added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / classifyotucommand.cpp

diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index f36631a0590725867dffc402f74fd73af6168e20..c8896375b016ef6c45462351a18e8e520bfe75c2 100644 (file)
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -182,7 +182,7 @@ ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
                        else if (refTaxonomy == "not open") { abort = true; }
        
                        namefile = validParameter.validFile(parameters, "name", true);
-                       if (namefile == "not open") { abort = true; }   
+                       if (namefile == "not open") { namefile = ""; abort = true; }    
                        else if (namefile == "not found") { namefile = ""; }
                        else { m->setNameFile(namefile); }
                        
@@ -206,7 +206,7 @@ ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
                        if ((basis != "otu") && (basis != "sequence")) { m->mothurOut("Invalid option for basis. basis options are otu and sequence, using otu."); m->mothurOutEndLine(); }
                        
                        string temp = validParameter.validFile(parameters, "cutoff", false);                    if (temp == "not found") { temp = "51"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        
                        temp = validParameter.validFile(parameters, "probs", false);                                    if (temp == "not found"){       temp = "true";                  }
                        probs = m->isTrue(temp);
@@ -214,6 +214,11 @@ ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
                        
                        if ((cutoff < 51) || (cutoff > 100)) { m->mothurOut("cutoff must be above 50, and no greater than 100."); m->mothurOutEndLine(); abort = true;  }
                        
+                       if (namefile == ""){
+                               vector<string> files; files.push_back(taxfile);
+                               parser.getNameFile(files);
+                       }
+                       
                }
        }
        catch(exception& e) {