added tree reader class to handle reading trees. Reworked the tree map to tree class...

[mothur.git] / unifracweightedcommand.h

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index e1ebd16c6151e373eb86971f53295d2036b4e4c2..ddbdc8548dad7e0545d75f8e98cd92fdb76a3419 100644 (file)
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -42,15 +42,12 @@ class UnifracWeightedCommand : public Command {
                        linePair(int i, int j) : start(i), num(j) {}
                };
                vector<linePair> lines;
-               
-               ReadTree* read;
-               SharedUtil* util;
+        TreeMap* tmap;
                FileOutput* output;
                vector<Tree*> T;           //user trees
                vector<double> utreeScores;  //user tree unweighted scores
                vector<double> WScoreSig;  //tree weighted score signifigance when compared to random trees - percentage of random trees with that score or lower.
                vector<string> groupComb; // AB. AC, BC...
-               TreeMap* tmap;
                string sumFile, outputDir;
                int iters, numGroups, numComp, counter;
                vector< vector<double> > rScores;  //vector<weighted scores for random trees.> each group comb has an entry
@@ -74,10 +71,8 @@ class UnifracWeightedCommand : public Command {
                void calculateFreqsCumuls();
                int createProcesses(Tree*,  vector< vector<string> >,  vector< vector<double> >&);
                int driver(Tree*, vector< vector<string> >, int, int,  vector< vector<double> >&);
-               int readNamesFile();
         int runRandomCalcs(Tree*, vector<double>);
-        int readTrees();
-        vector<Tree*> buildTrees(vector< vector<double> >&, int, TreeMap*);
+        vector<Tree*> buildTrees(vector< vector<double> >&, int, TreeMap&);
         int getConsensusTrees(vector< vector<double> >&, int);
         int getAverageSTDMatrices(vector< vector<double> >&, int);