globaldata.cpp

   1 #include "globaldata.hpp"
   2 #include "tree.h"
   3 #include "sparsematrix.hpp"
   4
   5 /*******************************************************/
   6
   7 /******************************************************/
   8 GlobalData* GlobalData::getInstance() {
   9         if( _uniqueInstance == 0 ) {
  10                 _uniqueInstance = new GlobalData();
  11         }
  12         return _uniqueInstance;
  13 }
  14 /*******************************************************/
  15
  16 /******************************************************/
  17 //This function parses through the option string of the command to remove its parameters
  18 void GlobalData::parseGlobalData(string commandString, string optionText){
  19         try {
  20                 commandName = commandString; //save command name to be used by other classes
  21
  22                 //set all non filename paramters to default
  23                 reset();
  24
  25                 //clears out data from previous read
  26                 if ((commandName == "read.dist") || (commandName == "read.otu") || (commandName == "read.tree")) {
  27                         clear();
  28                         gGroupmap = NULL;
  29                         gTree.clear();
  30                         Treenames.clear();
  31                         labels.clear(); lines.clear(); groups.clear();
  32                         allLines = 1;
  33                 }
  34
  35                 //saves help request
  36                 if (commandName =="help") {
  37                         helpRequest = optionText;
  38                 }
  39
  40                 if (commandName == "libshuff") {
  41                         iters = "10000";
  42                         cutoff = "1.0";
  43                 }
  44
  45                 string key, value;
  46                 //reads in parameters and values
  47                 if((optionText != "") && (commandName != "help")){
  48                         while((optionText.find_first_of(',') != -1)) {  //while there are parameters
  49                                 splitAtComma(value, optionText);
  50                                 splitAtEquals(key, value);
  51
  52                                 if (key == "phylip" )   { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";       }
  53                                 if (key == "column" )   { columnfile = value; inputFileName = value; fileroot = value; format = "column";       }
  54                                 if (key == "list" )             { listfile = value; inputFileName = value; fileroot = value; format = "list";           }
  55                                 if (key == "rabund" )   { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
  56                                 if (key == "sabund" )   { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       }
  57                                 if (key == "fasta" )    { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
  58                                 if (key == "nexus" )    { nexusfile = value; inputFileName = value; fileroot = value; format = "nexus";         }
  59                                 if (key == "clustal" )  { clustalfile = value; inputFileName = value; fileroot = value; format = "clustal"; }
  60                                 if (key == "tree" )             { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }
  61                                 if (key == "shared" )   { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile";   }
  62                                 if (key == "name" )             { namefile = value;             }
  63                                 if (key == "order" )    { orderfile = value;    }
  64                                 if (key == "group" )    { groupfile = value;    }
  65                                 if (key == "cutoff" )           { cutoff = value;               }
  66                                 if (key == "precision" )        { precision = value;    }
  67                                 if (key == "iters" )            { iters = value;                }
  68                                 if (key == "jumble" )           { jumble = value;               }
  69                                 if (key == "freq" )                     { freq = value;                 }
  70                                 if (key == "method" )           { method = value;               }
  71                                 if (key == "fileroot" )         { fileroot = value;             }
  72                                 if (key == "abund" )        { abund = value;        }
  73                                 if (key == "random" )           { randomtree = value;   }
  74                                 if (key == "calc")                      { calc = value;                 }
  75                                 if (key == "step")                      { step = value;                 }
  76                                 if (key == "form")                      { form = value;                 }
  77                                 if (key == "sorted")            { sorted = value;               }
  78                                 if (key == "vertical")          { vertical = value;             }
  79                                 if (key == "trump")                 { trump = value;            }
  80                                 if (key == "filter")            { filter = value;               }
  81                                 if (key == "soft")                  { soft = value;                 }
  82                                 if (key == "scale")                     { scale = value;                }
  83
  84
  85
  86
  87
  88                                 if (key == "line") {//stores lines to be used in a set
  89                                         lines.clear();
  90                                         labels.clear();
  91                                         line = value;
  92                                         label = "";
  93                                         splitAtDash(value, lines);
  94                                         allLines = 0;
  95                                 }
  96                                 if (key == "label") {//stores labels to be used in a set
  97                                         labels.clear();
  98                                         lines.clear();
  99                                         label = value;
 100                                         line = "";
 101                                         splitAtDash(value, labels);
 102                                         allLines = 0;
 103                                 }
 104
 105                                 if (key == "groups") {//stores groups to be used in a vector
 106                                         Groups.clear();
 107                                         groups = value;
 108                                         splitAtDash(value, Groups);
 109                                 }
 110
 111                         }
 112
 113                         //saves the last parameter
 114                         value = optionText;
 115                         splitAtEquals(key, value);
 116                         if (key == "phylip" )   { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";       }
 117                         if (key == "column" )   { columnfile = value; inputFileName = value; fileroot = value; format = "column";       }
 118                         if (key == "list" )             { listfile = value; inputFileName = value; fileroot = value; format = "list";           }
 119                         if (key == "rabund" )   { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
 120                         if (key == "sabund" )   { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       }
 121                         if (key == "fasta" )    { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
 122                         if (key == "nexus" )    { nexusfile = value; inputFileName = value; fileroot = value; format = "nexus";         }
 123                         if (key == "clustal" )  { clustalfile = value; inputFileName = value; fileroot = value; format = "clustal"; }
 124                         if (key == "tree" )             { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }
 125                         if (key == "shared" )   { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile";   }
 126                         if (key == "name" )             { namefile = value;             }
 127                         if (key == "order" )    { orderfile = value;    }
 128                         if (key == "group" )    { groupfile = value;    }
 129                         if (key == "cutoff" )           { cutoff = value;               }
 130                         if (key == "precision" )        { precision = value;    }
 131                         if (key == "iters" )            { iters = value;                }
 132                         if (key == "jumble" )           { jumble = value;               }
 133                         if (key == "freq" )                     { freq = value;                 }
 134                         if (key == "method" )           { method = value;               }
 135                         if (key == "fileroot" )         { fileroot = value;             }
 136                         if (key == "abund" )        { abund = value;        }
 137                         if (key == "random" )           { randomtree = value;   }
 138                         if (key == "calc")                      { calc = value;                 }
 139                         if (key == "step")                      { step = value;                 }
 140                         if (key == "form")                      { form = value;                 }
 141                         if (key == "sorted")            { sorted = value;               }
 142                         if (key == "vertical")          { vertical = value;             }
 143                         if (key == "trump")                 { trump = value;            }
 144                         if (key == "filter")            { filter = value;               }
 145                         if (key == "soft")                  { soft = value;                 }
 146                         if (key == "scale")                     { scale = value;                }
 147
 148
 149
 150
 151
 152                         if (key == "line") {//stores lines to be used in a vector
 153                                 lines.clear();
 154                                 labels.clear();
 155                                 line = value;
 156                                 label = "";
 157                                 if (line != "all") {  splitAtDash(value, lines);  allLines = 0;  }
 158                                 else { allLines = 1;  }
 159                         }
 160
 161                         if (key == "label") {//stores lines to be used in a vector
 162                                 labels.clear();
 163                                 lines.clear();
 164                                 label = value;
 165                                 line = "";
 166                                 if (label != "all") {  splitAtDash(value, labels);  allLines = 0;  }
 167                                 else { allLines = 1;  }
 168                         }
 169
 170                         if (key == "groups") {//stores groups to be used in a vector
 171                                         Groups.clear();
 172                                         groups = value;
 173                                         splitAtDash(value, Groups);
 174                         }
 175                 }
 176
 177                 //set format for shared
 178                 if ((listfile != "") && (groupfile != "")) { format = "shared"; }
 179                 if ((phylipfile != "") && (groupfile != "")) { format = "matrix"; }
 180
 181                 //input defaults for calculators
 182                 if (commandName == "collect.single") {
 183
 184                         if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
 185                         Estimators.clear();
 186                         splitAtDash(calc, Estimators);
 187                 }
 188                 if (commandName == "rarefaction.single") {
 189                         if ((calc == "default") || (calc == "")) { calc = "sobs"; }
 190                         Estimators.clear();
 191                         splitAtDash(calc, Estimators);
 192                 }
 193                 if (commandName == "collect.shared") {
 194
 195                         if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
 196                         Estimators.clear();
 197                         splitAtDash(calc, Estimators);
 198                 }
 199                 if (commandName == "summary.single") {
 200                         if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
 201                         Estimators.clear();
 202                         splitAtDash(calc, Estimators);
 203                 }
 204                 if (commandName == "summary.shared") {
 205                         if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
 206                         Estimators.clear();
 207                         splitAtDash(calc, Estimators);
 208                 }
 209                 if (commandName == "rarefaction.shared") {
 210                         if ((calc == "default") || (calc == "")) { calc = "sharedobserved"; }
 211                         Estimators.clear();
 212                         splitAtDash(calc, Estimators);
 213                 }
 214                 if (commandName == "venn") {
 215                         if ((calc == "default") || (calc == "")) {
 216                                 if (format == "list") { calc = "sobs"; }
 217                                 else { calc = "sharedsobs"; }
 218                         }
 219                         Estimators.clear();
 220                         splitAtDash(calc, Estimators);
 221                 }
 222                 if ((commandName == "tree.shared") || (commandName == "bootstrap.shared")) {
 223                         if (calc != "") {
 224                                 Estimators.clear();
 225                                 splitAtDash(calc, Estimators);
 226                         }else { cout << "You have not specified any calculators." << endl; }
 227                 }
 228
 229
 230                 //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
 231                 if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single")) {
 232                         if (listfile != "") { format = "list"; }
 233                         else if (sabundfile != "") { format = "sabund"; }
 234                         else if (rabundfile != "") { format = "rabund"; }
 235                 }
 236         }
 237         catch(exception& e) {
 238                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 239                 exit(1);
 240         }
 241         catch(...) {
 242                 cout << "An unknown error has occurred in the GlobalData class function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 243                 exit(1);
 244         }
 245 }
 246 /*******************************************************/
 247
 248 /******************************************************/
 249 // These functions give you the option parameters of the commands
 250 string GlobalData::getPhylipFile()              {       return phylipfile;      }
 251 string GlobalData::getColumnFile()              {       return columnfile;      }
 252 string GlobalData::getListFile()                {       return listfile;        }
 253 string GlobalData::getRabundFile()              {       return rabundfile;      }
 254 string GlobalData::getSabundFile()              {       return sabundfile;      }
 255 string GlobalData::getNameFile()                {       return namefile;        }
 256 string GlobalData::getGroupFile()               {       return groupfile;       }
 257 string GlobalData::getOrderFile()               {       return orderfile;       }
 258 string GlobalData::getTreeFile()                {       return treefile;        }
 259 string GlobalData::getSharedFile()              {       return sharedfile;      }
 260 string GlobalData::getFastaFile()               {       return fastafile;       }
 261 string GlobalData::getNexusFile()               {       return nexusfile;       }
 262 string GlobalData::getClustalFile()     {   return clustalfile; }
 263 string GlobalData::getCutOff()                  {       return cutoff;          }
 264 string GlobalData::getFormat()                  {       return format;          }
 265 string GlobalData::getPrecision()               {       return precision;       }
 266 string GlobalData::getMethod()                  {       return method;          }
 267 string GlobalData::getFileRoot()                {       return fileroot;        }
 268 string GlobalData::getIters()                   {       return iters;           }
 269 string GlobalData::getJumble()                  {       return jumble;          }
 270 string GlobalData::getFreq()                    {       return freq;            }
 271 string GlobalData::getAbund()           {   return abund;       }
 272 string GlobalData::getRandomTree()              {       return randomtree;      }
 273 string GlobalData::getGroups()                  {       return groups;          }
 274 string GlobalData::getStep()                    {       return step;            }
 275 string GlobalData::getForm()                    {       return form;            }
 276 string GlobalData::getSorted()                  {       return sorted;          }
 277 string GlobalData::getTrump()                   {   return trump;       }
 278 string GlobalData::getSoft()                    {   return soft;                }
 279 string GlobalData::getFilter()                  {   return filter;              }
 280 string GlobalData::getScale()                   {       return scale;           }
 281
 282 void GlobalData::setListFile(string file)       {       listfile = file;        inputFileName = file;}
 283 void GlobalData::setRabundFile(string file)     {       rabundfile = file;      inputFileName = file;}
 284 void GlobalData::setSabundFile(string file)     {       sabundfile = file;      inputFileName = file;}
 285 void GlobalData::setPhylipFile(string file)     {       phylipfile = file;    inputFileName = file;}
 286 void GlobalData::setColumnFile(string file)     {       columnfile = file;    inputFileName = file;}
 287 void GlobalData::setNameFile(string file)               {       namefile = file;                }
 288 void GlobalData::setFormat(string Format)               {       format = Format;                }
 289 void GlobalData::setRandomTree(string Random)   {       randomtree = Random;    }
 290 void GlobalData::setGroups(string g)                    {       groups = g;                             }
 291 void GlobalData::setCalc(string Calc)                   {       calc = Calc;                    }
 292
 293 /*******************************************************/
 294
 295 /******************************************************/
 296 GlobalData::GlobalData() {
 297         //option definitions should go here...
 298         helpRequest = "";
 299         clear();
 300         gListVector == NULL;
 301         gSparseMatrix == NULL;
 302 }
 303 /*******************************************************/
 304
 305 /******************************************************/
 306 void GlobalData::clear() {
 307         //option definitions should go here...
 308         phylipfile              =       "";
 309         columnfile              =       "";
 310         listfile                =       "";
 311         rabundfile              =       "";
 312         sabundfile              =       "";
 313         namefile                =       "";
 314         groupfile               =       "";
 315         orderfile               =       "";
 316         fastafile               =   "";
 317         nexusfile               =   "";
 318         clustalfile             =   "";
 319         treefile                =       "";
 320         sharedfile              =       "";
 321         cutoff                  =       "10.00";
 322         format                  =       "";
 323         precision               =       "100";
 324         iters                   =       "1000";
 325         line                    =   "";
 326         label                   =       "";
 327         groups                  =       "";
 328         jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
 329         randomtree              =       "";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
 330         freq                    =       "100";
 331         method                  =       "furthest";
 332         fileroot                =       "";
 333         abund           =   "10";
 334         step                    =       "0.01";
 335         form                    =       "integral";
 336         sorted                  =       "T";  //F means don't sort, T means sort.
 337         vertical        =   "";
 338         trump           =   "";
 339         filter          =   "";
 340         soft            =   "";
 341         scale                   =       "log10";
 342
 343 }
 344
 345 //*******************************************************/
 346
 347 /******************************************************/
 348 void GlobalData::reset() {
 349         cutoff                  =       "10.00";
 350         precision               =       "100";
 351         iters                   =       "1000";
 352         groups                  =       "";
 353         jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
 354         sorted                  =       "T";  //F means don't sort, T means sort.
 355         randomtree              =       "";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
 356         freq                    =       "100";
 357         method                  =       "furthest";
 358         calc                    =       "";
 359         abund                   =   "10";
 360         step                    =       "0.01";
 361         form                    =       "integral";
 362 }
 363 /*******************************************************/
 364
 365 /******************************************************/
 366 GlobalData::~GlobalData() {
 367         _uniqueInstance = 0;
 368         if(gListVector != NULL)         {       delete gListVector;             }
 369         if(gSparseMatrix != NULL)       {       delete gSparseMatrix;   }
 370         if(gorder != NULL)                      {       delete gorder;          }
 371 }
 372 /*******************************************************/
 373
 374 /*******************************************************/
 375 void GlobalData::parseTreeFile() {
 376         //only takes names from the first tree and assumes that all trees use the same names.
 377         try {
 378                 string filename = treefile;
 379                 ifstream filehandle;
 380                 openInputFile(filename, filehandle);
 381                 int c, comment;
 382                 comment = 0;
 383
 384                 //if you are not a nexus file
 385                 if ((c = filehandle.peek()) != '#') {
 386                         while((c = filehandle.peek()) != ';') {
 387                                 while ((c = filehandle.peek()) != ';') {
 388                                         // get past comments
 389                                         if(c == '[') {
 390                                                 comment = 1;
 391                                         }
 392                                         if(c == ']'){
 393                                                 comment = 0;
 394                                         }
 395                                         if((c == '(') && (comment != 1)){ break; }
 396                                         filehandle.get();
 397                                 }
 398
 399                                 readTreeString(filehandle);
 400                         }
 401                 //if you are a nexus file
 402                 }else if ((c = filehandle.peek()) == '#') {
 403                         string holder = "";
 404
 405                         // get past comments
 406                         while(holder != "translate" && holder != "Translate"){
 407                                 if(holder == "[" || holder == "[!"){
 408                                         comment = 1;
 409                                 }
 410                                 if(holder == "]"){
 411                                         comment = 0;
 412                                 }
 413                                 filehandle >> holder;
 414
 415                                 //if there is no translate then you must read tree string otherwise use translate to get names
 416                                 if(holder == "tree" && comment != 1){
 417                                         //pass over the "tree rep.6878900 = "
 418                                         while (((c = filehandle.get()) != '(') && ((c = filehandle.peek()) != EOF) ) {;}
 419
 420                                         if (c == EOF ) { break; }
 421                                         filehandle.putback(c);  //put back first ( of tree.
 422                                         readTreeString(filehandle);
 423                                         break;
 424                                 }
 425                         }
 426
 427                         //use nexus translation rather than parsing tree to save time
 428                         if ((holder == "translate") || (holder == "Translate")) {
 429
 430                                 string number, name, h;
 431                                 h = ""; // so it enters the loop the first time
 432                                 while((h != ";") && (number != ";")) {
 433                                         filehandle >> number;
 434                                         filehandle >> name;
 435
 436                                         //c = , until done with translation then c = ;
 437                                         h = name.substr(name.length()-1, name.length());
 438                                         name.erase(name.end()-1);  //erase the comma
 439                                         Treenames.push_back(number);
 440                                 }
 441                                 if (number == ";") { Treenames.pop_back(); }  //in case ';' from translation is on next line instead of next to last name
 442                         }
 443                 }
 444
 445         }
 446         catch(exception& e) {
 447                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 448                 exit(1);
 449         }
 450         catch(...) {
 451                 cout << "An unknown error has occurred in the GlobalData class function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 452                 exit(1);
 453         }
 454 }
 455 /*******************************************************/
 456
 457 /*******************************************************/
 458 void GlobalData::readTreeString(ifstream& filehandle)   {
 459         try {
 460                 int c;
 461                 string name; //k
 462
 463                 while((c = filehandle.peek()) != ';') {
 464                                 //if you are a name
 465                         if ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != '\t') && (c != 32)) { //32 is space
 466                                 name = "";
 467                                 c = filehandle.get();
 468         //              k = c;
 469 //cout << k << endl;
 470                                 while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {
 471                                         name += c;
 472                                         c = filehandle.get();
 473                 //      k = c;
 474 //cout << " in name while " << k << endl;
 475                                 }
 476
 477 //cout << "name = " << name << endl;
 478                                 Treenames.push_back(name);
 479                                 filehandle.putback(c);
 480 //k = c;
 481 //cout << " after putback" <<  k << endl;
 482                         }
 483
 484                         if (c  == ':') { //read until you reach the end of the branch length
 485                                 while ((c != '(') && (c != ')') && (c != ',') && (c != ';') && (c != '\n') && (c != '\t') && (c != 32)) {
 486                                         c = filehandle.get();
 487                                 //      k = c;
 488         //cout << " in branch while " << k << endl;
 489                                 }
 490                                 filehandle.putback(c);
 491                         }
 492                         c = filehandle.get();
 493                         if (c == ';') { break; }
 494                 //      k = c;
 495 //cout << k << endl;
 496
 497                 }
 498         }
 499         catch(exception& e) {
 500                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 501                 exit(1);
 502         }
 503         catch(...) {
 504                 cout << "An unknown error has occurred in the GlobalData class function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 505                 exit(1);
 506         }
 507 }
 508
 509 /*******************************************************/
 510
 511 /*******************************************************/
 512
 513