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::getRelAbundFile()    {       return relAbundfile;    }
  33 string GlobalData::getFormat()                  {       return format;                  }
  34
  35 void GlobalData::setListFile(string file)               {       listfile = file;        inputFileName = file;                                   }
  36 void GlobalData::setTreeFile(string file)               {       treefile = file;        inputFileName = 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::setRelAbundFile(string file)   {       relAbundfile = file;    inputFileName = file;                           }
  44 void GlobalData::setNameFile(string file)               {       namefile = file;                }
  45 void GlobalData::setOrderFile(string file)              {       orderfile = file;               }
  46 void GlobalData::setOrderGroupFile(string file) {       ordergroup = file;              }
  47 void GlobalData::setFormat(string Format)               {       format = Format;                }
  48
  49
  50 /*******************************************************/
  51
  52 /******************************************************/
  53 GlobalData::GlobalData() {
  54         m = MothurOut::getInstance();
  55         //option definitions should go here...
  56         clear();
  57         gListVector = NULL;
  58         gSparseMatrix = NULL;
  59         ginput = NULL;
  60         gorder = NULL;
  61         glist = NULL;
  62         gSharedList = NULL;
  63         sabund = NULL;
  64         rabund = NULL;
  65         gGroupmap = NULL;
  66         gMatrix = NULL;
  67         gTreemap = NULL;
  68         gSequenceDB = NULL;
  69         nameMap = NULL;
  70 }
  71 /*******************************************************/
  72
  73 /******************************************************/
  74 void GlobalData::clear() {
  75         //option definitions should go here...
  76         phylipfile              =       ""; //do we need this?
  77         columnfile              =       ""; //do we need this?
  78         listfile                =       "";
  79         rabundfile              =       "";
  80         sabundfile              =       "";
  81         namefile                =       ""; //do we need this?
  82         groupfile               =       ""; //do we need this?
  83         orderfile               =       "";
  84         ordergroup              =       "";
  85 //      fastafile               =   ""; //do we need this?
  86         treefile                =       "";
  87         sharedfile              =       "";
  88         relAbundfile    =       "";
  89         format = "";
  90 }
  91
  92
  93 /*******************************************************/
  94
  95 /******************************************************/
  96 void GlobalData::newRead() {
  97         try{
  98                         //remove old file names
  99                         clear();
 100
 101                         //free memory
 102                         if (gGroupmap != NULL) { delete gGroupmap; gGroupmap = NULL; }
 103
 104                         if (gListVector != NULL) { delete gListVector; gListVector = NULL;}
 105
 106                         if (gSparseMatrix != NULL) { delete gSparseMatrix; gSparseMatrix = NULL; }
 107
 108                         if (ginput != NULL) { delete ginput; ginput = NULL;}
 109
 110                         if (gorder != NULL) { delete gorder; gorder = NULL; }
 111
 112                         if (glist != NULL) { delete glist; glist = NULL;}
 113
 114                         if (gSharedList != NULL) { delete gSharedList; gSharedList = NULL; }
 115
 116                         if (sabund != NULL) { delete sabund; sabund = NULL;}
 117
 118                         if (rabund != NULL) { delete rabund; rabund = NULL; }
 119
 120                         if (gMatrix != NULL) { delete gMatrix; gMatrix = NULL;}
 121
 122                         if (gTreemap != NULL) { delete gTreemap; gTreemap = NULL; }
 123
 124                         if (gSequenceDB != NULL) { delete gSequenceDB; gSequenceDB = NULL;}
 125
 126                         if (nameMap != NULL) { delete nameMap; nameMap = NULL; }
 127
 128
 129                         gTree.clear();
 130                         Treenames.clear();
 131                         labels.clear(); Groups.clear();
 132                         allLines = 1;
 133                         runParse = true;
 134                         names.clear();
 135         }
 136         catch(exception& e) {
 137                 m->errorOut(e, "GlobalData", "newRead");
 138                 exit(1);
 139         }
 140 }
 141
 142 //******************************************************/
 143
 144 /******************************************************/
 145 GlobalData::~GlobalData() {
 146         _uniqueInstance = 0;
 147         try {
 148                 if (gGroupmap != NULL) { delete gGroupmap; gGroupmap = NULL; }
 149                 if (gListVector != NULL) { delete gListVector; gListVector = NULL;}
 150                 if (gSparseMatrix != NULL) { delete gSparseMatrix; gSparseMatrix = NULL; }
 151                 if (ginput != NULL) { delete ginput; ginput = NULL;}
 152                 if (gorder != NULL) { delete gorder; gorder = NULL; }
 153                 if (glist != NULL) { delete glist; glist = NULL;}
 154                 if (gSharedList != NULL) { delete gSharedList; gSharedList = NULL; }
 155                 if (sabund != NULL) { delete sabund; sabund = NULL;}
 156                 if (rabund != NULL) { delete rabund; rabund = NULL; }
 157                 if (gMatrix != NULL) { delete gMatrix; gMatrix = NULL;}
 158                 if (gTreemap != NULL) { delete gTreemap; gTreemap = NULL; }
 159                 if (gSequenceDB != NULL) { delete gSequenceDB; gSequenceDB = NULL;}
 160                 if (nameMap != NULL) { delete nameMap; nameMap = NULL; }
 161         }
 162         catch(exception& e) {
 163                 m->errorOut(e, "GlobalData", "~GlobalData");
 164                 exit(1);
 165         }
 166 }
 167 /*******************************************************/
 168
 169 /*******************************************************/
 170
 171