X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=secondarystructurecommand.cpp;h=24142e0cf4aa6174a8006f1e0a7a85c82f10ab24;hb=e339f9008daa7d37c9a9034829565620a6abe783;hp=fec93e6e9f5f94414a392a1220b86153999b1f9d;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index fec93e6..24142e0 100644
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -36,7 +36,7 @@ string AlignCheckCommand::getHelpString(){
 		helpString += "The align.check command parameters are fasta and map, both are required.\n";
 		helpString += "The align.check command should be in the following format: align.check(fasta=yourFasta, map=yourMap).\n";
 		helpString += "Example align.check(map=silva.ss.map, 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) {
@@ -66,6 +66,7 @@ AlignCheckCommand::AlignCheckCommand(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();
@@ -121,23 +122,28 @@ 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(); }
 				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"){	
 				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);
+			}
 		}
 
 	}
@@ -181,7 +187,7 @@ 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() != "") {
@@ -218,7 +224,7 @@ 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());
@@ -236,7 +242,7 @@ 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();