changed random forest output filename

[mothur.git] / summarycommand.h

diff --git a/summarycommand.h b/summarycommand.h
index 15b7f4066e9f17b263b30ac3d0b663d7cd414455..3c8420795550e1f39ef5529ad235d13e11e5e7a5 100644 (file)
--- a/summarycommand.h
+++ b/summarycommand.h
@@ -25,7 +25,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "summary.single";                      }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "http://www.mothur.org/wiki/Summary.single"; }
        string getDescription()         { return "generate summary file that has the calculator value for each line in the OTU data"; }
 
@@ -37,9 +39,9 @@ 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 +49,8 @@ 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&);
 
 
 };