X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unweighted.cpp;h=ba88049d7e9914231b326861c3abbccdf2af01b2;hb=bd93b1a6f9fe9a6a4a7ac2e9f106e5c83a438856;hp=c4548c9c5ada81a19405ef491a00b1d62672c2d8;hpb=f099fdc1e3a0d7b75d780a164e5bdb93496a7a1d;p=mothur.git

diff --git a/unweighted.cpp b/unweighted.cpp
index c4548c9..ba88049 100644
--- a/unweighted.cpp
+++ b/unweighted.cpp
@@ -11,73 +11,28 @@
 
 /**************************************************************************************************/
 
-EstOutput Unweighted::getValues(Tree* t) {
+EstOutput Unweighted::getValues(Tree* t, int p, string o) {
 	try {
 		globaldata = GlobalData::getInstance();
-		
-		vector<string> groups;
-		double UniqueBL;  //a branch length is unique if it's chidren are from the same group
-		double totalBL;	//all branch lengths
-		double UW;		//Unweighted Value = UniqueBL / totalBL;
-	
+		processors = p;
+		outputDir = o;
+			
 		//if the users enters no groups then give them the score of all groups
 		int numGroups = globaldata->Groups.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++) {
 				numComp++;
+				vector<string> groups; groups.push_back(globaldata->Groups[r]); groups.push_back(globaldata->Groups[l]);
+				namesOfGroupCombos.push_back(groups);
 			}
 		}
-
-		//numComp+1 for AB, AC, BC, ABC
-		data.resize(numComp+1,0);
-		
-		int count = 0;
-		for (int a=0; a<numGroups; a++) { 
-			for (int l = a+1; l < numGroups; l++) {
-				UniqueBL=0.0000;  //a branch length is unique if it's chidren are from the same group
-				totalBL = 0.00;	//all branch lengths
-				UW = 0.00;		//Unweighted Value = UniqueBL / totalBL;
-				//copyIpcount.clear();
-				
-				//groups in this combo
-				groups.push_back(globaldata->Groups[a]); groups.push_back(globaldata->Groups[l]);
-		
-				for(int i=0;i<t->getNumNodes();i++){
-					if (m->control_pressed) {  return data; }
-	
-					//pcountSize = 0, they are from a branch that is entirely from a group the user doesn't want
-					//pcountSize = 2, not unique to one group
-					//pcountSize = 1, unique to one group
-					
-					int pcountSize = 0;
-					for (int j = 0; j < groups.size(); j++) {
-						map<string, int>::iterator itGroup = t->tree[i].pcount.find(groups[j]);
-						if (itGroup != t->tree[i].pcount.end()) { pcountSize++; } 
-					}
-					
-					if (pcountSize == 0) { }
-					else if ((t->tree[i].getBranchLength() != -1) && (pcountSize == 1)) {  UniqueBL += abs(t->tree[i].getBranchLength());	}
-			
-					if ((t->tree[i].getBranchLength() != -1) && (pcountSize != 0)) {  
-						totalBL += abs(t->tree[i].getBranchLength()); 
-					}
-				}
-		
-				UW = (UniqueBL / totalBL);  
-	
-				if (isnan(UW) || isinf(UW)) { UW = 0; }
-	
-				data[count] = UW;
-				count++;
-				groups.clear();
-			}
-		}
-		
 		
 		if (numComp != 1) {
+			vector<string> groups;
 			if (numGroups == 0) {
 				//get score for all users groups
 				for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
@@ -85,15 +40,145 @@ EstOutput Unweighted::getValues(Tree* t) {
 						groups.push_back(tmap->namesOfGroups[i]);
 					}
 				}
+				namesOfGroupCombos.push_back(groups);
 			}else {
 				for (int i = 0; i < globaldata->Groups.size(); i++) {
 					groups.push_back(globaldata->Groups[i]);
 				}
+				namesOfGroupCombos.push_back(groups);
+			}
+		}
+
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			if(processors == 1){
+				data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
+			}else{
+				int numPairs = namesOfGroupCombos.size();
+				
+				int numPairsPerProcessor = numPairs / processors;
+				
+				for (int i = 0; i < processors; i++) {
+					int startPos = i * numPairsPerProcessor;
+					if(i == processors - 1){
+						numPairsPerProcessor = numPairs - i * numPairsPerProcessor;
+					}
+					lines.push_back(new linePair(startPos, numPairsPerProcessor));
+				}
+
+				data = createProcesses(t, namesOfGroupCombos);
+				
+				for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 			}
+		#else
+			data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
+		#endif
 		
-			UniqueBL=0.0000;  //a branch length is unique if it's chidren are from the same group
-			totalBL = 0.00;	//all branch lengths
-			UW = 0.00;		//Unweighted Value = UniqueBL / totalBL;
+		return data;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Unweighted", "getValues");
+		exit(1);
+	}
+}
+/**************************************************************************************************/
+
+EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos) {
+	try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		int process = 1;
+		int num = 0;
+		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){
+				EstOutput myresults;
+				myresults = driver(t, namesOfGroupCombos, lines[process]->start, lines[process]->num);
+				
+				if (m->control_pressed) { exit(0); }
+				
+				m->mothurOut("Merging results."); m->mothurOutEndLine();
+				
+				//pass numSeqs to parent
+				ofstream out;
+				string tempFile = outputDir + toString(getpid()) + ".unweighted.results.temp";
+				m->openOutputFile(tempFile, out);
+				out << myresults.size() << endl;
+				for (int i = 0; i < myresults.size(); i++) {  out << myresults[i] << '\t';  } out << endl;
+				out.close();
+				
+				exit(0);
+			}else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+		}
+		
+		results = driver(t, namesOfGroupCombos, lines[0]->start, lines[0]->num);
+		
+		//force parent to wait until all the processes are done
+		for (int i=0;i<(processors-1);i++) { 
+			int temp = processIDS[i];
+			wait(&temp);
+		}
+		
+		if (m->control_pressed) { return results; }
+		
+		//get data created by processes
+		for (int i=0;i<(processors-1);i++) { 
+			ifstream in;
+			string s = outputDir + toString(processIDS[i]) + ".unweighted.results.temp";
+			m->openInputFile(s, in);
+			
+			//get quantiles
+			if (!in.eof()) {
+				int num;
+				in >> num; m->gobble(in);
+				
+				if (m->control_pressed) { break; }
+				
+				double w; 
+				for (int j = 0; j < num; j++) {
+					in >> w;
+					results.push_back(w);
+				}
+				m->gobble(in);
+			}
+			in.close();
+			remove(s.c_str());
+		}
+		
+		m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
+		
+		return results;
+#endif		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Unweighted", "createProcesses");
+		exit(1);
+	}
+}
+/**************************************************************************************************/
+EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num) { 
+ try {
+		
+		EstOutput results; results.resize(num);
+		
+		int count = 0;
+		int total = num;
+		int twentyPercent = (total * 0.20);
+
+		for (int h = start; h < (start+num); h++) {
+		
+			if (m->control_pressed) { return results; }
+		
+			double UniqueBL=0.0000;  //a branch length is unique if it's chidren are from the same group
+			double totalBL = 0.00;	//all branch lengths
+			double UW = 0.00;		//Unweighted Value = UniqueBL / totalBL;
 				
 			for(int i=0;i<t->getNumNodes();i++){
 			
@@ -104,8 +189,8 @@ EstOutput Unweighted::getValues(Tree* t) {
 				//pcountSize = 1, unique to one group
 				
 				int pcountSize = 0;
-				for (int j = 0; j < groups.size(); j++) {
-					map<string, int>::iterator itGroup = t->tree[i].pcount.find(groups[j]);
+				for (int j = 0; j < namesOfGroupCombos[h].size(); j++) {
+					map<string, int>::iterator itGroup = t->tree[i].pcount.find(namesOfGroupCombos[h][j]);
 					if (itGroup != t->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } } 
 				}
 				
@@ -121,18 +206,22 @@ EstOutput Unweighted::getValues(Tree* t) {
 	
 			if (isnan(UW) || isinf(UW)) { UW = 0; }
 	
-			data[count] = UW;
-		}
+			results[count] = UW;
+			count++;
 
-		return data;
-	
+			//report progress
+			if((count) % twentyPercent == 0){	m->mothurOut("Percentage complete: " + toString(int((count / (float)total) * 100.0))); m->mothurOutEndLine();		}
+		}
+		
+		m->mothurOut("Percentage complete: 100"); m->mothurOutEndLine();
+		
+		return results; 
 	}
 	catch(exception& e) {
-		m->errorOut(e, "Unweighted", "getValues");
+		m->errorOut(e, "Unweighted", "driver");
 		exit(1);
 	}
 }
-
 /**************************************************************************************************/
 
 EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB) { 
@@ -277,6 +366,6 @@ EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB) {
 	}
 }
 
-
+/**************************************************************************************************/