X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=secondarystructurecommand.cpp;h=ee50ab14e6183af4b2fe9979c97336ac1d9b75a5;hb=0cefb55a2616975bd4a144fc345693695ffc9bb6;hp=2b84cc365d4796363bd3e4c5612abb246cfc5aab;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index 2b84cc3..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; 
@@ -122,23 +142,28 @@ 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);
+			}
 		}
 
 	}
@@ -165,7 +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);
 		
 				
@@ -182,7 +207,7 @@ 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 +244,7 @@ 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 +262,7 @@ 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();