globaldata.cpp

   1 #include "globaldata.hpp"
   2 #include "sparsematrix.hpp"
   3 #include "tree.h"
   4 #include "rabundvector.hpp"
   5 #include "sabundvector.hpp"
   6 #include "listvector.hpp"
   7
   8 /*******************************************************/
   9
  10 /******************************************************/
  11 GlobalData* GlobalData::getInstance() {
  12         if( _uniqueInstance == 0 ) {
  13                 _uniqueInstance = new GlobalData();
  14         }
  15         return _uniqueInstance;
  16 }
  17 /*******************************************************/
  18
  19 /******************************************************/
  20 //This function parses through the option string of the command to remove its parameters
  21 void GlobalData::parseGlobalData(string commandString, string optionText){
  22         try {
  23                 commandName = commandString; //save command name to be used by other classes
  24
  25                 //set all non filename paramters to default
  26                 reset();
  27
  28                 //clears out data from previous read
  29                 if ((commandName == "read.dist") || (commandName == "read.otu") || (commandName == "read.tree")) {
  30                         clear();
  31                         gGroupmap = NULL;
  32                         gTree.clear();
  33                         labels.clear(); lines.clear(); groups.clear();
  34                         allLines = 1;
  35                 }
  36
  37                 //saves help request
  38                 if (commandName =="help") {
  39                         helpRequest = optionText;
  40                 }
  41
  42                 string key, value;
  43                 //reads in parameters and values
  44                 if((optionText != "") && (commandName != "help")){
  45                         while((optionText.find_first_of(',') != -1)) {  //while there are parameters
  46                                 splitAtComma(value, optionText);
  47                                 splitAtEquals(key, value);
  48
  49                                 if (key == "phylip" )   { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";       }
  50                                 if (key == "column" )   { columnfile = value; inputFileName = value; fileroot = value; format = "column";       }
  51                                 if (key == "list" )             { listfile = value; inputFileName = value; fileroot = value; format = "list";           }
  52                                 if (key == "rabund" )   { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
  53                                 if (key == "sabund" )   { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       }
  54                                 if (key == "fasta" )    { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
  55                                 if (key == "tree" )             { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }
  56                                 if (key == "shared" )   { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile";   }
  57                                 if (key == "name" )             { namefile = value;             }
  58                                 if (key == "order" )    { orderfile = value;    }
  59                                 if (key == "group" )    { groupfile = value;    }
  60                                 if (key == "cutoff" )           { cutoff = value;               }
  61                                 if (key == "precision" )        { precision = value;    }
  62                                 if (key == "iters" )            { iters = value;                }
  63                                 if (key == "jumble" )           { jumble = value;               }
  64                                 if (key == "freq" )                     { freq = value;                 }
  65                                 if (key == "method" )           { method = value;               }
  66                                 if (key == "fileroot" )         { fileroot = value;             }
  67                                 if (key == "abund" )        { abund = value;        }
  68                                 if (key == "random" )           { randomtree = value;   }
  69                                 if (key == "calc")                      { calc = value;         }
  70
  71
  72                                 if (key == "line") {//stores lines to be used in a set
  73                                         lines.clear();
  74                                         line = value;
  75                                         label = "";
  76                                         splitAtDash(value, lines);
  77                                         allLines = 0;
  78                                 }
  79                                 if (key == "label") {//stores labels to be used in a set
  80                                         labels.clear();
  81                                         label = value;
  82                                         line = "";
  83                                         splitAtDash(value, labels);
  84                                         allLines = 0;
  85                                 }
  86
  87                                 if (key == "groups") {//stores groups to be used in a vector
  88                                         Groups.clear();
  89                                         groups = value;
  90                                         splitAtDash(value, Groups);
  91                                 }
  92
  93                         }
  94
  95                         //saves the last parameter
  96                         value = optionText;
  97                         splitAtEquals(key, value);
  98                         if (key == "phylip" )   { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";       }
  99                         if (key == "column" )   { columnfile = value; inputFileName = value; fileroot = value; format = "column";       }
 100                         if (key == "list" )             { listfile = value; inputFileName = value; fileroot = value; format = "list";           }
 101                         if (key == "rabund" )   { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
 102                         if (key == "sabund" )   { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       }
 103                         if (key == "fasta" )    { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
 104                         if (key == "tree" )             { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }
 105                         if (key == "shared" )   { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile";   }
 106                         if (key == "name" )             { namefile = value;             }
 107                         if (key == "order" )    { orderfile = value;    }
 108                         if (key == "group" )    { groupfile = value;    }
 109                         if (key == "cutoff" )           { cutoff = value;               }
 110                         if (key == "precision" )        { precision = value;    }
 111                         if (key == "iters" )            { iters = value;                }
 112                         if (key == "jumble" )           { jumble = value;               }
 113                         if (key == "freq" )                     { freq = value;                 }
 114                         if (key == "method" )           { method = value;               }
 115                         if (key == "fileroot" )         { fileroot = value;             }
 116                         if (key == "abund" )        { abund = value;        }
 117                         if (key == "random" )           { randomtree = value;   }
 118                         if (key == "calc")                      { calc = value;         }
 119
 120
 121                         if (key == "line") {//stores lines to be used in a vector
 122                                 lines.clear();
 123                                 line = value;
 124                                 label = "";
 125                                 if (line != "all") {  splitAtDash(value, lines);  allLines = 0;  }
 126                                 else { allLines = 1;  }
 127                         }
 128                         if (key == "label") {//stores lines to be used in a vector
 129                                 labels.clear();
 130                                 label = value;
 131                                 line = "";
 132                                 if (label != "all") {  splitAtDash(value, labels);  allLines = 0;  }
 133                                 else { allLines = 1;  }
 134                         }
 135
 136                         if (key == "groups") {//stores groups to be used in a vector
 137                                         Groups.clear();
 138                                         groups = value;
 139                                         splitAtDash(value, Groups);
 140                         }
 141                 }
 142
 143                 //set format for shared
 144                 if ((listfile != "") && (groupfile != "")) { format = "shared"; }
 145                 if ((phylipfile != "") && (groupfile != "")) { format = "matrix"; }
 146
 147                 //input defaults for calculators
 148                 if (commandName == "collect.single") {
 149                         if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; }
 150                         Estimators.clear();
 151                         splitAtDash(calc, Estimators);
 152                 }
 153                 if (commandName == "rarefaction.single") {
 154                         if ((calc == "default") || (calc == "")) { calc = "sobs"; }
 155                         Estimators.clear();
 156                         splitAtDash(calc, Estimators);
 157                 }
 158                 if (commandName == "collect.shared") {
 159                         if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan"; }
 160                         Estimators.clear();
 161                         splitAtDash(calc, Estimators);
 162                 }
 163                 if (commandName == "summary.single") {
 164                         if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; }
 165                         Estimators.clear();
 166                         splitAtDash(calc, Estimators);
 167                 }
 168                 if (commandName == "summary.shared") {
 169                         if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan"; }
 170                         Estimators.clear();
 171                         splitAtDash(calc, Estimators);
 172                 }
 173                 if (commandName == "rarefaction.shared") {
 174                         if ((calc == "default") || (calc == "")) { calc = "sharedobserved"; }
 175                         Estimators.clear();
 176                         splitAtDash(calc, Estimators);
 177                 }
 178
 179                 //if you have done a read.otu with a groupfile but don't want to use it anymore because you want to do single commands
 180                 if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single")) {
 181                         if (listfile != "") { format = "list"; }
 182                         else if (sabundfile != "") { format = "sabund"; }
 183                         else if (rabundfile != "") { format = "rabund"; }
 184                 }
 185         }
 186         catch(exception& e) {
 187                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 188                 exit(1);
 189         }
 190         catch(...) {
 191                 cout << "An unknown error has occurred in the GlobalData class function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 192                 exit(1);
 193         }
 194 }
 195 /*******************************************************/
 196
 197 /******************************************************/
 198 // These functions give you the option parameters of the commands
 199 string GlobalData::getPhylipFile()              {       return phylipfile;      }
 200 string GlobalData::getColumnFile()              {       return columnfile;      }
 201 string GlobalData::getListFile()                {       return listfile;        }
 202 string GlobalData::getRabundFile()              {       return rabundfile;      }
 203 string GlobalData::getSabundFile()              {       return sabundfile;      }
 204 string GlobalData::getNameFile()                {       return namefile;        }
 205 string GlobalData::getGroupFile()               {       return groupfile;       }
 206 string GlobalData::getOrderFile()               {       return orderfile;       }
 207 string GlobalData::getTreeFile()                {       return treefile;        }
 208 string GlobalData::getSharedFile()              {       return sharedfile;      }
 209 string GlobalData::getFastaFile()               {       return fastafile;       }
 210 string GlobalData::getCutOff()                  {       return cutoff;          }
 211 string GlobalData::getFormat()                  {       return format;          }
 212 string GlobalData::getPrecision()               {       return precision;       }
 213 string GlobalData::getMethod()                  {       return method;          }
 214 string GlobalData::getFileRoot()                {       return fileroot;        }
 215 string GlobalData::getIters()                   {       return iters;           }
 216 string GlobalData::getJumble()                  {       return jumble;          }
 217 string GlobalData::getFreq()                    {       return freq;            }
 218 string GlobalData::getAbund()           {   return abund;       }
 219 string GlobalData::getRandomTree()              {       return randomtree;      }
 220 string GlobalData::getGroups()                  {       return groups;          }
 221 void GlobalData::setListFile(string file)       {       listfile = file;        inputFileName = file;}
 222 void GlobalData::setRabundFile(string file)     {       rabundfile = file;      inputFileName = file;}
 223 void GlobalData::setSabundFile(string file)     {       sabundfile = file;      inputFileName = file;}
 224 void GlobalData::setPhylipFile(string file)     {       phylipfile = file;    inputFileName = file;}
 225 void GlobalData::setColumnFile(string file)     {       columnfile = file;    inputFileName = file;}
 226 void GlobalData::setNameFile(string file)               {       namefile = file;                }
 227 void GlobalData::setFormat(string Format)               {       format = Format;                }
 228 void GlobalData::setRandomTree(string Random)   {       randomtree = Random;    }
 229 void GlobalData::setGroups(string g)                    {       groups = g;                             }
 230 void GlobalData::setCalc(string Calc)                   {       calc = Calc;                    }
 231
 232 /*******************************************************/
 233
 234 /******************************************************/
 235 GlobalData::GlobalData() {
 236         //option definitions should go here...
 237         helpRequest = "";
 238         clear();
 239 }
 240 /*******************************************************/
 241
 242 /******************************************************/
 243 void GlobalData::clear() {
 244         //option definitions should go here...
 245         phylipfile              =       "";
 246         columnfile              =       "";
 247         listfile                =       "";
 248         rabundfile              =       "";
 249         sabundfile              =       "";
 250         namefile                =       "";
 251         groupfile               =       "";
 252         orderfile               =       "";
 253         fastafile               =   "";
 254         treefile                =       "";
 255         sharedfile              =       "";
 256         cutoff                  =       "10.00";
 257         format                  =       "";
 258         precision               =       "100";
 259         iters                   =       "1000";
 260         line                    =   "";
 261         label                   =       "";
 262         groups                  =       "";
 263         jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
 264         randomtree              =       "";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
 265         freq                    =       "100";
 266         method                  =       "furthest";
 267         fileroot                =       "";
 268         abund           =   "10";
 269 }
 270
 271 //*******************************************************/
 272
 273 /******************************************************/
 274 void GlobalData::reset() {
 275         cutoff                  =       "10.00";
 276         precision               =       "100";
 277         iters                   =       "1000";
 278         groups                  =       "";
 279         jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
 280         randomtree              =       "";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
 281         freq                    =       "100";
 282         method                  =       "furthest";
 283         calc                    =       "";
 284         abund = "10";
 285 }
 286 /*******************************************************/
 287
 288 /******************************************************/
 289 GlobalData::~GlobalData() {
 290         _uniqueInstance = 0;
 291         if(gListVector != NULL)         {       delete gListVector;             }
 292         if(gSparseMatrix != NULL)       {       delete gSparseMatrix;   }
 293         if(gorder != NULL)                      {       delete gorder;          }
 294 }
 295 /*******************************************************/