fixed Thomas' calculators

[mothur.git] / summarycommand.cpp

diff --git a/summarycommand.cpp b/summarycommand.cpp
index 05fc6e8c77057c00bd64e9c057f8784ea71a7188..b649582758636370f812a51cf182ce7813bc3e02 100644 (file)
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -22,6 +22,12 @@
 #include "qstat.h"
 #include "bergerparker.h"
 #include "bstick.h"
+#include "goodscoverage.h"
+#include "coverage.h"
+#include "efron.h"
+#include "boneh.h"
+#include "solow.h"
+#include "shen.h"
 
 //**********************************************************************************************************************
 
@@ -37,9 +43,11 @@ 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());
@@ -64,6 +72,20 @@ SummaryCommand::SummaryCommand(){
                                        sumCalculators.push_back(new Bootstrap());
                                }else if (globaldata->Estimators[i] == "nseqs") { 
                                        sumCalculators.push_back(new NSeqs());
+                               }else if (globaldata->Estimators[i] == "goodscoverage") { 
+                                       sumCalculators.push_back(new GoodsCoverage());
+                               }else if (globaldata->Estimators[i] == "efron") { 
+                                       convert(globaldata->getSize(), size);
+                                       sumCalculators.push_back(new Efron(size));
+                               }else if (globaldata->Estimators[i] == "boneh") { 
+                                       convert(globaldata->getSize(), size);
+                                       sumCalculators.push_back(new Boneh(size));
+                               }else if (globaldata->Estimators[i] == "solow") { 
+                                       convert(globaldata->getSize(), size);
+                                       sumCalculators.push_back(new Solow(size));
+                               }else if (globaldata->Estimators[i] == "shen") { 
+                                       convert(globaldata->getSize(), size);
+                                       sumCalculators.push_back(new Shen(size));
                                }
                        }
                }
@@ -101,7 +123,7 @@ 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++){