From 013ef8f1507c29ef442e47eb3538ecdd1ef6ddef Mon Sep 17 00:00:00 2001 From: Kathryn Iverson Date: Tue, 26 Jun 2012 15:43:31 -0400 Subject: [PATCH] added kruskalwallis command --- kruskalwalliscommand.cpp | 192 +++++++++++++++++++++++++++++++++++++++ kruskalwalliscommand.h | 42 +++++++++ 2 files changed, 234 insertions(+) create mode 100644 kruskalwalliscommand.cpp create mode 100644 kruskalwalliscommand.h diff --git a/kruskalwalliscommand.cpp b/kruskalwalliscommand.cpp new file mode 100644 index 0000000..263b1c5 --- /dev/null +++ b/kruskalwalliscommand.cpp @@ -0,0 +1,192 @@ +/* + * File: kruskalwalliscommand.cpp + * Author: kiverson + * + * Created on June 26, 2012, 11:06 AM + */ +#include "kruskalwalliscommand.h" + +//********************************************************************************************************************** +class groupRank { +public: + string group; + double value; + double rank; +}; +//********************************************************************************************************************** +vector KruskalWallisCommand::setParameters(){ + try { + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + + vector 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 >::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 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 myArray = setParameters(); + + OptionParser parser(option); + map parameters = parser.getParameters(); + map::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; } + } + + + //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 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; } + + //math goes here + + int N; + double ss, H; + double tmp = 0.0; + + //merge all groups into a vector + //rank function here + + //test statistic + for (int i=0;ierrorOut(e, "KruskalWallisCommand", "execute"); + exit(1); + } +} +//********************************************************************************************************************** +multimap KruskalWallisCommand::getRank(vector vec) { + try { + multimap rankMap; + double rank = 1; + double previous; + double tie = 0.0; + int tiecount = 0; + + sort (vec.begin(), vec.end()); + + for (int i=0;ierrorOut(e, "KruskalWallisCommand", "getRank"); + exit(1); + } + +} +//********************************************************************************************************************** + +//********************************************************************************************************************** +//********************************************************************************************************************** +//********************************************************************************************************************** \ No newline at end of file diff --git a/kruskalwalliscommand.h b/kruskalwalliscommand.h new file mode 100644 index 0000000..7e52613 --- /dev/null +++ b/kruskalwalliscommand.h @@ -0,0 +1,42 @@ +/* + * File: kruskalwalliscommand.h + * Author: kiverson + * + * Created on June 26, 2012, 11:07 AM + */ + +#ifndef KRUSKALWALLISCOMMAND_H +#define KRUSKALWALLISCOMMAND_H + +#include "command.hpp" + +class KruskalWallisCommand : public Command { + +public: + + KruskalWallisCommand(string); + KruskalWallisCommand(); + ~KruskalWallisCommand(){} + + vector 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."; } + + int execute(); + void help() { m->mothurOut(getHelpString()); } + multimap getRank(vector); + +private: + string outputDir; + vector counts; + vector rankSums; + vector rankMeans; + +}; + +#endif /* KRUSKALWALLISCOMMAND_H */ + -- 2.39.2