working on adding count file to mgcluster

[mothur.git] / unweighted.cpp

diff --git a/unweighted.cpp b/unweighted.cpp
index 98bfa45542bc7e17bb7b95dde67d40bd1e282e52..864a9f8bab16f5d1ea52480c37c141ddc934e199 100644 (file)
--- a/unweighted.cpp
+++ b/unweighted.cpp
@@ -15,9 +15,11 @@ EstOutput Unweighted::getValues(Tree* t, int p, string o) {
        try {
                processors = p;
                outputDir = o;
-                       
+        
+        TreeMap* tmap = t->getTreeMap();
+        
                //if the users enters no groups then give them the score of all groups
-               int numGroups = m->Groups.size();
+               int numGroups = m->getNumGroups();
                
                //calculate number of comparsions
                int numComp = 0;
@@ -25,7 +27,7 @@ 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(m->Groups[r]); groups.push_back(m->Groups[l]);
+                               vector<string> groups; groups.push_back((m->getGroups())[r]); groups.push_back((m->getGroups())[l]);
                                namesOfGroupCombos.push_back(groups);
                        }
                }
@@ -34,23 +36,23 @@ 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 < m->Groups.size(); i++) {
-                                       groups.push_back(m->Groups[i]);
+                               for (int i = 0; i < m->getNumGroups(); i++) {
+                                       groups.push_back((m->getGroups())[i]);
                                }
                                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());
+                               data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), tmap);
                        }else{
                                int numPairs = namesOfGroupCombos.size();
                                
@@ -65,11 +67,11 @@ EstOutput Unweighted::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;
@@ -81,9 +83,9 @@ EstOutput Unweighted::getValues(Tree* t, int p, string o) {
 }
 /**************************************************************************************************/
 
-EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos) {
+EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, TreeMap* tmap) {
        try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                int process = 1;
                vector<int> processIDS;
                
@@ -98,7 +100,7 @@ EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfG
                                process++;
                        }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);
                                
                                if (m->control_pressed) { exit(0); }
                                
@@ -120,7 +122,7 @@ EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfG
                        }
                }
                
-               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++) { 
@@ -165,7 +167,7 @@ EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfG
        }
 }
 /**************************************************************************************************/
-EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num) { 
+EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, TreeMap* tmap) { 
  try {
        
         
@@ -259,8 +261,10 @@ EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB, int p, st
                processors = p;
                outputDir = o;
                
+        TreeMap* tmap = t->getTreeMap();
+     
                //if the users enters no groups then give them the score of all groups
-               int numGroups = m->Groups.size();
+               int numGroups = m->getNumGroups();
                
                //calculate number of comparsions
                int numComp = 0;
@@ -268,7 +272,7 @@ 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(m->Groups[r]); groups.push_back(m->Groups[l]);
+                               vector<string> groups; groups.push_back((m->getGroups())[r]); groups.push_back((m->getGroups())[l]);
                                namesOfGroupCombos.push_back(groups);
                        }
                }
@@ -277,23 +281,23 @@ 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 < m->Groups.size(); i++) {
-                                       groups.push_back(m->Groups[i]);
+                               for (int i = 0; i < m->getNumGroups(); i++) {
+                                       groups.push_back((m->getGroups())[i]);
                                }
                                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(), true);
+                               data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true, tmap);
                        }else{
                                int numPairs = namesOfGroupCombos.size();
                                
@@ -307,12 +311,12 @@ EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB, int p, st
                                        lines.push_back(linePair(startPos, numPairsPerProcessor));
                                }
                                        
-                               data = createProcesses(t, namesOfGroupCombos, true);
+                               data = createProcesses(t, namesOfGroupCombos, true, tmap);
                                
                                lines.clear();
                        }
                #else
-                       data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true);
+                       data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true, tmap);
                #endif
        
                return data;
@@ -324,9 +328,9 @@ EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB, int p, st
 }
 /**************************************************************************************************/
 
-EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, bool usingGroups) {
+EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, bool usingGroups, TreeMap* tmap) {
        try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                int process = 1;
                vector<int> processIDS;
                
@@ -341,7 +345,7 @@ EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfG
                                process++;
                        }else if (pid == 0){
                                EstOutput myresults;
-                               myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, usingGroups);
+                               myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, usingGroups, tmap);
                                
                                if (m->control_pressed) { exit(0); }
                                
@@ -361,7 +365,7 @@ EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfG
                        }
                }
                
-               results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, usingGroups);
+               results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, usingGroups, tmap);
                
                //force parent to wait until all the processes are done
                for (int i=0;i<(processors-1);i++) { 
@@ -405,7 +409,7 @@ EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfG
        }
 }
 /**************************************************************************************************/
-EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, bool usingGroups) { 
+EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, bool usingGroups, TreeMap* tmap) { 
  try {
                
                EstOutput results; results.resize(num);