X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactsharedcommand.cpp;h=4a25cb3208f2695fc50308a8ff7df83deda163a8;hb=599af78a6ea4916919d460a131e2d0dffa28d35e;hp=6a4fe85b76b56dd5903b98155f0b01121f0f0002;hpb=9ca2caadbeac83bb84b3330d9204b1b659d62941;p=mothur.git

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index 6a4fe85..4a25cb3 100644
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -20,6 +20,7 @@ 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++) {
@@ -55,6 +56,7 @@ RareFactSharedCommand::~RareFactSharedCommand(){
 	delete input;
 	delete rCurve;
 	delete read;
+	delete util;
 }
 
 //**********************************************************************************************************************
@@ -66,24 +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
-		setGroups();
+		util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "rarefact");
 		
 		while(order != NULL){
 		
@@ -100,18 +92,8 @@ 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++;
 		}
 	
@@ -134,51 +116,3 @@ int RareFactSharedCommand::execute(){
 
 
 //**********************************************************************************************************************
-
-void RareFactSharedCommand::setGroups() {
-	try {
-		//if the user has not entered specific groups to analyze then do them all
-		if (globaldata->Groups.size() != 0) {
-			if (globaldata->Groups[0] != "all") {
-				//check that groups are valid
-				for (int i = 0; i < globaldata->Groups.size(); i++) {
-					if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
-						cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
-						// erase the invalid group from globaldata->Groups
-						globaldata->Groups.erase(globaldata->Groups.begin()+i);
-					}
-				}
-			
-				//if the user only entered invalid groups
-				if ((globaldata->Groups.size() == 0) || (globaldata->Groups.size() == 1)) { 
-					cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl; 
-					for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
-						globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
-					}
-				}
-			}else{//user has enter "all" and wants the default groups
-				globaldata->Groups.clear();
-				for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
-					globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
-				}
-				globaldata->setGroups("");
-			}
-		}else {
-			for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
-				globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
-			}
-		}
-		
-	}
-	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the RareFactSharedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}		
-
-}
-/***********************************************************/
-