+vector<string> GetLineageCommand::setParameters(){
+ try {
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pname);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(ptaxonomy);
+ CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(palignreport);
+ CommandParameter ptaxon("taxon", "String", "", "", "", "", "",false,true); parameters.push_back(ptaxon);
+ CommandParameter pdups("dups", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pdups);
+ 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, "GetLineageCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string GetLineageCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The get.lineage command reads a taxonomy file and any of the following file types: fasta, name, group, list or alignreport file.\n";
+ helpString += "It outputs a file containing only the sequences from the taxonomy file that are from the taxon requested.\n";
+ helpString += "The get.lineage command parameters are taxon, fasta, name, group, list, taxonomy, alignreport and dups. You must provide taxonomy unless you have a valid current taxonomy file.\n";
+ helpString += "The dups parameter allows you to add the entire line from a name file if you add any name from the line. default=false. \n";
+ helpString += "The taxon parameter allows you to select the taxons you would like to get and is required.\n";
+ helpString += "You may enter your taxons with confidence scores, doing so will get only those sequences that belong to the taxonomy and whose cofidence scores is above the scores you give.\n";
+ helpString += "If they belong to the taxonomy and have confidences below those you provide the sequence will not be selected.\n";
+ helpString += "The get.lineage command should be in the following format: get.lineage(taxonomy=yourTaxonomyFile, taxon=yourTaxons).\n";
+ helpString += "Example get.lineage(taxonomy=amazon.silva.taxonomy, taxon=Bacteria;Firmicutes;Bacilli;Lactobacillales;).\n";
+ helpString += "Note: If you are running mothur in script mode you must wrap the taxon in ' characters so mothur will ignore the ; in the taxon.\n";
+ helpString += "Example get.lineage(taxonomy=amazon.silva.taxonomy, taxon='Bacteria;Firmicutes;Bacilli;Lactobacillales;').\n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string GetLineageCommand::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 == "fasta") { outputFileName = "pick" + m->getExtension(inputName); }
+ else if (type == "taxonomy") { outputFileName = "pick" + m->getExtension(inputName); }
+ else if (type == "name") { outputFileName = "pick" + m->getExtension(inputName); }
+ else if (type == "group") { outputFileName = "pick" + m->getExtension(inputName); }
+ else if (type == "list") { outputFileName = "pick" + m->getExtension(inputName); }
+ else if (type == "alignreport") { outputFileName = "pick.align.report"; }
+ 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, "GetLineageCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetLineageCommand::GetLineageCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["taxonomy"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ outputTypes["alignreport"] = tempOutNames;
+ outputTypes["list"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "GetLineageCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************