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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) {
try {
m = MothurOut::getInstance();
if (option != "") {
string key, value;
//reads in parameters and values
while((option.find_first_of(',') != -1)) { //while there are parameters
m->splitAtComma(value, option);
m->splitAtEquals(key, value);
if ((key == "candidate") || (key == "query")) { key = "fasta"; }
if (key == "template") { key = "reference"; }
parameters[key] = value;
}
//in case there is no comma and to get last parameter after comma
m->splitAtEquals(key, option);
if ((key == "candidate") || (key == "query")) { key = "fasta"; }
if (key == "template") { key = "reference"; }
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();
if (option != "") {
string key, value;
//reads in parameters and values
while((option.find_first_of(',') != -1)) { //while there are parameters
m->splitAtComma(value, option);
m->splitAtEquals(key, value);
if ((key == "candidate") || (key == "query")) { key = "fasta"; }
if (key == "template") { key = "reference"; }
parameters[key] = value;
}
//in case there is no comma and to get last parameter after comma
m->splitAtEquals(key, option);
if ((key == "candidate") || (key == "query")) { key = "fasta"; }
if (key == "template") { key = "reference"; }
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 = m->getFastaFile();
}else if (it->first == "qfile") {
it->second = m->getQualFile();
}else if (it->first == "phylip") {
it->second = m->getPhylipFile();
}else if (it->first == "column") {
it->second = m->getColumnFile();
}else if (it->first == "list") {
it->second = m->getListFile();
}else if (it->first == "rabund") {
it->second = m->getRabundFile();
}else if (it->first == "sabund") {
it->second = m->getSabundFile();
}else if (it->first == "name") {
it->second = m->getNameFile();
}else if (it->first == "group") {
it->second = m->getGroupFile();
}else if (it->first == "order") {
it->second = m->getOrderFile();
}else if (it->first == "ordergroup") {
it->second = m->getOrderGroupFile();
}else if (it->first == "tree") {
it->second = m->getTreeFile();
}else if (it->first == "shared") {
it->second = m->getSharedFile();
}else if (it->first == "relabund") {
it->second = m->getRelAbundFile();
}else if (it->first == "design") {
it->second = m->getDesignFile();
}else if (it->first == "sff") {
it->second = m->getSFFFile();
}else if (it->first == "flow") {
it->second = m->getFlowFile();
}else if (it->first == "oligos") {
it->second = m->getOligosFile();
}else if (it->first == "accnos") {
it->second = m->getAccnosFile();
}else if (it->first == "taxonomy") {
it->second = m->getTaxonomyFile();
}else if (it->first == "biom") {
it->second = m->getBiomFile();
}else if (it->first == "count") {
it->second = m->getCountTableFile();
}else if (it->first == "summary") {
it->second = m->getSummaryFile();
}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."); m->mothurOutEndLine();
parameters.erase(it++);
}else {
m->mothurOut("Using " + it->second + " as input file for the " + it->first + " parameter."); m->mothurOutEndLine();
it++;
}
}else{ it++; }
}
return parameters;
}
catch(exception& e) {
m->errorOut(e, "OptionParser", "getParameters");
exit(1);
}
}
/***********************************************************************/
//pass a vector of filenames that may match the current namefile.
//this function will look at each one, if the rootnames match, mothur will warn
//the user that they may have neglected to provide a namefile.
//stops when it finds a match.
bool OptionParser::getNameFile(vector<string> files) {
try {
string namefile = m->getNameFile();
bool match = false;
if ((namefile != "")&&(!m->mothurCalling)) {
string temp = m->getRootName(m->getSimpleName(namefile));
vector<string> rootName;
m->splitAtChar(temp, rootName, '.');
for (int i = 0; i < files.size(); i++) {
temp = m->getRootName(m->getSimpleName(files[i]));
vector<string> root;
m->splitAtChar(temp, root, '.');
int smallest = rootName.size();
if (root.size() < smallest) { smallest = root.size(); }
int numMatches = 0;
for(int j = 0; j < smallest; j++) {
if (root[j] == rootName[j]) { numMatches++; }
}
if (smallest > 0) {
if ((numMatches >= (smallest-2)) && (root[0] == rootName[0])) {
m->mothurOut("[WARNING]: This command can take a namefile and you did not provide one. The current namefile is " + namefile + " which seems to match " + files[i] + ".");
m->mothurOutEndLine();
match = true;
break;
}
}
}
}
return match;
}
catch(exception& e) {
m->errorOut(e, "OptionParser", "getNameFile");
exit(1);
}
}
/***********************************************************************/
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