optionparser.cpp

   1 /*
   2  *  optionparser.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 6/8/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "optionparser.h"
  11
  12 /***********************************************************************/
  13
  14 OptionParser::OptionParser(string option) {
  15         try {
  16                 m = MothurOut::getInstance();
  17                 if (option != "") {
  18
  19                         string key, value;
  20                         //reads in parameters and values
  21                         while((option.find_first_of(',') != -1)) {  //while there are parameters
  22                                 m->splitAtComma(value, option);
  23                                 m->splitAtEquals(key, value);
  24                                 if ((key == "candidate") || (key == "query")) { key = "fasta"; }
  25                                 if (key == "template") { key = "reference"; }
  26                                 parameters[key] = value;
  27                         }
  28
  29                         //in case there is no comma and to get last parameter after comma
  30                         m->splitAtEquals(key, option);
  31                         if ((key == "candidate") || (key == "query")) { key = "fasta"; }
  32                         if (key == "template") { key = "reference"; }
  33                         parameters[key] = option;
  34                 }
  35         }
  36         catch(exception& e) {
  37                 m->errorOut(e, "OptionParser", "OptionParser");
  38                 exit(1);
  39         }
  40 }
  41
  42 /***********************************************************************/
  43
  44 map<string, string> OptionParser::getParameters() {
  45         try {
  46
  47                 //loop through parameters and look for "current" so you can return the appropriate file
  48                 //doing it here to avoid code duplication in each of the commands
  49
  50                 map<string, string>::iterator it;
  51                 for (it = parameters.begin(); it != parameters.end();) {
  52
  53                         if (it->second == "current") {
  54
  55                                 //look for file types
  56                                 if (it->first == "fasta") {
  57                                         it->second = m->getFastaFile();
  58                                 }else if (it->first == "qfile") {
  59                                         it->second = m->getQualFile();
  60                                 }else if (it->first == "phylip") {
  61                                         it->second = m->getPhylipFile();
  62                                 }else if (it->first == "column") {
  63                                         it->second = m->getColumnFile();
  64                                 }else if (it->first == "list") {
  65                                         it->second = m->getListFile();
  66                                 }else if (it->first == "rabund") {
  67                                         it->second = m->getRabundFile();
  68                                 }else if (it->first == "sabund") {
  69                                         it->second = m->getSabundFile();
  70                                 }else if (it->first == "name") {
  71                                         it->second = m->getNameFile();
  72                                 }else if (it->first == "group") {
  73                                         it->second = m->getGroupFile();
  74                                 }else if (it->first == "order") {
  75                                         it->second = m->getOrderFile();
  76                                 }else if (it->first == "ordergroup") {
  77                                         it->second = m->getOrderGroupFile();
  78                                 }else if (it->first == "tree") {
  79                                         it->second = m->getTreeFile();
  80                                 }else if (it->first == "shared") {
  81                                         it->second = m->getSharedFile();
  82                                 }else if (it->first == "relabund") {
  83                                         it->second = m->getRelAbundFile();
  84                                 }else if (it->first == "design") {
  85                                         it->second = m->getDesignFile();
  86                                 }else if (it->first == "sff") {
  87                                         it->second = m->getSFFFile();
  88                                 }else if (it->first == "oligos") {
  89                                         it->second = m->getOligosFile();
  90                                 }else if (it->first == "accnos") {
  91                                         it->second = m->getAccnosFile();
  92                                 }else if (it->first == "taxonomy") {
  93                                         it->second = m->getTaxonomyFile();
  94                 }else if (it->first == "biom") {
  95                         it->second = m->getBiomFile();
  96                                 }else {
  97                                         m->mothurOut("[ERROR]: mothur does not save a current file for " + it->first); m->mothurOutEndLine();
  98                                 }
  99
 100                                 if (it->second == "") { //no file was saved for that type, warn and remove from parameters
 101                                         m->mothurOut("[WARNING]: no file was saved for " + it->first + " parameter."); m->mothurOutEndLine();
 102                                         parameters.erase(it++);
 103                                 }else {
 104                                         m->mothurOut("Using " + it->second + " as input file for the " + it->first + " parameter."); m->mothurOutEndLine();
 105                                         it++;
 106                                 }
 107                         }else{ it++; }
 108                 }
 109
 110                 return parameters;
 111         }
 112         catch(exception& e) {
 113                 m->errorOut(e, "OptionParser", "getParameters");
 114                 exit(1);
 115         }
 116 }
 117
 118 /***********************************************************************/
 119 //pass a vector of filenames that may match the current namefile.
 120 //this function will look at each one, if the rootnames match, mothur will warn
 121 //the user that they may have neglected to provide a namefile.
 122 //stops when it finds a match.
 123 bool OptionParser::getNameFile(vector<string> files) {
 124         try {
 125                 string namefile = m->getNameFile();
 126                 bool match = false;
 127
 128                 if ((namefile != "")&&(!m->mothurCalling)) {
 129                         string temp = m->getRootName(m->getSimpleName(namefile));
 130                         vector<string> rootName;
 131                         m->splitAtChar(temp, rootName, '.');
 132
 133                         for (int i = 0; i < files.size(); i++) {
 134                                 temp = m->getRootName(m->getSimpleName(files[i]));
 135                                 vector<string> root;
 136                                 m->splitAtChar(temp, root, '.');
 137
 138                                 int smallest = rootName.size();
 139                                 if (root.size() < smallest) { smallest = root.size(); }
 140
 141                                 int numMatches = 0;
 142                                 for(int j = 0; j < smallest; j++) {
 143                                         if (root[j] == rootName[j]) { numMatches++; }
 144                                 }
 145
 146                                 if (smallest > 0) {
 147                                         if ((numMatches >= (smallest-2)) && (root[0] == rootName[0])) {
 148                                                 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] + ".");
 149                                                 m->mothurOutEndLine();
 150                                                 match = true;
 151                                                 break;
 152                                         }
 153                                 }
 154                         }
 155
 156                 }
 157
 158
 159                 return match;
 160         }
 161         catch(exception& e) {
 162                 m->errorOut(e, "OptionParser", "getNameFile");
 163                 exit(1);
 164         }
 165 }
 166
 167
 168 /***********************************************************************/