working on citations

[mothur.git] / unifracunweightedcommand.cpp

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index a8c656cb5c5ffdc4a1e0fb3fd62e8eed0f1bb25f..8ec2d06e75d3980b42cb9980ca1631a978418429 100644 (file)
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -48,7 +48,7 @@ string UnifracUnweightedCommand::getHelpString(){
                helpString += "Example unifrac.unweighted(groups=A-B-C, iters=500).\n";
                helpString += "The default value for groups is all the groups in your groupfile, and iters is 1000.\n";
                helpString += "The unifrac.unweighted command output two files: .unweighted and .uwsummary their descriptions are in the manual.\n";
-               helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -80,11 +80,10 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(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 {
-                       //valid paramters for this command
-                       string Array[] =  {"groups","iters","distance","random","root", "processors","outputdir","inputdir"};
-                       vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+                       vector<string> myArray = setParameters();
                        
                        OptionParser parser(option);
                        map<string,string> parameters = parser.getParameters();
@@ -135,6 +134,10 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
                        }
                        
                        m->runParse = true;
+                       m->Groups.clear();
+                       m->namesOfGroups.clear();
+                       m->Treenames.clear();
+                       m->names.clear();
                        
                        //check for required parameters
                        treefile = validParameter.validFile(parameters, "tree", true);
@@ -208,6 +211,8 @@ int UnifracUnweightedCommand::execute() {
                
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
+               m->setTreeFile(treefile);
+               
                if (groupfile != "") {
                        //read in group map info.
                        tmap = new TreeMap(groupfile);