added logfile feature

[mothur.git] / sharedlistvector.cpp

diff --git a/sharedlistvector.cpp b/sharedlistvector.cpp
index 3cb3e9e57c4da06f0589272cff4b3e97bd92eea4..ba2ac1f54082a44cc188611994ff4f5c61b65ad3 100644 (file)
--- a/sharedlistvector.cpp
+++ b/sharedlistvector.cpp
@@ -44,11 +44,7 @@ SharedListVector::SharedListVector(ifstream& f) : DataVector(), maxRank(0), numB
        
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function SharedListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedListVector class function SharedListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedListVector", "SharedListVector");
                exit(1);
        }
 }
@@ -67,11 +63,7 @@ void SharedListVector::set(int binNumber, string seqNames){
                numSeqs += (nNames_new - nNames_old);
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedListVector class function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedListVector", "set");
                exit(1);
        }
 }
@@ -96,11 +88,7 @@ void SharedListVector::push_back(string seqNames){
                numSeqs += nNames;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedListVector class function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedListVector", "push_back");
                exit(1);
        }
 }
@@ -140,11 +128,7 @@ void SharedListVector::print(ostream& output){
                output << endl;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedListVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedListVector", "print");
                exit(1);
        }
 }
@@ -175,11 +159,7 @@ RAbundVector SharedListVector::getRAbundVector(){
                return rav;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedListVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedListVector", "getRAbundVector");
                exit(1);
        }
 }
@@ -200,11 +180,7 @@ SAbundVector SharedListVector::getSAbundVector(){
                return sav;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedListVector class function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedListVector", "getSAbundVector");
                exit(1);
        }
 }
@@ -237,14 +213,9 @@ SharedOrderVector* SharedListVector::getSharedOrderVector(){
                return order;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getSharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedListVector", "getSharedOrderVector");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedListVector class function getSharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-
 }
 /***********************************************************************/
 SharedRAbundVector SharedListVector::getSharedRAbundVector(string groupName) {
@@ -277,11 +248,7 @@ SharedRAbundVector SharedListVector::getSharedRAbundVector(string groupName) {
                
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedListVector class function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedListVector", "getSharedRAbundVector");
                exit(1);
        }
 }
@@ -326,14 +293,9 @@ vector<SharedRAbundVector*> SharedListVector::getSharedRAbundVector() {
                return lookup;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedListVector class function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedListVector", "getSharedRAbundVector");
                exit(1);
        }
-       
 }
 
 /***********************************************************************/
@@ -348,11 +310,7 @@ SharedSAbundVector SharedListVector::getSharedSAbundVector(string groupName) {
                return sav;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getSharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedListVector class function getSharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedListVector", "getSharedSAbundVector");
                exit(1);
        }
 }
@@ -393,7 +351,7 @@ OrderVector SharedListVector::getOrderVector(map<string,int>* orderMap = NULL){
                                        }
                                        else{
                                                if(orderMap->count(seqName) == 0){
-                                                       cerr << seqName << " not found, check *.names file\n";
+                                                       mothurOut(seqName + " not found, check *.names file\n");
                                                        exit(1);
                                                }
                                        
@@ -403,7 +361,7 @@ OrderVector SharedListVector::getOrderVector(map<string,int>* orderMap = NULL){
                                }
                        
                                if(orderMap->count(seqName) == 0){
-                                       cerr << seqName << " not found, check *.names file\n";
+                                       mothurOut(seqName + " not found, check *.names file\n");
                                        exit(1);
                                }
                                ov.set((*orderMap)[seqName], i);        
@@ -416,11 +374,7 @@ OrderVector SharedListVector::getOrderVector(map<string,int>* orderMap = NULL){
                }
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedListVector class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedListVector", "getOrderVector");
                exit(1);
        }
 }