added tree reader class to handle reading trees. Reworked the tree map to tree class...

[mothur.git] / weighted.cpp

diff --git a/weighted.cpp b/weighted.cpp
index b0a642b1b5024710530e95de5b2a57cc87a7accd..85eed5207ff20d586bd999f670d59a4c8e840c67 100644 (file)
--- a/weighted.cpp
+++ b/weighted.cpp
@@ -18,6 +18,8 @@ EstOutput Weighted::getValues(Tree* t, int p, string o) {
                vector<double> D;
                processors = p;
                outputDir = o;
+        
+        TreeMap* tmap = t->getTreeMap();
                
                numGroups = m->getNumGroups();
                
@@ -36,7 +38,7 @@ EstOutput Weighted::getValues(Tree* t, int p, string o) {
                
                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                        if(processors == 1){
-                               data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
+                               data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), tmap);
                        }else{
                                int numPairs = namesOfGroupCombos.size();
                                
@@ -50,12 +52,12 @@ EstOutput Weighted::getValues(Tree* t, int p, string o) {
                                        lines.push_back(linePair(startPos, numPairsPerProcessor));
                                }
 
-                               data = createProcesses(t, namesOfGroupCombos);
+                               data = createProcesses(t, namesOfGroupCombos, tmap);
                                
                                lines.clear();
                        }
                #else
-                       data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
+                       data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), tmap);
                #endif
                
                return data;
@@ -67,7 +69,7 @@ EstOutput Weighted::getValues(Tree* t, int p, string o) {
 }
 /**************************************************************************************************/
 
-EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos) {
+EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, TreeMap* tmap) {
        try {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                int process = 1;
@@ -85,7 +87,7 @@ EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGro
                        }else if (pid == 0){
        
                                EstOutput Myresults;
-                               Myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num);
+                               Myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, tmap);
                        
                                //m->mothurOut("Merging results."); m->mothurOutEndLine();
                                
@@ -108,7 +110,7 @@ EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGro
                        }
                }
        
-               results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num);
+               results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, tmap);
        
                //force parent to wait until all the processes are done
                for (int i=0;i<(processors-1);i++) { 
@@ -153,7 +155,7 @@ EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGro
        }
 }
 /**************************************************************************************************/
-EstOutput Weighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num) { 
+EstOutput Weighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, TreeMap* tmap) { 
  try {
                EstOutput results;
                vector<double> D;
@@ -267,6 +269,8 @@ EstOutput Weighted::getValues(Tree* t, string groupA, string groupB) {
  try {
                
                data.clear(); //clear out old values
+     
+        TreeMap* tmap = t->getTreeMap();
                
                if (m->control_pressed) { return data; }