X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getmetacommunitycommand.h;h=d84a65d640605734b51efd9dd32a4e78e4038e48;hp=d7b163e93f1003fdb0dcd73bdb5984de2eee208b;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=875ab4b2eec77b920e9fa0042f9a2aae2faff2b0

diff --git a/getmetacommunitycommand.h b/getmetacommunitycommand.h
index d7b163e..d84a65d 100644
--- a/getmetacommunitycommand.h
+++ b/getmetacommunitycommand.h
@@ -12,6 +12,50 @@
 #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"
 
 /**************************************************************************************************/
 
@@ -40,18 +84,20 @@ private:
 		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>);
 
 };
 
@@ -63,111 +109,5 @@ struct summaryData {
     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