working on current change

[mothur.git] / clusterfragmentscommand.cpp

diff --git a/clusterfragmentscommand.cpp b/clusterfragmentscommand.cpp
index baea496ccb8b2b95aac764028493be1e51a302d1..71ce5eed4e6e21c63210be0e34eb9a6f72dac59b 100644 (file)
--- a/clusterfragmentscommand.cpp
+++ b/clusterfragmentscommand.cpp
@@ -58,7 +58,7 @@ string ClusterFragmentsCommand::getHelpString(){
                helpString += "The cluster.fragments command should be in the following format: \n";
                helpString += "cluster.fragments(fasta=yourFastaFile, names=yourNamesFile) \n";
                helpString += "Example cluster.fragments(fasta=amazon.fasta).\n";
-               helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -87,6 +87,7 @@ ClusterFragmentsCommand::ClusterFragmentsCommand(string option) {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -137,6 +138,7 @@ ClusterFragmentsCommand::ClusterFragmentsCommand(string option) {
                                else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }
                        else if (fastafile == "not open") { fastafile = ""; abort = true; }     
+                       else { m->setFastaFile(fastafile); }
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(fastafile);      }
@@ -146,7 +148,7 @@ ClusterFragmentsCommand::ClusterFragmentsCommand(string option) {
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not found") { namefile =  "";  }
                        else if (namefile == "not open") { abort = true; }      
-                       else {  readNameFile();  }
+                       else {  readNameFile(); m->setNameFile(namefile); }
                        
                        string temp;
                        temp = validParameter.validFile(parameters, "diffs", false);            if (temp == "not found"){       temp = "0";                             }