X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clusterfragmentscommand.cpp;h=71ce5eed4e6e21c63210be0e34eb9a6f72dac59b;hb=220dc345e493cddc569521111ce32ac4d965ab7f;hp=baea496ccb8b2b95aac764028493be1e51a302d1;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/clusterfragmentscommand.cpp b/clusterfragmentscommand.cpp
index baea496..71ce5ee 100644
--- 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";				}