modified some calculators and other stuff - pds

[mothur.git] / summarycommand.cpp

diff --git a/summarycommand.cpp b/summarycommand.cpp
index 5adf44ff8621e5ea6e5231abc9417cdb3ff93e80..39972cef649a1c34443b0ae36117a48f8b776cbd 100644 (file)
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -17,6 +17,12 @@
 #include "npshannon.h"
 #include "shannon.h"
 #include "jackknife.h"
+#include "geom.h"
+#include "logsd.h"
+#include "qstat.h"
+#include "bergerparker.h"
+#include "bstick.h"
+#include "coverage.h"
 
 //**********************************************************************************************************************
 
@@ -32,6 +38,18 @@ SummaryCommand::SummaryCommand(){
                                        sumCalculators.push_back(new Sobs());
                                }else if(globaldata->Estimators[i] == "chao"){
                                        sumCalculators.push_back(new Chao1());
+                               }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] == "logseries"){
+                                       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)
@@ -86,7 +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++){
@@ -107,16 +125,16 @@ 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);
                                }
+                               
                                outputFileHandle << endl;
                        }
-               
                        sabund = input->getSAbundVector();
                        count++;
                }