added multiple processors option for Windows users to align.seqs, dist.seqs, summary...

[mothur.git] / corraxescommand.cpp

diff --git a/corraxescommand.cpp b/corraxescommand.cpp
index 07c5707e0c195cf26596e5ef328af83994ebd031..f10fe4de4e385d943460998d62bfa75b61cc2637 100644 (file)
--- a/corraxescommand.cpp
+++ b/corraxescommand.cpp
@@ -158,7 +158,7 @@ CorrAxesCommand::CorrAxesCommand(string option)  {
                                pickedGroups = true;
                                m->splitAtDash(groups, Groups); 
                        }                       
-                       m->Groups = Groups;
+                       m->setGroups(Groups);
                        
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(inputFileName);  }
                        
@@ -776,7 +776,7 @@ int CorrAxesCommand::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>& thisloo
                                }
                                
                                //if there is a bin label use it otherwise make one
-                               string binLabel = "Otu" + (i+1);
+                               string binLabel = "Otu" + toString(i+1);
                                if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
                                
                                newBinLabels.push_back(binLabel);
@@ -907,12 +907,13 @@ int CorrAxesCommand::getMetadata(){
                //remove any groups the user does not want, and set globaldata->groups with only valid groups
                SharedUtil* util;
                util = new SharedUtil();
-               
-               util->setGroups(m->Groups, groupNames);
+               Groups = m->getGroups();
+               util->setGroups(Groups, groupNames);
+               m->setGroups(Groups);
                
                for (int i = 0; i < lookupFloat.size(); i++) {
                        //if this sharedrabund is not from a group the user wants then delete it.
-                       if (util->isValidGroup(lookupFloat[i]->getGroup(), m->Groups) == false) { 
+                       if (util->isValidGroup(lookupFloat[i]->getGroup(), m->getGroups()) == false) { 
                                delete lookupFloat[i]; lookupFloat[i] = NULL;
                                lookupFloat.erase(lookupFloat.begin()+i); 
                                i--;