changing command name classify.shared to classifyrf.shared

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index f99eac1917cbe2ce5a1ce278c66d27d1df71737e..3cf6fa4963672b5d69acb7de389eb266b957ba24 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);
@@ -151,6 +155,7 @@ 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
                int factorial(int num);