#include "command.hpp"
#include "inputdata.h"
#include "qFinderDMM.h"
+#include "pam.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"
/**************************************************************************************************/
unsigned long long end;
linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
};
- bool abort, allLines;
+ bool abort, allLines, subsample;
string outputDir;
vector<string> outputNames;
- string sharedfile;
- int minpartitions, maxpartitions, optimizegap, processors;
- vector<string> Groups;
+ string sharedfile, method, calc;
+ int minpartitions, maxpartitions, optimizegap, processors, iters, subsampleSize;
+ vector<string> Groups, Estimators;
set<string> labels;
+ vector<vector<double> > generateDistanceMatrix(vector<SharedRAbundVector*>& lookup);
+ int driver(vector<SharedRAbundVector*> thisLookup, vector< vector<seqDist> >& calcDists, Calculator*);
int processDriver(vector<SharedRAbundVector*>&, vector<int>&, string, vector<string>, vector<string>, vector<string>, int);
int createProcesses(vector<SharedRAbundVector*>&);
vector<double> generateDesignFile(int, map<string,string>);
- int generateSummaryFile(int, map<string,string>);
+ int generateSummaryFile(int, map<string,string>, vector<double>);
};
vector<double> partMean, partLCI, partUCI;
};
-/**************************************************************************************************/
-
-struct metaCommunityData {
- vector<SharedRAbundVector*> thislookup;
- MothurOut* m;
- string outputFileName;
- vector<string> relabunds, matrix, outputNames;
- int minpartitions, maxpartitions, optimizegap;
- vector<int> parts;
- int minPartition;
-
- metaCommunityData(){}
- metaCommunityData(vector<SharedRAbundVector*> lu, MothurOut* mout, vector<int> dp, string fit, vector<string> rels, vector<string> mat, int minp, int maxp, int opg) {
- m = mout;
- thislookup = lu;
- parts = dp;
- outputFileName = fit;
- relabunds = rels;
- matrix = mat;
- minpartitions = minp;
- maxpartitions = maxp;
- optimizegap = opg;
- minPartition = 0;
- }
-};
-/**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
-#else
-static DWORD WINAPI MyMetaCommunityThreadFunction(LPVOID lpParam){
- metaCommunityData* pDataArray;
- pDataArray = (metaCommunityData*)lpParam;
-
- try {
-
- double minLaplace = 1e10;
-
- ofstream fitData;
- pDataArray->m->openOutputFile(pDataArray->outputFileName, fitData);
- fitData.setf(ios::fixed, ios::floatfield);
- fitData.setf(ios::showpoint);
- cout.setf(ios::fixed, ios::floatfield);
- cout.setf(ios::showpoint);
-
- vector< vector<int> > sharedMatrix;
- for (int i = 0; i < pDataArray->thislookup.size(); i++) { sharedMatrix.push_back(pDataArray->thislookup[i]->getAbundances()); }
-
- pDataArray->m->mothurOut("K\tNLE\t\tlogDet\tBIC\t\tAIC\t\tLaplace\n");
- fitData << "K\tNLE\tlogDet\tBIC\tAIC\tLaplace" << endl;
-
- for(int i=0;i<pDataArray->parts.size();i++){
-
- int numPartitions = pDataArray->parts[i];
-
- if (pDataArray->m->debug) { pDataArray->m->mothurOut("[DEBUG]: running partition " + toString(numPartitions) + "\n"); }
-
- if (pDataArray->m->control_pressed) { break; }
-
- qFinderDMM* findQ = new qFinderDMM(sharedMatrix, numPartitions);
-
- if (pDataArray->m->debug) { pDataArray->m->mothurOut("[DEBUG]: done finding Q " + toString(numPartitions) + "\n"); }
-
- double laplace = findQ->getLaplace();
- pDataArray->m->mothurOut(toString(numPartitions) + '\t');
- cout << setprecision (2) << findQ->getNLL() << '\t' << findQ->getLogDet() << '\t';
- pDataArray->m->mothurOutJustToLog(toString(findQ->getNLL()) + '\t' + toString(findQ->getLogDet()) + '\t');
- cout << findQ->getBIC() << '\t' << findQ->getAIC() << '\t' << laplace;
- pDataArray->m->mothurOutJustToLog(toString(findQ->getBIC()) + '\t' + toString(findQ->getAIC()) + '\t' + toString(laplace));
-
- fitData << numPartitions << '\t';
- fitData << setprecision (2) << findQ->getNLL() << '\t' << findQ->getLogDet() << '\t';
- fitData << findQ->getBIC() << '\t' << findQ->getAIC() << '\t' << laplace << endl;
-
- if(laplace < minLaplace){
- pDataArray->minPartition = numPartitions;
- minLaplace = laplace;
- pDataArray->m->mothurOut("***");
- }
- pDataArray->m->mothurOutEndLine();
-
- pDataArray->outputNames.push_back(pDataArray->relabunds[i]);
- pDataArray->outputNames.push_back(pDataArray->matrix[i]);
-
- findQ->printZMatrix(pDataArray->matrix[i], pDataArray->m->getGroups());
- findQ->printRelAbund(pDataArray->relabunds[i], pDataArray->m->currentBinLabels);
-
- if(pDataArray->optimizegap != -1 && (numPartitions - pDataArray->minPartition) >= pDataArray->optimizegap && numPartitions >= pDataArray->minpartitions){ break; }
-
- delete findQ;
- }
- fitData.close();
-
- //minPartition = 4;
-
- if (pDataArray->m->control_pressed) { return 0; }
-
- return 0;
-
- }
- catch(exception& e) {
- pDataArray->m->errorOut(e, "GetMetaCommunityCommand", "MyMetaCommunityThreadFunction");
- exit(1);
- }
-}
-#endif
-
-
#endif
projects / mothur.git / blobdiff