some changes to trim.flows

[mothur.git] / collectcommand.h

diff --git a/collectcommand.h b/collectcommand.h
index 10894e7218b5d2d607f2c0fa931f7c10a0f6146d..20c863b81dfd79fad597cd6e1e83571256873969 100644 (file)
--- a/collectcommand.h
+++ b/collectcommand.h
@@ -38,7 +38,12 @@ class CollectCommand : public Command {
        
 public:
        CollectCommand(string); 
+       CollectCommand();
        ~CollectCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();  
        void help();
        
@@ -50,12 +55,19 @@ private:
        Collect* cCurve;
        ValidCalculators* validCalculator;
        vector<Display*> cDisplays;
-       int freq, abund, size;
+       int abund, size;
+       float freq;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
 
        bool abort, allLines;
        set<string> labels; //holds labels to be used
-       string label, calc;
+       string label, calc, outputDir;
        vector<string>  Estimators;
+       vector<string> inputFileNames;
+       vector<string> groups;
+       
+       vector<string> parseSharedFile(string);
 
 
 };