X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=indicatorcommand.cpp;h=ac7efcf5a40846dd8fcf6a2166dbc773f18d2b34;hb=4de093e3b92bdab1579565cb2873553412f6671e;hp=8e80d5331ed6265f7da9640258cb399c4c11a15d;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/indicatorcommand.cpp b/indicatorcommand.cpp
index 8e80d53..ac7efcf 100644
--- 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;