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#ifndef SUMMARYSHAREDCOMMAND_H
#define SUMMARYSHAREDCOMMAND_H
/*
* summarysharedcommand.h
* Dotur
*
* Created by Sarah Westcott on 1/2/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "command.hpp"
#include "inputdata.h"
#include "calculator.h"
#include "validcalculator.h"
#include "sharedsobscollectsummary.h"
#include "sharedchao1.h"
#include "sharedace.h"
#include "sharednseqs.h"
#include "sharedjabund.h"
#include "sharedsorabund.h"
#include "sharedjclass.h"
#include "sharedsorclass.h"
#include "sharedjest.h"
#include "sharedsorest.h"
#include "sharedthetayc.h"
#include "sharedthetan.h"
#include "sharedkstest.h"
#include "whittaker.h"
#include "sharedochiai.h"
#include "sharedanderbergs.h"
#include "sharedkulczynski.h"
#include "sharedkulczynskicody.h"
#include "sharedlennon.h"
#include "sharedmorisitahorn.h"
#include "sharedbraycurtis.h"
//#include "sharedjackknife.h"
#include "whittaker.h"
#include "odum.h"
#include "canberra.h"
#include "structeuclidean.h"
#include "structchord.h"
#include "hellinger.h"
#include "manhattan.h"
#include "structpearson.h"
#include "soergel.h"
#include "spearman.h"
#include "structkulczynski.h"
#include "structchi2.h"
#include "speciesprofile.h"
#include "hamming.h"
#include "gower.h"
#include "memchi2.h"
#include "memchord.h"
#include "memeuclidean.h"
#include "mempearson.h"
#include "sharedjsd.h"
#include "sharedrjsd.h"
class SummarySharedCommand : public Command {
public:
SummarySharedCommand(string);
~SummarySharedCommand() = default;
vector<string> setParameters();
string getCommandName() { return "summary.shared"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Summary.shared"; }
string getDescription() { return "generate a summary file containing calculator values for each line in the OTU data and for all possible comparisons between groups"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
vector<linePair> lines;
bool abort, allLines, mult, all, createPhylip, subsample, withReplacement;
set<string> labels; //holds labels to be used
string label, calc, groups, sharedfile, output;
vector<string> Estimators, Groups, outputNames, sumCalculatorsNames;
string format;
int numGroups, processors, subsampleSize, iters, numCalcs;
int process(SharedRAbundVectors*, string, string, vector<string>);
int printSims(ostream&, vector< vector<double> >&, vector<string>);
int runCalcs(SharedRAbundVectors*&, string, string, vector< vector<seqDist> >&);
};
/**************************************************************************************************/
//custom data structure for threads to use.
//main process handling the calcs that can do more than 2 groups
// This is passed by void pointer so it can be any data type
// that can be passed using a single void pointer (LPVOID).
struct summarySharedData {
vector<SharedRAbundVector*> thisLookup;
vector< vector<seqDist> > calcDists;
vector<string> Estimators;
unsigned long long start;
unsigned long long end;
MothurOut* m;
string sumFile, sumAllFile;
int count;
bool main, mult;
bool subsample;
Utils util;
summarySharedData(){}
summarySharedData(string sf, string sfa, MothurOut* mout, unsigned long long st, unsigned long long en, vector<string> est, SharedRAbundVectors*& lu, bool mai, bool mu, bool sub) {
sumFile = sf;
sumAllFile = sfa;
m = mout;
start = st;
end = en;
Estimators = est;
thisLookup = lu->getSharedRAbundVectors();
count=0;
main = mai;
mult = mu;
subsample = sub;
}
~summarySharedData() { for (int j = 0; j < thisLookup.size(); j++) { delete thisLookup[j]; } thisLookup.clear(); }
};
/**************************************************************************************************/
#endif
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