X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.h;h=cc8bfb6b101b13b0ebe45a2eb2f5472600d6e0fc;hb=e0ce7cbc93d7d2fbb753ca694182db092a0ea0e7;hp=2a6ba2de6316eb24ff281d703f8e27d4c94a45a3;hpb=f55cf350ca6643f8eb070d8336e1957699a3f109;p=mothur.git

diff --git a/mothurout.h b/mothurout.h
index 2a6ba2d..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);
@@ -128,7 +129,9 @@ class MothurOut {
 		void splitAtDash(string&, set<string>&);
 		void splitAtDash(string&, vector<string>&);
 		void splitAtChar(string&, vector<string>&, char);
+        void splitAtChar(string&, string&, char);
 		int removeConfidences(string&);
+        string makeList(vector<string>&);
 		
 		//math operation
 		int factorial(int num);
@@ -139,7 +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;		}
@@ -162,6 +165,7 @@ class MothurOut {
 		string getAccnosFile()		{ return accnosfile;		}
 		string getTaxonomyFile()	{ return taxonomyfile;		}
 		string getFlowFile()		{ return flowfile;			}
+        string getBiomFile()		{ return biomfile;			}
 		string getProcessors()		{ return processors;		}
 		
 		void setListFile(string f)			{ listfile = getFullPathName(f);			}
@@ -184,6 +188,7 @@ class MothurOut {
 		void setAccnosFile(string f)		{ accnosfile = getFullPathName(f);			}
 		void setTaxonomyFile(string f)		{ taxonomyfile = getFullPathName(f);		}
 		void setFlowFile(string f)			{ flowfile = getFullPathName(f);			}
+        void setBiomFile(string f)			{ biomfile = getFullPathName(f);			}
 		void setProcessors(string p)		{ processors = p;							}
 		
 		void printCurrentFiles();
@@ -217,10 +222,12 @@ class MothurOut {
 			taxonomyfile = "";
 			processors = "1";
 			flowfile = "";
+            biomfile = "";
 			gui = false;
 			printedHeaders = false;
 			commandInputsConvertError = false;
             mothurCalling = false;
+            debug = false;
 			sharedHeaderMode = "";
 		}
 		~MothurOut();
@@ -229,7 +236,7 @@ class MothurOut {
 		string defaultPath, outputDir;
 		string releaseDate, version;
 	
-		string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile;
+		string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile;
 		string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;
 
 		vector<string> Groups;