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 == "filter")            { filter = value;               }
  84                                 if (key == "soft")                  { soft = value;                 }
  85                                 if (key == "scale")                     { scale = value;                }
  86                                 if (key == "ends" )                     { ends = value;                 }
  87                                 if (key == "processors" )       { processors = value;   }
  88                                 if (key == "template")          { templatefile = value; }
  89                                 if (key == "search")            { search = value;               }
  90                                 if (key == "ksize")                     { ksize = value;                }
  91                                 if (key == "align")                 { align = value;            }
  92                                 if (key == "match")                     { match = value;                }
  93                                 if (key == "mismatch")          { mismatch = value;         }
  94                                 if (key == "gapopen")           { gapopen = value;              }
  95                                 if (key == "gapextend" )        { gapextend = value;    }
  96
  97                                 if (key == "line") {//stores lines to be used in a set
  98                                         lines.clear();
  99                                         labels.clear();
 100                                         line = value;
 101                                         label = "";
 102                                         splitAtDash(value, lines);
 103                                         allLines = 0;
 104                                 }
 105                                 if (key == "label") {//stores labels to be used in a set
 106                                         labels.clear();
 107                                         lines.clear();
 108                                         label = value;
 109                                         line = "";
 110                                         splitAtDash(value, labels);
 111                                         allLines = 0;
 112                                 }
 113
 114                                 if (key == "groups") {//stores groups to be used in a vector
 115                                         Groups.clear();
 116                                         groups = value;
 117                                         splitAtDash(value, Groups);
 118                                 }
 119
 120                         }
 121
 122                         //saves the last parameter
 123                         value = optionText;
 124                         splitAtEquals(key, value);
 125                         if (key == "phylip" )   { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";       }
 126                         if (key == "column" )   { columnfile = value; inputFileName = value; fileroot = value; format = "column";       }
 127                         if (key == "list" )             { listfile = value; inputFileName = value; fileroot = value; format = "list";           }
 128                         if (key == "rabund" )   { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
 129                         if (key == "sabund" )   { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       }
 130                         if (key == "fasta" )    { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
 131                         if (key == "nexus" )    { nexusfile = value; inputFileName = value; fileroot = value; format = "nexus";         }
 132                         if (key == "clustal" )  { clustalfile = value; inputFileName = value; fileroot = value; format = "clustal"; }
 133                         if (key == "tree" )             { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }
 134                         if (key == "shared" )   { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile";   }
 135                         if (key == "name" )             { namefile = value;             }
 136                         if (key == "order" )    { orderfile = value;    }
 137                         if (key == "group" )    { groupfile = value;    }
 138                         if (key == "cutoff" )           { cutoff = value;               }
 139                         if (key == "precision" )        { precision = value;    }
 140                         if (key == "iters" )            { iters = value;                }
 141                         if (key == "jumble" )           { jumble = value;               }
 142                         if (key == "freq" )                     { freq = value;                 }
 143                         if (key == "method" )           { method = value;               }
 144                         if (key == "fileroot" )         { fileroot = value;             }
 145                         if (key == "abund" )        { abund = value;        }
 146                         if (key == "random" )           { randomtree = value;   }
 147                         if (key == "calc")                      { calc = value;                 }
 148                         if (key == "step")                      { step = value;                 }
 149                         if (key == "form")                      { form = value;                 }
 150                         if (key == "sorted")            { sorted = value;               }
 151                         if (key == "vertical")          { vertical = value;             }
 152                         if (key == "trump")                 { trump = value;            }
 153                         if (key == "filter")            { filter = value;               }
 154                         if (key == "soft")                  { soft = value;                 }
 155                         if (key == "scale")                     { scale = value;                }
 156                         if (key == "ends" )                     { ends = value;                 }
 157                         if (key == "processors" )       { processors = value;   }
 158                         if (key == "template")          { templatefile = value; }
 159                         if (key == "search")            { search = value;               }
 160                         if (key == "ksize")                     { ksize = value;                }
 161                         if (key == "align")                 { align = value;            }
 162                         if (key == "match")                     { match = value;                }
 163                         if (key == "mismatch")          { mismatch = value;         }
 164                         if (key == "gapopen")           { gapopen = value;              }
 165                         if (key == "gapextend" )        { gapextend = value;    }
 166
 167                         if (key == "line") {//stores lines to be used in a vector
 168                                 lines.clear();
 169                                 labels.clear();
 170                                 line = value;
 171                                 label = "";
 172                                 if (line != "all") {  splitAtDash(value, lines);  allLines = 0;  }
 173                                 else { allLines = 1;  }
 174                         }
 175
 176                         if (key == "label") {//stores lines to be used in a vector
 177                                 labels.clear();
 178                                 lines.clear();
 179                                 label = value;
 180                                 line = "";
 181                                 if (label != "all") {  splitAtDash(value, labels);  allLines = 0;  }
 182                                 else { allLines = 1;  }
 183                         }
 184
 185                         if (key == "groups") {//stores groups to be used in a vector
 186                                         Groups.clear();
 187                                         groups = value;
 188                                         splitAtDash(value, Groups);
 189                         }
 190                 }
 191
 192                 //set format for shared
 193                 if ((listfile != "") && (groupfile != "")) { format = "shared"; }
 194                 if ((phylipfile != "") && (groupfile != "")) { format = "matrix"; }
 195
 196                 //input defaults for calculators
 197                 if (commandName == "collect.single") {
 198
 199                         if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
 200                         Estimators.clear();
 201                         splitAtDash(calc, Estimators);
 202                 }
 203                 if (commandName == "rarefaction.single") {
 204                         if ((calc == "default") || (calc == "")) { calc = "sobs"; }
 205                         Estimators.clear();
 206                         splitAtDash(calc, Estimators);
 207                 }
 208                 if (commandName == "collect.shared") {
 209
 210                         if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
 211                         Estimators.clear();
 212                         splitAtDash(calc, Estimators);
 213                 }
 214                 if (commandName == "summary.single") {
 215                         if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
 216                         Estimators.clear();
 217                         splitAtDash(calc, Estimators);
 218                 }
 219                 if (commandName == "summary.shared") {
 220                         if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
 221                         Estimators.clear();
 222                         splitAtDash(calc, Estimators);
 223                 }
 224                 if (commandName == "rarefaction.shared") {
 225                         if ((calc == "default") || (calc == "")) { calc = "sharedobserved"; }
 226                         Estimators.clear();
 227                         splitAtDash(calc, Estimators);
 228                 }
 229                 if (commandName == "dist.seqs") {
 230                         if ((calc == "default") || (calc == "")) {  calc = "onegap";  }
 231                         Estimators.clear();
 232                         splitAtDash(calc, Estimators);
 233                 }
 234                 if (commandName == "venn") {
 235                         if ((calc == "default") || (calc == "")) {
 236                                 if (format == "list") { calc = "sobs"; }
 237                                 else { calc = "sharedsobs"; }
 238                         }
 239                         Estimators.clear();
 240                         splitAtDash(calc, Estimators);
 241                 }
 242                 if ((commandName == "tree.shared") || (commandName == "bootstrap.shared")) {
 243                         if (calc != "") {
 244                                 Estimators.clear();
 245                                 splitAtDash(calc, Estimators);
 246                         }else { cout << "You have not specified any calculators." << endl; }
 247                 }
 248
 249
 250                 //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
 251                 if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single")) {
 252                         if (listfile != "") { format = "list"; }
 253                         else if (sabundfile != "") { format = "sabund"; }
 254                         else if (rabundfile != "") { format = "rabund"; }
 255                 }
 256         }
 257         catch(exception& e) {
 258                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 259                 exit(1);
 260         }
 261         catch(...) {
 262                 cout << "An unknown error has occurred in the GlobalData class function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 263                 exit(1);
 264         }
 265 }
 266 /*******************************************************/
 267
 268 /******************************************************/
 269 // These functions give you the option parameters of the commands
 270 string GlobalData::getPhylipFile()              {       return phylipfile;      }
 271 string GlobalData::getColumnFile()              {       return columnfile;      }
 272 string GlobalData::getListFile()                {       return listfile;        }
 273 string GlobalData::getRabundFile()              {       return rabundfile;      }
 274 string GlobalData::getSabundFile()              {       return sabundfile;      }
 275 string GlobalData::getNameFile()                {       return namefile;        }
 276 string GlobalData::getGroupFile()               {       return groupfile;       }
 277 string GlobalData::getOrderFile()               {       return orderfile;       }
 278 string GlobalData::getTreeFile()                {       return treefile;        }
 279 string GlobalData::getSharedFile()              {       return sharedfile;      }
 280 string GlobalData::getFastaFile()               {       return fastafile;       }
 281 string GlobalData::getNexusFile()               {       return nexusfile;       }
 282 string GlobalData::getClustalFile()     {   return clustalfile; }
 283 string GlobalData::getCutOff()                  {       return cutoff;          }
 284 string GlobalData::getFormat()                  {       return format;          }
 285 string GlobalData::getPrecision()               {       return precision;       }
 286 string GlobalData::getMethod()                  {       return method;          }
 287 string GlobalData::getFileRoot()                {       return fileroot;        }
 288 string GlobalData::getIters()                   {       return iters;           }
 289 string GlobalData::getJumble()                  {       return jumble;          }
 290 string GlobalData::getFreq()                    {       return freq;            }
 291 string GlobalData::getAbund()           {   return abund;       }
 292 string GlobalData::getRandomTree()              {       return randomtree;      }
 293 string GlobalData::getGroups()                  {       return groups;          }
 294 string GlobalData::getStep()                    {       return step;            }
 295 string GlobalData::getForm()                    {       return form;            }
 296 string GlobalData::getSorted()                  {       return sorted;          }
 297 string GlobalData::getTrump()                   {   return trump;       }
 298 string GlobalData::getSoft()                    {   return soft;                }
 299 string GlobalData::getFilter()                  {   return filter;              }
 300 string GlobalData::getScale()                   {       return scale;           }
 301 string GlobalData::getEnds()                    {   return ends;                }
 302 string GlobalData::getProcessors()              {       return processors;      }
 303 string GlobalData::getTemplateFile()    {       return templatefile;}
 304 string GlobalData::getSearch()                  {       return search;          }
 305 string GlobalData::getKSize()                   {       return ksize;           }
 306 string GlobalData::getAlign()                   {       return align;           }
 307 string GlobalData::getMatch()                   {       return match;           }
 308 string GlobalData::getMismatch()                {       return mismatch;        }
 309 string GlobalData::getGapopen()                 {       return gapopen;         }
 310 string GlobalData::getGapextend()               {       return gapextend;       }
 311
 312 void GlobalData::setListFile(string file)               {       listfile = file;        inputFileName = file;}
 313 void GlobalData::setGroupFile(string file)              {       groupfile = file;       }
 314 void GlobalData::setRabundFile(string file)             {       rabundfile = file;      inputFileName = file;}
 315 void GlobalData::setSabundFile(string file)             {       sabundfile = file;      inputFileName = file;}
 316 void GlobalData::setPhylipFile(string file)             {       phylipfile = file;    inputFileName = file;}
 317 void GlobalData::setColumnFile(string file)             {       columnfile = file;    inputFileName = file;}
 318 void GlobalData::setSharedFile(string file)             {       sharedfile = file;      inputFileName = file; fileroot = file;}
 319 void GlobalData::setNameFile(string file)               {       namefile = file;                }
 320 void GlobalData::setFormat(string Format)               {       format = Format;                }
 321 void GlobalData::setRandomTree(string Random)   {       randomtree = Random;    }
 322 void GlobalData::setGroups(string g)                    {       groups = g;                             }
 323 void GlobalData::setCalc(string Calc)                   {       calc = Calc;                    }
 324 void GlobalData::setEnds(string e)                              {   ends = e;                           }
 325 void GlobalData::setProcessors(string p)                {       processors = p;                 }
 326
 327
 328 /*******************************************************/
 329
 330 /******************************************************/
 331 GlobalData::GlobalData() {
 332         //option definitions should go here...
 333         helpRequest = "";
 334         clear();
 335         gListVector == NULL;
 336         gSparseMatrix == NULL;
 337 }
 338 /*******************************************************/
 339
 340 /******************************************************/
 341 void GlobalData::clear() {
 342         //option definitions should go here...
 343         phylipfile              =       "";
 344         columnfile              =       "";
 345         listfile                =       "";
 346         rabundfile              =       "";
 347         sabundfile              =       "";
 348         namefile                =       "";
 349         groupfile               =       "";
 350         orderfile               =       "";
 351         fastafile               =   "";
 352         nexusfile               =   "";
 353         clustalfile             =   "";
 354         treefile                =       "";
 355         sharedfile              =       "";
 356         templatefile    =       "";
 357         cutoff                  =       "10.00";
 358         format                  =       "";
 359         precision               =       "100";
 360         iters                   =       "1000";
 361         line                    =   "";
 362         label                   =       "";
 363         groups                  =       "";
 364         jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
 365         randomtree              =       "";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
 366         freq                    =       "100";
 367         method                  =       "furthest";
 368         fileroot                =       "";
 369         abund           =   "10";
 370         step                    =       "0.01";
 371         form                    =       "integral";
 372         sorted                  =       "T";  //F means don't sort, T means sort.
 373         vertical        =   "";
 374         trump           =   "";
 375         filter          =   "";
 376         soft            =   "";
 377         scale                   =       "log10";
 378         ends                    =   "T";  //yes
 379         processors              =       "1";
 380         search                  =       "suffix";
 381         ksize                   =       "7";
 382         align                   =       "blast";
 383         match                   =       "1.0";
 384         mismatch                =       "-1.0";
 385         gapopen                 =       "-5.0";
 386         gapextend               =       "-2.0";
 387
 388
 389 }
 390
 391 //*******************************************************/
 392
 393 /******************************************************/
 394 void GlobalData::reset() {
 395         cutoff                  =       "10.00";
 396         precision               =       "100";
 397         iters                   =       "1000";
 398         groups                  =       "";
 399         jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
 400         sorted                  =       "T";  //F means don't sort, T means sort.
 401         randomtree              =       "";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
 402         freq                    =       "100";
 403         method                  =       "furthest";
 404         calc                    =       "";
 405         abund                   =   "10";
 406         step                    =       "0.01";
 407         form                    =       "integral";
 408         ends                    =   "T";
 409         processors              =       "1";
 410         search                  =       "suffix";
 411         ksize                   =       "7";
 412         align                   =       "blast";
 413         match                   =       "1.0";
 414         mismatch                =       "-1.0";
 415         gapopen                 =       "-5.0";
 416         gapextend               =       "-2.0";
 417 }
 418 /*******************************************************/
 419
 420 /******************************************************/
 421 GlobalData::~GlobalData() {
 422         _uniqueInstance = 0;
 423         if(gListVector != NULL)         {       delete gListVector;             }
 424         if(gSparseMatrix != NULL)       {       delete gSparseMatrix;   }
 425         if(gorder != NULL)                      {       delete gorder;          }
 426 }
 427 /*******************************************************/
 428
 429 /*******************************************************/
 430 void GlobalData::parseTreeFile() {
 431         //only takes names from the first tree and assumes that all trees use the same names.
 432         try {
 433                 string filename = treefile;
 434                 ifstream filehandle;
 435                 openInputFile(filename, filehandle);
 436                 int c, comment;
 437                 comment = 0;
 438
 439                 //if you are not a nexus file
 440                 if ((c = filehandle.peek()) != '#') {
 441                         while((c = filehandle.peek()) != ';') {
 442                                 while ((c = filehandle.peek()) != ';') {
 443                                         // get past comments
 444                                         if(c == '[') {
 445                                                 comment = 1;
 446                                         }
 447                                         if(c == ']'){
 448                                                 comment = 0;
 449                                         }
 450                                         if((c == '(') && (comment != 1)){ break; }
 451                                         filehandle.get();
 452                                 }
 453
 454                                 readTreeString(filehandle);
 455                         }
 456                 //if you are a nexus file
 457                 }else if ((c = filehandle.peek()) == '#') {
 458                         string holder = "";
 459
 460                         // get past comments
 461                         while(holder != "translate" && holder != "Translate"){
 462                                 if(holder == "[" || holder == "[!"){
 463                                         comment = 1;
 464                                 }
 465                                 if(holder == "]"){
 466                                         comment = 0;
 467                                 }
 468                                 filehandle >> holder;
 469
 470                                 //if there is no translate then you must read tree string otherwise use translate to get names
 471                                 if(holder == "tree" && comment != 1){
 472                                         //pass over the "tree rep.6878900 = "
 473                                         while (((c = filehandle.get()) != '(') && ((c = filehandle.peek()) != EOF) ) {;}
 474
 475                                         if (c == EOF ) { break; }
 476                                         filehandle.putback(c);  //put back first ( of tree.
 477                                         readTreeString(filehandle);
 478                                         break;
 479                                 }
 480                         }
 481
 482                         //use nexus translation rather than parsing tree to save time
 483                         if ((holder == "translate") || (holder == "Translate")) {
 484
 485                                 string number, name, h;
 486                                 h = ""; // so it enters the loop the first time
 487                                 while((h != ";") && (number != ";")) {
 488                                         filehandle >> number;
 489                                         filehandle >> name;
 490
 491                                         //c = , until done with translation then c = ;
 492                                         h = name.substr(name.length()-1, name.length());
 493                                         name.erase(name.end()-1);  //erase the comma
 494                                         Treenames.push_back(number);
 495                                 }
 496                                 if (number == ";") { Treenames.pop_back(); }  //in case ';' from translation is on next line instead of next to last name
 497                         }
 498                 }
 499
 500         }
 501         catch(exception& e) {
 502                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 503                 exit(1);
 504         }
 505         catch(...) {
 506                 cout << "An unknown error has occurred in the GlobalData class function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 507                 exit(1);
 508         }
 509 }
 510 /*******************************************************/
 511
 512 /*******************************************************/
 513 void GlobalData::readTreeString(ifstream& filehandle)   {
 514         try {
 515                 int c;
 516                 string name; //k
 517
 518                 while((c = filehandle.peek()) != ';') {
 519                                 //if you are a name
 520                         if ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != '\t') && (c != 32)) { //32 is space
 521                                 name = "";
 522                                 c = filehandle.get();
 523         //              k = c;
 524 //cout << k << endl;
 525                                 while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {
 526                                         name += c;
 527                                         c = filehandle.get();
 528                 //      k = c;
 529 //cout << " in name while " << k << endl;
 530                                 }
 531
 532 //cout << "name = " << name << endl;
 533                                 Treenames.push_back(name);
 534                                 filehandle.putback(c);
 535 //k = c;
 536 //cout << " after putback" <<  k << endl;
 537                         }
 538
 539                         if (c  == ':') { //read until you reach the end of the branch length
 540                                 while ((c != '(') && (c != ')') && (c != ',') && (c != ';') && (c != '\n') && (c != '\t') && (c != 32)) {
 541                                         c = filehandle.get();
 542                                 //      k = c;
 543         //cout << " in branch while " << k << endl;
 544                                 }
 545                                 filehandle.putback(c);
 546                         }
 547                         c = filehandle.get();
 548                         if (c == ';') { break; }
 549                 //      k = c;
 550 //cout << k << endl;
 551
 552                 }
 553         }
 554         catch(exception& e) {
 555                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 556                 exit(1);
 557         }
 558         catch(...) {
 559                 cout << "An unknown error has occurred in the GlobalData class function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 560                 exit(1);
 561         }
 562 }
 563
 564 /*******************************************************/
 565
 566 /*******************************************************/
 567
 568