*** empty log message ***

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index cc13bae137577dc28e554c39d9088725114740f3..40b87583aaa2e472f788b2102f5daea0628c2f9e 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -39,7 +39,7 @@ public:
        GroupMap* gGroupmap;
        FullMatrix* gMatrix;
        TreeMap* gTreemap;
-       string inputFileName, helpRequest, commandName;
+       string inputFileName, helpRequest, commandName, vertical;
        bool allLines;
        vector<string>  Estimators, Groups; //holds estimators to be used
        set<int> lines; //hold lines to be used
@@ -55,6 +55,8 @@ public:
        string getGroupFile();
        string getOrderFile();
        string getFastaFile();
+       string getNexusFile();
+       string getClustalFile();
        string getTreeFile();
        string getSharedFile();
        string getCutOff();
@@ -71,8 +73,15 @@ public:
        string getStep();
        string getForm();
        string getSorted();
+
+       string getTrump();
+       string getSoft();
+       string getFilter();
+       
+
        string getScale();
 
+
        void setListFile(string);
        void setPhylipFile(string);
        void setColumnFile(string);
@@ -97,8 +106,10 @@ public:
 
                
 private:
-       string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, treefile, sharedfile, line, label, randomtree, groups;
-       string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted, scale;
+
+       string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, nexusfile, clustalfile, treefile, sharedfile, line, label, randomtree, groups;
+       string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted, trump, soft, filter, scale;
+
 
        static GlobalData* _uniqueInstance;
        GlobalData( const GlobalData& ); // Disable copy constructor