added the Calculators Thomas made in the fall. Added parameter and command error...

[mothur.git] / summarycommand.cpp

diff --git a/summarycommand.cpp b/summarycommand.cpp
index 5adf44ff8621e5ea6e5231abc9417cdb3ff93e80..8c8a2aadf93440ab0e6271381e641bdae2167686 100644 (file)
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -17,6 +17,11 @@
 #include "npshannon.h"
 #include "shannon.h"
 #include "jackknife.h"
+#include "geom.h"
+#include "logsd.h"
+#include "qstat.h"
+#include "bergerparker.h"
+#include "bstick.h"
 
 //**********************************************************************************************************************
 
@@ -28,10 +33,21 @@ SummaryCommand::SummaryCommand(){
                
                for (i=0; i<globaldata->Estimators.size(); i++) {
                        if (validCalculator->isValidCalculator("summary", globaldata->Estimators[i]) == true) { 
+                       
                                if(globaldata->Estimators[i] == "sobs"){
                                        sumCalculators.push_back(new Sobs());
                                }else if(globaldata->Estimators[i] == "chao"){
                                        sumCalculators.push_back(new Chao1());
+                               }else if(globaldata->Estimators[i] == "geom"){
+                                       sumCalculators.push_back(new Geom());
+                               }else if(globaldata->Estimators[i] == "logsd"){
+                                       sumCalculators.push_back(new LogSD());
+                               }else if(globaldata->Estimators[i] == "qstat"){
+                                       sumCalculators.push_back(new QStat());
+                               }else if(globaldata->Estimators[i] == "bergerparker"){
+                                       sumCalculators.push_back(new BergerParker());
+                               }else if(globaldata->Estimators[i] == "bstick"){
+                                       sumCalculators.push_back(new BStick());
                                }else if(globaldata->Estimators[i] == "ace"){
                                        convert(globaldata->getAbund(), abund);
                                        if(abund < 5)
@@ -107,16 +123,16 @@ int SummaryCommand::execute(){
                        if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(sabund->getLabel()) == 1){                      
        
                                cout << sabund->getLabel() << '\t' << count << endl;
-                       
+                               
                                outputFileHandle << sabund->getLabel();
                                for(int i=0;i<sumCalculators.size();i++){
                                        vector<double> data = sumCalculators[i]->getValues(sabund);
                                        outputFileHandle << '\t';
-                                       sumCalculators[i]->print(outputFileHandle);
+                                       //sumCalculators[i]->print(outputFileHandle);
                                }
+                               
                                outputFileHandle << endl;
                        }
-               
                        sabund = input->getSAbundVector();
                        count++;
                }