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 == "size" )         { size = value;         }
  89                                 if (key == "template")          { templatefile = 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 == "filter")            { filter = value;               }
 155                         if (key == "soft")                  { soft = value;                 }
 156                         if (key == "scale")                     { scale = value;                }
 157                         if (key == "ends" )                     { ends = value;                 }
 158                         if (key == "processors" )       { processors = value;   }
 159                         if (key == "size" )         { size = value;         }
 160                         if (key == "template")          { templatefile = 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-efron-boneh-solow-shen"; }
 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-efron-boneh-solow-shen"; }
 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                         Estimators.clear();
 234                         splitAtDash(calc, Estimators);
 235                 }
 236                 if (commandName == "venn") {
 237                         if ((calc == "default") || (calc == "")) {
 238                                 if (format == "list") { calc = "sobs"; }
 239                                 else { calc = "sharedsobs"; }
 240                         }
 241                         Estimators.clear();
 242                         splitAtDash(calc, Estimators);
 243                 }
 244                 if ((commandName == "tree.shared") || (commandName == "bootstrap.shared")) {
 245                         if (calc != "") {
 246                                 Estimators.clear();
 247                                 splitAtDash(calc, Estimators);
 248                         }else { cout << "You have not specified any calculators." << endl; }
 249                 }
 250
 251
 252                 //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
 253                 if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single")) {
 254                         if (listfile != "") { format = "list"; }
 255                         else if (sabundfile != "") { format = "sabund"; }
 256                         else if (rabundfile != "") { format = "rabund"; }
 257                 }
 258         }
 259         catch(exception& e) {
 260                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 261                 exit(1);
 262         }
 263         catch(...) {
 264                 cout << "An unknown error has occurred in the GlobalData class function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 265                 exit(1);
 266         }
 267 }
 268 /*******************************************************/
 269
 270 /******************************************************/
 271 // These functions give you the option parameters of the commands
 272 string GlobalData::getPhylipFile()              {       return phylipfile;      }
 273 string GlobalData::getColumnFile()              {       return columnfile;      }
 274 string GlobalData::getListFile()                {       return listfile;        }
 275 string GlobalData::getRabundFile()              {       return rabundfile;      }
 276 string GlobalData::getSabundFile()              {       return sabundfile;      }
 277 string GlobalData::getNameFile()                {       return namefile;        }
 278 string GlobalData::getGroupFile()               {       return groupfile;       }
 279 string GlobalData::getOrderFile()               {       return orderfile;       }
 280 string GlobalData::getTreeFile()                {       return treefile;        }
 281 string GlobalData::getSharedFile()              {       return sharedfile;      }
 282 string GlobalData::getFastaFile()               {       return fastafile;       }
 283 string GlobalData::getNexusFile()               {       return nexusfile;       }
 284 string GlobalData::getClustalFile()     {   return clustalfile; }
 285 string GlobalData::getCutOff()                  {       return cutoff;          }
 286 string GlobalData::getFormat()                  {       return format;          }
 287 string GlobalData::getPrecision()               {       return precision;       }
 288 string GlobalData::getMethod()                  {       return method;          }
 289 string GlobalData::getFileRoot()                {       return fileroot;        }
 290 string GlobalData::getIters()                   {       return iters;           }
 291 string GlobalData::getJumble()                  {       return jumble;          }
 292 string GlobalData::getFreq()                    {       return freq;            }
 293 string GlobalData::getAbund()           {   return abund;       }
 294 string GlobalData::getRandomTree()              {       return randomtree;      }
 295 string GlobalData::getGroups()                  {       return groups;          }
 296 string GlobalData::getStep()                    {       return step;            }
 297 string GlobalData::getForm()                    {       return form;            }
 298 string GlobalData::getSorted()                  {       return sorted;          }
 299 string GlobalData::getTrump()                   {   return trump;       }
 300 string GlobalData::getSoft()                    {   return soft;                }
 301 string GlobalData::getFilter()                  {   return filter;              }
 302 string GlobalData::getScale()                   {       return scale;           }
 303 string GlobalData::getEnds()                    {   return ends;                }
 304 string GlobalData::getProcessors()              {       return processors;      }
 305 string GlobalData::getSize()            {   return size;        }
 306 string GlobalData::getTemplateFile()    {       return templatefile;}
 307 string GlobalData::getSearch()                  {       return search;          }
 308 string GlobalData::getKSize()                   {       return ksize;           }
 309 string GlobalData::getAlign()                   {       return align;           }
 310 string GlobalData::getMatch()                   {       return match;           }
 311 string GlobalData::getMismatch()                {       return mismatch;        }
 312 string GlobalData::getGapopen()                 {       return gapopen;         }
 313 string GlobalData::getGapextend()               {       return gapextend;       }
 314
 315
 316 void GlobalData::setListFile(string file)       {       listfile = file;        inputFileName = file;}
 317 void GlobalData::setRabundFile(string file)     {       rabundfile = file;      inputFileName = file;}
 318 void GlobalData::setSabundFile(string file)     {       sabundfile = file;      inputFileName = file;}
 319 void GlobalData::setPhylipFile(string file)     {       phylipfile = file;    inputFileName = file;}
 320 void GlobalData::setColumnFile(string file)     {       columnfile = file;    inputFileName = file;}
 321 void GlobalData::setGroupFile(string file)              {       groupfile = file;       }
 322 void GlobalData::setSharedFile(string file)             {       sharedfile = file;      inputFileName = file; fileroot = file;}
 323 void GlobalData::setNameFile(string file)               {       namefile = file;                }
 324 void GlobalData::setFormat(string Format)               {       format = Format;                }
 325 void GlobalData::setRandomTree(string Random)   {       randomtree = Random;    }
 326 void GlobalData::setGroups(string g)                    {       groups = g;                             }
 327 void GlobalData::setCalc(string Calc)                   {       calc = Calc;                    }
 328 void GlobalData::setEnds(string e)                              {   ends = e;                           }
 329 void GlobalData::setProcessors(string p)                {       processors = p;                 }
 330
 331
 332 /*******************************************************/
 333
 334 /******************************************************/
 335 GlobalData::GlobalData() {
 336         //option definitions should go here...
 337         helpRequest = "";
 338         clear();
 339         gListVector == NULL;
 340         gSparseMatrix == NULL;
 341 }
 342 /*******************************************************/
 343
 344 /******************************************************/
 345 void GlobalData::clear() {
 346         //option definitions should go here...
 347         phylipfile              =       "";
 348         columnfile              =       "";
 349         listfile                =       "";
 350         rabundfile              =       "";
 351         sabundfile              =       "";
 352         namefile                =       "";
 353         groupfile               =       "";
 354         orderfile               =       "";
 355         fastafile               =   "";
 356         nexusfile               =   "";
 357         clustalfile             =   "";
 358         treefile                =       "";
 359         sharedfile              =       "";
 360         templatefile    =       "";
 361         cutoff                  =       "10.00";
 362         format                  =       "";
 363         precision               =       "100";
 364         iters                   =       "1000";
 365         line                    =   "";
 366         label                   =       "";
 367         groups                  =       "";
 368         jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
 369         randomtree              =       "";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
 370         freq                    =       "100";
 371         method                  =       "furthest";
 372         fileroot                =       "";
 373         abund           =   "10";
 374         step                    =       "0.01";
 375         form                    =       "integral";
 376         sorted                  =       "T";  //F means don't sort, T means sort.
 377         vertical        =   "";
 378         trump           =   "";
 379         filter          =   "";
 380         soft            =   "";
 381         scale                   =       "log10";
 382         ends                    =   "T";  //yes
 383         processors              =       "1";
 384         size            =   "1000";
 385         search                  =       "suffix";
 386         ksize                   =       "7";
 387         align                   =       "blast";
 388         match                   =       "1.0";
 389         mismatch                =       "-1.0";
 390         gapopen                 =       "-5.0";
 391         gapextend               =       "-2.0";
 392 }
 393
 394 //*******************************************************/
 395
 396 /******************************************************/
 397 void GlobalData::reset() {
 398         cutoff                  =       "10.00";
 399         precision               =       "100";
 400         iters                   =       "1000";
 401         groups                  =       "";
 402         jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
 403         sorted                  =       "T";  //F means don't sort, T means sort.
 404         randomtree              =       "";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
 405         freq                    =       "100";
 406         method                  =       "furthest";
 407         calc                    =       "";
 408         abund                   =   "10";
 409         step                    =       "0.01";
 410         form                    =       "integral";
 411         ends                    =   "T";
 412         processors              =       "1";
 413         size            =   "1000";
 414         search                  =       "suffix";
 415         ksize                   =       "7";
 416         align                   =       "blast";
 417         match                   =       "1.0";
 418         mismatch                =       "-1.0";
 419         gapopen                 =       "-5.0";
 420         gapextend               =       "-2.0";
 421 }
 422 /*******************************************************/
 423
 424 /******************************************************/
 425 GlobalData::~GlobalData() {
 426         _uniqueInstance = 0;
 427         if(gListVector != NULL)         {       delete gListVector;             }
 428         if(gSparseMatrix != NULL)       {       delete gSparseMatrix;   }
 429         if(gorder != NULL)                      {       delete gorder;          }
 430 }
 431 /*******************************************************/
 432
 433 /*******************************************************/
 434 void GlobalData::parseTreeFile() {
 435         //only takes names from the first tree and assumes that all trees use the same names.
 436         try {
 437                 string filename = treefile;
 438                 ifstream filehandle;
 439                 openInputFile(filename, filehandle);
 440                 int c, comment;
 441                 comment = 0;
 442
 443                 //if you are not a nexus file
 444                 if ((c = filehandle.peek()) != '#') {
 445                         while((c = filehandle.peek()) != ';') {
 446                                 while ((c = filehandle.peek()) != ';') {
 447                                         // get past comments
 448                                         if(c == '[') {
 449                                                 comment = 1;
 450                                         }
 451                                         if(c == ']'){
 452                                                 comment = 0;
 453                                         }
 454                                         if((c == '(') && (comment != 1)){ break; }
 455                                         filehandle.get();
 456                                 }
 457
 458                                 readTreeString(filehandle);
 459                         }
 460                 //if you are a nexus file
 461                 }else if ((c = filehandle.peek()) == '#') {
 462                         string holder = "";
 463
 464                         // get past comments
 465                         while(holder != "translate" && holder != "Translate"){
 466                                 if(holder == "[" || holder == "[!"){
 467                                         comment = 1;
 468                                 }
 469                                 if(holder == "]"){
 470                                         comment = 0;
 471                                 }
 472                                 filehandle >> holder;
 473
 474                                 //if there is no translate then you must read tree string otherwise use translate to get names
 475                                 if(holder == "tree" && comment != 1){
 476                                         //pass over the "tree rep.6878900 = "
 477                                         while (((c = filehandle.get()) != '(') && ((c = filehandle.peek()) != EOF) ) {;}
 478
 479                                         if (c == EOF ) { break; }
 480                                         filehandle.putback(c);  //put back first ( of tree.
 481                                         readTreeString(filehandle);
 482                                         break;
 483                                 }
 484                         }
 485
 486                         //use nexus translation rather than parsing tree to save time
 487                         if ((holder == "translate") || (holder == "Translate")) {
 488
 489                                 string number, name, h;
 490                                 h = ""; // so it enters the loop the first time
 491                                 while((h != ";") && (number != ";")) {
 492                                         filehandle >> number;
 493                                         filehandle >> name;
 494
 495                                         //c = , until done with translation then c = ;
 496                                         h = name.substr(name.length()-1, name.length());
 497                                         name.erase(name.end()-1);  //erase the comma
 498                                         Treenames.push_back(number);
 499                                 }
 500                                 if (number == ";") { Treenames.pop_back(); }  //in case ';' from translation is on next line instead of next to last name
 501                         }
 502                 }
 503
 504         }
 505         catch(exception& e) {
 506                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 507                 exit(1);
 508         }
 509         catch(...) {
 510                 cout << "An unknown error has occurred in the GlobalData class function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 511                 exit(1);
 512         }
 513 }
 514 /*******************************************************/
 515
 516 /*******************************************************/
 517 void GlobalData::readTreeString(ifstream& filehandle)   {
 518         try {
 519                 int c;
 520                 string name; //k
 521
 522                 while((c = filehandle.peek()) != ';') {
 523                                 //if you are a name
 524                         if ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != '\t') && (c != 32)) { //32 is space
 525                                 name = "";
 526                                 c = filehandle.get();
 527         //              k = c;
 528 //cout << k << endl;
 529                                 while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {
 530                                         name += c;
 531                                         c = filehandle.get();
 532                 //      k = c;
 533 //cout << " in name while " << k << endl;
 534                                 }
 535
 536 //cout << "name = " << name << endl;
 537                                 Treenames.push_back(name);
 538                                 filehandle.putback(c);
 539 //k = c;
 540 //cout << " after putback" <<  k << endl;
 541                         }
 542
 543                         if (c  == ':') { //read until you reach the end of the branch length
 544                                 while ((c != '(') && (c != ')') && (c != ',') && (c != ';') && (c != '\n') && (c != '\t') && (c != 32)) {
 545                                         c = filehandle.get();
 546                                 //      k = c;
 547         //cout << " in branch while " << k << endl;
 548                                 }
 549                                 filehandle.putback(c);
 550                         }
 551                         c = filehandle.get();
 552                         if (c == ';') { break; }
 553                 //      k = c;
 554 //cout << k << endl;
 555
 556                 }
 557         }
 558         catch(exception& e) {
 559                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 560                 exit(1);
 561         }
 562         catch(...) {
 563                 cout << "An unknown error has occurred in the GlobalData class function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 564                 exit(1);
 565         }
 566 }
 567
 568 /*******************************************************/
 569
 570 /*******************************************************/
 571
 572