X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=reversecommand.cpp;h=274240158068655fcbbc501d81e335238966edfa;hb=df92022fc75c08b91cefa2c6ca4fd7b23eb480b0;hp=15f63f6f17453082394a7ade3e7fc5244f66fe7e;hpb=64eee3a595ae53817f52807d7393b22e74e31f56;p=mothur.git

diff --git a/reversecommand.cpp b/reversecommand.cpp
index 15f63f6..2742401 100644
--- a/reversecommand.cpp
+++ b/reversecommand.cpp
@@ -13,19 +13,74 @@
 
 //***************************************************************************************************************
 
-ReverseSeqsCommand::ReverseSeqsCommand(){
+ReverseSeqsCommand::ReverseSeqsCommand(string option){
 	try {
-		globaldata = GlobalData::getInstance();
-		if(globaldata->getFastaFile() == "")		{	cout << "you need to at least enter a fasta file name" << endl;	}
+		abort = false;
+		
+		//allow user to run help
+		if(option == "help") { help(); abort = true; }
+		
+		else {
+			//valid paramters for this command
+			string Array[] =  {"fasta", "outputdir","inputdir"};
+			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+			
+			OptionParser parser(option);
+			map<string,string> parameters = parser.getParameters();
+			
+			ValidParameters validParameter;
+			map<string,string>::iterator it;
+			
+			//check to make sure all parameters are valid for command
+			for (it = parameters.begin(); it != parameters.end(); it++) { 
+				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+			}
+			
+			//if the user changes the input directory command factory will send this info to us in the output parameter 
+			string inputDir = validParameter.validFile(parameters, "inputdir", false);		
+			if (inputDir == "not found"){	inputDir = "";		}
+			else {
+				string path;
+				it = parameters.find("fasta");
+				//user has given a template file
+				if(it != parameters.end()){ 
+					path = hasPath(it->second);
+					//if the user has not given a path then, add inputdir. else leave path alone.
+					if (path == "") {	parameters["fasta"] = inputDir + it->second;		}
+				}
+			}
+
+			//check for required parameters
+			fasta = validParameter.validFile(parameters, "fasta", true);
+			if (fasta == "not open") { abort = true; }
+			else if (fasta == "not found") { fasta = ""; mothurOut("fasta is a required parameter for the reverse.seqs command."); mothurOutEndLine(); abort = true;  }	
+			
+			//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 += hasPath(fasta); //if user entered a file with a path then preserve it	
+			}
+
+		}
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ReverseSeqsCommand class Function ReverseSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ReverseSeqsCommand class function ReverseSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+
+void ReverseSeqsCommand::help(){
+	try {
+		mothurOut("The reverse.seqs command reads a fastafile and ....\n");
+		mothurOut("The reverse.seqs command parameter is fasta and it is required.\n");
+		mothurOut("The reverse.seqs command should be in the following format: \n");
+		mothurOut("reverse.seqs(fasta=yourFastaFile) \n");	
+	}
+	catch(exception& e) {
+		errorOut(e, "ReverseSeqsCommand", "help");
 		exit(1);
-	}	
+	}
 }
 
 //***************************************************************************************************************
@@ -38,17 +93,21 @@ ReverseSeqsCommand::~ReverseSeqsCommand(){	/*	do nothing	*/	}
 int ReverseSeqsCommand::execute(){
 	try{
 		
+		if (abort == true) { return 0; }
+		
 		ifstream inFASTA;
-		openInputFile(globaldata->getFastaFile(), inFASTA);
+		openInputFile(fasta, inFASTA);
 		
 		ofstream outFASTA;
-		string reverseFile = getRootName(globaldata->getFastaFile()) + "rc" + getExtension(globaldata->getFastaFile());
+		string reverseFile = outputDir + getRootName(getSimpleName(fasta)) + "rc" + getExtension(fasta);
 		openOutputFile(reverseFile, outFASTA);
 		
 		while(!inFASTA.eof()){
-			Sequence currSeq(inFASTA);
-			currSeq.reverseComplement();
-			currSeq.printSequence(outFASTA);
+			Sequence currSeq(inFASTA);  gobble(inFASTA);
+			if (currSeq.getName() != "") {
+				currSeq.reverseComplement();
+				currSeq.printSequence(outFASTA);
+			}
 		}
 		inFASTA.close();
 		outFASTA.close();
@@ -57,11 +116,7 @@ int ReverseSeqsCommand::execute(){
 		
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ReverseSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ReverseSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "ReverseSeqsCommand", "execute");
 		exit(1);
 	}
 }