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

[mothur.git] / unweighted.cpp

diff --git a/unweighted.cpp b/unweighted.cpp
index 08e83ec5ba4ccbbbefe36163c25d1075fb05a883..431323f066665bd07edce8da80c32dadb1600cf2 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->getNumGroups();
                
                //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->getGroups())[r]); groups.push_back((m->getGroups())[l]);
                                namesOfGroupCombos.push_back(groups);
                        }
                }
@@ -35,15 +34,15 @@ EstOutput Unweighted::getValues(Tree* t, int p, string o) {
                        vector<string> groups;
                        if (numGroups == 0) {
                                //get score for all users groups
-                               for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
-                                       if (tmap->namesOfGroups[i] != "xxx") {
-                                               groups.push_back(tmap->namesOfGroups[i]);
+                               for (int i = 0; i < (tmap->getNamesOfGroups()).size(); i++) {
+                                       if ((tmap->getNamesOfGroups())[i] != "xxx") {
+                                               groups.push_back((tmap->getNamesOfGroups())[i]);
                                        }
                                }
                                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->getNumGroups(); i++) {
+                                       groups.push_back((m->getGroups())[i]);
                                }
                                namesOfGroupCombos.push_back(groups);
                        }
@@ -152,7 +151,7 @@ EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfG
                                m->gobble(in);
                        }
                        in.close();
-                       remove(s.c_str());
+                       m->mothurRemove(s);
                }
                
                m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
@@ -199,14 +198,14 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
                                m->mothurOut(namesOfGroupCombos[h][namesOfGroupCombos[h].size()-1]);
                                m->mothurOut(", skipping."); m->mothurOutEndLine(); results[count] = UW;
                        }else{
-                               
+                               //cout << "trying to get root" << endl; 
                                //if including the root this clears rootForGrouping[namesOfGroupCombos[h]]
                                getRoot(t, nodeBelonging, namesOfGroupCombos[h]);
-                               
+                               //cout << "here" << endl;       
                                for(int i=0;i<t->getNumNodes();i++){
                                        
                                        if (m->control_pressed) {  return data; }
-                                       
+                                       //cout << i << endl;    
                                        //pcountSize = 0, they are from a branch that is entirely from a group the user doesn't want
                                        //pcountSize = 2, not unique to one group
                                        //pcountSize = 1, unique to one group
@@ -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->getNumGroups();
                
                //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->getGroups())[r]); groups.push_back((m->getGroups())[l]);
                                namesOfGroupCombos.push_back(groups);
                        }
                }
@@ -279,15 +277,15 @@ EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB, int p, st
                        vector<string> groups;
                        if (numGroups == 0) {
                                //get score for all users groups
-                               for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
-                                       if (tmap->namesOfGroups[i] != "xxx") {
-                                               groups.push_back(tmap->namesOfGroups[i]);
+                               for (int i = 0; i < (tmap->getNamesOfGroups()).size(); i++) {
+                                       if ((tmap->getNamesOfGroups())[i] != "xxx") {
+                                               groups.push_back((tmap->getNamesOfGroups())[i]);
                                        }
                                }
                                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->getNumGroups(); i++) {
+                                       groups.push_back((m->getGroups())[i]);
                                }
                                namesOfGroupCombos.push_back(groups);
                        }
@@ -395,7 +393,7 @@ EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfG
                                m->gobble(in);
                        }
                        in.close();
-                       remove(s.c_str());
+                       m->mothurRemove(s);
                }
                
                return results;
@@ -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++) {
                
@@ -497,17 +495,18 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
 int Unweighted::getRoot(Tree* t, int v, vector<string> grouping) { 
        try {
                //you are a leaf so get your parent
-               int index = t->tree[index].getParent();
+               int index = t->tree[v].getParent();
                
                if (includeRoot) { 
                        rootForGrouping[grouping].clear();
                }else {
+                       
                        //my parent is a potential root
                        rootForGrouping[grouping].insert(index);
                        
                        //while you aren't at root
                        while(t->tree[index].getParent() != -1){
-                               
+                               //cout << index << endl;        
                                if (m->control_pressed) {  return 0; }
                                
                                //am I the root for this grouping? if so I want to stop "early"