added citation function to commands

[mothur.git] / sharedcommand.h

diff --git a/sharedcommand.h b/sharedcommand.h
index 20e2ddb3981df57f471970da64e3631814a6c170..add6ee8d4a6ebdfd86d6a08d750c7fe88cc3bd35 100644 (file)
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -12,8 +12,6 @@
 #include "command.hpp"
 #include "sharedlistvector.h"
 #include "inputdata.h"
-#include "shared.h"
-#include "readmatrix.hpp"
 
 /* The shared() command:
        The shared command can only be executed after a successful read.shared command.  
@@ -22,25 +20,39 @@
        There are no shared command parameters.  The shared command should be in the following format: shared(). */
 
 
-class GlobalData;
-
 class SharedCommand : public Command {
        
 public:
-       SharedCommand();        
+       SharedCommand(string);  
+       SharedCommand();
        ~SharedCommand();
-       int execute();  
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "make.shared";                         }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Make.shared"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       void printSharedData();
-       GlobalData* globaldata;
-       ReadMatrix* read;
+       void printSharedData(vector<SharedRAbundVector*>);
+       int createMisMatchFile();
+       int readOrderFile();
+       bool isValidGroup(string, vector<string>);
+       int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+       
        SharedListVector* SharedList;
        InputData* input;
-       Shared* shared;
-       map<string, SharedRAbundVector*>::iterator it;
+       GroupMap* groupMap;
+       vector<string> Groups, outputNames, order;
+       set<string> labels;
        ofstream out;
-       string filename;
+       string filename, fileroot, outputDir, listfile, groupfile, ordergroupfile;
+       bool firsttime, pickedGroups, abort, allLines;
+       map<string, ofstream*> filehandles;
+       map<string, ofstream*>::iterator it3;
 
 };