This is mothur v 1.2.0 - the April ~24, 2009 release

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index bdd664a55d360fe753318900456828b69b8daa4f..e50fbaad53f0438a44bc25bf5b7c55fbf9146b83 100644 (file)
--- 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