fixed some bugs and added scriptengine

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 484b5536ec668fbf60b94cba6ae5244570d2f111..0f106c493d1d55f7e742ed1195e1557f435d6e49 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -66,7 +66,7 @@ TreeGroupCommand::TreeGroupCommand(string option){
                        else if (namefile == "not found") { namefile = ""; }
                        else {  globaldata->setNameFile(namefile);      }
                        
-//                     format = globaldata->getFormat();
+                       format = globaldata->getFormat();
                        
                        //error checking on files                       
                        if ((globaldata->getSharedFile() == "") && ((phylipfile == "") && (columnfile == "")))  { cout << "You must run the read.otu command or provide a distance file before running the tree.shared command." << endl; abort = true; }
@@ -234,6 +234,8 @@ int TreeGroupCommand::execute(){
                        
                        if (lookup.size() < 2) { cout << "You have not provided enough valid groups.  I cannot run the command." << endl; return 0; }
                
+                       globaldata->runParse = false;
+                       
                        //create tree file
                        makeSimsShared();
                }else{
@@ -269,7 +271,9 @@ int TreeGroupCommand::execute(){
                
                        //fills globaldatas tree names
                        globaldata->Treenames = globaldata->Groups;
-
+                       
+                       globaldata->runParse = false;
+                       
                        makeSimsDist();
 
                        //create a new filename
@@ -562,7 +566,7 @@ void TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
                                                        }
                                                }
                                        }
-                                       
+                               
                                        //creates tree from similarity matrix and write out file
                                        createTree();
                                }