X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clusterfragmentscommand.cpp;h=8d2d3eac9ba398dbce884d61c99dd81b3f2442b6;hb=ae57e166b2ed7b475ec3f466106bd76fabadd063;hp=2e37e7caedc35b67609e7c27e263261abd6f88f9;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/clusterfragmentscommand.cpp b/clusterfragmentscommand.cpp
index 2e37e7c..8d2d3ea 100644
--- a/clusterfragmentscommand.cpp
+++ b/clusterfragmentscommand.cpp
@@ -138,6 +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); 	}
@@ -147,7 +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";				}
@@ -225,7 +226,7 @@ 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; }
 		
@@ -237,7 +238,7 @@ 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();