fixed a trimming bug in sffinfo which occurs when the right trim point is smaller...

[mothur.git] / readtreecommand.cpp

diff --git a/readtreecommand.cpp b/readtreecommand.cpp
index 60654489ce6a1a848eb0dc9743f43e64b832a639..07aa5b3e4071289a25400e7cb03f616b34ad18ba 100644 (file)
--- a/readtreecommand.cpp
+++ b/readtreecommand.cpp
@@ -108,8 +108,10 @@ void ReadTreeCommand::help(){
        try {
                m->mothurOut("The read.tree command must be run before you execute a unifrac.weighted, unifrac.unweighted. \n");
                m->mothurOut("It also must be run before using the parsimony command, unless you are using the randomtree parameter.\n");
+               m->mothurOut("The read.tree command parameters are tree, group and name.\n");
                m->mothurOut("The read.tree command should be in the following format: read.tree(tree=yourTreeFile, group=yourGroupFile).\n");
                m->mothurOut("The tree and group parameters are both required.\n");
+               m->mothurOut("The name parameter allows you to enter a namefile.\n");
                m->mothurOut("Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile).\n\n");
        }
        catch(exception& e) {
@@ -147,7 +149,7 @@ int ReadTreeCommand::execute(){
                                delete globaldata->gTreemap;
                                return 0;
                        }
-                       
+       
                        T[i]->assembleTree();
                }
 
@@ -180,6 +182,8 @@ int ReadTreeCommand::execute(){
                                        }
                                }
                        }
+                       
+                       globaldata->gTreemap = treeMap;
                }
                
                return 0;