changed raredisplay to use vectors instead of files

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index 6f66cbe8bbd09577ff0ce709e7fc882d79eb8874..759bcae6fd7631988bf15407e7234330c2c9f659 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -42,12 +42,13 @@ public:
        TreeMap* gTreemap;
        SequenceDB* gSequenceDB;
        string inputFileName, argv;
-       bool allLines, runParse;
+       bool allLines, runParse, jumble;
        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;
        
+       
        string getPhylipFile();
        string getColumnFile();
        string getListFile();
@@ -56,18 +57,13 @@ public:
        string getNameFile();   //do we need this?
        string getGroupFile();  //do we need this?
        string getOrderFile();
-//     string getFastaFile();
        string getTreeFile();
        string getSharedFile();
        string getFormat();     //do we need this?
-//     string getCandidateFile();
-//     string getTemplateFile();
+
 
        void setListFile(string);
-//     void setFastaFile(string);
        void setTreeFile(string);
-//     void setCandidateFile(string);
-//     void setTemplateFile(string);
        void setGroupFile(string);              //do we need this?
        void setPhylipFile(string);
        void setColumnFile(string);