X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=reversecommand.cpp;h=a9b297731a346999b155c61d7cab47ff7089063c;hp=ea2ddeb8e718b44363409f0b332827feec41d6a9;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd

diff --git a/reversecommand.cpp b/reversecommand.cpp
index ea2ddeb..a9b2977 100644
--- a/reversecommand.cpp
+++ b/reversecommand.cpp
@@ -14,10 +14,10 @@
 //**********************************************************************************************************************
 vector<string> ReverseSeqsCommand::setParameters(){	
 	try {
-		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "fastaQual", "none",false,false); parameters.push_back(pfasta);
-		CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "fastaQual", "none",false,false); parameters.push_back(pqfile);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "fastaQual", "none","fasta",false,false,true); parameters.push_back(pfasta);
+		CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "fastaQual", "none","qfile",false,false,true); parameters.push_back(pqfile);
+		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
 		
 		vector<string> myArray;
 		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
@@ -43,7 +43,22 @@ string ReverseSeqsCommand::getHelpString(){
 		exit(1);
 	}
 }
-
+//**********************************************************************************************************************
+string ReverseSeqsCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "fasta") {  pattern = "[filename],rc,[extension]"; } 
+        else if (type == "qfile") {  pattern = "[filename],rc,[extension]"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "ReverseSeqsCommand", "getOutputPattern");
+        exit(1);
+    }
+}
 //**********************************************************************************************************************
 ReverseSeqsCommand::ReverseSeqsCommand(){	
 	try {
@@ -162,11 +177,14 @@ 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);
+            map<string, string> variables; 
+            variables["[filename]"] = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileName));
+            variables["[extension]"] = m->getExtension(fastaFileName);
+			fastaReverseFileName = getOutputFileName("fasta", variables);
 			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() != "") {
@@ -190,11 +208,14 @@ 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);
+            map<string, string> variables; 
+            variables["[filename]"] = tempOutputDir + m->getRootName(m->getSimpleName(qualFileName));
+            variables["[extension]"] = m->getExtension(qualFileName);
+			string qualReverseFileName = getOutputFileName("qfile", variables);
+            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);
@@ -204,7 +225,7 @@ 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 = "";
@@ -220,7 +241,7 @@ int ReverseSeqsCommand::execute(){
 		
 		
 		m->mothurOutEndLine();
-		m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 		for(int i=0;i<outputNames.size();i++){
 			m->mothurOut(outputNames[i]);
 			m->mothurOutEndLine();