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/*
* optionparser.cpp
* Mothur
*
* Created by Sarah Westcott on 6/8/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "optionparser.h"
/***********************************************************************/
OptionParser::OptionParser(string option, vector<string> parametersAllowedByThisCommand) {
try {
m = MothurOut::getInstance();
current = CurrentFile::getInstance();
ValidParameters validParameter;
fillFileTypes(fileTypes);
if (option != "") {
string key, value;
//reads in parameters and values
while((option.find_first_of(',') != -1)) { //while there are parameters
util.splitAtComma(value, option);
util.splitAtEquals(key, value);
if ((key == "candidate") || (key == "query")) { key = "fasta"; }
if (key == "template") { key = "reference"; }
key = util.splitWhiteSpace(key).front();
//if value is wrapped in '' preserve spaces
if ((value[0] == '\'') && (value[(value.length()-1)] == '\'')) { value = value.substr(1); value = value.substr(0, (value.length()-1)); }
else { trimWhiteSpace(value); }
if (!validParameter.isValidParameter(key, parametersAllowedByThisCommand, value)) {} //ignore invalid parameters
else { parameters[key] = value; }
}
//in case there is no comma and to get last parameter after comma
util.splitAtEquals(key, option);
if ((key == "candidate") || (key == "query")) { key = "fasta"; }
if (key == "template") { key = "reference"; }
key = util.splitWhiteSpace(key).front();
//if value is wrapped in '' preserve spaces
if ((option[0] == '\'') && (option[(option.length()-1)] == '\'')) { option = option.substr(1); option = option.substr(0, (option.length()-1)); }
else { trimWhiteSpace(option); }
if (!validParameter.isValidParameter(key, parametersAllowedByThisCommand, option)) {} //ignore invalid parameters
else { parameters[key] = option; }
}
}
catch(exception& e) {
m->errorOut(e, "OptionParser", "OptionParser");
exit(1);
}
}
/***********************************************************************/
OptionParser::OptionParser(string option, map<string, string>& copy) {
try {
m = MothurOut::getInstance();
current = CurrentFile::getInstance();
fillFileTypes(fileTypes);
if (option != "") {
string key, value;
//reads in parameters and values
while((option.find_first_of(',') != -1)) { //while there are parameters
util.splitAtComma(value, option);
util.splitAtEquals(key, value);
if ((key == "candidate") || (key == "query")) { key = "fasta"; }
if (key == "template") { key = "reference"; }
key = util.splitWhiteSpace(key).front();
//if value is wrapped in '' preserve spaces
if ((value[0] == '\'') && (value[(value.length()-1)] == '\'')) { value = value.substr(1); value = value.substr(0, (value.length()-1)); }
else {
value = util.splitWhiteSpace(value).front();
}
parameters[key] = value;
}
//in case there is no comma and to get last parameter after comma
util.splitAtEquals(key, option);
if ((key == "candidate") || (key == "query")) { key = "fasta"; }
if (key == "template") { key = "reference"; }
key = util.splitWhiteSpace(key).front();
//if value is wrapped in '' preserve spaces
if ((option[0] == '\'') && (option[(option.length()-1)] == '\'')) { option = option.substr(1); option = option.substr(0, (option.length()-1)); }
else {
option = util.splitWhiteSpace(option).front();
}
parameters[key] = option;
}
copy = parameters;
}
catch(exception& e) {
m->errorOut(e, "OptionParser", "OptionParser");
exit(1);
}
}
/***********************************************************************/
map<string, string> OptionParser::getParameters() {
try {
//loop through parameters and look for "current" so you can return the appropriate file
//doing it here to avoid code duplication in each of the commands
map<string, string>::iterator it;
for (it = parameters.begin(); it != parameters.end();) {
if (it->second == "current") {
//look for file types
if (it->first == "fasta") {
it->second = current->getFastaFile();
}else if (it->first == "qfile") {
it->second = current->getQualFile();
}else if (it->first == "phylip") {
it->second = current->getPhylipFile();
}else if (it->first == "column") {
it->second = current->getColumnFile();
}else if (it->first == "list") {
it->second = current->getListFile();
}else if (it->first == "rabund") {
it->second = current->getRabundFile();
}else if (it->first == "clr") {
it->second = current->getCLRFile();
}else if (it->first == "sabund") {
it->second = current->getSabundFile();
}else if (it->first == "name") {
it->second = current->getNameFile();
}else if (it->first == "group") {
it->second = current->getGroupFile();
}else if (it->first == "order") {
it->second = current->getOrderFile();
}else if (it->first == "ordergroup") {
it->second = current->getOrderGroupFile();
}else if (it->first == "tree") {
it->second = current->getTreeFile();
}else if (it->first == "shared") {
it->second = current->getSharedFile();
}else if (it->first == "relabund") {
it->second = current->getRelAbundFile();
}else if (it->first == "design") {
it->second = current->getDesignFile();
}else if (it->first == "sff") {
it->second = current->getSFFFile();
}else if (it->first == "flow") {
it->second = current->getFlowFile();
}else if (it->first == "oligos") {
it->second = current->getOligosFile();
}else if (it->first == "accnos") {
it->second = current->getAccnosFile();
}else if (it->first == "taxonomy") {
it->second = current->getTaxonomyFile();
}else if (it->first == "constaxonomy") {
it->second = current->getConsTaxonomyFile();
}else if (it->first == "contigsreport") {
it->second = current->getContigsReportFile();
}else if (it->first == "biom") {
it->second = current->getBiomFile();
}else if (it->first == "count") {
it->second = current->getCountFile();
}else if (it->first == "summary") {
it->second = current->getSummaryFile();
}else if (it->first == "file") {
it->second = current->getFileFile();
}else if (it->first == "sample") {
it->second = current->getSampleFile();
}else {
m->mothurOut("[ERROR]: mothur does not save a current file for " + it->first); m->mothurOutEndLine();
}
if (it->second == "") { //no file was saved for that type, warn and remove from parameters
m->mothurOut("[WARNING]: no file was saved for " + it->first + " parameter.\n");
parameters.erase(it++);
}else {
m->mothurOut("Using " + it->second + " as input file for the " + it->first + " parameter.\n");
it++;
}
}else{ it++; }
}
vector<string> inputDirs = current->getInputDir();
if (inputDirs.size() != 0) {
for (it = parameters.begin(); it != parameters.end(); it++) {
if (fileTypes.count(it->first) != 0) {
string path = util.hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") {
string inputLocation = it->second;
util.checkSpecificLocations(inputLocation, inputDirs, "");
it->second = inputLocation;
}
}
}
}
return parameters;
}
catch(exception& e) {
m->errorOut(e, "OptionParser", "getParameters");
exit(1);
}
}
/***********************************************************************/
void OptionParser::fillFileTypes(set<string>& fileTypes) {
try {
fileTypes.insert("fasta");
fileTypes.insert("qfile");
fileTypes.insert("phylip");
fileTypes.insert("column");
fileTypes.insert("list");
fileTypes.insert("rabund");
fileTypes.insert("clr");
fileTypes.insert("sabund");
fileTypes.insert("name");
fileTypes.insert("group");
fileTypes.insert("order");
fileTypes.insert("ordergroup");
fileTypes.insert("tree");
fileTypes.insert("shared");
fileTypes.insert("relabund");
fileTypes.insert("design");
fileTypes.insert("sff");
fileTypes.insert("sfftxt");
fileTypes.insert("flow");
fileTypes.insert("oligos");
fileTypes.insert("accnos");
fileTypes.insert("taxonomy");
fileTypes.insert("constaxonomy");
fileTypes.insert("contigsreport");
fileTypes.insert("biom");
fileTypes.insert("count");
fileTypes.insert("summary");
fileTypes.insert("file");
fileTypes.insert("sample");
fileTypes.insert("list");
fileTypes.insert("rabund");
fileTypes.insert("clr");
fileTypes.insert("sabund");
fileTypes.insert("reference");
fileTypes.insert("conservation");
fileTypes.insert("quantile");
fileTypes.insert("reffasta");
fileTypes.insert("refcolumn");
fileTypes.insert("reflist");
fileTypes.insert("refname");
fileTypes.insert("refcount");
fileTypes.insert("reftaxonomy");
fileTypes.insert("axes");
fileTypes.insert("metadata");
fileTypes.insert("refname");
fileTypes.insert("repfasta");
fileTypes.insert("oldfasta");
fileTypes.insert("hard");
fileTypes.insert("alignreport");
fileTypes.insert("report");
fileTypes.insert("corraxes");
fileTypes.insert("otucorr");
fileTypes.insert("accnos");
fileTypes.insert("phylip1");
fileTypes.insert("phylip2");
fileTypes.insert("picrust");
fileTypes.insert("ffastq");
fileTypes.insert("rfastq");
fileTypes.insert("ffasta");
fileTypes.insert("rfasta");
fileTypes.insert("fqfile");
fileTypes.insert("rqfile");
fileTypes.insert("findex");
fileTypes.insert("rindex");
fileTypes.insert("error");
fileTypes.insert("xml");
fileTypes.insert("ecoli");
fileTypes.insert("map");
fileTypes.insert("lookup");
fileTypes.insert("project");
fileTypes.insert("mimark");
fileTypes.insert("vsearch");
fileTypes.insert("blast");
fileTypes.insert("uchime");
fileTypes.insert("prefetch");
fileTypes.insert("fasterq-dump");
fileTypes.insert("input");
//uchime, vsearch, prefetch and fasterq-dump are not included
}
catch(exception& e) {
m->errorOut(e, "OptionParser", "fillFileTypes");
exit(1);
}
}
/***********************************************************************/
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