added hcluster command and fixed some bugs, namely one with smart distancing.

[mothur.git] / globaldata.cpp

diff --git a/globaldata.cpp b/globaldata.cpp
index 690a8c3400c802844dc71c49f13f898a0e822e0e..c2871694e2feaa9219ed5d31575e57a84a3022dc 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;                                   }
@@ -63,6 +61,7 @@ GlobalData::GlobalData() {
        gMatrix = NULL;
        gTreemap = NULL;
        gSequenceDB = NULL;
+       nameMap = NULL;
 }
 /*******************************************************/
 
@@ -115,6 +114,8 @@ void GlobalData::newRead() {
                        if (gTreemap != NULL) { delete gTreemap; gTreemap = NULL; }
 
                        if (gSequenceDB != NULL) { delete gSequenceDB; gSequenceDB = NULL;}
+                       
+                       if (nameMap != NULL) { delete nameMap; nameMap = NULL; }
 
 
                        gTree.clear();
@@ -147,6 +148,7 @@ 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");