more calculator edits and added coverage and whittaker

[mothur.git] / summarycommand.cpp

diff --git a/summarycommand.cpp b/summarycommand.cpp
index 05fc6e8c77057c00bd64e9c057f8784ea71a7188..39972cef649a1c34443b0ae36117a48f8b776cbd 100644 (file)
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -22,6 +22,7 @@
 #include "qstat.h"
 #include "bergerparker.h"
 #include "bstick.h"
+#include "coverage.h"
 
 //**********************************************************************************************************************
 
@@ -37,9 +38,11 @@ SummaryCommand::SummaryCommand(){
                                        sumCalculators.push_back(new Sobs());
                                }else if(globaldata->Estimators[i] == "chao"){
                                        sumCalculators.push_back(new Chao1());
-                               }else if(globaldata->Estimators[i] == "geom"){
+                               }else if(globaldata->Estimators[i] == "coverage"){
+                                       sumCalculators.push_back(new Coverage());
+                               }else if(globaldata->Estimators[i] == "geometric"){
                                        sumCalculators.push_back(new Geom());
-                               }else if(globaldata->Estimators[i] == "logsd"){
+                               }else if(globaldata->Estimators[i] == "logseries"){
                                        sumCalculators.push_back(new LogSD());
                                }else if(globaldata->Estimators[i] == "qstat"){
                                        sumCalculators.push_back(new QStat());
@@ -101,7 +104,7 @@ int SummaryCommand::execute(){
                openOutputFile(outputFileName, outputFileHandle);
                outputFileHandle << "label";
        
-               read = new ReadPhilFile(globaldata->inputFileName);     
+               read = new ReadOTUFile(globaldata->inputFileName);      
                read->read(&*globaldata); 
 
                for(int i=0;i<sumCalculators.size();i++){