added calcs to tree.shared. working on remove.rare command

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 626659501a531db80f5193bef33e88793414a874..6e32a373e41bd2aeb9ad3e9fe0cde110d583da37 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -8,6 +8,10 @@
  */
 
 #include "treegroupscommand.h"
+#include "sharedsobscollectsummary.h"
+#include "sharedchao1.h"
+#include "sharedace.h"
+#include "sharednseqs.h"
 #include "sharedjabund.h"
 #include "sharedsorabund.h"
 #include "sharedjclass.h"
@@ -16,8 +20,35 @@
 #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"
 
 //**********************************************************************************************************************
 vector<string> TreeGroupCommand::getValidParameters(){ 
@@ -210,7 +241,13 @@ TreeGroupCommand::TreeGroupCommand(string option)  {
                                        int i;
                                        for (i=0; i<Estimators.size(); i++) {
                                                if (validCalculator->isValidCalculator("treegroup", Estimators[i]) == true) { 
-                                                       if (Estimators[i] == "jabund") {        
+                                                       if (Estimators[i] == "sharedsobs") { 
+                                                               treeCalculators.push_back(new SharedSobsCS());
+                                                       }else if (Estimators[i] == "sharedchao") { 
+                                                               treeCalculators.push_back(new SharedChao1());
+                                                       }else if (Estimators[i] == "sharedace") { 
+                                                               treeCalculators.push_back(new SharedAce());
+                                                       }else if (Estimators[i] == "jabund") {  
                                                                treeCalculators.push_back(new JAbund());
                                                        }else if (Estimators[i] == "sorabund") { 
                                                                treeCalculators.push_back(new SorAbund());
@@ -226,10 +263,62 @@ TreeGroupCommand::TreeGroupCommand(string option)  {
                                                                treeCalculators.push_back(new ThetaYC());
                                                        }else if (Estimators[i] == "thetan") { 
                                                                treeCalculators.push_back(new ThetaN());
+                                                       }else if (Estimators[i] == "kstest") { 
+                                                               treeCalculators.push_back(new KSTest());
+                                                       }else if (Estimators[i] == "sharednseqs") { 
+                                                               treeCalculators.push_back(new SharedNSeqs());
+                                                       }else if (Estimators[i] == "ochiai") { 
+                                                               treeCalculators.push_back(new Ochiai());
+                                                       }else if (Estimators[i] == "anderberg") { 
+                                                               treeCalculators.push_back(new Anderberg());
+                                                       }else if (Estimators[i] == "kulczynski") { 
+                                                               treeCalculators.push_back(new Kulczynski());
+                                                       }else if (Estimators[i] == "kulczynskicody") { 
+                                                               treeCalculators.push_back(new KulczynskiCody());
+                                                       }else if (Estimators[i] == "lennon") { 
+                                                               treeCalculators.push_back(new Lennon());
                                                        }else if (Estimators[i] == "morisitahorn") { 
                                                                treeCalculators.push_back(new MorHorn());
                                                        }else if (Estimators[i] == "braycurtis") { 
                                                                treeCalculators.push_back(new BrayCurtis());
+                                                       }else if (Estimators[i] == "whittaker") { 
+                                                               treeCalculators.push_back(new Whittaker());
+                                                       }else if (Estimators[i] == "odum") { 
+                                                               treeCalculators.push_back(new Odum());
+                                                       }else if (Estimators[i] == "canberra") { 
+                                                               treeCalculators.push_back(new Canberra());
+                                                       }else if (Estimators[i] == "structeuclidean") { 
+                                                               treeCalculators.push_back(new StructEuclidean());
+                                                       }else if (Estimators[i] == "structchord") { 
+                                                               treeCalculators.push_back(new StructChord());
+                                                       }else if (Estimators[i] == "hellinger") { 
+                                                               treeCalculators.push_back(new Hellinger());
+                                                       }else if (Estimators[i] == "manhattan") { 
+                                                               treeCalculators.push_back(new Manhattan());
+                                                       }else if (Estimators[i] == "structpearson") { 
+                                                               treeCalculators.push_back(new StructPearson());
+                                                       }else if (Estimators[i] == "soergel") { 
+                                                               treeCalculators.push_back(new Soergel());
+                                                       }else if (Estimators[i] == "spearman") { 
+                                                               treeCalculators.push_back(new Spearman());
+                                                       }else if (Estimators[i] == "structkulczynski") { 
+                                                               treeCalculators.push_back(new StructKulczynski());
+                                                       }else if (Estimators[i] == "speciesprofile") { 
+                                                               treeCalculators.push_back(new SpeciesProfile());
+                                                       }else if (Estimators[i] == "hamming") { 
+                                                               treeCalculators.push_back(new Hamming());
+                                                       }else if (Estimators[i] == "structchi2") { 
+                                                               treeCalculators.push_back(new StructChi2());
+                                                       }else if (Estimators[i] == "gower") { 
+                                                               treeCalculators.push_back(new Gower());
+                                                       }else if (Estimators[i] == "memchi2") { 
+                                                               treeCalculators.push_back(new MemChi2());
+                                                       }else if (Estimators[i] == "memchord") { 
+                                                               treeCalculators.push_back(new MemChord());
+                                                       }else if (Estimators[i] == "memeuclidean") { 
+                                                               treeCalculators.push_back(new MemEuclidean());
+                                                       }else if (Estimators[i] == "mempearson") { 
+                                                               treeCalculators.push_back(new MemPearson());
                                                        }
                                                }
                                        }