#include "command.hpp"
#include "sharedlistvector.h"
#include "inputdata.h"
-#include "shared.h"
-#include "readotu.h"
/* The shared() command:
The shared command can only be executed after a successful read.shared command.
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();
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
- void printSharedData();
- GlobalData* globaldata;
- ReadOTUFile* 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;
};