X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.h;h=b2c638a167d1ebf507106cc300231f0f693471b0;hb=49d2b7459c5027557564b21e9487dadafbbbdc96;hp=db1a4f1ca4e6c4207a652d05ac20b24157dfa46d;hpb=42d411d3362186465347aeabdd3155bd3259671e;p=mothur.git

diff --git a/mothurout.h b/mothurout.h
index db1a4f1..b2c638a 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);
@@ -96,8 +97,15 @@ class MothurOut {
 		string getline(istringstream&);
 		void gobble(istream&);
 		void gobble(istringstream&);
-		map<string, int> readNames(string);
+        vector<string> splitWhiteSpace(string& rest, char[], int);
+        vector<string> splitWhiteSpace(string);
+        set<string> readAccnos(string);
+        int readAccnos(string, vector<string>&);
+        map<string, int> readNames(string);
+        int readTax(string, map<string, string>&);
+        int readNames(string, map<string, string>&, map<string, int>&);
 		int readNames(string, map<string, string>&);
+        int readNames(string, map<string, string>&, bool);
 		int readNames(string, map<string, vector<string> >&);
 		int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
 		int mothurRemove(string);
@@ -130,6 +138,7 @@ 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);
@@ -142,7 +151,7 @@ class MothurOut {
 		int control_pressed;
 		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.
+		//current files - if you add a new type you must edit optionParser->getParameters, get.current command and mothurOut->printCurrentFiles/clearCurrentFiles/getCurrentTypes.
 		string getPhylipFile()		{ return phylipfile;		}
 		string getColumnFile()		{ return columnfile;		}
 		string getListFile()		{ return listfile;			}
@@ -187,11 +196,12 @@ class MothurOut {
 		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 setProcessors(string p)		{ processors = p; mothurOut("\nUsing " + toString(p) + " processors.\n");	}
 		
 		void printCurrentFiles();
 		bool hasCurrentFiles();
 		void clearCurrentFiles();
+        set<string> getCurrentTypes(); 
 		
 	private:
 		static MothurOut* _uniqueInstance;