indicator command

[mothur.git] / getrelabundcommand.cpp

diff --git a/getrelabundcommand.cpp b/getrelabundcommand.cpp
index 74ec992a001e16a91d131a376944165aca1b4622..693e36d000891339b843115fa11bd338dbc7a103 100644 (file)
--- a/getrelabundcommand.cpp
+++ b/getrelabundcommand.cpp
@@ -69,6 +69,7 @@ GetRelAbundCommand::GetRelAbundCommand(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();
@@ -110,7 +111,7 @@ GetRelAbundCommand::GetRelAbundCommand(string option) {
                                sharedfile = m->getSharedFile(); 
                                if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }
+                       }else { m->setSharedFile(sharedfile); }
                        
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
@@ -174,6 +175,7 @@ int GetRelAbundCommand::execute(){
                        if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){                  
 
                                m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+                               if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
                                getRelAbundance(lookup, out);
                                
                                processedLabels.insert(lookup[0]->getLabel());
@@ -186,7 +188,7 @@ int GetRelAbundCommand::execute(){
                                for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }  
                                lookup = input->getSharedRAbundVectors(lastLabel);
                                m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
-                               
+                               if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
                                getRelAbundance(lookup, out);
                                
                                processedLabels.insert(lookup[0]->getLabel());
@@ -227,7 +229,7 @@ int GetRelAbundCommand::execute(){
                        lookup = input->getSharedRAbundVectors(lastLabel);
                        
                        m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
-                       
+                       if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
                        getRelAbundance(lookup, out);
                        
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }