+++ /dev/null
-/*
- * 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);
- }
-}
-
-/***********************************************************************/
-
-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 == "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 {
- 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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