X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=parsimony.cpp;h=6a0485c133b2868670e49e5873186e5d10df474d;hp=3b0f31759c0563031874aa16cb0d3d515a65653b;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc

diff --git a/parsimony.cpp b/parsimony.cpp
index 3b0f317..6a0485c 100644
--- a/parsimony.cpp
+++ b/parsimony.cpp
@@ -15,7 +15,7 @@ EstOutput Parsimony::getValues(Tree* t, int p, string o) {
 	try {
 		processors = p;
 		outputDir = o;
-        TreeMap* tmap = t->getTreeMap();
+        CountTable* ct = t->getCountTable();
 		
 		//if the users enters no groups then give them the score of all groups
 		vector<string> mGroups = m->getGroups();
@@ -38,7 +38,7 @@ EstOutput Parsimony::getValues(Tree* t, int p, string o) {
 			vector<string> groups;
 			if (numGroups == 0) {
 				//get score for all users groups
-				vector<string> tGroups = tmap->getNamesOfGroups();
+				vector<string> tGroups = ct->getNamesOfGroups();
 				for (int i = 0; i < tGroups.size(); i++) {
 					if (tGroups[i] != "xxx") {
 						groups.push_back(tGroups[i]);
@@ -57,7 +57,7 @@ EstOutput Parsimony::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(), tmap);
+			data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), ct);
 		}else{
 			lines.clear();
 			int numPairs = namesOfGroupCombos.size();
@@ -74,10 +74,10 @@ EstOutput Parsimony::getValues(Tree* t, int p, string o) {
 				lines.push_back(linePair(startPos, numPairsPerProcessor));
 			}
 			
-			data = createProcesses(t, namesOfGroupCombos, tmap);
+			data = createProcesses(t, namesOfGroupCombos, ct);
 		}
 	#else
-		data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), tmap);
+		data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), ct);
 	#endif
 		
 		return data;
@@ -90,7 +90,7 @@ EstOutput Parsimony::getValues(Tree* t, int p, string o) {
 }
 /**************************************************************************************************/
 
-EstOutput Parsimony::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, TreeMap* tmap) {
+EstOutput Parsimony::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, CountTable* ct) {
 	try {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		int process = 1;
@@ -107,7 +107,7 @@ EstOutput Parsimony::createProcesses(Tree* t, vector< vector<string> > namesOfGr
 				process++;
 			}else if (pid == 0){
 				EstOutput myresults;
-				myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, tmap);
+				myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, ct);
 				
 				if (m->control_pressed) { exit(0); }
 				
@@ -127,7 +127,7 @@ EstOutput Parsimony::createProcesses(Tree* t, vector< vector<string> > namesOfGr
 			}
 		}
 		
-		results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, tmap);
+		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<processIDS.size();i++) { 
@@ -170,12 +170,12 @@ EstOutput Parsimony::createProcesses(Tree* t, vector< vector<string> > namesOfGr
 	}
 }
 /**************************************************************************************************/
-EstOutput Parsimony::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, TreeMap* tmap) { 
+EstOutput Parsimony::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, CountTable* ct) { 
 	try {
 		
 		EstOutput results; results.resize(num);
 		
-		Tree* copyTree = new Tree(tmap);
+		Tree* copyTree = new Tree(ct);
 		int count = 0;
 		
 		for (int h = start; h < (start+num); h++) {