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
 100                                 if (key == "line") {//stores lines to be used in a set
 101                                         lines.clear();
 102                                         labels.clear();
 103                                         line = value;
 104                                         label = "";
 105                                         splitAtDash(value, lines);
 106                                         allLines = 0;
 107                                 }
 108                                 if (key == "label") {//stores labels to be used in a set
 109                                         labels.clear();
 110                                         lines.clear();
 111                                         label = value;
 112                                         line = "";
 113                                         splitAtDash(value, labels);
 114                                         allLines = 0;
 115                                 }
 116
 117                                 if (key == "groups") {//stores groups to be used in a vector
 118                                         Groups.clear();
 119                                         groups = value;
 120                                         splitAtDash(value, Groups);
 121                                 }
 122
 123                         }
 124
 125                         //saves the last parameter
 126                         value = optionText;
 127                         splitAtEquals(key, value);
 128                         if (key == "phylip" )   { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";       }
 129                         if (key == "column" )   { columnfile = value; inputFileName = value; fileroot = value; format = "column";       }
 130                         if (key == "list" )             { listfile = value; inputFileName = value; fileroot = value; format = "list";           }
 131                         if (key == "rabund" )   { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
 132                         if (key == "sabund" )   { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       }
 133                         if (key == "fasta" )    { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
 134                         if (key == "nexus" )    { nexusfile = value; inputFileName = value; fileroot = value; format = "nexus";         }
 135                         if (key == "clustal" )  { clustalfile = value; inputFileName = value; fileroot = value; format = "clustal"; }
 136                         if (key == "tree" )             { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }
 137                         if (key == "shared" )   { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile";   }
 138                         if (key == "name" )             { namefile = value;             }
 139                         if (key == "order" )    { orderfile = value;    }
 140                         if (key == "group" )    { groupfile = value;    }
 141                         if (key == "cutoff" )           { cutoff = value;               }
 142                         if (key == "precision" )        { precision = value;    }
 143                         if (key == "iters" )            { iters = value;                }
 144                         if (key == "jumble" )           { jumble = value;               }
 145                         if (key == "freq" )                     { freq = value;                 }
 146                         if (key == "method" )           { method = value;               }
 147                         if (key == "fileroot" )         { fileroot = value;             }
 148                         if (key == "abund" )        { abund = value;        }
 149                         if (key == "random" )           { randomtree = value;   }
 150                         if (key == "calc")                      { calc = value;                 }
 151                         if (key == "step")                      { step = value;                 }
 152                         if (key == "form")                      { form = value;                 }
 153                         if (key == "sorted")            { sorted = value;               }
 154                         if (key == "vertical")          { vertical = value;             }
 155                         if (key == "trump")                 { trump = value;            }
 156                         if (key == "hard")                      { hard = value;         }
 157                         if (key == "soft")                  { soft = value;                 }
 158                         if (key == "scale")                     { scale = value;                }
 159                         if (key == "countends" )        { countends = value;    }
 160                         if (key == "processors" )       { processors = value;   }
 161                         if (key == "size" )         { size = value;         }
 162                         if (key == "candidate")         { candidatefile = value;        }
 163                         if (key == "search")            { search = value;               }
 164                         if (key == "ksize")                     { ksize = value;                }
 165                         if (key == "align")                 { align = value;            }
 166                         if (key == "match")                     { match = value;                }
 167                         if (key == "mismatch")          { mismatch = value;         }
 168                         if (key == "gapopen")           { gapopen = value;              }
 169                         if (key == "gapextend" )        { gapextend = value;    }
 170
 171                         if (key == "line") {//stores lines to be used in a vector
 172                                 lines.clear();
 173                                 labels.clear();
 174                                 line = value;
 175                                 label = "";
 176                                 if (line != "all") {  splitAtDash(value, lines);  allLines = 0;  }
 177                                 else { allLines = 1;  }
 178                         }
 179
 180                         if (key == "label") {//stores lines to be used in a vector
 181                                 labels.clear();
 182                                 lines.clear();
 183                                 label = value;
 184                                 line = "";
 185                                 if (label != "all") {  splitAtDash(value, labels);  allLines = 0;  }
 186                                 else { allLines = 1;  }
 187                         }
 188
 189                         if (key == "groups") {//stores groups to be used in a vector
 190                                         Groups.clear();
 191                                         groups = value;
 192                                         splitAtDash(value, Groups);
 193                         }
 194                 }
 195
 196                 //set format for shared
 197                 if ((listfile != "") && (groupfile != "")) { format = "shared"; }
 198                 if ((phylipfile != "") && (groupfile != "")) { format = "matrix"; }
 199
 200                 //input defaults for calculators
 201                 if (commandName == "collect.single") {
 202
 203                         if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
 204                         Estimators.clear();
 205                         splitAtDash(calc, Estimators);
 206                 }
 207                 if (commandName == "rarefaction.single") {
 208                         if ((calc == "default") || (calc == "")) { calc = "sobs"; }
 209                         Estimators.clear();
 210                         splitAtDash(calc, Estimators);
 211                 }
 212                 if (commandName == "collect.shared") {
 213
 214                         if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
 215                         Estimators.clear();
 216                         splitAtDash(calc, Estimators);
 217                 }
 218                 if (commandName == "summary.single") {
 219                         if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
 220                         Estimators.clear();
 221                         splitAtDash(calc, Estimators);
 222                 }
 223                 if (commandName == "summary.shared") {
 224                         if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
 225                         Estimators.clear();
 226                         splitAtDash(calc, Estimators);
 227                 }
 228                 if (commandName == "rarefaction.shared") {
 229                         if ((calc == "default") || (calc == "")) { calc = "sharedobserved"; }
 230                         Estimators.clear();
 231                         splitAtDash(calc, Estimators);
 232                 }
 233                 if (commandName == "dist.seqs") {
 234                         if ((calc == "default") || (calc == "")) {  calc = "onegap";    }
 235                         if (countends == "")    { countends = "T"; }
 236                         Estimators.clear();
 237                         splitAtDash(calc, Estimators);
 238                 }
 239                 if (commandName == "venn") {
 240                         if ((calc == "default") || (calc == "")) {
 241                                 if (format == "list") { calc = "sobs"; }
 242                                 else { calc = "sharedsobs"; }
 243                         }
 244                         Estimators.clear();
 245                         splitAtDash(calc, Estimators);
 246                 }
 247                 if ((commandName == "tree.shared") || (commandName == "bootstrap.shared") || (commandName == "dist.shared")) {
 248                         if ((calc == "default") || (calc == "")) {
 249                                 calc = "jclass-thetayc";
 250                         }
 251                         Estimators.clear();
 252                         splitAtDash(calc, Estimators);
 253                 }
 254
 255                 if(commandName == "filter.seqs"){
 256                         if(trump == "" && vertical == "" && hard == "" && soft == ""){
 257                                 trump = '.';
 258                         }
 259
 260                 }
 261
 262                 //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
 263                 if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single")) {
 264                         if (listfile != "") { format = "list"; }
 265                         else if (sabundfile != "") { format = "sabund"; }
 266                         else if (rabundfile != "") { format = "rabund"; }
 267                 }
 268         }
 269         catch(exception& e) {
 270                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 271                 exit(1);
 272         }
 273         catch(...) {
 274                 cout << "An unknown error has occurred in the GlobalData class function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 275                 exit(1);
 276         }
 277 }
 278 /*******************************************************/
 279
 280 /******************************************************/
 281 // These functions give you the option parameters of the commands
 282 string GlobalData::getPhylipFile()              {       return phylipfile;      }
 283 string GlobalData::getColumnFile()              {       return columnfile;      }
 284 string GlobalData::getListFile()                {       return listfile;        }
 285 string GlobalData::getRabundFile()              {       return rabundfile;      }
 286 string GlobalData::getSabundFile()              {       return sabundfile;      }
 287 string GlobalData::getNameFile()                {       return namefile;        }
 288 string GlobalData::getGroupFile()               {       return groupfile;       }
 289 string GlobalData::getOrderFile()               {       return orderfile;       }
 290 string GlobalData::getTreeFile()                {       return treefile;        }
 291 string GlobalData::getSharedFile()              {       return sharedfile;      }
 292 string GlobalData::getFastaFile()               {       return fastafile;       }
 293 string GlobalData::getNexusFile()               {       return nexusfile;       }
 294 string GlobalData::getClustalFile()     {   return clustalfile; }
 295 string GlobalData::getCutOff()                  {       return cutoff;          }
 296 string GlobalData::getFormat()                  {       return format;          }
 297 string GlobalData::getPrecision()               {       return precision;       }
 298 string GlobalData::getMethod()                  {       return method;          }
 299 string GlobalData::getFileRoot()                {       return fileroot;        }
 300 string GlobalData::getIters()                   {       return iters;           }
 301 string GlobalData::getJumble()                  {       return jumble;          }
 302 string GlobalData::getFreq()                    {       return freq;            }
 303 string GlobalData::getAbund()           {   return abund;       }
 304 string GlobalData::getRandomTree()              {       return randomtree;      }
 305 string GlobalData::getGroups()                  {       return groups;          }
 306 string GlobalData::getStep()                    {       return step;            }
 307 string GlobalData::getForm()                    {       return form;            }
 308 string GlobalData::getSorted()                  {       return sorted;          }
 309 string GlobalData::getVertical()                {   return vertical;    }
 310 string GlobalData::getTrump()                   {   return trump;       }
 311 string GlobalData::getSoft()                    {   return soft;                }
 312 string GlobalData::getHard()                    {   return hard;                }
 313 string GlobalData::getScale()                   {       return scale;           }
 314 string GlobalData::getCountEnds()               {   return countends;   }
 315 string GlobalData::getProcessors()              {       return processors;      }
 316 string GlobalData::getSize()            {   return size;        }
 317 string GlobalData::getCandidateFile()   {       return candidatefile;}
 318 string GlobalData::getSearch()                  {       return search;          }
 319 string GlobalData::getKSize()                   {       return ksize;           }
 320 string GlobalData::getAlign()                   {       return align;           }
 321 string GlobalData::getMatch()                   {       return match;           }
 322 string GlobalData::getMismatch()                {       return mismatch;        }
 323 string GlobalData::getGapopen()                 {       return gapopen;         }
 324 string GlobalData::getGapextend()               {       return gapextend;       }
 325
 326
 327 void GlobalData::setListFile(string file)               {       listfile = file;        inputFileName = file;                                   }
 328 void GlobalData::setRabundFile(string file)             {       rabundfile = file;      inputFileName = file;                                   }
 329 void GlobalData::setSabundFile(string file)             {       sabundfile = file;      inputFileName = file;                                   }
 330 void GlobalData::setPhylipFile(string file)             {       phylipfile = file;    inputFileName = file;                                     }
 331 void GlobalData::setColumnFile(string file)             {       columnfile = file;    inputFileName = file;                                     }
 332 void GlobalData::setGroupFile(string file)              {       groupfile = file;                                                                                       }
 333 void GlobalData::setSharedFile(string file)             {       sharedfile = file;      inputFileName = file; fileroot = file;  }
 334 void GlobalData::setNameFile(string file)               {       namefile = file;                }
 335 void GlobalData::setFormat(string Format)               {       format = Format;                }
 336 void GlobalData::setRandomTree(string Random)   {       randomtree = Random;    }
 337 void GlobalData::setGroups(string g)                    {       groups = g;                             }
 338 void GlobalData::setCalc(string Calc)                   {       calc = Calc;                    }
 339 void GlobalData::setCountEnds(string e)                 {   countends = e;                      }
 340 void GlobalData::setProcessors(string p)                {       processors = p;                 }
 341
 342
 343 /*******************************************************/
 344
 345 /******************************************************/
 346 GlobalData::GlobalData() {
 347         //option definitions should go here...
 348         helpRequest = "";
 349         clear();
 350         gListVector == NULL;
 351         gSparseMatrix == NULL;
 352 }
 353 /*******************************************************/
 354
 355 /******************************************************/
 356 void GlobalData::clear() {
 357         //option definitions should go here...
 358         phylipfile              =       "";
 359         columnfile              =       "";
 360         listfile                =       "";
 361         rabundfile              =       "";
 362         sabundfile              =       "";
 363         namefile                =       "";
 364         groupfile               =       "";
 365         orderfile               =       "";
 366         fastafile               =   "";
 367         nexusfile               =   "";
 368         clustalfile             =   "";
 369         treefile                =       "";
 370         sharedfile              =       "";
 371         candidatefile   =       "";
 372         cutoff                  =       "10.00";
 373         format                  =       "";
 374         precision               =       "100";
 375         iters                   =       "1000";
 376         line                    =   "";
 377         label                   =       "";
 378         groups                  =       "";
 379         jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
 380         randomtree              =       "";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
 381         freq                    =       "100";
 382         method                  =       "furthest";
 383         fileroot                =       "";
 384         abund           =   "10";
 385         step                    =       "0.01";
 386         form                    =       "integral";
 387         sorted                  =       "T";  //F means don't sort, T means sort.
 388         vertical        =   "";
 389         trump           =       "";
 390         hard                    =   "";
 391         soft            =   "";
 392         scale                   =       "log10";
 393         countends               =   "T";  //yes
 394         processors              =       "1";
 395         size            =   "0";
 396         search                  =       "kmer";
 397         ksize                   =       "7";
 398         align                   =       "needleman";
 399         match                   =       "1.0";
 400         mismatch                =       "-1.0";
 401         gapopen                 =       "-1.0";
 402         gapextend               =       "-2.0";
 403 }
 404
 405 //*******************************************************/
 406
 407 /******************************************************/
 408 void GlobalData::reset() {
 409         cutoff                  =       "10.00";
 410         precision               =       "100";
 411         iters                   =       "1000";
 412         groups                  =       "";
 413         jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
 414         sorted                  =       "T";  //F means don't sort, T means sort.
 415         randomtree              =       "";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
 416         freq                    =       "100";
 417         method                  =       "furthest";
 418         calc                    =       "";
 419         abund                   =   "10";
 420         step                    =       "0.01";
 421         form                    =       "integral";
 422         countends               =   "T";
 423         processors              =       "1";
 424         size            =   "0";
 425         search                  =       "kmer";
 426         ksize                   =       "7";
 427         align                   =       "needleman";
 428         match                   =       "1.0";
 429         mismatch                =       "-1.0";
 430         gapopen                 =       "-1.0";
 431         gapextend               =       "-2.0";
 432         vertical        =   "";
 433         trump           =   "";
 434         hard                    =   "";
 435         soft            =   "";
 436
 437 }
 438 /*******************************************************/
 439
 440 /******************************************************/
 441 GlobalData::~GlobalData() {
 442         _uniqueInstance = 0;
 443         if(gListVector != NULL)         {       delete gListVector;             }
 444         if(gSparseMatrix != NULL)       {       delete gSparseMatrix;   }
 445         if(gorder != NULL)                      {       delete gorder;          }
 446 }
 447 /*******************************************************/
 448
 449 /*******************************************************/
 450 void GlobalData::parseTreeFile() {
 451         //only takes names from the first tree and assumes that all trees use the same names.
 452         try {
 453                 string filename = treefile;
 454                 ifstream filehandle;
 455                 openInputFile(filename, filehandle);
 456                 int c, comment;
 457                 comment = 0;
 458
 459                 //if you are not a nexus file
 460                 if ((c = filehandle.peek()) != '#') {
 461                         while((c = filehandle.peek()) != ';') {
 462                                 while ((c = filehandle.peek()) != ';') {
 463                                         // get past comments
 464                                         if(c == '[') {
 465                                                 comment = 1;
 466                                         }
 467                                         if(c == ']'){
 468                                                 comment = 0;
 469                                         }
 470                                         if((c == '(') && (comment != 1)){ break; }
 471                                         filehandle.get();
 472                                 }
 473
 474                                 readTreeString(filehandle);
 475                         }
 476                 //if you are a nexus file
 477                 }else if ((c = filehandle.peek()) == '#') {
 478                         string holder = "";
 479
 480                         // get past comments
 481                         while(holder != "translate" && holder != "Translate"){
 482                                 if(holder == "[" || holder == "[!"){
 483                                         comment = 1;
 484                                 }
 485                                 if(holder == "]"){
 486                                         comment = 0;
 487                                 }
 488                                 filehandle >> holder;
 489
 490                                 //if there is no translate then you must read tree string otherwise use translate to get names
 491                                 if(holder == "tree" && comment != 1){
 492                                         //pass over the "tree rep.6878900 = "
 493                                         while (((c = filehandle.get()) != '(') && ((c = filehandle.peek()) != EOF) ) {;}
 494
 495                                         if (c == EOF ) { break; }
 496                                         filehandle.putback(c);  //put back first ( of tree.
 497                                         readTreeString(filehandle);
 498                                         break;
 499                                 }
 500                         }
 501
 502                         //use nexus translation rather than parsing tree to save time
 503                         if ((holder == "translate") || (holder == "Translate")) {
 504
 505                                 string number, name, h;
 506                                 h = ""; // so it enters the loop the first time
 507                                 while((h != ";") && (number != ";")) {
 508                                         filehandle >> number;
 509                                         filehandle >> name;
 510
 511                                         //c = , until done with translation then c = ;
 512                                         h = name.substr(name.length()-1, name.length());
 513                                         name.erase(name.end()-1);  //erase the comma
 514                                         Treenames.push_back(number);
 515                                 }
 516                                 if (number == ";") { Treenames.pop_back(); }  //in case ';' from translation is on next line instead of next to last name
 517                         }
 518                 }
 519
 520         }
 521         catch(exception& e) {
 522                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 523                 exit(1);
 524         }
 525         catch(...) {
 526                 cout << "An unknown error has occurred in the GlobalData class function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 527                 exit(1);
 528         }
 529 }
 530 /*******************************************************/
 531
 532 /*******************************************************/
 533 void GlobalData::readTreeString(ifstream& filehandle)   {
 534         try {
 535                 int c;
 536                 string name; //k
 537
 538                 while((c = filehandle.peek()) != ';') {
 539                                 //if you are a name
 540                         if ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != '\t') && (c != 32)) { //32 is space
 541                                 name = "";
 542                                 c = filehandle.get();
 543         //              k = c;
 544 //cout << k << endl;
 545                                 while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {
 546                                         name += c;
 547                                         c = filehandle.get();
 548                 //      k = c;
 549 //cout << " in name while " << k << endl;
 550                                 }
 551
 552 //cout << "name = " << name << endl;
 553                                 Treenames.push_back(name);
 554                                 filehandle.putback(c);
 555 //k = c;
 556 //cout << " after putback" <<  k << endl;
 557                         }
 558
 559                         if (c  == ':') { //read until you reach the end of the branch length
 560                                 while ((c != '(') && (c != ')') && (c != ',') && (c != ';') && (c != '\n') && (c != '\t') && (c != 32)) {
 561                                         c = filehandle.get();
 562                                 //      k = c;
 563         //cout << " in branch while " << k << endl;
 564                                 }
 565                                 filehandle.putback(c);
 566                         }
 567                         c = filehandle.get();
 568                         if (c == ';') { break; }
 569                 //      k = c;
 570 //cout << k << endl;
 571
 572                 }
 573         }
 574         catch(exception& e) {
 575                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 576                 exit(1);
 577         }
 578         catch(...) {
 579                 cout << "An unknown error has occurred in the GlobalData class function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 580                 exit(1);
 581         }
 582 }
 583
 584 /*******************************************************/
 585
 586 /*******************************************************/
 587
 588