X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treegroupscommand.cpp;h=ac82da5e558d2965829de82f170b1514c8972c84;hb=ee27b6e01a979fdf832668eb87412b029f77e4d7;hp=7791d5ecd913c431114a9de5afb2ca651ec1232c;hpb=477e76a8a79b60f6cd4253324dd830bdea25e3e9;p=mothur.git

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 7791d5e..ac82da5 100644
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -17,6 +17,7 @@
 #include "sharedthetayc.h"
 #include "sharedthetan.h"
 #include "sharedmorisitahorn.h"
+#include "sharedbraycurtis.h"
 
 
 //**********************************************************************************************************************
@@ -49,6 +50,8 @@ TreeGroupCommand::TreeGroupCommand(){
 					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());
 				}
 			}
 		}
@@ -80,28 +83,20 @@ int TreeGroupCommand::execute(){
 	try {
 		int count = 1;	
 		EstOutput data;
-	
+		vector<SharedRAbundVector*> subset;
+		
 		//if the users entered no valid calculators don't execute command
 		if (treeCalculators.size() == 0) { return 0; }
 
-		if (format == "sharedfile") {
-			read = new ReadOTUFile(globaldata->inputFileName);	
-			read->read(&*globaldata); 
+		//you have groups
+		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 ReadOTUFile(globaldata->inputFileName);	
-			read->read(&*globaldata); 
-		
-			input = globaldata->ginput;
-			SharedList = globaldata->gSharedList;
-			order = SharedList->getSharedOrderVector();
-		}
+		input = globaldata->ginput;
+		lookup = input->getSharedRAbundVectors();
+				
+		if (lookup.size() < 2) { cout << "You have not provided enough valid groups.  I cannot run the command." << endl; }
 		
-		//set users groups
-		util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "treegroup");
 		numGroups = globaldata->Groups.size();
 		groupNames = "";
 		for (int i = 0; i < numGroups; i++) { groupNames += globaldata->Groups[i]; }
@@ -117,12 +112,11 @@ int TreeGroupCommand::execute(){
 		tmap->makeSim(globaldata->gGroupmap);
 		globaldata->gTreemap = tmap;
 			
-		while(order != NULL){
+		while(lookup[0] != NULL){
 		
-			if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){			
+			if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){			
 				
-				cout << order->getLabel() << '\t' << count << endl;
-				util->getSharedVectors(globaldata->Groups, lookup, order);  //fills group vectors from order vector.
+				cout << lookup[0]->getLabel() << '\t' << count << endl;
 				
 				//for each calculator												
 				for(int i = 0 ; i < treeCalculators.size(); i++) {
@@ -141,13 +135,18 @@ 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() + ".tre";
+					outputFile = getRootName(globaldata->inputFileName) + treeCalculators[i]->getName() + "." + lookup[0]->getLabel() + ".tre";
 							
 					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
-								data = treeCalculators[i]->getValues(lookup[k], lookup[l]); //saves the calculator outputs
+								
+								subset.clear(); //clear out old pair of sharedrabunds
+								//add new pair of sharedrabunds
+								subset.push_back(lookup[k]); subset.push_back(lookup[l]); 
+								
+								data = treeCalculators[i]->getValues(subset); //saves the calculator outputs
 								//save values in similarity matrix
 								simMatrix[k][l] = data[0];
 								simMatrix[l][k] = data[0];
@@ -161,17 +160,7 @@ int TreeGroupCommand::execute(){
 			}
 		
 			//get next line to process
-			if (format == "sharedfile") {
-				order = input->getSharedOrderVector();
-			}else {
-				//you are using a list and a groupfile
-				SharedList = input->getSharedListVector(); //get new list vector to process
-				if (SharedList != NULL) {
-					order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
-				}else {
-					break;
-				}
-			}
+			lookup = input->getSharedRAbundVectors();
 			count++;
 		}