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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 "sharedrabundvector.h"
#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();
~SummarySharedCommand() {}
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:
struct linePair {
int start;
int end;
};
vector<linePair> lines;
vector<Calculator*> sumCalculators;
InputData* input;
bool abort, allLines, mult, all, createPhylip, subsample;
set<string> labels; //holds labels to be used
string label, calc, groups, sharedfile, output;
vector<string> Estimators, Groups, outputNames;
vector<SharedRAbundVector*> lookup;
string format, outputDir;
int numGroups, processors, subsampleSize, iters;
int process(vector<SharedRAbundVector*>, string, string);
int driver(vector<SharedRAbundVector*>, int, int, string, string, vector< vector<seqDist> >&);
int printSims(ostream&, vector< vector<double> >&);
};
/**************************************************************************************************/
//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;
int count;
summarySharedData(){}
summarySharedData(string sf, MothurOut* mout, unsigned long long st, unsigned long long en, vector<string> est, vector<SharedRAbundVector*> lu) {
sumFile = sf;
m = mout;
start = st;
end = en;
Estimators = est;
thisLookup = lu;
count=0;
}
};
/**************************************************************************************************/
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
#else
static DWORD WINAPI MySummarySharedThreadFunction(LPVOID lpParam){
summarySharedData* pDataArray;
pDataArray = (summarySharedData*)lpParam;
try {
vector<Calculator*> sumCalculators;
ValidCalculators validCalculator;
for (int i=0; i<pDataArray->Estimators.size(); i++) {
if (validCalculator.isValidCalculator("sharedsummary", pDataArray->Estimators[i]) == true) {
if (pDataArray->Estimators[i] == "sharedsobs") {
sumCalculators.push_back(new SharedSobsCS());
}else if (pDataArray->Estimators[i] == "sharedchao") {
sumCalculators.push_back(new SharedChao1());
}else if (pDataArray->Estimators[i] == "sharedace") {
sumCalculators.push_back(new SharedAce());
}else if (pDataArray->Estimators[i] == "jabund") {
sumCalculators.push_back(new JAbund());
}else if (pDataArray->Estimators[i] == "sorabund") {
sumCalculators.push_back(new SorAbund());
}else if (pDataArray->Estimators[i] == "jclass") {
sumCalculators.push_back(new Jclass());
}else if (pDataArray->Estimators[i] == "sorclass") {
sumCalculators.push_back(new SorClass());
}else if (pDataArray->Estimators[i] == "jest") {
sumCalculators.push_back(new Jest());
}else if (pDataArray->Estimators[i] == "sorest") {
sumCalculators.push_back(new SorEst());
}else if (pDataArray->Estimators[i] == "thetayc") {
sumCalculators.push_back(new ThetaYC());
}else if (pDataArray->Estimators[i] == "thetan") {
sumCalculators.push_back(new ThetaN());
}else if (pDataArray->Estimators[i] == "kstest") {
sumCalculators.push_back(new KSTest());
}else if (pDataArray->Estimators[i] == "sharednseqs") {
sumCalculators.push_back(new SharedNSeqs());
}else if (pDataArray->Estimators[i] == "ochiai") {
sumCalculators.push_back(new Ochiai());
}else if (pDataArray->Estimators[i] == "anderberg") {
sumCalculators.push_back(new Anderberg());
}else if (pDataArray->Estimators[i] == "kulczynski") {
sumCalculators.push_back(new Kulczynski());
}else if (pDataArray->Estimators[i] == "kulczynskicody") {
sumCalculators.push_back(new KulczynskiCody());
}else if (pDataArray->Estimators[i] == "lennon") {
sumCalculators.push_back(new Lennon());
}else if (pDataArray->Estimators[i] == "morisitahorn") {
sumCalculators.push_back(new MorHorn());
}else if (pDataArray->Estimators[i] == "braycurtis") {
sumCalculators.push_back(new BrayCurtis());
}else if (pDataArray->Estimators[i] == "whittaker") {
sumCalculators.push_back(new Whittaker());
}else if (pDataArray->Estimators[i] == "odum") {
sumCalculators.push_back(new Odum());
}else if (pDataArray->Estimators[i] == "canberra") {
sumCalculators.push_back(new Canberra());
}else if (pDataArray->Estimators[i] == "structeuclidean") {
sumCalculators.push_back(new StructEuclidean());
}else if (pDataArray->Estimators[i] == "structchord") {
sumCalculators.push_back(new StructChord());
}else if (pDataArray->Estimators[i] == "hellinger") {
sumCalculators.push_back(new Hellinger());
}else if (pDataArray->Estimators[i] == "manhattan") {
sumCalculators.push_back(new Manhattan());
}else if (pDataArray->Estimators[i] == "structpearson") {
sumCalculators.push_back(new StructPearson());
}else if (pDataArray->Estimators[i] == "soergel") {
sumCalculators.push_back(new Soergel());
}else if (pDataArray->Estimators[i] == "spearman") {
sumCalculators.push_back(new Spearman());
}else if (pDataArray->Estimators[i] == "structkulczynski") {
sumCalculators.push_back(new StructKulczynski());
}else if (pDataArray->Estimators[i] == "speciesprofile") {
sumCalculators.push_back(new SpeciesProfile());
}else if (pDataArray->Estimators[i] == "hamming") {
sumCalculators.push_back(new Hamming());
}else if (pDataArray->Estimators[i] == "structchi2") {
sumCalculators.push_back(new StructChi2());
}else if (pDataArray->Estimators[i] == "gower") {
sumCalculators.push_back(new Gower());
}else if (pDataArray->Estimators[i] == "memchi2") {
sumCalculators.push_back(new MemChi2());
}else if (pDataArray->Estimators[i] == "memchord") {
sumCalculators.push_back(new MemChord());
}else if (pDataArray->Estimators[i] == "memeuclidean") {
sumCalculators.push_back(new MemEuclidean());
}else if (pDataArray->Estimators[i] == "mempearson") {
sumCalculators.push_back(new MemPearson());
}else if (pDataArray->Estimators[i] == "jsd") {
sumCalculators.push_back(new JSD());
}else if (pDataArray->Estimators[i] == "rjsd") {
sumCalculators.push_back(new RJSD());
}
}
}
pDataArray->calcDists.resize(sumCalculators.size());
ofstream outputFileHandle;
pDataArray->m->openOutputFile(pDataArray->sumFile, outputFileHandle);
vector<SharedRAbundVector*> subset;
for (int k = pDataArray->start; k < pDataArray->end; k++) { // pass cdd each set of groups to compare
pDataArray->count++;
for (int l = 0; l < k; l++) {
outputFileHandle << pDataArray->thisLookup[0]->getLabel() << '\t';
subset.clear(); //clear out old pair of sharedrabunds
//add new pair of sharedrabunds
subset.push_back(pDataArray->thisLookup[k]); subset.push_back(pDataArray->thisLookup[l]);
//sort groups to be alphanumeric
if (pDataArray->thisLookup[k]->getGroup() > pDataArray->thisLookup[l]->getGroup()) {
outputFileHandle << (pDataArray->thisLookup[l]->getGroup() +'\t' + pDataArray->thisLookup[k]->getGroup()) << '\t'; //print out groups
}else{
outputFileHandle << (pDataArray->thisLookup[k]->getGroup() +'\t' + pDataArray->thisLookup[l]->getGroup()) << '\t'; //print out groups
}
for(int i=0;i<sumCalculators.size();i++) {
//if this calc needs all groups to calculate the pair load all groups
if (sumCalculators[i]->getNeedsAll()) {
//load subset with rest of lookup for those calcs that need everyone to calc for a pair
for (int w = 0; w < pDataArray->thisLookup.size(); w++) {
if ((w != k) && (w != l)) { subset.push_back(pDataArray->thisLookup[w]); }
}
}
vector<double> tempdata = sumCalculators[i]->getValues(subset); //saves the calculator outputs
if (pDataArray->m->control_pressed) { for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } outputFileHandle.close(); return 1; }
outputFileHandle << '\t';
sumCalculators[i]->print(outputFileHandle);
seqDist temp(l, k, tempdata[0]);
pDataArray->calcDists[i].push_back(temp);
}
outputFileHandle << endl;
}
}
outputFileHandle.close();
for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; }
return 0;
}
catch(exception& e) {
pDataArray->m->errorOut(e, "SummarySharedCommand", "MySummarySharedThreadFunction");
exit(1);
}
}
#endif
#endif
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