X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.h;h=f839328cd2c304330fb18f31fb97eea531ef625a;hb=a5afca18544555fba2d9c3670ad1f8574916b0a0;hp=ba88f71fabffced9509deed545cecde7228b2b63;hpb=7b3c9ca940891c1b20b3b7ec13e05d7e7b316b63;p=mothur.git

diff --git a/mothur.h b/mothur.h
index ba88f71..f839328 100644
--- a/mothur.h
+++ b/mothur.h
@@ -21,6 +21,7 @@
 #include <iomanip>
 #include <fstream>
 #include <sstream>
+#include <signal.h>
 
 //exception
 #include <stdexcept>
@@ -45,10 +46,21 @@
 #include <ctime>
 #include <limits>
 
+/***********************************************************************/
 
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 	#include <sys/wait.h>
 	#include <unistd.h>
+	
+	#ifdef USE_READLINE
+		#include <readline/readline.h>
+		#include <readline/history.h>
+	#endif
+
+	//#include <readline/readline.h>
+	//#include <readline/history.h>
+#else
+	#include <conio.h> //allows unbuffered screen capture from stdin
 #endif
 
 using namespace std;
@@ -189,7 +201,6 @@ inline void gobble(istream& f){
 	f.putback(d);
 	
 }
-
 /***********************************************************************/
 
 inline string getline(ifstream& fileHandle) {
@@ -283,9 +294,6 @@ inline void errorOut(exception& e, string object, string function) {
 	
 }
 
-
-
-
 /***********************************************************************/
 
 inline bool isTrue(string f){
@@ -425,7 +433,21 @@ inline string getExtension(string longName){
 	
 	return extension;
 }
-
+/***********************************************************************/
+inline bool isBlank(string fileName){
+	
+	ifstream fileHandle;
+	fileHandle.open(fileName.c_str());
+	if(!fileHandle) {
+		mothurOut("Error: Could not open " + fileName);  mothurOutEndLine();
+		return false;
+	}else {
+		//check for blank file
+		gobble(fileHandle);
+		if (fileHandle.eof()) { fileHandle.close(); return true;  }
+	}
+	return false;
+}
 /***********************************************************************/
 
 inline int openInputFile(string fileName, ifstream& fileHandle){
@@ -469,7 +491,16 @@ inline int getNumSeqs(ifstream& file){
 	return numSeqs;
 
 }
+/***********************************************************************/
 
+inline bool inVector(string member, vector<string> group){
+	
+	for (int i = 0; i < group.size(); i++) {
+		if (group[i] == member) {  return true; 	}
+	}
+	
+	return false;
+}
 /***********************************************************************/
 
 //This function parses the estimator options and puts them in a vector