X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactsharedcommand.cpp;h=4a25cb3208f2695fc50308a8ff7df83deda163a8;hb=599af78a6ea4916919d460a131e2d0dffa28d35e;hp=45c2e2ebbdfc0004a8e1d6acb551649fe82b1239;hpb=09a01fb51eea9e81409d367410c831394193fd86;p=mothur.git

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index 45c2e2e..4a25cb3 100644
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -9,6 +9,7 @@
 
 #include "rarefactsharedcommand.h"
 #include "sharedsobs.h"
+#include "sharednseqs.h"
 
 //**********************************************************************************************************************
 
@@ -19,13 +20,17 @@ RareFactSharedCommand::RareFactSharedCommand(){
 		fileNameRoot = getRootName(globaldata->inputFileName);
 		format = globaldata->getFormat();
 		validCalculator = new ValidCalculators();
+		util = new SharedUtil();
 				
 		int i;
 		for (i=0; i<globaldata->Estimators.size(); i++) {
 			if (validCalculator->isValidCalculator("sharedrarefaction", globaldata->Estimators[i]) == true) { 
 				if (globaldata->Estimators[i] == "sharedobserved") { 
 					rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));
+				}else if (globaldata->Estimators[i] == "sharednseqs") { 
+					rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(fileNameRoot+"shared.r_nseqs", "")));
 				}
+
 			}
 		}
 		
@@ -51,6 +56,7 @@ RareFactSharedCommand::~RareFactSharedCommand(){
 	delete input;
 	delete rCurve;
 	delete read;
+	delete util;
 }
 
 //**********************************************************************************************************************
@@ -62,21 +68,14 @@ int RareFactSharedCommand::execute(){
 		//if the users entered no valid calculators don't execute command
 		if (rDisplays.size() == 0) { return 0; }
 
-		if (format == "sharedfile") {
-			read = new ReadPhilFile(globaldata->inputFileName);	
-			read->read(&*globaldata); 
+		read = new ReadOTUFile(globaldata->inputFileName);	
+		read->read(&*globaldata); 
 			
-			input = globaldata->ginput;
-			order = input->getSharedOrderVector();
-		}else {
-			//you are using a list and a groupfile
-			read = new ReadPhilFile(globaldata->inputFileName);	
-			read->read(&*globaldata); 
-		
-			input = globaldata->ginput;
-			SharedList = globaldata->gSharedList;
-			order = SharedList->getSharedOrderVector();
-		}
+		input = globaldata->ginput;
+		order = input->getSharedOrderVector();
+				
+		//set users groups
+		util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "rarefact");
 		
 		while(order != NULL){
 		
@@ -93,22 +92,16 @@ int RareFactSharedCommand::execute(){
 			}
 			
 			//get next line to process
-			if (format == "sharedfile") {
-				order = input->getSharedOrderVector();
-			}else {
-				//you are using a list and a groupfile
-				SharedList = input->getSharedListVector(); //get new list vector to process
-				if (SharedList != NULL) {
-					order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
-				}else {
-					break;
-				}
-			}
-			
+			delete order;
+			order = input->getSharedOrderVector();
 			count++;
 		}
 	
 		for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	}	
+		
+		//reset groups parameter
+		globaldata->Groups.clear();  globaldata->setGroups("");
+
 		return 0;
 	}
 	catch(exception& e) {