modified some calculators and other stuff - pds

[mothur.git] / summarycommand.cpp

diff --git a/summarycommand.cpp b/summarycommand.cpp
index c6170d10263a0b1e35fa4c03e39e61fc016e0087..39972cef649a1c34443b0ae36117a48f8b776cbd 100644 (file)
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -10,38 +10,70 @@
 #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 "coverage.h"
 
 //**********************************************************************************************************************
 
 SummaryCommand::SummaryCommand(){
        try {
                globaldata = GlobalData::getInstance();
+               validCalculator = new ValidCalculators();
                int i;
-               for (i=0; i<globaldata->summaryEstimators.size(); i++) {
-                       if(globaldata->summaryEstimators[i] == "sobs"){
-                               sumCalculators.push_back(new Sobs());
-                       }else if(globaldata->summaryEstimators[i] == "chao"){
-                               sumCalculators.push_back(new Chao1());
-                       }else if(globaldata->summaryEstimators[i] == "ace"){
-                               sumCalculators.push_back(new Ace());
-                       }else if(globaldata->summaryEstimators[i] == "jack"){
-                               sumCalculators.push_back(new Jackknife());
-                       }else if(globaldata->summaryEstimators[i] == "shannon"){
-                               sumCalculators.push_back(new Shannon());
-                       }else if(globaldata->summaryEstimators[i] == "npshannon"){
-                               sumCalculators.push_back(new NPShannon());
-                       }else if(globaldata->summaryEstimators[i] == "simpson"){
-                               sumCalculators.push_back(new Simpson());
-                       }else if(globaldata->summaryEstimators[i] == "bootstrap"){
-                               sumCalculators.push_back(new Bootstrap());
+               
+               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] == "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)
+                                               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"){
+                                       sumCalculators.push_back(new Shannon());
+                               }else if(globaldata->Estimators[i] == "npshannon"){
+                                       sumCalculators.push_back(new NPShannon());
+                               }else if(globaldata->Estimators[i] == "simpson"){
+                                       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());
+                               }
                        }
                }
+               
+               //reset calc for next command
+               globaldata->setCalc("");
+
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the SummaryCommand class Function SummaryCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -64,11 +96,15 @@ SummaryCommand::~SummaryCommand(){
 
 int SummaryCommand::execute(){
        try {
+       
+               //if the users entered no valid calculators don't execute command
+               if (sumCalculators.size() == 0) { return 0; }
+
                outputFileName = ((getRootName(globaldata->inputFileName)) + "summary");
                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++){
@@ -89,16 +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++;
                }