X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=weighted.cpp;h=a114d2ca0756c6fe671dc135acf0254ad1d5bf92;hb=b8f3e71c8a0310e25261464d27e6fcfe891483b0;hp=fa22716e397c4dddb1dd1ab29e2cd04d40b10311;hpb=fc7cf3aac8fd6106fd725b43baa8ab5ca6f836f8;p=mothur.git

diff --git a/weighted.cpp b/weighted.cpp
index fa22716..a114d2c 100644
--- a/weighted.cpp
+++ b/weighted.cpp
@@ -26,11 +26,16 @@ EstOutput Weighted::getValues(Tree* t) {
 				//initialize weighted scores
 				WScore[globaldata->Groups[i]+globaldata->Groups[l]] = 0.0;
 				
+				vector<string> groups; groups.push_back(globaldata->Groups[i]); groups.push_back(globaldata->Groups[l]);
+				
 				D.push_back(0.0000); //initialize a spot in D for each combination
 				
 				/********************************************************/
 				//calculate a D value for each group combo
 				for(int v=0;v<t->getNumLeaves();v++){
+				
+					if (m->control_pressed) { return data; }
+					
 					int index = v;
 					double sum = 0.0000;
 		
@@ -39,22 +44,38 @@ EstOutput Weighted::getValues(Tree* t) {
 							
 						//if you have a BL
 						if(t->tree[index].getBranchLength() != -1){
-							sum += t->tree[index].getBranchLength();
+							sum += abs(t->tree[index].getBranchLength());
 						}
 						index = t->tree[index].getParent();
 					}
 						
 					//get last breanch length added
 					if(t->tree[index].getBranchLength() != -1){
-						sum += t->tree[index].getBranchLength();
+						sum += abs(t->tree[index].getBranchLength());
 					}
 						
 					//is this sum from a sequence which is in one of the users groups
 					if (inUsersGroups(t->tree[v].getGroup(), globaldata->Groups) == true) {
 						//is this sum from a sequence which is in this groupCombo
-						if ((t->tree[v].getGroup() == globaldata->Groups[i]) || (t->tree[v].getGroup() == globaldata->Groups[l])) {
-							sum /= (double)tmap->seqsPerGroup[t->tree[v].getGroup()];
-							D[count] += sum; 
+						if (inUsersGroups(t->tree[v].getGroup(), groups)) {
+							int numSeqsInGroupI, numSeqsInGroupL;
+							
+							map<string, int>::iterator it;
+							it = t->tree[v].pcount.find(groups[0]);
+							if (it != t->tree[v].pcount.end()) { //this leaf node contains seqs from group i
+								numSeqsInGroupI = it->second;
+							}else{ numSeqsInGroupI = 0; }
+							
+							it = t->tree[v].pcount.find(groups[1]);
+							if (it != t->tree[v].pcount.end()) { //this leaf node contains seqs from group l
+								numSeqsInGroupL = it->second;
+							}else{ numSeqsInGroupL = 0; }
+							
+							double weightedSum = ((numSeqsInGroupI * sum) / (double)tmap->seqsPerGroup[groups[0]]) + ((numSeqsInGroupL * sum) / (double)tmap->seqsPerGroup[groups[1]]);
+
+							//sum /= (double)tmap->seqsPerGroup[t->tree[v].getGroup()];
+							
+							D[count] += weightedSum; 
 						}
 					}
 				}
@@ -69,6 +90,9 @@ EstOutput Weighted::getValues(Tree* t) {
 			//calculate weighted score for each of the group comb i.e. with groups A,B,C = AB, AC, BC.
 			for (int b=0; b<numGroups; b++) { 
 				for (int l = b+1; l < numGroups; l++) {
+				
+					if (m->control_pressed) { return data; }
+					
 					//calculate a u value for each combo
 					double u;
 					//does this node have descendants from group b-1
@@ -85,7 +109,7 @@ EstOutput Weighted::getValues(Tree* t) {
 						u -= (double) t->tree[i].pcount[globaldata->Groups[l]] / (double) tmap->seqsPerGroup[globaldata->Groups[l]];
 					}
 						
-					u = abs(u) * t->tree[i].getBranchLength();
+					u = abs(u * t->tree[i].getBranchLength());
 					
 					//save groupcombs u value
 					WScore[globaldata->Groups[b]+globaldata->Groups[l]] += u;
@@ -109,14 +133,9 @@ EstOutput Weighted::getValues(Tree* t) {
 		return data;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the Weighted class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the Weighted class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "Weighted", "getValues");
 		exit(1);
 	}
-
 }
 
 /**************************************************************************************************/
@@ -130,10 +149,13 @@ EstOutput Weighted::getValues(Tree* t, string groupA, string groupB) {
 		WScore[(groupA+groupB)] = 0.0;
 		float D = 0.0;
 		
+		vector<string> groups; groups.push_back(groupA); groups.push_back(groupB);
 						
 		/********************************************************/
 		//calculate a D value for the group combo
 		for(int v=0;v<t->getNumLeaves();v++){
+			if (m->control_pressed) { return data; }
+			
 			int index = v;
 			double sum = 0.0000;
 		
@@ -142,25 +164,44 @@ EstOutput Weighted::getValues(Tree* t, string groupA, string groupB) {
 							
 				//if you have a BL
 				if(t->tree[index].getBranchLength() != -1){
-					sum += t->tree[index].getBranchLength();
+					sum += abs(t->tree[index].getBranchLength());
 				}
 				index = t->tree[index].getParent();
 			}
 						
 			//get last breanch length added
 			if(t->tree[index].getBranchLength() != -1){
-				sum += t->tree[index].getBranchLength();
+				sum += abs(t->tree[index].getBranchLength());
 			}
 						
-			if ((t->tree[v].getGroup() == groupA) || (t->tree[v].getGroup() == groupB)) {
-				sum /= (double)tmap->seqsPerGroup[t->tree[v].getGroup()];
-				D += sum; 
+			if (inUsersGroups(t->tree[v].getGroup(), groups)) {
+				int numSeqsInGroupI, numSeqsInGroupL;
+							
+				map<string, int>::iterator it;
+				it = t->tree[v].pcount.find(groups[0]);
+				if (it != t->tree[v].pcount.end()) { //this leaf node contains seqs from group i
+					numSeqsInGroupI = it->second;
+				}else{ numSeqsInGroupI = 0; }
+				
+				it = t->tree[v].pcount.find(groups[1]);
+				if (it != t->tree[v].pcount.end()) { //this leaf node contains seqs from group l
+					numSeqsInGroupL = it->second;
+				}else{ numSeqsInGroupL = 0; }
+				
+				double weightedSum = ((numSeqsInGroupI * sum) / (double)tmap->seqsPerGroup[groups[0]]) + ((numSeqsInGroupL * sum) / (double)tmap->seqsPerGroup[groups[1]]);
+				
+				//sum /= (double)tmap->seqsPerGroup[t->tree[v].getGroup()];
+				
+				D += weightedSum; 
 			}
 		}
 		/********************************************************/				
 		
 		//calculate u for the group comb 
 		for(int i=0;i<t->getNumNodes();i++){
+		
+			if (m->control_pressed) { return data; }
+			
 			double u;
 			//does this node have descendants from groupA
 			it = t->tree[i].pcount.find(groupA);
@@ -177,7 +218,7 @@ EstOutput Weighted::getValues(Tree* t, string groupA, string groupB) {
 				u -= (double) t->tree[i].pcount[groupB] / (double) tmap->seqsPerGroup[groupB];
 			}
 						
-			u = abs(u) * t->tree[i].getBranchLength();
+			u = abs(u * t->tree[i].getBranchLength());
 					
 			//save groupcombs u value
 			WScore[(groupA+groupB)] += u;
@@ -195,14 +236,9 @@ EstOutput Weighted::getValues(Tree* t, string groupA, string groupB) {
 		return data; 
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the Weighted class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "Weighted", "getValues");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the Weighted class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-
 }