fixed seq. error align=f issue. added std and ave calcs to mothurout. working on...

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index ac47d79f7d92b113f58dbe421fdbaad892b2b175..84f9be31f82ebc2c27aa19563fb5366519e1cba8 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -111,6 +111,7 @@ class MothurOut {
                int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
                int mothurRemove(string);
                bool mothurConvert(string, int&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
+        bool mothurConvert(string, intDist&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
                bool mothurConvert(string, float&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
                bool mothurConvert(string, double&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
        
@@ -119,7 +120,9 @@ class MothurOut {
                bool checkReleaseVersion(ifstream&, string);
                bool anyLabelsToProcess(string, set<string>&, string);
                bool inUsersGroups(vector<string>, vector<string>);
+        bool inUsersGroups(vector<int>, vector< vector<int> >);
                bool inUsersGroups(string, vector<string>);
+        bool inUsersGroups(int, vector<int>);
                void getNumSeqs(ifstream&, int&);
                int getNumSeqs(ifstream&);
                int getNumNames(string);
@@ -138,8 +141,11 @@ class MothurOut {
                void splitAtDash(string&, vector<string>&);
                void splitAtChar(string&, vector<string>&, char);
         void splitAtChar(string&, string&, char);
+        vector<string> splitWhiteSpaceWithQuotes(string);
                int removeConfidences(string&);
+        string removeQuotes(string);
         string makeList(vector<string>&);
+        bool isSubset(vector<string>, vector<string>); //bigSet, subset
                
                //math operation
                int factorial(int num);
@@ -148,6 +154,10 @@ class MothurOut {
                float roundDist(float, int);
                unsigned int fromBase36(string);
                int getRandomIndex(int); //highest
+        double getStandardDeviation(vector<int>&);
+        vector<double> getStandardDeviation(vector< vector<double> >&);
+        vector<double> getStandardDeviation(vector< vector<double> >&, vector<double>&);
+        vector<double> getAverages(vector< vector<double> >&);
 
                int control_pressed;
                bool executing, runParse, jumble, gui, mothurCalling, debug;