fixed bug in read.tree updates help and validparameters strings, added ability for...

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index 6070dd7b2cdd6122b78c5833359ce487497fd0e3..0abdd28cd18bcfc617ab105069cf15db5ead241b 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -37,6 +37,7 @@ public:
        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();
@@ -60,6 +61,9 @@ public:
        string getAbund();
        string getRandomTree();
        string getGroups();
+       string getStep();
+       string getForm();
+       string getSorted();
 
        void setListFile(string);
        void setPhylipFile(string);
@@ -77,10 +81,16 @@ public:
        void clearAbund();
        
        void parseGlobalData(string, string);
+       
+       void parseTreeFile();           //parses through tree file to find names of nodes and number of them
+                                                       //this is required in case user has sequences in the names file that are
+                                                       //not included in the tree. 
+                                                       //only takes names from the first tree in the tree file and assumes that all trees use the same names.
+
                
 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;
+       string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted;
 
        static GlobalData* _uniqueInstance;
        GlobalData( const GlobalData& ); // Disable copy constructor
@@ -88,6 +98,7 @@ private:
        GlobalData();
        ~GlobalData();
        void reset();   //clears all non filename parameters
+       void readTreeString(ifstream&);