added topdown parameter to pre.cluster. added more debugging output to bayesian...

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index 77c5a804070eaa2dd3229375df999a5b9521dc92..0d2e86f24cb258b24e78367e1427fc7ee2bc7d31 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -120,7 +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);
@@ -139,8 +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);
@@ -149,6 +154,7 @@ class MothurOut {
                float roundDist(float, int);
                unsigned int fromBase36(string);
                int getRandomIndex(int); //highest
+        double getStandardDeviation(vector<int>&);
 
                int control_pressed;
                bool executing, runParse, jumble, gui, mothurCalling, debug;