Merge remote-tracking branch 'origin/master'

[mothur.git] / parsimonycommand.h

diff --git a/parsimonycommand.h b/parsimonycommand.h
index 81fa99ba06c691f9e0ee06f4b73521655b046e8c..79613f560746e443697e4e92bfed755605a6fe4a 100644 (file)
--- a/parsimonycommand.h
+++ b/parsimonycommand.h
@@ -28,6 +28,7 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "parsimony";                           }
        string getCommandCategory()             { return "Hypothesis Testing";          }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
        string getCitation() { return "Slatkin M, Maddison WP (1989). A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics 123: 603-13. \nSlatkin M, Maddison WP (1990). Detecting isolation by distance using phylogenies of genes. Genetics 126: 249-60. \nMartin AP (2002). Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl Environ Microbiol 68: 3673-82. \nSchloss PD, Handelsman J (2006). Introducing TreeClimber, a test to compare microbial community structure. Appl Environ Microbiol 72: 2379-84.\nhttp://www.mothur.org/wiki/Parsimony"; }
        string getDescription()         { return "generic test that describes whether two or more communities have the same structure"; }
@@ -36,15 +37,12 @@ public:
        void help() { m->mothurOut(getHelpString()); }
        
 private:
-       ReadTree* read;
-       SharedUtil* util;
        FileOutput* output;
        vector<Tree*> T;           //user trees
        Tree* randT;  //random tree
        Tree* copyUserTree; 
        TreeMap* tmap; 
        TreeMap* savetmap;
-       Parsimony* pars;
        vector<string> groupComb; // AB. AC, BC...
        string sumFile, randomtree, allGroups, outputDir, treefile, groupfile, namefile;
        int iters, numGroups, numComp, counter, processors, numUniquesInName;