changes while testing

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index f99eac1917cbe2ce5a1ce278c66d27d1df71737e..9987374e6c824cafe4aaf343c319d5bca14f209b 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -93,7 +93,9 @@ class MothurOut {
                string getRootName(string);
                bool isBlank(string);
                int openOutputFile(string, ofstream&);
+        int openOutputFileBinary(string, ofstream&);
                int openOutputFileAppend(string, ofstream&);
+        int openOutputFileBinaryAppend(string, ofstream&);
                int openInputFile(string, ifstream&);
                int openInputFile(string, ifstream&, string); //no error given 
                string getline(ifstream&);
@@ -107,6 +109,8 @@ class MothurOut {
         map<string, int> readNames(string);
         map<string, int> readNames(string, unsigned long int&);
         int readTax(string, map<string, string>&);
+        vector<consTax> readConsTax(string);
+        int readConsTax(string, map<string, consTax2>&);
         int readNames(string, map<string, string>&, map<string, int>&);
                int readNames(string, map<string, string>&);
         int readNames(string, map<string, string>&, bool);
@@ -134,6 +138,7 @@ class MothurOut {
                bool isTrue(string);
                bool isContainingOnlyDigits(string);
                bool isNumeric1(string);
+        string findEdianness();
        
                
                //string manipulation
@@ -151,13 +156,17 @@ class MothurOut {
         string makeList(vector<string>&);
         bool isSubset(vector<string>, vector<string>); //bigSet, subset
         int checkName(string&);
+        map<string, vector<string> > parseClasses(string);
                
                //math operation
+        double max(vector<double>&); //returns largest value in vector
+        double min(vector<double>&); //returns smallest value in vector
                int factorial(int num);
                vector<vector<double> > binomial(int);
                float ceilDist(float, int);
                float roundDist(float, int);
                unsigned int fromBase36(string);
+        double median(vector<double>);
                int getRandomIndex(int); //highest
         double getStandardDeviation(vector<int>&);
         vector<double> getStandardDeviation(vector< vector<double> >&);