#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"
/**************************************************************************************************/
~GetMetaCommunityCommand(){}
vector<string> setParameters();
- string getCommandName() { return "get.metacommunity"; }
+ string getCommandName() { return "get.communitytype"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getOutputPattern(string);
string getHelpString();
- string getCitation() { return "http://www.mothur.org/wiki/Get.metacommunity"; }
- string getDescription() { return "brief description"; }
+ string getCitation() { return "Holmes I, Harris K, Quince C (2012) Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics. PLoS ONE 7(2): e30126. doi:10.1371/journal.pone.0030126 http://www.mothur.org/wiki/get.communitytype"; }
+ string getDescription() { return "Assigns samples to bins using a Dirichlet multinomial mixture model"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
- bool abort, allLines;
+ struct linePair {
+ unsigned long long start;
+ unsigned long long end;
+ linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
+ };
+ bool abort, allLines, subsample;
string outputDir;
vector<string> outputNames;
- string sharedfile;
- int minpartitions, maxpartitions, optimizegap;
- vector<string> Groups;
+ string sharedfile, method, calc;
+ int minpartitions, maxpartitions, optimizegap, processors, iters, subsampleSize;
+ vector<string> Groups, Estimators;
set<string> labels;
- int process(vector<SharedRAbundVector*>&);
- vector<double> generateDesignFile(int, string);
- int generateSummaryFile(int, string, string, string, string);
+ 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>, vector<double>);
};
vector<double> partMean, partLCI, partUCI;
};
-/**************************************************************************************************/
-
-
-
#endif