X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clusterfragmentscommand.cpp;h=772113baf83e9fbbd057794103f46ffa21c21fda;hb=36a6b02cf7f09d2bc34376b588944a9ca73429c5;hp=baea496ccb8b2b95aac764028493be1e51a302d1;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/clusterfragmentscommand.cpp b/clusterfragmentscommand.cpp
index baea496..772113b 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); 	}
@@ -145,15 +147,20 @@ ClusterFragmentsCommand::ClusterFragmentsCommand(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 {  readNameFile();  }
+			else if (namefile == "not open") { namefile = ""; abort = true; }	
+			else {  readNameFile(); m->setNameFile(namefile); }
 			
 			string temp;
 			temp = validParameter.validFile(parameters, "diffs", false);		if (temp == "not found"){	temp = "0";				}
-			convert(temp, diffs); 
+			m->mothurConvert(temp, diffs); 
 			
 			temp = validParameter.validFile(parameters, "percent", false);		if (temp == "not found"){	temp = "0";				}
-			convert(temp, percent);
+			m->mothurConvert(temp, percent);
+			
+			if (namefile == "") {
+				vector<string> files; files.push_back(fastafile);
+				parser.getNameFile(files);
+			}
 			
 		}
 				
@@ -224,7 +231,7 @@ int ClusterFragmentsCommand::execute(){
 		string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));
 		
 		string newFastaFile = fileroot + "fragclust.fasta";
-		string newNamesFile = fileroot + "names";
+		string newNamesFile = fileroot + "fragclust.names";
 		
 		if (m->control_pressed) { return 0; }
 		
@@ -236,7 +243,7 @@ int ClusterFragmentsCommand::execute(){
 		
 		m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); 
 		
-		if (m->control_pressed) { remove(newFastaFile.c_str()); remove(newNamesFile.c_str()); return 0; }
+		if (m->control_pressed) { m->mothurRemove(newFastaFile); m->mothurRemove(newNamesFile); return 0; }
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();