removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / unweighted.cpp

diff --git a/unweighted.cpp b/unweighted.cpp
index a75ddc54058f878f63c579a4834754cb3890a374..90b6476543d67ee92d7c59624e2af8da2a7b2345 100644 (file)
--- a/unweighted.cpp
+++ b/unweighted.cpp
@@ -13,12 +13,11 @@
 
 EstOutput Unweighted::getValues(Tree* t, int p, string o) {
        try {
-               globaldata = GlobalData::getInstance();
                processors = p;
                outputDir = o;
                        
                //if the users enters no groups then give them the score of all groups
-               int numGroups = globaldata->Groups.size();
+               int numGroups = m->Groups.size();
                
                //calculate number of comparsions
                int numComp = 0;
@@ -26,7 +25,7 @@ EstOutput Unweighted::getValues(Tree* t, int p, string o) {
                for (int r=0; r<numGroups; r++) { 
                        for (int l = 0; l < r; l++) {
                                numComp++;
-                               vector<string> groups; groups.push_back(globaldata->Groups[r]); groups.push_back(globaldata->Groups[l]);
+                               vector<string> groups; groups.push_back(m->Groups[r]); groups.push_back(m->Groups[l]);
                                namesOfGroupCombos.push_back(groups);
                        }
                }
@@ -42,8 +41,8 @@ EstOutput Unweighted::getValues(Tree* t, int p, string o) {
                                }
                                namesOfGroupCombos.push_back(groups);
                        }else {
-                               for (int i = 0; i < globaldata->Groups.size(); i++) {
-                                       groups.push_back(globaldata->Groups[i]);
+                               for (int i = 0; i < m->Groups.size(); i++) {
+                                       groups.push_back(m->Groups[i]);
                                }
                                namesOfGroupCombos.push_back(groups);
                        }
@@ -257,12 +256,11 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
 
 EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB, int p, string o) { 
  try {
-               globaldata = GlobalData::getInstance();
                processors = p;
                outputDir = o;
                
                //if the users enters no groups then give them the score of all groups
-               int numGroups = globaldata->Groups.size();
+               int numGroups = m->Groups.size();
                
                //calculate number of comparsions
                int numComp = 0;
@@ -270,7 +268,7 @@ EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB, int p, st
                for (int r=0; r<numGroups; r++) { 
                        for (int l = 0; l < r; l++) {
                                numComp++;
-                               vector<string> groups; groups.push_back(globaldata->Groups[r]); groups.push_back(globaldata->Groups[l]);
+                               vector<string> groups; groups.push_back(m->Groups[r]); groups.push_back(m->Groups[l]);
                                namesOfGroupCombos.push_back(groups);
                        }
                }
@@ -286,8 +284,8 @@ EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB, int p, st
                                }
                                namesOfGroupCombos.push_back(groups);
                        }else {
-                               for (int i = 0; i < globaldata->Groups.size(); i++) {
-                                       groups.push_back(globaldata->Groups[i]);
+                               for (int i = 0; i < m->Groups.size(); i++) {
+                                       groups.push_back(m->Groups[i]);
                                }
                                namesOfGroupCombos.push_back(groups);
                        }
@@ -414,7 +412,7 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
                
                int count = 0;
                
-               Tree* copyTree = new Tree;
+               Tree* copyTree = new Tree(tmap);
                
                for (int h = start; h < (start+num); h++) {