testing public / private push error

[mothur.git] / preclustercommand.cpp

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index cac80b8d775d2e5bd4810198e69a2d5ad625c04d..582da493e4dc5cdf5267d65606181d1594f56a87 100644 (file)
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -147,7 +147,7 @@ PreClusterCommand::PreClusterCommand(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 {  m->setNameFile(namefile); }
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
@@ -162,7 +162,10 @@ PreClusterCommand::PreClusterCommand(string option) {
                        m->setProcessors(temp);
                        m->mothurConvert(temp, processors);
                        
-                       
+                       if (namefile == "") {
+                               vector<string> files; files.push_back(fastafile);
+                               parser.getNameFile(files);
+                       }
                }
                                
        }
@@ -372,9 +375,9 @@ int PreClusterCommand::createProcessesGroups(SequenceParser* parser, string newF
                
                //append output files
                for(int i=0;i<processIDS.size();i++){
-                       newFName = m->getFullPathName(".\\" + newFName);
-                       newNName = m->getFullPathName(".\\" + newNName);
-                       cout << newFName << endl;
+                       //newFName = m->getFullPathName(".\\" + newFName);
+                       //newNName = m->getFullPathName(".\\" + newNName);
+                       
                        m->appendFiles((newFName + toString(processIDS[i]) + ".temp"), newFName);
                        m->mothurRemove((newFName + toString(processIDS[i]) + ".temp"));