working on get.communitytype command

[mothur.git] / getmetacommunitycommand.cpp

diff --git a/getmetacommunitycommand.cpp b/getmetacommunitycommand.cpp
index b3160749e9031072ceafdea29b92a33a2909cff6..2b944153a92e5c919a0e2269916f0ffbbc9d2395 100644 (file)
--- a/getmetacommunitycommand.cpp
+++ b/getmetacommunitycommand.cpp
@@ -18,7 +18,7 @@ vector<string> GetMetaCommunityCommand::setParameters(){
         CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","outputType",false,true); parameters.push_back(pshared);
         CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
                CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
-        CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson-jsd", "jsd", "", "", "","",false,false,true); parameters.push_back(pcalc);
+        CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson-jsd-rjsd", "rjsd", "", "", "","",false,false,true); parameters.push_back(pcalc);
         CommandParameter psubsample("subsample", "String", "", "", "", "", "","",false,false); parameters.push_back(psubsample);
         CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
         CommandParameter pminpartitions("minpartitions", "Number", "", "5", "", "", "","",false,false,true); parameters.push_back(pminpartitions);
@@ -190,9 +190,9 @@ GetMetaCommunityCommand::GetMetaCommunityCommand(string option)  {
                        else { m->mothurOut("[ERROR]: " + method + " is not a valid method.  Valid algorithms are dmm, kmeans and pam."); m->mothurOutEndLine(); abort = true; }
             
             calc = validParameter.validFile(parameters, "calc", false);
-                       if (calc == "not found") { calc = "jsd";  }
+                       if (calc == "not found") { calc = "rjsd";  }
                        else {
-                if (calc == "default")  {  calc = "jsd";  }
+                if (calc == "default")  {  calc = "rjsd";  }
                        }
                        m->splitAtDash(calc, Estimators);
                        if (m->inUsersGroups("citation", Estimators)) {
@@ -611,6 +611,12 @@ int GetMetaCommunityCommand::processDriver(vector<SharedRAbundVector*>& thislook
                 finder = new qFinderDMM(sharedMatrix, numPartitions);
             }
             
+            string relabund = relabunds[i];
+            string matrixName = matrix[i];
+            outputNames.push_back(matrixName); outputTypes["matrix"].push_back(matrixName);
+            
+            finder->printZMatrix(matrixName, thisGroups);
+            
             double chi; vector<double> silhouettes;
             if (method == "dmm") {
                 double laplace = finder->getLaplace();
@@ -627,11 +633,6 @@ int GetMetaCommunityCommand::processDriver(vector<SharedRAbundVector*>& thislook
                     minSilhouettes = silhouettes;
                 }
             }
-            string relabund = relabunds[i];
-            string matrixName = matrix[i];
-            outputNames.push_back(matrixName); outputTypes["matrix"].push_back(matrixName);
-            
-            finder->printZMatrix(matrixName, thisGroups);
             
             if (method == "dmm") {
                 finder->printFitData(cout, minLaplace);
@@ -961,6 +962,8 @@ vector<vector<double> > GetMetaCommunityCommand::generateDistanceMatrix(vector<S
                 matrixCalculator = new MemPearson();
             }else if (Estimators[i] == "jsd") {
                 matrixCalculator = new JSD();
+            }else if (Estimators[i] == "rjsd") {
+                matrixCalculator = new RJSD();
             }else {
                 m->mothurOut("[ERROR]: " + Estimators[i] + " is not a valid calculator, please correct.\n"); m->control_pressed = true; return results;
             }