+//**********************************************************************************************************************
+vector<string> DeconvoluteCommand::setParameters(){
+ try {
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-name",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","name",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","count",false,false,true); parameters.push_back(pcount);
+ 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, "DeconvoluteCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string DeconvoluteCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The unique.seqs command reads a fastafile and creates a name or count file.\n";
+ helpString += "It creates a file where the first column is the groupname and the second column is a list of sequence names who have the same sequence. \n";
+ helpString += "If the sequence is unique the second column will just contain its name. \n";
+ helpString += "The unique.seqs command parameters are fasta and name. fasta is required, unless there is a valid current fasta file.\n";
+ helpString += "The unique.seqs command should be in the following format: \n";
+ helpString += "unique.seqs(fasta=yourFastaFile) \n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeconvoluteCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string DeconvoluteCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "fasta") { pattern = "[filename],unique,[extension]"; }
+ else if (type == "name") { pattern = "[filename],names-[filename],[tag],names"; }
+ else if (type == "count") { pattern = "[filename],count_table-[filename],[tag],count_table"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeconvoluteCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+DeconvoluteCommand::DeconvoluteCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand");
+ exit(1);
+ }
+}