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
  21 ListVector* GlobalData::getListVector()         {       return gListVector;             }
  22 /*******************************************************/
  23
  24 /******************************************************/
  25 void GlobalData::setListVector(ListVector* lv){
  26         try {
  27                 if(gListVector != NULL){        delete gListVector;     }
  28                 gListVector = new ListVector(*lv);
  29         }
  30         catch(exception& e) {
  31                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function setListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  32                 exit(1);
  33         }
  34         catch(...) {
  35                 cout << "An unknown error has occurred in the GlobalData class function setListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  36                 exit(1);
  37         }
  38 }
  39 /*******************************************************/
  40
  41 /******************************************************/
  42
  43 SparseMatrix* GlobalData::getSparseMatrix()     {       return gSparseMatrix;   }
  44 /*******************************************************/
  45
  46 /******************************************************/
  47 void GlobalData::setSparseMatrix(SparseMatrix* sm){
  48         try{
  49                 if(gSparseMatrix != NULL){      delete gSparseMatrix;   }
  50                 gSparseMatrix = new SparseMatrix(*sm);
  51         }
  52         catch(exception& e) {
  53                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function setSparseMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  54                 exit(1);
  55         }
  56         catch(...) {
  57                 cout << "An unknown error has occurred in the GlobalData class function setSparseMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  58                 exit(1);
  59         }
  60 }
  61 /*******************************************************/
  62
  63 /******************************************************/
  64 //This function parses through the option string of the command to remove its parameters
  65 void GlobalData::parseGlobalData(string commandString, string optionText){
  66         try {
  67                 allLines = 1;
  68                 commandName = commandString; //save command name to be used by other classes
  69
  70                 //set all non filename paramters to default
  71                 reset();
  72
  73                 //clears out data from previous read
  74                 if ((commandName == "read.dist") || (commandName == "read.otu") || (commandName == "read.tree") || (commandName == "read.shared")) {
  75                         clear();
  76                         gGroupmap = NULL;
  77                         gTree.clear();
  78                         labels.clear(); lines.clear(); groups.clear();
  79                 }
  80
  81                 //saves help request
  82                 if (commandName =="help") {
  83                         helpRequest = optionText;
  84                 }
  85
  86                 string key, value;
  87                 //reads in parameters and values
  88                 if((optionText != "") && (commandName != "help")){
  89                         while((optionText.find_first_of(',') != -1)) {  //while there are parameters
  90                                 splitAtComma(value, optionText);
  91                                 splitAtEquals(key, value);
  92
  93                                 if (key == "phylip" )   { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";       }
  94                                 if (key == "column" )   { columnfile = value; inputFileName = value; fileroot = value; format = "column";       }
  95                                 if (key == "list" )             { listfile = value; inputFileName = value; fileroot = value; format = "list";           }
  96                                 if (key == "rabund" )   { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
  97                                 if (key == "sabund" )   { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       }
  98                                 if (key == "fasta" )    { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
  99                                 if (key == "tree" )             { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }
 100                                 if (key == "shared" )   { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile";   }
 101                                 if (key == "name" )             { namefile = value;             }
 102                                 if (key == "order" )    { orderfile = value;    }
 103                                 if (key == "group" )    { groupfile = value;    }
 104                                 if (key == "cutoff" )           { cutoff = value;               }
 105                                 if (key == "precision" )        { precision = value;    }
 106                                 if (key == "iters" )            { iters = value;                }
 107                                 if (key == "jumble" )           { jumble = value;               }
 108                                 if (key == "freq" )                     { freq = value;                 }
 109                                 if (key == "method" )           { method = value;               }
 110                                 if (key == "fileroot" )         { fileroot = value;             }
 111                                 if (key == "abund" )        { abund = value;        }
 112                                 if (key == "random" )           { randomtree = value;   }
 113                                 if (key == "calc")                      { calc = value;         }
 114
 115
 116                                 if (key == "line") {//stores lines to be used in a set
 117                                         lines.clear();
 118                                         line = value;
 119                                         label = "";
 120                                         splitAtDash(value, lines);
 121                                         allLines = 0;
 122                                 }
 123                                 if (key == "label") {//stores labels to be used in a set
 124                                         labels.clear();
 125                                         label = value;
 126                                         line = "";
 127                                         splitAtDash(value, labels);
 128                                         allLines = 0;
 129                                 }
 130
 131                                 if (key == "groups") {//stores groups to be used in a vector
 132                                         Groups.clear();
 133                                         groups = value;
 134                                         splitAtDash(value, Groups);
 135                                 }
 136
 137                         }
 138
 139                         //saves the last parameter
 140                         value = optionText;
 141                         splitAtEquals(key, value);
 142                         if (key == "phylip" )   { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";       }
 143                         if (key == "column" )   { columnfile = value; inputFileName = value; fileroot = value; format = "column";       }
 144                         if (key == "list" )             { listfile = value; inputFileName = value; fileroot = value; format = "list";           }
 145                         if (key == "rabund" )   { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
 146                         if (key == "sabund" )   { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       }
 147                         if (key == "fasta" )    { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
 148                         if (key == "tree" )             { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }
 149                         if (key == "shared" )   { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile";   }
 150                         if (key == "name" )             { namefile = value;             }
 151                         if (key == "order" )    { orderfile = value;    }
 152                         if (key == "group" )    { groupfile = value;    }
 153                         if (key == "cutoff" )           { cutoff = value;               }
 154                         if (key == "precision" )        { precision = value;    }
 155                         if (key == "iters" )            { iters = value;                }
 156                         if (key == "jumble" )           { jumble = value;               }
 157                         if (key == "freq" )                     { freq = value;                 }
 158                         if (key == "method" )           { method = value;               }
 159                         if (key == "fileroot" )         { fileroot = value;             }
 160                         if (key == "abund" )        { abund = value;        }
 161                         if (key == "random" )           { randomtree = value;   }
 162                         if (key == "calc")                      { calc = value;         }
 163
 164
 165                         if (key == "line") {//stores lines to be used in a vector
 166                                 lines.clear();
 167                                 line = value;
 168                                 label = "";
 169                                 splitAtDash(value, lines);
 170                                 allLines = 0;
 171                         }
 172                         if (key == "label") {//stores lines to be used in a vector
 173                                 labels.clear();
 174                                 label = value;
 175                                 line = "";
 176                                 splitAtDash(value, labels);
 177                                 allLines = 0;
 178                         }
 179                         if (key == "groups") {//stores groups to be used in a vector
 180                                         Groups.clear();
 181                                         groups = value;
 182                                         splitAtDash(value, Groups);
 183                         }
 184                 }
 185
 186                 //set format for shared
 187                 if ((listfile != "") && (groupfile != "")) { format = "shared"; }
 188                 if ((phylipfile != "") && (groupfile != "")) { format = "matrix"; }
 189
 190                 //input defaults for calculators
 191                 if (commandName == "collect.single") {
 192                         if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; }
 193                         Estimators.clear();
 194                         splitAtDash(calc, Estimators);
 195                 }
 196                 if (commandName == "rarefaction.single") {
 197                         if ((calc == "default") || (calc == "")) { calc = "sobs"; }
 198                         Estimators.clear();
 199                         splitAtDash(calc, Estimators);
 200                 }
 201                 if (commandName == "collect.shared") {
 202                         if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan"; }
 203                         Estimators.clear();
 204                         splitAtDash(calc, Estimators);
 205                 }
 206                 if (commandName == "summary.single") {
 207                         if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; }
 208                         Estimators.clear();
 209                         splitAtDash(calc, Estimators);
 210                 }
 211                 if (commandName == "summary.shared") {
 212                         if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan"; }
 213                         Estimators.clear();
 214                         splitAtDash(calc, Estimators);
 215                 }
 216                 if (commandName == "rarefaction.shared") {
 217                         if ((calc == "default") || (calc == "")) { calc = "sharedobserved"; }
 218                         Estimators.clear();
 219                         splitAtDash(calc, Estimators);
 220                 }
 221
 222                 //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
 223                 if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single")) {
 224                         if (listfile != "") { format = "list"; }
 225                         else if (sabundfile != "") { format = "sabund"; }
 226                         else if (rabundfile != "") { format = "rabund"; }
 227                 }
 228         }
 229         catch(exception& e) {
 230                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 231                 exit(1);
 232         }
 233         catch(...) {
 234                 cout << "An unknown error has occurred in the GlobalData class function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 235                 exit(1);
 236         }
 237 }
 238 /*******************************************************/
 239
 240 /******************************************************/
 241 // These functions give you the option parameters of the commands
 242 string GlobalData::getPhylipFile()              {       return phylipfile;      }
 243 string GlobalData::getColumnFile()              {       return columnfile;      }
 244 string GlobalData::getListFile()                {       return listfile;        }
 245 string GlobalData::getRabundFile()              {       return rabundfile;      }
 246 string GlobalData::getSabundFile()              {       return sabundfile;      }
 247 string GlobalData::getNameFile()                {       return namefile;        }
 248 string GlobalData::getGroupFile()               {       return groupfile;       }
 249 string GlobalData::getOrderFile()               {       return orderfile;       }
 250 string GlobalData::getTreeFile()                {       return treefile;        }
 251 string GlobalData::getSharedFile()              {       return sharedfile;      }
 252 string GlobalData::getFastaFile()               {       return fastafile;       }
 253 string GlobalData::getCutOff()                  {       return cutoff;          }
 254 string GlobalData::getFormat()                  {       return format;          }
 255 string GlobalData::getPrecision()               {       return precision;       }
 256 string GlobalData::getMethod()                  {       return method;          }
 257 string GlobalData::getFileRoot()                {       return fileroot;        }
 258 string GlobalData::getIters()                   {       return iters;           }
 259 string GlobalData::getJumble()                  {       return jumble;          }
 260 string GlobalData::getFreq()                    {       return freq;            }
 261 string GlobalData::getAbund()           {   return abund;       }
 262 string GlobalData::getRandomTree()              {       return randomtree;      }
 263 string GlobalData::getGroups()                  {       return groups;          }
 264 void GlobalData::setListFile(string file)       {       listfile = file;        inputFileName = file;}
 265 void GlobalData::setRabundFile(string file)     {       rabundfile = file;      inputFileName = file;}
 266 void GlobalData::setSabundFile(string file)     {       sabundfile = file;      inputFileName = file;}
 267 void GlobalData::setPhylipFile(string file)     {       phylipfile = file;    inputFileName = file;}
 268 void GlobalData::setColumnFile(string file)     {       columnfile = file;    inputFileName = file;}
 269 void GlobalData::setNameFile(string file)               {       namefile = file;                }
 270 void GlobalData::setFormat(string Format)               {       format = Format;                }
 271 void GlobalData::setRandomTree(string Random)   {       randomtree = Random;    }
 272 void GlobalData::setGroups(string g)                    {       groups = g;                             }
 273 void GlobalData::setCalc(string Calc)                   {       calc = Calc;                    }
 274
 275 /*******************************************************/
 276
 277 /******************************************************/
 278 GlobalData::GlobalData() {
 279         //option definitions should go here...
 280         helpRequest = "";
 281         clear();
 282 }
 283 /*******************************************************/
 284
 285 /******************************************************/
 286 void GlobalData::clear() {
 287         //option definitions should go here...
 288         phylipfile              =       "";
 289         columnfile              =       "";
 290         listfile                =       "";
 291         rabundfile              =       "";
 292         sabundfile              =       "";
 293         namefile                =       "";
 294         groupfile               =       "";
 295         orderfile               =       "";
 296         fastafile               =   "";
 297         treefile                =       "";
 298         sharedfile              =       "";
 299         cutoff                  =       "10.00";
 300         format                  =       "";
 301         precision               =       "100";
 302         iters                   =       "1000";
 303         line                    =   "";
 304         label                   =       "";
 305         groups                  =       "";
 306         jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
 307         randomtree              =       "";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
 308         freq                    =       "100";
 309         method                  =       "furthest";
 310         fileroot                =       "";
 311         abund           =   "10";
 312 }
 313
 314 //*******************************************************/
 315
 316 /******************************************************/
 317 void GlobalData::reset() {
 318         cutoff                  =       "10.00";
 319         precision               =       "100";
 320         iters                   =       "1000";
 321         line                    =   "";
 322         label                   =       "";
 323         groups                  =       "";
 324         jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
 325         randomtree              =       "";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
 326         freq                    =       "100";
 327         method                  =       "furthest";
 328         calc                    =       "";
 329         abund = "10";
 330 }
 331 /*******************************************************/
 332
 333 /******************************************************/
 334 GlobalData::~GlobalData() {
 335         _uniqueInstance = 0;
 336         if(gListVector != NULL)         {       delete gListVector;             }
 337         if(gSparseMatrix != NULL)       {       delete gSparseMatrix;   }
 338         if(gorder != NULL)                      {       delete gorder;          }
 339 }
 340 /*******************************************************/