X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarycommand.cpp;h=39972cef649a1c34443b0ae36117a48f8b776cbd;hb=477e76a8a79b60f6cd4253324dd830bdea25e3e9;hp=c6170d10263a0b1e35fa4c03e39e61fc016e0087;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/summarycommand.cpp b/summarycommand.cpp
index c6170d1..39972ce 100644
--- 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++;
 		}