working on testing

[mothur.git] / globaldata.cpp

diff --git a/globaldata.cpp b/globaldata.cpp
index cdf819baa6badc6e89c65bb6c6428e01be41d40d..b18324b8766f9d498295a6e630caaec1b5cc9595 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -26,13 +26,13 @@ string GlobalData::getSabundFile()          {       return sabundfile;              }
 string GlobalData::getNameFile()               {       return namefile;                }
 string GlobalData::getGroupFile()              {       return groupfile;               }
 string GlobalData::getOrderFile()              {       return orderfile;               }
+string GlobalData::getOrderGroupFile() {       return ordergroup;              }
 string GlobalData::getTreeFile()               {       return treefile;                }
-string GlobalData::getSharedFile()             {       return sharedfile;              }
-//string GlobalData::getFastaFile()            {       return fastafile;               }       
+string GlobalData::getSharedFile()             {       return sharedfile;              }       
+string GlobalData::getRelAbundFile()   {       return relAbundfile;    }       
 string GlobalData::getFormat()                 {       return format;                  }
 
 void GlobalData::setListFile(string file)              {       listfile = file;        inputFileName = file;                                   }
-//void GlobalData::setFastaFile(string file)           {       fastafile = file;       inputFileName = file;                                   }
 void GlobalData::setTreeFile(string file)              {       treefile = file;        inputFileName = file;                                   }
 void GlobalData::setRabundFile(string file)            {       rabundfile = file;      inputFileName = file;                                   }
 void GlobalData::setSabundFile(string file)            {       sabundfile = file;      inputFileName = file;                                   }
@@ -40,8 +40,10 @@ void GlobalData::setPhylipFile(string file)          {       phylipfile = file;    inputFileNa
 void GlobalData::setColumnFile(string file)            {       columnfile = file;    inputFileName = file;                                     }
 void GlobalData::setGroupFile(string file)             {       groupfile = file;                                                                                       }
 void GlobalData::setSharedFile(string file)            {       sharedfile = file;      inputFileName = file;                                   }
+void GlobalData::setRelAbundFile(string file)  {       relAbundfile = file;    inputFileName = file;                           }
 void GlobalData::setNameFile(string file)              {       namefile = file;                }
 void GlobalData::setOrderFile(string file)             {       orderfile = file;               }
+void GlobalData::setOrderGroupFile(string file)        {       ordergroup = file;              }
 void GlobalData::setFormat(string Format)              {       format = Format;                }
 
 
@@ -49,6 +51,7 @@ void GlobalData::setFormat(string Format)             {       format = Format;                }
 
 /******************************************************/
 GlobalData::GlobalData() {
+       m = MothurOut::getInstance();
        //option definitions should go here...
        clear();
        gListVector = NULL;             
@@ -63,6 +66,8 @@ GlobalData::GlobalData() {
        gMatrix = NULL;
        gTreemap = NULL;
        gSequenceDB = NULL;
+       nameMap = NULL;
+       saveNextLabel = "";
 }
 /*******************************************************/
 
@@ -77,9 +82,13 @@ void GlobalData::clear() {
        namefile                =       ""; //do we need this?
        groupfile               =       ""; //do we need this?
        orderfile               =       "";
+       ordergroup              =       "";
 //     fastafile               =   ""; //do we need this?
        treefile                =       "";
        sharedfile              =       "";
+       relAbundfile    =       "";
+       format = "";
+       saveNextLabel = "";
 }
 
 
@@ -93,26 +102,41 @@ void GlobalData::newRead() {
                        
                        //free memory
                        if (gGroupmap != NULL) { delete gGroupmap; gGroupmap = NULL; }
+
                        if (gListVector != NULL) { delete gListVector; gListVector = NULL;}
+
                        if (gSparseMatrix != NULL) { delete gSparseMatrix; gSparseMatrix = NULL; }
+
                        if (ginput != NULL) { delete ginput; ginput = NULL;}
+
                        if (gorder != NULL) { delete gorder; gorder = NULL; }
+
                        if (glist != NULL) { delete glist; glist = NULL;}
+
                        if (gSharedList != NULL) { delete gSharedList; gSharedList = NULL; }
+
                        if (sabund != NULL) { delete sabund; sabund = NULL;}
+
                        if (rabund != NULL) { delete rabund; rabund = NULL; }
+
                        if (gMatrix != NULL) { delete gMatrix; gMatrix = NULL;}
+
                        if (gTreemap != NULL) { delete gTreemap; gTreemap = NULL; }
+
                        if (gSequenceDB != NULL) { delete gSequenceDB; gSequenceDB = NULL;}
+                       
+                       if (nameMap != NULL) { delete nameMap; nameMap = NULL; }
+
 
                        gTree.clear();
                        Treenames.clear();
-                       labels.clear(); lines.clear(); Groups.clear();
+                       labels.clear(); Groups.clear();
                        allLines = 1;
                        runParse = true;
+                       names.clear();
        }
        catch(exception& e) {
-               errorOut(e, "GlobalData", "newRead");
+               m->errorOut(e, "GlobalData", "newRead");
                exit(1);
        }
 }
@@ -135,9 +159,10 @@ GlobalData::~GlobalData() {
                if (gMatrix != NULL) { delete gMatrix; gMatrix = NULL;}
                if (gTreemap != NULL) { delete gTreemap; gTreemap = NULL; }
                if (gSequenceDB != NULL) { delete gSequenceDB; gSequenceDB = NULL;}
+               if (nameMap != NULL) { delete nameMap; nameMap = NULL; }
        }
        catch(exception& e) {
-               errorOut(e, "GlobalData", "~GlobalData");
+               m->errorOut(e, "GlobalData", "~GlobalData");
                exit(1);
        }
 }