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 OptionParser::OptionParser(string option, map<string, string>& copy) {
  44         try {
  45                 m = MothurOut::getInstance();
  46                 if (option != "") {
  47
  48                         string key, value;
  49                         //reads in parameters and values
  50                         while((option.find_first_of(',') != -1)) {  //while there are parameters
  51                                 m->splitAtComma(value, option);
  52                                 m->splitAtEquals(key, value);
  53                                 if ((key == "candidate") || (key == "query")) { key = "fasta"; }
  54                                 if (key == "template") { key = "reference"; }
  55                                 parameters[key] = value;
  56                         }
  57
  58                         //in case there is no comma and to get last parameter after comma
  59                         m->splitAtEquals(key, option);
  60                         if ((key == "candidate") || (key == "query")) { key = "fasta"; }
  61                         if (key == "template") { key = "reference"; }
  62                         parameters[key] = option;
  63                 }
  64
  65         copy = parameters;
  66         }
  67         catch(exception& e) {
  68                 m->errorOut(e, "OptionParser", "OptionParser");
  69                 exit(1);
  70         }
  71 }
  72 /***********************************************************************/
  73
  74 map<string, string> OptionParser::getParameters() {
  75         try {
  76
  77                 //loop through parameters and look for "current" so you can return the appropriate file
  78                 //doing it here to avoid code duplication in each of the commands
  79
  80
  81             map<string, string>::iterator it;
  82             for (it = parameters.begin(); it != parameters.end();) {
  83
  84                 if (it->second == "current") {
  85
  86                     //look for file types
  87                     if (it->first == "fasta") {
  88                         it->second = m->getFastaFile();
  89                     }else if (it->first == "qfile") {
  90                         it->second = m->getQualFile();
  91                     }else if (it->first == "phylip") {
  92                         it->second = m->getPhylipFile();
  93                     }else if (it->first == "column") {
  94                         it->second = m->getColumnFile();
  95                     }else if (it->first == "list") {
  96                         it->second = m->getListFile();
  97                     }else if (it->first == "rabund") {
  98                         it->second = m->getRabundFile();
  99                     }else if (it->first == "sabund") {
 100                         it->second = m->getSabundFile();
 101                     }else if (it->first == "name") {
 102                         it->second = m->getNameFile();
 103                     }else if (it->first == "group") {
 104                         it->second = m->getGroupFile();
 105                     }else if (it->first == "order") {
 106                         it->second = m->getOrderFile();
 107                     }else if (it->first == "ordergroup") {
 108                         it->second = m->getOrderGroupFile();
 109                     }else if (it->first == "tree") {
 110                         it->second = m->getTreeFile();
 111                     }else if (it->first == "shared") {
 112                         it->second = m->getSharedFile();
 113                     }else if (it->first == "relabund") {
 114                         it->second = m->getRelAbundFile();
 115                     }else if (it->first == "design") {
 116                         it->second = m->getDesignFile();
 117                     }else if (it->first == "sff") {
 118                         it->second = m->getSFFFile();
 119                     }else if (it->first == "flow") {
 120                             it->second = m->getFlowFile();
 121                     }else if (it->first == "oligos") {
 122                         it->second = m->getOligosFile();
 123                     }else if (it->first == "accnos") {
 124                         it->second = m->getAccnosFile();
 125                     }else if (it->first == "taxonomy") {
 126                         it->second = m->getTaxonomyFile();
 127                     }else if (it->first == "biom") {
 128                         it->second = m->getBiomFile();
 129                     }else if (it->first == "count") {
 130                             it->second = m->getCountTableFile();
 131                     }else if (it->first == "summary") {
 132                             it->second = m->getSummaryFile();
 133                     }else {
 134                         m->mothurOut("[ERROR]: mothur does not save a current file for " + it->first); m->mothurOutEndLine();
 135                     }
 136
 137                     if (it->second == "") { //no file was saved for that type, warn and remove from parameters
 138                         m->mothurOut("[WARNING]: no file was saved for " + it->first + " parameter."); m->mothurOutEndLine();
 139                         parameters.erase(it++);
 140                     }else {
 141                         m->mothurOut("Using " + it->second + " as input file for the " + it->first + " parameter."); m->mothurOutEndLine();
 142                         it++;
 143                     }
 144                 }else{ it++; }
 145             }
 146
 147                 return parameters;
 148         }
 149         catch(exception& e) {
 150                 m->errorOut(e, "OptionParser", "getParameters");
 151                 exit(1);
 152         }
 153 }
 154
 155 /***********************************************************************/
 156 //pass a vector of filenames that may match the current namefile.
 157 //this function will look at each one, if the rootnames match, mothur will warn
 158 //the user that they may have neglected to provide a namefile.
 159 //stops when it finds a match.
 160 bool OptionParser::getNameFile(vector<string> files) {
 161         try {
 162                 string namefile = m->getNameFile();
 163                 bool match = false;
 164
 165                 if ((namefile != "")&&(!m->mothurCalling)) {
 166                         string temp = m->getRootName(m->getSimpleName(namefile));
 167                         vector<string> rootName;
 168                         m->splitAtChar(temp, rootName, '.');
 169
 170                         for (int i = 0; i < files.size(); i++) {
 171                                 temp = m->getRootName(m->getSimpleName(files[i]));
 172                                 vector<string> root;
 173                                 m->splitAtChar(temp, root, '.');
 174
 175                                 int smallest = rootName.size();
 176                                 if (root.size() < smallest) { smallest = root.size(); }
 177
 178                                 int numMatches = 0;
 179                                 for(int j = 0; j < smallest; j++) {
 180                                         if (root[j] == rootName[j]) { numMatches++; }
 181                                 }
 182
 183                                 if (smallest > 0) {
 184                                         if ((numMatches >= (smallest-2)) && (root[0] == rootName[0])) {
 185                                                 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] + ".");
 186                                                 m->mothurOutEndLine();
 187                                                 match = true;
 188                                                 break;
 189                                         }
 190                                 }
 191                         }
 192
 193                 }
 194
 195
 196                 return match;
 197         }
 198         catch(exception& e) {
 199                 m->errorOut(e, "OptionParser", "getNameFile");
 200                 exit(1);
 201         }
 202 }
 203
 204
 205 /***********************************************************************/