//**********************************************************************************************************************
string SummarySharedCommand::getHelpString(){	
	try {
		string helpString = "";
		ValidCalculators validCalculator;
		helpString += "The summary.shared command parameters are shared, label, calc, distance, processors, subsample, iters and all.  shared is required if there is no current sharedfile.\n";
		helpString += "The summary.shared command should be in the following format: \n";
		helpString += "summary.shared(label=yourLabel, calc=yourEstimators, groups=yourGroups).\n";
		helpString += "Example summary.shared(label=unique-.01-.03, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n";
		helpString +=  validCalculator.printCalc("sharedsummary");
        helpString += "The iters parameter allows you to choose the number of times you would like to run the subsample.\n";
        helpString += "The subsample parameter allows you to enter the size pergroup of the sample or you can set subsample=T and mothur will use the size of your smallest group.\n";
        helpString += "The output parameter allows you to specify format of your distance matrix. Options are lt, and square. The default is lt.\n";
		helpString += "The default value for calc is sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan\n";
		helpString += "The default value for groups is all the groups in your groupfile.\n";
		helpString += "The distance parameter allows you to indicate you would like a distance file created for each calculator for each label, default=f.\n";
		helpString += "The label parameter is used to analyze specific labels in your input.\n";
		helpString += "The all parameter is used to specify if you want the estimate of all your groups together.  This estimate can only be made for sharedsobs and sharedchao calculators. The default is false.\n";
		helpString += "If you use sharedchao and run into memory issues, set all to false. \n";
		helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 2 valid groups.\n";
		helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n";
		return helpString;
	}
	catch(exception& e) {
		m->errorOut(e, "SummarySharedCommand", "getHelpString");
		exit(1);
	}
}

//**********************************************************************************************************************
string MatrixOutputCommand::getHelpString(){	
	try {
		string helpString = "";
		ValidCalculators validCalculator;
		helpString += "The dist.shared command parameters are shared, groups, calc, output, processors, subsample, iters, mode, and label.  shared is a required, unless you have a valid current file.\n";
		helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n";
		helpString += "The group names are separated by dashes. The label parameter allows you to select what distance levels you would like distance matrices created for, and is also separated by dashes.\n";
        helpString += "The iters parameter allows you to choose the number of times you would like to run the subsample.\n";
        helpString += "The subsample parameter allows you to enter the size pergroup of the sample or you can set subsample=T and mothur will use the size of your smallest group.\n";
		helpString += "The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n";
		helpString += "The output parameter allows you to specify format of your distance matrix. Options are lt, column and square. The default is lt.\n";
        helpString += "The mode parameter allows you to specify if you want the average or the median values reported when subsampling. Options are average, and median. The default is average.\n";
		helpString += "Example dist.shared(groups=A-B-C, calc=jabund-sorabund).\n";
		helpString += "The default value for groups is all the groups in your groupfile.\n";
		helpString += "The default value for calc is jclass and thetayc.\n";
		helpString += validCalculator.printCalc("matrix");
		helpString += "The dist.shared command outputs a .dist file for each calculator you specify at each distance you choose.\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, "MatrixOutputCommand", "getHelpString");
		exit(1);
	}
}

//**********************************************************************************************************************
string TreeGroupCommand::getHelpString(){	
	try {
		string helpString = "";
		ValidCalculators validCalculator;
		helpString += "The tree.shared command creates a .tre to represent the similiarity between groups or sequences.\n";
		helpString += "The tree.shared command parameters are shared, groups, calc, phylip, column, name, cutoff, precision, processors, subsample, iters and label.\n";
		helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n";
		helpString += "The group names are separated by dashes. The label allow you to select what distance levels you would like trees created for, and are also separated by dashes.\n";
		helpString += "The phylip or column parameter are required if you do not provide a sharedfile, and only one may be used.  If you use a column file the name filename is required. \n";
		helpString += "If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed.\n";
		helpString += "The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n";
        helpString += "The iters parameter allows you to choose the number of times you would like to run the subsample.\n";
        helpString += "The subsample parameter allows you to enter the size pergroup of the sample or you can set subsample=T and mothur will use the size of your smallest group. The subsample parameter may only be used with a shared file.\n";
		helpString += "Example tree.shared(groups=A-B-C, calc=jabund-sorabund).\n";
		helpString += "The default value for groups is all the groups in your groupfile.\n";
		helpString += "The default value for calc is jclass-thetayc.\n";
		helpString += "The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose.\n";
		helpString += validCalculator.printCalc("treegroup");
		helpString += "Or the tree.shared command can be in the following format: tree.shared(phylip=yourPhylipFile).\n";
		helpString += "Example tree.shared(phylip=abrecovery.dist).\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, "TreeGroupCommand", "getHelpString");
		exit(1);
	}
}

//**********************************************************************************************************************
string RareFactCommand::getHelpString(){	
	try {
		ValidCalculators validCalculator;
		string helpString = "";
		helpString += "The rarefaction.single command parameters are list, sabund, rabund, shared, label, iters, freq, calc, groupmode, groups, processors and abund.  list, sabund, rabund or shared is required unless you have a valid current file. \n";
		helpString += "The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n";
		helpString += "The rarefaction.single command should be in the following format: \n";
		helpString += "rarefaction.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n";
		helpString += "Example rarefaction.single(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson).\n";
		helpString += "The default values for iters is 1000, freq is 100, and calc is rarefaction which calculates the rarefaction curve for the observed richness.\n";
        helpString += "The alpha parameter is used to set the alpha value for the shannonrange calculator.\n";
		validCalculator.printCalc("rarefaction");
		helpString += "If you are running rarefaction.single with a shared file and would like your results collated in one file, set groupmode=t. (Default=true).\n";
		helpString += "The label parameter is used to analyze specific labels in your input.\n";
		return helpString;
	}
	catch(exception& e) {
		m->errorOut(e, "RareFactCommand", "getHelpString");
		exit(1);
	}
}

//**********************************************************************************************************************
string SummaryCommand::getHelpString() {
    try {
        string helpString = "";
        ValidCalculators validCalculator;
        helpString += "The summary.single command parameters are list, sabund, rabund, shared, subsample, iters, label, calc, abund and groupmode.  list, sabund, rabund or shared is required unless you have a valid current file.\n";
        helpString += "The summary.single command should be in the following format: \n";
        helpString += "summary.single(label=yourLabel, calc=yourEstimators).\n";
        helpString += "Example summary.single(label=unique-.01-.03, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson).\n";
        helpString += validCalculator.printCalc("summary");
        helpString += "The subsample parameter allows you to enter the size of the sample or you can set subsample=T and mothur will use the size of your smallest group in the case of a shared file. With a list, sabund or rabund file you must provide a subsample size.\n";
        helpString += "The iters parameter allows you to choose the number of times you would like to run the subsample.\n";
        helpString += "The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson\n";
        helpString += "If you are running summary.single with a shared file and would like your summary results collated in one file, set groupmode=t. (Default=true).\n";
        helpString += "The label parameter is used to analyze specific labels in your input.\n";
        helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n";
        return helpString;
    }
    catch(exception& e) {
        m->errorOut(e, "SummaryCommand", "getHelpString");
        exit(1);
    }
}

//**********************************************************************************************************************
string CollectSharedCommand::getHelpString(){	
	try {
		string helpString = "";
		ValidCalculators validCalculator;
		helpString += "The collect.shared command parameters are shared, label, freq, calc and groups.  shared is required if there is no current sharedfile. \n";
		helpString += "The collect.shared command should be in the following format: \n";
		helpString += "collect.shared(label=yourLabel, freq=yourFreq, calc=yourEstimators, groups=yourGroups).\n";
		helpString += "Example collect.shared(label=unique-.01-.03, freq=10, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n";
		helpString += "The default values for freq is 100 and calc are sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan.\n";
		helpString += "The default value for groups is all the groups in your groupfile.\n";
		helpString += "The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n";
		helpString += validCalculator.printCalc("shared");
		helpString += "The label parameter is used to analyze specific labels in your input.\n";
		helpString += "The all parameter is used to specify if you want the estimate of all your groups together.  This estimate can only be made for sharedsobs and sharedchao calculators. The default is false.\n";
		helpString += "If you use sharedchao and run into memory issues, set all to false. \n";
		helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 2 valid groups.\n";
		helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n";
		return helpString;
	}
	catch(exception& e) {
		m->errorOut(e, "CollectSharedCommand", "getHelpString");
		exit(1);
	}
}

MatrixOutputCommand::MatrixOutputCommand(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();
			map<string,string>::iterator it;
			
			ValidParameters validParameter;
		
			//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;  }
			}
			
			//initialize outputTypes
			vector<string> tempOutNames;
			outputTypes["phylip"] = tempOutNames;
			
			//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("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;		}
				}
			}
			
			sharedfile = validParameter.validFile(parameters, "shared", true);
			if (sharedfile == "not found") { 			
				//if there is a current shared file, use it
				sharedfile = m->getSharedFile(); 
				if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
				else { 	m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
			}else if (sharedfile == "not open") { sharedfile = ""; abort = true; }
			else { m->setSharedFile(sharedfile); }
			
			//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 = "";	
				outputDir += m->hasPath(sharedfile); //if user entered a file with a path then preserve it	
			}
			
			//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;  }
			}
			
			output = validParameter.validFile(parameters, "output", false);		if(output == "not found"){	output = "lt"; }
			if ((output != "lt") && (output != "square") && (output != "column")) { m->mothurOut(output + " is not a valid output form. Options are lt, column and square. I will use lt."); m->mothurOutEndLine(); output = "lt"; }
            
            mode = validParameter.validFile(parameters, "mode", false);		if(mode == "not found"){	mode = "average"; }
			if ((mode != "average") && (mode != "median")) { m->mothurOut(mode + " is not a valid mode. Options are average and medina. I will use average."); m->mothurOutEndLine(); output = "average"; }
			
			groups = validParameter.validFile(parameters, "groups", false);			
			if (groups == "not found") { groups = ""; }
			else { 
				m->splitAtDash(groups, Groups);
				m->setGroups(Groups);
			}
			
			string temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
			m->setProcessors(temp);
			m->mothurConvert(temp, processors); 
				
			calc = validParameter.validFile(parameters, "calc", false);			
			if (calc == "not found") { calc = "jclass-thetayc";  }
			else { 
				 if (calc == "default")  {  calc = "jclass-thetayc";  }
			}
			m->splitAtDash(calc, Estimators);
			if (m->inUsersGroups("citation", Estimators)) { 
				ValidCalculators validCalc; validCalc.printCitations(Estimators); 
				//remove citation from list of calcs
				for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
			}
            
            temp = validParameter.validFile(parameters, "iters", false);			if (temp == "not found") { temp = "1000"; }
			m->mothurConvert(temp, iters); 
            
            temp = validParameter.validFile(parameters, "subsample", false);		if (temp == "not found") { temp = "F"; }
			if (m->isNumeric1(temp)) { m->mothurConvert(temp, subsampleSize); subsample = true; }
            else {  
//.........这里部分代码省略.........

/////// need to fix to work with calcs and sequencedb
int DistanceCommand::driver(int startLine, int endLine, string dFileName, float cutoff){
	try {
		ValidCalculators validCalculator;
		Dist* distCalculator;
		if (m->isTrue(countends) == true) {
			for (int i=0; i<Estimators.size(); i++) {
				if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) { 
					if (Estimators[i] == "nogaps")			{	distCalculator = new ignoreGaps();	}
					else if (Estimators[i] == "eachgap")	{	distCalculator = new eachGapDist();	}
					else if (Estimators[i] == "onegap")		{	distCalculator = new oneGapDist();	}
				}
			}
		}else {
			for (int i=0; i<Estimators.size(); i++) {
				if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) { 
					if (Estimators[i] == "nogaps")		{	distCalculator = new ignoreGaps();					}
					else if (Estimators[i] == "eachgap"){	distCalculator = new eachGapIgnoreTermGapDist();	}
					else if (Estimators[i] == "onegap")	{	distCalculator = new oneGapIgnoreTermGapDist();		}
				}
			}
		}
		
		int startTime = time(NULL);
		
		//column file
		ofstream outFile(dFileName.c_str(), ios::trunc);
		outFile.setf(ios::fixed, ios::showpoint);
		outFile << setprecision(4);
		
		if((output == "lt") && startLine == 0){	outFile << alignDB.getNumSeqs() << endl;	}
		
		for(int i=startLine;i<endLine;i++){
			if(output == "lt")	{	
				string name = alignDB.get(i).getName();
				if (name.length() < 10) { //pad with spaces to make compatible
					while (name.length() < 10) {  name += " ";  }
				}
				outFile << name;
			}
			for(int j=0;j<i;j++){
				
				if (m->control_pressed) { delete distCalculator; outFile.close(); return 0;  }
                
				//if there was a column file given and we are appending, we don't want to calculate the distances that are already in the column file
				//the alignDB contains the new sequences and then the old, so if i an oldsequence and j is an old sequence then break out of this loop
				if ((i >= numNewFasta) && (j >= numNewFasta)) { break; }
				
				distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
				double dist = distCalculator->getDist();
				
				if(dist <= cutoff){
					if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
				}
                if (output == "lt") {  outFile  << '\t' << dist; }
			}
			
			if (output == "lt") { outFile << endl; }
            
            if(i % 100 == 0){
				m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n"); 
			}
			
		}
		m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
		
		outFile.close();
		delete distCalculator;
		
		return 1;
	}
	catch(exception& e) {
		m->errorOut(e, "DistanceCommand", "driver");
		exit(1);
	}
}

//.........这里部分代码省略.........
				}
			}
			
			//get shared file
			sharedfile = validParameter.validFile(parameters, "shared", true);
			if (sharedfile == "not open") { sharedfile = ""; abort = true; }	
			else if (sharedfile == "not found") { 
				//if there is a current shared file, use it
				sharedfile = m->getSharedFile(); 
				if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
				else { 	m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
			}else { m->setSharedFile(sharedfile); }
			
			
			//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 = m->hasPath(sharedfile);		}
			
			//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;  }
			}
			
			calc = validParameter.validFile(parameters, "calc", false);			
			if (calc == "not found") { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan";  }
			else { 
				 if (calc == "default")  {  calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan";  }
			}
			m->splitAtDash(calc, Estimators);
			if (m->inUsersGroups("citation", Estimators)) { 
				ValidCalculators validCalc; validCalc.printCitations(Estimators); 
				//remove citation from list of calcs
				for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
			}
			
			groups = validParameter.validFile(parameters, "groups", false);			
			if (groups == "not found") { groups = ""; }
			else { 
				m->splitAtDash(groups, Groups);
			}
			m->setGroups(Groups);
			
			string temp;
			temp = validParameter.validFile(parameters, "freq", false);			if (temp == "not found") { temp = "100"; }
			m->mothurConvert(temp, freq); 
			
			temp = validParameter.validFile(parameters, "all", false);				if (temp == "not found") { temp = "false"; }
			all = m->isTrue(temp);
						
			if (abort == false) {
				
				string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(sharedfile));
				
				ValidCalculators validCalculator;
				
				for (int i=0; i<Estimators.size(); i++) {
					if (validCalculator.isValidCalculator("shared", Estimators[i]) == true) { 
						if (Estimators[i] == "sharedchao") { 
							cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(fileNameRoot+"shared.chao")));
							outputNames.push_back(fileNameRoot+"shared.chao"); outputTypes["sharedchao"].push_back(fileNameRoot+"shared.chao");
						}else if (Estimators[i] == "sharedsobs") { 
							cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(fileNameRoot+"shared.sobs")));
							outputNames.push_back(fileNameRoot+"shared.sobs"); outputTypes["sharedsobs"].push_back(fileNameRoot+"shared.sobs");

int process(treeSharedData* params) {
    try{
        
        ValidCalculators validCalculator;
        vector<Calculator*> treeCalculators;
        for (int i=0; i<params->Estimators.size(); i++) {
            if (validCalculator.isValidCalculator("treegroup", params->Estimators[i]) ) {
                if (params->Estimators[i] == "sharedsobs") {
                    treeCalculators.push_back(new SharedSobsCS());
                }else if (params->Estimators[i] == "sharedchao") {
                    treeCalculators.push_back(new SharedChao1());
                }else if (params->Estimators[i] == "sharedace") {
                    treeCalculators.push_back(new SharedAce());
                }else if (params->Estimators[i] == "jabund") {
                    treeCalculators.push_back(new JAbund());
                }else if (params->Estimators[i] == "sorabund") {
                    treeCalculators.push_back(new SorAbund());
                }else if (params->Estimators[i] == "jclass") {
                    treeCalculators.push_back(new Jclass());
                }else if (params->Estimators[i] == "sorclass") {
                    treeCalculators.push_back(new SorClass());
                }else if (params->Estimators[i] == "jest") {
                    treeCalculators.push_back(new Jest());
                }else if (params->Estimators[i] == "sorest") {
                    treeCalculators.push_back(new SorEst());
                }else if (params->Estimators[i] == "thetayc") {
                    treeCalculators.push_back(new ThetaYC());
                }else if (params->Estimators[i] == "thetan") {
                    treeCalculators.push_back(new ThetaN());
                }else if (params->Estimators[i] == "kstest") {
                    treeCalculators.push_back(new KSTest());
                }else if (params->Estimators[i] == "sharednseqs") {
                    treeCalculators.push_back(new SharedNSeqs());
                }else if (params->Estimators[i] == "ochiai") {
                    treeCalculators.push_back(new Ochiai());
                }else if (params->Estimators[i] == "anderberg") {
                    treeCalculators.push_back(new Anderberg());
                }else if (params->Estimators[i] == "kulczynski") {
                    treeCalculators.push_back(new Kulczynski());
                }else if (params->Estimators[i] == "kulczynskicody") {
                    treeCalculators.push_back(new KulczynskiCody());
                }else if (params->Estimators[i] == "lennon") {
                    treeCalculators.push_back(new Lennon());
                }else if (params->Estimators[i] == "morisitahorn") {
                    treeCalculators.push_back(new MorHorn());
                }else if (params->Estimators[i] == "braycurtis") {
                    treeCalculators.push_back(new BrayCurtis());
                }else if (params->Estimators[i] == "whittaker") {
                    treeCalculators.push_back(new Whittaker());
                }else if (params->Estimators[i] == "odum") {
                    treeCalculators.push_back(new Odum());
                }else if (params->Estimators[i] == "canberra") {
                    treeCalculators.push_back(new Canberra());
                }else if (params->Estimators[i] == "structeuclidean") {
                    treeCalculators.push_back(new StructEuclidean());
                }else if (params->Estimators[i] == "structchord") {
                    treeCalculators.push_back(new StructChord());
                }else if (params->Estimators[i] == "hellinger") {
                    treeCalculators.push_back(new Hellinger());
                }else if (params->Estimators[i] == "manhattan") {
                    treeCalculators.push_back(new Manhattan());
                }else if (params->Estimators[i] == "structpearson") {
                    treeCalculators.push_back(new StructPearson());
                }else if (params->Estimators[i] == "soergel") {
                    treeCalculators.push_back(new Soergel());
                }else if (params->Estimators[i] == "spearman") {
                    treeCalculators.push_back(new Spearman());
                }else if (params->Estimators[i] == "structkulczynski") {
                    treeCalculators.push_back(new StructKulczynski());
                }else if (params->Estimators[i] == "speciesprofile") {
                    treeCalculators.push_back(new SpeciesProfile());
                }else if (params->Estimators[i] == "hamming") {
                    treeCalculators.push_back(new Hamming());
                }else if (params->Estimators[i] == "structchi2") {
                    treeCalculators.push_back(new StructChi2());
                }else if (params->Estimators[i] == "gower") {
                    treeCalculators.push_back(new Gower());
                }else if (params->Estimators[i] == "memchi2") {
                    treeCalculators.push_back(new MemChi2());
                }else if (params->Estimators[i] == "memchord") {
                    treeCalculators.push_back(new MemChord());
                }else if (params->Estimators[i] == "memeuclidean") {
                    treeCalculators.push_back(new MemEuclidean());
                }else if (params->Estimators[i] == "mempearson") {
                    treeCalculators.push_back(new MemPearson());
                }else if (params->Estimators[i] == "jsd") {
                    treeCalculators.push_back(new JSD());
                }else if (params->Estimators[i] == "rjsd") {
                    treeCalculators.push_back(new RJSD());
                }
            }
        }
        
        //if the users entered no valid calculators don't execute command
        if (treeCalculators.size() == 0) { params->m->mothurOut("You have given no valid calculators.\n");  return 0; }
        
        params->Estimators.clear();
        for (int i=0; i<treeCalculators.size(); i++) { params->Estimators.push_back(treeCalculators[i]->getName()); }
        
        vector< vector<seqDist>  > calcDists; calcDists.resize(treeCalculators.size());
//.........这里部分代码省略.........

int SummaryCommand::execute() {
    try {

        if (abort == true) {
            if (calledHelp) {
                return 0;
            }
            return 2;
        }

        if ((format != "sharedfile")) {
            inputFileNames.push_back(inputfile);
        }
        else {
            inputFileNames = parseSharedFile(sharedfile);
            format = "rabund";
        }

        if (m->control_pressed) {
            return 0;
        }

        int numLines = 0;
        int numCols = 0;
        map<string, string> groupIndex;

        for (int p = 0; p < inputFileNames.size(); p++) {

            numLines = 0;
            numCols = 0;

            map<string, string> variables;
            variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
            string fileNameRoot = getOutputFileName("summary",variables);
            variables["[tag]"] = "ave-std";
            string fileNameAve = getOutputFileName("summary",variables);
            outputNames.push_back(fileNameRoot);
            outputTypes["summary"].push_back(fileNameRoot);

            if (inputFileNames.size() > 1) {
                m->mothurOutEndLine();
                m->mothurOut("Processing group " + groups[p]);
                m->mothurOutEndLine();
                m->mothurOutEndLine();
                groupIndex[fileNameRoot] = groups[p];
            }

            sumCalculators.clear();

            ValidCalculators validCalculator;

            for (int i=0; i<Estimators.size(); i++) {
                if (validCalculator.isValidCalculator("summary", Estimators[i]) == true) {
                    if(Estimators[i] == "sobs") {
                        sumCalculators.push_back(new Sobs());
                    } else if(Estimators[i] == "chao") {
                        sumCalculators.push_back(new Chao1());
                    } else if(Estimators[i] == "coverage") {
                        sumCalculators.push_back(new Coverage());
                    } else if(Estimators[i] == "geometric") {
                        sumCalculators.push_back(new Geom());
                    } else if(Estimators[i] == "logseries") {
                        sumCalculators.push_back(new LogSD());
                    } else if(Estimators[i] == "qstat") {
                        sumCalculators.push_back(new QStat());
                    } else if(Estimators[i] == "bergerparker") {
                        sumCalculators.push_back(new BergerParker());
                    } else if(Estimators[i] == "bstick") {
                        sumCalculators.push_back(new BStick());
                    } else if(Estimators[i] == "ace") {
                        if(abund < 5)
                            abund = 10;
                        sumCalculators.push_back(new Ace(abund));
                    } else if(Estimators[i] == "jack") {
                        sumCalculators.push_back(new Jackknife());
                    } else if(Estimators[i] == "shannon") {
                        sumCalculators.push_back(new Shannon());
                    } else if(Estimators[i] == "shannoneven") {
                        sumCalculators.push_back(new ShannonEven());
                    } else if(Estimators[i] == "npshannon") {
                        sumCalculators.push_back(new NPShannon());
                    } else if(Estimators[i] == "heip") {
                        sumCalculators.push_back(new Heip());
                    } else if(Estimators[i] == "smithwilson") {
                        sumCalculators.push_back(new SmithWilson());
                    } else if(Estimators[i] == "simpson") {
                        sumCalculators.push_back(new Simpson());
                    } else if(Estimators[i] == "simpsoneven") {
                        sumCalculators.push_back(new SimpsonEven());
                    } else if(Estimators[i] == "invsimpson") {
                        sumCalculators.push_back(new InvSimpson());
                    } else if(Estimators[i] == "bootstrap") {
                        sumCalculators.push_back(new Bootstrap());
                    } else if (Estimators[i] == "nseqs") {
                        sumCalculators.push_back(new NSeqs());
                    } else if (Estimators[i] == "goodscoverage") {
                        sumCalculators.push_back(new GoodsCoverage());
                    } else if (Estimators[i] == "efron") {
                        sumCalculators.push_back(new Efron(size));
                    } else if (Estimators[i] == "boneh") {
//.........这里部分代码省略.........

//.........这里部分代码省略.........
			}
			
			//check for required parameters
			listfile = validParameter.validFile(parameters, "list", true);
			if (listfile == "not open") { listfile = ""; abort = true; }
			else if (listfile == "not found") { listfile = ""; }
			else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
			
			sabundfile = validParameter.validFile(parameters, "sabund", true);
			if (sabundfile == "not open") { sabundfile = ""; abort = true; }	
			else if (sabundfile == "not found") { sabundfile = ""; }
			else {  format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
			
			rabundfile = validParameter.validFile(parameters, "rabund", true);
			if (rabundfile == "not open") { rabundfile = ""; abort = true; }	
			else if (rabundfile == "not found") { rabundfile = ""; }
			else {  format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
			
			sharedfile = validParameter.validFile(parameters, "shared", true);
			if (sharedfile == "not open") { sharedfile = ""; abort = true; }	
			else if (sharedfile == "not found") { sharedfile = ""; }
			else {  format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
				
			if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) { 
				//is there are current file available for any of these?
				//give priority to shared, then list, then rabund, then sabund
				//if there is a current shared file, use it
				sharedfile = m->getSharedFile(); 
				if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
				else { 
					listfile = m->getListFile(); 
					if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
					else { 
						rabundfile = m->getRabundFile(); 
						if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
						else { 
							sabundfile = m->getSabundFile(); 
							if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
							else { 
								m->mothurOut("No valid current files. You must provide a list, sabund, rabund or shared file before you can use the collect.single command."); m->mothurOutEndLine(); 
								abort = true;
							}
						}
					}
				}
			}
			
			//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 = m->hasPath(inputfile);		}

			//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;  }
			}
				
			calc = validParameter.validFile(parameters, "calc", false);			
			if (calc == "not found") { calc = "sobs";  }
			else { 
				 if (calc == "default")  {  calc = "sobs";  }
			}
			m->splitAtDash(calc, Estimators);
			if (m->inUsersGroups("citation", Estimators)) { 
				ValidCalculators validCalc; validCalc.printCitations(Estimators); 
				//remove citation from list of calcs
				for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
			}

			string temp;
			temp = validParameter.validFile(parameters, "freq", false);			if (temp == "not found") { temp = "100"; }
			m->mothurConvert(temp, freq); 
			
			temp = validParameter.validFile(parameters, "abund", false);			if (temp == "not found") { temp = "10"; }
			m->mothurConvert(temp, abund); 
			
			temp = validParameter.validFile(parameters, "iters", false);			if (temp == "not found") { temp = "1000"; }
			m->mothurConvert(temp, nIters); 
			
			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
			m->setProcessors(temp);
			m->mothurConvert(temp, processors);
            
            temp = validParameter.validFile(parameters, "alpha", false);		if (temp == "not found") { temp = "1"; }
			m->mothurConvert(temp, alpha);
            
            if ((alpha != 0) && (alpha != 1) && (alpha != 2)) { m->mothurOut("[ERROR]: Not a valid alpha value. Valid values are 0, 1 and 2."); m->mothurOutEndLine(); abort=true; }
			
			temp = validParameter.validFile(parameters, "groupmode", false);		if (temp == "not found") { temp = "T"; }
			groupMode = m->isTrue(temp);
		}
		
	}
	catch(exception& e) {
		m->errorOut(e, "RareFactCommand", "RareFactCommand");
		exit(1);
	}
}

int TreeGroupCommand::execute(){
	try {
	
		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
		
		if (format == "sharedfile") {
			
			ValidCalculators validCalculator;
		
			for (int i=0; i<Estimators.size(); i++) {
				if (validCalculator.isValidCalculator("treegroup", Estimators[i]) == true) { 
					if (Estimators[i] == "sharedsobs") { 
						treeCalculators.push_back(new SharedSobsCS());
					}else if (Estimators[i] == "sharedchao") { 
						treeCalculators.push_back(new SharedChao1());
					}else if (Estimators[i] == "sharedace") { 
						treeCalculators.push_back(new SharedAce());
					}else if (Estimators[i] == "jabund") { 	
						treeCalculators.push_back(new JAbund());
					}else if (Estimators[i] == "sorabund") { 
						treeCalculators.push_back(new SorAbund());
					}else if (Estimators[i] == "jclass") { 
						treeCalculators.push_back(new Jclass());
					}else if (Estimators[i] == "sorclass") { 
						treeCalculators.push_back(new SorClass());
					}else if (Estimators[i] == "jest") { 
						treeCalculators.push_back(new Jest());
					}else if (Estimators[i] == "sorest") { 
						treeCalculators.push_back(new SorEst());
					}else if (Estimators[i] == "thetayc") { 
						treeCalculators.push_back(new ThetaYC());
					}else if (Estimators[i] == "thetan") { 
						treeCalculators.push_back(new ThetaN());
					}else if (Estimators[i] == "kstest") { 
						treeCalculators.push_back(new KSTest());
					}else if (Estimators[i] == "sharednseqs") { 
						treeCalculators.push_back(new SharedNSeqs());
					}else if (Estimators[i] == "ochiai") { 
						treeCalculators.push_back(new Ochiai());
					}else if (Estimators[i] == "anderberg") { 
						treeCalculators.push_back(new Anderberg());
					}else if (Estimators[i] == "kulczynski") { 
						treeCalculators.push_back(new Kulczynski());
					}else if (Estima