testing public / private push error

[mothur.git] / preclustercommand.cpp

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index cf4256851eb583a78b78fd5ab800bbfa5d46f5e8..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);
@@ -156,13 +156,16 @@ PreClusterCommand::PreClusterCommand(string option) {
                        else {   m->setGroupFile(groupfile); bygroup = true;  }
                        
                        string temp     = validParameter.validFile(parameters, "diffs", false);         if(temp == "not found"){        temp = "1"; }
-                       convert(temp, diffs); 
+                       m->mothurConvert(temp, diffs); 
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
-                       
+                       m->mothurConvert(temp, processors);
                        
+                       if (namefile == "") {
+                               vector<string> files; files.push_back(fastafile);
+                               parser.getNameFile(files);
+                       }
                }
                                
        }
@@ -372,6 +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);
+                       
                        m->appendFiles((newFName + toString(processIDS[i]) + ".temp"), newFName);
                        m->mothurRemove((newFName + toString(processIDS[i]) + ".temp"));