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

[mothur.git] / seqerrorcommand.cpp

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 253e03e2a1d380cb4d13f360fc9a5fecaaeb0808..d8ebe50fb11859367256a28286dec9789cc70d36 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -176,7 +176,7 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                                if (queryFileName != "") { m->mothurOut("Using " + queryFileName + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }
-                       else if (queryFileName == "not open") { abort = true; } 
+                       else if (queryFileName == "not open") { queryFileName = ""; abort = true; }     
                        else { m->setFastaFile(queryFileName); }
                        
                        referenceFileName = validParameter.validFile(parameters, "reference", true);
@@ -213,7 +213,7 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
                        temp = validParameter.validFile(parameters, "threshold", false);        if (temp == "not found") { temp = "1.00"; }
-                       convert(temp, threshold);  
+                       m->mothurConvert(temp, threshold);  
                        
                        temp = validParameter.validFile(parameters, "save", false);                     if (temp == "not found"){       temp = "f";                             }
                        save = m->isTrue(temp); 
@@ -242,10 +242,15 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors); 
+                       m->mothurConvert(temp, processors); 
 
                        substitutionMatrix.resize(6);
                        for(int i=0;i<6;i++){   substitutionMatrix[i].resize(6,0);      }
+                       
+                       if ((namesFileName == "") && (queryFileName != "")){
+                               vector<string> files; files.push_back(queryFileName); 
+                               parser.getNameFile(files);
+                       }
                }
        }
        catch(exception& e) {