X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=summarysharedcommand.h;h=8ba9b9fcf3e40b745cf75ddbaccd2f6df8cde652;hp=c0172645387d4846aca623d4bfbe7827ca08cd74;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=6446d2e9713a95db5f772135b7aa3387f7ebf7bb diff --git a/summarysharedcommand.h b/summarysharedcommand.h index c017264..8ba9b9f 100644 --- a/summarysharedcommand.h +++ b/summarysharedcommand.h @@ -14,18 +14,68 @@ #include "sharedrabundvector.h" #include "inputdata.h" #include "calculator.h" -#include "readotu.h" #include "validcalculator.h" - -class GlobalData; +#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" class SummarySharedCommand : public Command { public: SummarySharedCommand(string); - ~SummarySharedCommand(); - int execute(); - void help(); + SummarySharedCommand(); + ~SummarySharedCommand() {} + + vector 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 { @@ -33,22 +83,202 @@ private: int end; }; vector lines; - GlobalData* globaldata; - ReadOTUFile* read; vector sumCalculators; InputData* input; - ValidCalculators* validCalculator; - bool abort, allLines, mult, all, createPhylip; + bool abort, allLines, mult, all, createPhylip, subsample; set labels; //holds labels to be used - string label, calc, groups; + string label, calc, groups, sharedfile, output; vector Estimators, Groups, outputNames; vector lookup; string format, outputDir; - int numGroups, processors; + int numGroups, processors, subsampleSize, iters; int process(vector, string, string); int driver(vector, int, int, string, string, vector< vector >&); + int printSims(ostream&, vector< vector >&); }; +/**************************************************************************************************/ +//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 thisLookup; + vector< vector > calcDists; + vector 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 est, vector 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 sumCalculators; + ValidCalculators validCalculator; + for (int i=0; iEstimators.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()); + } + } + } + + pDataArray->calcDists.resize(sumCalculators.size()); + + ofstream outputFileHandle; + pDataArray->m->openOutputFile(pDataArray->sumFile, outputFileHandle); + + vector 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;igetNeedsAll()) { + //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 tempdata = sumCalculators[i]->getValues(subset); //saves the calculator outputs + + if (pDataArray->m->control_pressed) { for(int i=0;iprint(outputFileHandle); + + seqDist temp(l, k, tempdata[0]); + pDataArray->calcDists[i].push_back(temp); + } + outputFileHandle << endl; + } + } + + outputFileHandle.close(); + for(int i=0;im->errorOut(e, "SummarySharedCommand", "MySummarySharedThreadFunction"); + exit(1); + } +} +#endif + + #endif