added logfile feature

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index 1d38d63afc4df198599b77cf725b734c531a33ac..ff09a36c31727bb6d04e3b2dbe50b50574a2a19f 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -7,6 +7,10 @@
 #include "rabundvector.hpp"
 #include "sabundvector.hpp"
 #include "listvector.hpp"
+#include "tree.h"
+#include "sparsematrix.hpp"
+#include "sequencedb.h"
+
 
 class ListVector;
 class SharedListVector;
@@ -44,33 +48,36 @@ public:
        set<string> labels; //holds labels to be used
        vector<string> Treenames;
        
+       
        string getPhylipFile();
        string getColumnFile();
        string getListFile();
        string getRabundFile();
        string getSabundFile();
-       string getNameFile();
-       string getGroupFile();
+       string getNameFile();   //do we need this?
+       string getGroupFile();  //do we need this?
        string getOrderFile();
-       string getFastaFile();
+//     string getFastaFile();
        string getTreeFile();
        string getSharedFile();
-       string getFormat();
-       string getCandidateFile();
-               
+       string getFormat();     //do we need this?
+//     string getCandidateFile();
+//     string getTemplateFile();
+
        void setListFile(string);
-       void setFastaFile(string);
+//     void setFastaFile(string);
        void setTreeFile(string);
-       void setCandidateFile(string);
-       void setGroupFile(string);      
+//     void setCandidateFile(string);
+//     void setTemplateFile(string);
+       void setGroupFile(string);              //do we need this?
        void setPhylipFile(string);
        void setColumnFile(string);
-       void setNameFile(string);
+       void setNameFile(string);       //do we need this?
        void setRabundFile(string);
        void setSabundFile(string);
        void setSharedFile(string);
        void setOrderFile(string file);
-       void setFormat(string);
+       void setFormat(string); //do we need this?
        
        void clear(); 
        void clearLabels();
@@ -80,7 +87,7 @@ public:
        
 private:
 
-       string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, treefile, sharedfile, format, candidatefile;
+       string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, treefile, sharedfile, format;
 
        static GlobalData* _uniqueInstance;
        GlobalData( const GlobalData& ); // Disable copy constructor