added shannonrange calc.

[mothur.git] / summarycommand.h

diff --git a/summarycommand.h b/summarycommand.h
index 6f04fc721ad109545aa899b0a85871982bdc3c80..891d1570e3e55fd24f4d58260c023924584d7756 100644 (file)
--- a/summarycommand.h
+++ b/summarycommand.h
@@ -13,36 +13,44 @@
 #include "sabundvector.hpp"
 #include "inputdata.h"
 #include "calculator.h"
-#include "readotu.h"
 #include "validcalculator.h"
 
-class GlobalData;
-
 class SummaryCommand : public Command {
 
 public:
        SummaryCommand(string);
-       ~SummaryCommand();
-       int execute();
-       void help();
+       SummaryCommand();
+       ~SummaryCommand(){}
+       
+       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"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       GlobalData* globaldata;
-       ReadOTUFile* read;
        vector<Calculator*> sumCalculators;     
        InputData* input;
-       ValidCalculators* validCalculator;
        SAbundVector* sabund;
-       int abund, size;
+       int abund, size, iters, subsampleSize, alpha;
 
-       bool abort, allLines;
+       bool abort, allLines, groupMode, subsample;
        set<string> labels; //holds labels to be used
-       string label, calc, outputDir;
+       string label, calc, outputDir, sharedfile, listfile, rabundfile, sabundfile, format, inputfile;
        vector<string>  Estimators;
-       vector<string> inputFileNames;
+       vector<string> inputFileNames, outputNames;
        vector<string> groups;
        
        vector<string> parseSharedFile(string);
+       vector<string> createGroupSummaryFile(int, int, vector<string>&, map<string, string>);
+    int process(SAbundVector*&, ofstream&, ofstream&);
 
 
 };