X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clearcutcommand.cpp;h=d3c7fa48128246f8f4cb28ad53727329b3de856c;hb=36a6b02cf7f09d2bc34376b588944a9ca73429c5;hp=04dbc79aa15d3c4b6913a2e8131283b849dd90b9;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index 04dbc79..d3c7fa4 100644
--- a/clearcutcommand.cpp
+++ b/clearcutcommand.cpp
@@ -155,21 +155,21 @@ ClearcutCommand::ClearcutCommand(string option)  {
 			fastafile = validParameter.validFile(parameters, "fasta", true);
 			if (fastafile == "not open") { fastafile = ""; abort = true; }
 			else if (fastafile == "not found") { fastafile = ""; }	
-			else { inputFile = fastafile;  }
+			else { inputFile = fastafile;  m->setFastaFile(fastafile); }
 			
 			phylipfile = validParameter.validFile(parameters, "phylip", true);
 			if (phylipfile == "not open") { phylipfile = ""; abort = true; }
 			else if (phylipfile == "not found") { phylipfile = ""; }
-			else { inputFile = phylipfile;  }
+			else { inputFile = phylipfile;  m->setPhylipFile(phylipfile); }
 				
 			if ((phylipfile == "") && (fastafile == "")) {  
 				//is there are current file available for either of these?
 				//give priority to phylip, then fasta
 				phylipfile = m->getPhylipFile(); 
-				if (phylipfile != "") {  m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
+				if (phylipfile != "") {  inputFile = phylipfile; m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
 				else { 
 					fastafile = m->getFastaFile(); 
-					if (fastafile != "") {  m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+					if (fastafile != "") { inputFile = fastafile;  m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 					else { 
 						m->mothurOut("No valid current files. You must provide a phylip or fasta file before you can use the clearcut command."); m->mothurOutEndLine(); 
 						abort = true;