X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=reversecommand.cpp;h=cde88b71203ac3c5fe364c2d7a7bd112bc8da8f8;hb=49d2b7459c5027557564b21e9487dadafbbbdc96;hp=17924c9669b6b5338d15824b2920410fcf305af4;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/reversecommand.cpp b/reversecommand.cpp
index 17924c9..cde88b7 100644
--- a/reversecommand.cpp
+++ b/reversecommand.cpp
@@ -43,7 +43,27 @@ string ReverseSeqsCommand::getHelpString(){
 		exit(1);
 	}
 }
-
+//**********************************************************************************************************************
+string ReverseSeqsCommand::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 == "fasta")            {   outputFileName =  "rc" + m->getExtension(inputName);   }
+            else if (type == "qfile")       {   outputFileName =  "rc" + m->getExtension(inputName);   }
+            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, "ReverseSeqsCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 ReverseSeqsCommand::ReverseSeqsCommand(){	
 	try {
@@ -113,11 +133,13 @@ ReverseSeqsCommand::ReverseSeqsCommand(string option)  {
 			fastaFileName = validParameter.validFile(parameters, "fasta", true);
 			if (fastaFileName == "not open") { abort = true; }
 			else if (fastaFileName == "not found") { fastaFileName = "";}// m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true;  }	
+			else { m->setFastaFile(fastaFileName); }
 			
 			qualFileName = validParameter.validFile(parameters, "qfile", true);
 			if (qualFileName == "not open") { abort = true; }
 			else if (qualFileName == "not found") { qualFileName = ""; }//m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true;  }	
-
+			else { m->setQualFile(qualFileName); }
+			
 			if((fastaFileName == "") && (qualFileName == "")){
 				fastaFileName = m->getFastaFile(); 
 				if (fastaFileName != "") {  m->mothurOut("Using " + fastaFileName + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
@@ -160,11 +182,11 @@ int ReverseSeqsCommand::execute(){
 			ofstream outFASTA;
 			string tempOutputDir = outputDir;
 			if (outputDir == "") { tempOutputDir += m->hasPath(fastaFileName); } //if user entered a file with a path then preserve it
-			fastaReverseFileName = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileName)) + "rc" + m->getExtension(fastaFileName);
+			fastaReverseFileName = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileName)) + getOutputFileNameTag("fasta", fastaFileName);
 			m->openOutputFile(fastaReverseFileName, outFASTA);
 			
 			while(!inFASTA.eof()){
-				if (m->control_pressed) {  inFASTA.close();  outFASTA.close(); remove(fastaReverseFileName.c_str()); return 0; }
+				if (m->control_pressed) {  inFASTA.close();  outFASTA.close(); m->mothurRemove(fastaReverseFileName); return 0; }
 				 
 				Sequence currSeq(inFASTA);  m->gobble(inFASTA);
 				if (currSeq.getName() != "") {
@@ -188,11 +210,11 @@ int ReverseSeqsCommand::execute(){
 			ofstream outQual;
 			string tempOutputDir = outputDir;
 			if (outputDir == "") { tempOutputDir += m->hasPath(qualFileName); } //if user entered a file with a path then preserve it
-			string qualReverseFileName = tempOutputDir + m->getRootName(m->getSimpleName(qualFileName)) + "rc" + m->getExtension(qualFileName);
-			m->openOutputFile(qualReverseFileName, outQual);
+			string qualReverseFileName = tempOutputDir + m->getRootName(m->getSimpleName(qualFileName)) + getOutputFileNameTag("qfile", qualFileName);
+            m->openOutputFile(qualReverseFileName, outQual);
 
 			while(!inQual.eof()){
-				if (m->control_pressed) {  inQual.close();  outQual.close(); remove(qualReverseFileName.c_str()); return 0; }
+				if (m->control_pressed) {  inQual.close();  outQual.close(); m->mothurRemove(qualReverseFileName); return 0; }
 				currQual = QualityScores(inQual);  m->gobble(inQual);
 				currQual.flipQScores();	
 				currQual.printQScores(outQual);
@@ -202,7 +224,7 @@ int ReverseSeqsCommand::execute(){
 			outputNames.push_back(qualReverseFileName); outputTypes["qfile"].push_back(qualReverseFileName);
 		}
 		
-		if (m->control_pressed) {  remove(qualReverseFileName.c_str()); remove(fastaReverseFileName.c_str()); return 0; }
+		if (m->control_pressed) {  m->mothurRemove(qualReverseFileName); m->mothurRemove(fastaReverseFileName); return 0; }
 		
 		//set fasta file as new current fastafile
 		string current = "";