X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.h;h=efe1294245d915a66dc76e0baea439b8cf9caa1a;hb=6cf9539162b0fb0b5c0b99673e999df3cd717c55;hp=92363f5b6f26996b2e83badf681befa1ae9e3e0a;hpb=050220fe7822cc660615972a0054cf4a83eefbe4;p=mothur.git

diff --git a/mothurout.h b/mothurout.h
index 92363f5..efe1294 100644
--- a/mothurout.h
+++ b/mothurout.h
@@ -12,6 +12,7 @@
 
 #include "mothur.h"
 
+
 /***********************************************/
 
 class MothurOut {
@@ -27,17 +28,67 @@ class MothurOut {
 		void closeLog();
 		string getDefaultPath() { return defaultPath; }
 		void setDefaultPath(string);
+		string getOutputDir() { return outputDir; }
+		void setOutputDir(string);
 		
 		string getReleaseDate() { return releaseDate; }
 		void setReleaseDate(string r) { releaseDate = r; }
 		string getVersion() { return version; }
 		void setVersion(string r) { version = r; }
-
+		
+		//functions from mothur.h
+		//file operations
+		vector<unsigned long int> divideFile(string, int&);
+		vector<unsigned long int> setFilePosEachLine(string, int&);
+		vector<unsigned long int> setFilePosFasta(string, int&);
+		string sortFile(string, string);
+		void appendFiles(string, string);
+		int renameFile(string, string); //oldname, newname
+		string getFullPathName(string);
+		string hasPath(string);
+		string getExtension(string);
+		string getPathName(string);
+		string getSimpleName(string);
+		string getRootName(string);
+		bool isBlank(string);
+		int openOutputFile(string, ofstream&);
+		int openOutputFileAppend(string, ofstream&);
+		int openInputFile(string, ifstream&);
+		int openInputFile(string, ifstream&, string); //no error given 
+		string getline(ifstream&);
+		string getline(istringstream&);
+		void gobble(istream&);
+		void gobble(istringstream&);
+		
+		//searchs and checks
+		bool checkReleaseVersion(ifstream&, string);
+		bool anyLabelsToProcess(string, set<string>&, string);
+		bool inUsersGroups(vector<string>, vector<string>);
+		bool inUsersGroups(string, vector<string>);
+		void getNumSeqs(ifstream&, int&);
+		int getNumSeqs(ifstream&);
+		int getNumNames(string);
+		bool isTrue(string);
+	
+		
+		//string manipulation
+		void splitAtEquals(string&, string&);
+		void splitAtComma(string&, string&);	
+		void splitAtComma(string&, vector<string>&);
+		void splitAtDash(string&, set<int>&);
+		void splitAtDash(string&, set<string>&);
+		void splitAtDash(string&, vector<string>&);
+		void splitAtChar(string&, vector<string>&, char);
+		
+		//math operation
+		int factorial(int num);
+		vector<vector<double> > binomial(int);
+		float ceilDist(float, int);
+		float roundDist(float, int);
 
 		int control_pressed;
 		bool executing;
 		
-
 	private:
 		static MothurOut* _uniqueInstance;
 		MothurOut( const MothurOut& ); // Disable copy constructor
@@ -46,7 +97,7 @@ class MothurOut {
 		~MothurOut();
 
 		string logFileName;
-		string defaultPath;
+		string defaultPath, outputDir;
 		string releaseDate, version;
 		
 		ofstream out;