--- /dev/null
+/*
+ * getcurrentcommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 3/16/11.
+ * Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "getcurrentcommand.h"
+
+
+//**********************************************************************************************************************
+vector<string> GetCurrentCommand::getValidParameters(){
+ try {
+ string Array[] = {"outputdir","inputdir","clear"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetCurrentCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetCurrentCommand::GetCurrentCommand(){
+ try {
+ abort = true; calledHelp = true;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetCurrentCommand", "GetCurrentCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> GetCurrentCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetCurrentCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> GetCurrentCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetCurrentCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetCurrentCommand::GetCurrentCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"outputdir","inputdir","clear"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ 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; }
+ }
+
+ clearTypes = validParameter.validFile(parameters, "clear", false);
+ if (clearTypes == "not found") { clearTypes = ""; }
+ else { m->splitAtDash(clearTypes, types); }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetCurrentCommand", "GetCurrentCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+void GetCurrentCommand::help(){
+ try {
+ m->mothurOut("The get.current command outputs the current files saved by mothur.\n");
+ m->mothurOut("The get.current command has one parameter: clear.\n");
+ m->mothurOut("The clear paramter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n");
+ m->mothurOut("The get.current command should be in the following format: \n");
+ m->mothurOut("get.current() or get.current(clear=fasta-name-accnos)\n");
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetCurrentCommand", "help");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+GetCurrentCommand::~GetCurrentCommand(){}
+//**********************************************************************************************************************
+
+int GetCurrentCommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ //user wants to clear a type
+ if (types.size() != 0) {
+ for (int i = 0; i < types.size(); i++) {
+
+ if (m->control_pressed) { break; }
+
+ //look for file types
+ if (types[i] == "fasta") {
+ m->setFastaFile("");
+ }else if (types[i] == "qfile") {
+ m->setQualFile("");
+ }else if (types[i] == "phylip") {
+ m->setPhylipFile("");
+ }else if (types[i] == "column") {
+ m->setColumnFile("");
+ }else if (types[i] == "list") {
+ m->setListFile("");
+ }else if (types[i] == "rabund") {
+ m->setRabundFile("");
+ }else if (types[i] == "sabund") {
+ m->setSabundFile("");
+ }else if (types[i] == "name") {
+ m->setNameFile("");
+ }else if (types[i] == "group") {
+ m->setGroupFile("");
+ }else if (types[i] == "order") {
+ m->setOrderFile("");
+ }else if (types[i] == "ordergroup") {
+ m->setOrderGroupFile("");
+ }else if (types[i] == "tree") {
+ m->setTreeFile("");
+ }else if (types[i] == "shared") {
+ m->setSharedFile("");
+ }else if (types[i] == "relabund") {
+ m->setRelAbundFile("");
+ }else if (types[i] == "design") {
+ m->setDesignFile("");
+ }else if (types[i] == "sff") {
+ m->setSFFFile("");
+ }else if (types[i] == "oligos") {
+ m->setOligosFile("");
+ }else if (types[i] == "accnos") {
+ m->setAccnosFile("");
+ }else if (types[i] == "taxonomy") {
+ m->setTaxonomyFile("");
+ }else if (types[i] == "all") {
+ m->clearCurrentFiles();
+ }else {
+ m->mothurOut("[ERROR]: mothur does not save a current file for " + types[i]); m->mothurOutEndLine();
+ }
+ }
+ }
+
+ m->mothurOutEndLine(); m->mothurOut("Current files saved by mothur:"); m->mothurOutEndLine();
+ m->printCurrentFiles();
+
+ return 0;
+ }
+
+ catch(exception& e) {
+ m->errorOut(e, "GetCurrentCommand", "execute");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+
+
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