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

[mothur.git] / sharedordervector.cpp

diff --git a/sharedordervector.cpp b/sharedordervector.cpp
index 37cd28315a5c1928e965f7be8eef7ae0ef408692..ca26362672e130364f66ed8bd005ae8fa9d68d4c 100644 (file)
--- a/sharedordervector.cpp
+++ b/sharedordervector.cpp
@@ -41,9 +41,9 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {  //reads in a
                f >> label >> groupN >> num;
                holdLabel = label;
                
-               
+               vector<string> allGroups;
                //save group in groupmap
-               groupmap->namesOfGroups.push_back(groupN);
+               allGroups.push_back(groupN);
                groupmap->groupIndex[groupN] = 0;
                
                
@@ -67,7 +67,7 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {  //reads in a
                        
                        
                        //save group in groupmap
-                       groupmap->namesOfGroups.push_back(groupN);
+                       allGroups.push_back(groupN);
                        groupmap->groupIndex[groupN] = count;
                        
                        
@@ -88,8 +88,9 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {  //reads in a
                
                //put file pointer back since you are now at a new distance label
                for (int i = 0; i < nextLabel.length(); i++) { f.unget();  }
-       
-               m->namesOfGroups = groupmap->namesOfGroups;
+               
+               groupmap->setNamesOfGroups(allGroups);
+               m->setAllGroups(allGroups);
                
                updateStats();
                
@@ -285,8 +286,12 @@ vector<SharedRAbundVector*> SharedOrderVector::getSharedRAbundVector() {
                util = new SharedUtil();
                vector<SharedRAbundVector*> lookup;
                
-               util->setGroups(m->Groups, m->namesOfGroups);
-               util->getSharedVectors(m->Groups, lookup, this);
+               vector<string> Groups = m->getGroups();
+               vector<string> allGroups = m->getAllGroups();
+               util->setGroups(Groups, allGroups);
+               util->getSharedVectors(Groups, lookup, this);
+               m->setGroups(Groups);
+               m->setAllGroups(allGroups);
                
                return lookup;
        }