changed defaults for filter.seqs()

[mothur.git] / summarycommand.cpp

diff --git a/summarycommand.cpp b/summarycommand.cpp
index 7a3ad4a1e57e7f3f5dac9539fb2c974cd4e14cbe..b649582758636370f812a51cf182ce7813bc3e02 100644 (file)
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -10,12 +10,24 @@
 #include "summarycommand.h"
 #include "ace.h"
 #include "sobs.h"
+#include "nseqs.h"
 #include "chao1.h"
 #include "bootstrap.h"
 #include "simpson.h"
 #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 "goodscoverage.h"
+#include "coverage.h"
+#include "efron.h"
+#include "boneh.h"
+#include "solow.h"
+#include "shen.h"
 
 //**********************************************************************************************************************
 
@@ -31,8 +43,23 @@ 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"){
-                                       sumCalculators.push_back(new Ace());
+                                       convert(globaldata->getAbund(), abund);
+                                       if(abund < 5)
+                                               abund = 10;
+                                       sumCalculators.push_back(new Ace(abund));
                                }else if(globaldata->Estimators[i] == "jack"){
                                        sumCalculators.push_back(new Jackknife());
                                }else if(globaldata->Estimators[i] == "shannon"){
@@ -43,6 +70,22 @@ SummaryCommand::SummaryCommand(){
                                        sumCalculators.push_back(new Simpson());
                                }else if(globaldata->Estimators[i] == "bootstrap"){
                                        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));
                                }
                        }
                }
@@ -80,7 +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++){
@@ -101,16 +144,16 @@ 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++;
                }