fixed some bugs and added mgcluster command

[mothur.git] / libshuffcommand.cpp

diff --git a/libshuffcommand.cpp b/libshuffcommand.cpp
index 2d84767bc998d1e8db1d1ab40e7f9836f2045595..74acd841b676acc429df6df4e303210d82ae92ba 100644 (file)
--- a/libshuffcommand.cpp
+++ b/libshuffcommand.cpp
@@ -22,7 +22,6 @@
 
 LibShuffCommand::LibShuffCommand(string option){
        try {
-               
                globaldata = GlobalData::getInstance();
                abort = false;
                Groups.clear();
@@ -74,19 +73,19 @@ LibShuffCommand::LibShuffCommand(string option){
                        userform = validParameter.validFile(parameters, "form", false);                 if (userform == "not found") { userform = "integral"; }
                        
                        if (abort == false) {
-                       
+               
                                matrix = globaldata->gMatrix;                           //get the distance matrix
                                setGroups();                                                            //set the groups to be analyzed and sorts them
-                               
+       
                                /********************************************************************************************/
                                //this is needed because when we read the matrix we sort it into groups in alphabetical order
                                //the rest of the command and the classes used in this command assume specific order
                                /********************************************************************************************/
                                matrix->setGroups(globaldata->gGroupmap->namesOfGroups);
                                vector<int> sizes;
-                               for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {  sizes.push_back(globaldata->gGroupmap->getNumSeqs(globaldata->gGroupmap->namesOfGroups[i]));  }
+                               for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {   sizes.push_back(globaldata->gGroupmap->getNumSeqs(globaldata->gGroupmap->namesOfGroups[i]));  }
                                matrix->setSizes(sizes);
-                               
+                       
 
                                if(userform == "discrete"){
                                        form = new DLibshuff(matrix, iters, step, cutOff);
@@ -132,10 +131,10 @@ int LibShuffCommand::execute(){
        try {
                
                if (abort == true) {    return 0;       }
-               
+       
                savedDXYValues = form->evaluateAll();
                savedMinValues = form->getSavedMins();
-               
+       
                pValueCounts.resize(numGroups);
                for(int i=0;i<numGroups;i++){
                        pValueCounts[i].assign(numGroups, 0);