X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=parsimony.cpp;h=6a0485c133b2868670e49e5873186e5d10df474d;hp=54a3ffd93180376ff8a1efe67b121af3d36b9bc2;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6

diff --git a/parsimony.cpp b/parsimony.cpp
index 54a3ffd..6a0485c 100644
--- a/parsimony.cpp
+++ b/parsimony.cpp
@@ -15,17 +15,19 @@ EstOutput Parsimony::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();
+		vector<string> mGroups = m->getGroups();
+		int numGroups = mGroups.size();
 		
 		//calculate number of comparsions
 		int numComp = 0;
 		vector< vector<string> > namesOfGroupCombos;
 		for (int r=0; r<numGroups; r++) { 
-			for (int l = r+1; l < numGroups; l++) {
+			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(mGroups[r]); groups.push_back(mGroups[l]);
 				//cout << globaldata->Groups[r] << '\t' << globaldata->Groups[l] << endl;
 				namesOfGroupCombos.push_back(groups);
 			}
@@ -36,25 +38,26 @@ EstOutput Parsimony::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]);
+				vector<string> tGroups = ct->getNamesOfGroups();
+				for (int i = 0; i < tGroups.size(); i++) {
+					if (tGroups[i] != "xxx") {
+						groups.push_back(tGroups[i]);
 						//cout << tmap->namesOfGroups[i] << endl;
 					}
 				}
 				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 < mGroups.size(); i++) {
+					groups.push_back(mGroups[i]);
 					//cout << globaldata->Groups[i] << endl;
 				}
 				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{
 			lines.clear();
 			int numPairs = namesOfGroupCombos.size();
@@ -71,10 +74,10 @@ EstOutput Parsimony::getValues(Tree* t, int p, string o) {
 				lines.push_back(linePair(startPos, numPairsPerProcessor));
 			}
 			
-			data = createProcesses(t, namesOfGroupCombos);
+			data = createProcesses(t, namesOfGroupCombos, ct);
 		}
 	#else
-		data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
+		data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), ct);
 	#endif
 		
 		return data;
@@ -87,9 +90,9 @@ EstOutput Parsimony::getValues(Tree* t, int p, string o) {
 }
 /**************************************************************************************************/
 
-EstOutput Parsimony::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos) {
+EstOutput Parsimony::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;
 		
@@ -104,7 +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);
+				myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, ct);
 				
 				if (m->control_pressed) { exit(0); }
 				
@@ -124,7 +127,7 @@ EstOutput Parsimony::createProcesses(Tree* t, vector< vector<string> > namesOfGr
 			}
 		}
 		
-		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<processIDS.size();i++) { 
@@ -155,7 +158,7 @@ EstOutput Parsimony::createProcesses(Tree* t, vector< vector<string> > namesOfGr
 				m->gobble(in);
 			}
 			in.close();
-			remove(s.c_str());
+			m->mothurRemove(s);
 		}
 		
 		return results;
@@ -167,12 +170,12 @@ EstOutput Parsimony::createProcesses(Tree* t, vector< vector<string> > namesOfGr
 	}
 }
 /**************************************************************************************************/
-EstOutput Parsimony::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num) { 
+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++) {