+++ /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::setParameters(){
- try {
- CommandParameter pclear("clear", "String", "", "", "", "", "",false,false); parameters.push_back(pclear);
- 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, "GetCurrentCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string GetCurrentCommand::getHelpString(){
- try {
- string helpString = "";
- helpString += "The get.current command outputs the current files saved by mothur.\n";
- helpString += "The get.current command has one parameter: clear.\n";
- helpString += "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";
- helpString += "The get.current command should be in the following format: \n";
- helpString += "get.current() or get.current(clear=fasta-name-accnos)\n";
- return helpString;
- }
- catch(exception& e) {
- m->errorOut(e, "GetCurrentCommand", "getHelpString");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-GetCurrentCommand::GetCurrentCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- }
- catch(exception& e) {
- m->errorOut(e, "GetCurrentCommand", "GetCurrentCommand");
- 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 if(option == "citation") { citation(); abort = true; calledHelp = true;}
-
- else {
- vector<string> myArray = setParameters();
-
- 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);
- }
-}
-//**********************************************************************************************************************
-
-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] == "flow") {
- m->setFlowFile("");
- }else if (types[i] == "biom") {
- m->setBiomFile("");
- }else if (types[i] == "processors") {
- m->setProcessors("1");
- }else if (types[i] == "all") {
- m->clearCurrentFiles();
- }else {
- m->mothurOut("[ERROR]: mothur does not save a current file for " + types[i]); m->mothurOutEndLine();
- }
- }
- }
-
- if (m->hasCurrentFiles()) {
- 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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