X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=secondarystructurecommand.cpp;h=fe80b7810e716264152835060f25d1f2e45c1fed;hb=783b9ef8e739307aed392f35970701f6b53390fb;hp=2b84cc365d4796363bd3e4c5612abb246cfc5aab;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index 2b84cc3..fe80b78 100644
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -127,11 +127,12 @@ AlignCheckCommand::AlignCheckCommand(string option)  {
 				fastafile = m->getFastaFile(); 
 				if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
-			}	
+			}else { m->setFastaFile(fastafile); }	
 			
 			namefile = validParameter.validFile(parameters, "name", true);
 			if (namefile == "not open") { namefile = ""; abort = true; }
 			else if (namefile == "not found") { namefile = "";  }	
+			else { m->setNameFile(namefile); }
 			
 			//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"){	
@@ -182,7 +183,7 @@ int AlignCheckCommand::execute(){
 		
 		int count = 0;
 		while(!in.eof()){
-			if (m->control_pressed) { in.close(); out.close(); remove(outfile.c_str()); return 0; }
+			if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outfile); return 0; }
 			
 			Sequence seq(in);  m->gobble(in);
 			if (seq.getName() != "") {
@@ -219,7 +220,7 @@ int AlignCheckCommand::execute(){
 		in.close();
 		out.close();
 		
-		if (m->control_pressed) {  remove(outfile.c_str()); return 0; }
+		if (m->control_pressed) {  m->mothurRemove(outfile); return 0; }
 		
 		sort(pound.begin(), pound.end());
 		sort(dash.begin(), dash.end());
@@ -237,7 +238,7 @@ int AlignCheckCommand::execute(){
 		int ptile97_5	= int(size * 0.975);
 		int ptile100	= size - 1;
 		
-		if (m->control_pressed) {  remove(outfile.c_str()); return 0; }
+		if (m->control_pressed) {  m->mothurRemove(outfile); return 0; }
 		
 		m->mothurOutEndLine();
 		m->mothurOut("\t\tPound\tDash\tPlus\tEqual\tLoop\tTilde\tTotal"); m->mothurOutEndLine();