created mothurOut class to handle logfiles

[mothur.git] / globaldata.cpp

diff --git a/globaldata.cpp b/globaldata.cpp
index 0d728a128bd8fc43f0314c21894faf813533c7e2..58d00ffbee1166e3422cf070978c8c97fa964cc1 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -27,12 +27,10 @@ string GlobalData::getNameFile()            {       return namefile;                }
 string GlobalData::getGroupFile()              {       return groupfile;               }
 string GlobalData::getOrderFile()              {       return orderfile;               }
 string GlobalData::getTreeFile()               {       return treefile;                }
-string GlobalData::getSharedFile()             {       return sharedfile;              }
-//string GlobalData::getFastaFile()            {       return fastafile;               }       
+string GlobalData::getSharedFile()             {       return sharedfile;              }       
 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;                                   }
@@ -49,6 +47,7 @@ void GlobalData::setFormat(string Format)             {       format = Format;                }
 
 /******************************************************/
 GlobalData::GlobalData() {
+       m = MothurOut::getInstance();
        //option definitions should go here...
        clear();
        gListVector = NULL;             
@@ -63,6 +62,7 @@ GlobalData::GlobalData() {
        gMatrix = NULL;
        gTreemap = NULL;
        gSequenceDB = NULL;
+       nameMap = NULL;
 }
 /*******************************************************/
 
@@ -93,30 +93,41 @@ 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) {
-               cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function newRead. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the GlobalData class function newRead. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "GlobalData", "newRead");
                exit(1);
        }
 }
@@ -139,13 +150,10 @@ 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) {
-               cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function ~GlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the GlobalData class function ~GlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "GlobalData", "~GlobalData");
                exit(1);
        }
 }