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/*
* GetlabelCommand.cpp
* Mothur
*
* Created by Thomas Ryabin on 1/30/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "getlabelcommand.h"
//**********************************************************************************************************************
vector<string> GetlabelCommand::setParameters(){
try {
CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false, true); parameters.push_back(plist);
CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false, true); parameters.push_back(prabund);
CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false, true); parameters.push_back(psabund);
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, "GetlabelCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
GetlabelCommand::GetlabelCommand(){
try {
abort = true; calledHelp = true;
setParameters();
}
catch(exception& e) {
m->errorOut(e, "GetlabelCommand", "CollectCommand");
exit(1);
}
}
//**********************************************************************************************************************
string GetlabelCommand::getHelpString(){
try {
string helpString = "";
helpString += "The get.label command parameters are list, sabund and rabund file. \n";
helpString += "The get.label command should be in the following format: \n";
helpString += "get.label()\n";
helpString += "Example get.label().\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "GetlabelCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
GetlabelCommand::GetlabelCommand(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();
map<string,string>::iterator it;
ValidParameters validParameter;
//check to make sure all parameters are valid for command
for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
else {
string path;
it = parameters.find("rabund");
//user has given a template file
if(it != parameters.end()){
path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["rabund"] = inputDir + it->second; }
}
it = parameters.find("sabund");
//user has given a template file
if(it != parameters.end()){
path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["sabund"] = inputDir + it->second; }
}
it = parameters.find("list");
//user has given a template file
if(it != parameters.end()){
path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["list"] = inputDir + it->second; }
}
}
//check for required parameters
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not open") { listfile = ""; abort = true; }
else if (listfile == "not found") { listfile = ""; }
else { format = "list"; inputfile = listfile; m->setListFile(listfile); }
sabundfile = validParameter.validFile(parameters, "sabund", true);
if (sabundfile == "not open") { sabundfile = ""; abort = true; }
else if (sabundfile == "not found") { sabundfile = ""; }
else { format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
rabundfile = validParameter.validFile(parameters, "rabund", true);
if (rabundfile == "not open") { rabundfile = ""; abort = true; }
else if (rabundfile == "not found") { rabundfile = ""; }
else { format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
if ((listfile == "") && (rabundfile == "") && (sabundfile == "")) {
//is there are current file available for any of these?
//give priority to list, then rabund, then sabund
//if there is a current shared file, use it
listfile = m->getListFile();
if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
else {
rabundfile = m->getRabundFile();
if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
else {
sabundfile = m->getSabundFile();
if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
else {
m->mothurOut("No valid current files. You must provide a list, sabund or rabund file."); m->mothurOutEndLine();
abort = true;
}
}
}
}
}
}
catch(exception& e) {
m->errorOut(e, "GetlabelCommand", "GetlabelCommand");
exit(1);
}
}
//**********************************************************************************************************************
int GetlabelCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
InputData* input = new InputData(inputfile, format);
OrderVector* order = input->getOrderVector();
string label = order->getLabel();
while (order != NULL) {
if (m->control_pressed) { delete input; delete order; return 0; }
label = order->getLabel();
m->mothurOut(label); m->mothurOutEndLine();
delete order;
order = input->getOrderVector();
}
delete input;
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetlabelCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
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