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#ifndef SHAREDCOMMAND_H
#define SHAREDCOMMAND_H
/*
* sharedcommand.h
* Dotur
*
* Created by Sarah Westcott on 1/2/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "command.hpp"
#include "sharedlistvector.h"
#include "inputdata.h"
//**********************************************************************************************************************
struct tidy {
string otu;
string group;
int abund;
tidy() : group(""), otu(""), abund(0) {}
tidy(string o, string g, int a) : otu(o), group(g), abund(a) {}
};
//**********************************************************************************************************************
/* The shared() command:
The shared command can only be executed after a successful read.shared command.
The shared command parses a .list file and separates it into groups.
It outputs a .shared file containing the OTU information for each group.
There are no shared command parameters. The shared command should be in the following format: shared(). */
class SharedCommand : public Command {
public:
SharedCommand(string);
~SharedCommand();
vector<string> setParameters();
string getCommandName() { return "make.shared"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Make.shared"; }
string getDescription() { return "make a shared file from a list and group file"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
void printSharedData(SharedRAbundVectors*&, ofstream&, bool&);
int readOrderFile();
bool isValidGroup(string, vector<string>);
int ListGroupSameSeqs(vector<string>&, SharedListVector*);
int createSharedFromListGroup();
int createSharedFromBiom();
int createSharedFromCount();
void convertSharedFormat();
string findFormat();
string getTag(string&);
vector<string> readRows(string, int&);
int getDims(string, int&, int&);
SharedRAbundVectors* readData(string, string, string, vector<string>&, int);
vector<string> Groups, outputNames, order;
set<string> labels;
string fileroot, listfile, groupfile, biomfile, ordergroupfile, countfile, sharedfile;
bool firsttime, pickedGroups, abort, allLines, keepZeroes;
};
#endif
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