changes while testing

[mothur.git] / parsimonycommand.h

diff --git a/parsimonycommand.h b/parsimonycommand.h
index 79613f560746e443697e4e92bfed755605a6fe4a..7f7ad893b74140087248edfd7deb7b8c3441e671 100644 (file)
--- a/parsimonycommand.h
+++ b/parsimonycommand.h
@@ -11,7 +11,7 @@
 
 #include "command.hpp"
 #include "parsimony.h"
-#include "treemap.h"
+#include "counttable.h"
 #include "progress.hpp"
 #include "sharedutilities.h"
 #include "fileoutput.h"
@@ -28,8 +28,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "parsimony";                           }
        string getCommandCategory()             { return "Hypothesis Testing";          }
-       string getOutputFileNameTag(string, string);
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        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"; }
 
@@ -41,10 +42,10 @@ private:
        vector<Tree*> T;           //user trees
        Tree* randT;  //random tree
        Tree* copyUserTree; 
-       TreeMap* tmap; 
-       TreeMap* savetmap;
+       CountTable* ct; 
+       CountTable* savect;
        vector<string> groupComb; // AB. AC, BC...
-       string sumFile, randomtree, allGroups, outputDir, treefile, groupfile, namefile;
+       string sumFile, randomtree, allGroups, outputDir, treefile, groupfile, namefile, countfile;
        int iters, numGroups, numComp, counter, processors, numUniquesInName;
        vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
        vector< vector<float> > userTreeScores; //scores for users trees for each comb.