added check to make sure shhh.flows child processes finish properly. added subsamplin...

[mothur.git] / summarycommand.h

diff --git a/summarycommand.h b/summarycommand.h
index 15b7f4066e9f17b263b30ac3d0b663d7cd414455..1d93a333a8c971458ced6ca8803cb0b2027a48b2 100644 (file)
--- a/summarycommand.h
+++ b/summarycommand.h
@@ -37,9 +37,9 @@ private:
        vector<Calculator*> sumCalculators;     
        InputData* input;
        SAbundVector* sabund;
-       int abund, size;
+       int abund, size, iters, subsampleSize;
 
-       bool abort, allLines, groupMode;
+       bool abort, allLines, groupMode, subsample;
        set<string> labels; //holds labels to be used
        string label, calc, outputDir, sharedfile, listfile, rabundfile, sabundfile, format, inputfile;
        vector<string>  Estimators;
@@ -47,7 +47,8 @@ private:
        vector<string> groups;
        
        vector<string> parseSharedFile(string);
-       string createGroupSummaryFile(int, int, vector<string>&);
+       vector<string> createGroupSummaryFile(int, int, vector<string>&, map<string, string>);
+    int process(SAbundVector*&, ofstream&, ofstream&, ofstream&);
 
 
 };