more calculator edits and added coverage and whittaker

[mothur.git] / summarysharedcommand.cpp

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index bebdf2637edad951b4b766760d4d96ee86281f69..e6a7d9a7363a5d9a71d32fad38d6172248b0934a 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -21,7 +21,7 @@
 #include "sharedthetayc.h"
 #include "sharedthetan.h"
 #include "sharedkstest.h"
-#include "sharedbdiversity.h"
+#include "whittaker.h"
 #include "sharedochiai.h"
 #include "sharedanderbergs.h"
 #include "sharedkulczynski.h"
@@ -51,43 +51,43 @@ SummarySharedCommand::SummarySharedCommand(){
                                        sumCalculators.push_back(new SharedChao1());
                                }else if (globaldata->Estimators[i] == "sharedace") { 
                                        sumCalculators.push_back(new SharedAce());
-                               }else if (globaldata->Estimators[i] == "sharedjabund") {        
-                                       sumCalculators.push_back(new SharedJAbund());
-                               }else if (globaldata->Estimators[i] == "sharedsorensonabund") { 
-                                       sumCalculators.push_back(new SharedSorAbund());
-                               }else if (globaldata->Estimators[i] == "sharedjclass") { 
-                                       sumCalculators.push_back(new SharedJclass());
-                               }else if (globaldata->Estimators[i] == "sharedsorclass") { 
-                                       sumCalculators.push_back(new SharedSorClass());
-                               }else if (globaldata->Estimators[i] == "sharedjest") { 
-                                       sumCalculators.push_back(new SharedJest());
-                               }else if (globaldata->Estimators[i] == "sharedsorest") { 
-                                       sumCalculators.push_back(new SharedSorEst());
-                               }else if (globaldata->Estimators[i] == "sharedthetayc") { 
-                                       sumCalculators.push_back(new SharedThetaYC());
-                               }else if (globaldata->Estimators[i] == "sharedthetan") { 
-                                       sumCalculators.push_back(new SharedThetaN());
-                               }else if (globaldata->Estimators[i] == "sharedkstest") { 
-                                       sumCalculators.push_back(new SharedKSTest());
+                               }else if (globaldata->Estimators[i] == "jabund") {      
+                                       sumCalculators.push_back(new JAbund());
+                               }else if (globaldata->Estimators[i] == "sorabund") { 
+                                       sumCalculators.push_back(new SorAbund());
+                               }else if (globaldata->Estimators[i] == "jclass") { 
+                                       sumCalculators.push_back(new Jclass());
+                               }else if (globaldata->Estimators[i] == "sorclass") { 
+                                       sumCalculators.push_back(new SorClass());
+                               }else if (globaldata->Estimators[i] == "jest") { 
+                                       sumCalculators.push_back(new Jest());
+                               }else if (globaldata->Estimators[i] == "sorest") { 
+                                       sumCalculators.push_back(new SorEst());
+                               }else if (globaldata->Estimators[i] == "thetayc") { 
+                                       sumCalculators.push_back(new ThetaYC());
+                               }else if (globaldata->Estimators[i] == "thetan") { 
+                                       sumCalculators.push_back(new ThetaN());
+                               }else if (globaldata->Estimators[i] == "kstest") { 
+                                       sumCalculators.push_back(new KSTest());
                                }else if (globaldata->Estimators[i] == "sharednseqs") { 
                                        sumCalculators.push_back(new SharedNSeqs());
-                               }else if (globaldata->Estimators[i] == "sharedochiai") { 
-                                       sumCalculators.push_back(new SharedOchiai());
-                               }else if (globaldata->Estimators[i] == "sharedanderberg") { 
-                                       sumCalculators.push_back(new SharedAnderberg());
-                               }else if (globaldata->Estimators[i] == "sharedkulczynski") { 
-                                       sumCalculators.push_back(new SharedKulczynski());
-                               }else if (globaldata->Estimators[i] == "sharedkulczynskicody") { 
-                                       sumCalculators.push_back(new SharedKulczynskiCody());
-                               }else if (globaldata->Estimators[i] == "sharedlennon") { 
-                                       sumCalculators.push_back(new SharedLennon());
-                               }else if (globaldata->Estimators[i] == "sharedmorisitahorn") { 
-                                       sumCalculators.push_back(new SharedMorHorn());
-                               }else if (globaldata->Estimators[i] == "sharedbraycurtis") { 
-                                       sumCalculators.push_back(new SharedBrayCurtis());
+                               }else if (globaldata->Estimators[i] == "ochiai") { 
+                                       sumCalculators.push_back(new Ochiai());
+                               }else if (globaldata->Estimators[i] == "anderberg") { 
+                                       sumCalculators.push_back(new Anderberg());
+                               }else if (globaldata->Estimators[i] == "kulczynski") { 
+                                       sumCalculators.push_back(new Kulczynski());
+                               }else if (globaldata->Estimators[i] == "kulczynskicody") { 
+                                       sumCalculators.push_back(new KulczynskiCody());
+                               }else if (globaldata->Estimators[i] == "lennon") { 
+                                       sumCalculators.push_back(new Lennon());
+                               }else if (globaldata->Estimators[i] == "morisitahorn") { 
+                                       sumCalculators.push_back(new MorHorn());
+                               }else if (globaldata->Estimators[i] == "braycurtis") { 
+                                       sumCalculators.push_back(new BrayCurtis());
                                }
-                               else if (globaldata->Estimators[i] == "sharedbdiversity") { 
-                                       sumCalculators.push_back(new SharedBDiversity());
+                               else if (globaldata->Estimators[i] == "whittaker") { 
+                                       sumCalculators.push_back(new Whittaker());
                                }
                                
                        }
@@ -123,14 +123,14 @@ int SummarySharedCommand::execute(){
                if (sumCalculators.size() == 0) { return 0; }
 
                if (format == "sharedfile") {
-                       read = new ReadPhilFile(globaldata->inputFileName);     
+                       read = new ReadOTUFile(globaldata->inputFileName);      
                        read->read(&*globaldata); 
                        
                        input = globaldata->ginput;
                        order = input->getSharedOrderVector();
                }else {
                        //you are using a list and a groupfile
-                       read = new ReadPhilFile(globaldata->inputFileName);     
+                       read = new ReadOTUFile(globaldata->inputFileName);      
                        read->read(&*globaldata); 
                
                        input = globaldata->ginput;