added indicator command

[mothur.git] / summarycommand.h

diff --git a/summarycommand.h b/summarycommand.h
index 6ee8c4a522d517b563318d92b840f708b20603e5..d225109359d4950ad88be6a1ff41dd49cf062251 100644 (file)
--- a/summarycommand.h
+++ b/summarycommand.h
@@ -22,7 +22,12 @@ class SummaryCommand : public Command {
 
 public:
        SummaryCommand(string);
+       SummaryCommand();
        ~SummaryCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
@@ -33,14 +38,19 @@ private:
        InputData* input;
        ValidCalculators* validCalculator;
        SAbundVector* sabund;
-       string outputFileName;
-       ofstream outputFileHandle;
        int abund, size;
 
-       bool abort, allLines;
+       bool abort, allLines, groupMode;
        set<string> labels; //holds labels to be used
-       string label, calc;
+       string label, calc, outputDir;
        vector<string>  Estimators;
+       vector<string> inputFileNames, outputNames;
+       map<string, vector<string> > outputTypes;
+       vector<string> groups;
+       
+       vector<string> parseSharedFile(string);
+       string createGroupSummaryFile(int, int, vector<string>&);
+
 
 };
 #endif