added pipeline commands which involved change to command factory and command class...

[mothur.git] / sharedcommand.h

diff --git a/sharedcommand.h b/sharedcommand.h
index 08314b56590b70dcb56b29f0c08a454da9ebac5d..2c5ab237a2d39b006dee4eca4e9b9b2c65a57ebe 100644 (file)
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -12,7 +12,6 @@
 #include "command.hpp"
 #include "sharedlistvector.h"
 #include "inputdata.h"
-#include "shared.h"
 #include "readotu.h"
 
 /* The shared() command:
@@ -27,21 +26,35 @@ class GlobalData;
 class SharedCommand : public Command {
        
 public:
-       SharedCommand();        
+       SharedCommand(string);  
+       SharedCommand();
        ~SharedCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();  
        void help() {}
        
 private:
-       void printSharedData();
+       void printSharedData(vector<SharedRAbundVector*>);
+       int createMisMatchFile();
+       int readOrderFile();
+       bool isValidGroup(string, vector<string>);
+       int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+       map<string, vector<string> > outputTypes;
+       
        GlobalData* globaldata;
        ReadOTUFile* read;
        SharedListVector* SharedList;
        InputData* input;
-       Shared* shared;
-       map<string, SharedRAbundVector*>::iterator it;
+       GroupMap* groupMap;
+       vector<string> groups, outputNames, order;
        ofstream out;
-       string filename;
+       string filename, fileroot, outputDir;
+       bool firsttime, pickedGroups;
+       map<string, ofstream*> filehandles;
+       map<string, ofstream*>::iterator it3;
 
 };