added stricter compilation requirements and fixed resulting errors

[mothur.git] / mothur.h

diff --git a/mothur.h b/mothur.h
index 20d3b4b64725d0428248b47b22a3146a0a3a52c9..2efdda8bda209ec303dd7e6bc1b8650b5eb65949 100644 (file)
--- a/mothur.h
+++ b/mothur.h
@@ -60,7 +60,7 @@ using namespace std;
 #endif
 
 
-typedef unsigned long long ull;
+typedef unsigned long ull;
 
 struct IntNode {
        int lvalue;
@@ -153,14 +153,13 @@ string toString(const T&x, int i){
        
     return output.str();
 }
-
 /***********************************************************************/
 
 inline int openOutputFileAppend(string fileName, ofstream& fileHandle){
        
        fileHandle.open(fileName.c_str(), ios::app);
        if(!fileHandle) {
-               cerr << "Error: Could not open " << fileName << endl;
+               cout << "Error: Could not open " <<  fileName << endl; 
                return 1;
        }
        else {
@@ -169,7 +168,6 @@ inline int openOutputFileAppend(string fileName, ofstream& fileHandle){
 
 }
 
-
 /**************************************************************************************************/
 
 inline void mothurOut(string message) {
@@ -233,12 +231,14 @@ inline void errorOut(exception& e, string object, string function) {
        
                mothurOut("Error: ");
                mothurOut(toString(e.what()));
-               mothurOut(" has occurred in the " + object + " class function " + function + "Please contact Pat Schloss at pschloss@microbio.umass.edu, and be sure to include the mothur.logFile with your inquiry.");
+               mothurOut(" has occurred in the " + object + " class function " + function + ". Please contact Pat Schloss at pschloss@microbio.umass.edu, and be sure to include the mothur.logFile with your inquiry.");
                mothurOutEndLine();
        
 }
 
 
+
+
 /***********************************************************************/
 
 inline void gobble(istream& f){
@@ -394,7 +394,7 @@ inline int openInputFile(string fileName, ifstream& fileHandle){
 
        fileHandle.open(fileName.c_str());
        if(!fileHandle) {
-               cerr << "Error: Could not open " << fileName << endl;
+               mothurOut("Error: Could not open " + fileName);  mothurOutEndLine();
                return 1;
        }
        else {
@@ -409,7 +409,7 @@ inline int openOutputFile(string fileName, ofstream& fileHandle){
        
        fileHandle.open(fileName.c_str(), ios::trunc);
        if(!fileHandle) {
-               cerr << "Error: Could not open " << fileName << endl;
+               mothurOut("Error: Could not open " + fileName);  mothurOutEndLine();
                return 1;
        }
        else {