X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=parsimony.cpp;h=6a0485c133b2868670e49e5873186e5d10df474d;hp=e76a7b039c4e91afec85c27f375b22f120185f7b;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=9099173ea17b13be96563c7579ecc8dc2ef65d20

diff --git a/parsimony.cpp b/parsimony.cpp
index e76a7b0..6a0485c 100644
--- a/parsimony.cpp
+++ b/parsimony.cpp
@@ -10,54 +10,223 @@
 #include "parsimony.h"
 
 /**************************************************************************************************/
-EstOutput Parsimony::getValues(Tree* t) {
+
+EstOutput Parsimony::getValues(Tree* t, int p, string o) {
 	try {
-		globaldata = GlobalData::getInstance();
+		processors = p;
+		outputDir = o;
+        CountTable* ct = t->getCountTable();
 		
-		data.resize(1,0);
-			
-		int score = 0;
+		//if the users enters no groups then give them the score of all groups
+		vector<string> mGroups = m->getGroups();
+		int numGroups = mGroups.size();
 		
-		//create pgroups that reflect the groups the user want to use
-		for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
-			t->tree[i].pGroups = (t->mergeUserGroups(i));
+		//calculate number of comparsions
+		int numComp = 0;
+		vector< vector<string> > namesOfGroupCombos;
+		for (int r=0; r<numGroups; r++) { 
+			for (int l = 0; l < r; l++) {
+				numComp++;
+				vector<string> groups; groups.push_back(mGroups[r]); groups.push_back(mGroups[l]);
+				//cout << globaldata->Groups[r] << '\t' << globaldata->Groups[l] << endl;
+				namesOfGroupCombos.push_back(groups);
+			}
+		}
+
+		//numComp+1 for AB, AC, BC, ABC
+		if (numComp != 1) {
+			vector<string> groups;
+			if (numGroups == 0) {
+				//get score for all users groups
+				vector<string> tGroups = ct->getNamesOfGroups();
+				for (int i = 0; i < tGroups.size(); i++) {
+					if (tGroups[i] != "xxx") {
+						groups.push_back(tGroups[i]);
+						//cout << tmap->namesOfGroups[i] << endl;
+					}
+				}
+				namesOfGroupCombos.push_back(groups);
+			}else {
+				for (int i = 0; i < mGroups.size(); i++) {
+					groups.push_back(mGroups[i]);
+					//cout << globaldata->Groups[i] << endl;
+				}
+				namesOfGroupCombos.push_back(groups);
+			}
 		}
 		
-		for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
-			int lc = t->tree[i].getLChild();
-			int rc = t->tree[i].getRChild();
+	#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+		if(processors == 1){
+			data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), ct);
+		}else{
+			lines.clear();
+			int numPairs = namesOfGroupCombos.size();
 			
-			int iSize = t->tree[i].pGroups.size();
-			int rcSize = t->tree[rc].pGroups.size();
-			int lcSize = t->tree[lc].pGroups.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(linePair(startPos, numPairsPerProcessor));
+			}
+			
+			data = createProcesses(t, namesOfGroupCombos, ct);
+		}
+	#else
+		data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), ct);
+	#endif
+		
+		return data;
 		
-			//if isize are 0 then that branch is to be ignored
-			if (iSize == 0) { }
-			else if ((rcSize == 0) || (lcSize == 0)) { }
-			//if you have more groups than either of your kids then theres been a change.
-			else if(iSize > rcSize || iSize > lcSize){
-				score++;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Parsimony", "getValues");
+		exit(1);
+	}
+}
+/**************************************************************************************************/
+
+EstOutput Parsimony::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, CountTable* ct) {
+	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){
+				EstOutput myresults;
+				myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, ct);
+				
+				if (m->control_pressed) { exit(0); }
+				
+				//pass numSeqs to parent
+				ofstream out;
+				string tempFile = outputDir + toString(getpid()) + ".pars.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("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
+				for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+				exit(0); 
 			}
-			cout << i << ' ' << score << ": ";
-			t->tree[i].printNode();
-		} 
+		}
 		
-		string hold;
-		cin >> hold;
+		results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, ct);
 		
-		data[0] = score;
+		//force parent to wait until all the processes are done
+		for (int i=0;i<processIDS.size();i++) { 
+			int temp = processIDS[i];
+			wait(&temp);
+		}
 		
-		return data;
+		if (m->control_pressed) { return results; }
+			
+		//get data created by processes
+		for (int i=0;i<processIDS.size();i++) { 
+			ifstream in;
+			string s = outputDir + toString(processIDS[i]) + ".pars.results.temp";
+			m->openInputFile(s, in);
+			
+			//get scores
+			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();
+			m->mothurRemove(s);
+		}
+		
+		return results;
+#endif		
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the Parsimony class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "Parsimony", "createProcesses");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the Parsimony class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+/**************************************************************************************************/
+EstOutput Parsimony::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, CountTable* ct) { 
+	try {
+		
+		EstOutput results; results.resize(num);
+		
+		Tree* copyTree = new Tree(ct);
+		int count = 0;
+		
+		for (int h = start; h < (start+num); h++) {
+					
+			if (m->control_pressed) { delete copyTree; return results; }
+	
+			int score = 0;
+			
+			//groups in this combo
+			vector<string> groups = namesOfGroupCombos[h];
+			
+			//copy users tree so that you can redo pgroups 
+			copyTree->getCopy(t);
+			
+			//create pgroups that reflect the groups the user want to use
+			for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
+				copyTree->tree[i].pGroups = (copyTree->mergeUserGroups(i, groups));
+			}
+			
+			for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
+				
+				if (m->control_pressed) { return data; }
+				
+				int lc = copyTree->tree[i].getLChild();
+				int rc = copyTree->tree[i].getRChild();
+				
+				int iSize = copyTree->tree[i].pGroups.size();
+				int rcSize = copyTree->tree[rc].pGroups.size();
+				int lcSize = copyTree->tree[lc].pGroups.size();
+				
+				//if isize are 0 then that branch is to be ignored
+				if (iSize == 0) { }
+				else if ((rcSize == 0) || (lcSize == 0)) { }
+				//if you have more groups than either of your kids then theres been a change.
+				else if(iSize > rcSize || iSize > lcSize){
+					score++;
+				}
+			} 
+			
+			results[count] = score;
+			count++;
+		}
+					
+		delete copyTree;
+			
+		return results; 
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Parsimony", "driver");
 		exit(1);
 	}
-
 }
 
 /**************************************************************************************************/