#include "command.hpp"
#include "parsimony.h"
-#include "treemap.h"
+#include "counttable.h"
#include "progress.hpp"
#include "sharedutilities.h"
#include "fileoutput.h"
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.