fixed a bug in calculating the # of ambig bases

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index 0c2548971555b599ea87eba61623fb2dfcf9a8ac..f97d98b311ff46f21d5479c15795eaa3e69fd892 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -75,10 +75,10 @@ public:
        string getStep();
        string getForm();
        string getSorted();
-       string getEnds();
+       string getCountEnds();
        string getProcessors();
        string getSize();
-       string getTemplateFile();
+       string getCandidateFile();
        string getSearch();
        string getKSize();
        string getAlign();
@@ -86,11 +86,17 @@ public:
        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); 
@@ -104,7 +110,7 @@ public:
        void setRandomTree(string);
        void setGroups(string);
        void setCalc(string);
-       void setEnds(string);
+       void setCountEnds(string);
        void setProcessors(string);
 
        void clear(); 
@@ -113,7 +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.
@@ -121,9 +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, ends, processors, templatefile, search, ksize, align, match, size;
-       string mismatch, gapopen, gapextend;
+       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;