unifrac parallelization done, changed dist.seqs output=square to calc all distance...

[mothur.git] / unifracweightedcommand.h

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index b6aea7dad9215a131691019445c2f911c77084a4..7317c8a43092a5712a06dda00589d1eb4528c649 100644 (file)
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -34,7 +34,7 @@ class UnifracWeightedCommand : public Command {
                        int num;
                        linePair(int i, int j) : start(i), num(j) {}
                };
-               vector<linePair*> lines;
+               vector<linePair> lines;
                
                GlobalData* globaldata;
                SharedUtil* util;
@@ -43,7 +43,6 @@ class UnifracWeightedCommand : public Command {
                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...
-               Tree* randT;  //random tree
                TreeMap* tmap;
                Weighted* weighted;
                string sumFile, outputDir;
@@ -70,8 +69,8 @@ class UnifracWeightedCommand : public Command {
                //void removeValidScoresDuplicates();
                int findIndex(float, int);
                void calculateFreqsCumuls();
-               int createProcesses(Tree*, Tree*, vector< vector<string> >, vector<double>&, vector< vector<double> >&);
-               int driver(Tree*, Tree*, vector< vector<string> >, int, int, vector<double>&, vector< vector<double> >&);
+               int createProcesses(Tree*,  vector< vector<string> >, vector<double>&, vector< vector<double> >&);
+               int driver(Tree*, vector< vector<string> >, int, int, vector<double>&, vector< vector<double> >&);
                
 };