added chimera.uchime

[mothur.git] / indicatorcommand.cpp

diff --git a/indicatorcommand.cpp b/indicatorcommand.cpp
index 8e80d5331ed6265f7da9640258cb399c4c11a15d..ac7efcf5a40846dd8fcf6a2166dbc773f18d2b34 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) {
@@ -74,6 +74,7 @@ IndicatorCommand::IndicatorCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -90,6 +91,10 @@ 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 +236,7 @@ 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;