fixed bug in unifrac commands with unrooted trees

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 6e32a373e41bd2aeb9ad3e9fe0cde110d583da37..a31c15192f1f27dcc1b84ddf114d0dcf485d41a3 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -65,7 +65,7 @@ vector<string> TreeGroupCommand::getValidParameters(){
 //**********************************************************************************************************************
 TreeGroupCommand::TreeGroupCommand(){  
        try {
-               abort = true;
+               abort = true; calledHelp = true;
                globaldata = GlobalData::getInstance();
                //initialize outputTypes
                vector<string> tempOutNames;
@@ -104,14 +104,14 @@ vector<string> TreeGroupCommand::getRequiredFiles(){
 TreeGroupCommand::TreeGroupCommand(string option)  {
        try {
                globaldata = GlobalData::getInstance();
-               abort = false;
+               abort = false; calledHelp = false;   
                allLines = 1;
                labels.clear();
                Groups.clear();
                Estimators.clear();
                
                //allow user to run help
-               if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+               if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; calledHelp = true; }
                
                else {
                        //valid paramters for this command
@@ -380,7 +380,7 @@ TreeGroupCommand::~TreeGroupCommand(){
 int TreeGroupCommand::execute(){
        try {
        
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                if (format == "sharedfile") {
                        //if the users entered no valid calculators don't execute command
@@ -747,6 +747,14 @@ int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
                                                                //add new pair of sharedrabunds
                                                                subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]); 
                                                                
+                                                               //if this calc needs all groups to calculate the pair load all groups
+                                                               if (treeCalculators[i]->getNeedsAll()) { 
+                                                                       //load subset with rest of lookup for those calcs that need everyone to calc for a pair
+                                                                       for (int w = 0; w < thisLookup.size(); w++) {
+                                                                               if ((w != k) && (w != l)) { subset.push_back(thisLookup[w]); }
+                                                                       }
+                                                               }
+                                                               
                                                                data = treeCalculators[i]->getValues(subset); //saves the calculator outputs
                                                //cout << thisLookup[k]->getGroup() << '\t' << thisLookup[l]->getGroup() << '\t' << (1.0 - data[0]) << endl;
                                                                if (m->control_pressed) { return 1; }