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/*
* 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 parameter 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; }
cFactory = CommandFactory::getInstance();
//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] == "count") {
m->setCountTableFile("");
}else if (types[i] == "summary") {
m->setSummaryFile("");
}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();
}
string inputDir = cFactory->getInputDir();
if (inputDir != "") {
m->mothurOutEndLine(); m->mothurOut("Current input directory saved by mothur: " + inputDir); m->mothurOutEndLine();
}
string outputDir = cFactory->getOutputDir();
if (outputDir != "") {
m->mothurOutEndLine(); m->mothurOut("Current output directory saved by mothur: " + outputDir); m->mothurOutEndLine();
}
string defaultPath = m->getDefaultPath();
if (defaultPath != "") {
m->mothurOutEndLine(); m->mothurOut("Current default directory saved by mothur: " + defaultPath); m->mothurOutEndLine();
}
string temp = "./";
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
#else
temp = ".\\";
#endif
temp = m->getFullPathName(temp);
m->mothurOutEndLine(); m->mothurOut("Current working directory: " + temp); m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetCurrentCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
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