--- /dev/null
+//
+// getmimarkspackagecommand.cpp
+// Mothur
+//
+// Created by Sarah Westcott on 3/25/14.
+// Copyright (c) 2014 Schloss Lab. All rights reserved.
+//
+
+#include "getmimarkspackagecommand.h"
+
+//**********************************************************************************************************************
+vector<string> GetMIMarksPackageCommand::setParameters(){
+ try {
+ //files that have dependancies
+ CommandParameter pgroup("group", "InputTypes", "", "", "groupOligos", "none", "none","",false,false); parameters.push_back(pgroup);
+ CommandParameter poligos("oligos", "InputTypes", "", "", "groupOligos", "none", "none","",false,false); parameters.push_back(poligos);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetMIMarksPackageCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string GetMIMarksPackageCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The get.mimarkspackage command creates a mimarks package form with your groups. The required fields are flagged with * characters.\n";
+ helpString += "Further documentation on the different packages and required formats can be found here, http://www.mothur.org/wiki/MIMarks_Data_Packages.\n";
+ helpString += "The get.mimarkspackage command parameters are: oligos, group and package. oligos or group is required.\n";
+ helpString += "The oligos parameter is used to provide your oligos file so mothur can extract your group names.\n";
+ helpString += "The group parameter is used to provide your group file so mothur can extract your group names.\n";
+ helpString += "The package parameter is used to select the mimarks package you would like to use. Default=???\n";
+ helpString += "The get.mimarkspackage command should be in the following format: get.mimarkspackage(oligos=yourOligosFile, package=yourPackage)\n";
+ helpString += "get.mimarkspackage(oligos=GQY1XT001.oligos, package=???)\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetMIMarksPackageCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string GetMIMarksPackageCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "tsv") { pattern = "[filename],tsv"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetMIMarksPackageCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetMIMarksPackageCommand::GetMIMarksPackageCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["tsv"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetMIMarksPackageCommand", "GetMIMarksPackageCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetMIMarksPackageCommand::GetMIMarksPackageCommand(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 {
+ //valid paramters for this command
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string,string>::iterator it;
+ //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; }
+ }
+
+ vector<string> tempOutNames;
+ outputTypes["tsv"] = 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("oligos");
+ //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["oligos"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("group");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["group"] = inputDir + it->second; }
+ }
+
+ }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { groupfile = ""; abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; }
+ else { m->setGroupFile(groupfile); }
+
+ oligosfile = validParameter.validFile(parameters, "oligos", true);
+ if (oligosfile == "not found") { oligosfile = ""; }
+ else if(oligosfile == "not open") { abort = true; }
+ else { m->setOligosFile(oligosfile); }
+
+ if ((groupfile != "") && (oligosfile != "")) {
+ m->mothurOut("[ERROR]: You may not use a group file and an oligos file, only one."); m->mothurOutEndLine(); abort = true;
+ }
+
+ if ((groupfile == "") && (oligosfile == "")) {
+ oligosfile = m->getOligosFile();
+ if (oligosfile != "") { m->mothurOut("Using " + oligosfile + " as input file for the oligos parameter."); m->mothurOutEndLine(); }
+ else {
+ groupfile = m->getGroupFile();
+ if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("[ERROR]: You must provide groupfile or oligos file for the get.mimarkspackage command."); m->mothurOutEndLine(); abort = true;
+ }
+ }
+ }
+
+ package = validParameter.validFile(parameters, "package", false); if (package == "not found") { package = "package"; }
+ //if (!checkCasesPackage(package)) { abort = true; } //error message in function
+
+ //turn _ to spaces mothur's work around
+ for (int i = 0; i < package.length(); i++) { if (package[i] == '_') { package[i] = ' '; } }
+
+
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetMIMarksPackageCommand", "GetMIMarksPackageCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int GetMIMarksPackageCommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+
+
+
+
+ //output files created by command
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetMIMarksPackageCommand", "GetMIMarksPackageCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+
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