X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedcommand.h;h=2c5ab237a2d39b006dee4eca4e9b9b2c65a57ebe;hb=cdf9083dc32543cc640e72e9ca3aee0323cbad45;hp=318fe9820e0444c444cd0bcb73f1e1559e763a37;hpb=4761e165b4a196fefa57755d3176d9ced19df6b1;p=mothur.git

diff --git a/sharedcommand.h b/sharedcommand.h
index 318fe98..2c5ab23 100644
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -9,15 +9,10 @@
  *
  */
 
-#include <Carbon/Carbon.h>
-#include <iostream>
-#include <fstream>
-#include <map>
 #include "command.hpp"
 #include "sharedlistvector.h"
 #include "inputdata.h"
-#include "shared.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
 
 /* The shared() command:
 	The shared command can only be executed after a successful read.shared command.  
@@ -31,21 +26,36 @@ 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;
-	ReadMatrix* read;
+	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;
 
 };
 
-#endif
\ No newline at end of file
+#endif