X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=rarefact.cpp;h=0454d9e253473b368af34f35021dabbc4a50ae1b;hp=f5e7952688cdbb1dd182ca44df9c152ef46879d9;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3

diff --git a/rarefact.cpp b/rarefact.cpp
index f5e7952..0454d9e 100644
--- a/rarefact.cpp
+++ b/rarefact.cpp
@@ -12,13 +12,57 @@
 
 /***********************************************************************/
 
-int Rarefact::getCurve(int increment = 1, int nIters = 1000){
+int Rarefact::getCurve(float percentFreq = 0.01, int nIters = 1000){
 	try {
 		RarefactionCurveData* rcd = new RarefactionCurveData();
 		for(int i=0;i<displays.size();i++){
 			rcd->registerDisplay(displays[i]);
 		}
-	
+		
+		//convert freq percentage to number
+		int increment = 1;
+		if (percentFreq < 1.0) {  increment = numSeqs * percentFreq;  }
+		else { increment = percentFreq;  }	
+		
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+				if(processors == 1){
+					driver(rcd, increment, nIters);	
+				}else{
+					vector<int> procIters;
+					
+					int numItersPerProcessor = nIters / processors;
+					
+					//divide iters between processes
+					for (int i = 0; i < processors; i++) {
+						if(i == processors - 1){
+							numItersPerProcessor = nIters - i * numItersPerProcessor;
+						}
+						procIters.push_back(numItersPerProcessor);
+					}
+					
+					createProcesses(procIters, rcd, increment); 
+				}
+
+		#else
+			driver(rcd, increment, nIters);	
+		#endif
+
+		for(int i=0;i<displays.size();i++){
+			displays[i]->close();
+		}
+		
+		delete rcd;
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Rarefact", "getCurve");
+		exit(1);
+	}
+}
+/***********************************************************************/
+int Rarefact::driver(RarefactionCurveData* rcd, int increment, int nIters = 1000){
+	try {
+			
 		for(int iter=0;iter<nIters;iter++){
 		
 			for(int i=0;i<displays.size();i++){
@@ -42,12 +86,12 @@ int Rarefact::getCurve(int increment = 1, 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);
 			}
 
@@ -59,21 +103,75 @@ int Rarefact::getCurve(int increment = 1, int nIters = 1000){
 			delete rank;
 		}
 
-		for(int i=0;i<displays.size();i++){
-			displays[i]->close();
-		}
-		delete rcd;
 		return 0;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "Rarefact", "getCurve");
+		m->errorOut(e, "Rarefact", "driver");
 		exit(1);
 	}
 }
+/**************************************************************************************************/
 
+int Rarefact::createProcesses(vector<int>& procIters, RarefactionCurveData* rcd, int increment) {
+	try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+		int process = 1;
+		
+		vector<int> processIDS;
+		
+		EstOutput results;
+		
+		//loop through and create all the processes you want
+		while (process != processors) {
+			int pid = fork();
+			
+			if (pid > 0) {
+				processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
+				process++;
+			}else if (pid == 0){
+				driver(rcd, increment, procIters[process]);
+			
+				//pass numSeqs to parent
+				for(int i=0;i<displays.size();i++){
+					string tempFile = toString(getpid()) + toString(i) + ".rarefact.temp";
+					displays[i]->outputTempFiles(tempFile);
+				}
+				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]);
+		
+		//force parent to wait until all the processes are done
+		for (int i=0;i<(processors-1);i++) { 
+			int temp = processIDS[i];
+			wait(&temp);
+		}
+		
+		//get data created by processes
+		for (int i=0;i<(processors-1);i++) { 
+			for(int j=0;j<displays.size();j++){
+				string s = toString(processIDS[i]) + toString(j) + ".rarefact.temp";
+				displays[j]->inputTempFiles(s);
+				m->mothurRemove(s);
+			}
+		}
+		
+		return 0;
+#endif		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Rarefact", "createProcesses");
+		exit(1);
+	}
+}
 /***********************************************************************/
 
-int Rarefact::getSharedCurve(int increment = 1, int nIters = 1000){
+int Rarefact::getSharedCurve(float percentFreq = 0.01, int nIters = 1000){
 try {
 		SharedRarefactionCurveData* rcd = new SharedRarefactionCurveData();
 		
@@ -85,7 +183,12 @@ 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;
+		if (percentFreq < 1.0) {  increment = numSeqs * percentFreq;  }
+		else { increment = percentFreq;  }
 		
 		for(int iter=0;iter<nIters;iter++){
 		
@@ -93,7 +196,7 @@ try {
 				displays[i]->init(label);		  
 			}
 			
-			if (globaldata->jumble == true)  {
+			if (m->jumble == true)  {
 				//randomize the groups
 				random_shuffle(lookup.begin(), lookup.end());
 			}