modified chimera.slayer template=self

[mothur.git] / indicatorcommand.cpp

diff --git a/indicatorcommand.cpp b/indicatorcommand.cpp
index 8e80d5331ed6265f7da9640258cb399c4c11a15d..c25e4fa13b4b7cc8eaf7f320d66b1806a3bf194d 100644 (file)
--- a/indicatorcommand.cpp
+++ b/indicatorcommand.cpp
@@ -44,7 +44,7 @@ string IndicatorCommand::getHelpString(){
                helpString += "The groups parameter allows you to specify which of the groups in your shared or relabund you would like analyzed, or if you provide a design file the groups in your design file.  The groups may be entered separated by dashes.\n";
                helpString += "The label parameter indicates at what distance your tree relates to the shared or relabund.\n";
                helpString += "The indicator command should be used in the following format: indicator(tree=test.tre, shared=test.shared, label=0.03)\n";
-               helpString += "Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile).\n\n"; 
+               helpString += "Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile).\n"; 
                return helpString;
        }
        catch(exception& e) {
@@ -90,6 +90,10 @@ IndicatorCommand::IndicatorCommand(string option)  {
                        }
                        
                        m->runParse = true;
+                       m->Groups.clear();
+                       m->namesOfGroups.clear();
+                       m->Treenames.clear();
+                       m->names.clear();
                        
                        vector<string> tempOutNames;
                        outputTypes["tree"] = tempOutNames;
@@ -231,6 +235,7 @@ int IndicatorCommand::execute(){
                //    reading tree info                                                    //
                /***************************************************/
                string groupfile = ""; 
+               m->setTreeFile(treefile);
                Tree* tree = new Tree(treefile); delete tree;  //extracts names from tree to make faked out groupmap
                treeMap = new TreeMap();
                bool mismatch = false;