more calculator edits and added coverage and whittaker

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index a6e1918ffdefcf34d6052730f5161d011d644567..7791d5ecd913c431114a9de5afb2ca651ec1232c 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -33,7 +33,7 @@ TreeGroupCommand::TreeGroupCommand(){
                        if (validCalculator->isValidCalculator("treegroup", globaldata->Estimators[i]) == true) { 
                                if (globaldata->Estimators[i] == "jabund") {    
                                        treeCalculators.push_back(new JAbund());
-                               }else if (globaldata->Estimators[i] == "sorensonabund") { 
+                               }else if (globaldata->Estimators[i] == "sorabund") { 
                                        treeCalculators.push_back(new SorAbund());
                                }else if (globaldata->Estimators[i] == "jclass") { 
                                        treeCalculators.push_back(new Jclass());
@@ -85,14 +85,14 @@ 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 +141,9 @@ 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