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 // These functions give you the option parameters of the commands
  18 string GlobalData::getPhylipFile()              {       return phylipfile;              }
  19 string GlobalData::getColumnFile()              {       return columnfile;              }
  20 string GlobalData::getListFile()                {       return listfile;                }
  21 string GlobalData::getRabundFile()              {       return rabundfile;              }
  22 string GlobalData::getSabundFile()              {       return sabundfile;              }
  23 string GlobalData::getNameFile()                {       return namefile;                }
  24 string GlobalData::getGroupFile()               {       return groupfile;               }
  25 string GlobalData::getOrderFile()               {       return orderfile;               }
  26 string GlobalData::getTreeFile()                {       return treefile;                }
  27 string GlobalData::getSharedFile()              {       return sharedfile;              }
  28 string GlobalData::getFastaFile()               {       return fastafile;               }
  29 string GlobalData::getFormat()                  {       return format;                  }
  30 string GlobalData::getCandidateFile()   {       return candidatefile;   }
  31
  32
  33 void GlobalData::setListFile(string file)               {       listfile = file;        inputFileName = file;                                   }
  34 void GlobalData::setFastaFile(string file)              {       fastafile = file;       inputFileName = file;                                   }
  35 void GlobalData::setTreeFile(string file)               {       treefile = file;        inputFileName = file;                                   }
  36 void GlobalData::setCandidateFile(string file)  {       candidatefile = file;                                                                           }
  37 void GlobalData::setRabundFile(string file)             {       rabundfile = file;      inputFileName = file;                                   }
  38 void GlobalData::setSabundFile(string file)             {       sabundfile = file;      inputFileName = file;                                   }
  39 void GlobalData::setPhylipFile(string file)             {       phylipfile = file;    inputFileName = file;                                     }
  40 void GlobalData::setColumnFile(string file)             {       columnfile = file;    inputFileName = file;                                     }
  41 void GlobalData::setGroupFile(string file)              {       groupfile = file;                                                                                       }
  42 void GlobalData::setSharedFile(string file)             {       sharedfile = file;      inputFileName = file;                                   }
  43 void GlobalData::setNameFile(string file)               {       namefile = file;                }
  44 void GlobalData::setOrderFile(string file)              {       orderfile = file;               }
  45 void GlobalData::setFormat(string Format)               {       format = Format;                }
  46
  47
  48 /*******************************************************/
  49
  50 /******************************************************/
  51 GlobalData::GlobalData() {
  52         //option definitions should go here...
  53         clear();
  54         gListVector = NULL;
  55         gSparseMatrix = NULL;
  56 }
  57 /*******************************************************/
  58
  59 /******************************************************/
  60 void GlobalData::clear() {
  61         //option definitions should go here...
  62         phylipfile              =       "";
  63         columnfile              =       "";
  64         listfile                =       "";
  65         rabundfile              =       "";
  66         sabundfile              =       "";
  67         namefile                =       "";
  68         groupfile               =       "";
  69         orderfile               =       "";
  70         fastafile               =   "";
  71         treefile                =       "";
  72         sharedfile              =       "";
  73         candidatefile   =       "";
  74 }
  75 /*******************************************************/
  76
  77 /******************************************************/
  78 void GlobalData::newRead() {
  79         try{
  80                         clear();
  81                         gGroupmap = NULL;
  82                         gListVector = NULL;
  83                         gSparseMatrix = NULL;
  84                         gTree.clear();
  85                         Treenames.clear();
  86                         labels.clear(); lines.clear(); Groups.clear();
  87                         allLines = 1;
  88                         runParse = true;
  89         }
  90         catch(exception& e) {
  91                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function newRead. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  92                 exit(1);
  93         }
  94         catch(...) {
  95                 cout << "An unknown error has occurred in the GlobalData class function newRead. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  96                 exit(1);
  97         }
  98 }
  99
 100 //******************************************************/
 101
 102 /******************************************************/
 103 GlobalData::~GlobalData() {
 104         _uniqueInstance = 0;
 105         if(gListVector != NULL)         {       delete gListVector;             }
 106         if(gSparseMatrix != NULL)       {       delete gSparseMatrix;   }
 107         if(gorder != NULL)                      {       delete gorder;          }
 108 }
 109 /*******************************************************/
 110
 111 /*******************************************************/
 112
 113