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