added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / weighted.cpp

diff --git a/weighted.cpp b/weighted.cpp
index d0defc3394b8aa3dc7010837c12ad4a8d0cfc472..d8a4b857ad19d8057ed4eb11a592aa11e6787721 100644 (file)
--- a/weighted.cpp
+++ b/weighted.cpp
@@ -19,7 +19,7 @@ EstOutput Weighted::getValues(Tree* t, int p, string o) {
                processors = p;
                outputDir = o;
                
-               numGroups = m->Groups.size();
+               numGroups = m->getNumGroups();
                
                if (m->control_pressed) { return data; }
                
@@ -29,7 +29,7 @@ EstOutput Weighted::getValues(Tree* t, int p, string o) {
                        for (int l = 0; l < i; l++) {   
                                //initialize weighted scores
                                //WScore[globaldata->Groups[i]+globaldata->Groups[l]] = 0.0;
-                               vector<string> groups; groups.push_back(m->Groups[i]); groups.push_back(m->Groups[l]);
+                               vector<string> groups; groups.push_back((m->getGroups())[i]); groups.push_back((m->getGroups())[l]);
                                namesOfGroupCombos.push_back(groups);
                        }
                }
@@ -139,7 +139,7 @@ EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGro
                                m->gobble(in);
                        }
                        in.close();
-                       remove(s.c_str());
+                       m->mothurRemove(s);
                }
                
                m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();