added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / clusterfragmentscommand.cpp

diff --git a/clusterfragmentscommand.cpp b/clusterfragmentscommand.cpp
index 8d2d3eac9ba398dbce884d61c99dd81b3f2442b6..772113baf83e9fbbd057794103f46ffa21c21fda 100644 (file)
--- a/clusterfragmentscommand.cpp
+++ b/clusterfragmentscommand.cpp
@@ -147,15 +147,20 @@ ClusterFragmentsCommand::ClusterFragmentsCommand(string option) {
                        // ...at some point should added some additional type checking...
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not found") { namefile =  "";  }
-                       else if (namefile == "not open") { abort = true; }      
+                       else if (namefile == "not open") { namefile = ""; abort = true; }       
                        else {  readNameFile(); m->setNameFile(namefile); }
                        
                        string temp;
                        temp = validParameter.validFile(parameters, "diffs", false);            if (temp == "not found"){       temp = "0";                             }
-                       convert(temp, diffs); 
+                       m->mothurConvert(temp, diffs); 
                        
                        temp = validParameter.validFile(parameters, "percent", false);          if (temp == "not found"){       temp = "0";                             }
-                       convert(temp, percent);
+                       m->mothurConvert(temp, percent);
+                       
+                       if (namefile == "") {
+                               vector<string> files; files.push_back(fastafile);
+                               parser.getNameFile(files);
+                       }
                        
                }