sped up unifrac unweighted.

[mothur.git] / unifracweightedcommand.cpp

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index 9cda8f2ec14c4accb670c174602fb5c9ab2d5502..0201776b041e3637351bd3402c43cbdebf0223ce 100644 (file)
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -58,7 +58,7 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
                        string temp = validParameter.validFile(parameters, "distance", false);                  if (temp == "not found") { temp = "false"; }
                        phylip = m->isTrue(temp);
                
-                       temp = validParameter.validFile(parameters, "random", false);                                   if (temp == "not found") { temp = "true"; }
+                       temp = validParameter.validFile(parameters, "random", false);                                   if (temp == "not found") { temp = "F"; }
                        random = m->isTrue(temp);
                        
                        if (!random) {  iters = 0;  } //turn off random calcs
@@ -97,7 +97,7 @@ void UnifracWeightedCommand::help(){
                m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 2 valid groups.\n");
                m->mothurOut("The group names are separated by dashes.  The iters parameter allows you to specify how many random trees you would like compared to your tree.\n");
                m->mothurOut("The distance parameter allows you to create a distance file from the results. The default is false.\n");
-               m->mothurOut("The random parameter allows you to shut off the comparison to random trees. The default is true, meaning compare your trees with randomly generated trees.\n");
+               m->mothurOut("The random parameter allows you to shut off the comparison to random trees. The default is false, meaning don't compare your trees with randomly generated trees.\n");
                m->mothurOut("The unifrac.weighted command should be in the following format: unifrac.weighted(groups=yourGroups, iters=yourIters).\n");
                m->mothurOut("Example unifrac.weighted(groups=A-B-C, iters=500).\n");
                m->mothurOut("The default value for groups is all the groups in your groupfile, and iters is 1000.\n");