X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=secondarystructurecommand.cpp;h=ee50ab14e6183af4b2fe9979c97336ac1d9b75a5;hb=f509429e06e545bde69c97cacc0eb436775bd329;hp=fe80b7810e716264152835060f25d1f2e45c1fed;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index fe80b78..ee50ab1 100644
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -45,6 +45,26 @@ string AlignCheckCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string AlignCheckCommand::getOutputFileNameTag(string type, string inputName=""){	
+	try {
+        string outputFileName = "";
+		map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "aligncheck")            {   outputFileName =  "align.check";   }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "AlignCheckCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 AlignCheckCommand::AlignCheckCommand(){	
 	try {
 		abort = true; calledHelp = true; 
@@ -122,7 +142,7 @@ 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 +159,11 @@ 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);
+			}
 		}
 
 	}
@@ -166,7 +190,7 @@ int AlignCheckCommand::execute(){
 		m->openInputFile(fastafile, in);
 		
 		ofstream out;
-		string outfile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "align.check";
+		string outfile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("aligncheck");
 		m->openOutputFile(outfile, out);