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                 //set default value for cutoff
  46                 if (commandName == "dist.seqs") {       cutoff = "1.0";         }
  47
  48                 string key, value;
  49                 //reads in parameters and values
  50                 if((optionText != "") && (commandName != "help")){
  51                         while((optionText.find_first_of(',') != -1)) {  //while there are parameters
  52                                 splitAtComma(value, optionText);
  53                                 splitAtEquals(key, value);
  54
  55                                 if (key == "phylip" )   { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";       }
  56                                 if (key == "column" )   { columnfile = value; inputFileName = value; fileroot = value; format = "column";       }
  57                                 if (key == "list" )             { listfile = value; inputFileName = value; fileroot = value; format = "list";           }
  58                                 if (key == "rabund" )   { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
  59                                 if (key == "sabund" )   { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       }
  60                                 if (key == "fasta" )    { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
  61                                 if (key == "nexus" )    { nexusfile = value; inputFileName = value; fileroot = value; format = "nexus";         }
  62                                 if (key == "clustal" )  { clustalfile = value; inputFileName = value; fileroot = value; format = "clustal"; }
  63                                 if (key == "tree" )             { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }
  64                                 if (key == "shared" )   { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile";   }
  65                                 if (key == "name" )             { namefile = value;             }
  66                                 if (key == "order" )    { orderfile = value;    }
  67                                 if (key == "group" )    { groupfile = value;    }
  68                                 if (key == "cutoff" )           { cutoff = value;               }
  69                                 if (key == "precision" )        { precision = value;    }
  70                                 if (key == "iters" )            { iters = value;                }
  71                                 if (key == "jumble" )           { jumble = value;               }
  72                                 if (key == "freq" )                     { freq = value;                 }
  73                                 if (key == "method" )           { method = value;               }
  74                                 if (key == "fileroot" )         { fileroot = value;             }
  75                                 if (key == "abund" )        { abund = value;        }
  76                                 if (key == "random" )           { randomtree = value;   }
  77                                 if (key == "calc")                      { calc = value;                 }
  78                                 if (key == "step")                      { step = value;                 }
  79                                 if (key == "form")                      { form = value;                 }
  80                                 if (key == "sorted")            { sorted = value;               }
  81                                 if (key == "vertical")          { vertical = value;             }
  82                                 if (key == "trump")                 { trump = value;            }
  83                                 if (key == "hard")                      { hard = value;         }
  84                                 if (key == "soft")                  { soft = value;                 }
  85                                 if (key == "scale")                     { scale = value;                }
  86                                 if (key == "countends" )        { countends = value;    }
  87                                 if (key == "processors" )       { processors = value;   }
  88                                 if (key == "size" )         { size = value;         }
  89                                 if (key == "candidate")         { candidatefile = value;        }
  90                                 if (key == "search")            { search = value;               }
  91                                 if (key == "ksize")                     { ksize = value;                }
  92                                 if (key == "align")                 { align = value;            }
  93                                 if (key == "match")                     { match = value;                }
  94                                 if (key == "mismatch")          { mismatch = value;         }
  95                                 if (key == "gapopen")           { gapopen = value;              }
  96                                 if (key == "gapextend" )        { gapextend = value;    }
  97
  98                                 if (key == "line") {//stores lines to be used in a set
  99                                         lines.clear();
 100                                         labels.clear();
 101                                         line = value;
 102                                         label = "";
 103                                         splitAtDash(value, lines);
 104                                         allLines = 0;
 105                                 }
 106                                 if (key == "label") {//stores labels to be used in a set
 107                                         labels.clear();
 108                                         lines.clear();
 109                                         label = value;
 110                                         line = "";
 111                                         splitAtDash(value, labels);
 112                                         allLines = 0;
 113                                 }
 114
 115                                 if (key == "groups") {//stores groups to be used in a vector
 116                                         Groups.clear();
 117                                         groups = value;
 118                                         splitAtDash(value, Groups);
 119                                 }
 120
 121                         }
 122
 123                         //saves the last parameter
 124                         value = optionText;
 125                         splitAtEquals(key, value);
 126                         if (key == "phylip" )   { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";       }
 127                         if (key == "column" )   { columnfile = value; inputFileName = value; fileroot = value; format = "column";       }
 128                         if (key == "list" )             { listfile = value; inputFileName = value; fileroot = value; format = "list";           }
 129                         if (key == "rabund" )   { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
 130                         if (key == "sabund" )   { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       }
 131                         if (key == "fasta" )    { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
 132                         if (key == "nexus" )    { nexusfile = value; inputFileName = value; fileroot = value; format = "nexus";         }
 133                         if (key == "clustal" )  { clustalfile = value; inputFileName = value; fileroot = value; format = "clustal"; }
 134                         if (key == "tree" )             { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }
 135                         if (key == "shared" )   { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile";   }
 136                         if (key == "name" )             { namefile = value;             }
 137                         if (key == "order" )    { orderfile = value;    }
 138                         if (key == "group" )    { groupfile = value;    }
 139                         if (key == "cutoff" )           { cutoff = value;               }
 140                         if (key == "precision" )        { precision = value;    }
 141                         if (key == "iters" )            { iters = value;                }
 142                         if (key == "jumble" )           { jumble = value;               }
 143                         if (key == "freq" )                     { freq = value;                 }
 144                         if (key == "method" )           { method = value;               }
 145                         if (key == "fileroot" )         { fileroot = value;             }
 146                         if (key == "abund" )        { abund = value;        }
 147                         if (key == "random" )           { randomtree = value;   }
 148                         if (key == "calc")                      { calc = value;                 }
 149                         if (key == "step")                      { step = value;                 }
 150                         if (key == "form")                      { form = value;                 }
 151                         if (key == "sorted")            { sorted = value;               }
 152                         if (key == "vertical")          { vertical = value;             }
 153                         if (key == "trump")                 { trump = value;            }
 154                         if (key == "hard")                      { hard = value;         }
 155                         if (key == "soft")                  { soft = value;                 }
 156                         if (key == "scale")                     { scale = value;                }
 157                         if (key == "countends" )        { countends = value;    }
 158                         if (key == "processors" )       { processors = value;   }
 159                         if (key == "size" )         { size = value;         }
 160                         if (key == "candidate")         { candidatefile = value;        }
 161                         if (key == "search")            { search = value;               }
 162                         if (key == "ksize")                     { ksize = value;                }
 163                         if (key == "align")                 { align = value;            }
 164                         if (key == "match")                     { match = value;                }
 165                         if (key == "mismatch")          { mismatch = value;         }
 166                         if (key == "gapopen")           { gapopen = value;              }
 167                         if (key == "gapextend" )        { gapextend = value;    }
 168
 169                         if (key == "line") {//stores lines to be used in a vector
 170                                 lines.clear();
 171                                 labels.clear();
 172                                 line = value;
 173                                 label = "";
 174                                 if (line != "all") {  splitAtDash(value, lines);  allLines = 0;  }
 175                                 else { allLines = 1;  }
 176                         }
 177
 178                         if (key == "label") {//stores lines to be used in a vector
 179                                 labels.clear();
 180                                 lines.clear();
 181                                 label = value;
 182                                 line = "";
 183                                 if (label != "all") {  splitAtDash(value, labels);  allLines = 0;  }
 184                                 else { allLines = 1;  }
 185                         }
 186
 187                         if (key == "groups") {//stores groups to be used in a vector
 188                                         Groups.clear();
 189                                         groups = value;
 190                                         splitAtDash(value, Groups);
 191                         }
 192                 }
 193
 194                 //set format for shared
 195                 if ((listfile != "") && (groupfile != "")) { format = "shared"; }
 196                 if ((phylipfile != "") && (groupfile != "")) { format = "matrix"; }
 197
 198                 //input defaults for calculators
 199                 if (commandName == "collect.single") {
 200
 201                         if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
 202                         Estimators.clear();
 203                         splitAtDash(calc, Estimators);
 204                 }
 205                 if (commandName == "rarefaction.single") {
 206                         if ((calc == "default") || (calc == "")) { calc = "sobs"; }
 207                         Estimators.clear();
 208                         splitAtDash(calc, Estimators);
 209                 }
 210                 if (commandName == "collect.shared") {
 211
 212                         if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
 213                         Estimators.clear();
 214                         splitAtDash(calc, Estimators);
 215                 }
 216                 if (commandName == "summary.single") {
 217                         if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
 218                         Estimators.clear();
 219                         splitAtDash(calc, Estimators);
 220                 }
 221                 if (commandName == "summary.shared") {
 222                         if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
 223                         Estimators.clear();
 224                         splitAtDash(calc, Estimators);
 225                 }
 226                 if (commandName == "rarefaction.shared") {
 227                         if ((calc == "default") || (calc == "")) { calc = "sharedobserved"; }
 228                         Estimators.clear();
 229                         splitAtDash(calc, Estimators);
 230                 }
 231                 if (commandName == "dist.seqs") {
 232                         if ((calc == "default") || (calc == "")) {  calc = "onegap";    }
 233                         if (countends == "")    { countends = "T"; }
 234                         Estimators.clear();
 235                         splitAtDash(calc, Estimators);
 236                 }
 237                 if (commandName == "venn") {
 238                         if ((calc == "default") || (calc == "")) {
 239                                 if (format == "list") { calc = "sobs"; }
 240                                 else { calc = "sharedsobs"; }
 241                         }
 242                         Estimators.clear();
 243                         splitAtDash(calc, Estimators);
 244                 }
 245                 if ((commandName == "tree.shared") || (commandName == "bootstrap.shared") || (commandName == "dist.shared")) {
 246                         if ((calc == "default") || (calc == "")) {
 247                                 calc = "jclass-thetayc";
 248                         }
 249                         Estimators.clear();
 250                         splitAtDash(calc, Estimators);
 251                 }
 252                 if(commandName == "filter.seqs"){
 253                         if(trump == "" && vertical == "" && hard == "" && soft == ""){
 254                                 trump = '.';
 255                         }
 256                 }
 257
 258                 //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
 259                 if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single")) {
 260                         if (listfile != "") { format = "list"; }
 261                         else if (sabundfile != "") { format = "sabund"; }
 262                         else if (rabundfile != "") { format = "rabund"; }
 263                 }
 264         }
 265         catch(exception& e) {
 266                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 267                 exit(1);
 268         }
 269         catch(...) {
 270                 cout << "An unknown error has occurred in the GlobalData class function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 271                 exit(1);
 272         }
 273 }
 274 /*******************************************************/
 275
 276 /******************************************************/
 277 // These functions give you the option parameters of the commands
 278 string GlobalData::getPhylipFile()              {       return phylipfile;      }
 279 string GlobalData::getColumnFile()              {       return columnfile;      }
 280 string GlobalData::getListFile()                {       return listfile;        }
 281 string GlobalData::getRabundFile()              {       return rabundfile;      }
 282 string GlobalData::getSabundFile()              {       return sabundfile;      }
 283 string GlobalData::getNameFile()                {       return namefile;        }
 284 string GlobalData::getGroupFile()               {       return groupfile;       }
 285 string GlobalData::getOrderFile()               {       return orderfile;       }
 286 string GlobalData::getTreeFile()                {       return treefile;        }
 287 string GlobalData::getSharedFile()              {       return sharedfile;      }
 288 string GlobalData::getFastaFile()               {       return fastafile;       }
 289 string GlobalData::getNexusFile()               {       return nexusfile;       }
 290 string GlobalData::getClustalFile()     {   return clustalfile; }
 291 string GlobalData::getCutOff()                  {       return cutoff;          }
 292 string GlobalData::getFormat()                  {       return format;          }
 293 string GlobalData::getPrecision()               {       return precision;       }
 294 string GlobalData::getMethod()                  {       return method;          }
 295 string GlobalData::getFileRoot()                {       return fileroot;        }
 296 string GlobalData::getIters()                   {       return iters;           }
 297 string GlobalData::getJumble()                  {       return jumble;          }
 298 string GlobalData::getFreq()                    {       return freq;            }
 299 string GlobalData::getAbund()           {   return abund;       }
 300 string GlobalData::getRandomTree()              {       return randomtree;      }
 301 string GlobalData::getGroups()                  {       return groups;          }
 302 string GlobalData::getStep()                    {       return step;            }
 303 string GlobalData::getForm()                    {       return form;            }
 304 string GlobalData::getSorted()                  {       return sorted;          }
 305 string GlobalData::getVertical()                {   return vertical;    }
 306 string GlobalData::getTrump()                   {   return trump;       }
 307 string GlobalData::getSoft()                    {   return soft;                }
 308 string GlobalData::getHard()                    {   return hard;                }
 309 string GlobalData::getScale()                   {       return scale;           }
 310 string GlobalData::getCountEnds()               {   return countends;   }
 311 string GlobalData::getProcessors()              {       return processors;      }
 312 string GlobalData::getSize()            {   return size;        }
 313 string GlobalData::getCandidateFile()   {       return candidatefile;}
 314 string GlobalData::getSearch()                  {       return search;          }
 315 string GlobalData::getKSize()                   {       return ksize;           }
 316 string GlobalData::getAlign()                   {       return align;           }
 317 string GlobalData::getMatch()                   {       return match;           }
 318 string GlobalData::getMismatch()                {       return mismatch;        }
 319 string GlobalData::getGapopen()                 {       return gapopen;         }
 320 string GlobalData::getGapextend()               {       return gapextend;       }
 321
 322
 323 void GlobalData::setListFile(string file)               {       listfile = file;        inputFileName = file;                                   }
 324 void GlobalData::setRabundFile(string file)             {       rabundfile = file;      inputFileName = file;                                   }
 325 void GlobalData::setSabundFile(string file)             {       sabundfile = file;      inputFileName = file;                                   }
 326 void GlobalData::setPhylipFile(string file)             {       phylipfile = file;    inputFileName = file;                                     }
 327 void GlobalData::setColumnFile(string file)             {       columnfile = file;    inputFileName = file;                                     }
 328 void GlobalData::setGroupFile(string file)              {       groupfile = file;                                                                                       }
 329 void GlobalData::setSharedFile(string file)             {       sharedfile = file;      inputFileName = file; fileroot = file;  }
 330 void GlobalData::setNameFile(string file)               {       namefile = file;                }
 331 void GlobalData::setFormat(string Format)               {       format = Format;                }
 332 void GlobalData::setRandomTree(string Random)   {       randomtree = Random;    }
 333 void GlobalData::setGroups(string g)                    {       groups = g;                             }
 334 void GlobalData::setCalc(string Calc)                   {       calc = Calc;                    }
 335 void GlobalData::setCountEnds(string e)                 {   countends = e;                      }
 336 void GlobalData::setProcessors(string p)                {       processors = p;                 }
 337
 338
 339 /*******************************************************/
 340
 341 /******************************************************/
 342 GlobalData::GlobalData() {
 343         //option definitions should go here...
 344         helpRequest = "";
 345         clear();
 346         gListVector == NULL;
 347         gSparseMatrix == NULL;
 348 }
 349 /*******************************************************/
 350
 351 /******************************************************/
 352 void GlobalData::clear() {
 353         //option definitions should go here...
 354         phylipfile              =       "";
 355         columnfile              =       "";
 356         listfile                =       "";
 357         rabundfile              =       "";
 358         sabundfile              =       "";
 359         namefile                =       "";
 360         groupfile               =       "";
 361         orderfile               =       "";
 362         fastafile               =   "";
 363         nexusfile               =   "";
 364         clustalfile             =   "";
 365         treefile                =       "";
 366         sharedfile              =       "";
 367         candidatefile   =       "";
 368         cutoff                  =       "10.00";
 369         format                  =       "";
 370         precision               =       "100";
 371         iters                   =       "1000";
 372         line                    =   "";
 373         label                   =       "";
 374         groups                  =       "";
 375         jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
 376         randomtree              =       "";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
 377         freq                    =       "100";
 378         method                  =       "furthest";
 379         fileroot                =       "";
 380         abund           =   "10";
 381         step                    =       "0.01";
 382         form                    =       "integral";
 383         sorted                  =       "T";  //F means don't sort, T means sort.
 384         vertical        =   "";
 385         trump           =       "";
 386         hard                    =   "";
 387         soft            =   "";
 388         scale                   =       "log10";
 389         countends               =   "T";  //yes
 390         processors              =       "1";
 391         size            =   "0";
 392         search                  =       "kmer";
 393         ksize                   =       "7";
 394         align                   =       "needleman";
 395         match                   =       "1.0";
 396         mismatch                =       "-1.0";
 397         gapopen                 =       "-1.0";
 398         gapextend               =       "-2.0";
 399 }
 400
 401 //*******************************************************/
 402
 403 /******************************************************/
 404 void GlobalData::reset() {
 405         cutoff                  =       "10.00";
 406         precision               =       "100";
 407         iters                   =       "1000";
 408         groups                  =       "";
 409         jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
 410         sorted                  =       "T";  //F means don't sort, T means sort.
 411         randomtree              =       "";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
 412         freq                    =       "100";
 413         method                  =       "furthest";
 414         calc                    =       "";
 415         abund                   =   "10";
 416         step                    =       "0.01";
 417         form                    =       "integral";
 418         countends               =   "T";
 419         processors              =       "1";
 420         size            =   "0";
 421         search                  =       "kmer";
 422         ksize                   =       "7";
 423         align                   =       "needleman";
 424         match                   =       "1.0";
 425         mismatch                =       "-1.0";
 426         gapopen                 =       "-1.0";
 427         gapextend               =       "-2.0";
 428         vertical        =   "";
 429         trump           =   "";
 430         hard                    =   "";
 431         soft            =   "";
 432
 433 }
 434 /*******************************************************/
 435
 436 /******************************************************/
 437 GlobalData::~GlobalData() {
 438         _uniqueInstance = 0;
 439         if(gListVector != NULL)         {       delete gListVector;             }
 440         if(gSparseMatrix != NULL)       {       delete gSparseMatrix;   }
 441         if(gorder != NULL)                      {       delete gorder;          }
 442 }
 443 /*******************************************************/
 444
 445 /*******************************************************/
 446 void GlobalData::parseTreeFile() {
 447         //only takes names from the first tree and assumes that all trees use the same names.
 448         try {
 449                 string filename = treefile;
 450                 ifstream filehandle;
 451                 openInputFile(filename, filehandle);
 452                 int c, comment;
 453                 comment = 0;
 454
 455                 //if you are not a nexus file
 456                 if ((c = filehandle.peek()) != '#') {
 457                         while((c = filehandle.peek()) != ';') {
 458                                 while ((c = filehandle.peek()) != ';') {
 459                                         // get past comments
 460                                         if(c == '[') {
 461                                                 comment = 1;
 462                                         }
 463                                         if(c == ']'){
 464                                                 comment = 0;
 465                                         }
 466                                         if((c == '(') && (comment != 1)){ break; }
 467                                         filehandle.get();
 468                                 }
 469
 470                                 readTreeString(filehandle);
 471                         }
 472                 //if you are a nexus file
 473                 }else if ((c = filehandle.peek()) == '#') {
 474                         string holder = "";
 475
 476                         // get past comments
 477                         while(holder != "translate" && holder != "Translate"){
 478                                 if(holder == "[" || holder == "[!"){
 479                                         comment = 1;
 480                                 }
 481                                 if(holder == "]"){
 482                                         comment = 0;
 483                                 }
 484                                 filehandle >> holder;
 485
 486                                 //if there is no translate then you must read tree string otherwise use translate to get names
 487                                 if(holder == "tree" && comment != 1){
 488                                         //pass over the "tree rep.6878900 = "
 489                                         while (((c = filehandle.get()) != '(') && ((c = filehandle.peek()) != EOF) ) {;}
 490
 491                                         if (c == EOF ) { break; }
 492                                         filehandle.putback(c);  //put back first ( of tree.
 493                                         readTreeString(filehandle);
 494                                         break;
 495                                 }
 496                         }
 497
 498                         //use nexus translation rather than parsing tree to save time
 499                         if ((holder == "translate") || (holder == "Translate")) {
 500
 501                                 string number, name, h;
 502                                 h = ""; // so it enters the loop the first time
 503                                 while((h != ";") && (number != ";")) {
 504                                         filehandle >> number;
 505                                         filehandle >> name;
 506
 507                                         //c = , until done with translation then c = ;
 508                                         h = name.substr(name.length()-1, name.length());
 509                                         name.erase(name.end()-1);  //erase the comma
 510                                         Treenames.push_back(number);
 511                                 }
 512                                 if (number == ";") { Treenames.pop_back(); }  //in case ';' from translation is on next line instead of next to last name
 513                         }
 514                 }
 515
 516         }
 517         catch(exception& e) {
 518                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 519                 exit(1);
 520         }
 521         catch(...) {
 522                 cout << "An unknown error has occurred in the GlobalData class function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 523                 exit(1);
 524         }
 525 }
 526 /*******************************************************/
 527
 528 /*******************************************************/
 529 void GlobalData::readTreeString(ifstream& filehandle)   {
 530         try {
 531                 int c;
 532                 string name; //k
 533
 534                 while((c = filehandle.peek()) != ';') {
 535                                 //if you are a name
 536                         if ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != '\t') && (c != 32)) { //32 is space
 537                                 name = "";
 538                                 c = filehandle.get();
 539         //              k = c;
 540 //cout << k << endl;
 541                                 while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {
 542                                         name += c;
 543                                         c = filehandle.get();
 544                 //      k = c;
 545 //cout << " in name while " << k << endl;
 546                                 }
 547
 548 //cout << "name = " << name << endl;
 549                                 Treenames.push_back(name);
 550                                 filehandle.putback(c);
 551 //k = c;
 552 //cout << " after putback" <<  k << endl;
 553                         }
 554
 555                         if (c  == ':') { //read until you reach the end of the branch length
 556                                 while ((c != '(') && (c != ')') && (c != ',') && (c != ';') && (c != '\n') && (c != '\t') && (c != 32)) {
 557                                         c = filehandle.get();
 558                                 //      k = c;
 559         //cout << " in branch while " << k << endl;
 560                                 }
 561                                 filehandle.putback(c);
 562                         }
 563                         c = filehandle.get();
 564                         if (c == ';') { break; }
 565                 //      k = c;
 566 //cout << k << endl;
 567
 568                 }
 569         }
 570         catch(exception& e) {
 571                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 572                 exit(1);
 573         }
 574         catch(...) {
 575                 cout << "An unknown error has occurred in the GlobalData class function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 576                 exit(1);
 577         }
 578 }
 579
 580 /*******************************************************/
 581
 582 /*******************************************************/
 583
 584