C++ SharedUtil类代码示例

SequenceParser::SequenceParser(string groupFile, string fastaFile, vector<string> groupsSelected) {
	try {
		
		m = MothurOut::getInstance();
		int error;
		
		//read group file
		groupMap = new GroupMap(groupFile);
		error = groupMap->readMap();
		
		if (error == 1) { m->control_pressed = true; }
		
		//initialize maps
        vector<string> namesOfGroups = groupMap->getNamesOfGroups();
        set<string> selectedGroups;
        if (groupsSelected.size() != 0) {
            SharedUtil util;  util.setGroups(groupsSelected, namesOfGroups);
            namesOfGroups = groupsSelected;
        }
        
		for (int i = 0; i < namesOfGroups.size(); i++) {
			vector<Sequence> temp;
			seqs[namesOfGroups[i]] = temp;
            selectedGroups.insert(namesOfGroups[i]);
		}
		
		//read fasta file making sure each sequence is in the group file
		ifstream in;
		m->openInputFile(fastaFile, in);
		
		while (!in.eof()) {
			
			if (m->control_pressed) { break; }
			
			Sequence seq(in); m->gobble(in);
			
			if (seq.getName() != "") {
                
				string group = groupMap->getGroup(seq.getName());
                if (selectedGroups.count(group) != 0) { //this is a group we want
                    if (group == "not found") {  error = 1; m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file and not in your groupfile, please correct."); m->mothurOutEndLine();  }
                    else {
                        seqs[group].push_back(seq);
                    }
                }
			}
		}
		in.close();
		
		if (error == 1) { m->control_pressed = true; }
		
	}
	catch(exception& e) {
		m->errorOut(e, "SequenceParser", "SequenceParser");
		exit(1);
	}
}

int MergeGroupsCommand::processGroupFile(DesignMap*& designMap){
	try {
		
		string thisOutputDir = outputDir;
		if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
        map<string, string> variables; 
        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
        variables["[extension]"] = m->getExtension(groupfile);
		string outputFileName = getOutputFileName("group", variables);
		outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName);
		
		ofstream out;
		m->openOutputFile(outputFileName, out);
		
		//read groupfile
		GroupMap groupMap(groupfile);
		groupMap.readMap();
		
		//fill Groups - checks for "all" and for any typo groups
		SharedUtil* util = new SharedUtil();
		vector<string> nameGroups = groupMap.getNamesOfGroups();
		util->setGroups(Groups, nameGroups);
		delete util;
		
		vector<string> namesOfSeqs = groupMap.getNamesSeqs();
		bool error = false;
		
		for (int i = 0; i < namesOfSeqs.size(); i++) {
			
			if (m->control_pressed) { break; }
			
			string thisGroup = groupMap.getGroup(namesOfSeqs[i]);
			
			//are you in a group the user wants
			if (m->inUsersGroups(thisGroup, Groups)) {
				string thisGrouping = designMap->get(thisGroup);
				
				if (thisGrouping == "not found") { m->mothurOut("[ERROR]: " + namesOfSeqs[i] + " is from group " + thisGroup + " which is not in your design file, please correct."); m->mothurOutEndLine();  error = true; }
				else {
					out << namesOfSeqs[i] << '\t' << thisGrouping << endl;
				}
			}
		}
		
		if (error) { m->control_pressed = true; }

		out.close();
		
		return 0;
		
	}
	catch(exception& e) {
		m->errorOut(e, "MergeGroupsCommand", "processGroupFile");
		exit(1);
	}
}

int GetOtusCommand::execute(){
	try {
		
		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
		
		groupMap = new GroupMap(groupfile);
		groupMap->readMap();
		
		//get groups you want to get
		if (accnosfile != "") { m->readAccnos(accnosfile, Groups); m->setGroups(Groups); }
		
		//make sure groups are valid
		//takes care of user setting groupNames that are invalid or setting groups=all
		SharedUtil* util = new SharedUtil();
		vector<string> gNamesOfGroups = groupMap->getNamesOfGroups();
		util->setGroups(Groups, gNamesOfGroups);
		groupMap->setNamesOfGroups(gNamesOfGroups);
		delete util;
		
		if (m->control_pressed) { delete groupMap; return 0; }
		
		//read through the list file keeping any otus that contain any sequence from the groups selected
		readListGroup();
		
		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } return 0; }
				
		if (outputNames.size() != 0) {
			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();
			
			//set list file as new current listfile
			string 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); }
			}
		}
		
		return 0;		
	}
	
	catch(exception& e) {
		m->errorOut(e, "GetOtusCommand", "execute");
		exit(1);
	}
}

int ParsimonyCommand::execute() {
	try {
	
		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
		
		
		//randomtree will tell us if user had their own treefile or if they just want the random distribution
		//user has entered their own tree
		if (randomtree == "") { 
			
			m->setTreeFile(treefile);
			
            TreeReader* reader;
            if (countfile == "") { reader = new TreeReader(treefile, groupfile, namefile); }
            else { reader = new TreeReader(treefile, countfile); }
            T = reader->getTrees();
            ct = T[0]->getCountTable();
            delete reader;
	
			if(outputDir == "") { outputDir += m->hasPath(treefile); }
            map<string, string> variables; 
            variables["[filename]"] = outputDir + m->getSimpleName(treefile) +  ".";
            
			output = new ColumnFile(getOutputFileName("parsimony",variables), itersString);
			outputNames.push_back(getOutputFileName("parsimony",variables));
			outputTypes["parsimony"].push_back(getOutputFileName("parsimony",variables));
				
			sumFile = getOutputFileName("psummary",variables);
			m->openOutputFile(sumFile, outSum);
			outputNames.push_back(sumFile);
			outputTypes["psummary"].push_back(sumFile);
		}else { //user wants random distribution
			getUserInput();
				
			if(outputDir == "") { outputDir += m->hasPath(randomtree); }
			output = new ColumnFile(outputDir+ m->getSimpleName(randomtree), itersString);
			outputNames.push_back(outputDir+ m->getSimpleName(randomtree));
			outputTypes["parsimony"].push_back(outputDir+ m->getSimpleName(randomtree));
		}
			
		//set users groups to analyze
		SharedUtil util;
		vector<string> mGroups = m->getGroups();
		vector<string> tGroups = ct->getNamesOfGroups();
		util.setGroups(mGroups, tGroups, allGroups, numGroups, "parsimony");	//sets the groups the user wants to analyze
		util.getCombos(groupComb, mGroups, numComp);
		m->setGroups(mGroups);
			
		if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }
			
		Parsimony pars;
		counter = 0;
	
		Progress* reading;
		reading = new Progress("Comparing to random:", iters);
		
		if (m->control_pressed) { 
			delete reading; delete output;
			delete ct; for (int i = 0; i < T.size(); i++) { delete T[i]; }
			if (randomtree == "") {  outSum.close();  }
			for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
			m->clearGroups();
			return 0;
		}
			
		
		//get pscore for users tree
		userData.resize(numComp,0);  //data = AB, AC, BC, ABC.
		randomData.resize(numComp,0);  //data = AB, AC, BC, ABC.
		rscoreFreq.resize(numComp);  
		uscoreFreq.resize(numComp);  
		rCumul.resize(numComp);  
		uCumul.resize(numComp);  
		userTreeScores.resize(numComp);  
		UScoreSig.resize(numComp); 
				
		if (randomtree == "") {
			//get pscores for users trees
			for (int i = 0; i < T.size(); i++) {
				userData = pars.getValues(T[i], processors, outputDir);  //data = AB, AC, BC, ABC.
				
				if (m->control_pressed) { 
					delete reading; delete output;
					delete ct; for (int i = 0; i < T.size(); i++) { delete T[i]; }
					if (randomtree == "") {  outSum.close();  }
					for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
					m->clearGroups();
					return 0;
				}


				//output scores for each combination
				for(int k = 0; k < numComp; k++) {

					//update uscoreFreq
					map<int,double>::iterator it = uscoreFreq[k].find(userData[k]);
					if (it == uscoreFreq[k].end()) {//new score
						uscoreFreq[k][userData[k]] = 1;
					}else{ uscoreFreq[k][userData[k]]++; }
					
//.........这里部分代码省略.........

int CorrAxesCommand::getMetadata(){
	try {
		vector<string> groupNames;
		
		ifstream in;
		m->openInputFile(metadatafile, in);
		
		string headerLine = m->getline(in); m->gobble(in);
		istringstream iss (headerLine,istringstream::in);
		
		//read the first label, because it refers to the groups
		string columnLabel;
		iss >> columnLabel; m->gobble(iss); 
		
		//save names of columns you are reading
		while (!iss.eof()) {
			iss >> columnLabel; m->gobble(iss);
			metadataLabels.push_back(columnLabel);
		}
		int count = metadataLabels.size();
			
		//read rest of file
		while (!in.eof()) {
			
			if (m->control_pressed) { in.close(); return 0; }
			
			string group = "";
			in >> group; m->gobble(in);
			groupNames.push_back(group);
				
			SharedRAbundFloatVector* tempLookup = new SharedRAbundFloatVector();
			tempLookup->setGroup(group);
			tempLookup->setLabel("1");
			
			for (int i = 0; i < count; i++) {
				float temp = 0.0;
				in >> temp; 
				tempLookup->push_back(temp, group);
			}
			
			lookupFloat.push_back(tempLookup);
			
			m->gobble(in);
		}
		in.close();
		
		//remove any groups the user does not want, and set globaldata->groups with only valid groups
		SharedUtil* util;
		util = new SharedUtil();
		Groups = m->getGroups();
		util->setGroups(Groups, groupNames);
		m->setGroups(Groups);
		
		for (int i = 0; i < lookupFloat.size(); i++) {
			//if this sharedrabund is not from a group the user wants then delete it.
			if (util->isValidGroup(lookupFloat[i]->getGroup(), m->getGroups()) == false) { 
				delete lookupFloat[i]; lookupFloat[i] = NULL;
				lookupFloat.erase(lookupFloat.begin()+i); 
				i--; 
			}
		}
		
		delete util;
		
		return 0;
	}
	catch(exception& e) {
		m->errorOut(e, "CorrAxesCommand", "getMetadata");	
		exit(1);
	}
}

int GetSharedOTUCommand::runShared() {
	try {
        InputData input(sharedfile, "sharedfile");
		vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
		string lastLabel = lookup[0]->getLabel();
        
        if (Groups.size() == 0) {
            Groups = m->getGroups();
            
            //make string for outputfile name
            userGroups = "unique.";
            for(int i = 0; i < Groups.size(); i++) {  userGroups += Groups[i] + "-";  }
            userGroups = userGroups.substr(0, userGroups.length()-1);
        }else {
            //sanity check for group names
            SharedUtil util;
            vector<string> allGroups = m->getAllGroups();
            util.setGroups(Groups, allGroups);
        }
        
        //put groups in map to find easier
        for(int i = 0; i < Groups.size(); i++) {
            groupFinder[Groups[i]] = Groups[i];
        }

		//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;
        
		//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) {
                outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); }
                for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); return 0;
			}
            
            
			if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
				m->mothurOut(lookup[0]->getLabel()); 
				process(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()); 
                process(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();
            
			//get next line to process
			//prevent memory leak
			for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
			lookup = input.getSharedRAbundVectors();
		}
		
		if (m->control_pressed) {
            outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); }
            for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); 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()); 
            process(lookup);
            for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
		}
        
		//reset groups parameter
		m->clearGroups();  
		
//.........这里部分代码省略.........

int CollectSharedCommand::execute(){
	try {
		
		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
		
		//if the users entered no valid calculators don't execute command
		if (cDisplays.size() == 0) { return 0; }
		for(int i=0;i<cDisplays.size();i++){	cDisplays[i]->setAll(all);	}	
	
		input = new InputData(sharedfile, "sharedfile");
		order = input->getSharedOrderVector();
		string lastLabel = order->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;
			
		//set users groups
		SharedUtil* util = new SharedUtil();
		Groups = m->getGroups();
		vector<string> allGroups = m->getAllGroups();
		util->setGroups(Groups, allGroups, "collect");
		m->setGroups(Groups);
		m->setAllGroups(allGroups);
		delete util;

		while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
			if (m->control_pressed) { 
					for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	}  outputTypes.clear();
					for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}
					delete order; delete input;
					m->clearGroups();
					return 0;
			}

			if(allLines == 1 || labels.count(order->getLabel()) == 1){
			
				m->mothurOut(order->getLabel()); m->mothurOutEndLine();
				//create collectors curve
				cCurve = new Collect(order, cDisplays);
				cCurve->getSharedCurve(freq);
				delete cCurve;
			
				processedLabels.insert(order->getLabel());
				userLabels.erase(order->getLabel());
			}
			
			//you have a label the user want that is smaller than this label and the last label has not already been processed
			if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
				string saveLabel = order->getLabel();
				
				delete order;
				order = input->getSharedOrderVector(lastLabel);
				
				m->mothurOut(order->getLabel()); m->mothurOutEndLine();
				//create collectors curve
				cCurve = new Collect(order, cDisplays);
				cCurve->getSharedCurve(freq);
				delete cCurve;
				
				processedLabels.insert(order->getLabel());
				userLabels.erase(order->getLabel());
				
				//restore real lastlabel to save below
				order->setLabel(saveLabel);
			}
			
			
			lastLabel = order->getLabel();			
			
			//get next line to process
			delete order;
			order = input->getSharedOrderVector();
		}
		
		if (m->control_pressed) { 
					for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	}   outputTypes.clear();
					for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}
					m->clearGroups();
					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 (order != NULL) {  delete order;  }
			order = input->getSharedOrderVector(lastLabel);
//.........这里部分代码省略.........

int RemoveGroupsCommand::execute(){
	try {
		
		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
		
		//get groups you want to remove
		if (accnosfile != "") { m->readAccnos(accnosfile, Groups); m->setGroups(Groups);  }
		
		if (groupfile != "") {
			groupMap = new GroupMap(groupfile);
			groupMap->readMap();
			
			//make sure groups are valid
			//takes care of user setting groupNames that are invalid or setting groups=all
			vector<string> namesGroups = groupMap->getNamesOfGroups();
			vector<string> checkedGroups;
            for (int i = 0; i < Groups.size(); i++) {
                if (m->inUsersGroups(Groups[i], namesGroups)) { checkedGroups.push_back(Groups[i]); }
                else {  m->mothurOut("[WARNING]: " + Groups[i] + " is not a valid group in your groupfile, ignoring.\n"); }
            }
            
            if (checkedGroups.size() == 0) { m->mothurOut("[ERROR]: no valid groups, aborting.\n"); delete groupMap; return 0; }
			else {
                Groups = checkedGroups;
                m->setGroups(Groups);
            }
            
			//fill names with names of sequences that are from the groups we want to remove 
			fillNames();
			
			delete groupMap;
		}else if (countfile != ""){
            if ((fastafile != "") || (listfile != "") || (taxfile != "")) { 
                m->mothurOut("\n[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.\n\n");
            }
            CountTable ct;
            ct.readTable(countfile, true, false);
            if (!ct.hasGroupInfo()) { m->mothurOut("[ERROR]: your count file does not contain group info, aborting.\n"); return 0; }
            
            vector<string> gNamesOfGroups = ct.getNamesOfGroups();
            SharedUtil util;
            util.setGroups(Groups, gNamesOfGroups);
            vector<string> namesOfSeqs = ct.getNamesOfSeqs();
            sort(Groups.begin(), Groups.end());
            
            for (int i = 0; i < namesOfSeqs.size(); i++) {
                vector<string> thisSeqsGroups = ct.getGroups(namesOfSeqs[i]);
                if (m->isSubset(Groups, thisSeqsGroups)) { //you only have seqs from these groups so remove you
                    names.insert(namesOfSeqs[i]);
                }
            }
        }

				
		if (m->control_pressed) { return 0; }
		
		//read through the correct file and output lines you want to keep
		if (namefile != "")			{		readName();		}
		if (fastafile != "")		{		readFasta();	}
		if (groupfile != "")		{		readGroup();	}
        if (countfile != "")		{		readCount();	}
		if (listfile != "")			{		readList();		}
		if (taxfile != "")			{		readTax();		}
		if (sharedfile != "")		{		readShared();	}
        if (designfile != "")		{		readDesign();	}
		
		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } return 0; }
				
		if (outputNames.size() != 0) {
			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();
			
			//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("taxonomy");
			if (itTypes != outputTypes.end()) {
				if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
			}
//.........这里部分代码省略.........

int MergeGroupsCommand::processCountFile(DesignMap*& designMap){
    try {
        CountTable countTable;
        if (!countTable.testGroups(countfile)) { m->mothurOut("[ERROR]: your countfile contains no group information, please correct.\n"); m->control_pressed = true; return 0; }
        
        //read countTable
        countTable.readTable(countfile, true, false);
        
        //fill Groups - checks for "all" and for any typo groups
        SharedUtil util;
        vector<string> nameGroups = countTable.getNamesOfGroups();
        util.setGroups(Groups, nameGroups);
        
        vector<string> dnamesGroups = designMap->getNamesGroups();
        
        //sanity check
        bool error = false;
        if (nameGroups.size() == dnamesGroups.size()) { //at least there are the same number
            //is every group in counttable also in designmap
            for (int i = 0; i < nameGroups.size(); i++) {
                if (m->control_pressed) { break; }
                if (!m->inUsersGroups(nameGroups[i], dnamesGroups)) { error = true; break; }
            }
            
        }
        if (error) { m->mothurOut("[ERROR]: Your countfile does not contain the same groups as your design file, please correct\n"); m->control_pressed = true; return 0; }
        
        //user selected groups - remove some groups from table
        if (Groups.size() != nameGroups.size()) {
            for (int i = 0; i < nameGroups.size(); i++) {
                if (!m->inUsersGroups(nameGroups[i], Groups)) { countTable.removeGroup(nameGroups[i]); }
            }
        }
        //ask again in case order changed
        nameGroups = countTable.getNamesOfGroups();
        int numGroups = nameGroups.size();
        
        //create new table
        CountTable newTable;
        vector<string> treatments = designMap->getCategory();
        map<string, vector<int> > clearedMap;
        for (int i = 0; i < treatments.size(); i++) {
            newTable.addGroup(treatments[i]);
            vector<int> temp;
            clearedMap[treatments[i]] = temp;
        }
        treatments = newTable.getNamesOfGroups();
        
        set<string> namesToRemove;
        vector<string> namesOfSeqs = countTable.getNamesOfSeqs();
        for (int i = 0; i < namesOfSeqs.size(); i++) {
            
            if (m->control_pressed) { break; }
            
            vector<int> thisSeqsCounts = countTable.getGroupCounts(namesOfSeqs[i]);
            map<string, vector<int> > thisSeqsMap = clearedMap;
            
            for (int j = 0; j < numGroups; j++) {
                thisSeqsMap[designMap->get(nameGroups[j])].push_back(thisSeqsCounts[j]);
            }
        
            //create new counts for seq for new table
            vector<int> newCounts; int totalAbund = 0;
            for (int j = 0; j < treatments.size(); j++){
                int abund = mergeAbund(thisSeqsMap[treatments[j]]);
                newCounts.push_back(abund);  //order matters, add in count for each treatment in new table.
                totalAbund += abund;
            }
            
            //add seq to new table
            if(totalAbund == 0) {
                namesToRemove.insert(namesOfSeqs[i]);
            }else { newTable.push_back(namesOfSeqs[i], newCounts); }
        }
        
        if (error) { m->control_pressed = true; return 0; }
        
        //remove sequences zeroed out by median method
        if (namesToRemove.size() != 0) {
            //print names
            ofstream out;
            string accnosFile = "accnosFile.temp";
            m->openOutputFile(accnosFile, out);
            
            //output to .accnos file
            for (set<string>::iterator it = namesToRemove.begin(); it != namesToRemove.end(); it++) {
                if (m->control_pressed) {  out.close(); m->mothurRemove(accnosFile); return 0; }
                out << *it << endl;
            }
            out.close();

            //run remove.seqs
            string inputString = "accnos=" + accnosFile + ", fasta=" + fastafile;
            
            m->mothurOut("/******************************************/"); m->mothurOutEndLine();
            m->mothurOut("Running command: remove.seqs(" + inputString + ")"); m->mothurOutEndLine();
            m->mothurCalling = true;
            
            Command* removeCommand = new RemoveSeqsCommand(inputString);
            removeCommand->execute();
//.........这里部分代码省略.........

//**********************************************************************************************************************
int RemoveRareCommand::processList(){
	try {
		string thisOutputDir = outputDir;
		if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" +  m->getExtension(listfile);
		string outputGroupFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" +  m->getExtension(groupfile);
		
		ofstream out, outGroup;
		m->openOutputFile(outputFileName, out);
		
		bool wroteSomething = false;
		
		//you must provide a label because the names in the listfile need to be consistent
		string thisLabel = "";
		if (allLines) { m->mothurOut("For the listfile you must select one label, using first label in your listfile."); m->mothurOutEndLine(); }
		else if (labels.size() > 1) { m->mothurOut("For the listfile you must select one label, using " + (*labels.begin()) + "."); m->mothurOutEndLine(); thisLabel = *labels.begin(); }
		else { thisLabel = *labels.begin(); }
		
		InputData input(listfile, "list");
		ListVector* list = input.getListVector();
		
		//get first one or the one we want
		if (thisLabel != "") { 	
			//use smart distancing
			set<string> userLabels; userLabels.insert(thisLabel);
			set<string> processedLabels;
			string lastLabel = list->getLabel();
			while((list != NULL) && (userLabels.size() != 0)) {
				if(userLabels.count(list->getLabel()) == 1){
					processedLabels.insert(list->getLabel());
					userLabels.erase(list->getLabel());
					break;
				}
				
				if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
					processedLabels.insert(list->getLabel());
					userLabels.erase(list->getLabel());
					delete list;
					list = input.getListVector(lastLabel);
					break;
				}
				lastLabel = list->getLabel();
				delete list;
				list = input.getListVector();
			}
			if (userLabels.size() != 0) { 
				m->mothurOut("Your file does not include the label " + thisLabel + ". I will use " + lastLabel + ".");  m->mothurOutEndLine();
				list = input.getListVector(lastLabel); 
			}
		}
		
		//if groupfile is given then use it
		GroupMap* groupMap;
		if (groupfile != "") { 
			groupMap = new GroupMap(groupfile); groupMap->readMap(); 
			SharedUtil util;
			vector<string> namesGroups = groupMap->getNamesOfGroups();
			util.setGroups(Groups, namesGroups);
			m->openOutputFile(outputGroupFileName, outGroup);
		}
		
		
		if (list != NULL) {	
			//make a new list vector
			ListVector newList;
			newList.setLabel(list->getLabel());
			
			//for each bin
			for (int i = 0; i < list->getNumBins(); i++) {
				if (m->control_pressed) {  if (groupfile != "") { delete groupMap; outGroup.close(); m->mothurRemove(outputGroupFileName); } out.close();  m->mothurRemove(outputFileName);  return 0; }
				
				//parse out names that are in accnos file
				string binnames = list->get(i);
				vector<string> names;
				string saveBinNames = binnames;
				m->splitAtComma(binnames, names);
				
				vector<string> newGroupFile;
				if (groupfile != "") {
					vector<string> newNames;
					saveBinNames = "";
					for(int k = 0; k < names.size(); k++) {
						string group = groupMap->getGroup(names[k]);
						
						if (m->inUsersGroups(group, Groups)) {
							newGroupFile.push_back(names[k] + "\t" + group); 
								
							newNames.push_back(names[k]);	
							saveBinNames += names[k] + ",";
						}
					}
					names = newNames;
					saveBinNames = saveBinNames.substr(0, saveBinNames.length()-1);
				}

				if (names.size() > nseqs) { //keep bin
					newList.push_back(saveBinNames);
					for(int k = 0; k < newGroupFile.size(); k++) { outGroup << newGroupFile[k] << endl; }
				}
//.........这里部分代码省略.........

int HomovaCommand::execute(){
	try {
		
		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
		
		//read design file
		designMap = new GroupMap(designFileName);
		designMap->readDesignMap();
		
		if (outputDir == "") { outputDir = m->hasPath(phylipFileName); }
		
		//read in distance matrix and square it
		ReadPhylipVector readMatrix(phylipFileName);
		vector<string> sampleNames = readMatrix.read(distanceMatrix);
		
        if (Sets.size() != 0) { //user selected sets, so we want to remove the samples not in those sets
            SharedUtil util; 
            vector<string> dGroups = designMap->getNamesOfGroups();
            util.setGroups(Sets, dGroups);  
            
            for(int i=0;i<distanceMatrix.size();i++){
                
                if (m->control_pressed) { delete designMap; return 0; }
                
                string group = designMap->getGroup(sampleNames[i]);
                
                if (group == "not found") {
                    m->mothurOut("[ERROR]: " + sampleNames[i] + " is not in your design file, please correct."); m->mothurOutEndLine(); m->control_pressed = true;
                }else if (!m->inUsersGroups(group, Sets)){  //not in set we want remove it
                    //remove from all other rows
                    for(int j=0;j<distanceMatrix.size();j++){
                        distanceMatrix[j].erase(distanceMatrix[j].begin()+i);
                    }
                    distanceMatrix.erase(distanceMatrix.begin()+i);
                    sampleNames.erase(sampleNames.begin()+i);
                    i--;
                }
            }
        }

		for(int i=0;i<distanceMatrix.size();i++){
			for(int j=0;j<i;j++){
				distanceMatrix[i][j] *= distanceMatrix[i][j];	
			}
		}
		
		//link designMap to rows/columns in distance matrix
		map<string, vector<int> > origGroupSampleMap;
		for(int i=0;i<sampleNames.size();i++){
			string group = designMap->getGroup(sampleNames[i]);
			
			if (group == "not found") {
				m->mothurOut("[ERROR]: " + sampleNames[i] + " is not in your design file, please correct."); m->mothurOutEndLine(); m->control_pressed = true;
			}else { origGroupSampleMap[group].push_back(i); }
		}
		int numGroups = origGroupSampleMap.size();
		
		if (m->control_pressed) { delete designMap; return 0; }
		
		//create a new filename
		ofstream HOMOVAFile;
        map<string, string> variables; 
		variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(phylipFileName));
		string HOMOVAFileName = getOutputFileName("homova", variables);				
		m->openOutputFile(HOMOVAFileName, HOMOVAFile);
		outputNames.push_back(HOMOVAFileName); outputTypes["homova"].push_back(HOMOVAFileName);
		
		HOMOVAFile << "HOMOVA\tBValue\tP-value\tSSwithin/(Ni-1)_values" << endl;
		m->mothurOut("HOMOVA\tBValue\tP-value\tSSwithin/(Ni-1)_values\n");
		
		double fullHOMOVAPValue = runHOMOVA(HOMOVAFile, origGroupSampleMap, experimentwiseAlpha);

		if(fullHOMOVAPValue <= experimentwiseAlpha && numGroups > 2){
			
			int numCombos = numGroups * (numGroups-1) / 2;
			double pairwiseAlpha = experimentwiseAlpha / (double) numCombos;
			
			map<string, vector<int> >::iterator itA;
			map<string, vector<int> >::iterator itB;
			
			for(itA=origGroupSampleMap.begin();itA!=origGroupSampleMap.end();itA++){
				itB = itA;itB++;
				for(;itB!=origGroupSampleMap.end();itB++){
					map<string, vector<int> > pairwiseGroupSampleMap;
					pairwiseGroupSampleMap[itA->first] = itA->second;
					pairwiseGroupSampleMap[itB->first] = itB->second;
					
					runHOMOVA(HOMOVAFile, pairwiseGroupSampleMap, pairwiseAlpha);
				}			
			}
			HOMOVAFile << endl;
			m->mothurOutEndLine();
			
			m->mothurOut("Experiment-wise error rate: " + toString(experimentwiseAlpha) + '\n');
			m->mothurOut("Pair-wise error rate (Bonferroni): " + toString(pairwiseAlpha) + '\n');
		}
		else{
			m->mothurOut("Experiment-wise error rate: " + toString(experimentwiseAlpha) + '\n');
		}
		
//.........这里部分代码省略.........

void CModManager::DumpCoreLog ( CExceptionInformation* pExceptionInformation )
{
    // Write a log with the generic exception information
    FILE* pFile = fopen ( CalcMTASAPath ( "mta\\core.log" ), "a+" );
    if ( pFile )
    {
        // Header
        fprintf ( pFile, "%s", "** -- Unhandled exception -- **\n\n" );

        // Write the mod name
        //fprintf ( pFile, "Mod name = %s\n", "TODO" );

        // Write the time
        time_t timeTemp;
        time ( &timeTemp );
        fprintf ( pFile, "Time = %s", ctime ( &timeTemp ) );

#define MAX_MODULE_PATH 512
        char * szModulePath = new char[MAX_MODULE_PATH];
        if ( pExceptionInformation->GetModule( szModulePath, MAX_MODULE_PATH ) )
        {
           fprintf ( pFile, "Module = %s\n", szModulePath );
        }
        delete [] szModulePath;
#undef MAX_MODULE_PATH

        // Write the basic exception information
        fprintf ( pFile, "Code = 0x%08X\n", pExceptionInformation->GetCode () );
        fprintf ( pFile, "Offset = 0x%08X\n\n", pExceptionInformation->GetOffset () );
        //fprintf ( pFile, "Referencing offset = 0x%08X\n\n", pExceptionInformation->GetReferencingOffset () );

        // Write the register info
        fprintf ( pFile, "EAX=%08X  EBX=%08X  ECX=%08X  EDX=%08X  ESI=%08X\n" \
                         "EDI=%08X  EBP=%08X  ESP=%08X  EIP=%08X  FLG=%08X\n" \
                         "CS=%04X   DS=%04X  SS=%04X  ES=%04X   " \
                         "FS=%04X  GS=%04X\n\n",
                         pExceptionInformation->GetEAX (),
                         pExceptionInformation->GetEBX (),
                         pExceptionInformation->GetECX (),
                         pExceptionInformation->GetEDX (),
                         pExceptionInformation->GetESI (),
                         pExceptionInformation->GetEDI (),
                         pExceptionInformation->GetEBP (),
                         pExceptionInformation->GetESP (),
                         pExceptionInformation->GetEIP (),
                         pExceptionInformation->GetEFlags (),
                         pExceptionInformation->GetCS (),
                         pExceptionInformation->GetDS (),
                         pExceptionInformation->GetSS (),
                         pExceptionInformation->GetES (),
                         pExceptionInformation->GetFS (),
                         pExceptionInformation->GetGS () );

        // End of unhandled exception
        fprintf ( pFile, "%s", "** -- End of unhandled exception -- **\n\n\n" );
        
        // Close the file
        fclose ( pFile );
    }
}

void CCore::CreateXML ( )
{
    // Create function pointer type and variable.
    typedef CXML* (*pfnXMLInitializer) ( );
    pfnXMLInitializer pfnXMLInit;

    CFilePathTranslator     FileTranslator;
    string                  WorkingDirectory;
    char                    szCurDir [ 1024 ];

    // Set the current directory.
    FileTranslator.SetCurrentWorkingDirectory ( "MTA" );
    FileTranslator.GetCurrentWorkingDirectory ( WorkingDirectory );
    GetCurrentDirectory ( sizeof ( szCurDir ), szCurDir );
    SetCurrentDirectory ( WorkingDirectory.c_str ( ) );

    // Load approrpiate compilation-specific library.
#ifdef MTA_DEBUG
    m_XMLModule.LoadModule ( "xmll_d.dll" );
#else
    m_XMLModule.LoadModule ( "xmll.dll" );
#endif

    // Get client initializer function from DLL's routine.
    pfnXMLInit = static_cast< pfnXMLInitializer > 
    ( m_XMLModule.GetFunctionPointer ( "InitXMLInterface" ) );

    // If we have a valid initializer, call it.
    if ( pfnXMLInit != NULL )
    {
        WriteDebugEvent ( "XML loaded." );
        m_pXML = pfnXMLInit ( );
    }
    else
    {
        // USE CLANGUAGELOCALE HERE.
        MessageBox ( 0, "XML module could not be located!", "Error", MB_OK|MB_ICONEXCLAMATION );
        TerminateProcess ( GetCurrentProcess (), 0 );
    }

	SetCurrentDirectory ( szCurDir );

    
    // Load config XML file
    m_pConfigFile = m_pXML->CreateXML ( CalcMTASAPath ( MTA_CONFIG_PATH ) );
    if ( !m_pConfigFile ) {
        assert ( false );
        return;
    }
    m_pConfigFile->Parse ();

    // Load the keybinds (loads defaults if the subnode doesn't exist)
    GetKeyBinds ()->LoadFromXML ( GetConfig ()->FindSubNode ( CONFIG_NODE_KEYBINDS ) );

    // Load XML-dependant subsystems
    m_ClientVariables.Load ( );
}

void CCore::CreateGame ( )
{
    // Create function pointer type and variable.
    typedef CGame* (*pfnGameInitializer) ( );
    pfnGameInitializer pfnGameInit;

    // Load approrpiate compilation-specific library.
#ifdef MTA_DEBUG
    m_GameModule.LoadModule ( CalcMTASAPath ( "mta/game_sa_d.dll" ) );
# else
    m_GameModule.LoadModule ( CalcMTASAPath ( "mta/game_sa.dll" ) );

#endif


    // Get client initializer function from DLL's routine.
    pfnGameInit = static_cast< pfnGameInitializer > 
    ( m_GameModule.GetFunctionPointer ( "GetGameInterface" ) );

    // If we have a valid initializer, call it.
    if ( pfnGameInit != NULL )
    {
        WriteDebugEvent ( "Game loaded." );
        m_pGame = pfnGameInit ( );

        if ( m_pGame->GetGameVersion () >= VERSION_11 )
        {
            MessageBox ( 0, "Only GTA:SA version 1.0 is supported!", "Error", MB_OK|MB_ICONEXCLAMATION );
            TerminateProcess ( GetCurrentProcess (), 0 );
        }
    }
    else
    {
        // USE CLANGUAGELOCALE HERE.
        MessageBox ( 0, "Game module could not be located!", "Error", MB_OK|MB_ICONEXCLAMATION );
        TerminateProcess ( GetCurrentProcess (), 0 );
    }
}

void CCore::CreateMultiplayer ( )
{
    // Check to see if our game has been created.
    if ( m_pGame == NULL )
    {
        // Inform user that loading failed.
        return;
    }

    // Create function pointer type and variable.
    typedef CMultiplayer* (*pfnMultiplayerInitializer) ( CGame * );
    pfnMultiplayerInitializer pfnMultiplayerInit;

    // Load appropriate compilation-specific library.
#ifdef MTA_DEBUG
    m_MultiplayerModule.LoadModule ( CalcMTASAPath ( "mta/multiplayer_sa_d.dll" ) );
# else
    m_MultiplayerModule.LoadModule ( CalcMTASAPath ( "mta/multiplayer_sa.dll" ) );
#endif

    // Get client initializer function from DLL's routine.
    pfnMultiplayerInit = static_cast< pfnMultiplayerInitializer > 
    ( m_MultiplayerModule.GetFunctionPointer ( "InitMultiplayerInterface" ) );

    // If we have a valid initializer, call it.
    if ( pfnMultiplayerInit != NULL )
    {
        WriteDebugEvent ( "Multiplayer loaded." );
        m_pMultiplayer = pfnMultiplayerInit ( m_pGame );
    }
    else
    {
        // USE CLANGUAGELOCALE HERE.
        MessageBox ( 0, "Multiplayer module could not be located!", "Error", MB_OK|MB_ICONEXCLAMATION );
        TerminateProcess ( GetCurrentProcess (), 0 );
    }
}