made make.table alias to count.seqs command. added large parameter to count.seqs...

[mothur.git] / shhhercommand.h

diff --git a/shhhercommand.h b/shhhercommand.h
index c9772af6f0e87e32d24518ee0419885770e11998..03f171e8a85cf0ebe363381793fbaea7e69950ab 100644 (file)
--- a/shhhercommand.h
+++ b/shhhercommand.h
@@ -41,6 +41,7 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "shhh.flows";  }
        string getCommandCategory()             { return "Sequence Processing";         }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
        string getCitation() { return "http://www.mothur.org/wiki/Shhh.flows"; }
        string getDescription()         { return "shhh.flows"; }
@@ -56,10 +57,10 @@ private:
                linePair(int i, int j) : start(i), end(j) {}
        };
     
-       int abort;
+       bool abort, large;
        string outputDir, flowFileName, flowFilesFileName, lookupFileName, compositeFASTAFileName, compositeNamesFileName;
 
-       int processors, maxIters;
+       int processors, maxIters, largeSize;
        float cutoff, sigma, minDelta;
        string flowOrder;
     
@@ -68,6 +69,7 @@ private:
        vector<double> jointLookUp;
     vector<string> flowFileVector;
        
+    vector<string> parseFlowFiles(string);
     int driver(vector<string>, string, string, int, int);
     int createProcesses(vector<string>);
     int getFlowData(string, vector<string>&, vector<int>&, vector<short>&, map<string, int>&, int&);
@@ -90,7 +92,7 @@ private:
     void writeQualities(int, int, string, vector<int>, vector<int>&, vector<int>&, vector<double>&, vector<short>&, vector<short>&, vector<int>&, vector<int>&, vector<string>&, vector<int>&, vector<vector<int> >&);
     void writeSequences(string, int, int, string, vector<int>, vector<short>&, vector<string>&, vector<vector<int> >&, vector<int>&);
     void writeNames(string, int, string, vector<int>, vector<string>&, vector<vector<int> >&, vector<int>&);
-    void writeGroups(string, int, vector<string>&);
+    void writeGroups(string, string, int, vector<string>&);
     void writeClusters(string, int, int, vector<int>, vector<int>&, vector<short>&, vector<string>&, vector<vector<int> >&, vector<int>&, vector<int>&, vector<short>&);
     
        void getSingleLookUp();