sped up align.seqs appending of files

[mothur.git] / sharedcommand.h

diff --git a/sharedcommand.h b/sharedcommand.h
index 5b922b6d6255eb993f8607fedc9696d4054f7caa..2c5ab237a2d39b006dee4eca4e9b9b2c65a57ebe 100644 (file)
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -26,25 +26,32 @@ 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(vector<SharedRAbundVector*>);
-       void createMisMatchFile();
+       int createMisMatchFile();
+       int readOrderFile();
        bool isValidGroup(string, vector<string>);
-       void eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+       int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+       map<string, vector<string> > outputTypes;
        
        GlobalData* globaldata;
        ReadOTUFile* read;
        SharedListVector* SharedList;
        InputData* input;
        GroupMap* groupMap;
-       vector<string> groups;
+       vector<string> groups, outputNames, order;
        ofstream out;
-       string filename, fileroot;
+       string filename, fileroot, outputDir;
        bool firsttime, pickedGroups;
        map<string, ofstream*> filehandles;
        map<string, ofstream*>::iterator it3;