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                         Treenames.clear();
  34                         labels.clear(); lines.clear(); groups.clear();
  35                         allLines = 1;
  36                 }
  37
  38                 //saves help request
  39                 if (commandName =="help") {
  40                         helpRequest = optionText;
  41                 }
  42
  43                 if (commandName == "libshuff") {
  44                         iters = "10000";
  45                         cutoff = "1.0";
  46                 }
  47
  48                 string key, value;
  49                 //reads in parameters and values
  50                 if((optionText != "") && (commandName != "help")){
  51                         while((optionText.find_first_of(',') != -1)) {  //while there are parameters
  52                                 splitAtComma(value, optionText);
  53                                 splitAtEquals(key, value);
  54
  55                                 if (key == "phylip" )   { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";       }
  56                                 if (key == "column" )   { columnfile = value; inputFileName = value; fileroot = value; format = "column";       }
  57                                 if (key == "list" )             { listfile = value; inputFileName = value; fileroot = value; format = "list";           }
  58                                 if (key == "rabund" )   { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
  59                                 if (key == "sabund" )   { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       }
  60                                 if (key == "fasta" )    { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
  61                                 if (key == "tree" )             { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }
  62                                 if (key == "shared" )   { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile";   }
  63                                 if (key == "name" )             { namefile = value;             }
  64                                 if (key == "order" )    { orderfile = value;    }
  65                                 if (key == "group" )    { groupfile = value;    }
  66                                 if (key == "cutoff" )           { cutoff = value;               }
  67                                 if (key == "precision" )        { precision = value;    }
  68                                 if (key == "iters" )            { iters = value;                }
  69                                 if (key == "jumble" )           { jumble = value;               }
  70                                 if (key == "freq" )                     { freq = value;                 }
  71                                 if (key == "method" )           { method = value;               }
  72                                 if (key == "fileroot" )         { fileroot = value;             }
  73                                 if (key == "abund" )        { abund = value;        }
  74                                 if (key == "random" )           { randomtree = value;   }
  75                                 if (key == "calc")                      { calc = value;                 }
  76                                 if (key == "step")                      { step = value;                 }
  77                                 if (key == "form")                      { form = value;                 }
  78                                 if (key == "sorted")            { sorted = value;               }
  79
  80
  81
  82                                 if (key == "line") {//stores lines to be used in a set
  83                                         lines.clear();
  84                                         labels.clear();
  85                                         line = value;
  86                                         label = "";
  87                                         splitAtDash(value, lines);
  88                                         allLines = 0;
  89                                 }
  90                                 if (key == "label") {//stores labels to be used in a set
  91                                         labels.clear();
  92                                         lines.clear();
  93                                         label = value;
  94                                         line = "";
  95                                         splitAtDash(value, labels);
  96                                         allLines = 0;
  97                                 }
  98
  99                                 if (key == "groups") {//stores groups to be used in a vector
 100                                         Groups.clear();
 101                                         groups = value;
 102                                         splitAtDash(value, Groups);
 103                                 }
 104
 105                         }
 106
 107                         //saves the last parameter
 108                         value = optionText;
 109                         splitAtEquals(key, value);
 110                         if (key == "phylip" )   { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";       }
 111                         if (key == "column" )   { columnfile = value; inputFileName = value; fileroot = value; format = "column";       }
 112                         if (key == "list" )             { listfile = value; inputFileName = value; fileroot = value; format = "list";           }
 113                         if (key == "rabund" )   { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
 114                         if (key == "sabund" )   { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       }
 115                         if (key == "fasta" )    { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
 116                         if (key == "tree" )             { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }
 117                         if (key == "shared" )   { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile";   }
 118                         if (key == "name" )             { namefile = value;             }
 119                         if (key == "order" )    { orderfile = value;    }
 120                         if (key == "group" )    { groupfile = value;    }
 121                         if (key == "cutoff" )           { cutoff = value;               }
 122                         if (key == "precision" )        { precision = value;    }
 123                         if (key == "iters" )            { iters = value;                }
 124                         if (key == "jumble" )           { jumble = value;               }
 125                         if (key == "freq" )                     { freq = value;                 }
 126                         if (key == "method" )           { method = value;               }
 127                         if (key == "fileroot" )         { fileroot = value;             }
 128                         if (key == "abund" )        { abund = value;        }
 129                         if (key == "random" )           { randomtree = value;   }
 130                         if (key == "calc")                      { calc = value;                 }
 131                         if (key == "step")                      { step = value;                 }
 132                         if (key == "form")                      { form = value;                 }
 133                         if (key == "sorted")            { sorted = value;               }
 134
 135                         if (key == "line") {//stores lines to be used in a vector
 136                                 lines.clear();
 137                                 labels.clear();
 138                                 line = value;
 139                                 label = "";
 140                                 if (line != "all") {  splitAtDash(value, lines);  allLines = 0;  }
 141                                 else { allLines = 1;  }
 142                         }
 143                         if (key == "label") {//stores lines to be used in a vector
 144                                 labels.clear();
 145                                 lines.clear();
 146                                 label = value;
 147                                 line = "";
 148                                 if (label != "all") {  splitAtDash(value, labels);  allLines = 0;  }
 149                                 else { allLines = 1;  }
 150                         }
 151
 152                         if (key == "groups") {//stores groups to be used in a vector
 153                                         Groups.clear();
 154                                         groups = value;
 155                                         splitAtDash(value, Groups);
 156                         }
 157                 }
 158
 159                 //set format for shared
 160                 if ((listfile != "") && (groupfile != "")) { format = "shared"; }
 161                 if ((phylipfile != "") && (groupfile != "")) { format = "matrix"; }
 162
 163                 //input defaults for calculators
 164                 if (commandName == "collect.single") {
 165                         if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-geom-qstat-logsd-bergerparker-bstick"; }
 166                         Estimators.clear();
 167                         splitAtDash(calc, Estimators);
 168                 }
 169                 if (commandName == "rarefaction.single") {
 170                         if ((calc == "default") || (calc == "")) { calc = "sobs"; }
 171                         Estimators.clear();
 172                         splitAtDash(calc, Estimators);
 173                 }
 174                 if (commandName == "collect.shared") {
 175                         if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan-sharedkstest-sharedbdiversity"; }
 176                         Estimators.clear();
 177                         splitAtDash(calc, Estimators);
 178                 }
 179                 if (commandName == "summary.single") {
 180                         if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-geom-logsd-qstat-bergerparker-bstick"; }
 181                         Estimators.clear();
 182                         splitAtDash(calc, Estimators);
 183                 }
 184                 if (commandName == "summary.shared") {
 185                         if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan-sharedkstest-sharedbdiversity"; }
 186                         Estimators.clear();
 187                         splitAtDash(calc, Estimators);
 188                 }
 189                 if (commandName == "rarefaction.shared") {
 190                         if ((calc == "default") || (calc == "")) { calc = "sharedobserved"; }
 191                         Estimators.clear();
 192                         splitAtDash(calc, Estimators);
 193                 }
 194                 if (commandName == "venn") {
 195                         if ((calc == "default") || (calc == "")) {
 196                                 if (format == "list") { calc = "sobs"; }
 197                                 else { calc = "sharedsobs"; }
 198                         }
 199                         Estimators.clear();
 200                         splitAtDash(calc, Estimators);
 201                 }
 202
 203                 //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
 204                 if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single")) {
 205                         if (listfile != "") { format = "list"; }
 206                         else if (sabundfile != "") { format = "sabund"; }
 207                         else if (rabundfile != "") { format = "rabund"; }
 208                 }
 209         }
 210         catch(exception& e) {
 211                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 212                 exit(1);
 213         }
 214         catch(...) {
 215                 cout << "An unknown error has occurred in the GlobalData class function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 216                 exit(1);
 217         }
 218 }
 219 /*******************************************************/
 220
 221 /******************************************************/
 222 // These functions give you the option parameters of the commands
 223 string GlobalData::getPhylipFile()              {       return phylipfile;      }
 224 string GlobalData::getColumnFile()              {       return columnfile;      }
 225 string GlobalData::getListFile()                {       return listfile;        }
 226 string GlobalData::getRabundFile()              {       return rabundfile;      }
 227 string GlobalData::getSabundFile()              {       return sabundfile;      }
 228 string GlobalData::getNameFile()                {       return namefile;        }
 229 string GlobalData::getGroupFile()               {       return groupfile;       }
 230 string GlobalData::getOrderFile()               {       return orderfile;       }
 231 string GlobalData::getTreeFile()                {       return treefile;        }
 232 string GlobalData::getSharedFile()              {       return sharedfile;      }
 233 string GlobalData::getFastaFile()               {       return fastafile;       }
 234 string GlobalData::getCutOff()                  {       return cutoff;          }
 235 string GlobalData::getFormat()                  {       return format;          }
 236 string GlobalData::getPrecision()               {       return precision;       }
 237 string GlobalData::getMethod()                  {       return method;          }
 238 string GlobalData::getFileRoot()                {       return fileroot;        }
 239 string GlobalData::getIters()                   {       return iters;           }
 240 string GlobalData::getJumble()                  {       return jumble;          }
 241 string GlobalData::getFreq()                    {       return freq;            }
 242 string GlobalData::getAbund()           {   return abund;       }
 243 string GlobalData::getRandomTree()              {       return randomtree;      }
 244 string GlobalData::getGroups()                  {       return groups;          }
 245 string GlobalData::getStep()                    {       return step;            }
 246 string GlobalData::getForm()                    {       return form;            }
 247 string GlobalData::getSorted()                  {       return sorted;          }
 248 void GlobalData::setListFile(string file)       {       listfile = file;        inputFileName = file;}
 249 void GlobalData::setRabundFile(string file)     {       rabundfile = file;      inputFileName = file;}
 250 void GlobalData::setSabundFile(string file)     {       sabundfile = file;      inputFileName = file;}
 251 void GlobalData::setPhylipFile(string file)     {       phylipfile = file;    inputFileName = file;}
 252 void GlobalData::setColumnFile(string file)     {       columnfile = file;    inputFileName = file;}
 253 void GlobalData::setNameFile(string file)               {       namefile = file;                }
 254 void GlobalData::setFormat(string Format)               {       format = Format;                }
 255 void GlobalData::setRandomTree(string Random)   {       randomtree = Random;    }
 256 void GlobalData::setGroups(string g)                    {       groups = g;                             }
 257 void GlobalData::setCalc(string Calc)                   {       calc = Calc;                    }
 258
 259 /*******************************************************/
 260
 261 /******************************************************/
 262 GlobalData::GlobalData() {
 263         //option definitions should go here...
 264         helpRequest = "";
 265         clear();
 266 }
 267 /*******************************************************/
 268
 269 /******************************************************/
 270 void GlobalData::clear() {
 271         //option definitions should go here...
 272         phylipfile              =       "";
 273         columnfile              =       "";
 274         listfile                =       "";
 275         rabundfile              =       "";
 276         sabundfile              =       "";
 277         namefile                =       "";
 278         groupfile               =       "";
 279         orderfile               =       "";
 280         fastafile               =   "";
 281         treefile                =       "";
 282         sharedfile              =       "";
 283         cutoff                  =       "10.00";
 284         format                  =       "";
 285         precision               =       "100";
 286         iters                   =       "1000";
 287         line                    =   "";
 288         label                   =       "";
 289         groups                  =       "";
 290         jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
 291         randomtree              =       "";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
 292         freq                    =       "100";
 293         method                  =       "furthest";
 294         fileroot                =       "";
 295         abund           =   "10";
 296         step                    =       "0.01";
 297         form                    =       "integral";
 298         sorted                  =       "1";  //0 means don't sort, 1 means sort.
 299 }
 300
 301 //*******************************************************/
 302
 303 /******************************************************/
 304 void GlobalData::reset() {
 305         cutoff                  =       "10.00";
 306         precision               =       "100";
 307         iters                   =       "1000";
 308         groups                  =       "";
 309         jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
 310         sorted                  =       "1";  //0 means don't sort, 1 means sort.
 311         randomtree              =       "";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
 312         freq                    =       "100";
 313         method                  =       "furthest";
 314         calc                    =       "";
 315         abund                   =   "10";
 316         step                    =       "0.01";
 317         form                    =       "integral";
 318 }
 319 /*******************************************************/
 320
 321 /******************************************************/
 322 GlobalData::~GlobalData() {
 323         _uniqueInstance = 0;
 324         if(gListVector != NULL)         {       delete gListVector;             }
 325         if(gSparseMatrix != NULL)       {       delete gSparseMatrix;   }
 326         if(gorder != NULL)                      {       delete gorder;          }
 327 }
 328 /*******************************************************/
 329
 330 /*******************************************************/
 331 void GlobalData::parseTreeFile() {
 332         //only takes names from the first tree and assumes that all trees use the same names.
 333         try {
 334                 string filename = treefile;
 335                 ifstream filehandle;
 336                 openInputFile(filename, filehandle);
 337                 int c, comment;
 338                 comment = 0;
 339
 340                 //if you are not a nexus file
 341                 if ((c = filehandle.peek()) != '#') {
 342                         while((c = filehandle.peek()) != ';') {
 343                                 while ((c = filehandle.peek()) != ';') {
 344                                         // get past comments
 345                                         if(c == '[') {
 346                                                 comment = 1;
 347                                         }
 348                                         if(c == ']'){
 349                                                 comment = 0;
 350                                         }
 351                                         if((c == '(') && (comment != 1)){ break; }
 352                                         filehandle.get();
 353                                 }
 354
 355                                 readTreeString(filehandle);
 356                         }
 357                 //if you are a nexus file
 358                 }else if ((c = filehandle.peek()) == '#') {
 359                         string holder = "";
 360
 361                         // get past comments
 362                         while(holder != "translate" && holder != "Translate"){
 363                                 if(holder == "[" || holder == "[!"){
 364                                         comment = 1;
 365                                 }
 366                                 if(holder == "]"){
 367                                         comment = 0;
 368                                 }
 369                                 filehandle >> holder;
 370
 371                                 //if there is no translate then you must read tree string otherwise use translate to get names
 372                                 if(holder == "tree" && comment != 1){
 373                                         //pass over the "tree rep.6878900 = "
 374                                         while (((c = filehandle.get()) != '(') && ((c = filehandle.peek()) != EOF) ) {;}
 375
 376                                         if (c == EOF ) { break; }
 377                                         filehandle.putback(c);  //put back first ( of tree.
 378                                         readTreeString(filehandle);
 379                                         break;
 380                                 }
 381                         }
 382
 383                         //use nexus translation rather than parsing tree to save time
 384                         if ((holder == "translate") || (holder == "Translate")) {
 385 cout << "there is a translate " << endl;
 386                                 string number, name, h;
 387                                 h = ""; // so it enters the loop the first time
 388                                 while((h != ";") && (number != ";")) {
 389                                         filehandle >> number;
 390                                         filehandle >> name;
 391
 392                                         //c = , until done with translation then c = ;
 393                                         h = name.substr(name.length()-1, name.length());
 394                                         name.erase(name.end()-1);  //erase the comma
 395                                         Treenames.push_back(number);
 396                                 }
 397                                 if (number == ";") { Treenames.pop_back(); }  //in case ';' from translation is on next line instead of next to last name
 398                         }
 399                 }
 400
 401         }
 402         catch(exception& e) {
 403                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 404                 exit(1);
 405         }
 406         catch(...) {
 407                 cout << "An unknown error has occurred in the GlobalData class function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 408                 exit(1);
 409         }
 410 }
 411 /*******************************************************/
 412
 413 /*******************************************************/
 414 void GlobalData::readTreeString(ifstream& filehandle)   {
 415         try {
 416                 int c;
 417                 string name; //k
 418
 419                 while((c = filehandle.peek()) != ';') {
 420                                 //if you are a name
 421                         if ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != '\t') && (c != 32)) { //32 is space
 422                                 name = "";
 423                                 c = filehandle.get();
 424         //              k = c;
 425 //cout << k << endl;
 426                                 while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {
 427                                         name += c;
 428                                         c = filehandle.get();
 429                 //      k = c;
 430 //cout << " in name while " << k << endl;
 431                                 }
 432
 433 //cout << "name = " << name << endl;
 434                                 Treenames.push_back(name);
 435                                 filehandle.putback(c);
 436 //k = c;
 437 //cout << " after putback" <<  k << endl;
 438                         }
 439
 440                         if (c  == ':') { //read until you reach the end of the branch length
 441                                 while ((c != '(') && (c != ')') && (c != ',') && (c != ';') && (c != '\n') && (c != '\t') && (c != 32)) {
 442                                         c = filehandle.get();
 443                                 //      k = c;
 444         //cout << " in branch while " << k << endl;
 445                                 }
 446                                 filehandle.putback(c);
 447                         }
 448                         c = filehandle.get();
 449                         if (c == ';') { break; }
 450                 //      k = c;
 451 //cout << k << endl;
 452
 453                 }
 454         }
 455         catch(exception& e) {
 456                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 457                 exit(1);
 458         }
 459         catch(...) {
 460                 cout << "An unknown error has occurred in the GlobalData class function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 461                 exit(1);
 462         }
 463 }
 464
 465 /*******************************************************/
 466
 467 /*******************************************************/
 468
 469