globaldata.cpp

   1 #include "globaldata.hpp"
   2 #include "sparsematrix.hpp"
   3 #include "tree.h"
   4 #include "rabundvector.hpp"
   5 #include "sabundvector.hpp"
   6 #include "listvector.hpp"
   7
   8 /*******************************************************/
   9
  10 /******************************************************/
  11 GlobalData* GlobalData::getInstance() {
  12         if( _uniqueInstance == 0 ) {
  13                 _uniqueInstance = new GlobalData();
  14         }
  15         return _uniqueInstance;
  16 }
  17 /*******************************************************/
  18
  19 /******************************************************/
  20 //This function parses through the option string of the command to remove its parameters
  21 void GlobalData::parseGlobalData(string commandString, string optionText){
  22         try {
  23                 commandName = commandString; //save command name to be used by other classes
  24
  25                 //set all non filename paramters to default
  26                 reset();
  27
  28                 //clears out data from previous read
  29                 if ((commandName == "read.dist") || (commandName == "read.otu") || (commandName == "read.tree")) {
  30                         clear();
  31                         gGroupmap = NULL;
  32                         gTree.clear();
  33                         labels.clear(); lines.clear(); groups.clear();
  34                         allLines = 1;
  35                 }
  36
  37                 //saves help request
  38                 if (commandName =="help") {
  39                         helpRequest = optionText;
  40                 }
  41
  42                 if (commandName == "libshuff") {
  43                         iters = "10000";
  44                         cutoff = "1.0";
  45                 }
  46
  47                 string key, value;
  48                 //reads in parameters and values
  49                 if((optionText != "") && (commandName != "help")){
  50                         while((optionText.find_first_of(',') != -1)) {  //while there are parameters
  51                                 splitAtComma(value, optionText);
  52                                 splitAtEquals(key, value);
  53
  54                                 if (key == "phylip" )   { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";       }
  55                                 if (key == "column" )   { columnfile = value; inputFileName = value; fileroot = value; format = "column";       }
  56                                 if (key == "list" )             { listfile = value; inputFileName = value; fileroot = value; format = "list";           }
  57                                 if (key == "rabund" )   { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
  58                                 if (key == "sabund" )   { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       }
  59                                 if (key == "fasta" )    { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
  60                                 if (key == "tree" )             { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }
  61                                 if (key == "shared" )   { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile";   }
  62                                 if (key == "name" )             { namefile = value;             }
  63                                 if (key == "order" )    { orderfile = value;    }
  64                                 if (key == "group" )    { groupfile = value;    }
  65                                 if (key == "cutoff" )           { cutoff = value;               }
  66                                 if (key == "precision" )        { precision = value;    }
  67                                 if (key == "iters" )            { iters = value;                }
  68                                 if (key == "jumble" )           { jumble = value;               }
  69                                 if (key == "freq" )                     { freq = value;                 }
  70                                 if (key == "method" )           { method = value;               }
  71                                 if (key == "fileroot" )         { fileroot = value;             }
  72                                 if (key == "abund" )        { abund = value;        }
  73                                 if (key == "random" )           { randomtree = value;   }
  74                                 if (key == "calc")                      { calc = value;                 }
  75                                 if (key == "step")                      { step = value;                 }
  76                                 if (key == "form")                      { form = value;                 }
  77                                 if (key == "sorted")            { sorted = value;               }
  78
  79
  80
  81                                 if (key == "line") {//stores lines to be used in a set
  82                                         lines.clear();
  83                                         labels.clear();
  84                                         line = value;
  85                                         label = "";
  86                                         splitAtDash(value, lines);
  87                                         allLines = 0;
  88                                 }
  89                                 if (key == "label") {//stores labels to be used in a set
  90                                         labels.clear();
  91                                         lines.clear();
  92                                         label = value;
  93                                         line = "";
  94                                         splitAtDash(value, labels);
  95                                         allLines = 0;
  96                                 }
  97
  98                                 if (key == "groups") {//stores groups to be used in a vector
  99                                         Groups.clear();
 100                                         groups = value;
 101                                         splitAtDash(value, Groups);
 102                                 }
 103
 104                         }
 105
 106                         //saves the last parameter
 107                         value = optionText;
 108                         splitAtEquals(key, value);
 109                         if (key == "phylip" )   { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";       }
 110                         if (key == "column" )   { columnfile = value; inputFileName = value; fileroot = value; format = "column";       }
 111                         if (key == "list" )             { listfile = value; inputFileName = value; fileroot = value; format = "list";           }
 112                         if (key == "rabund" )   { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
 113                         if (key == "sabund" )   { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       }
 114                         if (key == "fasta" )    { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
 115                         if (key == "tree" )             { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }
 116                         if (key == "shared" )   { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile";   }
 117                         if (key == "name" )             { namefile = value;             }
 118                         if (key == "order" )    { orderfile = value;    }
 119                         if (key == "group" )    { groupfile = value;    }
 120                         if (key == "cutoff" )           { cutoff = value;               }
 121                         if (key == "precision" )        { precision = value;    }
 122                         if (key == "iters" )            { iters = value;                }
 123                         if (key == "jumble" )           { jumble = value;               }
 124                         if (key == "freq" )                     { freq = value;                 }
 125                         if (key == "method" )           { method = value;               }
 126                         if (key == "fileroot" )         { fileroot = value;             }
 127                         if (key == "abund" )        { abund = value;        }
 128                         if (key == "random" )           { randomtree = value;   }
 129                         if (key == "calc")                      { calc = value;                 }
 130                         if (key == "step")                      { step = value;                 }
 131                         if (key == "form")                      { form = value;                 }
 132                         if (key == "sorted")            { sorted = value;               }
 133
 134                         if (key == "line") {//stores lines to be used in a vector
 135                                 lines.clear();
 136                                 labels.clear();
 137                                 line = value;
 138                                 label = "";
 139                                 if (line != "all") {  splitAtDash(value, lines);  allLines = 0;  }
 140                                 else { allLines = 1;  }
 141                         }
 142                         if (key == "label") {//stores lines to be used in a vector
 143                                 labels.clear();
 144                                 lines.clear();
 145                                 label = value;
 146                                 line = "";
 147                                 if (label != "all") {  splitAtDash(value, labels);  allLines = 0;  }
 148                                 else { allLines = 1;  }
 149                         }
 150
 151                         if (key == "groups") {//stores groups to be used in a vector
 152                                         Groups.clear();
 153                                         groups = value;
 154                                         splitAtDash(value, Groups);
 155                         }
 156                 }
 157
 158                 //set format for shared
 159                 if ((listfile != "") && (groupfile != "")) { format = "shared"; }
 160                 if ((phylipfile != "") && (groupfile != "")) { format = "matrix"; }
 161
 162                 //input defaults for calculators
 163                 if (commandName == "collect.single") {
 164                         if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-geom-qstat-logsd-bergerparker-bstick"; }
 165                         Estimators.clear();
 166                         splitAtDash(calc, Estimators);
 167                 }
 168                 if (commandName == "rarefaction.single") {
 169                         if ((calc == "default") || (calc == "")) { calc = "sobs"; }
 170                         Estimators.clear();
 171                         splitAtDash(calc, Estimators);
 172                 }
 173                 if (commandName == "collect.shared") {
 174                         if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan-sharedkstest-sharedbdiversity"; }
 175                         Estimators.clear();
 176                         splitAtDash(calc, Estimators);
 177                 }
 178                 if (commandName == "summary.single") {
 179                         if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-geom-logsd-qstat-bergerparker-bstick"; }
 180                         Estimators.clear();
 181                         splitAtDash(calc, Estimators);
 182                 }
 183                 if (commandName == "summary.shared") {
 184                         if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan-sharedkstest-sharedbdiversity"; }
 185                         Estimators.clear();
 186                         splitAtDash(calc, Estimators);
 187                 }
 188                 if (commandName == "rarefaction.shared") {
 189                         if ((calc == "default") || (calc == "")) { calc = "sharedobserved"; }
 190                         Estimators.clear();
 191                         splitAtDash(calc, Estimators);
 192                 }
 193
 194                 //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
 195                 if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single")) {
 196                         if (listfile != "") { format = "list"; }
 197                         else if (sabundfile != "") { format = "sabund"; }
 198                         else if (rabundfile != "") { format = "rabund"; }
 199                 }
 200         }
 201         catch(exception& e) {
 202                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 203                 exit(1);
 204         }
 205         catch(...) {
 206                 cout << "An unknown error has occurred in the GlobalData class function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 207                 exit(1);
 208         }
 209 }
 210 /*******************************************************/
 211
 212 /******************************************************/
 213 // These functions give you the option parameters of the commands
 214 string GlobalData::getPhylipFile()              {       return phylipfile;      }
 215 string GlobalData::getColumnFile()              {       return columnfile;      }
 216 string GlobalData::getListFile()                {       return listfile;        }
 217 string GlobalData::getRabundFile()              {       return rabundfile;      }
 218 string GlobalData::getSabundFile()              {       return sabundfile;      }
 219 string GlobalData::getNameFile()                {       return namefile;        }
 220 string GlobalData::getGroupFile()               {       return groupfile;       }
 221 string GlobalData::getOrderFile()               {       return orderfile;       }
 222 string GlobalData::getTreeFile()                {       return treefile;        }
 223 string GlobalData::getSharedFile()              {       return sharedfile;      }
 224 string GlobalData::getFastaFile()               {       return fastafile;       }
 225 string GlobalData::getCutOff()                  {       return cutoff;          }
 226 string GlobalData::getFormat()                  {       return format;          }
 227 string GlobalData::getPrecision()               {       return precision;       }
 228 string GlobalData::getMethod()                  {       return method;          }
 229 string GlobalData::getFileRoot()                {       return fileroot;        }
 230 string GlobalData::getIters()                   {       return iters;           }
 231 string GlobalData::getJumble()                  {       return jumble;          }
 232 string GlobalData::getFreq()                    {       return freq;            }
 233 string GlobalData::getAbund()           {   return abund;       }
 234 string GlobalData::getRandomTree()              {       return randomtree;      }
 235 string GlobalData::getGroups()                  {       return groups;          }
 236 string GlobalData::getStep()                    {       return step;            }
 237 string GlobalData::getForm()                    {       return form;            }
 238 string GlobalData::getSorted()                  {       return sorted;          }
 239 void GlobalData::setListFile(string file)       {       listfile = file;        inputFileName = file;}
 240 void GlobalData::setRabundFile(string file)     {       rabundfile = file;      inputFileName = file;}
 241 void GlobalData::setSabundFile(string file)     {       sabundfile = file;      inputFileName = file;}
 242 void GlobalData::setPhylipFile(string file)     {       phylipfile = file;    inputFileName = file;}
 243 void GlobalData::setColumnFile(string file)     {       columnfile = file;    inputFileName = file;}
 244 void GlobalData::setNameFile(string file)               {       namefile = file;                }
 245 void GlobalData::setFormat(string Format)               {       format = Format;                }
 246 void GlobalData::setRandomTree(string Random)   {       randomtree = Random;    }
 247 void GlobalData::setGroups(string g)                    {       groups = g;                             }
 248 void GlobalData::setCalc(string Calc)                   {       calc = Calc;                    }
 249
 250 /*******************************************************/
 251
 252 /******************************************************/
 253 GlobalData::GlobalData() {
 254         //option definitions should go here...
 255         helpRequest = "";
 256         clear();
 257 }
 258 /*******************************************************/
 259
 260 /******************************************************/
 261 void GlobalData::clear() {
 262         //option definitions should go here...
 263         phylipfile              =       "";
 264         columnfile              =       "";
 265         listfile                =       "";
 266         rabundfile              =       "";
 267         sabundfile              =       "";
 268         namefile                =       "";
 269         groupfile               =       "";
 270         orderfile               =       "";
 271         fastafile               =   "";
 272         treefile                =       "";
 273         sharedfile              =       "";
 274         cutoff                  =       "10.00";
 275         format                  =       "";
 276         precision               =       "100";
 277         iters                   =       "1000";
 278         line                    =   "";
 279         label                   =       "";
 280         groups                  =       "";
 281         jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
 282         randomtree              =       "";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
 283         freq                    =       "100";
 284         method                  =       "furthest";
 285         fileroot                =       "";
 286         abund           =   "10";
 287         step                    =       "0.01";
 288         form                    =       "integral";
 289         sorted                  =       "1";  //0 means don't sort, 1 means sort.
 290 }
 291
 292 //*******************************************************/
 293
 294 /******************************************************/
 295 void GlobalData::reset() {
 296         cutoff                  =       "10.00";
 297         precision               =       "100";
 298         iters                   =       "1000";
 299         groups                  =       "";
 300         jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
 301         sorted                  =       "1";  //0 means don't sort, 1 means sort.
 302         randomtree              =       "";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
 303         freq                    =       "100";
 304         method                  =       "furthest";
 305         calc                    =       "";
 306         abund                   =   "10";
 307         step                    =       "0.01";
 308         form                    =       "integral";
 309 }
 310 /*******************************************************/
 311
 312 /******************************************************/
 313 GlobalData::~GlobalData() {
 314         _uniqueInstance = 0;
 315         if(gListVector != NULL)         {       delete gListVector;             }
 316         if(gSparseMatrix != NULL)       {       delete gSparseMatrix;   }
 317         if(gorder != NULL)                      {       delete gorder;          }
 318 }
 319 /*******************************************************/