fixed a bug in calculating the # of ambig bases

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index aa68dc2c1dffd0fe90f82e8eabff554e0c8c0000..f97d98b311ff46f21d5479c15795eaa3e69fd892 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -41,7 +41,7 @@ public:
        FullMatrix* gMatrix;
        TreeMap* gTreemap;
        SequenceDB* gSequenceDB;
-       string inputFileName, helpRequest, commandName, vertical;
+       string inputFileName, helpRequest, commandName, vertical, argv;
        bool allLines;
        vector<string>  Estimators, Groups; //holds estimators to be used
        set<int> lines; //hold lines to be used
@@ -75,25 +75,43 @@ public:
        string getStep();
        string getForm();
        string getSorted();
-
+       string getCountEnds();
+       string getProcessors();
+       string getSize();
+       string getCandidateFile();
+       string getSearch();
+       string getKSize();
+       string getAlign();
+       string getMatch();
+       string getMismatch();
+       string getGapopen();
+       string getGapextend();
+       string getVertical();
        string getTrump();
        string getSoft();
-       string getFilter();
-       
-
+       string getHard();
        string getScale();
-
+       string getStartPos();
+       string getEndPos();
+       string getMaxAmbig();
+       string getMaxHomoPolymer();
+       string getMinLength();
+       string getMaxLength();
 
        void setListFile(string);
+       void setGroupFile(string file); 
        void setPhylipFile(string);
        void setColumnFile(string);
        void setNameFile(string);
        void setRabundFile(string);
        void setSabundFile(string);
+       void setSharedFile(string);
        void setFormat(string);
        void setRandomTree(string);
        void setGroups(string);
        void setCalc(string);
+       void setCountEnds(string);
+       void setProcessors(string);
 
        void clear(); 
        void clearLabels();
@@ -101,7 +119,7 @@ public:
        
        void parseGlobalData(string, string);
        
-       void parseTreeFile();           //parses through tree file to find names of nodes and number of them
+       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.
@@ -109,8 +127,7 @@ public:
                
 private:
 
-       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;
+       string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, nexusfile, clustalfile, treefile, sharedfile, line, label, randomtree, groups, cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted, trump, soft, hard, scale, countends, processors, candidatefile, search, ksize, align, match, size, mismatch, gapopen, gapextend, minLength, maxLength, startPos, endPos, maxAmbig, maxHomoPolymer;
 
 
        static GlobalData* _uniqueInstance;