X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treegroupscommand.cpp;h=e50fbaad53f0438a44bc25bf5b7c55fbf9146b83;hb=fd00cd216d3a38ccea22eae258e601df64218b05;hp=bdd664a55d360fe753318900456828b69b8daa4f;hpb=c5c7502f435e1413c19e373dab1dfebcaa67588d;p=mothur.git

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index bdd664a..e50fbaa 100644
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -17,6 +17,7 @@
 #include "sharedthetayc.h"
 #include "sharedthetan.h"
 #include "sharedmorisitahorn.h"
+#include "sharedbraycurtis.h"
 
 
 //**********************************************************************************************************************
@@ -31,24 +32,26 @@ TreeGroupCommand::TreeGroupCommand(){
 		int i;
 		for (i=0; i<globaldata->Estimators.size(); i++) {
 			if (validCalculator->isValidCalculator("treegroup", globaldata->Estimators[i]) == true) { 
-				if (globaldata->Estimators[i] == "sharedjabund") { 	
-					treeCalculators.push_back(new SharedJAbund());
-				}else if (globaldata->Estimators[i] == "sharedsorensonabund") { 
-					treeCalculators.push_back(new SharedSorAbund());
-				}else if (globaldata->Estimators[i] == "sharedjclass") { 
-					treeCalculators.push_back(new SharedJclass());
-				}else if (globaldata->Estimators[i] == "sharedsorclass") { 
-					treeCalculators.push_back(new SharedSorClass());
-				}else if (globaldata->Estimators[i] == "sharedjest") { 
-					treeCalculators.push_back(new SharedJest());
-				}else if (globaldata->Estimators[i] == "sharedsorest") { 
-					treeCalculators.push_back(new SharedSorEst());
-				}else if (globaldata->Estimators[i] == "sharedthetayc") { 
-					treeCalculators.push_back(new SharedThetaYC());
-				}else if (globaldata->Estimators[i] == "sharedthetan") { 
-					treeCalculators.push_back(new SharedThetaN());
-				}else if (globaldata->Estimators[i] == "sharedmorisitahorn") { 
-					treeCalculators.push_back(new SharedMorHorn());
+				if (globaldata->Estimators[i] == "jabund") { 	
+					treeCalculators.push_back(new JAbund());
+				}else if (globaldata->Estimators[i] == "sorabund") { 
+					treeCalculators.push_back(new SorAbund());
+				}else if (globaldata->Estimators[i] == "jclass") { 
+					treeCalculators.push_back(new Jclass());
+				}else if (globaldata->Estimators[i] == "sorclass") { 
+					treeCalculators.push_back(new SorClass());
+				}else if (globaldata->Estimators[i] == "jest") { 
+					treeCalculators.push_back(new Jest());
+				}else if (globaldata->Estimators[i] == "sorest") { 
+					treeCalculators.push_back(new SorEst());
+				}else if (globaldata->Estimators[i] == "thetayc") { 
+					treeCalculators.push_back(new ThetaYC());
+				}else if (globaldata->Estimators[i] == "thetan") { 
+					treeCalculators.push_back(new ThetaN());
+				}else if (globaldata->Estimators[i] == "morisitahorn") { 
+					treeCalculators.push_back(new MorHorn());
+				}else if (globaldata->Estimators[i] == "braycurtis") { 
+					treeCalculators.push_back(new BrayCurtis());
 				}
 			}
 		}
@@ -85,14 +88,14 @@ int TreeGroupCommand::execute(){
 		if (treeCalculators.size() == 0) { return 0; }
 
 		if (format == "sharedfile") {
-			read = new ReadPhilFile(globaldata->inputFileName);	
+			read = new ReadOTUFile(globaldata->inputFileName);	
 			read->read(&*globaldata); 
 			
 			input = globaldata->ginput;
 			order = input->getSharedOrderVector();
 		}else {
 			//you are using a list and a groupfile
-			read = new ReadPhilFile(globaldata->inputFileName);	
+			read = new ReadOTUFile(globaldata->inputFileName);	
 			read->read(&*globaldata); 
 		
 			input = globaldata->ginput;
@@ -141,9 +144,9 @@ int TreeGroupCommand::execute(){
 					for (int g = 0; g < numGroups; g++) {	index[g] = g;	}
 		
 					//create a new filename
-					outputFile = getRootName(globaldata->inputFileName) + treeCalculators[i]->getName() + "." + order->getLabel() + groupNames + ".tre";
+					outputFile = getRootName(globaldata->inputFileName) + treeCalculators[i]->getName() + "." + order->getLabel() + ".tre";
 							
-					for (int k = 0; k < lookup.size(); k++) { // pass cdd each set of groups to commpare
+					for (int k = 0; k < lookup.size(); k++) { 
 						for (int l = k; l < lookup.size(); l++) {
 							if (k != l) { //we dont need to similiarity of a groups to itself
 								//get estimated similarity between 2 groups