle) {
                
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function FullMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the FullMatrix class function FullMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "FullMatrix", "FullMatrix");
                exit(1);
        }
 }
@@ -104,7 +100,7 @@ void FullMatrix::readSquareMatrix(ifstream& filehandle) {
                        index[i].groupName = group;
                        index[i].seqName = name;
                        
-                       if(group == "not found") {      cout << "Error: Sequence '" << name << "' was not found in the group file, please correct." << endl; exit(1); }
+                       if(group == "not found") {      mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); mothurOutEndLine(); exit(1); }
                                
                        for(int j=0;j<numSeqs;j++){
                                filehandle >> matrix[i][j];
@@ -117,14 +113,9 @@ void FullMatrix::readSquareMatrix(ifstream& filehandle) {
                delete reading;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function readSquareMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the FullMatrix class function readSquareMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "FullMatrix", "readSquareMatrix");
                exit(1);
        }
-
 } 
 /**************************************************************************/
 void FullMatrix::readLTMatrix(ifstream& filehandle) {
@@ -144,7 +135,7 @@ void FullMatrix::readLTMatrix(ifstream& filehandle) {
                        index[i].groupName = group;
                        index[i].seqName = name;
        
-                       if(group == "not found") {      cout << "Error: Sequence '" << name << "' was not found in the group file, please correct." << endl;  exit(1); }
+                       if(group == "not found") {      mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); mothurOutEndLine();  exit(1); }
                                
                        for(int j=0;j<i;j++){
                                filehandle >> distance;
@@ -159,14 +150,9 @@ void FullMatrix::readLTMatrix(ifstream& filehandle) {
                delete reading;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function readLTMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the FullMatrix class function readLTMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "FullMatrix", "readLTMatrix");
                exit(1);
        }
-
 }
 
 /**************************************************************************/
@@ -231,14 +217,9 @@ void FullMatrix::sortGroups(int low, int high){
        
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function sortGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the FullMatrix class function sortGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "FullMatrix", "sortGroups");
                exit(1);
        }
-
 }
 
 /**************************************************************************/   
@@ -274,14 +255,9 @@ void FullMatrix::printMatrix(ostream& out) {
                }
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function printMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "FullMatrix", "printMatrix");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the FullMatrix class function printMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-
 }
 
 /**************************************************************************/