X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=rarefact.cpp;h=0454d9e253473b368af34f35021dabbc4a50ae1b;hp=d04885f4333e3f224bddbfa99aa9614e9f171b4c;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=a537fefa3bd2c2eba7d532249375b6a11b295e25

diff --git a/rarefact.cpp b/rarefact.cpp
index d04885f..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);
 			}
 
@@ -114,9 +114,9 @@ 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;
-		int num = 0;
+		
 		vector<int> processIDS;
 		
 		EstOutput results;
@@ -137,7 +137,11 @@ int Rarefact::createProcesses(vector<int>& procIters, RarefactionCurveData* rcd,
 					displays[i]->outputTempFiles(tempFile);
 				}
 				exit(0);
-			}else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+			}else { 
+				m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
+				for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+				exit(0);
+			}
 		}
 		
 		driver(rcd, increment, procIters[0]);
@@ -153,7 +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);
 			}
 		}
 		
@@ -179,7 +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;
@@ -192,7 +196,7 @@ try {
 				displays[i]->init(label);		  
 			}
 			
-			if (globaldata->jumble == true)  {
+			if (m->jumble == true)  {
 				//randomize the groups
 				random_shuffle(lookup.begin(), lookup.end());
 			}