+}
+//**********************************************************************************************************************
+string UnifracWeightedCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The unifrac.weighted command parameters are tree, group, name, groups, iters, distance, processors, root and random. tree parameter is required unless you have valid current tree file.\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 += "The group names are separated by dashes. The iters parameter allows you to specify how many random trees you would like compared to your tree.\n";
+ helpString += "The distance parameter allows you to create a distance file from the results. The default is false.\n";
+ helpString += "The random parameter allows you to shut off the comparison to random trees. The default is false, meaning don't compare your trees with randomly generated trees.\n";
+ helpString += "The root parameter allows you to include the entire root in your calculations. The default is false, meaning stop at the root for this comparision instead of the root of the entire tree.\n";
+ helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
+ helpString += "The unifrac.weighted command should be in the following format: unifrac.weighted(groups=yourGroups, iters=yourIters).\n";
+ helpString += "Example unifrac.weighted(groups=A-B-C, iters=500).\n";
+ helpString += "The default value for groups is all the groups in your groupfile, and iters is 1000.\n";
+ helpString += "The unifrac.weighted command output two files: .weighted and .wsummary their descriptions are in the manual.\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, "UnifracWeightedCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+UnifracWeightedCommand::UnifracWeightedCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["weighted"] = tempOutNames;
+ outputTypes["wsummary"] = tempOutNames;
+ outputTypes["phylip"] = tempOutNames;
+ outputTypes["column"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "UnifracWeightedCommand", "UnifracWeightedCommand");
+ exit(1);
+ }
+}
+
+/***********************************************************/
+UnifracWeightedCommand::UnifracWeightedCommand(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 (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["weighted"] = tempOutNames;
+ outputTypes["wsummary"] = tempOutNames;
+ outputTypes["phylip"] = tempOutNames;
+ outputTypes["column"] = 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("tree");
+ //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["tree"] = 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; }
+ }
+
+ it = parameters.find("name");
+ //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["name"] = inputDir + it->second; }
+ }
+ }
+
+ m->runParse = true;
+ m->clearGroups();
+ m->clearAllGroups();
+ m->Treenames.clear();
+ m->names.clear();
+
+ //check for required parameters
+ treefile = validParameter.validFile(parameters, "tree", true);
+ if (treefile == "not open") { treefile = ""; abort = true; }
+ else if (treefile == "not found") { //if there is a current design file, use it
+ treefile = m->getTreeFile();
+ if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current tree file and the tree parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setTreeFile(treefile); }
+
+ //check for required parameters
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; }
+ else { m->setGroupFile(groupfile); }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { namefile = ""; abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
+
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
+
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ m->splitAtDash(groups, Groups);
+ m->setGroups(Groups);
+ }
+
+ itersString = validParameter.validFile(parameters, "iters", false); if (itersString == "not found") { itersString = "1000"; }
+ m->mothurConvert(itersString, iters);
+
+ string temp = validParameter.validFile(parameters, "distance", false);
+ if (temp == "not found") { phylip = false; outputForm = ""; }
+ else{
+ if ((temp == "lt") || (temp == "column") || (temp == "square")) { phylip = true; outputForm = temp; }
+ else { m->mothurOut("Options for distance are: lt, square, or column. Using lt."); m->mothurOutEndLine(); phylip = true; outputForm = "lt"; }
+ }
+
+ temp = validParameter.validFile(parameters, "random", false); if (temp == "not found") { temp = "F"; }
+ random = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "root", false); if (temp == "not found") { temp = "F"; }
+ includeRoot = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ m->mothurConvert(temp, processors);
+
+ if (!random) { iters = 0; } //turn off random calcs
+
+ if (namefile == "") {
+ vector<string> files; files.push_back(treefile);
+ parser.getNameFile(files);
+ }
+ }
+
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "UnifracWeightedCommand", "UnifracWeightedCommand");