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

[mothur.git] / subsamplecommand.cpp

diff --git a/subsamplecommand.cpp b/subsamplecommand.cpp
index e22bfdeee61af9b179b5ec5af4254157494b9d56..651ee028426f2713954557c4cdaf44af29112104 100644 (file)
--- a/subsamplecommand.cpp
+++ b/subsamplecommand.cpp
@@ -229,7 +229,7 @@ SubSampleCommand::SubSampleCommand(string option) {
                        else { 
                                pickedGroups = true;
                                m->splitAtDash(groups, Groups);
-                               m->Groups = Groups;
+                               m->setGroups(Groups);
                        }
                        
                        string temp = validParameter.validFile(parameters, "size", false);              if (temp == "not found"){       temp = "0";             }
@@ -349,7 +349,8 @@ int SubSampleCommand::getSubSampleFasta() {
                        
                        //takes care of user setting groupNames that are invalid or setting groups=all
                        SharedUtil* util = new SharedUtil();
-                       util->setGroups(Groups, groupMap->namesOfGroups);
+                       vector<string> namesGroups = groupMap->getNamesOfGroups();
+                       util->setGroups(Groups, namesGroups);
                        delete util;
                        
                        //file mismatch quit
@@ -672,19 +673,20 @@ int SubSampleCommand::getSubSampleShared() {
                                if (thisSize < size) {  size = thisSize;        }
                        }
                }else {
-                       m->Groups.clear();
+                       m->clearGroups();
+                       Groups.clear();
                        vector<SharedRAbundVector*> temp;
                        for (int i = 0; i < lookup.size(); i++) {
                                if (lookup[i]->getNumSeqs() < size) { 
                                        m->mothurOut(lookup[i]->getGroup() + " contains " + toString(lookup[i]->getNumSeqs()) + ". Eliminating."); m->mothurOutEndLine();
                                        delete lookup[i];
                                }else { 
-                                       m->Groups.push_back(lookup[i]->getGroup()); 
+                                       Groups.push_back(lookup[i]->getGroup()); 
                                        temp.push_back(lookup[i]);
                                }
                        } 
                        lookup = temp;
-                       Groups = m->Groups;
+                       m->setGroups(Groups);
                }
                
                if (lookup.size() == 0) {  m->mothurOut("The size you selected is too large, skipping shared file."); m->mothurOutEndLine(); delete input; return 0; }
@@ -878,7 +880,8 @@ int SubSampleCommand::getSubSampleList() {
                        
                        //takes care of user setting groupNames that are invalid or setting groups=all
                        SharedUtil* util = new SharedUtil();
-                       util->setGroups(Groups, groupMap->namesOfGroups);
+                       vector<string> namesGroups = groupMap->getNamesOfGroups();
+                       util->setGroups(Groups, namesGroups);
                        delete util;
                        
                        //create outputfiles