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
  82                 //saves help request
  83                 if (commandName =="help") {
  84                         helpRequest = optionText;
  85                 }
  86
  87                 string key, value;
  88                 //reads in parameters and values
  89                 if((optionText != "") && (commandName != "help")){
  90                         while((optionText.find_first_of(',') != -1)) {  //while there are parameters
  91                                 splitAtComma(value, optionText);
  92                                 splitAtEquals(key, value);
  93
  94                                 if (key == "phylip" )   { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";       }
  95                                 if (key == "column" )   { columnfile = value; inputFileName = value; fileroot = value; format = "column";       }
  96                                 if (key == "list" )             { listfile = value; inputFileName = value; fileroot = value; format = "list";           }
  97                                 if (key == "rabund" )   { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
  98                                 if (key == "sabund" )   { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       }
  99                                 if (key == "fasta" )    { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
 100                                 if (key == "tree" )             { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }
 101                                 if (key == "shared" )   { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile";   }
 102                                 if (key == "name" )             { namefile = value;             }
 103                                 if (key == "order" )    { orderfile = value;    }
 104                                 if (key == "group" )    { groupfile = value;    }
 105                                 if (key == "cutoff" )           { cutoff = value;               }
 106                                 if (key == "precision" )        { precision = value;    }
 107                                 if (key == "iters" )            { iters = value;                }
 108                                 if (key == "jumble" )           { jumble = value;               }
 109                                 if (key == "freq" )                     { freq = value;                 }
 110                                 if (key == "method" )           { method = value;               }
 111                                 if (key == "fileroot" )         { fileroot = value;             }
 112                                 if (key == "random" )           { randomtree = value;   }
 113                                 if (key == "groups" )           { groups = value;       }
 114                                 if (key == "calc")                      { calc = value;         }
 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                                 if (key == "groups") {//stores groups to be used in a vector
 131                                         Groups.clear();
 132                                         groups = value;
 133                                         splitAtDash(value, Groups);
 134                                 }
 135                         }
 136
 137                         //saves the last parameter
 138                         value = optionText;
 139                         splitAtEquals(key, value);
 140                         if (key == "phylip" )   { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";       }
 141                         if (key == "column" )   { columnfile = value; inputFileName = value; fileroot = value; format = "column";       }
 142                         if (key == "list" )             { listfile = value; inputFileName = value; fileroot = value; format = "list";           }
 143                         if (key == "rabund" )   { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
 144                         if (key == "sabund" )   { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       }
 145                         if (key == "fasta" )    { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
 146                         if (key == "tree" )             { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }
 147                         if (key == "shared" )   { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile";   }
 148                         if (key == "name" )             { namefile = value;             }
 149                         if (key == "order" )    { orderfile = value;    }
 150                         if (key == "group" )    { groupfile = value;    }
 151                         if (key == "cutoff" )           { cutoff = value;               }
 152                         if (key == "precision" )        { precision = value;    }
 153                         if (key == "iters" )            { iters = value;                }
 154                         if (key == "jumble" )           { jumble = value;               }
 155                         if (key == "freq" )                     { freq = value;                 }
 156                         if (key == "method" )           { method = value;               }
 157                         if (key == "fileroot" )         { fileroot = value;             }
 158                         if (key == "random" )           { randomtree = value;   }
 159                         if (key == "groups" )           { groups = value;       }
 160                         if (key == "calc")                      { calc = value;         }
 161
 162
 163                         if (key == "line") {//stores lines to be used in a vector
 164                                 lines.clear();
 165                                 line = value;
 166                                 label = "";
 167                                 splitAtDash(value, lines);
 168                                 allLines = 0;
 169                         }
 170                         if (key == "label") {//stores lines to be used in a vector
 171                                 labels.clear();
 172                                 label = value;
 173                                 line = "";
 174                                 splitAtDash(value, labels);
 175                                 allLines = 0;
 176                         }
 177                         if (key == "groups") {//stores groups to be used in a vector
 178                                         Groups.clear();
 179                                         groups = value;
 180                                         splitAtDash(value, Groups);
 181                         }
 182                 }
 183
 184                 //set format for shared
 185                 if ((listfile != "") && (groupfile != "")) { format = "shared"; }
 186
 187                 //input defaults for calculators
 188                 if (commandName == "collect.single") {
 189                         if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; }
 190                         Estimators.clear();
 191                         splitAtDash(calc, Estimators);
 192                 }
 193                 if (commandName == "rarefaction.single") {
 194                         if ((calc == "default") || (calc == "")) { calc = "sobs"; }
 195                         Estimators.clear();
 196                         splitAtDash(calc, Estimators);
 197                 }
 198                 if (commandName == "collect.shared") {
 199                         if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan"; }
 200                         Estimators.clear();
 201                         splitAtDash(calc, Estimators);
 202                 }
 203                 if (commandName == "summary.single") {
 204                         if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; }
 205                         Estimators.clear();
 206                         splitAtDash(calc, Estimators);
 207                 }
 208                 if (commandName == "summary.shared") {
 209                         if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan"; }
 210                         Estimators.clear();
 211                         splitAtDash(calc, Estimators);
 212                 }
 213                 if (commandName == "rarefaction.shared") {
 214                         if ((calc == "default") || (calc == "")) { calc = "sharedobserved"; }
 215                         Estimators.clear();
 216                         splitAtDash(calc, Estimators);
 217                 }
 218
 219                 //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
 220                 if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single")) {
 221                         if (listfile != "") { format = "list"; }
 222                         else if (sabundfile != "") { format = "sabund"; }
 223                         else if (rabundfile != "") { format = "rabund"; }
 224                 }
 225         }
 226         catch(exception& e) {
 227                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 228                 exit(1);
 229         }
 230         catch(...) {
 231                 cout << "An unknown error has occurred in the GlobalData class function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 232                 exit(1);
 233         }
 234 }
 235 /*******************************************************/
 236
 237 /******************************************************/
 238 // These functions give you the option parameters of the commands
 239 string GlobalData::getPhylipFile()              {       return phylipfile;      }
 240 string GlobalData::getColumnFile()              {       return columnfile;      }
 241 string GlobalData::getListFile()                {       return listfile;        }
 242 string GlobalData::getRabundFile()              {       return rabundfile;      }
 243 string GlobalData::getSabundFile()              {       return sabundfile;      }
 244 string GlobalData::getNameFile()                {       return namefile;        }
 245 string GlobalData::getGroupFile()               {       return groupfile;       }
 246 string GlobalData::getOrderFile()               {       return orderfile;       }
 247 string GlobalData::getTreeFile()                {       return treefile;        }
 248 string GlobalData::getSharedFile()              {       return sharedfile;      }
 249 string GlobalData::getFastaFile()               {       return fastafile;       }
 250 string GlobalData::getCutOff()                  {       return cutoff;          }
 251 string GlobalData::getFormat()                  {       return format;          }
 252 string GlobalData::getPrecision()               {       return precision;       }
 253 string GlobalData::getMethod()                  {       return method;          }
 254 string GlobalData::getFileRoot()                {       return fileroot;        }
 255 string GlobalData::getIters()                   {       return iters;           }
 256 string GlobalData::getJumble()                  {       return jumble;          }
 257 string GlobalData::getFreq()                    {       return freq;            }
 258 string GlobalData::getRandomTree()              {       return randomtree;      }
 259 void GlobalData::setListFile(string file)       {       listfile = file;        inputFileName = file;}
 260 void GlobalData::setRabundFile(string file)     {       rabundfile = file;      inputFileName = file;}
 261 void GlobalData::setSabundFile(string file)     {       sabundfile = file;      inputFileName = file;}
 262 void GlobalData::setPhylipFile(string file)     {       phylipfile = file;    inputFileName = file;}
 263 void GlobalData::setColumnFile(string file)     {       columnfile = file;    inputFileName = file;}
 264 void GlobalData::setNameFile(string file)               {       namefile = file;                }
 265 void GlobalData::setFormat(string Format)               {       format = Format;                }
 266 void GlobalData::setRandomTree(string Random)   {       randomtree = Random;    }
 267 void GlobalData::setCalc(string Calc)                   {       calc = Calc;    }
 268
 269 /*******************************************************/
 270
 271 /******************************************************/
 272 GlobalData::GlobalData() {
 273         //option definitions should go here...
 274         helpRequest = "";
 275         clear();
 276 }
 277 /*******************************************************/
 278
 279 /******************************************************/
 280 void GlobalData::clear() {
 281         //option definitions should go here...
 282         phylipfile              =       "";
 283         columnfile              =       "";
 284         listfile                =       "";
 285         rabundfile              =       "";
 286         sabundfile              =       "";
 287         namefile                =       "";
 288         groupfile               =       "";
 289         orderfile               =       "";
 290         fastafile               =   "";
 291         treefile                =       "";
 292         sharedfile              =       "";
 293         cutoff                  =       "10.00";
 294         format                  =       "";
 295         precision               =       "100";
 296         iters                   =       "1000";
 297         line                    =   "";
 298         label                   =       "";
 299         groups                  =       "";
 300         jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
 301         randomtree              =       "";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
 302         freq                    =       "100";
 303         method                  =       "furthest";
 304         fileroot                =       "";
 305         calc                    =       "";
 306 }
 307 /*******************************************************/
 308
 309 /******************************************************/
 310 void GlobalData::reset() {
 311         cutoff                  =       "10.00";
 312         precision               =       "100";
 313         iters                   =       "1000";
 314         line                    =   "";
 315         label                   =       "";
 316         groups                  =       "";
 317         jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
 318         randomtree              =       "";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
 319         freq                    =       "100";
 320         method                  =       "furthest";
 321         calc                    =       "";
 322 }
 323 /*******************************************************/
 324
 325 /******************************************************/
 326 GlobalData::~GlobalData() {
 327         _uniqueInstance = 0;
 328         if(gListVector != NULL)         {       delete gListVector;             }
 329         if(gSparseMatrix != NULL)       {       delete gSparseMatrix;   }
 330         if(gorder != NULL)                      {       delete gorder;          }
 331 }
 332 /*******************************************************/
 333
 334 /******************************************************/
 335