X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.h;h=c5afe86a79a9e92c789735ea3b1be3d33accf66a;hb=952a85d59a12e664f5efa6d01681be189e4fff9c;hp=20d3b4b64725d0428248b47b22a3146a0a3a52c9;hpb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2;p=mothur.git

diff --git a/mothur.h b/mothur.h
index 20d3b4b..c5afe86 100644
--- a/mothur.h
+++ b/mothur.h
@@ -45,22 +45,23 @@
 #include <ctime>
 #include <limits>
 
-using namespace std;
 
-#ifdef _WIN32
-	#define exp(x) (exp((double) x))
-	#define sqrt(x) (sqrt((double) x))
-	#define log10(x) (log10((double) x))
-	#define log2(x) (log10(x)/log10(2))
-	#define isnan(x) ((x) != (x))
-	#define isinf(x) (fabs(x) == std::numeric_limits<double>::infinity())
-#else
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 	#include <sys/wait.h>
 	#include <unistd.h>
 #endif
 
+using namespace std;
+
+#define exp(x) (exp((double) x))
+#define sqrt(x) (sqrt((double) x))
+#define log10(x) (log10((double) x))
+#define log2(x) (log10(x)/log10(2))
+#define isnan(x) ((x) != (x))
+#define isinf(x) (fabs(x) == std::numeric_limits<double>::infinity())
 
-typedef unsigned long long ull;
+
+typedef unsigned long ull;
 
 struct IntNode {
 	int lvalue;
@@ -96,6 +97,7 @@ inline void convert(const string& s, T& x, bool failIfLeftoverChars = true){
 	if (!(i >> x) || (failIfLeftoverChars && i.get(c)))
 		throw BadConversion(s);
 }
+
 //**********************************************************************************************************************
 
 template<typename T>
@@ -153,14 +155,13 @@ 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 {
@@ -168,7 +169,30 @@ inline int openOutputFileAppend(string fileName, ofstream& fileHandle){
 	}
 
 }
+/***********************************************************************/
 
+inline string getline(ifstream& fileHandle) {
+	try {
+	
+		string line = "";
+		
+		while (!fileHandle.eof())	{
+			//get next character
+			char c = fileHandle.get(); 
+			
+			//are you at the end of the line
+			if ((c == '\n') || (c == '\r') || (c == '\f')){   break;	}	
+			else {		line += c;		}
+		}
+		
+		return line;
+		
+	}
+	catch(exception& e) {
+		cout << "Error in mothur function getline" << endl;
+		exit(1);
+	}
+}
 
 /**************************************************************************************************/
 
@@ -233,12 +257,14 @@ 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@umich.edu, and be sure to include the mothur.logFile with your inquiry.");
 		mothurOutEndLine();
 	
 }
 
 
+
+
 /***********************************************************************/
 
 inline void gobble(istream& f){
@@ -394,7 +420,7 @@ 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 +435,7 @@ 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 {