fixes while testing 1.33.0

[mothur.git] / getmetacommunitycommand.h

diff --git a/getmetacommunitycommand.h b/getmetacommunitycommand.h
index 62070d6191ca75a09b6980f6cd5aabe73af89023..d84a65d640605734b51efd9dd32a4e78e4038e48 100644 (file)
--- a/getmetacommunitycommand.h
+++ b/getmetacommunitycommand.h
@@ -11,6 +11,51 @@
 
 #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"
 
 /**************************************************************************************************/
 
@@ -21,30 +66,38 @@ public:
     ~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>);
 
 };
 
@@ -56,9 +109,5 @@ struct summaryData {
     vector<double> partMean, partLCI, partUCI;
     
 };
-/**************************************************************************************************/
-
-
-
 
 #endif