added MPI code, broke up chimera.seqs into 5 separated commands, added parse.sff...

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index 1d38d63afc4df198599b77cf725b734c531a33ac..35415c70c874039c99c758c24a77b7b43eeb6079 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -7,6 +7,11 @@
 #include "rabundvector.hpp"
 #include "sabundvector.hpp"
 #include "listvector.hpp"
+#include "tree.h"
+#include "sparsematrix.hpp"
+#include "sequencedb.h"
+#include "nameassignment.hpp"
+
 
 class ListVector;
 class SharedListVector;
@@ -38,39 +43,39 @@ public:
        TreeMap* gTreemap;
        SequenceDB* gSequenceDB;
        string inputFileName, argv;
-       bool allLines, runParse;
+       bool allLines, runParse, jumble, sim;
        vector<string>  Estimators, Groups; //holds estimators to be used
-       set<int> lines; //hold lines to be used
        set<string> labels; //holds labels to be used
        vector<string> Treenames;
+       map<string, string> names;
+       
        
        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 getTreeFile();
        string getSharedFile();
-       string getFormat();
-       string getCandidateFile();
-               
+       string getFormat();     //do we need this?
+
+
        void setListFile(string);
-       void setFastaFile(string);
        void setTreeFile(string);
-       void setCandidateFile(string);
-       void setGroupFile(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?
+       
+       NameAssignment* nameMap;
        
        void clear(); 
        void clearLabels();
@@ -79,8 +84,8 @@ public:
        void newRead();
        
 private:
-
-       string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, treefile, sharedfile, format, candidatefile;
+       MothurOut* m;
+       string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, treefile, sharedfile, format, distfile;
 
        static GlobalData* _uniqueInstance;
        GlobalData( const GlobalData& ); // Disable copy constructor