globaldata.cpp

   1
   2
   3 #include "globaldata.hpp"
   4 #include "sharedlistvector.h"
   5 #include "inputdata.h"
   6 #include "fullmatrix.h"
   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 // These functions give you the option parameters of the commands
  21 string GlobalData::getPhylipFile()              {       return phylipfile;              }
  22 string GlobalData::getColumnFile()              {       return columnfile;              }
  23 string GlobalData::getListFile()                {       return listfile;                }
  24 string GlobalData::getRabundFile()              {       return rabundfile;              }
  25 string GlobalData::getSabundFile()              {       return sabundfile;              }
  26 string GlobalData::getNameFile()                {       return namefile;                }
  27 string GlobalData::getGroupFile()               {       return groupfile;               }
  28 string GlobalData::getOrderFile()               {       return orderfile;               }
  29 string GlobalData::getOrderGroupFile()  {       return ordergroup;              }
  30 string GlobalData::getTreeFile()                {       return treefile;                }
  31 string GlobalData::getSharedFile()              {       return sharedfile;              }
  32 string GlobalData::getFormat()                  {       return format;                  }
  33
  34 void GlobalData::setListFile(string file)               {       listfile = file;        inputFileName = file;                                   }
  35 void GlobalData::setTreeFile(string file)               {       treefile = file;        inputFileName = file;                                   }
  36 void GlobalData::setRabundFile(string file)             {       rabundfile = file;      inputFileName = file;                                   }
  37 void GlobalData::setSabundFile(string file)             {       sabundfile = file;      inputFileName = file;                                   }
  38 void GlobalData::setPhylipFile(string file)             {       phylipfile = file;    inputFileName = file;                                     }
  39 void GlobalData::setColumnFile(string file)             {       columnfile = file;    inputFileName = file;                                     }
  40 void GlobalData::setGroupFile(string file)              {       groupfile = file;                                                                                       }
  41 void GlobalData::setSharedFile(string file)             {       sharedfile = file;      inputFileName = file;                                   }
  42 void GlobalData::setNameFile(string file)               {       namefile = file;                }
  43 void GlobalData::setOrderFile(string file)              {       orderfile = file;               }
  44 void GlobalData::setOrderGroupFile(string file) {       ordergroup = file;              }
  45 void GlobalData::setFormat(string Format)               {       format = Format;                }
  46
  47
  48 /*******************************************************/
  49
  50 /******************************************************/
  51 GlobalData::GlobalData() {
  52         m = MothurOut::getInstance();
  53         //option definitions should go here...
  54         clear();
  55         gListVector = NULL;
  56         gSparseMatrix = NULL;
  57         ginput = NULL;
  58         gorder = NULL;
  59         glist = NULL;
  60         gSharedList = NULL;
  61         sabund = NULL;
  62         rabund = NULL;
  63         gGroupmap = NULL;
  64         gMatrix = NULL;
  65         gTreemap = NULL;
  66         gSequenceDB = NULL;
  67         nameMap = NULL;
  68 }
  69 /*******************************************************/
  70
  71 /******************************************************/
  72 void GlobalData::clear() {
  73         //option definitions should go here...
  74         phylipfile              =       ""; //do we need this?
  75         columnfile              =       ""; //do we need this?
  76         listfile                =       "";
  77         rabundfile              =       "";
  78         sabundfile              =       "";
  79         namefile                =       ""; //do we need this?
  80         groupfile               =       ""; //do we need this?
  81         orderfile               =       "";
  82         ordergroup              =       "";
  83 //      fastafile               =   ""; //do we need this?
  84         treefile                =       "";
  85         sharedfile              =       "";
  86         format = "";
  87 }
  88
  89
  90 /*******************************************************/
  91
  92 /******************************************************/
  93 void GlobalData::newRead() {
  94         try{
  95                         //remove old file names
  96                         clear();
  97
  98                         //free memory
  99                         if (gGroupmap != NULL) { delete gGroupmap; gGroupmap = NULL; }
 100
 101                         if (gListVector != NULL) { delete gListVector; gListVector = NULL;}
 102
 103                         if (gSparseMatrix != NULL) { delete gSparseMatrix; gSparseMatrix = NULL; }
 104
 105                         if (ginput != NULL) { delete ginput; ginput = NULL;}
 106
 107                         if (gorder != NULL) { delete gorder; gorder = NULL; }
 108
 109                         if (glist != NULL) { delete glist; glist = NULL;}
 110
 111                         if (gSharedList != NULL) { delete gSharedList; gSharedList = NULL; }
 112
 113                         if (sabund != NULL) { delete sabund; sabund = NULL;}
 114
 115                         if (rabund != NULL) { delete rabund; rabund = NULL; }
 116
 117                         if (gMatrix != NULL) { delete gMatrix; gMatrix = NULL;}
 118
 119                         if (gTreemap != NULL) { delete gTreemap; gTreemap = NULL; }
 120
 121                         if (gSequenceDB != NULL) { delete gSequenceDB; gSequenceDB = NULL;}
 122
 123                         if (nameMap != NULL) { delete nameMap; nameMap = NULL; }
 124
 125
 126                         gTree.clear();
 127                         Treenames.clear();
 128                         labels.clear(); Groups.clear();
 129                         allLines = 1;
 130                         runParse = true;
 131                         names.clear();
 132         }
 133         catch(exception& e) {
 134                 m->errorOut(e, "GlobalData", "newRead");
 135                 exit(1);
 136         }
 137 }
 138
 139 //******************************************************/
 140
 141 /******************************************************/
 142 GlobalData::~GlobalData() {
 143         _uniqueInstance = 0;
 144         try {
 145                 if (gGroupmap != NULL) { delete gGroupmap; gGroupmap = NULL; }
 146                 if (gListVector != NULL) { delete gListVector; gListVector = NULL;}
 147                 if (gSparseMatrix != NULL) { delete gSparseMatrix; gSparseMatrix = NULL; }
 148                 if (ginput != NULL) { delete ginput; ginput = NULL;}
 149                 if (gorder != NULL) { delete gorder; gorder = NULL; }
 150                 if (glist != NULL) { delete glist; glist = NULL;}
 151                 if (gSharedList != NULL) { delete gSharedList; gSharedList = NULL; }
 152                 if (sabund != NULL) { delete sabund; sabund = NULL;}
 153                 if (rabund != NULL) { delete rabund; rabund = NULL; }
 154                 if (gMatrix != NULL) { delete gMatrix; gMatrix = NULL;}
 155                 if (gTreemap != NULL) { delete gTreemap; gTreemap = NULL; }
 156                 if (gSequenceDB != NULL) { delete gSequenceDB; gSequenceDB = NULL;}
 157                 if (nameMap != NULL) { delete nameMap; nameMap = NULL; }
 158         }
 159         catch(exception& e) {
 160                 m->errorOut(e, "GlobalData", "~GlobalData");
 161                 exit(1);
 162         }
 163 }
 164 /*******************************************************/
 165
 166 /*******************************************************/
 167
 168