X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactsharedcommand.cpp;h=58f73f34e45b61b30e5355ebd38cfa63f988448d;hb=39ef0543b73cb12dfc64529522b66ad3df7527d0;hp=4ed479555ab7ac66a75e789e71f9be5053ec3ae2;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index 4ed4795..58f73f3 100644
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -15,22 +15,23 @@
 RareFactSharedCommand::RareFactSharedCommand(){
 	try {
 		globaldata = GlobalData::getInstance();
-		string fileNameRoot, groups;
+		string fileNameRoot;
 		fileNameRoot = getRootName(globaldata->inputFileName);
-		groupmap = globaldata->gGroupmap;
-		
-		//initialize groups for label
-		groups = "";
-		for (int i = 0; i < groupmap->namesOfGroups.size(); i++) {
-			groups = groups + groupmap->namesOfGroups[i];
-		}
-		
+		format = globaldata->getFormat();
+		validCalculator = new ValidCalculators();
+				
 		int i;
-		for (i=0; i<globaldata->sharedRareEstimators.size(); i++) {
-			if (globaldata->sharedRareEstimators[i] == "sharedobserved") { 
-				rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"sharedObserved", groups)));
+		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", "")));
+				}
 			}
 		}
+		
+		//reset calc for next command
+		globaldata->setCalc("");
+
 	}
 	catch(exception& e) {
 		cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function RareFactSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -57,12 +58,28 @@ RareFactSharedCommand::~RareFactSharedCommand(){
 int RareFactSharedCommand::execute(){
 	try {
 		int count = 1;
-		read = new ReadPhilFile(globaldata->inputFileName);	
-		read->read(&*globaldata); 
 		
-		input = globaldata->ginput;
-		list = globaldata->glist;
-		order = list->getSharedOrderVector();
+		//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); 
+			
+			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();
+		}
+		
+		//set users groups
+		setGroups();
 		
 		while(order != NULL){
 		
@@ -78,17 +95,27 @@ int RareFactSharedCommand::execute(){
 				cout << order->getLabel() << '\t' << count << endl;
 			}
 			
-			list = input->getListVector(); //get new list vector to process
-			if (list != NULL) {
-				order = list->getSharedOrderVector(); //gets new order vector with group info.
-				count++;
+			//get next line to process
+			if (format == "sharedfile") {
+				order = input->getSharedOrderVector();
 			}else {
-				break;
+				//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;
+				}
 			}
-		
+			
+			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) {
@@ -103,3 +130,51 @@ 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);
+	}		
+
+}
+/***********************************************************/
+