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                 allLines = 1;
  24                 commandName = commandString; //save command name to be used by other classes
  25
  26                 //set all non filename paramters to default
  27                 reset();
  28
  29                 //clears out data from previous read
  30                 if ((commandName == "read.dist") || (commandName == "read.otu") || (commandName == "read.tree") || (commandName == "read.shared")) {
  31                         clear();
  32                         gGroupmap = NULL;
  33                         gTree.clear();
  34                         labels.clear(); lines.clear(); groups.clear();
  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                                 splitAtDash(value, lines);
 126                                 allLines = 0;
 127                         }
 128                         if (key == "label") {//stores lines to be used in a vector
 129                                 labels.clear();
 130                                 label = value;
 131                                 line = "";
 132                                 splitAtDash(value, labels);
 133                                 allLines = 0;
 134                         }
 135                         if (key == "groups") {//stores groups to be used in a vector
 136                                         Groups.clear();
 137                                         groups = value;
 138                                         splitAtDash(value, Groups);
 139                         }
 140                 }
 141
 142                 //set format for shared
 143                 if ((listfile != "") && (groupfile != "")) { format = "shared"; }
 144                 if ((phylipfile != "") && (groupfile != "")) { format = "matrix"; }
 145
 146                 //input defaults for calculators
 147                 if (commandName == "collect.single") {
 148                         if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; }
 149                         Estimators.clear();
 150                         splitAtDash(calc, Estimators);
 151                 }
 152                 if (commandName == "rarefaction.single") {
 153                         if ((calc == "default") || (calc == "")) { calc = "sobs"; }
 154                         Estimators.clear();
 155                         splitAtDash(calc, Estimators);
 156                 }
 157                 if (commandName == "collect.shared") {
 158                         if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan"; }
 159                         Estimators.clear();
 160                         splitAtDash(calc, Estimators);
 161                 }
 162                 if (commandName == "summary.single") {
 163                         if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; }
 164                         Estimators.clear();
 165                         splitAtDash(calc, Estimators);
 166                 }
 167                 if (commandName == "summary.shared") {
 168                         if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan"; }
 169                         Estimators.clear();
 170                         splitAtDash(calc, Estimators);
 171                 }
 172                 if (commandName == "rarefaction.shared") {
 173                         if ((calc == "default") || (calc == "")) { calc = "sharedobserved"; }
 174                         Estimators.clear();
 175                         splitAtDash(calc, Estimators);
 176                 }
 177
 178                 //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
 179                 if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single")) {
 180                         if (listfile != "") { format = "list"; }
 181                         else if (sabundfile != "") { format = "sabund"; }
 182                         else if (rabundfile != "") { format = "rabund"; }
 183                 }
 184         }
 185         catch(exception& e) {
 186                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 187                 exit(1);
 188         }
 189         catch(...) {
 190                 cout << "An unknown error has occurred in the GlobalData class function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 191                 exit(1);
 192         }
 193 }
 194 /*******************************************************/
 195
 196 /******************************************************/
 197 // These functions give you the option parameters of the commands
 198 string GlobalData::getPhylipFile()              {       return phylipfile;      }
 199 string GlobalData::getColumnFile()              {       return columnfile;      }
 200 string GlobalData::getListFile()                {       return listfile;        }
 201 string GlobalData::getRabundFile()              {       return rabundfile;      }
 202 string GlobalData::getSabundFile()              {       return sabundfile;      }
 203 string GlobalData::getNameFile()                {       return namefile;        }
 204 string GlobalData::getGroupFile()               {       return groupfile;       }
 205 string GlobalData::getOrderFile()               {       return orderfile;       }
 206 string GlobalData::getTreeFile()                {       return treefile;        }
 207 string GlobalData::getSharedFile()              {       return sharedfile;      }
 208 string GlobalData::getFastaFile()               {       return fastafile;       }
 209 string GlobalData::getCutOff()                  {       return cutoff;          }
 210 string GlobalData::getFormat()                  {       return format;          }
 211 string GlobalData::getPrecision()               {       return precision;       }
 212 string GlobalData::getMethod()                  {       return method;          }
 213 string GlobalData::getFileRoot()                {       return fileroot;        }
 214 string GlobalData::getIters()                   {       return iters;           }
 215 string GlobalData::getJumble()                  {       return jumble;          }
 216 string GlobalData::getFreq()                    {       return freq;            }
 217 string GlobalData::getAbund()           {   return abund;       }
 218 string GlobalData::getRandomTree()              {       return randomtree;      }
 219 string GlobalData::getGroups()                  {       return groups;          }
 220 void GlobalData::setListFile(string file)       {       listfile = file;        inputFileName = file;}
 221 void GlobalData::setRabundFile(string file)     {       rabundfile = file;      inputFileName = file;}
 222 void GlobalData::setSabundFile(string file)     {       sabundfile = file;      inputFileName = file;}
 223 void GlobalData::setPhylipFile(string file)     {       phylipfile = file;    inputFileName = file;}
 224 void GlobalData::setColumnFile(string file)     {       columnfile = file;    inputFileName = file;}
 225 void GlobalData::setNameFile(string file)               {       namefile = file;                }
 226 void GlobalData::setFormat(string Format)               {       format = Format;                }
 227 void GlobalData::setRandomTree(string Random)   {       randomtree = Random;    }
 228 void GlobalData::setGroups(string g)                    {       groups = g;                             }
 229 void GlobalData::setCalc(string Calc)                   {       calc = Calc;                    }
 230
 231 /*******************************************************/
 232
 233 /******************************************************/
 234 GlobalData::GlobalData() {
 235         //option definitions should go here...
 236         helpRequest = "";
 237         clear();
 238 }
 239 /*******************************************************/
 240
 241 /******************************************************/
 242 void GlobalData::clear() {
 243         //option definitions should go here...
 244         phylipfile              =       "";
 245         columnfile              =       "";
 246         listfile                =       "";
 247         rabundfile              =       "";
 248         sabundfile              =       "";
 249         namefile                =       "";
 250         groupfile               =       "";
 251         orderfile               =       "";
 252         fastafile               =   "";
 253         treefile                =       "";
 254         sharedfile              =       "";
 255         cutoff                  =       "10.00";
 256         format                  =       "";
 257         precision               =       "100";
 258         iters                   =       "1000";
 259         line                    =   "";
 260         label                   =       "";
 261         groups                  =       "";
 262         jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
 263         randomtree              =       "";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
 264         freq                    =       "100";
 265         method                  =       "furthest";
 266         fileroot                =       "";
 267         abund           =   "10";
 268 }
 269
 270 //*******************************************************/
 271
 272 /******************************************************/
 273 void GlobalData::reset() {
 274         cutoff                  =       "10.00";
 275         precision               =       "100";
 276         iters                   =       "1000";
 277         line                    =   "";
 278         label                   =       "";
 279         groups                  =       "";
 280         jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
 281         randomtree              =       "";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
 282         freq                    =       "100";
 283         method                  =       "furthest";
 284         calc                    =       "";
 285         abund = "10";
 286 }
 287 /*******************************************************/
 288
 289 /******************************************************/
 290 GlobalData::~GlobalData() {
 291         _uniqueInstance = 0;
 292         if(gListVector != NULL)         {       delete gListVector;             }
 293         if(gSparseMatrix != NULL)       {       delete gSparseMatrix;   }
 294         if(gorder != NULL)                      {       delete gorder;          }
 295 }
 296 /*******************************************************/