X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedcommand.cpp;h=cb4b4e6ced702b08d2b1dda3668f376a82e1e624;hb=836150c0a3666899ad58426388f4999d6cf8829a;hp=26ba2211906fa025e3807aedf8c13ef3d913e413;hpb=29c0d3ec01be5372807eb86261100d77de253787;p=mothur.git

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index 26ba221..cb4b4e6 100644
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -8,95 +8,353 @@
  */
 
 #include "sharedcommand.h"
-
+//********************************************************************************************************************
+//sorts lowest to highest
+inline bool compareSharedRabunds(SharedRAbundVector* left, SharedRAbundVector* right){
+	return (left->getGroup() < right->getGroup());	
+}
+//**********************************************************************************************************************
+vector<string> SharedCommand::setParameters(){	
+	try {
+		CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
+		CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
+		CommandParameter pordergroup("ordergroup", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pordergroup);
+		CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+		CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		
+		vector<string> myArray;
+		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SharedCommand", "setParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+string SharedCommand::getHelpString(){	
+	try {
+		string helpString = "";
+		helpString += "The make.shared command reads a list and group file and creates a shared file, as well as a rabund file for each group.\n";
+		helpString += "The make.shared command parameters are list, group, ordergroup, groups and label. list and group are required unless a current file is available.\n";
+		helpString += "The groups parameter allows you to indicate which groups you want to include, group names should be separated by dashes. ex. groups=A-B-C. Default is all groups in your groupfile.\n";
+		helpString += "The label parameter allows you to indicate which labels you want to include, label names should be separated by dashes. Default is all labels in your list file.\n";
+		helpString += "The ordergroup parameter allows you to indicate the order of the groups in the sharedfile, by default the groups are listed alphabetically.\n";
+		return helpString;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SharedCommand", "getHelpString");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+SharedCommand::SharedCommand(){	
+	try {
+		abort = true; calledHelp = true; 
+		setParameters();
+		//initialize outputTypes
+		vector<string> tempOutNames;
+		outputTypes["rabund"] = tempOutNames;
+		outputTypes["shared"] = tempOutNames;
+		outputTypes["group"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SharedCommand", "SharedCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+SharedCommand::SharedCommand(string option)  {
+	try {
+		abort = false; calledHelp = false;   
+		allLines = 1;
+		
+		//allow user to run help
+		if(option == "help") { help(); abort = true; calledHelp = true; }
+		
+		else {
+			
+			 vector<string> myArray = setParameters();
+			 
+			 OptionParser parser(option);
+			 map<string, string> parameters = parser.getParameters();
+			 
+			 ValidParameters validParameter;
+			 map<string, string>::iterator it;
+			 
+			 //check to make sure all parameters are valid for command
+			 for (it = parameters.begin(); it != parameters.end(); it++) { 
+				 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+			 }
+			 
+			 //if the user changes the input directory command factory will send this info to us in the output parameter 
+			string inputDir = validParameter.validFile(parameters, "inputdir", false);		
+			 if (inputDir == "not found"){	inputDir = "";		}
+			 else {
+				 string path;
+				 it = parameters.find("list");
+				 //user has given a template file
+				 if(it != parameters.end()){ 
+					 path = m->hasPath(it->second);
+					 //if the user has not given a path then, add inputdir. else leave path alone.
+					 if (path == "") {	parameters["list"] = inputDir + it->second;		}
+				 }
+			 
+				 it = parameters.find("group");
+				 //user has given a template file
+				 if(it != parameters.end()){ 
+					 path = m->hasPath(it->second);
+					 //if the user has not given a path then, add inputdir. else leave path alone.
+					 if (path == "") {	parameters["group"] = inputDir + it->second;		}
+				 }
+			 
+				 it = parameters.find("ordergroup");
+				 //user has given a template file
+				 if(it != parameters.end()){ 
+					 path = m->hasPath(it->second);
+					 //if the user has not given a path then, add inputdir. else leave path alone.
+					 if (path == "") {	parameters["ordergroup"] = inputDir + it->second;		}
+				 }
+			 }
+			 
+			 
+			 //if the user changes the output directory command factory will send this info to us in the output parameter 
+			 outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	outputDir = "";	}
+			 
+			 //check for required parameters
+			 listfile = validParameter.validFile(parameters, "list", true);
+			 if (listfile == "not open") { listfile = ""; abort = true; }
+			 else if (listfile == "not found") { 
+				 listfile = m->getListFile(); 
+				 if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
+				 else { 	m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
+			 }	
+							
+			 ordergroupfile = validParameter.validFile(parameters, "ordergroup", true);
+			 if (ordergroupfile == "not open") { abort = true; }	
+			 else if (ordergroupfile == "not found") { ordergroupfile = ""; }
+			 			 
+			 groupfile = validParameter.validFile(parameters, "group", true);
+			 if (groupfile == "not open") { groupfile = ""; abort = true; }	
+			 else if (groupfile == "not found") { 
+				 groupfile = m->getGroupFile(); 
+				 if (groupfile != "") { 
+					 m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine();
+					 groupMap = new GroupMap(groupfile);
+					 
+					 int error = groupMap->readMap();
+					 if (error == 1) { abort = true; }
+					 m->namesOfGroups = groupMap->namesOfGroups;
+				 }
+				 else { 	m->mothurOut("You have no current group file and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
+			 }else {  
+				 groupMap = new GroupMap(groupfile);
+			 
+				 int error = groupMap->readMap();
+				 if (error == 1) { abort = true; }
+				 m->namesOfGroups = groupMap->namesOfGroups;
+				 m->setGroupFile(groupfile);
+			 }
+			 
+			 string groups = validParameter.validFile(parameters, "groups", false);			
+			 if (groups == "not found") { groups = ""; }
+			 else { 
+				 m->splitAtDash(groups, Groups);
+				 m->Groups = Groups;
+			 }
+			 
+			 //check for optional parameter and set defaults
+			 // ...at some point should added some additional type checking...
+			 string label = validParameter.validFile(parameters, "label", false);			
+			 if (label == "not found") { label = ""; }
+			 else { 
+				 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
+				 else { allLines = 1;  }
+			 }
+		}
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SharedCommand", "SharedCommand");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 
-SharedCommand::SharedCommand(){
+int SharedCommand::execute(){
 	try {
-		globaldata = GlobalData::getInstance();
+		
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		//getting output filename
-		filename = globaldata->inputFileName;
-		filename = getRootName(filename);
+		filename = listfile;
+		
+		if (outputDir == "") { outputDir += m->hasPath(filename); }
+		
+		filename = outputDir + m->getRootName(m->getSimpleName(filename));
 		filename = filename + "shared";
-		openOutputFile(filename, out);
+		outputTypes["shared"].push_back(filename);
 		
-		groupMap = globaldata->gGroupmap;
+		m->openOutputFile(filename, out);
+		pickedGroups = false;
+		
+		//if hte user has not specified any groups then use them all
+		if (Groups.size() == 0) {
+			Groups = groupMap->namesOfGroups; m->Groups = Groups;
+		}else { pickedGroups = true; }
 		
 		//fill filehandles with neccessary ofstreams
 		int i;
 		ofstream* temp;
-		for (i=0; i<groupMap->getNumGroups(); i++) {
+		for (i=0; i<Groups.size(); i++) {
 			temp = new ofstream;
-			filehandles[groupMap->namesOfGroups[i]] = temp;
+			filehandles[Groups[i]] = temp;
 		}
 		
 		//set fileroot
-		fileroot = getRootName(globaldata->getListFile());
+		fileroot = outputDir + m->getRootName(m->getSimpleName(listfile));
 		
 		//clears file before we start to write to it below
-		for (int i=0; i<groupMap->getNumGroups(); i++) {
-			remove((fileroot + groupMap->namesOfGroups[i] + ".rabund").c_str());
+		for (int i=0; i<Groups.size(); i++) {
+			remove((fileroot + Groups[i] + ".rabund").c_str());
+			outputNames.push_back((fileroot + Groups[i] + ".rabund"));
+			outputTypes["rabund"].push_back((fileroot + Groups[i] + ".rabund"));
 		}
-
-	}
-	catch(exception& e) {
-		errorOut(e, "SharedCommand", "SharedCommand");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************
-
-int SharedCommand::execute(){
-	try {
 		
 		//lookup.clear();
-		int count = 1;
 		string errorOff = "no error";
-			
-		//read in listfile
-		read = new ReadOTUFile(globaldata->inputFileName);	
-		read->read(&*globaldata); 
-
-		input = globaldata->ginput;
-		SharedList = globaldata->gSharedList;
+		//errorOff = "";
+		
+		//if user provided an order file containing the order the shared file should be in read it
+		if (ordergroupfile != "") { readOrderFile(); }
+		
+		input = new InputData(listfile, "shared");
+		SharedList = input->getSharedListVector();
 		string lastLabel = SharedList->getLabel();
 		vector<SharedRAbundVector*> lookup; 
+		
+		if (m->control_pressed) { 
+			delete input; delete SharedList; delete groupMap; 
+			for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
+			out.close(); remove(filename.c_str()); 
+			for (int i=0; i<Groups.size(); i++) {  remove((fileroot + Groups[i] + ".rabund").c_str());		}
+			return 0; 
+		}
 				
+		if ((m->Groups.size() == 0) && (SharedList->getNumSeqs() != groupMap->getNumSeqs())) {  //if the user has not specified any groups and their files don't match exit with error
+			m->mothurOut("Your group file contains " + toString(groupMap->getNumSeqs()) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct."); m->mothurOutEndLine(); 
+			
+			out.close();
+			remove(filename.c_str()); //remove blank shared file you made
+			
+			createMisMatchFile();
+			
+			//delete memory
+			for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+				delete it3->second;
+			}
+		
+			delete input; delete SharedList; delete groupMap; 
+			
+			return 0; 
+		}
+		
+		//if user has specified groups make new groupfile for them
+		if (pickedGroups) { //make new group file
+			string groups = "";
+			if (m->Groups.size() < 4) {
+				for (int i = 0; i < m->Groups.size(); i++) {
+					groups += m->Groups[i] + ".";
+				}
+			}else { groups = "merge"; }
+		
+			string newGroupFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + groups + "groups";
+			outputTypes["group"].push_back(newGroupFile); 
+			outputNames.push_back(newGroupFile);
+			ofstream outGroups;
+			m->openOutputFile(newGroupFile, outGroups);
+		
+			vector<string> names = groupMap->getNamesSeqs();
+			string groupName;
+			for (int i = 0; i < names.size(); i++) {
+				groupName = groupMap->getGroup(names[i]);
+				if (isValidGroup(groupName, m->Groups)) {
+					outGroups << names[i] << '\t' << groupName << endl;
+				}
+			}
+			outGroups.close();
+		}
+		
 		//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 		set<string> processedLabels;
-		set<string> userLabels = globaldata->labels;
-		set<int> userLines = globaldata->lines;
-		
+		set<string> userLabels = labels;	
+	
+		while((SharedList != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+			if (m->control_pressed) { 
+				delete input; delete SharedList; delete groupMap;
+				for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
+				out.close(); remove(filename.c_str()); 
+				for (int i=0; i<Groups.size(); i++) {  remove((fileroot + Groups[i] + ".rabund").c_str());		}
+				return 0; 
+			}
 		
-		while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
-			
-
-			if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
+			if(allLines == 1 || labels.count(SharedList->getLabel()) == 1){
 					
 					lookup = SharedList->getSharedRAbundVector();
-					mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+					
+					m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+					if (pickedGroups) { //check for otus with no seqs in them
+						eliminateZeroOTUS(lookup);
+					}
+					
+					if (m->control_pressed) { 
+						delete input; delete SharedList; delete groupMap; 
+						for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
+						for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
+						out.close(); remove(filename.c_str()); 
+						for (int i=0; i<Groups.size(); i++) {  remove((fileroot + Groups[i] + ".rabund").c_str());		}
+						return 0; 
+					}
 					
 					printSharedData(lookup); //prints info to the .shared file
 					for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 				
 					processedLabels.insert(SharedList->getLabel());
 					userLabels.erase(SharedList->getLabel());
-					userLines.erase(count);
 			}
 			
-			if ((anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
+			if ((m->anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
+					string saveLabel = SharedList->getLabel();
+					
 					delete SharedList;
 					SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
 					
 					lookup = SharedList->getSharedRAbundVector();
-					mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+					m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+					if (pickedGroups) { //check for otus with no seqs in them
+						eliminateZeroOTUS(lookup);
+					}
+					
+					
+					if (m->control_pressed) { 
+						delete input; delete SharedList; delete groupMap; 
+						for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
+						for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
+						out.close(); remove(filename.c_str()); 
+						for (int i=0; i<Groups.size(); i++) {  remove((fileroot + Groups[i] + ".rabund").c_str());		}
+						return 0; 
+					}
 					
 					printSharedData(lookup); //prints info to the .shared file
 					for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 					
 					processedLabels.insert(SharedList->getLabel());
 					userLabels.erase(SharedList->getLabel());
+					
+					//restore real lastlabel to save below
+					SharedList->setLabel(saveLabel);
 			}
 			
 		
@@ -104,8 +362,6 @@ int SharedCommand::execute(){
 				
 			delete SharedList;
 			SharedList = input->getSharedListVector(); //get new list vector to process
-			
-			count++;		
 		}
 		
 		//output error messages about any remaining user labels
@@ -117,33 +373,71 @@ int SharedCommand::execute(){
 			}
 		}
 		
-		//run last line if you need to
+		//run last label if you need to
 		if (needToRun == true)  {
-			delete SharedList;
+			if (SharedList != NULL) {	delete SharedList;	}
 			SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
 					
 			lookup = SharedList->getSharedRAbundVector();
-			mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+			m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+			if (pickedGroups) { //check for otus with no seqs in them
+				eliminateZeroOTUS(lookup);
+			}
+			
+			if (m->control_pressed) { 
+				delete input;  delete groupMap;
+					for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;   }
+					out.close(); remove(filename.c_str()); 
+					for (int i=0; i<Groups.size(); i++) {  remove((fileroot + Groups[i] + ".rabund").c_str());		}
+					return 0; 
+			}
 			
 			printSharedData(lookup); //prints info to the .shared file
 			for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 			delete SharedList;
 		}
 		
-		globaldata->gSharedList = NULL;
-		delete read;
-		
 		out.close();
 		
 		for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 			delete it3->second;
 		}
 
+		delete input; delete groupMap;
+		
+		if (m->control_pressed) { 
+				remove(filename.c_str()); 
+				for (int i=0; i<Groups.size(); i++) {  remove((fileroot + Groups[i] + ".rabund").c_str());		}
+				return 0; 
+		}
+		
+		//set rabund file as new current rabundfile
+		string current = "";
+		itTypes = outputTypes.find("rabund");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
+		}
+		
+		itTypes = outputTypes.find("shared");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
+		}	
+		
+		itTypes = outputTypes.find("group");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
+		}
+		
+		m->mothurOutEndLine();
+		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+		for (int i = 0; i < outputNames.size(); i++) {	m->mothurOut(outputNames[i]); m->mothurOutEndLine();	}
+		m->mothurOut(filename); m->mothurOutEndLine();
+		m->mothurOutEndLine();
 		
 		return 0;
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedCommand", "execute");
+		m->errorOut(e, "SharedCommand", "execute");
 		exit(1);
 	}
 }
@@ -151,20 +445,208 @@ int SharedCommand::execute(){
 void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
 	try {
 		
-		//initialize bin values
+		if (order.size() == 0) { //user has not specified an order so do aplabetically
+			sort(thislookup.begin(), thislookup.end(), compareSharedRabunds);
+			
+			m->Groups.clear();
+			
+			//initialize bin values
+			for (int i = 0; i < thislookup.size(); i++) {
+				out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
+				thislookup[i]->print(out);
+				
+				m->Groups.push_back(thislookup[i]->getGroup());
+				
+				RAbundVector rav = thislookup[i]->getRAbundVector();
+				m->openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
+				rav.print(*(filehandles[thislookup[i]->getGroup()]));
+				(*(filehandles[thislookup[i]->getGroup()])).close();
+			}
+		}else{
+			//create a map from groupName to each sharedrabund
+			map<string, SharedRAbundVector*> myMap;
+			map<string, SharedRAbundVector*>::iterator myIt;
+			
+			for (int i = 0; i < thislookup.size(); i++) {
+				myMap[thislookup[i]->getGroup()] = thislookup[i];
+			}
+			
+			m->Groups.clear();
+			
+			//loop through ordered list and print the rabund
+			for (int i = 0; i < order.size(); i++) {
+				myIt = myMap.find(order[i]);
+				
+				if(myIt != myMap.end()) { //we found it
+					out << (myIt->second)->getLabel() << '\t' << (myIt->second)->getGroup() << '\t';
+					(myIt->second)->print(out);
+					
+					m->Groups.push_back((myIt->second)->getGroup());
+				
+					RAbundVector rav = (myIt->second)->getRAbundVector();
+					m->openOutputFileAppend(fileroot + (myIt->second)->getGroup() + ".rabund", *(filehandles[(myIt->second)->getGroup()]));
+					rav.print(*(filehandles[(myIt->second)->getGroup()]));
+					(*(filehandles[(myIt->second)->getGroup()])).close();
+				}else{
+					m->mothurOut("Can't find shared info for " + order[i] + ", skipping."); m->mothurOutEndLine();
+				}
+			}
+		
+		}
+ 
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SharedCommand", "printSharedData");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+int SharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
+	try {
+		
+		vector<SharedRAbundVector*> newLookup;
 		for (int i = 0; i < thislookup.size(); i++) {
-			out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
-			thislookup[i]->print(out);
+			SharedRAbundVector* temp = new SharedRAbundVector();
+			temp->setLabel(thislookup[i]->getLabel());
+			temp->setGroup(thislookup[i]->getGroup());
+			newLookup.push_back(temp);
+		}
+		
+		//for each bin
+		for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
+			if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
+		
+			//look at each sharedRabund and make sure they are not all zero
+			bool allZero = true;
+			for (int j = 0; j < thislookup.size(); j++) {
+				if (thislookup[j]->getAbundance(i) != 0) { allZero = false;  break;  }
+			}
 			
-			openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
-			(*filehandles[thislookup[i]->getGroup()]) << thislookup[i]->getLabel()  << '\t' << thislookup[i]->getGroup()  << '\t';
-			thislookup[i]->print(*(filehandles[thislookup[i]->getGroup()]));
-			(*(filehandles[thislookup[i]->getGroup()])).close();
+			//if they are not all zero add this bin
+			if (!allZero) {
+				for (int j = 0; j < thislookup.size(); j++) {
+					newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
+				}
+			}
+			//else{  cout << "bin # " << i << " is all zeros" << endl;  }
 		}
+	
+		for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
+		thislookup = newLookup;
+		
+		return 0;
  
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedCommand", "printSharedData");
+		m->errorOut(e, "SharedCommand", "eliminateZeroOTUS");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+int SharedCommand::createMisMatchFile() {
+	try {
+		ofstream outMisMatch;
+		string outputMisMatchName = outputDir + m->getRootName(m->getSimpleName(listfile));
+		
+		//you have sequences in your list file that are not in your group file
+		if (SharedList->getNumSeqs() > groupMap->getNumSeqs()) { 
+			outputMisMatchName += "missing.group";
+			m->mothurOut("For a list of names that are in your list file and not in your group file, please refer to " + outputMisMatchName + "."); m->mothurOutEndLine();
+			
+			m->openOutputFile(outputMisMatchName, outMisMatch);
+			
+			map<string, string> listNames;
+			map<string, string>::iterator itList;
+			
+			//go through list and if group returns "not found" output it
+			for (int i = 0; i < SharedList->getNumBins(); i++) {
+				if (m->control_pressed) { outMisMatch.close(); remove(outputMisMatchName.c_str()); return 0; } 
+			
+				string names = SharedList->get(i); 
+				
+				while (names.find_first_of(',') != -1) { 
+					string name = names.substr(0,names.find_first_of(','));
+					names = names.substr(names.find_first_of(',')+1, names.length());
+					string group = groupMap->getGroup(name);
+					
+					if(group == "not found") {	outMisMatch << name << endl;  }
+					
+					itList = listNames.find(name);
+					if (itList != listNames.end()) {  m->mothurOut(name + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
+					else { listNames[name] = name; }
+				}
+			
+				//get last name
+				string group = groupMap->getGroup(names);
+				if(group == "not found") {	outMisMatch << names << endl;  }	
+				
+				itList = listNames.find(names);
+				if (itList != listNames.end()) {  m->mothurOut(names + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
+				else { listNames[names] = names; }
+
+			}
+			
+			outMisMatch.close();
+			
+		
+		}else {//you have sequences in your group file that are not in you list file
+			
+			outputMisMatchName += "missing.name";
+			m->mothurOut("For a list of names that are in your group file and not in your list file, please refer to " + outputMisMatchName + "."); m->mothurOutEndLine();
+			
+			map<string, string> namesInList;
+			map<string, string>::iterator itList;
+			
+			//go through listfile and get names
+			for (int i = 0; i < SharedList->getNumBins(); i++) {
+				if (m->control_pressed) {  return 0; } 
+
+				
+				string names = SharedList->get(i); 
+		
+				while (names.find_first_of(',') != -1) { 
+					string name = names.substr(0,names.find_first_of(','));
+					names = names.substr(names.find_first_of(',')+1, names.length());
+					
+					itList = namesInList.find(name);
+					if (itList != namesInList.end()) {  m->mothurOut(name + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
+
+					namesInList[name] = name;
+					
+				}
+				
+				itList = namesInList.find(names);
+				if (itList != namesInList.end()) {  m->mothurOut(names + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
+
+				//get last name
+				namesInList[names] = names;				
+			}
+			
+			//get names of sequences in groupfile
+			vector<string> seqNames = groupMap->getNamesSeqs();
+		
+			map<string, string>::iterator itMatch;
+			
+			m->openOutputFile(outputMisMatchName, outMisMatch);
+			
+			//loop through names in seqNames and if they aren't in namesIn list output them
+			for (int i = 0; i < seqNames.size(); i++) {
+				if (m->control_pressed) { outMisMatch.close(); remove(outputMisMatchName.c_str()); return 0; } 
+				
+				itMatch = namesInList.find(seqNames[i]);
+				
+				if (itMatch == namesInList.end()) {
+				
+					outMisMatch << seqNames[i] << endl; 
+				}
+			}		
+			outMisMatch.close();
+		}
+		
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SharedCommand", "createMisMatchFile");
 		exit(1);
 	}
 }
@@ -176,5 +658,47 @@ SharedCommand::~SharedCommand(){
 	
 	
 }
-
 //**********************************************************************************************************************
+int SharedCommand::readOrderFile() {
+	try {
+		//remove old names
+		order.clear();
+		
+		ifstream in;
+		m->openInputFile(ordergroupfile, in);
+		string thisGroup;
+		
+		while(!in.eof()){
+			in >> thisGroup; m->gobble(in);
+						
+			order.push_back(thisGroup);
+			
+			if (m->control_pressed) { order.clear(); break; }
+		}
+		in.close();		
+		
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SharedCommand", "readOrderFile");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+
+bool SharedCommand::isValidGroup(string groupname, vector<string> groups) {
+	try {
+		for (int i = 0; i < groups.size(); i++) {
+			if (groupname == groups[i]) { return true; }
+		}
+		
+		return false;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SharedCommand", "isValidGroup");
+		exit(1);
+	}
+}
+/************************************************************/
+
+