added cutoff change to mgcluster

[mothur.git] / classifyseqscommand.cpp

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 9d5a625308f8970888833ec7e74ec4b2e2ec32dd..72ca1d00fed7815ef68a8f1dc321c8c911eaeff0 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -106,6 +106,7 @@ ClassifySeqsCommand::ClassifySeqsCommand(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();
@@ -238,6 +239,8 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                                                        //erase from file list
                                                        fastaFileNames.erase(fastaFileNames.begin()+i);
                                                        i--;
+                                               }else {
+                                                       m->setFastaFile(fastaFileNames[i]);
                                                }
                                        }
                                        
@@ -318,6 +321,8 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                                                        //erase from file list
                                                        namefileNames.erase(namefileNames.begin()+i);
                                                        i--;
+                                               }else {
+                                                       m->setNameFile(namefileNames[i]);
                                                }
                                        }
                                }
@@ -374,6 +379,8 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                                                //erase from file list
                                                groupfileNames.erase(groupfileNames.begin()+i);
                                                i--;
+                                       }else {
+                                               m->setGroupFile(groupfileNames[i]);
                                        }
                                }
                        }