X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=secondarystructurecommand.cpp;h=24142e0cf4aa6174a8006f1e0a7a85c82f10ab24;hb=36a6b02cf7f09d2bc34376b588944a9ca73429c5;hp=fe80b7810e716264152835060f25d1f2e45c1fed;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index fe80b78..24142e0 100644
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -122,7 +122,7 @@ AlignCheckCommand::AlignCheckCommand(string option)  {
 			else if (mapfile == "not found") {  mapfile = "";  m->mothurOut("You must provide an map file."); m->mothurOutEndLine(); abort = true; }	
 			
 			fastafile = validParameter.validFile(parameters, "fasta", true);
-			if (fastafile == "not open") { abort = true; }
+			if (fastafile == "not open") { fastafile = ""; abort = true; }
 			else if (fastafile == "not found") {  				
 				fastafile = m->getFastaFile(); 
 				if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
@@ -139,7 +139,11 @@ AlignCheckCommand::AlignCheckCommand(string option)  {
 				outputDir = "";	
 				outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it	
 			}
-
+			
+			if ((namefile == "") && (fastafile != "")){
+				vector<string> files; files.push_back(fastafile); 
+				parser.getNameFile(files);
+			}
 		}
 
 	}