paralellized rarefaction.single

[mothur.git] / unifracweightedcommand.cpp

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index 1417b5a34a6e4ca8a133cc6f2c8ae390ffb81271..e8add90a259bac0da04bf2b8d52be247e9fc1fd1 100644 (file)
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -96,11 +96,12 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
 void UnifracWeightedCommand::help(){
        try {
                m->mothurOut("The unifrac.weighted command can only be executed after a successful read.tree command.\n");
-               m->mothurOut("The unifrac.weighted command parameters are groups, iters, distance and random.  No parameters are required.\n");
+               m->mothurOut("The unifrac.weighted command parameters are groups, iters, distance, processors and random.  No parameters are required.\n");
                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 false, meaning don't compare your trees with randomly generated trees.\n");
+               m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\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");
@@ -158,7 +159,7 @@ int UnifracWeightedCommand::execute() {
                                //calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
                                vector< vector<string> > namesOfGroupCombos;
                                for (int a=0; a<numGroups; a++) { 
-                                       for (int l = a+1; l < numGroups; l++) { 
+                                       for (int l = 0; l < a; l++) {   
                                                vector<string> groups; groups.push_back(globaldata->Groups[a]); groups.push_back(globaldata->Groups[l]);
                                                namesOfGroupCombos.push_back(groups);
                                        }