From: westcott <westcott>
Date: Mon, 17 May 2010 14:01:43 +0000 (+0000)
Subject: change to phylo.diversity to make output = total branch length seen so far for each... 
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=29b2a01f3daf8f16438b16f0e44b1c36d989d60b

change to phylo.diversity to make output = total branch length seen so far for each group instead of total branch length seen so far for each group / total branch length for that group
---

diff --git a/phylodiversity.cpp b/phylodiversity.cpp
index 96d49d4..37884c4 100644
--- a/phylodiversity.cpp
+++ b/phylodiversity.cpp
@@ -66,10 +66,11 @@ EstOutput PhyloDiversity::getValues(Tree* t, vector<int> treeNodes) {
 		
 	
 		for (int i=0; i<globaldata->Groups.size(); i++) {   
-			if (groupTotals[globaldata->Groups[i]] != 0.0) { //avoid divide by zero error
-				float percent = DScore[globaldata->Groups[i]] / groupTotals[globaldata->Groups[i]];
-				data.push_back(percent);  
-			}else {  data.push_back(0.0);  }
+			//if (groupTotals[globaldata->Groups[i]] != 0.0) { //avoid divide by zero error
+				//float percent = DScore[globaldata->Groups[i]] / groupTotals[globaldata->Groups[i]];
+			float percent = DScore[globaldata->Groups[i]]; 
+			data.push_back(percent);  
+			//}else {  data.push_back(0.0);  }
 		}
 		
 		return data;
diff --git a/phylodiversitycommand.cpp b/phylodiversitycommand.cpp
index 19c65ce..0c2f72d 100644
--- a/phylodiversitycommand.cpp
+++ b/phylodiversitycommand.cpp
@@ -113,7 +113,7 @@ int PhyloDiversityCommand::execute(){
 		
 			if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	} return 0; }
 			
-			phylo.setTotalGroupBranchLengths(trees[i]);
+			//phylo.setTotalGroupBranchLengths(trees[i]);
 			
 			string outFile = outputDir + getRootName(getSimpleName(globaldata->getTreeFile()))  + toString(i+1) + ".phylo.diversity";
 			if (rarefy) { outFile += ".rarefaction"; }