--- /dev/null
+/*
+ * File: kruskalwalliscommand.cpp
+ * Author: kiverson
+ *
+ * Created on June 26, 2012, 11:06 AM
+ */
+
+#include "kruskalwalliscommand.h"
+
+//**********************************************************************************************************************
+vector<string> KruskalWallisCommand::setParameters(){
+ try {
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
+
+ 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, "KruskalWallisCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string KruskalWallisCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The kruskalwallis command parameter options are \n";
+ helpString += "Kruskal–Wallis one-way analysis of variance is a non-parametric method for testing whether samples originate from the same distribution.";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "KruskalWallisCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string KruskalWallisCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "summary") { outputFileName = "cooccurence.summary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "KruskalWallisCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+KruskalWallisCommand::KruskalWallisCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "KruskalWallisCommand", "KruskalWallisCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+KruskalWallisCommand::KruskalWallisCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+
+ //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; }
+ }
+
+ //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); }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ m->splitAtDash(groups, Groups);
+ }
+ m->setGroups(Groups);
+
+ //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; }
+ }
+ }
+
+ vector<string> tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+
+
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "KruskalWallisCommand", "KruskalWallisCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int KruskalWallisCommand::execute(){
+ try {
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ 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;
+
+ ofstream out;
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("summary");
+ m->openOutputFile(outputFileName, out);
+ outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+ out << "H\tpvalue\n";
+
+ //math goes here
+
+ int N = m->getNumGroups();
+ double H;
+ double tmp = 0.0;
+ vector<groupRank> vec;
+ vector<string> groups = m->getGroups();
+ string group;
+ int count;
+ double sum;
+
+ //merge all groups into a vector
+
+
+
+ //rank function here
+ assignRank(vec);
+
+ //populate counts and ranSums vectors
+ for (int i=0;i<N;i++) {
+ count = 0;
+ sum = 0;
+ group = groups[i];
+ for(int j;j<vec.size();j++) {
+ if (vec[j].group == group) {
+ count++;
+ sum = sum + vec[j].rank;
+ }
+ }
+ counts[i] = count;
+ rankSums[i] = sum;
+ }
+
+ //test statistic
+ for (int i=0;i<N;i++) { tmp = tmp + (pow(rankSums[i],2) / counts[i]); }
+
+ H = (12 / (N*(N+1))) * tmp - (3*(N+1));
+
+ //ss = tmp - pow(accumulate(rankSums.begin(), rankSums.end(), 0), 2);
+
+ //H = ss / ( (N * (N + 1))/12 );
+
+ //correction for ties?
+
+ //p-value calculation
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "KruskalWallisCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+void KruskalWallisCommand::assignRank(vector<groupRank> &vec) {
+ try {
+ double rank = 1;
+ double numRanks, avgRank, j;
+ vector<groupRank>::iterator it, oldit;
+
+ sort (vec.begin(), vec.end(), comparevalue);
+
+ it = vec.begin();
+
+ while ( it != vec.end() ) {
+ j = rank;
+ oldit = it;
+ if (!equalvalue(*it, *(it+1))) {
+ (*it).rank = rank;
+ rank = rank+1;
+ it++; }
+ else {
+ while(equalrank(*it, *(it+1))) {
+ j = j + (j+1);
+ rank++;
+ it++;
+ }
+ numRanks = double (distance(oldit, it));
+ avgRank = j / numRanks;
+ while(oldit != it) {
+ (*oldit).rank = avgRank;
+ oldit++;
+ }
+ }
+
+ }
+
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "KruskalWallisCommand", "getRank");
+ exit(1);
+ }
+
+}
+//**********************************************************************************************************************
+void KruskalWallisCommand::assignValue(vector<groupRank> &vec) {
+
+}
+//**********************************************************************************************************************
+//**********************************************************************************************************************
+//**********************************************************************************************************************
\ No newline at end of file
--- /dev/null
+/*
+ * File: kruskalwalliscommand.h
+ * Author: kiverson
+ *
+ * Created on June 26, 2012, 11:07 AM
+ */
+
+#ifndef KRUSKALWALLISCOMMAND_H
+#define KRUSKALWALLISCOMMAND_H
+
+#include "command.hpp"
+#include "inputdata.h"
+#include "sharedrabundvector.h"
+
+
+class KruskalWallisCommand : public Command {
+
+public:
+
+ KruskalWallisCommand(string);
+ KruskalWallisCommand();
+ ~KruskalWallisCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "kruskalwallis"; }
+ string getCommandCategory() { return "Hypothesis Testing"; }
+ string getOutputFileNameTag(string, string);
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/kruskalwallis"; }
+ string getDescription() { return "Non-parametric method for testing whether samples originate from the same distribution."; }
+
+ struct groupRank {
+ string group;
+ double value;
+ double rank;
+ };
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+ void assignRank(vector<groupRank>&);
+ void assignValue(vector<groupRank>&);
+
+
+private:
+ string outputDir, sharedfile, groups;
+ bool abort;
+ set<string> labels;
+ vector<string> outputNames, Groups;
+ vector<int> counts;
+ vector<double> rankSums;
+ vector<double> rankMeans;
+
+
+
+ static bool comparevalue(const groupRank &a, const groupRank &b) { return a.value < b.value; }
+ static bool equalvalue(const groupRank &a, const groupRank &b) { return a.value == b.value; }
+ static bool comparerank(const groupRank &a, const groupRank &b) { return a.rank < b.rank; }
+ static bool equalrank(const groupRank &a, const groupRank &b) { return a.rank == b.rank; }
+ static bool equalgroup(const groupRank &a, const groupRank &b) { return a.group == b.group; }
+
+};
+
+#endif /* KRUSKALWALLISCOMMAND_H */
+
try {
CommandParameter pblast("blast", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pblast);
CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter plarge("large", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(plarge);
+ CommandParameter pcount("count", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pcount);
+ //CommandParameter plarge("large", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(plarge);
CommandParameter plength("length", "Number", "", "5", "", "", "",false,false); parameters.push_back(plength);
CommandParameter ppenalty("penalty", "Number", "", "0.10", "", "", "",false,false); parameters.push_back(ppenalty);
CommandParameter pcutoff("cutoff", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pcutoff);
if (namefile == "not open") { abort = true; }
else if (namefile == "not found") { namefile = ""; }
else { m->setNameFile(namefile); }
+
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { abort = true; }
+ else if (countfile == "not found") { countfile = ""; }
+ else { m->setCountTableFile(countfile); }
+
+ if (countfile != "" && namefile != "") { m->mothurOut("Cannot have both a name file and count file. Please use one or the other."); m->mothurOutEndLine(); abort = true; }
if ((blastfile == "")) { m->mothurOut("When executing a mgcluster command you must provide a blastfile."); m->mothurOutEndLine(); abort = true; }
list = new ListVector(nameMap->getListVector());
RAbundVector* rabund = NULL;
- if(large) {
- map<string, int> nameMapCounts = m->readNames(namefile);
- createRabund(nameMapCounts);
+ if(countfile != "") {
+ //map<string, int> nameMapCounts = m->readNames(namefile);
+ ct = new CountTable();
+ ct->readTable(countfile);
+ createRabund(ct, list);
rabund = &rav;
}else {
rabund = new RAbundVector(list->getRAbundVector());
//**********************************************************************************************************************
-void MGClusterCommand::createRabund(map<string, int> nameMapCounts){
+void MGClusterCommand::createRabund(CountTable* ct, ListVector* list){
try {
+ //vector<string> names = ct.getNamesOfSeqs();
+
+ //for ( int i; i < ct.getNumGroups(); i++ ) { rav.push_back( ct.getNumSeqs(names[i]) ); }
+ //return rav;
+
+ for(int i = 0; i < list->getNumBins(); i++) {
+ vector<string> binNames;
+ string bin = list->get(i);
+ m->splitAtComma(bin, binNames);
+ int total = 0;
+ for (int j = 0; j < binNames.size(); j++) {
+ total += ct->getNumSeqs(binNames[j]);
+ }
+ rav.push_back(total);
+ }
+
+
}
catch(exception& e) {
m->errorOut(e, "MGClusterCommand", "createRabund");
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