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                         gListVector = NULL;
  30                         gSparseMatrix = NULL;
  31                         gTree.clear();
  32                         Treenames.clear();
  33                         labels.clear(); lines.clear(); Groups.clear();
  34                         allLines = 1;
  35                 }
  36
  37                 //saves help request
  38                 if (commandName =="help") {
  39                         helpRequest = optionText;
  40                 }
  41
  42                 if (commandName == "libshuff") {
  43                         iters = "10000";
  44                         cutoff = "1.0";
  45                 }
  46
  47                 //set default value for cutoff
  48                 if (commandName == "dist.seqs") {       cutoff = "1.0";         }
  49
  50                 string key, value;
  51                 //reads in parameters and values
  52                 if((optionText != "") && (commandName != "help")){
  53                         while((optionText.find_first_of(',') != -1)) {  //while there are parameters
  54                                 splitAtComma(value, optionText);
  55                                 splitAtEquals(key, value);
  56
  57                                 if (key == "phylip" )   { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";       }
  58                                 if (key == "column" )   { columnfile = value; inputFileName = value; fileroot = value; format = "column";       }
  59                                 if (key == "list" )             { listfile = value; inputFileName = value; fileroot = value; format = "list";           }
  60                                 if (key == "rabund" )   { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
  61                                 if (key == "sabund" )   { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       }
  62                                 if (key == "fasta" )    { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
  63                                 if (key == "nexus" )    { nexusfile = value; inputFileName = value; fileroot = value; format = "nexus";         }
  64                                 if (key == "clustal" )  { clustalfile = value; inputFileName = value; fileroot = value; format = "clustal"; }
  65                                 if (key == "tree" )             { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }
  66                                 if (key == "shared" )   { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile";   }
  67                                 if (key == "name" )             { namefile = value;             }
  68                                 if (key == "order" )    { orderfile = value;    }
  69                                 if (key == "group" )    { groupfile = value;    }
  70                                 if (key == "cutoff" )           { cutoff = value;               }
  71                                 if (key == "precision" )        { precision = value;    }
  72                                 if (key == "iters" )            { iters = value;                }
  73                                 if (key == "jumble" )           { jumble = value;               }
  74                                 if (key == "freq" )                     { freq = value;                 }
  75                                 if (key == "method" )           { method = value;               }
  76                                 if (key == "fileroot" )         { fileroot = value;             }
  77                                 if (key == "abund" )        { abund = value;        }
  78                                 if (key == "random" )           { randomtree = value;   }
  79                                 if (key == "calc")                      { calc = value;                 }
  80                                 if (key == "step")                      { step = value;                 }
  81                                 if (key == "form")                      { form = value;                 }
  82                                 if (key == "sorted")            { sorted = value;               }
  83                                 if (key == "vertical")          { vertical = value;             }
  84                                 if (key == "trump")                 { trump = value;            }
  85                                 if (key == "hard")                      { hard = value;         }
  86                                 if (key == "soft")                  { soft = value;                 }
  87                                 if (key == "scale")                     { scale = value;                }
  88                                 if (key == "countends" )        { countends = value;    }
  89                                 if (key == "processors" )       { processors = value;   }
  90                                 if (key == "size" )         { size = value;         }
  91                                 if (key == "candidate")         { candidatefile = value;        }
  92                                 if (key == "search")            { search = value;               }
  93                                 if (key == "ksize")                     { ksize = value;                }
  94                                 if (key == "align")                 { align = value;            }
  95                                 if (key == "match")                     { match = value;                }
  96                                 if (key == "mismatch")          { mismatch = value;         }
  97                                 if (key == "gapopen")           { gapopen = value;              }
  98                                 if (key == "gapextend" )        { gapextend = value;    }
  99                                 if (key == "start" )            { startPos = value;     }
 100                                 if (key == "end" )                      { endPos = value;       }
 101                                 if (key == "maxambig" )         { maxAmbig = value;     }
 102                                 if (key == "maxhomop" )         { maxHomoPolymer = value;       }
 103                                 if (key == "minlength" )        { minLength = value;    }
 104                                 if (key == "maxlength" )        { maxLength = value;    }
 105
 106                                 if (key == "line") {//stores lines to be used in a vector
 107                                         lines.clear();
 108                                         labels.clear();
 109                                         line = value;
 110                                         label = "";
 111                                         if (line != "all") {  splitAtDash(value, lines);  allLines = 0;  }
 112                                         else { allLines = 1;  }
 113                                 }
 114
 115                                 if (key == "label") {//stores lines to be used in a vector
 116                                         labels.clear();
 117                                         lines.clear();
 118                                         label = value;
 119                                         line = "";
 120                                         if (label != "all") {  splitAtDash(value, labels);  allLines = 0;  }
 121                                         else { allLines = 1;  }
 122                                 }
 123
 124                                 if (key == "groups") {//stores groups to be used in a vector
 125                                         Groups.clear();
 126                                         groups = value;
 127                                         splitAtDash(value, Groups);
 128                                 }
 129
 130                         }
 131
 132                         //saves the last parameter
 133                         value = optionText;
 134                         splitAtEquals(key, value);
 135                         if (key == "phylip" )   { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";       }
 136                         if (key == "column" )   { columnfile = value; inputFileName = value; fileroot = value; format = "column";       }
 137                         if (key == "list" )             { listfile = value; inputFileName = value; fileroot = value; format = "list";           }
 138                         if (key == "rabund" )   { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
 139                         if (key == "sabund" )   { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       }
 140                         if (key == "fasta" )    { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
 141                         if (key == "nexus" )    { nexusfile = value; inputFileName = value; fileroot = value; format = "nexus";         }
 142                         if (key == "clustal" )  { clustalfile = value; inputFileName = value; fileroot = value; format = "clustal"; }
 143                         if (key == "tree" )             { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }
 144                         if (key == "shared" )   { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile";   }
 145                         if (key == "name" )             { namefile = value;             }
 146                         if (key == "order" )    { orderfile = value;    }
 147                         if (key == "group" )    { groupfile = value;    }
 148                         if (key == "cutoff" )           { cutoff = value;               }
 149                         if (key == "precision" )        { precision = value;    }
 150                         if (key == "iters" )            { iters = value;                }
 151                         if (key == "jumble" )           { jumble = value;               }
 152                         if (key == "freq" )                     { freq = value;                 }
 153                         if (key == "method" )           { method = value;               }
 154                         if (key == "fileroot" )         { fileroot = value;             }
 155                         if (key == "abund" )        { abund = value;        }
 156                         if (key == "random" )           { randomtree = value;   }
 157                         if (key == "calc")                      { calc = value;                 }
 158                         if (key == "step")                      { step = value;                 }
 159                         if (key == "form")                      { form = value;                 }
 160                         if (key == "sorted")            { sorted = value;               }
 161                         if (key == "vertical")          { vertical = value;             }
 162                         if (key == "trump")                 { trump = value;            }
 163                         if (key == "hard")                      { hard = value;         }
 164                         if (key == "soft")                  { soft = value;                 }
 165                         if (key == "scale")                     { scale = value;                }
 166                         if (key == "countends" )        { countends = value;    }
 167                         if (key == "processors" )       { processors = value;   }
 168                         if (key == "size" )         { size = value;         }
 169                         if (key == "candidate")         { candidatefile = value;        }
 170                         if (key == "search")            { search = value;               }
 171                         if (key == "ksize")                     { ksize = value;                }
 172                         if (key == "align")                 { align = value;            }
 173                         if (key == "match")                     { match = value;                }
 174                         if (key == "mismatch")          { mismatch = value;         }
 175                         if (key == "gapopen")           { gapopen = value;              }
 176                         if (key == "gapextend" )        { gapextend = value;    }
 177                         if (key == "start" )            { startPos = value;     }
 178                         if (key == "end" )                      { endPos = value;       }
 179                         if (key == "maxambig" )         { maxAmbig = value;     }
 180                         if (key == "maxhomop" )         { maxHomoPolymer = value;       }
 181                         if (key == "minlength" )        { minLength = value;    }
 182                         if (key == "maxlength" )        { maxLength = value;    }
 183
 184
 185                         if (key == "line") {//stores lines to be used in a vector
 186                                 lines.clear();
 187                                 labels.clear();
 188                                 line = value;
 189                                 label = "";
 190                                 if (line != "all") {  splitAtDash(value, lines);  allLines = 0;  }
 191                                 else { allLines = 1;  }
 192                         }
 193
 194                         if (key == "label") {//stores lines to be used in a vector
 195                                 labels.clear();
 196                                 lines.clear();
 197                                 label = value;
 198                                 line = "";
 199                                 if (label != "all") {  splitAtDash(value, labels);  allLines = 0;  }
 200                                 else { allLines = 1;  }
 201                         }
 202
 203                         if (key == "groups") {//stores groups to be used in a vector
 204                                         Groups.clear();
 205                                         groups = value;
 206                                         splitAtDash(value, Groups);
 207                         }
 208                 }
 209
 210                 //set format for shared
 211                 if ((listfile != "") && (groupfile != "")) { format = "shared"; }
 212                 if ((phylipfile != "") && (groupfile != "")) { format = "matrix"; }
 213
 214                 //input defaults for calculators
 215                 if (commandName == "collect.single") {
 216
 217                         if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
 218                         Estimators.clear();
 219                         splitAtDash(calc, Estimators);
 220                 }
 221                 if (commandName == "rarefaction.single") {
 222                         if ((calc == "default") || (calc == "")) { calc = "sobs"; }
 223                         Estimators.clear();
 224                         splitAtDash(calc, Estimators);
 225                 }
 226                 if (commandName == "collect.shared") {
 227                         if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
 228                         Estimators.clear();
 229                         splitAtDash(calc, Estimators);
 230                 }
 231                 if (commandName == "summary.single") {
 232                         if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
 233                         Estimators.clear();
 234                         splitAtDash(calc, Estimators);
 235                 }
 236                 if (commandName == "summary.shared") {
 237                         if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
 238                         Estimators.clear();
 239                         splitAtDash(calc, Estimators);
 240                 }
 241                 if (commandName == "rarefaction.shared") {
 242                         if ((calc == "default") || (calc == "")) { calc = "sharedobserved"; }
 243                         Estimators.clear();
 244                         splitAtDash(calc, Estimators);
 245                 }
 246                 if (commandName == "dist.seqs") {
 247                         if ((calc == "default") || (calc == "")) {  calc = "onegap";    }
 248                         if (countends == "")    { countends = "T"; }
 249                         Estimators.clear();
 250                         splitAtDash(calc, Estimators);
 251                 }
 252                 if (commandName == "venn") {
 253                         if ((calc == "default") || (calc == "")) {
 254                                 if (format == "list") { calc = "sobs"; }
 255                                 else { calc = "sharedsobs"; }
 256                         }
 257                         Estimators.clear();
 258                         splitAtDash(calc, Estimators);
 259                 }
 260                 if ((commandName == "tree.shared") || (commandName == "bootstrap.shared") || (commandName == "dist.shared")) {
 261                         if ((calc == "default") || (calc == "")) {
 262                                 calc = "jclass-thetayc";
 263                         }
 264                         Estimators.clear();
 265                         splitAtDash(calc, Estimators);
 266                 }
 267
 268                 if(commandName == "filter.seqs"){
 269                         if(trump == "" && vertical == "" && hard == "" && soft == ""){
 270                                 trump = '.';
 271                         }
 272
 273                 }
 274
 275                 //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
 276                 if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single")) {
 277                         if (listfile != "") { format = "list"; }
 278                         else if (sabundfile != "") { format = "sabund"; }
 279                         else if (rabundfile != "") { format = "rabund"; }
 280                 }
 281         }
 282         catch(exception& e) {
 283                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 284                 exit(1);
 285         }
 286         catch(...) {
 287                 cout << "An unknown error has occurred in the GlobalData class function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 288                 exit(1);
 289         }
 290 }
 291 /*******************************************************/
 292
 293 /******************************************************/
 294 // These functions give you the option parameters of the commands
 295 string GlobalData::getPhylipFile()              {       return phylipfile;      }
 296 string GlobalData::getColumnFile()              {       return columnfile;      }
 297 string GlobalData::getListFile()                {       return listfile;        }
 298 string GlobalData::getRabundFile()              {       return rabundfile;      }
 299 string GlobalData::getSabundFile()              {       return sabundfile;      }
 300 string GlobalData::getNameFile()                {       return namefile;        }
 301 string GlobalData::getGroupFile()               {       return groupfile;       }
 302 string GlobalData::getOrderFile()               {       return orderfile;       }
 303 string GlobalData::getTreeFile()                {       return treefile;        }
 304 string GlobalData::getSharedFile()              {       return sharedfile;      }
 305 string GlobalData::getFastaFile()               {       return fastafile;       }
 306 string GlobalData::getNexusFile()               {       return nexusfile;       }
 307 string GlobalData::getClustalFile()     {   return clustalfile; }
 308 string GlobalData::getCutOff()                  {       return cutoff;          }
 309 string GlobalData::getFormat()                  {       return format;          }
 310 string GlobalData::getPrecision()               {       return precision;       }
 311 string GlobalData::getMethod()                  {       return method;          }
 312 string GlobalData::getFileRoot()                {       return fileroot;        }
 313 string GlobalData::getIters()                   {       return iters;           }
 314 string GlobalData::getJumble()                  {       return jumble;          }
 315 string GlobalData::getFreq()                    {       return freq;            }
 316 string GlobalData::getAbund()           {   return abund;       }
 317 string GlobalData::getRandomTree()              {       return randomtree;      }
 318 string GlobalData::getGroups()                  {       return groups;          }
 319 string GlobalData::getStep()                    {       return step;            }
 320 string GlobalData::getForm()                    {       return form;            }
 321 string GlobalData::getSorted()                  {       return sorted;          }
 322 string GlobalData::getVertical()                {   return vertical;    }
 323 string GlobalData::getTrump()                   {   return trump;       }
 324 string GlobalData::getSoft()                    {   return soft;                }
 325 string GlobalData::getHard()                    {   return hard;                }
 326 string GlobalData::getScale()                   {       return scale;           }
 327 string GlobalData::getCountEnds()               {   return countends;   }
 328 string GlobalData::getProcessors()              {       return processors;      }
 329 string GlobalData::getSize()            {   return size;        }
 330 string GlobalData::getCandidateFile()   {       return candidatefile;}
 331 string GlobalData::getSearch()                  {       return search;          }
 332 string GlobalData::getKSize()                   {       return ksize;           }
 333 string GlobalData::getAlign()                   {       return align;           }
 334 string GlobalData::getMatch()                   {       return match;           }
 335 string GlobalData::getMismatch()                {       return mismatch;        }
 336 string GlobalData::getGapopen()                 {       return gapopen;         }
 337 string GlobalData::getGapextend()               {       return gapextend;       }
 338 string GlobalData::getStartPos()                {       return startPos;        }
 339 string GlobalData::getEndPos()                  {       return endPos;          }
 340 string GlobalData::getMaxAmbig()                {       return maxAmbig;        }
 341 string GlobalData::getMaxHomoPolymer()  {       return maxHomoPolymer;  }
 342 string GlobalData::getMinLength()               {       return minLength;       }
 343 string GlobalData::getMaxLength()               {       return maxLength;       }
 344
 345
 346 void GlobalData::setListFile(string file)               {       listfile = file;        inputFileName = file;                                   }
 347 void GlobalData::setRabundFile(string file)             {       rabundfile = file;      inputFileName = file;                                   }
 348 void GlobalData::setSabundFile(string file)             {       sabundfile = file;      inputFileName = file;                                   }
 349 void GlobalData::setPhylipFile(string file)             {       phylipfile = file;    inputFileName = file;                                     }
 350 void GlobalData::setColumnFile(string file)             {       columnfile = file;    inputFileName = file;                                     }
 351 void GlobalData::setGroupFile(string file)              {       groupfile = file;                                                                                       }
 352 void GlobalData::setSharedFile(string file)             {       sharedfile = file;      inputFileName = file; fileroot = file;  }
 353 void GlobalData::setNameFile(string file)               {       namefile = file;                }
 354 void GlobalData::setFormat(string Format)               {       format = Format;                }
 355 void GlobalData::setRandomTree(string Random)   {       randomtree = Random;    }
 356 void GlobalData::setGroups(string g)                    {       groups = g;                             }
 357 void GlobalData::setCalc(string Calc)                   {       calc = Calc;                    }
 358 void GlobalData::setCountEnds(string e)                 {   countends = e;                      }
 359 void GlobalData::setProcessors(string p)                {       processors = p;                 }
 360
 361
 362 /*******************************************************/
 363
 364 /******************************************************/
 365 GlobalData::GlobalData() {
 366         //option definitions should go here...
 367         helpRequest = "";
 368         clear();
 369         gListVector == NULL;
 370         gSparseMatrix == NULL;
 371 }
 372 /*******************************************************/
 373
 374 /******************************************************/
 375 void GlobalData::clear() {
 376         //option definitions should go here...
 377         phylipfile              =       "";
 378         columnfile              =       "";
 379         listfile                =       "";
 380         rabundfile              =       "";
 381         sabundfile              =       "";
 382         namefile                =       "";
 383         groupfile               =       "";
 384         orderfile               =       "";
 385         fastafile               =   "";
 386         nexusfile               =   "";
 387         clustalfile             =   "";
 388         treefile                =       "";
 389         sharedfile              =       "";
 390         candidatefile   =       "";
 391         cutoff                  =       "10.00";
 392         format                  =       "";
 393         precision               =       "100";
 394         iters                   =       "1000";
 395         line                    =   "";
 396         label                   =       "";
 397         groups                  =       "";
 398         jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
 399         randomtree              =       "";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
 400         freq                    =       "100";
 401         method                  =       "furthest";
 402         fileroot                =       "";
 403         abund           =   "10";
 404         step                    =       "0.01";
 405         form                    =       "integral";
 406         sorted                  =       "T";  //F means don't sort, T means sort.
 407         vertical        =   "";
 408         trump           =       "";
 409         hard                    =   "";
 410         soft            =   "";
 411         scale                   =       "log10";
 412         countends               =   "T";  //yes
 413         processors              =       "1";
 414         size            =   "0";
 415         search                  =       "kmer";
 416         ksize                   =       "8";
 417         align                   =       "needleman";
 418         match                   =       "1.0";
 419         mismatch                =       "-1.0";
 420         gapopen                 =       "-1.0";
 421         gapextend               =       "-2.0";
 422         startPos                =       "-1";
 423         endPos                  =       "-1";
 424         maxAmbig                =       "-1";
 425         maxHomoPolymer  =       "-1";
 426         minLength               =       "-1";
 427         maxLength               =       "-1";
 428
 429 }
 430
 431 //*******************************************************/
 432
 433 /******************************************************/
 434 void GlobalData::reset() {
 435         cutoff                  =       "10.00";
 436         precision               =       "100";
 437         iters                   =       "1000";
 438         groups                  =       "";
 439         jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
 440         sorted                  =       "T";  //F means don't sort, T means sort.
 441         randomtree              =       "";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
 442         freq                    =       "100";
 443         method                  =       "furthest";
 444         calc                    =       "";
 445         abund                   =   "10";
 446         step                    =       "0.01";
 447         form                    =       "integral";
 448         countends               =   "T";
 449         processors              =       "1";
 450         size            =   "0";
 451         search                  =       "kmer";
 452         ksize                   =       "8";
 453         align                   =       "needleman";
 454         match                   =       "1.0";
 455         mismatch                =       "-1.0";
 456         gapopen                 =       "-1.0";
 457         gapextend               =       "-2.0";
 458         vertical        =   "";
 459         trump           =   "";
 460         hard                    =   "";
 461         soft            =   "";
 462         startPos                =       "-1";
 463         endPos                  =       "-1";
 464         maxAmbig                =       "-1";
 465         maxHomoPolymer  =       "-1";
 466         minLength               =       "-1";
 467         maxLength               =       "-1";
 468
 469 }
 470 /*******************************************************/
 471
 472 /******************************************************/
 473 GlobalData::~GlobalData() {
 474         _uniqueInstance = 0;
 475         if(gListVector != NULL)         {       delete gListVector;             }
 476         if(gSparseMatrix != NULL)       {       delete gSparseMatrix;   }
 477         if(gorder != NULL)                      {       delete gorder;          }
 478 }
 479 /*******************************************************/
 480
 481 /*******************************************************/
 482 void GlobalData::parseTreeFile() {
 483         //Why is THIS in GlobalData??? - PDS
 484
 485         //only takes names from the first tree and assumes that all trees use the same names.
 486         try {
 487                 string filename = treefile;
 488                 ifstream filehandle;
 489                 openInputFile(filename, filehandle);
 490                 int c, comment;
 491                 comment = 0;
 492
 493                 //if you are not a nexus file
 494                 if ((c = filehandle.peek()) != '#') {
 495                         while((c = filehandle.peek()) != ';') {
 496                                 while ((c = filehandle.peek()) != ';') {
 497                                         // get past comments
 498                                         if(c == '[') {
 499                                                 comment = 1;
 500                                         }
 501                                         if(c == ']'){
 502                                                 comment = 0;
 503                                         }
 504                                         if((c == '(') && (comment != 1)){ break; }
 505                                         filehandle.get();
 506                                 }
 507
 508                                 readTreeString(filehandle);
 509                         }
 510                 //if you are a nexus file
 511                 }else if ((c = filehandle.peek()) == '#') {
 512                         string holder = "";
 513
 514                         // get past comments
 515                         while(holder != "translate" && holder != "Translate"){
 516                                 if(holder == "[" || holder == "[!"){
 517                                         comment = 1;
 518                                 }
 519                                 if(holder == "]"){
 520                                         comment = 0;
 521                                 }
 522                                 filehandle >> holder;
 523
 524                                 //if there is no translate then you must read tree string otherwise use translate to get names
 525                                 if(holder == "tree" && comment != 1){
 526                                         //pass over the "tree rep.6878900 = "
 527                                         while (((c = filehandle.get()) != '(') && ((c = filehandle.peek()) != EOF) ) {;}
 528
 529                                         if (c == EOF ) { break; }
 530                                         filehandle.putback(c);  //put back first ( of tree.
 531                                         readTreeString(filehandle);
 532                                         break;
 533                                 }
 534                         }
 535
 536                         //use nexus translation rather than parsing tree to save time
 537                         if ((holder == "translate") || (holder == "Translate")) {
 538
 539                                 string number, name, h;
 540                                 h = ""; // so it enters the loop the first time
 541                                 while((h != ";") && (number != ";")) {
 542                                         filehandle >> number;
 543                                         filehandle >> name;
 544
 545                                         //c = , until done with translation then c = ;
 546                                         h = name.substr(name.length()-1, name.length());
 547                                         name.erase(name.end()-1);  //erase the comma
 548                                         Treenames.push_back(number);
 549                                 }
 550                                 if (number == ";") { Treenames.pop_back(); }  //in case ';' from translation is on next line instead of next to last name
 551                         }
 552                 }
 553
 554         }
 555         catch(exception& e) {
 556                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 557                 exit(1);
 558         }
 559         catch(...) {
 560                 cout << "An unknown error has occurred in the GlobalData class function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 561                 exit(1);
 562         }
 563 }
 564 /*******************************************************/
 565
 566 /*******************************************************/
 567 void GlobalData::readTreeString(ifstream& filehandle)   {
 568         try {
 569                 int c;
 570                 string name; //k
 571
 572                 while((c = filehandle.peek()) != ';') {
 573                                 //if you are a name
 574                         if ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != '\t') && (c != 32)) { //32 is space
 575                                 name = "";
 576                                 c = filehandle.get();
 577         //              k = c;
 578 //cout << k << endl;
 579                                 while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {
 580                                         name += c;
 581                                         c = filehandle.get();
 582                 //      k = c;
 583 //cout << " in name while " << k << endl;
 584                                 }
 585
 586 //cout << "name = " << name << endl;
 587                                 Treenames.push_back(name);
 588                                 filehandle.putback(c);
 589 //k = c;
 590 //cout << " after putback" <<  k << endl;
 591                         }
 592
 593                         if (c  == ':') { //read until you reach the end of the branch length
 594                                 while ((c != '(') && (c != ')') && (c != ',') && (c != ';') && (c != '\n') && (c != '\t') && (c != 32)) {
 595                                         c = filehandle.get();
 596                                 //      k = c;
 597         //cout << " in branch while " << k << endl;
 598                                 }
 599                                 filehandle.putback(c);
 600                         }
 601                         c = filehandle.get();
 602                         if (c == ';') { break; }
 603                 //      k = c;
 604 //cout << k << endl;
 605
 606                 }
 607         }
 608         catch(exception& e) {
 609                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 610                 exit(1);
 611         }
 612         catch(...) {
 613                 cout << "An unknown error has occurred in the GlobalData class function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 614                 exit(1);
 615         }
 616 }
 617
 618 /*******************************************************/
 619
 620 /*******************************************************/
 621
 622