/*
 *  subsamplecommand.cpp
 *  Mothur
 *
 *  Created by westcott on 10/27/10.
 *  Copyright 2010 Schloss Lab. All rights reserved.
 *
 */

#include "subsamplecommand.h"
#include "sharedutilities.h"
#include "deconvolutecommand.h"
#include "getseqscommand.h"
#include "subsample.h"

//**********************************************************************************************************************
vector<string> SubSampleCommand::setParameters(){	
	try {		
		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FLSSR", "none","fasta",false,false,true); parameters.push_back(pfasta);
        CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
        CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","taxonomy",false,false,true); parameters.push_back(ptaxonomy);
        CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount);
		CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","group",false,false,true); parameters.push_back(pgroup);
		CommandParameter plist("list", "InputTypes", "", "", "none", "FLSSR", "none","list",false,false,true); parameters.push_back(plist);
		CommandParameter pshared("shared", "InputTypes", "", "", "none", "FLSSR", "none","shared",false,false,true); parameters.push_back(pshared);
		CommandParameter prabund("rabund", "InputTypes", "", "", "none", "FLSSR", "none","rabund",false,false); parameters.push_back(prabund);
		CommandParameter psabund("sabund", "InputTypes", "", "", "none", "FLSSR", "none","sabund",false,false); parameters.push_back(psabund);
		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
		CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
		CommandParameter psize("size", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(psize);
		CommandParameter ppersample("persample", "Boolean", "", "F", "", "", "","",false,false,true); parameters.push_back(ppersample);
		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, "SubSampleCommand", "setParameters");
		exit(1);
	}
}
//**********************************************************************************************************************
string SubSampleCommand::getHelpString(){	
	try {
		string helpString = "";
		helpString += "The sub.sample command is designed to be used as a way to normalize your data, or create a smaller set from your original set.\n";
		helpString += "The sub.sample command parameters are fasta, name, list, group, count, rabund, sabund, shared, taxonomy, groups, size, persample and label.  You must provide a fasta, list, sabund, rabund or shared file as an input file.\n";
		helpString += "The namefile is only used with the fasta file, not with the listfile, because the list file should contain all sequences.\n";
		helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included. The group names are separated by dashes.\n";
		helpString += "The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n";
		helpString += "The size parameter allows you indicate the size of your subsample.\n";
		helpString += "The persample parameter allows you indicate you want to select subsample of the same size from each of your groups, default=false. It is only used with the list and fasta files if a groupfile is given.\n";
		helpString += "persample=false will select a random set of sequences of the size you select, but the number of seqs from each group may differ.\n";
		helpString += "The size parameter is not set: with shared file size=number of seqs in smallest sample, with all other files if a groupfile is given and persample=true, then size=number of seqs in smallest sample, otherwise size=10% of number of seqs.\n";
		helpString += "The sub.sample command should be in the following format: sub.sample(list=yourListFile, group=yourGroupFile, groups=yourGroups, label=yourLabels).\n";
		helpString += "Example sub.sample(list=abrecovery.fn.list, group=abrecovery.groups, groups=B-C, size=20).\n";
		helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
		helpString += "The sub.sample command outputs a .subsample file.\n";
		helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
		return helpString;
	}
	catch(exception& e) {
		m->errorOut(e, "SubSampleCommand", "getHelpString");
		exit(1);
	}
}
//**********************************************************************************************************************
string SubSampleCommand::getOutputPattern(string type) {
    try {
        string pattern = "";
        
        if (type == "fasta")            {   pattern = "[filename],subsample,[extension]";    }
        else if (type == "sabund")      {   pattern = "[filename],subsample,[extension]";    }
        else if (type == "name")        {   pattern = "[filename],subsample,[extension]";    }
        else if (type == "group")       {   pattern = "[filename],subsample,[extension]";    }
        else if (type == "count")       {   pattern = "[filename],subsample,[extension]";    }
        else if (type == "list")        {   pattern = "[filename],[distance],subsample,[extension]";    }
        else if (type == "taxonomy")    {   pattern = "[filename],subsample,[extension]";    }
        else if (type == "shared")      {   pattern = "[filename],[distance],subsample,[extension]";    }
        else if (type == "rabund")      {   pattern = "[filename],subsample,[extension]";    }
        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
        
        return pattern;
    }
    catch(exception& e) {
        m->errorOut(e, "SubSampleCommand", "getOutputPattern");
        exit(1);
    }
}
//**********************************************************************************************************************
SubSampleCommand::SubSampleCommand(){	
	try {
		abort = true; calledHelp = true; 
		setParameters();
		vector<string> tempOutNames;
		outputTypes["shared"] = tempOutNames;
		outputTypes["list"] = tempOutNames;
		outputTypes["rabund"] = tempOutNames;
		outputTypes["sabund"] = tempOutNames;
		outputTypes["fasta"] = tempOutNames;
		outputTypes["name"] = tempOutNames;
		outputTypes["group"] = tempOutNames;
        outputTypes["count"] = tempOutNames;
        outputTypes["taxonomy"] = tempOutNames;
	}
	catch(exception& e) {
		m->errorOut(e, "SubSampleCommand", "GetRelAbundCommand");
		exit(1);
	}
}
//**********************************************************************************************************************
SubSampleCommand::SubSampleCommand(string option) {
	try {
		abort = false; calledHelp = false;   
		allLines = 1;
		
		//allow user to run help
		if(option == "help") { help(); abort = true; calledHelp = true; }
		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
		
		else {
			vector<string> myArray = setParameters();
			
			OptionParser parser(option);
			map<string,string> parameters = parser.getParameters();
			
			ValidParameters validParameter;
			
			//check to make sure all parameters are valid for command
			map<string,string>::iterator it;
			for (it = parameters.begin(); it != parameters.end(); it++) { 
				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
			}
			
			//initialize outputTypes
			vector<string> tempOutNames;
			outputTypes["shared"] = tempOutNames;
			outputTypes["list"] = tempOutNames;
			outputTypes["rabund"] = tempOutNames;
			outputTypes["sabund"] = tempOutNames;
			outputTypes["fasta"] = tempOutNames;
			outputTypes["name"] = tempOutNames;
			outputTypes["group"] = tempOutNames;
            outputTypes["count"] = tempOutNames;
            outputTypes["taxonomy"] = tempOutNames;
					
			//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 = "";	}
			
			//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("fasta");
				//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["fasta"] = inputDir + it->second;		}
				}
				
				it = parameters.find("shared");
				//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["shared"] = 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("sabund");
				//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["sabund"] = inputDir + it->second;		}
				}
				
				it = parameters.find("rabund");
				//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["rabund"] = inputDir + it->second;		}
				}
				
				it = parameters.find("name");
				//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["name"] = inputDir + it->second;		}
				}
                
                it = parameters.find("count");
				//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["count"] = inputDir + it->second;		}
				}
                
                it = parameters.find("taxonomy");
				//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["taxonomy"] = inputDir + it->second;		}
				}
			}
			
			//check for required parameters
			listfile = validParameter.validFile(parameters, "list", true);
			if (listfile == "not open") { listfile = ""; abort = true; }
			else if (listfile == "not found") { listfile = ""; }
			else { m->setListFile(listfile); }
			
			sabundfile = validParameter.validFile(parameters, "sabund", true);
			if (sabundfile == "not open") { sabundfile = ""; abort = true; }	
			else if (sabundfile == "not found") { sabundfile = ""; }
			else { m->setSabundFile(sabundfile); }
			
			rabundfile = validParameter.validFile(parameters, "rabund", true);
			if (rabundfile == "not open") { rabundfile = ""; abort = true; }	
			else if (rabundfile == "not found") { rabundfile = ""; }
			else { m->setRabundFile(rabundfile); }
			
			fastafile = validParameter.validFile(parameters, "fasta", true);
			if (fastafile == "not open") { fastafile = ""; abort = true; }	
			else if (fastafile == "not found") { fastafile = ""; }
			else { m->setFastaFile(fastafile); }
			
			sharedfile = validParameter.validFile(parameters, "shared", true);
			if (sharedfile == "not open") { sharedfile = ""; abort = true; }	
			else if (sharedfile == "not found") { sharedfile = ""; }
			else { m->setSharedFile(sharedfile); }
			
			namefile = validParameter.validFile(parameters, "name", true);
			if (namefile == "not open") { namefile = ""; abort = true; }	
			else if (namefile == "not found") { namefile = ""; }
			else { m->setNameFile(namefile); }
			
			groupfile = validParameter.validFile(parameters, "group", true);
			if (groupfile == "not open") { groupfile = ""; abort = true; }	
			else if (groupfile == "not found") { groupfile = ""; }
			else { m->setGroupFile(groupfile); }
            
            taxonomyfile = validParameter.validFile(parameters, "taxonomy", true);
			if (taxonomyfile == "not open") { taxonomyfile = ""; abort = true; }
			else if (taxonomyfile == "not found") { taxonomyfile = ""; }
			else { m->setTaxonomyFile(taxonomyfile); }
			
            countfile = validParameter.validFile(parameters, "count", true);
			if (countfile == "not open") { countfile = ""; abort = true; }
			else if (countfile == "not found") { countfile = "";  }	
			else {
                m->setCountTableFile(countfile); 
                ct.readTable(countfile, true, false);
            }
            
            if ((namefile != "") && (countfile != "")) {
                m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
            }
			
            if ((groupfile != "") && (countfile != "")) {
                m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
            }
            
			//check for optional parameter and set defaults
			// ...at some point should added some additional type checking...
			label = validParameter.validFile(parameters, "label", false);			
			if (label == "not found") { label = ""; }
			else { 
				if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
				else { allLines = 1;  }
			}
			
			groups = validParameter.validFile(parameters, "groups", false);			
			if (groups == "not found") { groups = ""; pickedGroups = false; }
			else { 
				pickedGroups = true;
				m->splitAtDash(groups, Groups);
				m->setGroups(Groups);
			}
			
			string temp = validParameter.validFile(parameters, "size", false);		if (temp == "not found"){	temp = "0";		}
			m->mothurConvert(temp, size);  
			
			temp = validParameter.validFile(parameters, "persample", false);		if (temp == "not found"){	temp = "f";		}
			persample = m->isTrue(temp);
			
			if ((groupfile == "") && (countfile == "")) { persample = false; }
            if (countfile != "") {
                if (!ct.hasGroupInfo()) { 
                    persample = false; 
                    if (pickedGroups) { m->mothurOut("You cannot pick groups without group info in your count file."); m->mothurOutEndLine(); abort = true; }
                }
            }
			
			if ((namefile != "") && ((fastafile == "") && (taxonomyfile == ""))) { m->mothurOut("You may only use a name file with a fasta file or taxonomy file."); m->mothurOutEndLine(); abort = true; }
            
            if ((taxonomyfile != "") && ((fastafile == "") && (listfile == ""))) { m->mothurOut("You may only use a taxonomyfile with a fastafile or listfile."); m->mothurOutEndLine(); abort = true; }
            
			
			if ((fastafile == "") && (listfile == "") && (sabundfile == "") && (rabundfile == "") && (sharedfile == "")) {
				m->mothurOut("You must provide a fasta, list, sabund, rabund or shared file as an input file."); m->mothurOutEndLine(); abort = true; }
			
			if (pickedGroups && ((groupfile == "") && (sharedfile == "") && (countfile == ""))) { 
				m->mothurOut("You cannot pick groups without a valid group, count or shared file."); m->mothurOutEndLine(); abort = true; }
			
			if (((groupfile != "") || (countfile != "")) && ((fastafile == "") && (listfile == ""))) { 
				m->mothurOut("Group or count files are only valid with listfile or fastafile."); m->mothurOutEndLine(); abort = true; }
			
			if (((groupfile != "") || (countfile != "")) && ((fastafile != "") && (listfile != ""))) { 
				m->mothurOut("A new group or count file can only be made from the subsample of a listfile or fastafile, not both. Please correct."); m->mothurOutEndLine(); abort = true; }
			
            if (countfile == "") {
                if ((fastafile != "") && (namefile == "")) {
                    vector<string> files; files.push_back(fastafile);
                    parser.getNameFile(files);
                }
            }
		}

	}
	catch(exception& e) {
		m->errorOut(e, "SubSampleCommand", "SubSampleCommand");
		exit(1);
	}
}
//**********************************************************************************************************************

int SubSampleCommand::execute(){
	try {
	
		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
		
		if (sharedfile != "")	{   getSubSampleShared();	}
		if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); return 0; } }
		
		if (listfile != "")		{   getSubSampleList();		}
		if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); return 0; } }
		
		if (rabundfile != "")	{   getSubSampleRabund();	}
		if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); return 0; } }
		
		if (sabundfile != "")	{   getSubSampleSabund();	}
		if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); return 0; } }
		
		if (fastafile != "")	{   getSubSampleFasta();	}
		if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); return 0; } }
			
		//set fasta file as new current fastafile
		string current = "";
		itTypes = outputTypes.find("fasta");
		if (itTypes != outputTypes.end()) {
			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
		}
		
		itTypes = outputTypes.find("name");
		if (itTypes != outputTypes.end()) {
			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
		}
		
		itTypes = outputTypes.find("group");
		if (itTypes != outputTypes.end()) {
			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
		}
		
		itTypes = outputTypes.find("list");
		if (itTypes != outputTypes.end()) {
			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
		}
		
		itTypes = outputTypes.find("shared");
		if (itTypes != outputTypes.end()) {
			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
		}
		
		itTypes = outputTypes.find("rabund");
		if (itTypes != outputTypes.end()) {
			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
		}
		
		itTypes = outputTypes.find("sabund");
		if (itTypes != outputTypes.end()) {
			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }
		}
        
        itTypes = outputTypes.find("count");
		if (itTypes != outputTypes.end()) {
			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
		}
		
        itTypes = outputTypes.find("taxonomy");
		if (itTypes != outputTypes.end()) {
			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(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->mothurOutEndLine();
		
		return 0;
	}
	catch(exception& e) {
		m->errorOut(e, "SubSampleCommand", "execute");
		exit(1);
	}
}
//**********************************************************************************************************************
int SubSampleCommand::getSubSampleFasta() {
	try {
		
		if (namefile != "") { readNames(); }	//fills names with all names in namefile.
		else { getNames(); }//no name file, so get list of names to pick from
		
		GroupMap groupMap;
		if (groupfile != "") {
			groupMap.readMap(groupfile);
			
			//takes care of user setting groupNames that are invalid or setting groups=all
			SharedUtil util;
			vector<string> namesGroups = groupMap.getNamesOfGroups();
			util.setGroups(Groups, namesGroups);
			
			//file mismatch quit
			if (names.size() != groupMap.getNumSeqs()) { 
				m->mothurOut("[ERROR]: your fasta file contains " + toString(names.size()) + " sequences, and your groupfile contains " + toString(groupMap.getNumSeqs()) + ", please correct."); 
				m->mothurOutEndLine();
				return 0;
			}			
		}else if (countfile != "") {
            if (ct.hasGroupInfo()) {
                SharedUtil util;
                vector<string> namesGroups = ct.getNamesOfGroups();
                util.setGroups(Groups, namesGroups);
            }
            
            //file mismatch quit
			if (names.size() != ct.getNumUniqueSeqs()) { 
				m->mothurOut("[ERROR]: your fasta file contains " + toString(names.size()) + " sequences, and your count file contains " + toString(ct.getNumUniqueSeqs()) + " unique sequences, please correct."); 
				m->mothurOutEndLine();
				return 0;
			}	
        }
		
		if (m->control_pressed) { return 0; }
		
		//make sure that if your picked groups size is not too big
		int thisSize = 0;
        if (countfile == "") { thisSize = names.size();  }
        else {  thisSize = ct. getNumSeqs();  }  //all seqs not just unique
        
		if (persample) { 
			if (size == 0) { //user has not set size, set size = smallest samples size
				if (countfile == "") { size = groupMap.getNumSeqs(Groups[0]); }
                else {  size = ct.getGroupCount(Groups[0]);  }
                
				for (int i = 1; i < Groups.size(); i++) {
					int thisSize = 0;
                    if (countfile == "") { thisSize = groupMap.getNumSeqs(Groups[i]); }
                    else {  thisSize = ct.getGroupCount(Groups[i]);  }
					
					if (thisSize < size) {	size = thisSize;	}
				}
			}else { //make sure size is not too large
				vector<string> newGroups;
				for (int i = 0; i < Groups.size(); i++) {
					int thisSize = 0;
                    if (countfile == "") { thisSize = groupMap.getNumSeqs(Groups[i]); }
                    else {  thisSize = ct.getGroupCount(Groups[i]);  }
					
					if (thisSize >= size) {	newGroups.push_back(Groups[i]);	}
					else {  m->mothurOut("You have selected a size that is larger than " + Groups[i] + " number of sequences, removing " + Groups[i] + "."); m->mothurOutEndLine(); }
				}
				Groups = newGroups;
                if (newGroups.size() == 0) {  m->mothurOut("[ERROR]: all groups removed."); m->mothurOutEndLine(); m->control_pressed = true; }
			}
			
			m->mothurOut("Sampling " + toString(size) + " from each group."); m->mothurOutEndLine();			
		}else {
			if (pickedGroups) {
				int total = 0;
				for(int i = 0; i < Groups.size(); i++) {
                    if (countfile == "") { total += groupMap.getNumSeqs(Groups[i]); }
                    else {  total += ct.getGroupCount(Groups[i]);  }
				}
				
				if (size == 0) { //user has not set size, set size = 10% samples size
					size = int (total * 0.10);
				}
				
				if (total < size) { 
					if (size != 0) { 
						m->mothurOut("Your size is too large for the number of groups you selected. Adjusting to " + toString(int (total * 0.10)) + "."); m->mothurOutEndLine();
					}
					size = int (total * 0.10);
				}
				
				m->mothurOut("Sampling " + toString(size) + " from " + toString(total) + "."); m->mothurOutEndLine();
			}
			
			if (size == 0) { //user has not set size, set size = 10% samples size
				if (countfile == "") {  size = int (names.size() * 0.10); }
                else {  size = int (ct.getNumSeqs() * 0.10); }
			}
			
            
            if (size > thisSize) { m->mothurOut("Your fasta file only contains " + toString(thisSize) + " sequences. Setting size to " + toString(thisSize) + "."); m->mothurOutEndLine();
                    size = thisSize;
            }
            
            if (!pickedGroups) { m->mothurOut("Sampling " + toString(size) + " from " + toString(thisSize) + "."); m->mothurOutEndLine(); }

		}
		random_shuffle(names.begin(), names.end());
		
		set<string> subset; //dont want repeat sequence names added
		if (persample) {
            if (countfile == "") {
                //initialize counts
                map<string, int> groupCounts;
                map<string, int>::iterator itGroupCounts;
                for (int i = 0; i < Groups.size(); i++) { groupCounts[Groups[i]] = 0; }
			
                for (int j = 0; j < names.size(); j++) {
					
                    if (m->control_pressed) { return 0; }
												
                    string group = groupMap.getGroup(names[j]);
                    if (group == "not found") { m->mothurOut("[ERROR]: " + names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
                    else{
                        itGroupCounts = groupCounts.find(group);
                        if (itGroupCounts != groupCounts.end()) {
                            if (itGroupCounts->second < size) {	subset.insert(names[j]); 	(itGroupCounts->second)++; }
                        }
                    }				
                }
            }else {
                SubSample sample;
                CountTable sampledCt = sample.getSample(ct, size, Groups);
                vector<string> sampledSeqs = sampledCt.getNamesOfSeqs();
                for (int i = 0; i < sampledSeqs.size(); i++) { subset.insert(sampledSeqs[i]); }
                
                string countOutputDir = outputDir;
                if (outputDir == "") {  countOutputDir += m->hasPath(countfile);  }
                map<string, string> variables; 
                variables["[filename]"] = countOutputDir + m->getRootName(m->getSimpleName(countfile));
                variables["[extension]"] = m->getExtension(countfile);
                string countOutputFileName = getOutputFileName("count", variables);
                outputTypes["count"].push_back(countOutputFileName);  outputNames.push_back(countOutputFileName);
                sampledCt.printTable(countOutputFileName);
            }
		}else {
			if (countfile == "") {
                //randomly select a subset of those names to include in the subsample
                //since names was randomly shuffled just grab the next one
                for (int j = 0; j < names.size(); j++) {
                    
                    if (m->control_pressed) { return 0; }
                    
                    if (groupfile != "") { //if there is a groupfile given fill in group info
                        string group = groupMap.getGroup(names[j]);
                        if (group == "not found") { m->mothurOut("[ERROR]: " + names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
                        
                        if (pickedGroups) { //if hte user picked groups, we only want to keep the names of sequences from those groups
                            if (m->inUsersGroups(group, Groups)) {  subset.insert(names[j]); }
                        }else{  subset.insert(names[j]); }
                    }else{ //save everyone, group
                        subset.insert(names[j]); 
                    }					
                    
                    //do we have enough??
                    if (subset.size() == size) { break; }
                }
            }else {
                SubSample sample;
                CountTable sampledCt = sample.getSample(ct, size, Groups, pickedGroups);
                vector<string> sampledSeqs = sampledCt.getNamesOfSeqs();
                for (int i = 0; i < sampledSeqs.size(); i++) { subset.insert(sampledSeqs[i]); }
                
                string countOutputDir = outputDir;
                if (outputDir == "") {  countOutputDir += m->hasPath(countfile);  }
                map<string, string> variables; 
                variables["[filename]"] = countOutputDir + m->getRootName(m->getSimpleName(countfile));
                variables["[extension]"] = m->getExtension(countfile);
                string countOutputFileName = getOutputFileName("count", variables);
                outputTypes["count"].push_back(countOutputFileName);  outputNames.push_back(countOutputFileName);
                sampledCt.printTable(countOutputFileName);
            }
		}
		
		if (subset.size() == 0) {  m->mothurOut("The size you selected is too large, skipping fasta file."); m->mothurOutEndLine();  return 0; }
		
		string thisOutputDir = outputDir;
		if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
        map<string, string> variables; 
        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
        variables["[extension]"] = m->getExtension(fastafile);
		string outputFileName = getOutputFileName("fasta", variables);		
		ofstream out;
		m->openOutputFile(outputFileName, out);
		
		//read through fasta file outputting only the names on the subsample list
		ifstream in;
		m->openInputFile(fastafile, in);
		
		string thisname;
		int count = 0;
		map<string, vector<string> >::iterator itNameMap;
		
		while(!in.eof()){
			
			if (m->control_pressed) { in.close(); out.close();  return 0; }
			
			Sequence currSeq(in);
			thisname = currSeq.getName();
			
			if (thisname != "") {
				
				//does the subset contain a sequence that this sequence represents
				itNameMap = nameMap.find(thisname);
				if (itNameMap != nameMap.end()) {
					vector<string> nameRepresents = itNameMap->second;
				
					for (int i = 0; i < nameRepresents.size(); i++){
						if (subset.count(nameRepresents[i]) != 0) {
							out << ">" << nameRepresents[i] << endl << currSeq.getAligned() << endl;
							count++;
						}
					}
				}else{
					m->mothurOut("[ERROR]: " + thisname + " is not in your namefile, please correct."); m->mothurOutEndLine();
				}
			}
			m->gobble(in);
		}
		in.close();	
		out.close();
        
		
		if (count != subset.size()) {
			m->mothurOut("[ERROR]: The subset selected contained " + toString(subset.size()) + " sequences, but I only found " + toString(count) + " of those in the fastafile."); m->mothurOutEndLine();
		}
		
		if (namefile != "") {
			m->mothurOut("Deconvoluting subsampled fasta file... "); m->mothurOutEndLine();
			map<string, string> variables; 
            variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile));
            variables["[extension]"] = m->getExtension(namefile);
            string outputNameFileName = getOutputFileName("name", variables);
			//use unique.seqs to create new name and fastafile
			string inputString = "fasta=" + outputFileName;
			m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
			m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine(); 
			m->mothurCalling = true;
            
			Command* uniqueCommand = new DeconvoluteCommand(inputString);
			uniqueCommand->execute();
			
			map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
			
			delete uniqueCommand;
			m->mothurCalling = false;
            
            m->renameFile(filenames["name"][0], outputNameFileName); 
            m->renameFile(filenames["fasta"][0], outputFileName);  
            
			outputTypes["name"].push_back(outputNameFileName);  outputNames.push_back(outputNameFileName);

			m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
			
			m->mothurOut("Done."); m->mothurOutEndLine();
            
            if (taxonomyfile != "") {
                set<string> tempSubset;
                //get new unique names from fasta file
                //read through fasta file outputting only the names on the subsample list after deconvolute
                ifstream in2;
                m->openInputFile(outputFileName, in2);
                
                while (!in2.eof()) {
                    Sequence seq(in2); m->gobble(in2);
                    if (seq.getName() != "") {
                        tempSubset.insert(seq.getName());
                    }
                }
                in2.close();
                
                //send that list to getTax
                int tcount = getTax(tempSubset);
                if (tcount != tempSubset.size()) { m->mothurOut("[ERROR]: subsampled fasta file contains " + toString(tempSubset.size()) + " sequences, but I only found " + toString(tcount) + " in your taxonomy file, please correct."); m->mothurOutEndLine(); }
            }
		}else {
            if (taxonomyfile != "") {
                int tcount = getTax(subset);
                if (tcount != subset.size()) { m->mothurOut("[ERROR]: subsampled fasta file contains " + toString(subset.size()) + " sequences, but I only found " + toString(tcount) + " in your taxonomy file, please correct."); m->mothurOutEndLine(); }
            
            }  //should only contain uniques.
        }
		
		outputTypes["fasta"].push_back(outputFileName);  outputNames.push_back(outputFileName);
		
		//if a groupfile is provided read through the group file only outputting the names on the subsample list
		if (groupfile != "") {
			
			string groupOutputDir = outputDir;
			if (outputDir == "") {  groupOutputDir += m->hasPath(groupfile);  }
            map<string, string> variables; 
            variables["[filename]"] = groupOutputDir + m->getRootName(m->getSimpleName(groupfile));
            variables["[extension]"] = m->getExtension(groupfile);
			string groupOutputFileName = getOutputFileName("group", variables);
			
			ofstream outGroup;
			m->openOutputFile(groupOutputFileName, outGroup);
			outputTypes["group"].push_back(groupOutputFileName);  outputNames.push_back(groupOutputFileName);
			
			ifstream inGroup;
			m->openInputFile(groupfile, inGroup);
			string name, group;
			
			while(!inGroup.eof()){
				
				if (m->control_pressed) { inGroup.close(); outGroup.close(); return 0; }
				
				inGroup >> name;	m->gobble(inGroup);			//read from first column
				inGroup >> group;			//read from second column
				
				//if this name is in the accnos file
				if (subset.count(name) != 0) {
					outGroup << name << '\t' << group << endl;
					subset.erase(name);
				}
				
				m->gobble(inGroup);
			}
			inGroup.close();
			outGroup.close();	
			
			//sanity check
			if (subset.size() != 0) {  
				m->mothurOut("Your groupfile does not match your fasta file."); m->mothurOutEndLine();
				for (set<string>::iterator it = subset.begin(); it != subset.end(); it++) {
					m->mothurOut("[ERROR]: " + *it + " is missing from your groupfile."); m->mothurOutEndLine();
				}
			}
		}
			
		return 0;
		
	}
	catch(exception& e) {
		m->errorOut(e, "SubSampleCommand", "getSubSampleFasta");
		exit(1);
	}
}
//**********************************************************************************************************************
int SubSampleCommand::getNames() {
	try {
		
		ifstream in;
		m->openInputFile(fastafile, in);
		
		string thisname;
		while(!in.eof()){
			
			if (m->control_pressed) { in.close(); return 0; }
			
			Sequence currSeq(in);
			thisname = currSeq.getName();
			
			if (thisname != "") {
				vector<string> temp; temp.push_back(thisname);
				nameMap[thisname] = temp;
				names.push_back(thisname);
			}
			m->gobble(in);
		}
		in.close();	
		
		return 0;
		
	}
	catch(exception& e) {
		m->errorOut(e, "SubSampleCommand", "getNames");
		exit(1);
	}
}	
//**********************************************************************************************************************
int SubSampleCommand::readNames() {
	try {
		
        nameMap.clear();
        m->readNames(namefile, nameMap);
        
        //save names of all sequences
        map<string, vector<string> >::iterator it;
        for (it = nameMap.begin(); it != nameMap.end(); it++) { for (int i = 0; i < (it->second).size(); i++) { names.push_back((it->second)[i]); } }
        
		return 0;
		
	}
	catch(exception& e) {
		m->errorOut(e, "SubSampleCommand", "readNames");
		exit(1);
	}
}		
//**********************************************************************************************************************
int SubSampleCommand::getSubSampleShared() {
	try {
		
		InputData* input = new InputData(sharedfile, "sharedfile");
		vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
		string lastLabel = lookup[0]->getLabel();
		
		//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 = labels;
		
		if (size == 0) { //user has not set size, set size = smallest samples size
			size = lookup[0]->getNumSeqs();
			for (int i = 1; i < lookup.size(); i++) {
				int thisSize = lookup[i]->getNumSeqs();
				
				if (thisSize < size) {	size = thisSize;	}
			}
		}else {
			m->clearGroups();
			Groups.clear();
			vector<SharedRAbundVector*> temp;
			for (int i = 0; i < lookup.size(); i++) {
				if (lookup[i]->getNumSeqs() < size) { 
					m->mothurOut(lookup[i]->getGroup() + " contains " + toString(lookup[i]->getNumSeqs()) + ". Eliminating."); m->mothurOutEndLine();
					delete lookup[i];
				}else { 
					Groups.push_back(lookup[i]->getGroup()); 
					temp.push_back(lookup[i]);
				}
			} 
			lookup = temp;
			m->setGroups(Groups);
		}
		
		if (lookup.size() == 0) {  m->mothurOut("The size you selected is too large, skipping shared file."); m->mothurOutEndLine(); delete input; return 0; }
		
		m->mothurOut("Sampling " + toString(size) + " from each group."); m->mothurOutEndLine();
		
		//as long as you are not at the end of the file or done wih the lines you want
		while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
			if (m->control_pressed) {  delete input; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }  return 0;  }
			
			if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){			
				
				m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
				
				processShared(lookup);
				
				processedLabels.insert(lookup[0]->getLabel());
				userLabels.erase(lookup[0]->getLabel());
			}
			
			if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
				string saveLabel = lookup[0]->getLabel();
				
				for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }  
				
				lookup = input->getSharedRAbundVectors(lastLabel);
				m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
				
				processShared(lookup);
				
				processedLabels.insert(lookup[0]->getLabel());
				userLabels.erase(lookup[0]->getLabel());
				
				//restore real lastlabel to save below
				lookup[0]->setLabel(saveLabel);
			}
			
			lastLabel = lookup[0]->getLabel();
			//prevent memory leak
			for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
			
			//get next line to process
			lookup = input->getSharedRAbundVectors();				
		}
		
		
		if (m->control_pressed) {   return 0;  }
		
		//output error messages about any remaining user labels
		set<string>::iterator it;
		bool needToRun = false;
		for (it = userLabels.begin(); it != userLabels.end(); it++) {  
			m->mothurOut("Your file does not include the label " + *it); 
			if (processedLabels.count(lastLabel) != 1) {
				m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
				needToRun = true;
			}else {
				m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
			}
		}
		
		//run last label if you need to
		if (needToRun == true)  {
			for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }  
			lookup = input->getSharedRAbundVectors(lastLabel);
			
			m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
			
			processShared(lookup);
			
			for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
		}
		
		delete input;
		
		return 0;
		
	}
	catch(exception& e) {
		m->errorOut(e, "SubSampleCommand", "getSubSampleShared");
		exit(1);
	}
}
//**********************************************************************************************************************
int SubSampleCommand::processShared(vector<SharedRAbundVector*>& thislookup) {
	try {
		
		//save mothurOut's binLabels to restore for next label
		vector<string> saveBinLabels = m->currentSharedBinLabels;
		
		string thisOutputDir = outputDir;
		if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }
        map<string, string> variables; 
        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile));
        variables["[extension]"] = m->getExtension(sharedfile);
        variables["[distance]"] = thislookup[0]->getLabel();
		string outputFileName = getOutputFileName("shared", variables);        
        SubSample sample;
        vector<string> subsampledLabels = sample.getSample(thislookup, size);
        
        if (m->control_pressed) {  return 0; }
        
        ofstream out;
		m->openOutputFile(outputFileName, out);
		outputTypes["shared"].push_back(outputFileName);  outputNames.push_back(outputFileName);
		
        m->currentSharedBinLabels = subsampledLabels;
        
		thislookup[0]->printHeaders(out);
		
		for (int i = 0; i < thislookup.size(); i++) {
			out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
			thislookup[i]->print(out);
		}
		out.close();
        
        
        //save mothurOut's binLabels to restore for next label
		m->currentSharedBinLabels = saveBinLabels;
		
		return 0;
		
	}
	catch(exception& e) {
		m->errorOut(e, "SubSampleCommand", "processShared");
		exit(1);
	}
}			
//**********************************************************************************************************************
int SubSampleCommand::getSubSampleList() {
	try {
        
		if (namefile != "") { m->readNames(namefile, nameMap); }
        
		InputData* input = new InputData(listfile, "list");
		ListVector* list = input->getListVector();
		string lastLabel = list->getLabel();
		
        //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 = labels;

		ofstream outGroup;
		GroupMap groupMap;
		if (groupfile != "") {
			groupMap.readMap(groupfile);
			
			//takes care of user setting groupNames that are invalid or setting groups=all
			SharedUtil util; vector<string> namesGroups = groupMap.getNamesOfGroups(); util.setGroups(Groups, namesGroups);
			
			//create outputfiles
			string groupOutputDir = outputDir;
			if (outputDir == "") {  groupOutputDir += m->hasPath(groupfile);  }
			string groupOutputFileName = groupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "subsample" + m->getExtension(groupfile);
			m->openOutputFile(groupOutputFileName, outGroup);
			outputTypes["group"].push_back(groupOutputFileName);  outputNames.push_back(groupOutputFileName);
			
			//file mismatch quit
			if (list->getNumSeqs() != groupMap.getNumSeqs()) { 
				m->mothurOut("[ERROR]: your list file contains " + toString(list->getNumSeqs()) + " sequences, and your groupfile contains " + toString(groupMap.getNumSeqs()) + ", please correct."); 
				m->mothurOutEndLine(); delete list; delete input;  outGroup.close(); return 0;
			}			
		}else if (countfile != "") {
            if (ct.hasGroupInfo()) {
                SharedUtil util;
                vector<string> namesGroups = ct.getNamesOfGroups();
                util.setGroups(Groups, namesGroups);
            }
            
            //file mismatch quit
			if (list->getNumSeqs() != ct.getNumUniqueSeqs()) { 
				m->mothurOut("[ERROR]: your list file contains " + toString(list->getNumSeqs()) + " sequences, and your count file contains " + toString(ct.getNumUniqueSeqs()) + " unique sequences, please correct."); 
				m->mothurOutEndLine();
				return 0;
			}	
        }

		//make sure that if your picked groups size is not too big
		if (persample) {
			if (size == 0) { //user has not set size, set size = smallest samples size
				if (countfile == "") { size = groupMap.getNumSeqs(Groups[0]); }
                else {  size = ct.getGroupCount(Groups[0]);  }
                
				for (int i = 1; i < Groups.size(); i++) {
					int thisSize = 0;
                    if (countfile == "") { thisSize = groupMap.getNumSeqs(Groups[i]); }
                    else {  thisSize = ct.getGroupCount(Groups[i]);  }
					
					if (thisSize < size) {	size = thisSize;	}
				}
			}else { //make sure size is not too large
				vector<string> newGroups;
				for (int i = 0; i < Groups.size(); i++) {
					int thisSize = 0;
                    if (countfile == "") { thisSize = groupMap.getNumSeqs(Groups[i]); }
                    else {  thisSize = ct.getGroupCount(Groups[i]);  }
					
					if (thisSize >= size) {	newGroups.push_back(Groups[i]);	}
					else {  m->mothurOut("You have selected a size that is larger than " + Groups[i] + " number of sequences, removing " + Groups[i] + "."); m->mothurOutEndLine(); }
				}
				Groups = newGroups;
                if (newGroups.size() == 0) {  m->mothurOut("[ERROR]: all groups removed."); m->mothurOutEndLine(); m->control_pressed = true; }
			}
			
			m->mothurOut("Sampling " + toString(size) + " from each group."); m->mothurOutEndLine();		
		}else{
            if (pickedGroups) {
				int total = 0;
				for(int i = 0; i < Groups.size(); i++) {
                    if (countfile == "") { total += groupMap.getNumSeqs(Groups[i]); }
                    else {  total += ct.getGroupCount(Groups[i]);  }
				}
				
				if (size == 0) { //user has not set size, set size = 10% samples size
					size = int (total * 0.10);
				}
				
				if (total < size) { 
					if (size != 0) { 
						m->mothurOut("Your size is too large for the number of groups you selected. Adjusting to " + toString(int (total * 0.10)) + "."); m->mothurOutEndLine();
					}
					size = int (total * 0.10);
				}
				
				m->mothurOut("Sampling " + toString(size) + " from " + toString(total) + "."); m->mothurOutEndLine();
			}else {
                if (size == 0) { //user has not set size, set size = 10% samples size
					if (countfile == "") {  size = int (list->getNumSeqs() * 0.10);  }
                    else { size = int (ct.getNumSeqs() * 0.10);  }
				}
				
				int thisSize = 0;
                if (countfile == "") { thisSize = list->getNumSeqs();  }
                else { thisSize = ct.getNumSeqs(); }
                
				if (size > thisSize) { m->mothurOut("Your list file only contains " + toString(thisSize) + " sequences. Setting size to " + toString(thisSize) + "."); m->mothurOutEndLine();
					size = thisSize;
				}
				
				m->mothurOut("Sampling " + toString(size) + " from " + toString(thisSize) + "."); m->mothurOutEndLine();
            }
        }
		
        set<string> subset; //dont want repeat sequence names added
		if (countfile == "") {
            //fill names
            for (int i = 0; i < list->getNumBins(); i++) {
                string binnames = list->get(i);
                vector<string> thisBin;
                m->splitAtComma(binnames, thisBin);
                
                for(int j=0;j<thisBin.size();j++){
                    if (groupfile != "") { //if there is a groupfile given fill in group info
                        string group = groupMap.getGroup(thisBin[j]);
                        if (group == "not found") { m->mothurOut("[ERROR]: " + thisBin[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
                        
						//if hte user picked groups, we only want to keep the names of sequences from those groups
						if (pickedGroups) { if (m->inUsersGroups(group, Groups)) { names.push_back(thisBin[j]); }  }
						else{ names.push_back(thisBin[j]); } 
                    }//save everyone, group
                    else{ names.push_back(thisBin[j]); }
                }
            }
            
            random_shuffle(names.begin(), names.end());
			
            //randomly select a subset of those names to include in the subsample
            if (persample) {
                //initialize counts
                map<string, int> groupCounts;
                map<string, int>::iterator itGroupCounts;
                for (int i = 0; i < Groups.size(); i++) { groupCounts[Groups[i]] = 0; }
                
                for (int j = 0; j < names.size(); j++) {
                    
                    if (m->control_pressed) { delete list; delete input;  return 0; }
                    
                    string group = groupMap.getGroup(names[j]);
                    if (group == "not found") { m->mothurOut("[ERROR]: " + names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
                    else{
                        itGroupCounts = groupCounts.find(group);
                        if (itGroupCounts != groupCounts.end()) {
                            if (groupCounts[group] < size) {	subset.insert(names[j]); 	groupCounts[group]++; }
                        }
                    }				
                }
            }else{
                for (int j = 0; j < size; j++) {
                    if (m->control_pressed) { break; }
                    subset.insert(names[j]); 
                }	
            }
            
            if (groupfile != "") { 
                //write out new groupfile
                for (set<string>::iterator it = subset.begin(); it != subset.end(); it++) {
                    string group = groupMap.getGroup(*it);
                    if (group == "not found") { group = "NOTFOUND"; }
                    outGroup << *it << '\t' << group << endl;
                }
                outGroup.close(); 
            }
		}else {
            SubSample sample; CountTable sampledCt;
            
            if (persample)  { sampledCt = sample.getSample(ct, size, Groups);               }
            else            { sampledCt = sample.getSample(ct, size, Groups, pickedGroups); }
            
            vector<string> sampledSeqs = sampledCt.getNamesOfSeqs();
            for (int i = 0; i < sampledSeqs.size(); i++) { subset.insert(sampledSeqs[i]); }
        
            string countOutputDir = outputDir;
            if (outputDir == "") {  countOutputDir += m->hasPath(countfile);  }
            map<string, string> variables; 
            variables["[filename]"] = countOutputDir + m->getRootName(m->getSimpleName(countfile));
            variables["[extension]"] = m->getExtension(countfile);
            string countOutputFileName = getOutputFileName("count", variables);
            outputTypes["count"].push_back(countOutputFileName);  outputNames.push_back(countOutputFileName);
            sampledCt.printTable(countOutputFileName);
        }
						
		//as long as you are not at the end of the file or done wih the lines you want
		while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
			
			if (m->control_pressed) {  delete list; delete input;  return 0;  }
			
			if(allLines == 1 || labels.count(list->getLabel()) == 1){			
				
				m->mothurOut(list->getLabel()); m->mothurOutEndLine();
				
				processList(list,  subset);
				
				processedLabels.insert(list->getLabel());
				userLabels.erase(list->getLabel());
			}
			
			if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
				string saveLabel = list->getLabel();
				
				delete list; 
				
				list = input->getListVector(lastLabel);
				m->mothurOut(list->getLabel()); m->mothurOutEndLine();
				
				processList(list,  subset);
				
				processedLabels.insert(list->getLabel());
				userLabels.erase(list->getLabel());
				
				//restore real lastlabel to save below
				list->setLabel(saveLabel);
			}
			
			lastLabel = list->getLabel();
			
			delete list; list = NULL;
			
			//get next line to process
			list = input->getListVector();				
		}
		
		
		if (m->control_pressed) {  if (list != NULL) { delete list; } delete input;  return 0;  }
		
		//output error messages about any remaining user labels
		set<string>::iterator it;
		bool needToRun = false;
		for (it = userLabels.begin(); it != userLabels.end(); it++) {  
			m->mothurOut("Your file does not include the label " + *it); 
			if (processedLabels.count(lastLabel) != 1) {
				m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
				needToRun = true;
			}else {
				m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
			}
		}
		
		//run last label if you need to
		if (needToRun == true)  {
			if (list != NULL) { delete list; }
			
			list = input->getListVector(lastLabel);
			
			m->mothurOut(list->getLabel()); m->mothurOutEndLine();
			
			processList(list, subset);
			
			delete list; list = NULL;
		}
		
		if (list != NULL) { delete list; }
		delete input;
        
        if (taxonomyfile != "") {
            if (namefile == "") {
                InputData input(listfile, "list");
                ListVector* list = input.getListVector();
                string lastLabel = list->getLabel();
                
                for (int i = 0; i < list->getNumBins(); i++) {
                    vector<string> temp;
                    string bin = list->get(i);
                    m->splitAtComma(bin, temp);
                    for (int j = 0; j < temp.size(); j++) { vector<string> tempFakeOut; tempFakeOut.push_back(temp[j]); nameMap[temp[j]] = tempFakeOut; }
                }
                delete list;
                    
                int tcount = getTax(subset);
                if (tcount != subset.size()) { m->mothurOut("[ERROR]: subsampled list file contains " + toString(subset.size()) + " sequences, but I only found " + toString(tcount) + " in your taxonomy file, did you forget a name file? Please correct."); m->mothurOutEndLine(); }
            }else {
                string tempAccnos = "temp.accnos";
                ofstream outAccnos;
                m->openOutputFile(tempAccnos, outAccnos);
                for (set<string>::iterator it = subset.begin(); it != subset.end(); it++) { outAccnos << *it << endl; }
                outAccnos.close();
                
                m->mothurOut("Sampling taxonomy and name file... "); m->mothurOutEndLine();
                string thisNameOutputDir = outputDir;
                if (outputDir == "") {  thisNameOutputDir += m->hasPath(namefile);  }
                map<string, string> variables;
                variables["[filename]"] = thisNameOutputDir + m->getRootName(m->getSimpleName(namefile));
                variables["[extension]"] = m->getExtension(namefile);
                string outputNameFileName = getOutputFileName("name", variables);
                
                string thisTaxOutputDir = outputDir;
                if (outputDir == "") {  thisTaxOutputDir += m->hasPath(taxonomyfile);  }
                variables["[filename]"] = thisTaxOutputDir + m->getRootName(m->getSimpleName(taxonomyfile));
                variables["[extension]"] = m->getExtension(taxonomyfile);
                string outputTaxFileName = getOutputFileName("taxonomy", variables);
                
                
                //use unique.seqs to create new name and fastafile
                string inputString = "dups=f, name=" + namefile + ", taxonomy=" + taxonomyfile + ", accnos=" + tempAccnos;
                m->mothurOut("/******************************************/"); m->mothurOutEndLine();
                m->mothurOut("Running command: get.seqs(" + inputString + ")"); m->mothurOutEndLine();
                m->mothurCalling = true;
                
                Command* getCommand = new GetSeqsCommand(inputString);
                getCommand->execute();
                
                map<string, vector<string> > filenames = getCommand->getOutputFiles();
                
                delete getCommand;
                m->mothurCalling = false;
                
                m->renameFile(filenames["name"][0], outputNameFileName);
                m->renameFile(filenames["taxonomy"][0], outputTaxFileName);
                
                outputTypes["name"].push_back(outputNameFileName);  outputNames.push_back(outputNameFileName);
                outputNames.push_back(outputTaxFileName); outputTypes["taxonomy"].push_back(outputTaxFileName);
                
                m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
                
                m->mothurOut("Done."); m->mothurOutEndLine();
            }
        }
						
		return 0;
 
	}
	catch(exception& e) {
		m->errorOut(e, "SubSampleCommand", "getSubSampleList");
		exit(1);
	}
}
//**********************************************************************************************************************
int SubSampleCommand::processList(ListVector*& list, set<string>& subset) {
	try {
		string thisOutputDir = outputDir;
		if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
		map<string, string> variables;
        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
        variables["[extension]"] = m->getExtension(listfile);
        variables["[distance]"] = list->getLabel();
		string outputFileName = getOutputFileName("list", variables);
		ofstream out;
		m->openOutputFile(outputFileName, out);
		outputTypes["list"].push_back(outputFileName);  outputNames.push_back(outputFileName);
		
		int numBins = list->getNumBins();

		ListVector* temp = new ListVector();
		temp->setLabel(list->getLabel());
		
        vector<string> binLabels = list->getLabels();
        vector<string> newLabels;
		for (int i = 0; i < numBins; i++) {
			
			if (m->control_pressed) { break; }
			
			string bin = list->get(i);
            vector<string> binnames;
            m->splitAtComma(bin, binnames);
			
            string newNames = "";
			for(int j=0;j<binnames.size();j++){ if (subset.count(binnames[j]) != 0) {  newNames += binnames[j] + ",";  } }
			
			//if there are names in this bin add to new list
			if (newNames != "") { 
				newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
				temp->push_back(newNames);
                newLabels.push_back(binLabels[i]);
			}
		}
		
        temp->setLabels(newLabels);
		delete list;
		list = temp;
		
		if (m->control_pressed) { out.close(); return 0; }
		
        list->printHeaders(out);
		list->print(out);
        out.close();
		
		return 0;
		
	}
	catch(exception& e) {
		m->errorOut(e, "SubSampleCommand", "processList");
		exit(1);
	}
}
//**********************************************************************************************************************
int SubSampleCommand::getSubSampleRabund() {
	try {
		InputData* input = new InputData(rabundfile, "rabund");
		RAbundVector* rabund = input->getRAbundVector();
		string lastLabel = rabund->getLabel();
		
		//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 = labels;
		
		if (size == 0) { //user has not set size, set size = 10%
			size = int((rabund->getNumSeqs()) * 0.10);
		}else if (size > rabund->getNumSeqs()) { m->mothurOut("The size you selected is too large, skipping rabund file."); m->mothurOutEndLine(); delete input; delete rabund; return 0; }
		
		m->mothurOut("Sampling " + toString(size) + " from " + toString(rabund->getNumSeqs()) + "."); m->mothurOutEndLine();
		
		string thisOutputDir = outputDir;
		if (outputDir == "") {  thisOutputDir += m->hasPath(rabundfile);  }
        map<string, string> variables; 
		variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile));
        variables["[extension]"] = m->getExtension(rabundfile);
		string outputFileName = getOutputFileName("rabund", variables);		
		ofstream out;
		m->openOutputFile(outputFileName, out);
		outputTypes["rabund"].push_back(outputFileName);  outputNames.push_back(outputFileName);
		
		//as long as you are not at the end of the file or done wih the lines you want
		while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
			if (m->control_pressed) {  delete input; delete rabund; out.close(); return 0;  }
			
			if(allLines == 1 || labels.count(rabund->getLabel()) == 1){			
				
				m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
				
				processRabund(rabund, out);
				
				processedLabels.insert(rabund->getLabel());
				userLabels.erase(rabund->getLabel());
			}
			
			if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
				string saveLabel = rabund->getLabel();
				
				delete rabund; 
				
				rabund = input->getRAbundVector(lastLabel);
				m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
				
				processRabund(rabund, out);
				
				processedLabels.insert(rabund->getLabel());
				userLabels.erase(rabund->getLabel());
				
				//restore real lastlabel to save below
				rabund->setLabel(saveLabel);
			}
			
			lastLabel = rabund->getLabel();
			
			//prevent memory leak
			delete rabund; rabund = NULL;
			
			//get next line to process
			rabund = input->getRAbundVector();				
		}
		
		
		if (m->control_pressed) {  out.close(); return 0;  }
		
		//output error messages about any remaining user labels
		set<string>::iterator it;
		bool needToRun = false;
		for (it = userLabels.begin(); it != userLabels.end(); it++) {  
			m->mothurOut("Your file does not include the label " + *it); 
			if (processedLabels.count(lastLabel) != 1) {
				m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
				needToRun = true;
			}else {
				m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
			}
		}
		
		//run last label if you need to
		if (needToRun == true)  {
			if (rabund != NULL) { delete rabund; }
			
			rabund = input->getRAbundVector(lastLabel);
			
			m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
			
			processRabund(rabund, out);
			
			delete rabund;
		}
		
		delete input;
		out.close();  
		
		return 0;
		
	}
	catch(exception& e) {
		m->errorOut(e, "SubSampleCommand", "getSubSampleRabund");
		exit(1);
	}
}
//**********************************************************************************************************************
int SubSampleCommand::processRabund(RAbundVector*& rabund, ofstream& out) {
	try {
		
		int numBins = rabund->getNumBins();
		int thisSize = rabund->getNumSeqs();
			
		if (thisSize != size) {
				
			OrderVector* order = new OrderVector();
			for(int p=0;p<numBins;p++){
				for(int j=0;j<rabund->get(p);j++){
					order->push_back(p);
				}
			}
			random_shuffle(order->begin(), order->end());
			
			RAbundVector* temp = new RAbundVector(numBins);
			temp->setLabel(rabund->getLabel());
			
			delete rabund;
			rabund = temp;
			
			for (int j = 0; j < size; j++) {
				
				if (m->control_pressed) { delete order; return 0; }
				
				int bin = order->get(j);
				
				int abund = rabund->get(bin);
				rabund->set(bin, (abund+1));
			}
			
			delete order;
		}
		
		if (m->control_pressed) { return 0; }
		
		rabund->print(out);
		
		return 0;
		
	}
	catch(exception& e) {
		m->errorOut(e, "SubSampleCommand", "processRabund");
		exit(1);
	}
}	
//**********************************************************************************************************************
int SubSampleCommand::getSubSampleSabund() {
	try {
				
		InputData* input = new InputData(sabundfile, "sabund");
		SAbundVector* sabund = input->getSAbundVector();
		string lastLabel = sabund->getLabel();
		
		//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 = labels;
		
		if (size == 0) { //user has not set size, set size = 10%
			size = int((sabund->getNumSeqs()) * 0.10);
		}else if (size > sabund->getNumSeqs()) { m->mothurOut("The size you selected is too large, skipping sabund file."); m->mothurOutEndLine(); delete input; delete sabund; return 0; }
		
		
		m->mothurOut("Sampling " + toString(size) + " from " + toString(sabund->getNumSeqs()) + "."); m->mothurOutEndLine();
		
		string thisOutputDir = outputDir;
		if (outputDir == "") {  thisOutputDir += m->hasPath(sabundfile);  }
        map<string, string> variables; 
		variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile));
        variables["[extension]"] = m->getExtension(sabundfile);
		string outputFileName = getOutputFileName("sabund", variables);		
		ofstream out;
		m->openOutputFile(outputFileName, out);
		outputTypes["sabund"].push_back(outputFileName);  outputNames.push_back(outputFileName);
		
		
		//as long as you are not at the end of the file or done wih the lines you want
		while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
			if (m->control_pressed) {  delete input; delete sabund; out.close(); return 0;  }
			
			if(allLines == 1 || labels.count(sabund->getLabel()) == 1){			
				
				m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
				
				processSabund(sabund, out);
				
				processedLabels.insert(sabund->getLabel());
				userLabels.erase(sabund->getLabel());
			}
			
			if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
				string saveLabel = sabund->getLabel();
				
				delete sabund; 
				
				sabund = input->getSAbundVector(lastLabel);
				m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
				
				processSabund(sabund, out);
				
				processedLabels.insert(sabund->getLabel());
				userLabels.erase(sabund->getLabel());
				
				//restore real lastlabel to save below
				sabund->setLabel(saveLabel);
			}
			
			lastLabel = sabund->getLabel();
			
			//prevent memory leak
			delete sabund; sabund = NULL;
			
			//get next line to process
			sabund = input->getSAbundVector();				
		}
		
		
		if (m->control_pressed) {  out.close(); return 0;  }
		
		//output error messages about any remaining user labels
		set<string>::iterator it;
		bool needToRun = false;
		for (it = userLabels.begin(); it != userLabels.end(); it++) {  
			m->mothurOut("Your file does not include the label " + *it); 
			if (processedLabels.count(lastLabel) != 1) {
				m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
				needToRun = true;
			}else {
				m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
			}
		}
		
		//run last label if you need to
		if (needToRun == true)  {
			if (sabund != NULL) { delete sabund; }
			
			sabund = input->getSAbundVector(lastLabel);
			
			m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
			
			processSabund(sabund, out);
			
			delete sabund;
		}
		
		delete input;
		out.close();  
		
		return 0;
		
	}
	catch(exception& e) {
		m->errorOut(e, "SubSampleCommand", "getSubSampleSabund");
		exit(1);
	}
}
//**********************************************************************************************************************
int SubSampleCommand::processSabund(SAbundVector*& sabund, ofstream& out) {
	try {
		
		RAbundVector* rabund = new RAbundVector();
		*rabund = sabund->getRAbundVector();
		
		int numBins = rabund->getNumBins();
		int thisSize = rabund->getNumSeqs();
	
		if (thisSize != size) {
			
			OrderVector* order = new OrderVector();
			for(int p=0;p<numBins;p++){
				for(int j=0;j<rabund->get(p);j++){
					order->push_back(p);
				}
			}
			random_shuffle(order->begin(), order->end());
			
			RAbundVector* temp = new RAbundVector(numBins);
			temp->setLabel(rabund->getLabel());
			
			delete rabund;
			rabund = temp;
			
			for (int j = 0; j < size; j++) {
	
				if (m->control_pressed) { delete order; return 0; }
				
				int bin = order->get(j);
				
				int abund = rabund->get(bin);
				rabund->set(bin, (abund+1));
			}
			
			delete order;
		}
		
		if (m->control_pressed) { return 0; }

		delete sabund;
		sabund = new SAbundVector();
		*sabund = rabund->getSAbundVector();
		delete rabund;
	
		sabund->print(out);
		
		return 0;
		
	}
	catch(exception& e) {
		m->errorOut(e, "SubSampleCommand", "processSabund");
		exit(1);
	}
}

//**********************************************************************************************************************
int SubSampleCommand::getTax(set<string>& subset) {
	try {

        string thisTaxOutputDir = outputDir;
        if (outputDir == "") {  thisTaxOutputDir += m->hasPath(taxonomyfile);  }
        map<string, string> variables;
        variables["[filename]"] = thisTaxOutputDir + m->getRootName(m->getSimpleName(taxonomyfile));
        variables["[extension]"] = m->getExtension(taxonomyfile);
        string outputTaxFileName = getOutputFileName("taxonomy", variables);
        ofstream outTax;
        m->openOutputFile(outputTaxFileName, outTax);
        outputNames.push_back(outputTaxFileName); outputTypes["taxonomy"].push_back(outputTaxFileName);
        
        //read through fasta file outputting only the names on the subsample list
        ifstream inTax;
        m->openInputFile(taxonomyfile, inTax);
        
        string tname, tax;
        int tcount = 0;
        map<string, vector<string> >::iterator itNameMap;
        
        while(!inTax.eof()){
            
            if (m->control_pressed) { inTax.close(); outTax.close();  return 0; }
            
            inTax >> tname;	m->gobble(inTax);			//read from first column
            inTax >> tax;	m->gobble(inTax);		//read from second column
            
            //does the subset contain a sequence that this sequence represents
            itNameMap = nameMap.find(tname);
            if (itNameMap != nameMap.end()) {
                vector<string> nameRepresents = itNameMap->second;
                
            
                for (int i = 0; i < nameRepresents.size(); i++){
                    if (subset.count(nameRepresents[i]) != 0) {
                        outTax << nameRepresents[i] << '\t' << tax << endl;
                        tcount++;
                       
                    }
                }
            }else{ m->mothurOut("[ERROR]: " + tname + " is missing, please correct."); m->mothurOutEndLine(); }
        }
        inTax.close();
        outTax.close();
        
        return tcount;
    }
    catch(exception& e) {
        m->errorOut(e, "SubSampleCommand", "getTax");
        exit(1);
    }
}

//**********************************************************************************************************************