initialized numLinkers and numSpacers in trim.seqs and trim.flows

[mothur.git] / weighted.cpp

diff --git a/weighted.cpp b/weighted.cpp
index cae2b92885632b697852babccd84d463b7a78564..7a31da4d55d398f47d022de7b80396bb44f6c6b4 100644 (file)
--- a/weighted.cpp
+++ b/weighted.cpp
@@ -13,15 +13,13 @@
 
 EstOutput Weighted::getValues(Tree* t, int p, string o) {
     try {
-               globaldata = GlobalData::getInstance();
-               
                data.clear(); //clear out old values
                int numGroups;
                vector<double> D;
                processors = p;
                outputDir = o;
                
-               numGroups = globaldata->Groups.size();
+               numGroups = m->getNumGroups();
                
                if (m->control_pressed) { return data; }
                
@@ -31,12 +29,12 @@ 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(globaldata->Groups[i]); groups.push_back(globaldata->Groups[l]);
+                               vector<string> groups; groups.push_back((m->getGroups())[i]); groups.push_back((m->getGroups())[l]);
                                namesOfGroupCombos.push_back(groups);
                        }
                }
                
-               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                        if(processors == 1){
                                data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
                        }else{
@@ -71,7 +69,7 @@ EstOutput Weighted::getValues(Tree* t, int p, string o) {
 
 EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos) {
        try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                int process = 1;
                vector<int> processIDS;
                
@@ -141,7 +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();
@@ -267,7 +265,6 @@ EstOutput Weighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos,
 /**************************************************************************************************/
 EstOutput Weighted::getValues(Tree* t, string groupA, string groupB) { 
  try {
-               globaldata = GlobalData::getInstance();
                
                data.clear(); //clear out old values