X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unweighted.cpp;h=56694e32e3a977b08df087dfc8deeabb2524564c;hb=1a968f34ae2d2680eaf189a197d1a21b8dfd6c03;hp=98bfa45542bc7e17bb7b95dde67d40bd1e282e52;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git

diff --git a/unweighted.cpp b/unweighted.cpp
index 98bfa45..56694e3 100644
--- a/unweighted.cpp
+++ b/unweighted.cpp
@@ -15,9 +15,11 @@ EstOutput Unweighted::getValues(Tree* t, int p, string o) {
 	try {
 		processors = p;
 		outputDir = o;
-			
+        
+        CountTable* ct = t->getCountTable();
+        
 		//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 < (ct->getNamesOfGroups()).size(); i++) {
+					if ((ct->getNamesOfGroups())[i] != "xxx") {
+						groups.push_back((ct->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(), ct);
 			}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, ct);
 				lines.clear();
 			}
 		#else
-			data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
+			data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), ct);
 		#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, CountTable* ct) {
 	try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		int process = 1;
 		vector<int> processIDS;
 		
@@ -98,11 +100,11 @@ 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, ct);
 				
 				if (m->control_pressed) { exit(0); }
 				
-				m->mothurOut("Merging results."); m->mothurOutEndLine();
+				//m->mothurOut("Merging results."); m->mothurOutEndLine();
 				
 				//pass numSeqs to parent
 				ofstream out;
@@ -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, ct);
 		
 		//force parent to wait until all the processes are done
 		for (int i=0;i<(processors-1);i++) { 
@@ -154,7 +156,7 @@ EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfG
 			m->mothurRemove(s);
 		}
 		
-		m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
+		//m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
 		
 		return results;
 #endif		
@@ -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, CountTable* ct) { 
  try {
 	
 	 
@@ -259,8 +261,10 @@ EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB, int p, st
 		processors = p;
 		outputDir = o;
 		
+        CountTable* ct = t->getCountTable();
+     
 		//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 < (ct->getNamesOfGroups()).size(); i++) {
+					if ((ct->getNamesOfGroups())[i] != "xxx") {
+						groups.push_back((ct->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, ct);
 			}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, ct);
 				
 				lines.clear();
 			}
 		#else
-			data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true);
+			data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true, ct);
 		#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, CountTable* ct) {
 	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, ct);
 				
 				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, ct);
 		
 		//force parent to wait until all the processes are done
 		for (int i=0;i<(processors-1);i++) { 
@@ -405,14 +409,14 @@ 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, CountTable* ct) { 
  try {
 		
 		EstOutput results; results.resize(num);
 		
 		int count = 0;
 		
-		Tree* copyTree = new Tree(tmap);
+		Tree* copyTree = new Tree(ct);
 		
 		for (int h = start; h < (start+num); h++) {