From: westcott <westcott>
Date: Wed, 23 Feb 2011 13:34:08 +0000 (+0000)
Subject: fixed bug in unifrac commands with unrooted trees
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=5334a314651228c55fd0f206dec0209bc3148b24

fixed bug in unifrac commands with unrooted trees
---

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 902e927..e479725 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -1625,7 +1625,7 @@
 			attributes = {
 				ORGANIZATIONNAME = "Schloss Lab";
 			};
-			buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */;
+			buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */;
 			compatibilityVersion = "Xcode 3.1";
 			developmentRegion = English;
 			hasScannedForEncodings = 1;
@@ -2048,7 +2048,7 @@
 			defaultConfigurationIsVisible = 0;
 			defaultConfigurationName = Release;
 		};
-		1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */ = {
+		1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */ = {
 			isa = XCConfigurationList;
 			buildConfigurations = (
 				1DEB928A08733DD80010E9CD /* Debug */,
diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 53bdc7e..dd5bf34 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -349,7 +349,7 @@ int TrimSeqsCommand::execute(){
 					createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, outputGroupFileName, fastaFileNames, qualFileNames); 
 				}	
 		#else
-				driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, outputGroupFile, fastaFileNames, qualFileNames, lines[0], qLines[0]);
+				driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, outputGroupFileName, fastaFileNames, qualFileNames, lines[0], qLines[0]);
 		#endif
 		
 		if (m->control_pressed) {  return 0; }			
diff --git a/unweighted.cpp b/unweighted.cpp
index ea66294..fb2f0b2 100644
--- a/unweighted.cpp
+++ b/unweighted.cpp
@@ -232,7 +232,11 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
 						}
 					}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
-						tempTotals[i] = tempTotals[lc] + tempTotals[rc] + abs(t->tree[i].getBranchLength()); 
+						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;
 				}
@@ -482,7 +486,11 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
 						}
 					}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
-						tempTotals[i] = tempTotals[lc] + tempTotals[rc] + abs(copyTree->tree[i].getBranchLength()); 
+						if (t->tree[i].getBranchLength() != -1) {
+							tempTotals[i] = tempTotals[lc] + tempTotals[rc] + abs(copyTree->tree[i].getBranchLength()); 
+						}else {
+							tempTotals[i] = tempTotals[lc] + tempTotals[rc];
+						}
 					}
 					
 				}
diff --git a/weighted.cpp b/weighted.cpp
index 30e4a76..a0d593c 100644
--- a/weighted.cpp
+++ b/weighted.cpp
@@ -231,10 +231,13 @@ EstOutput Weighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos,
 				
 				//if this is not the root then add it
 				if (rootForGrouping[namesOfGroupCombos[h]].count(i) == 0) {
-					u = abs(u * t->tree[i].getBranchLength());
-					WScore[(groupA+groupB)] += u; 
+					if (t->tree[i].getBranchLength() != -1) {
+						u = abs(u * t->tree[i].getBranchLength());
+						WScore[(groupA+groupB)] += u; 
+					}
 				}
 				
+				
 			}
 		}
 		
@@ -244,7 +247,6 @@ EstOutput Weighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos,
 		count = 0;
 		for (int h = start; h < (start+num); h++) {
 			UN = (WScore[namesOfGroupCombos[h][0]+namesOfGroupCombos[h][1]] / D[count]);
-		
 			if (isnan(UN) || isinf(UN)) { UN = 0; } 
 			results.push_back(UN);
 			count++;
@@ -319,12 +321,14 @@ EstOutput Weighted::getValues(Tree* t, string groupA, string groupB) {
 			
 			//if this is not the root then add it
 			if (rootForGrouping[groups].count(i) == 0) {
-				u = abs(u * t->tree[i].getBranchLength());
-				WScore[(groupA+groupB)] += u; 
+				if (t->tree[i].getBranchLength() != -1) {
+					u = abs(u * t->tree[i].getBranchLength());
+					WScore[(groupA+groupB)] += u;
+				}
 			}
 		}		
 		/********************************************************/
-		
+	 
 		//calculate weighted score for the group combination
 		double UN;	
 		UN = (WScore[(groupA+groupB)] / D);