X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=parsimony.cpp;h=1b08e8a3fe8470e5d34944722e186fdca7e0731b;hp=2a673b0cb622bd97b8f91dc4f1c2e9c69de19e8d;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=692e0c1f69a78b568dc85cbdcea9fb6c189e2e6c

diff --git a/parsimony.cpp b/parsimony.cpp
index 2a673b0..1b08e8a 100644
--- a/parsimony.cpp
+++ b/parsimony.cpp
@@ -10,87 +10,251 @@
 #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;
-			
-		for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
-			int lc = t->tree[i].getLChild();
-			int rc = t->tree[i].getRChild();
-			
-			int iSize = 0;
-			int rcSize = 0;
-			int lcSize = 0;
+		//if the users enters no groups then give them the score of all groups
+		vector<string> mGroups = m->getGroups();
+		int numGroups = mGroups.size();
+		
+		//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);
+			}
+		}
 
-			//add in all the groups the users wanted
-			for (it = t->tree[i].pGroups.begin(); it != t->tree[i].pGroups.end(); it++) {
-				if (inUsersGroups(it->first) == true) {  iSize++;  }
+		//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);
 			}
+		}
+        
+        lines.clear();
+        int remainingPairs = namesOfGroupCombos.size();
+        int startIndex = 0;
+        for (int remainingProcessors = processors; remainingProcessors > 0; remainingProcessors--) {
+            int numPairs = remainingPairs; //case for last processor
+            if (remainingProcessors != 1) { numPairs = ceil(remainingPairs / remainingProcessors); }
+            lines.push_back(linePair(startIndex, numPairs)); //startIndex, numPairs
+            startIndex = startIndex + numPairs;
+            remainingPairs = remainingPairs - numPairs;
+        }
+        
+        data = createProcesses(t, namesOfGroupCombos, ct);
+		
+		return data;
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Parsimony", "getValues");
+		exit(1);
+	}
+}
+/**************************************************************************************************/
 
-			//if that leaves no groups give it 1 so it will cause no change to parent
-			if (iSize == 0) { iSize++; }
-			
-			//add in all the groups the users wanted
-			for (it = t->tree[rc].pGroups.begin(); it != t->tree[rc].pGroups.end(); it++) {
+EstOutput Parsimony::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, CountTable* ct) {
+	try {
+        int process = 1;
+		vector<int> processIDS;
+		
+		EstOutput results;
 
-				if (inUsersGroups(it->first) == true) {  rcSize++;  }
-			}
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+				
+		//loop through and create all the processes you want
+		while (process != processors) {
+			int pid = fork();
 			
-			//if that leaves no groups give it 1 so it will cause no change to parent
-			if (rcSize == 0) { rcSize++; }
-
+			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);
 				
-			//add in all the groups the users wanted
-			for (it = t->tree[lc].pGroups.begin(); it != t->tree[lc].pGroups.end(); it++) {
-
-				if (inUsersGroups(it->first) == true) {  lcSize++;  }
+				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); 
 			}
+		}
+		
+		results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, ct);
+		
+		//force parent to wait until all the processes are done
+		for (int i=0;i<processIDS.size();i++) { 
+			int temp = processIDS[i];
+			wait(&temp);
+		}
+		
+		if (m->control_pressed) { return results; }
 			
-			//if that leaves no groups give it 1 so it will cause no change to parent
-			if (lcSize == 0) { lcSize++; }
-
-
-			//if you have more groups than either of your kids then theres been a change.
-			 if(iSize > rcSize || iSize > lcSize){
-				score++;
-
+		//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);
+		}
+#else
+        //fill in functions
+        vector<parsData*> pDataArray;
+		DWORD   dwThreadIdArray[processors-1];
+		HANDLE  hThreadArray[processors-1];
+        vector<CountTable*> cts;
+        vector<Tree*> trees;
 		
-		data[0] = score;
+		//Create processor worker threads.
+		for( int i=1; i<processors; i++ ){
+            CountTable* copyCount = new CountTable();
+            copyCount->copy(ct);
+            Tree* copyTree = new Tree(copyCount);
+            copyTree->getCopy(t);
+            
+            cts.push_back(copyCount);
+            trees.push_back(copyTree);
+            
+            parsData* temppars = new parsData(m, lines[i].start, lines[i].num, namesOfGroupCombos, copyTree, copyCount);
+			pDataArray.push_back(temppars);
+			processIDS.push_back(i);
+            
+			hThreadArray[i-1] = CreateThread(NULL, 0, MyParsimonyThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
+		}
 		
-		return data;
+		results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, ct);
+		
+		//Wait until all threads have terminated.
+		WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
+		
+		//Close all thread handles and free memory allocations.
+		for(int i=0; i < pDataArray.size(); i++){
+            for (int j = 0; j < pDataArray[i]->results.size(); j++) {  results.push_back(pDataArray[i]->results[j]);  }
+			delete cts[i];
+            delete trees[i];
+			CloseHandle(hThreadArray[i]);
+			delete pDataArray[i];
+		}
+		
+#endif		
+        return results;
 	}
 	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";
-		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";
+		m->errorOut(e, "Parsimony", "createProcesses");
 		exit(1);
 	}
-
 }
 /**************************************************************************************************/
-
-bool Parsimony::inUsersGroups(string groupname) {
+EstOutput Parsimony::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, CountTable* ct) { 
 	try {
-		for (int i = 0; i < globaldata->Groups.size(); i++) {
-			if (groupname == globaldata->Groups[i]) { return true; }
+		
+		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++;
 		}
-		return false;
+					
+		delete copyTree;
+			
+		return results; 
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the Parsimony class Function inUsersGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the Parsimony class function inUsersGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "Parsimony", "driver");
 		exit(1);
 	}
 }
+
 /**************************************************************************************************/
+