X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.h;h=cc8bfb6b101b13b0ebe45a2eb2f5472600d6e0fc;hb=791f42d21a85f794529fd4c912dcc27d873c25e8;hp=9ce698be4e1963e6af9abee67673ded3e1743fde;hpb=7dab6ac3ae5a5f1ce37dca8cfacaa719881fd5b2;p=mothur.git

diff --git a/mothurout.h b/mothurout.h
index 9ce698b..cc8bfb6 100644
--- a/mothurout.h
+++ b/mothurout.h
@@ -82,6 +82,7 @@ class MothurOut {
 		int appendFiles(string, string);
 		int renameFile(string, string); //oldname, newname
 		string getFullPathName(string);
+        string findProgramPath(string programName);
 		string hasPath(string);
 		string getExtension(string);
 		string getPathName(string);
@@ -130,6 +131,7 @@ class MothurOut {
 		void splitAtChar(string&, vector<string>&, char);
         void splitAtChar(string&, string&, char);
 		int removeConfidences(string&);
+        string makeList(vector<string>&);
 		
 		//math operation
 		int factorial(int num);
@@ -140,7 +142,7 @@ class MothurOut {
 		int getRandomIndex(int); //highest
 
 		int control_pressed;
-		bool executing, runParse, jumble, gui, mothurCalling;
+		bool executing, runParse, jumble, gui, mothurCalling, debug;
 		
 		//current files - if you add a new type you must edit optionParser->getParameters, get.current command and mothurOut->printCurrentFiles/clearCurrentFiles.
 		string getPhylipFile()		{ return phylipfile;		}
@@ -225,6 +227,7 @@ class MothurOut {
 			printedHeaders = false;
 			commandInputsConvertError = false;
             mothurCalling = false;
+            debug = false;
 			sharedHeaderMode = "";
 		}
 		~MothurOut();