X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefact.cpp;h=0454d9e253473b368af34f35021dabbc4a50ae1b;hb=bd27c2b0612942815b7417c79f7ee41f669a2a34;hp=032cd93752db10521d18495aa141888e37720963;hpb=5694c92fbf646fe01abc87bde2af59e14a9a56b6;p=mothur.git

diff --git a/rarefact.cpp b/rarefact.cpp
index 032cd93..0454d9e 100644
--- a/rarefact.cpp
+++ b/rarefact.cpp
@@ -24,7 +24,7 @@ int Rarefact::getCurve(float percentFreq = 0.01, int nIters = 1000){
 		if (percentFreq < 1.0) {  increment = numSeqs * percentFreq;  }
 		else { increment = percentFreq;  }	
 		
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 				if(processors == 1){
 					driver(rcd, increment, nIters);	
 				}else{
@@ -86,12 +86,12 @@ int Rarefact::driver(RarefactionCurveData* rcd, int increment, int nIters = 1000
 				lookup->set(binNumber, abundance);
 				rank->set(abundance, rank->get(abundance)+1);
 
-				if((i == 0) || (i+1) % increment == 0){
+				if((i == 0) || ((i+1) % increment == 0) || (ends.count(i+1) != 0)){
 					rcd->updateRankData(rank);
 				}
 			}
 	
-			if(numSeqs % increment != 0){
+			if((numSeqs % increment != 0) || (ends.count(numSeqs) != 0)){
 				rcd->updateRankData(rank);
 			}
 
@@ -114,7 +114,7 @@ int Rarefact::driver(RarefactionCurveData* rcd, int increment, int nIters = 1000
 
 int Rarefact::createProcesses(vector<int>& procIters, RarefactionCurveData* rcd, int increment) {
 	try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		int process = 1;
 		
 		vector<int> processIDS;
@@ -157,7 +157,7 @@ int Rarefact::createProcesses(vector<int>& procIters, RarefactionCurveData* rcd,
 			for(int j=0;j<displays.size();j++){
 				string s = toString(processIDS[i]) + toString(j) + ".rarefact.temp";
 				displays[j]->inputTempFiles(s);
-				remove(s.c_str());
+				m->mothurRemove(s);
 			}
 		}
 		
@@ -183,7 +183,7 @@ try {
 		}
 		
 		//if jumble is false all iters will be the same
-		if (globaldata->jumble == false)  {  nIters = 1;  }
+		if (m->jumble == false)  {  nIters = 1;  }
 		
 		//convert freq percentage to number
 		int increment = 1;
@@ -196,7 +196,7 @@ try {
 				displays[i]->init(label);		  
 			}
 			
-			if (globaldata->jumble == true)  {
+			if (m->jumble == true)  {
 				//randomize the groups
 				random_shuffle(lookup.begin(), lookup.end());
 			}