X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=weighted.cpp;h=b0a642b1b5024710530e95de5b2a57cc87a7accd;hb=03dca3b32a903c3f29fbcf5b410b19d6ab6dae63;hp=d0defc3394b8aa3dc7010837c12ad4a8d0cfc472;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/weighted.cpp b/weighted.cpp
index d0defc3..b0a642b 100644
--- a/weighted.cpp
+++ b/weighted.cpp
@@ -19,7 +19,7 @@ EstOutput Weighted::getValues(Tree* t, int p, string o) {
 		processors = p;
 		outputDir = o;
 		
-		numGroups = m->Groups.size();
+		numGroups = m->getNumGroups();
 		
 		if (m->control_pressed) { return data; }
 		
@@ -29,12 +29,12 @@ EstOutput Weighted::getValues(Tree* t, int p, string o) {
 			for (int l = 0; l < i; l++) {	
 				//initialize weighted scores
 				//WScore[globaldata->Groups[i]+globaldata->Groups[l]] = 0.0;
-				vector<string> groups; groups.push_back(m->Groups[i]); groups.push_back(m->Groups[l]);
+				vector<string> groups; groups.push_back((m->getGroups())[i]); groups.push_back((m->getGroups())[l]);
 				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());
 			}else{
@@ -69,7 +69,7 @@ EstOutput Weighted::getValues(Tree* t, int p, string o) {
 
 EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos) {
 	try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		int process = 1;
 		vector<int> processIDS;
 		
@@ -87,7 +87,7 @@ EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGro
 				EstOutput Myresults;
 				Myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num);
 			
-				m->mothurOut("Merging results."); m->mothurOutEndLine();
+				//m->mothurOut("Merging results."); m->mothurOutEndLine();
 				
 				//pass numSeqs to parent
 				ofstream out;
@@ -139,10 +139,10 @@ EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGro
 				m->gobble(in);
 			}
 			in.close();
-			remove(s.c_str());
+			m->mothurRemove(s);
 		}
 		
-		m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
+		//m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
 		
 		return results;
 #endif