added sorted parameter to get.oturep, added error checking to chimera classes in...

[mothur.git] / mothur.h

diff --git a/mothur.h b/mothur.h
index 5c1880d569eeb7f37089c1a2d418f8fadf7b4ab7..f839328cd2c304330fb18f31fb97eea531ef625a 100644 (file)
--- a/mothur.h
+++ b/mothur.h
@@ -46,10 +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;
@@ -190,7 +201,6 @@ inline void gobble(istream& f){
        f.putback(d);
        
 }
-
 /***********************************************************************/
 
 inline string getline(ifstream& fileHandle) {
@@ -481,7 +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