minor mods to seq.error

[mothur.git] / removerarecommand.cpp

diff --git a/removerarecommand.cpp b/removerarecommand.cpp
index 41355b9560e910c03be93e527524e4363b86be11..c320fa4d8854f003486bc71c8e6b0806ec7ae0e3 100644 (file)
--- a/removerarecommand.cpp
+++ b/removerarecommand.cpp
@@ -50,7 +50,7 @@ string RemoveRareCommand::getHelpString(){
                helpString += "The nseqs parameter allows you to set the cutoff for an otu to be deemed rare. It is required.\n";
                helpString += "The remove.rare command should be in the following format: remove.rare(shared=yourSharedFile, nseqs=yourRareCutoff).\n";
                helpString += "Example remove.rare(shared=amazon.fn.shared, nseqs=2).\n";
-               helpString += "Note: No spaces between parameter labels (i.e. shared), '=' and parameters (i.e.yourSharedFile).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. shared), '=' and parameters (i.e.yourSharedFile).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -83,6 +83,7 @@ RemoveRareCommand::RemoveRareCommand(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();
@@ -159,23 +160,28 @@ RemoveRareCommand::RemoveRareCommand(string option)  {
                        //check for file parameters
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
-                       else if (listfile == "not found") {  listfile = "";  }  
+                       else if (listfile == "not found") {  listfile = "";  }
+                       else { m->setListFile(listfile); }
                        
                        sabundfile = validParameter.validFile(parameters, "sabund", true);
                        if (sabundfile == "not open") { abort = true; }
                        else if (sabundfile == "not found") {  sabundfile = "";  }      
+                       else { m->setSabundFile(sabundfile); }
                        
                        rabundfile = validParameter.validFile(parameters, "rabund", true);
                        if (rabundfile == "not open") { abort = true; }
                        else if (rabundfile == "not found") {  rabundfile = "";  }                              
+                       else { m->setRabundFile(rabundfile); }
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { groupfile = ""; abort = true; }
                        else if (groupfile == "not found") {  groupfile = "";  }        
+                       else { m->setGroupFile(groupfile); }
                        
                        sharedfile = validParameter.validFile(parameters, "shared", true);
                        if (sharedfile == "not open") { sharedfile = "";  abort = true; }
                        else if (sharedfile == "not found") {  sharedfile = "";  }
+                       else { m->setSharedFile(sharedfile); }
                        
                        if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) { 
                                //is there are current file available for any of these?
@@ -645,6 +651,7 @@ int RemoveRareCommand::processShared(){
                                processedLabels.insert(lookup[0]->getLabel());
                                userLabels.erase(lookup[0]->getLabel());
                                
+                               if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
                                processLookup(lookup, out);
                        }
                        
@@ -658,6 +665,7 @@ int RemoveRareCommand::processShared(){
                                processedLabels.insert(lookup[0]->getLabel());
                                userLabels.erase(lookup[0]->getLabel());
                                
+                               if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
                                processLookup(lookup, out);                     
                                
                                //restore real lastlabel to save below
@@ -692,6 +700,7 @@ int RemoveRareCommand::processShared(){
                        
                        m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
                        
+                       if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
                        processLookup(lookup, out);     
                        
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }