working on current change

[mothur.git] / removerarecommand.cpp

diff --git a/removerarecommand.cpp b/removerarecommand.cpp
index 255448ece9d1ed6eb5c8d65b4d562644ddf73051..c320fa4d8854f003486bc71c8e6b0806ec7ae0e3 100644 (file)
--- a/removerarecommand.cpp
+++ b/removerarecommand.cpp
@@ -160,23 +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?