X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unweighted.cpp;h=fb2f0b22afa3cc2143ad95afe6c45e4e093db222;hb=5334a314651228c55fd0f206dec0209bc3148b24;hp=8103688fb04d34542ee2174728d3399055a5d452;hpb=4745a956b3116a719f52f341d2a2db84df4817da;p=mothur.git

diff --git a/unweighted.cpp b/unweighted.cpp
index 8103688..fb2f0b2 100644
--- a/unweighted.cpp
+++ b/unweighted.cpp
@@ -66,7 +66,6 @@ EstOutput Unweighted::getValues(Tree* t, int p, string o) {
 		
 					lines.push_back(linePair(startPos, numPairsPerProcessor));
 				}
-
 				data = createProcesses(t, namesOfGroupCombos);
 				lines.clear();
 			}
@@ -87,7 +86,6 @@ EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfG
 	try {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 		int process = 1;
-		int num = 0;
 		vector<int> processIDS;
 		
 		EstOutput results;
@@ -116,7 +114,11 @@ EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfG
 				out.close();
 				
 				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); 
+			}
 		}
 		
 		results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num);
@@ -170,17 +172,22 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
 		EstOutput results; results.resize(num);
 		
 		int count = 0;
+		int numLeaves = t->getNumLeaves();
 		int total = num;
 		int twentyPercent = (total * 0.20);
 		if (twentyPercent == 0) { twentyPercent = 1; }
 		
-		for (int h = start; h < (start+num); h++) {
 		
+		for (int h = start; h < (start+num); h++) {
+	//cout << namesOfGroupCombos[h][0] << '\t' << namesOfGroupCombos[h][1] << endl;		
 			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;
+			map<int, double> tempTotals; //maps node to total Branch Length
+			map<int, int> nodePcountSize; //maps node to pcountSize
+			map<int, int>::iterator itCount;
 				
 			for(int i=0;i<t->getNumNodes();i++){
 			
@@ -195,15 +202,47 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
 					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; } } 
 				}
+
+				nodePcountSize[i] = pcountSize;
 				
+				//cout << i << '\t' << t->tree[i].getName() << " br = " << abs(t->tree[i].getBranchLength()) << '\t';		
 				if (pcountSize == 0) { }
-				else if ((t->tree[i].getBranchLength() != -1) && (pcountSize == 1)) {  UniqueBL += abs(t->tree[i].getBranchLength());	}
+				else if ((t->tree[i].getBranchLength() != -1) && (pcountSize == 1)) {  UniqueBL += abs(t->tree[i].getBranchLength()); }
+				
+				//if you are a leaf from a users group add to total
+				if (i < numLeaves) {
+					if ((t->tree[i].getBranchLength() != -1) && pcountSize != 0) { 
+					//cout << "added to total" << endl; 
+						totalBL += abs(t->tree[i].getBranchLength()); 
+					}
+					tempTotals[i] = 0.0;  //we don't care about you, or we have already added you
+				}else{ //if you are not a leaf 
+					//do both your chidren have have descendants from the users groups? 
+					int lc = t->tree[i].getLChild();
+					int rc = t->tree[i].getRChild();
 					
-				if ((t->tree[i].getBranchLength() != -1) && (pcountSize != 0)) {  
-					totalBL += abs(t->tree[i].getBranchLength()); 
+					//if yes, add your childrens tempTotals
+					if ((nodePcountSize[lc] != 0) && (nodePcountSize[rc] != 0)) {
+						totalBL += tempTotals[lc] + tempTotals[rc]; 
+						//cout << "added to total " << tempTotals[lc] << '\t' << tempTotals[rc] << endl;
+						if (t->tree[i].getBranchLength() != -1) {
+							tempTotals[i] = abs(t->tree[i].getBranchLength());
+						}else {
+							tempTotals[i] = 0.0;
+						}
+					}else if ((nodePcountSize[lc] == 0) && (nodePcountSize[rc] == 0)) { tempTotals[i] = 0.0;  //we don't care about you
+					}else { //if no, your tempTotal is your childrens temp totals + your branch length
+						if (t->tree[i].getBranchLength() != -1) {
+							tempTotals[i] = tempTotals[lc] + tempTotals[rc] + abs(t->tree[i].getBranchLength()); 
+						}else {
+							tempTotals[i] = tempTotals[lc] + tempTotals[rc];
+						}
+					}
+					//cout << "temptotal = "<< tempTotals[i] << endl;
 				}
+
 			}
-	
+	//cout << UniqueBL << '\t' << totalBL << endl;		
 			UW = (UniqueBL / totalBL);  
 	
 			if (isnan(UW) || isinf(UW)) { UW = 0; }
@@ -281,7 +320,7 @@ EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB, int p, st
 					}
 					lines.push_back(linePair(startPos, numPairsPerProcessor));
 				}
-
+					
 				data = createProcesses(t, namesOfGroupCombos, true);
 				
 				lines.clear();
@@ -303,7 +342,6 @@ EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfG
 	try {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 		int process = 1;
-		int num = 0;
 		vector<int> processIDS;
 		
 		EstOutput results;
@@ -330,7 +368,11 @@ EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfG
 				out.close();
 				
 				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); 
+			}
 		}
 		
 		results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, usingGroups);
@@ -353,12 +395,13 @@ EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfG
 			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);
@@ -382,8 +425,7 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
 		EstOutput results; results.resize(num);
 		
 		int count = 0;
-		int total = num;
-		int twentyPercent = (total * 0.20);
+		int numLeaves = t->getNumLeaves();
 		
 		Tree* copyTree = new Tree;
 		
@@ -400,8 +442,10 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
 			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;
+			map<int, double> tempTotals; //maps node to total Branch Length
+			map<int, int> nodePcountSize; //maps node to pcountSize
 				
-			for(int i=0;i<t->getNumNodes();i++){
+			for(int i=0;i<copyTree->getNumNodes();i++){
 			
 				if (m->control_pressed) {  return data; }
 				
@@ -411,16 +455,46 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
 				
 				int pcountSize = 0;
 				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; } } 
+					map<string, int>::iterator itGroup = copyTree->tree[i].pcount.find(namesOfGroupCombos[h][j]);
+					if (itGroup != copyTree->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } } 
 				}
 				
+				nodePcountSize[i] = pcountSize;
+			
 				if (pcountSize == 0) { }
-				else if ((t->tree[i].getBranchLength() != -1) && (pcountSize == 1)) {  UniqueBL += abs(t->tree[i].getBranchLength());	}
+				else if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize == 1)) {  UniqueBL += abs(copyTree->tree[i].getBranchLength());	 }
+				
+				//if you are a leaf from a users group add to total
+				if (i < numLeaves) {
+					if ((copyTree->tree[i].getBranchLength() != -1) && pcountSize != 0) { 
+						totalBL += abs(copyTree->tree[i].getBranchLength()); 
+					}
+					tempTotals[i] = 0.0;  //we don't care about you, or we have already added you
+				}else{ //if you are not a leaf 
+					//do both your chidren have have descendants from the users groups? 
+					int lc = copyTree->tree[i].getLChild();
+					int rc = copyTree->tree[i].getRChild();
+					
+					//if yes, add your childrens tempTotals
+					if ((nodePcountSize[lc] != 0) && (nodePcountSize[rc] != 0)) {
+						totalBL += tempTotals[lc] + tempTotals[rc]; 
+						
+						if (copyTree->tree[i].getBranchLength() != -1) {
+							tempTotals[i] = abs(copyTree->tree[i].getBranchLength());
+						}else {
+							tempTotals[i] = 0.0;
+						}
+					}else if ((nodePcountSize[lc] == 0) && (nodePcountSize[rc] == 0)) { tempTotals[i] = 0.0;  //we don't care about you
+					}else { //if no, your tempTotal is your childrens temp totals + your branch length
+						if (t->tree[i].getBranchLength() != -1) {
+							tempTotals[i] = tempTotals[lc] + tempTotals[rc] + abs(copyTree->tree[i].getBranchLength()); 
+						}else {
+							tempTotals[i] = tempTotals[lc] + tempTotals[rc];
+						}
+					}
 					
-				if ((t->tree[i].getBranchLength() != -1) && (pcountSize != 0)) {  
-					totalBL += abs(t->tree[i].getBranchLength()); 
 				}
+
 			}
 		
 			UW = (UniqueBL / totalBL);