From 1d58557e4ce9f1b2d54db61937c161d889d6558b Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Sun, 2 Aug 2009 20:55:29 +0000
Subject: [PATCH] bugs fixes while testing for 1.5 release

---
 collectsharedcommand.cpp |  3 +--
 engine.cpp               |  7 ++++---
 fileoutput.cpp           | 18 +++++++++---------
 mothur.h                 |  5 ++++-
 4 files changed, 18 insertions(+), 15 deletions(-)

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 3fed167..e158dbb 100644
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -255,10 +255,9 @@ int CollectSharedCommand::execute(){
 				processedLabels.insert(order->getLabel());
 				userLabels.erase(order->getLabel());
 				userLines.erase(count);
-
-			//you have a label the user want that is smaller than this line and the last line has not already been processed 
 			}
 			
+			//you have a label the user want that is smaller than this line and the last line has not already been processed
 			if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 				delete order;
 				order = input->getSharedOrderVector(lastLabel);
diff --git a/engine.cpp b/engine.cpp
index 95c0ff0..e589803 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -119,9 +119,10 @@ bool BatchEngine::getInput(){
 		while(quitCommandCalled == 0){
 	
 			if (inputBatchFile.eof()) { input = "quit()"; }
-			else { input = getline(inputBatchFile); }
-			
-			
+			else { getline(inputBatchFile, input); }
+	//cout << "input = ";		
+	//for (int i = 0; i < input.size();  i++) {  cout << input[i];  if ((input[i] == '\n') || (input[i] == '\r')) {  char c = input[i]; cout << "line feed = " << c << endl; } }
+	//cout << endl;		
 			
 			if (input[0] != '#') {
 				
diff --git a/fileoutput.cpp b/fileoutput.cpp
index 597a05a..df1bfec 100644
--- a/fileoutput.cpp
+++ b/fileoutput.cpp
@@ -27,7 +27,7 @@ void ThreeColumnFile::initFile(string label){
 			openInputFile(inName, inFile);
 
 			string inputBuffer;
-			inputBuffer = getline(inFile);
+			getline(inFile, inputBuffer);
 		
 			outFile	<<  inputBuffer << '\t' << label << "\tlci\thci" << endl;
 		}
@@ -51,7 +51,7 @@ void ThreeColumnFile::output(int nSeqs, vector<double> data){
 	try {
 		if(counter != 0){		
 			string inputBuffer;
-			inputBuffer = getline(inFile);
+			getline(inFile, inputBuffer);
 		
 			outFile	<<  inputBuffer << setprecision(4) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
 		}
@@ -110,7 +110,7 @@ void ColumnFile::initFile(string label, vector<string> tags){
 			openInputFile(inName, inFile);
 
 			string inputBuffer;
-			inputBuffer = getline(inFile);
+			getline(inFile, inputBuffer);
 		
 			outFile	<<  inputBuffer << '\t'; 
 			for(int i = 0; i < tags.size(); i++) {
@@ -142,7 +142,7 @@ void ColumnFile::output(vector<double> data){
 	
 		if(counter != 0){		
 			string inputBuffer;
-			inputBuffer = getline(inFile);
+			getline(inFile, inputBuffer);
 
 			outFile << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(iters.length());
 			for (int i = 1; i< data.size(); i++) {
@@ -210,7 +210,7 @@ void SharedThreeColumnFile::initFile(string label){
 			openInputFile(inName, inFile);
 
 			string inputBuffer;
-			inputBuffer = getline(inFile);
+			getline(inFile, inputBuffer);
 		
 			outFile	<<  inputBuffer << '\t' << label << "\tlci\thci" << endl;
 		}
@@ -234,7 +234,7 @@ void SharedThreeColumnFile::output(int nSeqs, vector<double> data){
 	try {
 		if(counter != 0){		
 			string inputBuffer;
-			inputBuffer = getline(inFile);
+			getline(inFile, inputBuffer);
 		
 			outFile	<<  inputBuffer << setprecision(4) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
 		}
@@ -294,7 +294,7 @@ void OneColumnFile::initFile(string label){
 			openInputFile(inName, inFile);
 		
 			string inputBuffer;
-			inputBuffer = getline(inFile);
+			getline(inFile, inputBuffer);
 		
 			outFile	<<  inputBuffer << '\t' << label << endl;
 		}
@@ -318,7 +318,7 @@ void OneColumnFile::output(int nSeqs, vector<double> data){
 	try {	
 		if(counter != 0){		
 			string inputBuffer;
-			inputBuffer = getline(inFile);
+			getline(inFile, inputBuffer);
 		
 			outFile	<<  inputBuffer << setprecision(4) << '\t'  << data[0] << endl;
 		}
@@ -376,7 +376,7 @@ void SharedOneColumnFile::initFile(string label){
 			openInputFile(inName, inFile);
 		
 			string inputBuffer;
-			inputBuffer = getline(inFile);
+			getline(inFile, inputBuffer);
 		
 			outFile	<<  inputBuffer << '\t' << label  << endl;
 
diff --git a/mothur.h b/mothur.h
index b27c5ad..7d6b1d8 100644
--- a/mothur.h
+++ b/mothur.h
@@ -44,9 +44,12 @@
 #include <cerrno>
 #include <ctime>
 #include <limits>
-#include <sys/wait.h>
 #include <unistd.h>
 
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+	#include <sys/wait.h>
+#endif
+
 using namespace std;
 
 #define exp(x) (exp((double) x))
-- 
2.39.2