major change to the tree class to use the count table class instead of tree map....

[mothur.git] / parsimonycommand.h

diff --git a/parsimonycommand.h b/parsimonycommand.h
index 79613f560746e443697e4e92bfed755605a6fe4a..38a7505125e52b39ad37f36df592dfc9cac3b54c 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"
@@ -41,10 +41,10 @@ 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.