fixed Thomas' calculators

[mothur.git] / summarycommand.cpp

diff --git a/summarycommand.cpp b/summarycommand.cpp
index 8c8a2aadf93440ab0e6271381e641bdae2167686..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"
 
 //**********************************************************************************************************************
 
@@ -33,14 +39,15 @@ 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"){
+                               }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());
@@ -65,6 +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));
                                }
                        }
                }
@@ -102,7 +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++){
@@ -128,7 +149,7 @@ int SummaryCommand::execute(){
                                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;